Multiple sequence alignment - TraesCS1B01G087600

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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 TraesCS1B01G087600 chr1B 100.000 3839 0 0 1 3839 82740130 82743968 0 7090
1 TraesCS1B01G087600 chr1B 95.196 3872 148 17 1 3839 671068633 671064767 0 6085
2 TraesCS1B01G087600 chr1B 94.662 3859 167 34 1 3839 340978779 340982618 0 5949
3 TraesCS1B01G087600 chr1B 94.297 3875 151 23 1 3839 394861835 394865675 0 5867
4 TraesCS1B01G087600 chr1B 92.387 3862 214 45 1 3839 143682624 143678820 0 5430
5 TraesCS1B01G087600 chr1B 90.811 1861 150 15 741 2590 426966882 426968732 0 2470
6 TraesCS1B01G087600 chr5B 95.583 3871 136 10 1 3839 513857605 513861472 0 6168
7 TraesCS1B01G087600 chr7B 95.102 3879 144 16 1 3839 667388825 667392697 0 6069
8 TraesCS1B01G087600 chr7B 95.019 3875 127 19 1 3839 590850302 590854146 0 6026
9 TraesCS1B01G087600 chr7B 96.019 3291 96 8 1 3257 726142224 726145513 0 5319
10 TraesCS1B01G087600 chr7B 91.911 3041 189 31 826 3839 747731984 747728974 0 4200
11 TraesCS1B01G087600 chr7B 89.839 1860 155 19 741 2590 697874059 697875894 0 2357
12 TraesCS1B01G087600 chr3B 94.735 3875 157 23 1 3839 751335082 751331219 0 5982
13 TraesCS1B01G087600 chr3B 90.850 1858 149 18 742 2590 726421758 726419913 0 2470
14 TraesCS1B01G087600 chr3B 94.407 751 31 10 1 747 193604479 193603736 0 1144
15 TraesCS1B01G087600 chr6B 94.175 3296 140 26 583 3839 209592584 209595866 0 4975
16 TraesCS1B01G087600 chr6B 89.628 752 60 16 1 747 392473262 392472524 0 941
17 TraesCS1B01G087600 chr4B 93.440 2637 130 13 1 2600 523184518 523187148 0 3871
18 TraesCS1B01G087600 chr1A 88.845 753 67 16 1 747 472448199 472447458 0 909
19 TraesCS1B01G087600 chr1A 87.782 753 75 15 1 747 494766093 494766834 0 865
20 TraesCS1B01G087600 chr7A 88.815 751 68 16 1 747 61561341 61560603 0 907
21 TraesCS1B01G087600 chr6A 88.181 753 72 15 1 747 116931592 116930851 0 881
22 TraesCS1B01G087600 chrUn 92.819 557 34 6 8 561 200665327 200665880 0 802
23 TraesCS1B01G087600 chrUn 92.819 557 34 6 8 561 253418993 253418440 0 802


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 TraesCS1B01G087600 chr1B 82740130 82743968 3838 False 7090 7090 100.000 1 3839 1 chr1B.!!$F1 3838
1 TraesCS1B01G087600 chr1B 671064767 671068633 3866 True 6085 6085 95.196 1 3839 1 chr1B.!!$R2 3838
2 TraesCS1B01G087600 chr1B 340978779 340982618 3839 False 5949 5949 94.662 1 3839 1 chr1B.!!$F2 3838
3 TraesCS1B01G087600 chr1B 394861835 394865675 3840 False 5867 5867 94.297 1 3839 1 chr1B.!!$F3 3838
4 TraesCS1B01G087600 chr1B 143678820 143682624 3804 True 5430 5430 92.387 1 3839 1 chr1B.!!$R1 3838
