Multiple sequence alignment - TraesCS3A01G184100

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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 TraesCS3A01G184100 chr3A 100.000 2411 0 0 1 2411 214130147 214127737 0.000000e+00 4453
1 TraesCS3A01G184100 chr3A 77.859 411 87 4 321 729 690083267 690083675 3.980000e-63 252
2 TraesCS3A01G184100 chr2A 96.699 818 27 0 1 818 196509761 196510578 0.000000e+00 1362
3 TraesCS3A01G184100 chr2A 97.809 639 14 0 804 1442 196512068 196512706 0.000000e+00 1103
4 TraesCS3A01G184100 chr3B 92.181 972 57 11 1444 2411 253671370 253670414 0.000000e+00 1356
5 TraesCS3A01G184100 chr3D 88.830 949 76 20 1444 2370 174913945 174913005 0.000000e+00 1138
6 TraesCS3A01G184100 chr3D 85.678 391 45 7 1 390 614684519 614684139 3.730000e-108 401
7 TraesCS3A01G184100 chrUn 86.207 377 41 7 12 387 37627467 37627833 4.830000e-107 398
8 TraesCS3A01G184100 chr6A 74.440 759 186 7 5 759 140031199 140031953 1.080000e-83 320
9 TraesCS3A01G184100 chr6A 74.328 744 183 7 5 744 140053341 140054080 2.330000e-80 309
10 TraesCS3A01G184100 chr6B 76.491 587 129 8 1 583 1678838 1678257 6.470000e-81 311
11 TraesCS3A01G184100 chr4A 74.621 725 164 16 5 720 120377147 120377860 3.900000e-78 302
12 TraesCS3A01G184100 chr5D 74.874 597 129 19 210 795 510922702 510922116 3.980000e-63 252
13 TraesCS3A01G184100 chr5D 74.954 543 128 8 191 729 259521434 259521972 2.390000e-60 243
14 TraesCS3A01G184100 chr1D 74.688 561 134 8 191 747 492531560 492531004 2.390000e-60 243
15 TraesCS3A01G184100 chr7D 74.510 561 135 8 191 747 117764825 117764269 1.110000e-58 237
16 TraesCS3A01G184100 chr6D 76.998 413 87 8 321 729 424732614 424733022 1.860000e-56 230


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 TraesCS3A01G184100 chr3A 214127737 214130147 2410 True 4453.0 4453 100.000 1 2411 1 chr3A.!!$R1 2410
1 TraesCS3A01G184100 chr2A 196509761 196512706 2945 False 1232.5 1362 97.254 1 1442 2 chr2A.!!$F1 1441
2 TraesCS3A01G184100 chr3B 253670414 253671370 956 True 1356.0 1356 92.181 1444 2411 1 chr3B.!!$R1 967
3 TraesCS3A01G184100 chr3D 174913005 174913945 940 True 1138.0 1138 88.830 1444 2370 1 chr3D.!!$R1 926
4 TraesCS3A01G184100 chr6A 140031199 140031953 754 False 320.0 320 74.440 5 759 1 chr6A.!!$F1 754
5 TraesCS3A01G184100 chr6A 140053341 140054080 739 False 309.0 309 74.328 5 744 1 chr6A.!!$F2 739
6 TraesCS3A01G184100 chr6B 1678257 1678838 581 True 311.0 311 76.491 1 583 1 chr6B.!!$R1 582
7 TraesCS3A01G184100 chr4A 120377147 120377860 713 False 302.0 302 74.621 5 720 1 chr4A.!!$F1 715
8 TraesCS3A01G184100 chr5D 510922116 510922702 586 True 252.0 252 74.874 210 795 1 chr5D.!!$R1 585
9 TraesCS3A01G184100 chr5D 259521434 259521972 538 False 243.0 243 74.954 191 729 1 chr5D.!!$F1 538
10 TraesCS3A01G184100 chr1D 492531004 492531560 556 True 243.0 243 74.688 191 747 1 chr1D.!!$R1 556
11 TraesCS3A01G184100 chr7D 117764269 117764825 556 True 237.0 237 74.510 191 747 1 chr7D.!!$R1 556

