Multiple sequence alignment - TraesCS3D01G052200

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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 TraesCS3D01G052200 chr3D 100.000 3258 0 0 1 3258 21770838 21767581 0.000000e+00 6017
1 TraesCS3D01G052200 chr3D 90.612 245 19 3 1546 1787 384660715 384660958 4.060000e-84 322
2 TraesCS3D01G052200 chr3D 90.541 148 7 4 1311 1457 384655904 384656045 4.290000e-44 189
3 TraesCS3D01G052200 chr7D 96.006 2854 83 9 432 3258 544156025 544153176 0.000000e+00 4610
4 TraesCS3D01G052200 chr7D 93.369 1312 72 9 4 1307 142215309 142214005 0.000000e+00 1927
5 TraesCS3D01G052200 chr7D 95.804 715 14 9 1775 2473 548186216 548185502 0.000000e+00 1140
6 TraesCS3D01G052200 chr7D 96.785 622 19 1 2472 3092 142213176 142212555 0.000000e+00 1037
7 TraesCS3D01G052200 chr7D 93.740 623 29 5 2473 3092 548185403 548184788 0.000000e+00 926
8 TraesCS3D01G052200 chr7D 98.169 437 7 1 1 436 544161753 544161317 0.000000e+00 761
9 TraesCS3D01G052200 chr7D 95.545 202 9 0 2891 3092 539123222 539123021 1.130000e-84 324
10 TraesCS3D01G052200 chr7D 98.830 171 2 0 3088 3258 142211586 142211416 4.080000e-79 305
11 TraesCS3D01G052200 chr7A 94.869 2436 99 6 4 2417 675750777 675748346 0.000000e+00 3783
12 TraesCS3D01G052200 chr4A 94.385 1870 80 7 1 1849 504677845 504675980 0.000000e+00 2848
13 TraesCS3D01G052200 chr4A 94.258 714 26 3 1775 2473 658574117 658574830 0.000000e+00 1077
14 TraesCS3D01G052200 chr4A 97.368 418 10 1 1871 2288 504675924 504675508 0.000000e+00 710
15 TraesCS3D01G052200 chr1B 95.853 1447 41 8 1828 3257 659103957 659102513 0.000000e+00 2322
16 TraesCS3D01G052200 chr1B 92.967 910 54 4 1 900 659196386 659195477 0.000000e+00 1317
17 TraesCS3D01G052200 chr1B 90.844 972 63 8 612 1557 659105039 659104068 0.000000e+00 1279
18 TraesCS3D01G052200 chr1B 94.595 518 23 2 1 513 659105556 659105039 0.000000e+00 797
19 TraesCS3D01G052200 chr1B 85.535 159 16 3 1149 1307 121032282 121032433 3.360000e-35 159
20 TraesCS3D01G052200 chr5B 96.841 1203 37 1 2056 3258 89069715 89068514 0.000000e+00 2010
21 TraesCS3D01G052200 chr7B 96.432 1205 39 3 2056 3258 130902782 130901580 0.000000e+00 1984
22 TraesCS3D01G052200 chr7B 97.011 435 13 0 2824 3258 543521493 543521059 0.000000e+00 732
23 TraesCS3D01G052200 chr4D 92.852 1315 55 14 1 1307 410093571 410094854 0.000000e+00 1871
24 TraesCS3D01G052200 chr4D 94.754 629 18 4 1860 2473 410095630 410096258 0.000000e+00 965
25 TraesCS3D01G052200 chr2D 93.258 890 53 5 378 1263 291609651 291608765 0.000000e+00 1304
26 TraesCS3D01G052200 chr2D 94.803 712 22 3 1775 2471 614385073 614384362 0.000000e+00 1096
27 TraesCS3D01G052200 chr2D 95.974 621 23 2 2472 3090 291597588 291596968 0.000000e+00 1007
