Multiple sequence alignment - TraesCS3B01G384100

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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 TraesCS3B01G384100 chr3B 100.000 2783 0 0 1 2783 604142034 604139252 0.000000e+00 5140
1 TraesCS3B01G384100 chr3B 95.720 771 20 3 1509 2267 576053728 576052959 0.000000e+00 1229
2 TraesCS3B01G384100 chr3B 93.981 515 31 0 2269 2783 596728289 596727775 0.000000e+00 780
3 TraesCS3B01G384100 chr2B 97.216 1257 35 0 1015 2271 358758455 358759711 0.000000e+00 2128
4 TraesCS3B01G384100 chr2B 97.554 1022 22 3 1 1020 358756443 358757463 0.000000e+00 1746
5 TraesCS3B01G384100 chr2B 89.935 308 28 1 713 1020 579976455 579976759 7.220000e-106 394
6 TraesCS3B01G384100 chr4B 97.209 1254 31 3 1015 2268 535286557 535287806 0.000000e+00 2119
7 TraesCS3B01G384100 chr4B 96.335 1255 26 2 1018 2271 449519095 449520330 0.000000e+00 2045
8 TraesCS3B01G384100 chr4B 96.610 1003 30 4 16 1017 449516887 449517886 0.000000e+00 1661
9 TraesCS3B01G384100 chr4B 96.142 985 37 1 37 1020 535284450 535285434 0.000000e+00 1607
10 TraesCS3B01G384100 chr7A 94.374 1262 56 9 1018 2267 297775788 297774530 0.000000e+00 1923
11 TraesCS3B01G384100 chr7A 93.495 907 52 6 119 1020 297786601 297785697 0.000000e+00 1341
12 TraesCS3B01G384100 chr6A 93.459 1269 64 6 1018 2270 571575077 571576342 0.000000e+00 1866
13 TraesCS3B01G384100 chr6A 92.637 910 56 9 119 1020 571572986 571573892 0.000000e+00 1299
14 TraesCS3B01G384100 chr6A 93.333 510 34 0 2274 2783 131933634 131933125 0.000000e+00 754
15 TraesCS3B01G384100 chr6A 93.120 407 26 2 1863 2268 554477586 554477991 1.850000e-166 595
16 TraesCS3B01G384100 chr5D 93.664 1231 55 6 1018 2236 420019679 420020898 0.000000e+00 1820
17 TraesCS3B01G384100 chr5D 89.796 931 75 11 1018 1933 538687420 538688345 0.000000e+00 1175
18 TraesCS3B01G384100 chr5D 91.699 771 43 14 119 884 420017634 420018388 0.000000e+00 1050
19 TraesCS3B01G384100 chr5D 84.553 123 11 8 1 119 474296910 474297028 6.300000e-22 115
20 TraesCS3B01G384100 chr1B 94.930 1006 37 4 1275 2268 400360012 400361015 0.000000e+00 1563
21 TraesCS3B01G384100 chr1B 95.486 864 33 6 121 980 400359148 400360009 0.000000e+00 1375
22 TraesCS3B01G384100 chr3D 86.987 1268 115 25 1018 2270 339817451 339818683 0.000000e+00 1382
23 TraesCS3B01G384100 chr3D 89.894 752 68 6 272 1020 148505217 148504471 0.000000e+00 961
24 TraesCS3B01G384100 chr3D 93.385 514 34 0 2269 2782 277626067 277626580 0.000000e+00 761
