Multiple sequence alignment - TraesCS1B01G110000

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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 TraesCS1B01G110000 chr1B 100.000 3359 0 0 1 3359 122360159 122356801 0.000000e+00 6204.0
1 TraesCS1B01G110000 chr1B 96.205 2793 72 14 588 3359 123352973 123350194 0.000000e+00 4540.0
2 TraesCS1B01G110000 chr1B 90.641 2511 144 39 1 2478 121851119 121848667 0.000000e+00 3251.0
3 TraesCS1B01G110000 chr1B 90.989 2286 148 32 386 2630 122978448 122976180 0.000000e+00 3027.0
4 TraesCS1B01G110000 chr1B 91.155 2035 138 31 514 2524 121791913 121789897 0.000000e+00 2723.0
5 TraesCS1B01G110000 chr1B 97.403 385 10 0 1 385 122979911 122979527 0.000000e+00 656.0
6 TraesCS1B01G110000 chr1B 96.707 334 10 1 3 335 121833471 121833138 3.790000e-154 555.0
7 TraesCS1B01G110000 chr1B 97.101 69 2 0 400 468 121793567 121793499 2.120000e-22 117.0
8 TraesCS1B01G110000 chr1B 89.552 67 6 1 320 385 121793621 121793555 2.150000e-12 84.2
9 TraesCS1B01G110000 chr1B 93.750 48 2 1 2778 2824 121846334 121846287 1.670000e-08 71.3
10 TraesCS1B01G110000 chr1B 91.489 47 4 0 3048 3094 122357053 122357007 7.780000e-07 65.8
11 TraesCS1B01G110000 chr1B 91.489 47 4 0 3107 3153 122357112 122357066 7.780000e-07 65.8
12 TraesCS1B01G110000 chr1B 91.489 47 4 0 3048 3094 123350448 123350402 7.780000e-07 65.8
13 TraesCS1B01G110000 chr1B 100.000 31 0 0 2993 3023 123350434 123350464 1.300000e-04 58.4
14 TraesCS1B01G110000 chr1D 87.665 2278 170 51 400 2630 78131548 78129335 0.000000e+00 2547.0
15 TraesCS1B01G110000 chr1D 97.561 41 1 0 2784 2824 78128654 78128614 1.670000e-08 71.3
16 TraesCS1B01G110000 chrUn 72.629 369 83 13 1848 2202 155963890 155964254 4.580000e-19 106.0


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 TraesCS1B01G110000 chr1B 122356801 122360159 3358 True 2111.866667 6204 94.326000 1 3359 3 chr1B.!!$R4 3358
1 TraesCS1B01G110000 chr1B 123350194 123352973 2779 True 2302.900000 4540 93.847000 588 3359 2 chr1B.!!$R6 2771
2 TraesCS1B01G110000 chr1B 122976180 122979911 3731 True 1841.500000 3027 94.196000 1 2630 2 chr1B.!!$R5 2629
3 TraesCS1B01G110000 chr1B 121846287 121851119 4832 True 1661.150000 3251 92.195500 1 2824 2 chr1B.!!$R3 2823
4 TraesCS1B01G110000 chr1B 121789897 121793621 3724 True 974.733333 2723 92.602667 320 2524 3 chr1B.!!$R2 2204
5 TraesCS1B01G110000 chr1D 78128614 78131548 2934 True 1309.150000 2547 92.613000 400 2824 2 chr1D.!!$R1 2424

