Multiple sequence alignment - TraesCS1B01G034700

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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 TraesCS1B01G034700 chr1B 100.000 4063 0 0 1 4063 16531045 16535107 0.000000e+00 7504
1 TraesCS1B01G034700 chr1B 99.187 4061 32 1 3 4063 16545968 16550027 0.000000e+00 7315
2 TraesCS1B01G034700 chr1B 84.719 2009 293 11 804 2803 17342036 17344039 0.000000e+00 1997
3 TraesCS1B01G034700 chr1B 93.176 806 49 5 3 806 16519192 16519993 0.000000e+00 1179
4 TraesCS1B01G034700 chr1B 92.650 585 40 2 3479 4063 595027449 595028030 0.000000e+00 839
5 TraesCS1B01G034700 chr1B 80.899 801 121 23 7 801 17339933 17340707 1.620000e-168 603
6 TraesCS1B01G034700 chr1B 89.149 470 43 4 335 797 16927065 16927533 2.720000e-161 579
7 TraesCS1B01G034700 chr1B 88.323 471 46 4 335 797 16857675 16858144 1.280000e-154 556
8 TraesCS1B01G034700 chr1B 90.637 267 20 2 3 268 16857416 16857678 2.320000e-92 350
9 TraesCS1B01G034700 chr1B 90.226 266 22 1 3 268 16926807 16927068 1.080000e-90 344
10 TraesCS1B01G034700 chr1D 86.640 2006 251 15 804 2799 11495991 11497989 0.000000e+00 2204
11 TraesCS1B01G034700 chr1D 85.636 2005 273 13 804 2799 11178597 11180595 0.000000e+00 2093
12 TraesCS1B01G034700 chr1D 83.683 2004 306 18 806 2796 11319763 11321758 0.000000e+00 1869
13 TraesCS1B01G034700 chr1A 85.198 2020 288 9 804 2816 13571340 13573355 0.000000e+00 2063
14 TraesCS1B01G034700 chr1A 85.325 1983 269 19 828 2799 13415808 13417779 0.000000e+00 2030
15 TraesCS1B01G034700 chr1A 79.898 786 123 25 26 806 12589773 12589018 9.930000e-151 544
16 TraesCS1B01G034700 chr1A 87.701 374 44 2 434 806 13454430 13454802 6.240000e-118 435
17 TraesCS1B01G034700 chr1A 79.730 444 66 15 360 789 13315681 13316114 2.370000e-77 300
18 TraesCS1B01G034700 chr1A 98.519 135 2 0 3 137 13454295 13454429 5.250000e-59 239
19 TraesCS1B01G034700 chrUn 84.612 2021 297 11 804 2815 2472442 2470427 0.000000e+00 1997
20 TraesCS1B01G034700 chrUn 84.719 2009 293 11 804 2803 345524821 345526824 0.000000e+00 1997
21 TraesCS1B01G034700 chrUn 100.000 399 0 0 3178 3576 478801246 478800848 0.000000e+00 737
22 TraesCS1B01G034700 chrUn 81.149 801 119 23 7 801 317984165 317983391 7.460000e-172 614
23 TraesCS1B01G034700 chrUn 80.563 391 56 15 7 395 317004365 317003993 2.390000e-72 283
24 TraesCS1B01G034700 chrUn 80.563 391 56 15 7 395 346218134 346218506 2.390000e-72 283
25 TraesCS1B01G034700 chr4D 93.504 585 34 2 3479 4063 488127082 488127662 0.000000e+00 867
26 TraesCS1B01G034700 chr3B 93.333 585 37 1 3479 4063 10245619 10246201 0.000000e+00 863
27 TraesCS1B01G034700 chr3B 89.165 563 57 3 3502 4063 781366426 781365867 0.000000e+00 699
28 TraesCS1B01G034700 chr7B 93.162 585 38 1 3479 4063 55064630 55065212 0.000000e+00 857
29 TraesCS1B01G034700 chr7B 93.162 585 38 1 3479 4063 245621522 245622104 0.000000e+00 857
30 TraesCS1B01G034700 chr2B 92.821 585 40 1 3479 4063 509704905 509705487 0.000000e+00 846
31 TraesCS1B01G034700 chr3A 91.453 585 48 1 3479 4063 94098736 94098154 0.000000e+00 802