25 TraesCS3B01G384100 chr3D 92.816 515 37 0 2269 2783 335355389 335355903 0.000000e+00 747
26 TraesCS3B01G384100 chr4D 89.689 931 76 11 1018 1933 145379791 145378866 0.000000e+00 1170
27 TraesCS3B01G384100 chr4D 93.204 515 35 0 2269 2783 440497129 440496615 0.000000e+00 758
28 TraesCS3B01G384100 chr4A 89.259 931 81 13 1018 1933 629935919 629936845 0.000000e+00 1147
29 TraesCS3B01G384100 chr7D 87.712 765 83 8 133 890 578491108 578490348 0.000000e+00 881
30 TraesCS3B01G384100 chr7D 93.204 515 35 0 2269 2783 154519628 154519114 0.000000e+00 758
31 TraesCS3B01G384100 chr7D 93.010 515 35 1 2269 2783 326071256 326071769 0.000000e+00 750
32 TraesCS3B01G384100 chr1D 94.175 515 30 0 2269 2783 223043087 223043601 0.000000e+00 785
33 TraesCS3B01G384100 chr6D 93.137 510 35 0 2271 2780 71952004 71952513 0.000000e+00 749


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 TraesCS3B01G384100 chr3B 604139252 604142034 2782 True 5140.0 5140 100.0000 1 2783 1 chr3B.!!$R3 2782
1 TraesCS3B01G384100 chr3B 576052959 576053728 769 True 1229.0 1229 95.7200 1509 2267 1 chr3B.!!$R1 758
2 TraesCS3B01G384100 chr3B 596727775 596728289 514 True 780.0 780 93.9810 2269 2783 1 chr3B.!!$R2 514
3 TraesCS3B01G384100 chr2B 358756443 358759711 3268 False 1937.0 2128 97.3850 1 2271 2 chr2B.!!$F2 2270
4 TraesCS3B01G384100 chr4B 535284450 535287806 3356 False 1863.0 2119 96.6755 37 2268 2 chr4B.!!$F2 2231
5 TraesCS3B01G384100 chr4B 449516887 449520330 3443 False 1853.0 2045 96.4725 16 2271 2 chr4B.!!$F1 2255
6 TraesCS3B01G384100 chr7A 297774530 297775788 1258 True 1923.0 1923 94.3740 1018 2267 1 chr7A.!!$R1 1249
7 TraesCS3B01G384100 chr7A 297785697 297786601 904 True 1341.0 1341 93.4950 119 1020 1 chr7A.!!$R2 901
8 TraesCS3B01G384100 chr6A 571572986 571576342 3356 False 1582.5 1866 93.0480 119 2270 2 chr6A.!!$F2 2151
9 TraesCS3B01G384100 chr6A 131933125 131933634 509 True 754.0 754 93.3330 2274 2783 1 chr6A.!!$R1 509
10 TraesCS3B01G384100 chr5D 420017634 420020898 3264 False 1435.0 1820 92.6815 119 2236 2 chr5D.!!$F3 2117
11 TraesCS3B01G384100 chr5D 538687420 538688345 925 False 1175.0 1175 89.7960 1018 1933 1 chr5D.!!$F2 915
12 TraesCS3B01G384100 chr1B 400359148 400361015 1867 False 1469.0 1563 95.2080 121 2268 2 chr1B.!!$F1 2147
13 TraesCS3B01G384100 chr3D 339817451 339818683 1232 False 1382.0 1382 86.9870 1018 2270 1 chr3D.!!$F3 1252
14 TraesCS3B01G384100 chr3D 148504471 148505217 746 True 961.0 961 89.8940 272 1020 1 chr3D.!!$R1 748
15 TraesCS3B01G384100 chr3D 277626067 277626580 513 False 761.0 761 93.3850 2269 2782 1 chr3D.!!$F1 513