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
666 3339 0.670546 GAGCTGCTACACTTCGGCAA 60.671 55.0 0.15 0.0 37.06 4.52 F
1806 4486 0.253160 ATAAGTGGACCTCCCTGCCA 60.253 55.0 0.00 0.0 35.38 4.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2151 4837 0.811616 GCGGGTATTCCTCAGCACTG 60.812 60.000 0.00 0.00 0.00 3.66 R
2933 7700 1.741706 ACCGGTCACGTGTAGATACAG 59.258 52.381 16.51 6.47 36.78 2.74 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
44 51 5.121811 AGATCATGGAGCTTGTGACATAAC 58.878 41.667 0.00 0.00 0.00 1.89
96 103 7.658525 AGCAAATCAATATGTGGTTGGATAA 57.341 32.000 0.00 0.00 28.19 1.75
133 140 7.370383 GTGTTAATCACAACTCATCATGGTTT 58.630 34.615 0.00 0.00 45.51 3.27
186 193 7.009540 GCATTTTCCTGGTTTTATTTCAGATCG 59.990 37.037 0.00 0.00 0.00 3.69
666 3339 0.670546 GAGCTGCTACACTTCGGCAA 60.671 55.000 0.15 0.00 37.06 4.52
762 3441 4.226394 TCCGATTCCAGGTCCAAATCTTTA 59.774 41.667 0.00 0.00 0.00 1.85
763 3442 5.104109 TCCGATTCCAGGTCCAAATCTTTAT 60.104 40.000 0.00 0.00 0.00 1.40
1021 3701 0.459759 GGGGACGTGTAGCTTAGTGC 60.460 60.000 0.00 0.00 43.29 4.40
1280 3960 0.737715 GACCTCATTCGTGCGAGCTT 60.738 55.000 0.00 0.00 0.00 3.74
1380 4060 2.122167 CCTCTACGCCTCCGAAGCT 61.122 63.158 0.00 0.00 38.29 3.74
1486 4166 0.842635 GCATCTCATTGGGTCCTCCT 59.157 55.000 0.00 0.00 36.20 3.69
1800 4480 5.011840 GGTAGGTGATTATAAGTGGACCTCC 59.988 48.000 9.58 8.21 35.44 4.30
1806 4486 0.253160 ATAAGTGGACCTCCCTGCCA 60.253 55.000 0.00 0.00 35.38 4.92
2151 4837 1.394917 CGTAGTCAGTTGCAATGCCTC 59.605 52.381 0.59 0.00 0.00 4.70
2678 6906 4.539870 CCATTATGATCATTTCGGTGTGC 58.460 43.478 14.65 0.00 0.00 4.57
2741 6969 4.022849 CGGGCATCTTTTCAAGTCTTCTTT 60.023 41.667 0.00 0.00 0.00 2.52
2844 7611 4.963373 TGGAAGACAAGTTTTCCATCGTA 58.037 39.130 18.12 0.00 45.40 3.43
2928 7695 3.476552 TGCCTGTAGAGTTTTTCCAGTG 58.523 45.455 0.00 0.00 0.00 3.66
2933 7700 5.278022 CCTGTAGAGTTTTTCCAGTGAAAGC 60.278 44.000 0.00 0.00 41.31 3.51
3190 7958 5.103000 CGAAACAGATATATGGATCCGACC 58.897 45.833 7.39 0.00 0.00 4.79
3229 7997 1.655484 TGACTTGCATGATACCAGCG 58.345 50.000 6.60 0.00 0.00 5.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 51 9.713740 GAAGAAATGCTAGATTTGACACAATAG 57.286 33.333 0.00 0.00 0.00 1.73
133 140 5.011329 ACACCGATGTCAAGTTTAGGACTTA 59.989 40.000 0.00 0.00 46.75 2.24
186 193 1.132643 ACAGAATCCACGTCGCTAGAC 59.867 52.381 0.00 0.00 43.72 2.59
478 3126 3.000819 TGCCTTCCGTCCGATGGT 61.001 61.111 6.53 0.00 37.96 3.55
666 3339 4.352298 AGAGAAGGAACAAACCAGAGGAAT 59.648 41.667 0.00 0.00 0.00 3.01
787 3466 1.803334 AGTAGTGCCGCGAAATTTGA 58.197 45.000 8.23 0.00 0.00 2.69
971 3651 7.321153 AGAAATTGCAAAATCTGATCTTCTGG 58.679 34.615 14.50 0.00 0.00 3.86
1021 3701 2.133553 CTGCAGTAAGCTCATCATCCG 58.866 52.381 5.25 0.00 45.94 4.18
1280 3960 1.597854 CGCCAGAAGGAGCACACAA 60.598 57.895 0.00 0.00 36.89 3.33
1380 4060 0.976641 AAGCTCCGTTCTCACCATCA 59.023 50.000 0.00 0.00 0.00 3.07
1486 4166 3.772572 TCAGCAGTAACTAACCAGCCATA 59.227 43.478 0.00 0.00 31.72 2.74
1559 4239 1.381327 GTGATCACCGAGGGGAGGA 60.381 63.158 15.31 0.00 36.97 3.71
1626 4306 7.292356 TCCTGCTCTAAATCCCACATCTTATAA 59.708 37.037 0.00 0.00 0.00 0.98
1662 4342 3.840666 AGAGGCAGTCAGGAAACTCATTA 59.159 43.478 0.00 0.00 40.21 1.90
1800 4480 1.833630 TCATAGTTCTCACCTGGCAGG 59.166 52.381 31.62 31.62 42.49 4.85
1806 4486 4.910195 TGCATTGTTCATAGTTCTCACCT 58.090 39.130 0.00 0.00 0.00 4.00
2151 4837 0.811616 GCGGGTATTCCTCAGCACTG 60.812 60.000 0.00 0.00 0.00 3.66
2678 6906 7.713942 TCTCCATCAAATACAGAGATGAACATG 59.286 37.037 0.00 0.00 41.18 3.21
2741 6969 8.541899 AAAAAGAGGGGAGTACAAATTGTTAA 57.458 30.769 3.17 0.00 0.00 2.01
2844 7611 4.187694 TGCCAATTTCTTGCGAACTTTTT 58.812 34.783 0.00 0.00 0.00 1.94
2858 7625 5.644636 CAGTGATATTTTGGCTTGCCAATTT 59.355 36.000 25.17 17.85 0.00 1.82
2928 7695 3.858238 GGTCACGTGTAGATACAGCTTTC 59.142 47.826 16.51 0.00 36.78 2.62
2933 7700 1.741706 ACCGGTCACGTGTAGATACAG 59.258 52.381 16.51 6.47 36.78 2.74
3097 7865 9.642343 ATGTAAACAGGAGTAGTCTACATATGA 57.358 33.333 10.38 0.00 29.17 2.15
3190 7958 9.868277 CAAGTCATAGATTTATCTAGCTTAGGG 57.132 37.037 0.00 0.00 42.20 3.53
3229 7997 7.040755 ACACTGCATGATGTAGAGTAGATAGTC 60.041 40.741 17.41 0.00 32.99 2.59


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

AutoCloner maintained by Alex Coulton.