28 TraesCS3D01G052200 chr2D 98.830 171 2 0 3088 3258 291595956 291595786 4.080000e-79 305
29 TraesCS3D01G052200 chr2D 84.906 159 17 5 1149 1307 614385239 614385088 1.570000e-33 154
30 TraesCS3D01G052200 chr6D 95.098 714 20 4 1775 2473 322698257 322698970 0.000000e+00 1110
31 TraesCS3D01G052200 chr6D 95.098 714 19 5 1775 2473 384195982 384195270 0.000000e+00 1110
32 TraesCS3D01G052200 chr6D 93.878 588 28 7 668 1249 67658270 67658855 0.000000e+00 880
33 TraesCS3D01G052200 chr6D 87.538 650 65 14 1 643 283305122 283304482 0.000000e+00 737
34 TraesCS3D01G052200 chr6D 81.761 159 18 3 1149 1307 384196144 384195997 4.410000e-24 122
35 TraesCS3D01G052200 chr2A 94.678 714 23 3 1775 2473 722101816 722101103 0.000000e+00 1094
36 TraesCS3D01G052200 chr2A 90.671 343 14 5 2472 2804 656373066 656372732 1.070000e-119 440
37 TraesCS3D01G052200 chrUn 94.382 712 25 4 1775 2471 162682686 162683397 0.000000e+00 1079
38 TraesCS3D01G052200 chr1D 93.322 569 30 5 676 1240 408917434 408916870 0.000000e+00 833
39 TraesCS3D01G052200 chr6A 96.782 435 10 1 2826 3256 595723350 595723784 0.000000e+00 723
40 TraesCS3D01G052200 chr6A 94.643 336 15 2 2472 2804 291914781 291915116 4.820000e-143 518
41 TraesCS3D01G052200 chr6B 83.079 656 86 17 2 643 104303955 104304599 1.010000e-159 573
42 TraesCS3D01G052200 chr3A 90.987 233 17 3 1546 1775 507287819 507288050 8.780000e-81 311
43 TraesCS3D01G052200 chr3A 90.604 149 6 4 1311 1457 507273790 507273932 1.190000e-44 191
44 TraesCS3D01G052200 chr3A 94.595 74 1 2 1349 1421 507287474 507287545 9.560000e-21 111
45 TraesCS3D01G052200 chr5A 97.041 169 5 0 3088 3256 345322620 345322452 5.320000e-73 285
46 TraesCS3D01G052200 chr3B 88.841 233 22 3 1546 1775 500540929 500541160 1.910000e-72 283


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 TraesCS3D01G052200 chr3D 21767581 21770838 3257 True 6017.000000 6017 100.0000 1 3258 1 chr3D.!!$R1 3257
1 TraesCS3D01G052200 chr7D 544153176 544156025 2849 True 4610.000000 4610 96.0060 432 3258 1 chr7D.!!$R2 2826
2 TraesCS3D01G052200 chr7D 142211416 142215309 3893 True 1089.666667 1927 96.3280 4 3258 3 chr7D.!!$R4 3254
3 TraesCS3D01G052200 chr7D 548184788 548186216 1428 True 1033.000000 1140 94.7720 1775 3092 2 chr7D.!!$R5 1317
4 TraesCS3D01G052200 chr7A 675748346 675750777 2431 True 3783.000000 3783 94.8690 4 2417 1 chr7A.!!$R1 2413
5 TraesCS3D01G052200 chr4A 504675508 504677845 2337 True 1779.000000 2848 95.8765 1 2288 2 chr4A.!!$R1 2287
6 TraesCS3D01G052200 chr4A 658574117 658574830 713 False 1077.000000 1077 94.2580 1775 2473 1 chr4A.!!$F1 698
7 TraesCS3D01G052200 chr1B 659102513 659105556 3043 True 1466.000000 2322 93.7640 1 3257 3 chr1B.!!$R2 3256
8 TraesCS3D01G052200 chr1B 659195477 659196386 909 True 1317.000000 1317 92.9670 1 900 1 chr1B.!!$R1 899