5 TraesCS1B01G087600 chr1B 426966882 426968732 1850 False 2470 2470 90.811 741 2590 1 chr1B.!!$F4 1849
6 TraesCS1B01G087600 chr5B 513857605 513861472 3867 False 6168 6168 95.583 1 3839 1 chr5B.!!$F1 3838
7 TraesCS1B01G087600 chr7B 667388825 667392697 3872 False 6069 6069 95.102 1 3839 1 chr7B.!!$F2 3838
8 TraesCS1B01G087600 chr7B 590850302 590854146 3844 False 6026 6026 95.019 1 3839 1 chr7B.!!$F1 3838
9 TraesCS1B01G087600 chr7B 726142224 726145513 3289 False 5319 5319 96.019 1 3257 1 chr7B.!!$F4 3256
10 TraesCS1B01G087600 chr7B 747728974 747731984 3010 True 4200 4200 91.911 826 3839 1 chr7B.!!$R1 3013
11 TraesCS1B01G087600 chr7B 697874059 697875894 1835 False 2357 2357 89.839 741 2590 1 chr7B.!!$F3 1849
12 TraesCS1B01G087600 chr3B 751331219 751335082 3863 True 5982 5982 94.735 1 3839 1 chr3B.!!$R3 3838
13 TraesCS1B01G087600 chr3B 726419913 726421758 1845 True 2470 2470 90.850 742 2590 1 chr3B.!!$R2 1848
14 TraesCS1B01G087600 chr3B 193603736 193604479 743 True 1144 1144 94.407 1 747 1 chr3B.!!$R1 746
15 TraesCS1B01G087600 chr6B 209592584 209595866 3282 False 4975 4975 94.175 583 3839 1 chr6B.!!$F1 3256
16 TraesCS1B01G087600 chr6B 392472524 392473262 738 True 941 941 89.628 1 747 1 chr6B.!!$R1 746
17 TraesCS1B01G087600 chr4B 523184518 523187148 2630 False 3871 3871 93.440 1 2600 1 chr4B.!!$F1 2599
18 TraesCS1B01G087600 chr1A 472447458 472448199 741 True 909 909 88.845 1 747 1 chr1A.!!$R1 746
19 TraesCS1B01G087600 chr1A 494766093 494766834 741 False 865 865 87.782 1 747 1 chr1A.!!$F1 746
20 TraesCS1B01G087600 chr7A 61560603 61561341 738 True 907 907 88.815 1 747 1 chr7A.!!$R1 746
21 TraesCS1B01G087600 chr6A 116930851 116931592 741 True 881 881 88.181 1 747 1 chr6A.!!$R1 746
22 TraesCS1B01G087600 chrUn 200665327 200665880 553 False 802 802 92.819 8 561 1 chrUn.!!$F1 553
23 TraesCS1B01G087600 chrUn 253418440 253418993 553 True 802 802 92.819 8 561 1 chrUn.!!$R1 553

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
285 292 7.272731 CACATGCTTTTTCATTGTGACATCTAG 59.727 37.037 0.0 0.0 32.42 2.43 F
1111 1167 0.323957 GGTAACTGTCCACACCCTCC 59.676 60.000 0.0 0.0 0.00 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1391 1449 1.028905 GCAGGCTCGTAGATCTCACT 58.971 55.0 0.0 0.0 33.89 3.41 R
3094 3312 0.107993 CATCGGTGTCCTGATGCACT 60.108 55.0 0.0 0.0 35.97 4.40 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
285 292 7.272731 CACATGCTTTTTCATTGTGACATCTAG 59.727 37.037 0.00 0.00 32.42 2.43
794 817 9.719279 CAACATTTTGTTTTCAAGTGCATTTAT 57.281 25.926 0.00 0.00 38.77 1.40
