Multiple sequence alignment - TraesCS6A01G049300

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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 TraesCS6A01G049300 chr6A 100.000 4139 0 0 1 4139 25222508 25226646 0.000000e+00 7644.0
1 TraesCS6A01G049300 chr6A 97.280 4155 71 17 1 4117 16549380 16545230 0.000000e+00 7009.0
2 TraesCS6A01G049300 chr6A 97.050 4135 79 12 1 4120 396387841 396391947 0.000000e+00 6920.0
3 TraesCS6A01G049300 chr6A 94.899 3156 135 19 821 3955 11515756 11518906 0.000000e+00 4913.0
4 TraesCS6A01G049300 chr7A 97.676 4131 74 8 1 4117 309551601 309555723 0.000000e+00 7077.0
5 TraesCS6A01G049300 chr7A 94.857 3286 157 5 675 3955 572342839 572346117 0.000000e+00 5121.0
6 TraesCS6A01G049300 chr7A 95.652 161 7 0 3957 4117 572346278 572346438 4.100000e-65 259.0
7 TraesCS6A01G049300 chr5A 97.461 4135 70 10 1 4117 320485348 320489465 0.000000e+00 7022.0
8 TraesCS6A01G049300 chr3D 95.476 3404 119 22 675 4062 126047564 126050948 0.000000e+00 5400.0
9 TraesCS6A01G049300 chr3D 94.669 2720 124 13 675 3380 4875397 4878109 0.000000e+00 4200.0
10 TraesCS6A01G049300 chr6B 94.876 2947 129 8 451 3380 331029784 331032725 0.000000e+00 4586.0
11 TraesCS6A01G049300 chr6B 90.272 257 15 5 1 256 331029419 331029666 1.110000e-85 327.0
12 TraesCS6A01G049300 chr6B 94.521 73 3 1 263 334 331029714 331029786 1.220000e-20 111.0
13 TraesCS6A01G049300 chr7B 93.390 469 15 3 451 907 231202754 231203218 0.000000e+00 680.0
14 TraesCS6A01G049300 chr7B 90.347 259 14 6 1 257 231202388 231202637 3.080000e-86 329.0
15 TraesCS6A01G049300 chr7B 94.521 73 3 1 263 334 231202684 231202756 1.220000e-20 111.0
16 TraesCS6A01G049300 chr2B 93.987 449 14 3 451 887 157788606 157789053 0.000000e+00 667.0
17 TraesCS6A01G049300 chr2B 89.189 259 16 6 1 256 157788239 157788488 3.110000e-81 313.0
18 TraesCS6A01G049300 chr2B 88.372 258 19 6 1 256 691195006 691194758 2.420000e-77 300.0
19 TraesCS6A01G049300 chr2B 96.000 75 2 1 450 524 691194640 691194567 2.020000e-23 121.0
20 TraesCS6A01G049300 chr2B 95.833 72 2 1 263 333 691194710 691194639 9.400000e-22 115.0
21 TraesCS6A01G049300 chr2B 94.521 73 3 1 263 334 157788536 157788608 1.220000e-20 111.0
22 TraesCS6A01G049300 chr3B 92.641 462 32 1 3475 3934 769138687 769139148 0.000000e+00 664.0
23 TraesCS6A01G049300 chr3B 82.474 97 16 1 3969 4065 491531847 491531942 2.650000e-12 84.2
24 TraesCS6A01G049300 chr4A 90.667 225 10 1 452 665 658969386 658969162 5.240000e-74 289.0
25 TraesCS6A01G049300 chr2A 90.441 136 13 0 3977 4112 752779660 752779525 3.290000e-41 180.0