9 TraesCS3D01G052200 chr5B 89068514 89069715 1201 True 2010.000000 2010 96.8410 2056 3258 1 chr5B.!!$R1 1202
10 TraesCS3D01G052200 chr7B 130901580 130902782 1202 True 1984.000000 1984 96.4320 2056 3258 1 chr7B.!!$R1 1202
11 TraesCS3D01G052200 chr4D 410093571 410096258 2687 False 1418.000000 1871 93.8030 1 2473 2 chr4D.!!$F1 2472
12 TraesCS3D01G052200 chr2D 291608765 291609651 886 True 1304.000000 1304 93.2580 378 1263 1 chr2D.!!$R1 885
13 TraesCS3D01G052200 chr2D 291595786 291597588 1802 True 656.000000 1007 97.4020 2472 3258 2 chr2D.!!$R2 786
14 TraesCS3D01G052200 chr2D 614384362 614385239 877 True 625.000000 1096 89.8545 1149 2471 2 chr2D.!!$R3 1322
15 TraesCS3D01G052200 chr6D 322698257 322698970 713 False 1110.000000 1110 95.0980 1775 2473 1 chr6D.!!$F2 698
16 TraesCS3D01G052200 chr6D 67658270 67658855 585 False 880.000000 880 93.8780 668 1249 1 chr6D.!!$F1 581
17 TraesCS3D01G052200 chr6D 283304482 283305122 640 True 737.000000 737 87.5380 1 643 1 chr6D.!!$R1 642
18 TraesCS3D01G052200 chr6D 384195270 384196144 874 True 616.000000 1110 88.4295 1149 2473 2 chr6D.!!$R2 1324
19 TraesCS3D01G052200 chr2A 722101103 722101816 713 True 1094.000000 1094 94.6780 1775 2473 1 chr2A.!!$R2 698
20 TraesCS3D01G052200 chrUn 162682686 162683397 711 False 1079.000000 1079 94.3820 1775 2471 1 chrUn.!!$F1 696
21 TraesCS3D01G052200 chr1D 408916870 408917434 564 True 833.000000 833 93.3220 676 1240 1 chr1D.!!$R1 564
22 TraesCS3D01G052200 chr6B 104303955 104304599 644 False 573.000000 573 83.0790 2 643 1 chr6B.!!$F1 641
23 TraesCS3D01G052200 chr3A 507287474 507288050 576 False 211.000000 311 92.7910 1349 1775 2 chr3A.!!$F2 426

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
806 829 1.338107 CCCTATCTCCATACCGCACA 58.662 55.0 0.00 0.00 0.0 4.57 F
1023 1058 0.742281 CGAAGCTGTACATGCAGGCT 60.742 55.0 16.27 9.73 37.0 4.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1736 1979 2.143122 GACGAAGATGGAGTTGCACAA 58.857 47.619 0.00 0.0 0.0 3.33 R
2878 3920 4.324669 CGTGCACTTGATGTCTTGTACTAG 59.675 45.833 16.19 0.0 0.0 2.57 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
311 317 7.508687 ACATACAACATGAGGCTAATATGTCA 58.491 34.615 0.00 0.00 34.18 3.58
320 326 8.554528 CATGAGGCTAATATGTCAAGTGTTTAG 58.445 37.037 0.00 0.00 0.00 1.85
340 347 6.990341 TTAGCCGAAATAAGAGGGTAAAAC 57.010 37.500 3.28 0.00 42.70 2.43
477 486 3.058341 TCTCACCATCCATCCATCCATT 58.942 45.455 0.00 0.00 0.00 3.16
514 528 2.183679 GGATCACCTCAGTCACCTCTT 58.816 52.381 0.00 0.00 0.00 2.85
806 829 1.338107 CCCTATCTCCATACCGCACA 58.662 55.000 0.00 0.00 0.00 4.57
902 935 2.602676 CCTTCCTCCGCCCCTTGAA 61.603 63.158 0.00 0.00 0.00 2.69
1023 1058 0.742281 CGAAGCTGTACATGCAGGCT 60.742 55.000 16.27 9.73 37.00 4.58
1241 1294 1.451067 CTTACACGTCCTCGACTCCT 58.549 55.000 0.00 0.00 40.62 3.69