1111 1167 0.323957 GGTAACTGTCCACACCCTCC 59.676 60.000 0.00 0.00 0.00 4.30
1222 1280 4.769688 ACAACTGATCACTTTGTGTCTGA 58.230 39.130 14.49 0.00 34.79 3.27
1233 1291 5.457799 CACTTTGTGTCTGATTTTTGCAGAG 59.542 40.000 0.00 0.00 42.57 3.35
1270 1328 1.743252 CAGAGCCTCCCAAGAACGC 60.743 63.158 0.00 0.00 0.00 4.84
1391 1449 0.464036 CCCTGTATGCGACTGGCTTA 59.536 55.000 8.49 0.00 44.02 3.09
1675 1733 4.973168 TGTACCTCATCTCAGCTGTTTTT 58.027 39.130 14.67 0.00 0.00 1.94
1723 1781 3.364549 CAACAAATGCTTCCCCATCCTA 58.635 45.455 0.00 0.00 0.00 2.94
1811 1871 3.253188 GCTAATGTCTGCCAGTGTTTTCA 59.747 43.478 0.00 0.00 0.00 2.69
1820 1880 6.533367 GTCTGCCAGTGTTTTCAATGTTTTTA 59.467 34.615 0.00 0.00 43.29 1.52
1914 1977 5.056480 TGTGAAGAACATGAACTGGTGTAG 58.944 41.667 0.00 0.00 32.36 2.74
2057 2126 0.828022 ATTCATGCATGGCAACCTGG 59.172 50.000 25.97 0.00 43.62 4.45
2101 2216 4.521639 CCATAATGACAATATGGCAGCTGT 59.478 41.667 16.64 0.00 39.76 4.40
2218 2427 8.347771 AGCATATACATAATGCAACTTCTTGTG 58.652 33.333 10.37 0.00 43.25 3.33
2225 2434 9.762933 ACATAATGCAACTTCTTGTGTTTATTT 57.237 25.926 0.00 0.00 0.00 1.40
2383 2597 3.671971 CGACTGTCTTGATCTGTCCACTC 60.672 52.174 6.21 0.00 32.69 3.51
2558 2773 3.924144 TGGCATGCTTACAAATTTGACC 58.076 40.909 24.64 11.67 0.00 4.02
2611 2829 8.946935 GCATGCTTACAATTTCTTTTTGTTTTC 58.053 29.630 11.37 0.00 38.26 2.29
2767 2985 4.000325 CCGTGGATTACTTGTTGATGTCA 59.000 43.478 0.00 0.00 0.00 3.58
2881 3099 4.002797 GGAATGACCGGCTTGCTT 57.997 55.556 0.00 0.00 0.00 3.91
2901 3119 0.251209 GGGAAGTTGGTTGAGGGGTC 60.251 60.000 0.00 0.00 0.00 4.46
3094 3312 5.934043 GGATGACGATGATGACATGGATAAA 59.066 40.000 0.00 0.00 36.82 1.40
3115 3333 0.832626 TGCATCAGGACACCGATGAT 59.167 50.000 18.68 6.71 37.01 2.45
3142 3360 0.250467 ATGCTGAAGTTCGCACAGGT 60.250 50.000 19.62 6.25 39.21 4.00
3201 3419 5.643777 CACCGGAGAAAGTGAAAGAACATAT 59.356 40.000 9.46 0.00 36.01 1.78
3608 3837 0.109643 TACGACGATGACCAACACCG 60.110 55.000 0.00 0.00 41.97 4.94
3745 3977 6.488006 AGCTTGTCACATGTTCTTCTGTTATT 59.512 34.615 0.00 0.00 0.00 1.40
3797 4029 8.836268 TCCAAATGATTTCTTCCTTCATTTTG 57.164 30.769 7.24 5.28 43.83 2.44
3809 4043 7.716123 TCTTCCTTCATTTTGTTAGTTTACGGA 59.284 33.333 0.00 0.00 0.00 4.69
3811 4045 7.641760 TCCTTCATTTTGTTAGTTTACGGAAC 58.358 34.615 0.00 0.00 38.58 3.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
463 475 4.406972 ACACTGTCATATCTGCAGTATGGT 59.593 41.667 23.97 16.41 37.53 3.55
913 956 4.832266 TGCCACCTAACAGAAAATGTCAAT 59.168 37.500 0.00 0.00 43.00 2.57
1109 1165 5.435041 ACCAATAACATAAATCAGGAGGGGA 59.565 40.000 0.00 0.00 0.00 4.81
1111 1167 6.040842 CCAACCAATAACATAAATCAGGAGGG 59.959 42.308 0.00 0.00 0.00 4.30