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 TraesCS6A01G049300 chr6A 25222508 25226646 4138 False 7644.000000 7644 100.000000 1 4139 1 chr6A.!!$F2 4138
1 TraesCS6A01G049300 chr6A 16545230 16549380 4150 True 7009.000000 7009 97.280000 1 4117 1 chr6A.!!$R1 4116
2 TraesCS6A01G049300 chr6A 396387841 396391947 4106 False 6920.000000 6920 97.050000 1 4120 1 chr6A.!!$F3 4119
3 TraesCS6A01G049300 chr6A 11515756 11518906 3150 False 4913.000000 4913 94.899000 821 3955 1 chr6A.!!$F1 3134
4 TraesCS6A01G049300 chr7A 309551601 309555723 4122 False 7077.000000 7077 97.676000 1 4117 1 chr7A.!!$F1 4116
5 TraesCS6A01G049300 chr7A 572342839 572346438 3599 False 2690.000000 5121 95.254500 675 4117 2 chr7A.!!$F2 3442
6 TraesCS6A01G049300 chr5A 320485348 320489465 4117 False 7022.000000 7022 97.461000 1 4117 1 chr5A.!!$F1 4116
7 TraesCS6A01G049300 chr3D 126047564 126050948 3384 False 5400.000000 5400 95.476000 675 4062 1 chr3D.!!$F2 3387
8 TraesCS6A01G049300 chr3D 4875397 4878109 2712 False 4200.000000 4200 94.669000 675 3380 1 chr3D.!!$F1 2705
9 TraesCS6A01G049300 chr6B 331029419 331032725 3306 False 1674.666667 4586 93.223000 1 3380 3 chr6B.!!$F1 3379
10 TraesCS6A01G049300 chr7B 231202388 231203218 830 False 373.333333 680 92.752667 1 907 3 chr7B.!!$F1 906
11 TraesCS6A01G049300 chr2B 157788239 157789053 814 False 363.666667 667 92.565667 1 887 3 chr2B.!!$F1 886

