Multiple sequence alignment - TraesCS1D01G037100

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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 TraesCS1D01G037100 chr1D 100.000 4077 0 0 1 4077 17264163 17268239 0.000000e+00 7529
1 TraesCS1D01G037100 chr1D 97.470 4071 94 9 2 4071 17289051 17293113 0.000000e+00 6938
2 TraesCS1D01G037100 chr1D 96.735 4074 98 9 1 4072 17393613 17397653 0.000000e+00 6754
3 TraesCS1D01G037100 chr1D 96.392 4074 116 8 1 4072 17334817 17338861 0.000000e+00 6680
4 TraesCS1D01G037100 chrUn 97.579 3842 85 7 1 3841 307553987 307557821 0.000000e+00 6573
5 TraesCS1D01G037100 chrUn 97.579 3842 85 7 1 3841 307578857 307582691 0.000000e+00 6573
6 TraesCS1D01G037100 chrUn 97.466 2960 69 6 1112 4071 250127013 250124060 0.000000e+00 5046
7 TraesCS1D01G037100 chrUn 97.795 2903 60 4 939 3841 327528538 327525640 0.000000e+00 5003
8 TraesCS1D01G037100 chrUn 97.848 976 20 1 317 1291 455092401 455091426 0.000000e+00 1685
9 TraesCS1D01G037100 chrUn 97.911 766 12 3 1 765 366683374 366682612 0.000000e+00 1323
10 TraesCS1D01G037100 chrUn 97.635 761 14 3 1 760 420455020 420455777 0.000000e+00 1303
11 TraesCS1D01G037100 chrUn 96.807 595 17 1 1 595 369793701 369793109 0.000000e+00 992
12 TraesCS1D01G037100 chrUn 99.739 383 0 1 3695 4077 353838329 353838710 0.000000e+00 701
13 TraesCS1D01G037100 chrUn 99.739 383 0 1 3695 4077 353975072 353974691 0.000000e+00 701
14 TraesCS1D01G037100 chr1B 92.664 3026 179 23 829 3845 25473168 25476159 0.000000e+00 4318
15 TraesCS1D01G037100 chr1B 91.463 82 5 2 752 832 25569610 25569690 1.200000e-20 111
16 TraesCS1D01G037100 chr1A 93.421 2660 156 13 1193 3846 19640521 19643167 0.000000e+00 3925
17 TraesCS1D01G037100 chr1A 93.659 2208 131 6 829 3028 19263874 19261668 0.000000e+00 3293
18 TraesCS1D01G037100 chr1A 94.282 752 39 3 1 750 19625904 19626653 0.000000e+00 1147
19 TraesCS1D01G037100 chr1A 92.308 221 15 2 3853 4073 145873299 145873517 3.060000e-81 313
20 TraesCS1D01G037100 chr1A 92.771 83 4 1 752 832 19264002 19263920 7.160000e-23 119
21 TraesCS1D01G037100 chr1A 91.358 81 7 0 752 832 19688429 19688509 1.200000e-20 111
22 TraesCS1D01G037100 chr7D 93.607 219 12 2 3853 4071 291379592 291379808 3.930000e-85 326
23 TraesCS1D01G037100 chr7D 92.035 226 16 2 3846 4070 160037172 160036948 2.370000e-82 316
24 TraesCS1D01G037100 chr2A 92.576 229 14 3 3846 4074 374137284 374137509 3.930000e-85 326
25 TraesCS1D01G037100 chr5D 92.793 222 14 2 3853 4074 53753838 53754057 1.830000e-83 320