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 TraesCS1B01G034700 chr1B 16531045 16535107 4062 False 7504.0 7504 100.0000 1 4063 1 chr1B.!!$F2 4062
1 TraesCS1B01G034700 chr1B 16545968 16550027 4059 False 7315.0 7315 99.1870 3 4063 1 chr1B.!!$F3 4060
2 TraesCS1B01G034700 chr1B 17339933 17344039 4106 False 1300.0 1997 82.8090 7 2803 2 chr1B.!!$F7 2796
3 TraesCS1B01G034700 chr1B 16519192 16519993 801 False 1179.0 1179 93.1760 3 806 1 chr1B.!!$F1 803
4 TraesCS1B01G034700 chr1B 595027449 595028030 581 False 839.0 839 92.6500 3479 4063 1 chr1B.!!$F4 584
5 TraesCS1B01G034700 chr1B 16926807 16927533 726 False 461.5 579 89.6875 3 797 2 chr1B.!!$F6 794
6 TraesCS1B01G034700 chr1B 16857416 16858144 728 False 453.0 556 89.4800 3 797 2 chr1B.!!$F5 794
7 TraesCS1B01G034700 chr1D 11495991 11497989 1998 False 2204.0 2204 86.6400 804 2799 1 chr1D.!!$F3 1995
8 TraesCS1B01G034700 chr1D 11178597 11180595 1998 False 2093.0 2093 85.6360 804 2799 1 chr1D.!!$F1 1995
9 TraesCS1B01G034700 chr1D 11319763 11321758 1995 False 1869.0 1869 83.6830 806 2796 1 chr1D.!!$F2 1990
10 TraesCS1B01G034700 chr1A 13571340 13573355 2015 False 2063.0 2063 85.1980 804 2816 1 chr1A.!!$F3 2012
11 TraesCS1B01G034700 chr1A 13415808 13417779 1971 False 2030.0 2030 85.3250 828 2799 1 chr1A.!!$F2 1971
12 TraesCS1B01G034700 chr1A 12589018 12589773 755 True 544.0 544 79.8980 26 806 1 chr1A.!!$R1 780
13 TraesCS1B01G034700 chr1A 13454295 13454802 507 False 337.0 435 93.1100 3 806 2 chr1A.!!$F4 803
14 TraesCS1B01G034700 chrUn 2470427 2472442 2015 True 1997.0 1997 84.6120 804 2815 1 chrUn.!!$R1 2011
15 TraesCS1B01G034700 chrUn 345524821 345526824 2003 False 1997.0 1997 84.7190 804 2803 1 chrUn.!!$F1 1999
16 TraesCS1B01G034700 chrUn 317983391 317984165 774 True 614.0 614 81.1490 7 801 1 chrUn.!!$R3 794
17 TraesCS1B01G034700 chr4D 488127082 488127662 580 False 867.0 867 93.5040 3479 4063 1 chr4D.!!$F1 584
18 TraesCS1B01G034700 chr3B 10245619 10246201 582 False 863.0 863 93.3330 3479 4063 1 chr3B.!!$F1 584
19 TraesCS1B01G034700 chr3B 781365867 781366426 559 True 699.0 699 89.1650 3502 4063 1 chr3B.!!$R1 561
20 TraesCS1B01G034700 chr7B 55064630 55065212 582 False 857.0 857 93.1620 3479 4063 1 chr7B.!!$F1 584
21 TraesCS1B01G034700 chr7B 245621522 245622104 582 False 857.0 857 93.1620 3479 4063 1 chr7B.!!$F2 584
22 TraesCS1B01G034700 chr2B 509704905 509705487 582 False 846.0 846 92.8210 3479 4063 1 chr2B.!!$F1 584
23 TraesCS1B01G034700 chr3A 94098154 94098736 582 True 802.0 802 91.4530 3479 4063 1 chr3A.!!$R1 584