16 TraesCS3B01G384100 chr3D 335355389 335355903 514 False 747.0 747 92.8160 2269 2783 1 chr3D.!!$F2 514
17 TraesCS3B01G384100 chr4D 145378866 145379791 925 True 1170.0 1170 89.6890 1018 1933 1 chr4D.!!$R1 915
18 TraesCS3B01G384100 chr4D 440496615 440497129 514 True 758.0 758 93.2040 2269 2783 1 chr4D.!!$R2 514
19 TraesCS3B01G384100 chr4A 629935919 629936845 926 False 1147.0 1147 89.2590 1018 1933 1 chr4A.!!$F1 915
20 TraesCS3B01G384100 chr7D 578490348 578491108 760 True 881.0 881 87.7120 133 890 1 chr7D.!!$R2 757
21 TraesCS3B01G384100 chr7D 154519114 154519628 514 True 758.0 758 93.2040 2269 2783 1 chr7D.!!$R1 514
22 TraesCS3B01G384100 chr7D 326071256 326071769 513 False 750.0 750 93.0100 2269 2783 1 chr7D.!!$F1 514
23 TraesCS3B01G384100 chr1D 223043087 223043601 514 False 785.0 785 94.1750 2269 2783 1 chr1D.!!$F1 514
24 TraesCS3B01G384100 chr6D 71952004 71952513 509 False 749.0 749 93.1370 2271 2780 1 chr6D.!!$F1 509

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
60 61 0.106619 GCCGTCCCTCTTCCTCTCTA 60.107 60.0 0.0 0.0 0.0 2.43 F
1314 2621 0.178924 ACAAAGCTGATGCCCCCTTT 60.179 50.0 0.0 0.0 40.8 3.11 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1567 2874 0.821301 TTCACAAGTGCATCGGCCAA 60.821 50.0 2.24 0.0 40.13 4.52 R
2705 4033 0.951558 TGGCACCTTTCGAAGCTTTC 59.048 50.0 0.00 0.0 0.00 2.62 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
38 39 2.765356 CCTCTACAGCTCTCGCGCA 61.765 63.158 8.75 0.00 42.32 6.09
60 61 0.106619 GCCGTCCCTCTTCCTCTCTA 60.107 60.000 0.00 0.00 0.00 2.43
85 86 0.690411 CCATGCCTCTCCCTCTCTGT 60.690 60.000 0.00 0.00 0.00 3.41
650 666 1.075542 TCGCTTTTGTGGCATACTCG 58.924 50.000 0.00 0.00 0.00 4.18
774 791 8.712285 ATTTCAGCCAATTTTTGTAGATCATG 57.288 30.769 0.00 0.00 0.00 3.07
837 854 3.199880 AGGGGAGCTTCGTAATGATTG 57.800 47.619 0.00 0.00 0.00 2.67
861 878 3.524095 AACACCACCATCATTGGAGAA 57.476 42.857 0.00 0.00 46.92 2.87
1072 2378 5.012239 AGCAATTCAAGCTTTCTATCACCA 58.988 37.500 0.00 0.00 39.87 4.17
1253 2560 7.280205 ACCCTACAAATCTGATGTCGTTTTATC 59.720 37.037 0.00 0.00 32.27 1.75
1314 2621 0.178924 ACAAAGCTGATGCCCCCTTT 60.179 50.000 0.00 0.00 40.80 3.11
1351 2658 2.189594 GCACTATCATGCCATGGCTA 57.810 50.000 35.53 22.71 39.86 3.93
1567 2874 6.790232 TTCTCAAAGATGGGTTCAAACTTT 57.210 33.333 0.00 0.00 35.58 2.66
1578 2885 1.035923 TCAAACTTTTGGCCGATGCA 58.964 45.000 0.00 0.00 40.13 3.96
1890 3214 2.929161 GCGTGTGTGGCTGTCAAGTATA 60.929 50.000 0.00 0.00 0.00 1.47
