Multiple sequence alignment - TraesCS1A01G233100

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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 TraesCS1A01G233100 chr1A 100.000 4217 0 0 1 4217 406581596 406585812 0.000000e+00 7788
1 TraesCS1A01G233100 chr1A 98.392 3482 33 4 1 3482 407519142 407515684 0.000000e+00 6098
2 TraesCS1A01G233100 chr1A 97.962 2503 41 5 981 3482 425257928 425255435 0.000000e+00 4331
3 TraesCS1A01G233100 chr1A 97.403 2503 53 3 981 3482 421637974 421640465 0.000000e+00 4252
4 TraesCS1A01G233100 chr1A 84.710 1864 248 26 1402 3247 417389158 417387314 0.000000e+00 1829
5 TraesCS1A01G233100 chr1A 99.728 735 2 0 3483 4217 406593001 406593735 0.000000e+00 1347
6 TraesCS1A01G233100 chr1A 95.118 635 28 2 236 869 421637240 421637872 0.000000e+00 998
7 TraesCS1A01G233100 chr1A 90.405 740 45 20 3483 4217 583214502 583215220 0.000000e+00 950
8 TraesCS1A01G233100 chr1A 95.751 353 14 1 1054 1406 417395645 417395294 6.120000e-158 568
9 TraesCS1A01G233100 chr1A 93.675 332 11 6 1 332 425258816 425258495 4.900000e-134 488
10 TraesCS1A01G233100 chr1A 92.192 333 17 6 1 332 417396585 417396261 2.970000e-126 462
11 TraesCS1A01G233100 chr1A 97.131 244 1 1 1 244 421635877 421636114 1.410000e-109 407
12 TraesCS1A01G233100 chr1A 86.175 217 15 9 588 796 425258283 425258074 1.970000e-53 220
13 TraesCS1A01G233100 chr1A 83.796 216 17 7 588 796 417396071 417395867 5.570000e-44 189
14 TraesCS1A01G233100 chr1A 88.272 162 12 2 820 981 421637761 421637915 2.000000e-43 187
15 TraesCS1A01G233100 chr1A 91.071 112 7 1 761 872 407518320 407518212 9.450000e-32 148
16 TraesCS1A01G233100 chr1B 96.784 3141 83 6 343 3482 435360002 435363125 0.000000e+00 5225
17 TraesCS1A01G233100 chr1B 87.816 2889 274 42 334 3201 326928119 326925288 0.000000e+00 3314
18 TraesCS1A01G233100 chr1B 89.799 1539 147 6 1040 2576 435927071 435928601 0.000000e+00 1964
19 TraesCS1A01G233100 chr1B 96.697 333 10 1 1 332 442621789 442621457 1.710000e-153 553
20 TraesCS1A01G233100 chr1B 95.509 334 6 5 1 334 435359597 435359921 3.740000e-145 525
21 TraesCS1A01G233100 chr1B 93.846 325 7 7 1 323 326928475 326928162 1.060000e-130 477
22 TraesCS1A01G233100 chr1B 93.464 153 9 1 717 869 435808496 435808647 4.240000e-55 226
23 TraesCS1A01G233100 chr1B 85.965 171 10 6 588 750 442621242 442621078 2.020000e-38 171
24 TraesCS1A01G233100 chr1B 92.857 112 5 1 758 869 435360474 435360582 4.360000e-35 159
25 TraesCS1A01G233100 chr1B 89.286 112 10 2 761 872 326927656 326927547 5.690000e-29 139
26 TraesCS1A01G233100 chr1B 89.815 108 4 4 874 981 435814228 435814328 9.510000e-27 132
27 TraesCS1A01G233100 chr1D 96.286 2504 81 4 981 3482 322380989 322383482 0.000000e+00 4098
28 TraesCS1A01G233100 chr1D 88.894 2080 206 11 1040 3116 323636534 323638591 0.000000e+00 2538
29 TraesCS1A01G233100 chr1D 86.696 2285 258 30 981 3247 328445991 328443735 0.000000e+00 2494
30 TraesCS1A01G233100 chr1D 96.014 878 22 4 1 869 322380014 322380887 0.000000e+00 1415
31 TraesCS1A01G233100 chr1D 90.237 338 10 15 1 332 328453301 328452981 1.810000e-113 420
32 TraesCS1A01G233100 chr1D 87.097 217 14 6 588 796 328446363 328446153 2.540000e-57 233
33 TraesCS1A01G233100 chr1D 91.045 134 9 1 820 950 322380773 322380906 1.200000e-40 178
34 TraesCS1A01G233100 chr4B 98.777 736 6 2 3483 4217 41401535 41400802 0.000000e+00 1306
35 TraesCS1A01G233100 chr4B 98.370 736 9 2 3483 4217 41393430 41392697 0.000000e+00 1290
36 TraesCS1A01G233100 chr4B 94.407 751 20 13 3481 4217 262954250 262953508 0.000000e+00 1134
37 TraesCS1A01G233100 chrUn 98.345 725 8 3 3483 4207 239762830 239762110 0.000000e+00 1269
38 TraesCS1A01G233100 chrUn 98.207 725 9 3 3483 4207 239770814 239770094 0.000000e+00 1264
39 TraesCS1A01G233100 chrUn 94.126 749 22 13 3483 4217 338968046 338967306 0.000000e+00 1120
40 TraesCS1A01G233100 chr7B 98.345 725 8 3 3483 4207 193660884 193661604 0.000000e+00 1269
41 TraesCS1A01G233100 chr2B 84.768 604 62 27 3483 4066 563353218 563352625 2.830000e-161 579
42 TraesCS1A01G233100 chr3B 76.935 672 119 29 3476 4130 509860285 509859633 2.410000e-92 350