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
779 798 4.733887 CGAGTTCGTTTCTGAATATACGCT 59.266 41.667 7.94 1.89 34.24 5.07 F
1682 3030 2.039084 AGCCTCTCAGAAATTTCACGGT 59.961 45.455 19.99 3.59 0.00 4.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2091 3444 1.370900 GCCAAGCTCTTGTGCAACG 60.371 57.895 14.07 0.0 42.39 4.10 R
3642 4998 3.604629 GCTCTGCGGTGTCCTCTA 58.395 61.111 0.00 0.0 0.00 2.43 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
751 770 6.405731 GGTTATCAAGTTTAAGATGCATGCCA 60.406 38.462 16.68 3.52 0.00 4.92
779 798 4.733887 CGAGTTCGTTTCTGAATATACGCT 59.266 41.667 7.94 1.89 34.24 5.07
1682 3030 2.039084 AGCCTCTCAGAAATTTCACGGT 59.961 45.455 19.99 3.59 0.00 4.83
1801 3149 4.023707 CAGACTGTAAGCTTTGGGAAAGTG 60.024 45.833 3.20 0.00 40.64 3.16
2091 3444 5.512232 GGGAATATTGGTCTCTCTGGACATC 60.512 48.000 0.00 0.00 37.91 3.06
2547 3903 4.229876 GCTGTATGGTTGACTTTTGCTTC 58.770 43.478 0.00 0.00 0.00 3.86
2873 4229 5.545658 TTCTCGTTTCTTTACATGGATGC 57.454 39.130 0.00 0.00 0.00 3.91
2914 4270 7.630242 ATGTATATCCCGGCATAATTTCTTG 57.370 36.000 0.00 0.00 0.00 3.02
3048 4404 2.558795 GCTCCTTCCTCGCTCATATACA 59.441 50.000 0.00 0.00 0.00 2.29
3176 4532 5.765182 ACTTTTATCAGTGTTGTCTTGAGGG 59.235 40.000 0.00 0.00 0.00 4.30
3878 5235 3.340034 ACGGCATGGAAAGAACGAAATA 58.660 40.909 0.00 0.00 0.00 1.40
3883 5240 4.717991 CATGGAAAGAACGAAATACGCAA 58.282 39.130 0.00 0.00 46.94 4.85
3979 5336 1.006832 CCGGCCGTAACAAGATCAAG 58.993 55.000 26.12 0.00 0.00 3.02
4019 5376 6.829811 ACCTCTAGAACCAGACTAGACATTAC 59.170 42.308 0.00 0.00 40.57 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.194121 ACAGGCTTGAAATTGGGCCC 61.194 55.000 17.59 17.59 45.07 5.80
1 2 1.555967 TACAGGCTTGAAATTGGGCC 58.444 50.000 1.40 0.00 44.38 5.80
779 798 5.722441 TGGGTGGAACTACACATCTATAACA 59.278 40.000 0.00 0.00 43.08 2.41
852 2198 9.563898 CACAATTTTTCATCCCATATATCATCG 57.436 33.333 0.00 0.00 0.00 3.84
1682 3030 8.234136 AGTAATTGACCTCACTCGTGATATAA 57.766 34.615 0.00 0.00 39.13 0.98
2091 3444 1.370900 GCCAAGCTCTTGTGCAACG 60.371 57.895 14.07 0.00 42.39 4.10
2153 3506 9.206870 CAAAACATTCATACAAAGCCAAACTAT 57.793 29.630 0.00 0.00 0.00 2.12
2873 4229 5.673337 ATACATAAAGCGTACCAAGCATG 57.327 39.130 0.00 0.00 37.01 4.06
2914 4270 9.084164 CAAATGAGAAAGGAAATGTGAATGATC 57.916 33.333 0.00 0.00 0.00 2.92
3642 4998 3.604629 GCTCTGCGGTGTCCTCTA 58.395 61.111 0.00 0.00 0.00 2.43
3878 5235 5.408604 AGAACTTGTTATCGAAGATTTGCGT 59.591 36.000 0.00 0.00 45.12 5.24
3979 5336 1.484240 AGAGGTCTATGCAGCAGGTTC 59.516 52.381 0.00 0.00 0.00 3.62
4019 5376 1.227147 ACCACCGCATTCCGTATCG 60.227 57.895 0.00 0.00 34.38 2.92


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

AutoCloner maintained by Alex Coulton.