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 TraesCS1D01G037100 chr1D 17264163 17268239 4076 False 7529 7529 100.000 1 4077 1 chr1D.!!$F1 4076
1 TraesCS1D01G037100 chr1D 17289051 17293113 4062 False 6938 6938 97.470 2 4071 1 chr1D.!!$F2 4069
2 TraesCS1D01G037100 chr1D 17393613 17397653 4040 False 6754 6754 96.735 1 4072 1 chr1D.!!$F4 4071
3 TraesCS1D01G037100 chr1D 17334817 17338861 4044 False 6680 6680 96.392 1 4072 1 chr1D.!!$F3 4071
4 TraesCS1D01G037100 chrUn 307553987 307557821 3834 False 6573 6573 97.579 1 3841 1 chrUn.!!$F1 3840
5 TraesCS1D01G037100 chrUn 307578857 307582691 3834 False 6573 6573 97.579 1 3841 1 chrUn.!!$F2 3840
6 TraesCS1D01G037100 chrUn 250124060 250127013 2953 True 5046 5046 97.466 1112 4071 1 chrUn.!!$R1 2959
7 TraesCS1D01G037100 chrUn 327525640 327528538 2898 True 5003 5003 97.795 939 3841 1 chrUn.!!$R2 2902
8 TraesCS1D01G037100 chrUn 455091426 455092401 975 True 1685 1685 97.848 317 1291 1 chrUn.!!$R6 974
9 TraesCS1D01G037100 chrUn 366682612 366683374 762 True 1323 1323 97.911 1 765 1 chrUn.!!$R4 764
10 TraesCS1D01G037100 chrUn 420455020 420455777 757 False 1303 1303 97.635 1 760 1 chrUn.!!$F4 759
11 TraesCS1D01G037100 chrUn 369793109 369793701 592 True 992 992 96.807 1 595 1 chrUn.!!$R5 594
12 TraesCS1D01G037100 chr1B 25473168 25476159 2991 False 4318 4318 92.664 829 3845 1 chr1B.!!$F1 3016
13 TraesCS1D01G037100 chr1A 19640521 19643167 2646 False 3925 3925 93.421 1193 3846 1 chr1A.!!$F2 2653
14 TraesCS1D01G037100 chr1A 19261668 19264002 2334 True 1706 3293 93.215 752 3028 2 chr1A.!!$R1 2276
15 TraesCS1D01G037100 chr1A 19625904 19626653 749 False 1147 1147 94.282 1 750 1 chr1A.!!$F1 749