1222 1280 4.918810 ACGTTTCTTCCTCTGCAAAAAT 57.081 36.364 0.00 0.00 0.00 1.82
1233 1291 3.430895 TCTGTTGCGAATACGTTTCTTCC 59.569 43.478 0.00 0.00 41.98 3.46
1270 1328 7.424803 TGAATTTGTTAATCAACACAGTCAGG 58.575 34.615 0.00 0.00 41.74 3.86
1369 1427 2.028125 GCCAGTCGCATACAGGGCTA 62.028 60.000 12.08 0.00 43.68 3.93
1371 1429 2.876368 AAGCCAGTCGCATACAGGGC 62.876 60.000 11.64 11.64 46.00 5.19
1391 1449 1.028905 GCAGGCTCGTAGATCTCACT 58.971 55.000 0.00 0.00 33.89 3.41
1675 1733 2.765250 GAAGAGAAGTGGTCGGCGCA 62.765 60.000 10.83 0.00 0.00 6.09
1761 1819 2.270352 TGACATCGGAGCCAAAAAGT 57.730 45.000 0.00 0.00 0.00 2.66
1811 1871 9.757227 TCAGAAATCAAACGGAATAAAAACATT 57.243 25.926 0.00 0.00 0.00 2.71
1820 1880 4.380867 GCCACATCAGAAATCAAACGGAAT 60.381 41.667 0.00 0.00 0.00 3.01
1914 1977 2.014857 GGAGGAAGTCGGCAATAAACC 58.985 52.381 0.00 0.00 0.00 3.27
2057 2126 2.351738 GCAGTTGCCACCTTGTTATGAC 60.352 50.000 0.00 0.00 34.31 3.06
2101 2216 6.075762 GCAGTTGCCATATTGTCATTATGA 57.924 37.500 13.84 0.00 34.31 2.15
2218 2427 7.872163 TGTGCATGACAAGAATGAAATAAAC 57.128 32.000 0.00 0.00 0.00 2.01
2225 2434 4.763279 AGTTGATGTGCATGACAAGAATGA 59.237 37.500 0.00 0.00 38.36 2.57
2383 2597 2.171448 CTCCTACCCCAGTGAAATCCAG 59.829 54.545 0.00 0.00 0.00 3.86
2558 2773 2.738521 CACGGACGGTTGCCTCAG 60.739 66.667 0.00 0.00 0.00 3.35
2611 2829 1.527844 GCTTGGCCATCAGCTAGGG 60.528 63.158 20.18 0.00 43.05 3.53
2881 3099 0.996762 ACCCCTCAACCAACTTCCCA 60.997 55.000 0.00 0.00 0.00 4.37
2901 3119 1.139095 GAGGCACTAAGGGACGTCG 59.861 63.158 9.92 0.00 41.55 5.12
3094 3312 0.107993 CATCGGTGTCCTGATGCACT 60.108 55.000 0.00 0.00 35.97 4.40
3115 3333 2.160219 GCGAACTTCAGCATGTTCATCA 59.840 45.455 0.00 0.00 41.67 3.07
3142 3360 1.155859 ATCCTTGCCCTTGTTGCCA 59.844 52.632 0.00 0.00 0.00 4.92
3201 3419 2.997315 CCCTCGCCTCTCACACCA 60.997 66.667 0.00 0.00 0.00 4.17
3441 3669 4.405680 CACTACACATAACAGATGGAGGGA 59.594 45.833 0.00 0.00 0.00 4.20
3476 3705 2.826128 TCTTCATAACTGCTCGTCCACT 59.174 45.455 0.00 0.00 0.00 4.00
3558 3787 1.500783 CCTGGTGGAAGGGGTGTCAT 61.501 60.000 0.00 0.00 33.28 3.06
3597 3826 2.530661 ATCCCCCGGTGTTGGTCA 60.531 61.111 0.00 0.00 0.00 4.02
3608 3837 0.250338 GCAACACGATAGGATCCCCC 60.250 60.000 8.55 0.00 43.77 5.40
3797 4029 5.814188 CCAATAGGAGGTTCCGTAAACTAAC 59.186 44.000 0.00 0.00 42.75 2.34
3809 4043 5.755849 CCATGTAAAGACCAATAGGAGGTT 58.244 41.667 0.00 0.00 40.09 3.50
3811 4045 4.137543 GCCATGTAAAGACCAATAGGAGG 58.862 47.826 0.00 0.00 38.69 4.30


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

AutoCloner maintained by Alex Coulton.