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 TraesCS1A01G233100 chr1A 406581596 406585812 4216 False 7788.000000 7788 100.000000 1 4217 1 chr1A.!!$F1 4216
1 TraesCS1A01G233100 chr1A 407515684 407519142 3458 True 3123.000000 6098 94.731500 1 3482 2 chr1A.!!$R2 3481
2 TraesCS1A01G233100 chr1A 417387314 417389158 1844 True 1829.000000 1829 84.710000 1402 3247 1 chr1A.!!$R1 1845
3 TraesCS1A01G233100 chr1A 425255435 425258816 3381 True 1679.666667 4331 92.604000 1 3482 3 chr1A.!!$R4 3481
4 TraesCS1A01G233100 chr1A 421635877 421640465 4588 False 1461.000000 4252 94.481000 1 3482 4 chr1A.!!$F4 3481
5 TraesCS1A01G233100 chr1A 406593001 406593735 734 False 1347.000000 1347 99.728000 3483 4217 1 chr1A.!!$F2 734
6 TraesCS1A01G233100 chr1A 583214502 583215220 718 False 950.000000 950 90.405000 3483 4217 1 chr1A.!!$F3 734
7 TraesCS1A01G233100 chr1A 417395294 417396585 1291 True 406.333333 568 90.579667 1 1406 3 chr1A.!!$R3 1405
8 TraesCS1A01G233100 chr1B 435359597 435363125 3528 False 1969.666667 5225 95.050000 1 3482 3 chr1B.!!$F4 3481
9 TraesCS1A01G233100 chr1B 435927071 435928601 1530 False 1964.000000 1964 89.799000 1040 2576 1 chr1B.!!$F3 1536
10 TraesCS1A01G233100 chr1B 326925288 326928475 3187 True 1310.000000 3314 90.316000 1 3201 3 chr1B.!!$R1 3200
11 TraesCS1A01G233100 chr1B 442621078 442621789 711 True 362.000000 553 91.331000 1 750 2 chr1B.!!$R2 749
12 TraesCS1A01G233100 chr1D 323636534 323638591 2057 False 2538.000000 2538 88.894000 1040 3116 1 chr1D.!!$F1 2076
13 TraesCS1A01G233100 chr1D 322380014 322383482 3468 False 1897.000000 4098 94.448333 1 3482 3 chr1D.!!$F2 3481
14 TraesCS1A01G233100 chr1D 328443735 328446363 2628 True 1363.500000 2494 86.896500 588 3247 2 chr1D.!!$R2 2659
15 TraesCS1A01G233100 chr4B 41400802 41401535 733 True 1306.000000 1306 98.777000 3483 4217 1 chr4B.!!$R2 734
16 TraesCS1A01G233100 chr4B 41392697 41393430 733 True 1290.000000 1290 98.370000 3483 4217 1 chr4B.!!$R1 734
17 TraesCS1A01G233100 chr4B 262953508 262954250 742 True 1134.000000 1134 94.407000 3481 4217 1 chr4B.!!$R3 736
18 TraesCS1A01G233100 chrUn 239762110 239762830 720 True 1269.000000 1269 98.345000 3483 4207 1 chrUn.!!$R1 724
19 TraesCS1A01G233100 chrUn 239770094 239770814 720 True 1264.000000 1264 98.207000 3483 4207 1 chrUn.!!$R2 724
20 TraesCS1A01G233100 chrUn 338967306 338968046 740 True 1120.000000 1120 94.126000 3483 4217 1 chrUn.!!$R3 734
21 TraesCS1A01G233100 chr7B 193660884 193661604 720 False 1269.000000 1269 98.345000 3483 4207 1 chr7B.!!$F1 724
22 TraesCS1A01G233100 chr2B 563352625 563353218 593 True 579.000000 579 84.768000 3483 4066 1 chr2B.!!$R1 583
23 TraesCS1A01G233100 chr3B 509859633 509860285 652 True 350.000000 350 76.935000 3476 4130 1 chr3B.!!$R1 654