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
284 287 0.034767 CAGCTTCCTGCCCTTGATCA 60.035 55.000 0.0 0.0 44.23 2.92 F
1407 1468 3.057526 CACGTCATCTGTAGTGTCTTCCA 60.058 47.826 0.0 0.0 0.00 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1451 1512 0.964358 GCACTCATGCCAAGCCTCTT 60.964 55.0 0.00 0.0 46.97 2.85 R
3143 3212 2.537625 GACAGCTGCAGTAAGATAAGCG 59.462 50.0 15.27 0.0 38.90 4.68 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
284 287 0.034767 CAGCTTCCTGCCCTTGATCA 60.035 55.000 0.00 0.00 44.23 2.92
394 397 8.772250 AGTCTAATTATCCCTTGATCTTCAACA 58.228 33.333 0.00 0.00 32.21 3.33
834 891 5.230942 AGTCAAGAAAGTATGTCAACTCCG 58.769 41.667 0.00 0.00 0.00 4.63
836 893 5.346281 GTCAAGAAAGTATGTCAACTCCGAG 59.654 44.000 0.00 0.00 0.00 4.63
1407 1468 3.057526 CACGTCATCTGTAGTGTCTTCCA 60.058 47.826 0.00 0.00 0.00 3.53
1827 1888 7.485418 AATACGTTTTGATGTGAGTTGTACA 57.515 32.000 0.00 0.00 0.00 2.90
1868 1929 4.727507 AGTGAAGAGTACATGTGCTAGG 57.272 45.455 16.96 0.00 0.00 3.02
2188 2255 2.548920 GGAGACCACCACTCTTCAGTTG 60.549 54.545 0.00 0.00 35.10 3.16
2302 2369 2.581354 GACACCTCAGAGCGCCAT 59.419 61.111 2.29 0.00 0.00 4.40
2303 2370 1.676678 GGACACCTCAGAGCGCCATA 61.677 60.000 2.29 0.00 0.00 2.74
2541 2608 6.607689 CACGACTTGGATGCTTGTTTATTTA 58.392 36.000 0.00 0.00 0.00 1.40
2597 2665 4.565028 GGCATGAGATCTAGCAATCATGGA 60.565 45.833 21.91 0.00 45.85 3.41
2630 2698 2.357952 GGTTGTGGAGTGAGTGGTTTTC 59.642 50.000 0.00 0.00 0.00 2.29
2759 2827 2.679450 TCAAAGCAGCATGTTGAATGC 58.321 42.857 14.38 7.24 44.85 3.56
3115 3184 6.884832 TGGACATATGTAGAAAGGTTACCAG 58.115 40.000 8.71 0.00 0.00 4.00
3425 3495 7.122204 TCGTAATTGTCCTAGATGAGTTCTGAA 59.878 37.037 0.00 0.00 35.79 3.02
3513 3583 4.067192 TGCAATGCACGCAGATATTAGAT 58.933 39.130 2.72 0.00 33.55 1.98
3910 3981 5.061721 ACCCTACTTGAACTGATGGTTTT 57.938 39.130 0.00 0.00 38.41 2.43
3911 3982 4.827284 ACCCTACTTGAACTGATGGTTTTG 59.173 41.667 0.00 0.00 38.41 2.44
4055 4127 8.954950 TTTGCAAAATCATCAAGGTTTAAGAA 57.045 26.923 10.02 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 7.287061 ACGGAGTGAATATTGGGATTTTGATA 58.713 34.615 0.00 0.00 42.51 2.15
106 107 4.792068 AGGCTCGGAAATCATGGATTTTA 58.208 39.130 5.74 0.00 41.56 1.52
284 287 5.066246 CGTCTTCCTTAGAACTTCGATAGGT 59.934 44.000 0.00 0.00 33.81 3.08
394 397 2.423538 GCATCCGTGCCTAACTTTTGAT 59.576 45.455 0.00 0.00 45.76 2.57
863 920 4.119862 CCACATTAGTCGGATGGTACTTG 58.880 47.826 0.00 0.00 0.00 3.16
987 1048 8.520119 TTCCCCTATATAGAGTTAAAGGCAAT 57.480 34.615 11.53 0.00 0.00 3.56
1385 1446 3.057526 TGGAAGACACTACAGATGACGTG 60.058 47.826 0.00 0.00 0.00 4.49
1451 1512 0.964358 GCACTCATGCCAAGCCTCTT 60.964 55.000 0.00 0.00 46.97 2.85
1868 1929 6.462323 CGCAAAAATAGCAAAACAATGTATGC 59.538 34.615 13.95 13.95 39.06 3.14
1910 1972 8.143193 TCTGAGTAAAGTTACGTGGTGAAATAA 58.857 33.333 0.00 0.00 38.65 1.40
1932 1994 9.961264 ATACCTATCGATGAATACTAGTTCTGA 57.039 33.333 8.54 0.00 0.00 3.27
2188 2255 5.747951 CAGATTTTAGCATCTGGTTCTCC 57.252 43.478 4.26 0.00 44.57 3.71
2302 2369 6.540189 GCTTCATATTCTCCTTGAACAAGCTA 59.460 38.462 8.81 0.00 37.52 3.32
2303 2370 5.356470 GCTTCATATTCTCCTTGAACAAGCT 59.644 40.000 8.81 0.00 37.52 3.74
2541 2608 3.056607 GCAACCATGACAGCCTACAAAAT 60.057 43.478 0.00 0.00 0.00 1.82
2597 2665 4.280677 CACTCCACAACCCATACATTGTTT 59.719 41.667 0.00 0.00 36.92 2.83
2736 2804 4.201685 GCATTCAACATGCTGCTTTGATTC 60.202 41.667 0.00 0.00 41.52 2.52
2759 2827 6.260936 AGAAGACATAGAAAATTATGGCGTGG 59.739 38.462 0.00 0.00 42.68 4.94
2822 2890 5.163322 TGCCAAAAAGGATCATTGACAAAGT 60.163 36.000 0.00 0.00 41.22 2.66
3143 3212 2.537625 GACAGCTGCAGTAAGATAAGCG 59.462 50.000 15.27 0.00 38.90 4.68
3393 3463 6.124340 TCATCTAGGACAATTACGAGGTACA 58.876 40.000 0.00 0.00 0.00 2.90
3910 3981 1.262417 TCATCAGTACAACCGCCTCA 58.738 50.000 0.00 0.00 0.00 3.86
3911 3982 2.604046 ATCATCAGTACAACCGCCTC 57.396 50.000 0.00 0.00 0.00 4.70


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

AutoCloner maintained by Alex Coulton.