1309 1362 1.221466 TTGCTTCGTGCGGTCAGAAG 61.221 55.000 0.55 0.55 46.63 2.85
1326 1379 5.239525 GTCAGAAGTTAGCCTGTCAAATGTT 59.760 40.000 0.00 0.00 0.00 2.71
1458 1528 8.638873 TGATTAGCAAAATTCTCCGTAGATCTA 58.361 33.333 0.00 0.00 0.00 1.98
1459 1529 9.646427 GATTAGCAAAATTCTCCGTAGATCTAT 57.354 33.333 5.57 0.00 0.00 1.98
1536 1606 7.337184 TGTGAACATAACAAGTGGAGTACAAAA 59.663 33.333 0.00 0.00 0.00 2.44
1708 1951 2.591715 GCGCCTTGGTGTCAGTGT 60.592 61.111 0.00 0.00 0.00 3.55
1721 1964 2.698274 TGTCAGTGTCTGTTAGAAGGCA 59.302 45.455 0.00 0.00 32.61 4.75
1844 2087 0.531657 CATTCGCCAATCCTGCCAAA 59.468 50.000 0.00 0.00 0.00 3.28
2606 3641 5.830799 TCACCTGCCATCTGATAACATAT 57.169 39.130 0.00 0.00 0.00 1.78
2850 3892 7.061557 GCTTGTCTTATGCAATTCTTCTTGTTC 59.938 37.037 0.00 0.00 0.00 3.18
3244 6273 6.798427 ATCTCTAGTTGACCTATTGCTTCA 57.202 37.500 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
235 241 4.209703 GTGTATCTTCGGACGACAAACAAA 59.790 41.667 0.00 0.00 0.00 2.83
311 317 4.941873 CCCTCTTATTTCGGCTAAACACTT 59.058 41.667 0.00 0.00 0.00 3.16
320 326 5.830000 ATGTTTTACCCTCTTATTTCGGC 57.170 39.130 0.00 0.00 0.00 5.54
477 486 1.894756 CCGCGGTGGGTTTCTTCAA 60.895 57.895 19.50 0.00 0.00 2.69
514 528 2.687566 GGGCGGAAGGAAGGGAGA 60.688 66.667 0.00 0.00 0.00 3.71
585 606 2.901042 GACGGGGAGCTAGGGTTG 59.099 66.667 0.00 0.00 0.00 3.77
902 935 1.043673 GGTAGGGCGACACAGAGGAT 61.044 60.000 0.00 0.00 0.00 3.24
979 1012 2.948801 GATCCCCTCGCCCTACCAGT 62.949 65.000 0.00 0.00 0.00 4.00
1213 1262 0.324091 GGACGTGTAAGGGAGGGAGA 60.324 60.000 0.00 0.00 0.00 3.71
1241 1294 3.810941 GAGGTAAACAAACACGATCCACA 59.189 43.478 0.00 0.00 0.00 4.17
1309 1362 6.092807 CCTCTTAGAACATTTGACAGGCTAAC 59.907 42.308 0.00 0.00 0.00 2.34
1326 1379 4.284490 TGAGAGAAGCAAAAGCCTCTTAGA 59.716 41.667 0.00 0.00 36.25 2.10
1458 1528 7.432148 TGTACAGTACCATGGTTGAGAATAT 57.568 36.000 25.38 1.55 0.00 1.28
1459 1529 6.860790 TGTACAGTACCATGGTTGAGAATA 57.139 37.500 25.38 0.00 0.00 1.75
1597 1837 6.291377 AGATTATTCAGTATTGCGGTCACAT 58.709 36.000 0.00 0.00 0.00 3.21
1708 1951 7.039434 CCATCTATGACTATGCCTTCTAACAGA 60.039 40.741 0.00 0.00 0.00 3.41
1721 1964 4.694760 TGCACAAGCCATCTATGACTAT 57.305 40.909 0.00 0.00 41.13 2.12
1736 1979 2.143122 GACGAAGATGGAGTTGCACAA 58.857 47.619 0.00 0.00 0.00 3.33
2386 3321 8.732746 AGATGTTACTAACAAGTGTTCTTTGT 57.267 30.769 5.73 0.00 45.86 2.83
2668 3708 8.978874 AATTGCATATAAATGTGACTGGTCTA 57.021 30.769 2.38 0.00 35.38 2.59
2850 3892 8.621286 AGTTAAGAACACATAAAACTGAACTGG 58.379 33.333 0.00 0.00 32.91 4.00
2877 3919 5.230942 GTGCACTTGATGTCTTGTACTAGT 58.769 41.667 10.32 0.00 0.00 2.57
2878 3920 4.324669 CGTGCACTTGATGTCTTGTACTAG 59.675 45.833 16.19 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.