2277 3604 7.269316 CAACCAAACACACCCTAACTAAATTT 58.731 34.615 0.00 0.00 0.00 1.82
2302 3629 2.234661 CCAGTGGCACTGTATCTCTCAA 59.765 50.000 37.43 0.00 44.50 3.02
2360 3687 2.878406 CTGGGAAACGTGAAACACATCT 59.122 45.455 0.00 0.00 35.74 2.90
2387 3715 3.112263 TCCTGACAATCCTTCGGGTAAT 58.888 45.455 0.00 0.00 40.11 1.89
2393 3721 4.668636 ACAATCCTTCGGGTAATTCCAAA 58.331 39.130 0.00 0.00 38.11 3.28
2401 3729 5.438698 TCGGGTAATTCCAAATTGTAGGA 57.561 39.130 0.00 0.00 38.11 2.94
2516 3844 4.202020 GGTGACACACGAAGATATGCTCTA 60.202 45.833 8.08 0.00 34.83 2.43
2522 3850 6.264292 ACACACGAAGATATGCTCTATCTCTT 59.736 38.462 9.05 0.00 35.59 2.85
2554 3882 5.186996 ACTACCTTCTTGCATTTTGTGTG 57.813 39.130 0.00 0.00 0.00 3.82
2705 4033 1.139853 GTCCTGCACCTCCTTCCATAG 59.860 57.143 0.00 0.00 0.00 2.23
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 2.760385 GAGCTGTAGAGGGGCGGT 60.760 66.667 0.00 0.0 0.00 5.68
38 39 4.698625 AGGAAGAGGGACGGCGGT 62.699 66.667 13.24 0.0 0.00 5.68
203 208 0.183492 ATGGGTGTGCTTGACTGTGT 59.817 50.000 0.00 0.0 0.00 3.72
206 211 1.002888 AGAGATGGGTGTGCTTGACTG 59.997 52.381 0.00 0.0 0.00 3.51
637 653 0.468226 GATCCCCGAGTATGCCACAA 59.532 55.000 0.00 0.0 0.00 3.33
774 791 1.097547 ATAGATGCTGGTTGTGCCGC 61.098 55.000 0.00 0.0 41.21 6.53
837 854 3.441496 CCAATGATGGTGGTGTTATGC 57.559 47.619 0.00 0.0 42.18 3.14
1072 2378 4.723309 AGATGGTTTTTGACTTGCTCTCT 58.277 39.130 0.00 0.0 0.00 3.10
1314 2621 5.450818 AGTGCTCAATTGGGGTATTTAGA 57.549 39.130 7.59 0.0 0.00 2.10
1351 2658 3.383223 CCCCAATTGTCCCATAAATGGT 58.617 45.455 4.43 0.0 46.65 3.55
1567 2874 0.821301 TTCACAAGTGCATCGGCCAA 60.821 50.000 2.24 0.0 40.13 4.52
1578 2885 5.080337 TCATCTCCACTAGACTTCACAAGT 58.920 41.667 0.00 0.0 46.38 3.16
1890 3214 6.627953 GCAATAAAGCCATACATGTCCAAGTT 60.628 38.462 0.00 0.0 0.00 2.66
2159 3486 2.897969 AGGAGCAAAAGAGAGTAACGGA 59.102 45.455 0.00 0.0 0.00 4.69
2302 3629 2.289945 GCAGAGATGGCCGATATTCCTT 60.290 50.000 0.00 0.0 0.00 3.36
2360 3687 3.664107 CGAAGGATTGTCAGGAGTTCAA 58.336 45.455 0.00 0.0 0.00 2.69
2387 3715 4.263331 GGAGAGGTGTCCTACAATTTGGAA 60.263 45.833 0.78 0.0 31.76 3.53
2393 3721 2.642171 TGGGAGAGGTGTCCTACAAT 57.358 50.000 0.00 0.0 36.75 2.71
2401 3729 1.043673 GGAGCGTATGGGAGAGGTGT 61.044 60.000 0.00 0.0 0.00 4.16
2539 3867 2.955477 TGCACACACAAAATGCAAGA 57.045 40.000 0.00 0.0 45.96 3.02
2705 4033 0.951558 TGGCACCTTTCGAAGCTTTC 59.048 50.000 0.00 0.0 0.00 2.62


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

AutoCloner maintained by Alex Coulton.