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
546 1852 2.046507 ACGAGCGTCTCCCTACGT 60.047 61.111 0.00 0.00 44.64 3.57 F
878 2196 2.518349 CACCACCACCACCACCAC 60.518 66.667 0.00 0.00 0.00 4.16 F
1602 3196 3.583806 CAGAGCATATGATTCCGGAGAC 58.416 50.000 6.97 3.42 0.00 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1602 3196 1.302431 TGTTCCATGCCCTGTGTCG 60.302 57.895 0.0 0.0 0.0 4.35 R
2700 4303 1.065926 TGATGCTGCTCGTCCAAGATT 60.066 47.619 0.0 0.0 0.0 2.40 R
3243 4846 2.183478 ACATGTGCGATTCTCCAACA 57.817 45.000 0.0 0.0 0.0 3.33 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
546 1852 2.046507 ACGAGCGTCTCCCTACGT 60.047 61.111 0.00 0.00 44.64 3.57
770 2088 3.056749 GGTAGAGTGAGCGAAAGAGGAAA 60.057 47.826 0.00 0.00 0.00 3.13
878 2196 2.518349 CACCACCACCACCACCAC 60.518 66.667 0.00 0.00 0.00 4.16
879 2197 3.816090 ACCACCACCACCACCACC 61.816 66.667 0.00 0.00 0.00 4.61
880 2198 3.814906 CCACCACCACCACCACCA 61.815 66.667 0.00 0.00 0.00 4.17
1602 3196 3.583806 CAGAGCATATGATTCCGGAGAC 58.416 50.000 6.97 3.42 0.00 3.36
3054 4657 2.680841 GTCTCTCACAGTGCGAGTCTAT 59.319 50.000 18.12 0.00 0.00 1.98
3243 4846 5.889853 AGGAAAAGCATGTGTGACATATGAT 59.110 36.000 23.73 16.17 36.53 2.45
3365 4968 4.443913 CATCCATTGCTGTCACAATTCA 57.556 40.909 0.00 0.00 38.19 2.57
3723 5341 7.452189 GTCTCCTACTATTGTTAGGGAGCTATT 59.548 40.741 14.06 0.00 36.80 1.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
546 1852 1.271840 GCCCTGACACCCCTACATGA 61.272 60.000 0.00 0.0 0.00 3.07
770 2088 2.036346 GGTGGAGAGCAGCAAATGTTTT 59.964 45.455 0.00 0.0 0.00 2.43
773 2091 0.957395 CGGTGGAGAGCAGCAAATGT 60.957 55.000 0.00 0.0 0.00 2.71
878 2196 2.289072 TGCGTCTTCCTCTTTCTCTTGG 60.289 50.000 0.00 0.0 0.00 3.61
879 2197 3.032017 TGCGTCTTCCTCTTTCTCTTG 57.968 47.619 0.00 0.0 0.00 3.02
880 2198 3.971245 ATGCGTCTTCCTCTTTCTCTT 57.029 42.857 0.00 0.0 0.00 2.85
1006 2594 3.456277 GGGATCATGAGGTTCTACTGGTT 59.544 47.826 0.09 0.0 0.00 3.67
1007 2595 3.041946 GGGATCATGAGGTTCTACTGGT 58.958 50.000 0.09 0.0 0.00 4.00
1008 2596 3.041211 TGGGATCATGAGGTTCTACTGG 58.959 50.000 0.09 0.0 0.00 4.00
1009 2597 3.708631 AGTGGGATCATGAGGTTCTACTG 59.291 47.826 0.09 0.0 0.00 2.74
1010 2598 4.000928 AGTGGGATCATGAGGTTCTACT 57.999 45.455 0.09 0.0 0.00 2.57
1011 2599 4.762289 AAGTGGGATCATGAGGTTCTAC 57.238 45.455 0.09 0.0 0.00 2.59
1012 2600 5.488919 AGAAAAGTGGGATCATGAGGTTCTA 59.511 40.000 0.09 0.0 0.00 2.10
1013 2601 4.290722 AGAAAAGTGGGATCATGAGGTTCT 59.709 41.667 0.09 0.0 0.00 3.01
1014 2602 4.593956 AGAAAAGTGGGATCATGAGGTTC 58.406 43.478 0.09 0.0 0.00 3.62
1602 3196 1.302431 TGTTCCATGCCCTGTGTCG 60.302 57.895 0.00 0.0 0.00 4.35
1845 3439 2.083774 GCAACCGGATCATCAGTGAAA 58.916 47.619 9.46 0.0 38.01 2.69
2700 4303 1.065926 TGATGCTGCTCGTCCAAGATT 60.066 47.619 0.00 0.0 0.00 2.40
2979 4582 5.485353 TGAATTTATTGGCCCCACATTTGTA 59.515 36.000 0.00 0.0 0.00 2.41
3243 4846 2.183478 ACATGTGCGATTCTCCAACA 57.817 45.000 0.00 0.0 0.00 3.33
3384 4987 6.976934 AACACTGTTGATAAGTTGGGAAAT 57.023 33.333 0.00 0.0 0.00 2.17


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

AutoCloner maintained by Alex Coulton.