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
806 863 0.671796 TCGTTGATATCCGGTGCGAT 59.328 50.000 0.0 0.0 0.00 4.58 F
987 1045 1.221466 TTTGCTCAGCAGGACGTTCG 61.221 55.000 0.0 0.0 40.61 3.95 F
2714 2808 2.711174 AGATCCTATGGCTGATTGGGT 58.289 47.619 0.0 0.0 0.00 4.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2714 2808 1.072173 CAGTGAGGGTGACATGTTGGA 59.928 52.381 0.00 0.0 0.00 3.53 R
2796 2890 7.502120 AAGGATATTGAATTGATCACTTCGG 57.498 36.000 17.86 0.0 37.92 4.30 R
3820 3947 3.937706 GACCTCAATCCAACAGACTCATG 59.062 47.826 0.00 0.0 0.00 3.07 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
43 44 4.071423 TGTAGCTGCAGTTTAGCATTCAA 58.929 39.130 16.64 0.00 44.68 2.69
246 250 2.487762 TCGGCAAATTTTACTCTGCTGG 59.512 45.455 6.54 0.00 40.78 4.85
418 463 3.120338 GCGTGCTGCATAAGAAGTAACAA 60.120 43.478 5.27 0.00 45.45 2.83
446 491 9.819267 GGTTAGAAGATGTAGTTAATGCTTAGT 57.181 33.333 0.00 0.00 0.00 2.24
750 807 8.436046 CTCTGATTAGAAAAATGGAAGAGGAG 57.564 38.462 0.00 0.00 31.21 3.69
806 863 0.671796 TCGTTGATATCCGGTGCGAT 59.328 50.000 0.00 0.00 0.00 4.58
987 1045 1.221466 TTTGCTCAGCAGGACGTTCG 61.221 55.000 0.00 0.00 40.61 3.95
1055 1113 7.332926 TGAAGAAGATGTTGACTATGAAGAAGC 59.667 37.037 0.00 0.00 0.00 3.86
1098 1165 7.250032 TGAGGATGATGAAGAAGAAGAAGAA 57.750 36.000 0.00 0.00 0.00 2.52
1101 1168 8.093118 AGGATGATGAAGAAGAAGAAGAAGAT 57.907 34.615 0.00 0.00 0.00 2.40
1102 1169 7.988599 AGGATGATGAAGAAGAAGAAGAAGATG 59.011 37.037 0.00 0.00 0.00 2.90
1103 1170 7.986320 GGATGATGAAGAAGAAGAAGAAGATGA 59.014 37.037 0.00 0.00 0.00 2.92
2151 2243 4.216257 CCAATTCTTGATGTTCCAACTCGT 59.784 41.667 0.00 0.00 0.00 4.18
2530 2623 6.813152 GGACCCACAATTCAAGTTGAAATATG 59.187 38.462 21.57 20.38 40.12 1.78
2535 2628 9.426837 CCACAATTCAAGTTGAAATATGTTGAT 57.573 29.630 25.04 13.02 40.12 2.57
2714 2808 2.711174 AGATCCTATGGCTGATTGGGT 58.289 47.619 0.00 0.00 0.00 4.51
2756 2850 6.150976 ACTGCTCGATCAACAAATTTGGATTA 59.849 34.615 21.74 5.34 0.00 1.75
2796 2890 0.035820 TGTCAAAGGTACCCATCCGC 60.036 55.000 8.74 0.00 0.00 5.54
3492 3606 0.324614 ATGTTGCGGAGTGGATGACA 59.675 50.000 0.00 0.00 0.00 3.58
3865 3992 7.078228 GTCATTAGCTTGACGTTCTTTGAAAT 58.922 34.615 2.87 0.00 36.93 2.17
3866 3993 7.269297 GTCATTAGCTTGACGTTCTTTGAAATC 59.731 37.037 2.87 0.00 36.93 2.17
3955 4082 6.872628 TGTAATCTCATGATCTTGCCATTC 57.127 37.500 0.00 1.58 31.51 2.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
94 95 3.181516 CGAAAGGCTAAACTGCAGCTAAG 60.182 47.826 15.27 9.5 39.09 2.18
98 99 3.683581 CGAAAGGCTAAACTGCAGC 57.316 52.632 15.27 0.0 38.35 5.25
246 250 5.730296 ACATATGCACTACTCCATCCTAC 57.270 43.478 1.58 0.0 0.00 3.18
408 453 9.877178 CTACATCTTCTAACCATTGTTACTTCT 57.123 33.333 0.00 0.0 35.87 2.85
732 788 5.044846 CCCTTCCTCCTCTTCCATTTTTCTA 60.045 44.000 0.00 0.0 0.00 2.10
750 807 1.649271 ATGCCTCATGGTCCCCTTCC 61.649 60.000 0.00 0.0 35.27 3.46
900 957 5.857268 GCAACCATTAATTTGCATCCCTAT 58.143 37.500 16.48 0.0 46.13 2.57
941 999 8.662141 GGACACGAGTGTTAACATTACAATTAT 58.338 33.333 12.26 0.0 45.05 1.28
987 1045 2.683968 TCAACCATACGAGTGTCTTGC 58.316 47.619 0.00 0.0 0.00 4.01
1055 1113 4.099881 CCTCATCTTCTTCTCCTTCCTCTG 59.900 50.000 0.00 0.0 0.00 3.35
1098 1165 8.706521 TCTTCTTCTTCTTCATCATCATCATCT 58.293 33.333 0.00 0.0 0.00 2.90
1101 1168 8.537858 TCTTCTTCTTCTTCTTCATCATCATCA 58.462 33.333 0.00 0.0 0.00 3.07
1102 1169 8.945481 TCTTCTTCTTCTTCTTCATCATCATC 57.055 34.615 0.00 0.0 0.00 2.92
1103 1170 7.988599 CCTCTTCTTCTTCTTCTTCATCATCAT 59.011 37.037 0.00 0.0 0.00 2.45
1537 1628 9.224267 GCATATCATCTTGAAGCTAGGATTTAA 57.776 33.333 0.00 0.0 0.00 1.52
2132 2224 4.811555 CAACGAGTTGGAACATCAAGAA 57.188 40.909 8.01 0.0 39.30 2.52
2151 2243 5.497464 TCATCATGTAGGTTGAGTTCCAA 57.503 39.130 0.00 0.0 0.00 3.53
2530 2623 3.945285 TCTAGGCCAAATCGGAAATCAAC 59.055 43.478 5.01 0.0 36.56 3.18
2535 2628 3.713826 AACTCTAGGCCAAATCGGAAA 57.286 42.857 5.01 0.0 36.56 3.13
2714 2808 1.072173 CAGTGAGGGTGACATGTTGGA 59.928 52.381 0.00 0.0 0.00 3.53
2796 2890 7.502120 AAGGATATTGAATTGATCACTTCGG 57.498 36.000 17.86 0.0 37.92 4.30
3161 3261 7.544804 ACATGGCACTATATACATCAGAAGA 57.455 36.000 0.00 0.0 0.00 2.87
3820 3947 3.937706 GACCTCAATCCAACAGACTCATG 59.062 47.826 0.00 0.0 0.00 3.07
3865 3992 6.285224 TCGAACAAGACCAAAAGATTACAGA 58.715 36.000 0.00 0.0 0.00 3.41
3866 3993 6.539649 TCGAACAAGACCAAAAGATTACAG 57.460 37.500 0.00 0.0 0.00 2.74
3955 4082 7.830739 ACCCAGAATTTAGCAAATGTTTCTAG 58.169 34.615 0.00 0.0 0.00 2.43


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

AutoCloner maintained by Alex Coulton.