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
928 2434 1.376942 CCTGAGCAGTGGAGCAAGG 60.377 63.158 0.0 0.0 35.28 3.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2085 3611 1.532523 TGCTGATCATTGTGGCGAAA 58.467 45.0 0.0 0.0 0.0 3.46 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
93 94 3.614630 CGACGTCCTATCGACCTATCTCT 60.615 52.174 10.58 0.00 42.25 3.10
426 428 3.034923 TGCGTTTTTGCATGGCGC 61.035 55.556 15.25 15.25 47.00 6.53
499 501 3.131933 AGCGATATCTGACATATGCTCCC 59.868 47.826 1.58 0.00 0.00 4.30
654 656 2.386661 TTCTTCATCTCCTTGACGGC 57.613 50.000 0.00 0.00 0.00 5.68
732 734 7.793927 TGTACGCAATGAAATATACCATGAA 57.206 32.000 0.00 0.00 0.00 2.57
761 763 1.672030 CACCTGTGGAAGCATCGCA 60.672 57.895 0.00 0.00 0.00 5.10
861 2367 6.717084 AGATGGTTATCTCATACGATCACTCA 59.283 38.462 0.00 0.00 39.46 3.41
862 2368 6.709018 TGGTTATCTCATACGATCACTCAA 57.291 37.500 0.00 0.00 0.00 3.02
870 2376 5.836347 TCATACGATCACTCAAGATCCAAG 58.164 41.667 0.00 0.00 41.03 3.61
928 2434 1.376942 CCTGAGCAGTGGAGCAAGG 60.377 63.158 0.00 0.00 35.28 3.61
994 2500 2.438434 CTGATGGAACCGGTGGCC 60.438 66.667 8.52 14.39 0.00 5.36
1008 2514 0.834687 GTGGCCCGGGGATGATACTA 60.835 60.000 25.28 0.00 0.00 1.82
1144 2650 4.521062 GCATGGCGCCTCTCGTCT 62.521 66.667 29.70 0.06 44.46 4.18
1251 2757 2.838637 AGAGGAAGCTAGCTGTAGGT 57.161 50.000 20.16 0.68 38.70 3.08
1263 2769 1.123077 CTGTAGGTAGGGAGCATGCA 58.877 55.000 21.98 0.00 0.00 3.96
1329 2835 0.236711 CGCAAATGGGATGCTCGATC 59.763 55.000 0.00 0.00 41.64 3.69
1471 2977 3.873801 GCCACCACATCACCAGAATTAGT 60.874 47.826 0.00 0.00 0.00 2.24
1479 2985 7.309990 CCACATCACCAGAATTAGTCCAAAAAT 60.310 37.037 0.00 0.00 0.00 1.82
1481 2987 9.479549 ACATCACCAGAATTAGTCCAAAAATAT 57.520 29.630 0.00 0.00 0.00 1.28
1688 3211 8.702438 ACGCTAATCATTTTGTGAAAATTTGAG 58.298 29.630 0.00 0.00 40.97 3.02
1689 3212 7.685304 CGCTAATCATTTTGTGAAAATTTGAGC 59.315 33.333 0.00 0.00 40.97 4.26
1888 3412 7.565190 ATCAAGCAAAGATGGAGAGGATATA 57.435 36.000 0.00 0.00 0.00 0.86
2065 3591 9.780413 ATGCATTTTCGTTGTGTTTTTATTTTT 57.220 22.222 0.00 0.00 0.00 1.94
2118 3644 6.964807 ATGATCAGCATGGCAGTTTTAATA 57.035 33.333 0.09 0.00 35.42 0.98
2127 3653 9.942850 AGCATGGCAGTTTTAATATTTTAAACT 57.057 25.926 16.57 16.57 37.10 2.66
2357 3884 7.206981 AGTCTTCAATACATGTCAAAACCTG 57.793 36.000 0.00 0.00 0.00 4.00
2375 3902 2.575532 CTGCCAGAAAGTTGGAGTTCA 58.424 47.619 0.00 0.00 40.87 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 4.652131 ATTGCCGACCCGCCACAA 62.652 61.111 0.00 0.00 0.00 3.33
159 160 4.499188 CGAAAGTATTGGCGGAGTAGATCA 60.499 45.833 0.00 0.00 0.00 2.92
499 501 0.389296 TCGCGTTCCATACCACACAG 60.389 55.000 5.77 0.00 0.00 3.66
567 569 0.316841 ATGTTTTCGCCATTGCCGTT 59.683 45.000 0.00 0.00 0.00 4.44
654 656 2.398429 CGCTCATCGTTGCTGCAG 59.602 61.111 10.11 10.11 0.00 4.41
761 763 4.518249 GATGTAGCTGCTTAGGAACCTTT 58.482 43.478 7.79 0.00 0.00 3.11
861 2367 1.202879 TCACGTTTGCCCTTGGATCTT 60.203 47.619 0.00 0.00 0.00 2.40
862 2368 0.400213 TCACGTTTGCCCTTGGATCT 59.600 50.000 0.00 0.00 0.00 2.75
870 2376 1.652563 GGTCACTTCACGTTTGCCC 59.347 57.895 0.00 0.00 0.00 5.36
912 2418 2.033141 GCCTTGCTCCACTGCTCA 59.967 61.111 0.00 0.00 0.00 4.26
994 2500 2.195741 TCTCGTAGTATCATCCCCGG 57.804 55.000 0.00 0.00 0.00 5.73
1008 2514 1.938657 CTGCTCCCACGTGATCTCGT 61.939 60.000 19.30 16.56 45.10 4.18
1084 2590 0.475475 CCCTCCATGCAGGCTGATAA 59.525 55.000 20.86 2.69 37.29 1.75
1092 2598 3.788672 GGTAACTCCCTCCATGCAG 57.211 57.895 0.00 0.00 0.00 4.41
1144 2650 0.321919 GCAGCACAGTCCATCTCCAA 60.322 55.000 0.00 0.00 0.00 3.53
1251 2757 1.216064 ACCTGATTGCATGCTCCCTA 58.784 50.000 20.33 0.00 0.00 3.53
1371 2877 5.825679 ACAGTCTTGCTTACATAAACCAACA 59.174 36.000 0.00 0.00 0.00 3.33
1442 2948 2.241941 TGGTGATGTGGTGGCTGATTAT 59.758 45.455 0.00 0.00 0.00 1.28
1471 2977 8.728596 TTTCTGGACCCTTTAATATTTTTGGA 57.271 30.769 0.00 0.00 0.00 3.53
1481 2987 9.554395 GATTTCAAATTTTTCTGGACCCTTTAA 57.446 29.630 0.00 0.00 0.00 1.52
1663 3186 7.685304 GCTCAAATTTTCACAAAATGATTAGCG 59.315 33.333 0.00 0.00 40.05 4.26
1688 3211 9.230583 GTATTTTTATTACGTTTGCGAAAAAGC 57.769 29.630 1.27 0.00 42.00 3.51
1729 3253 6.793479 TTCGTCGTTAAATTTTGACCAAAC 57.207 33.333 0.00 0.00 0.00 2.93
1744 3268 5.927689 TGTATGGACAGTTTATTTCGTCGTT 59.072 36.000 0.00 0.00 0.00 3.85
1747 3271 9.620660 AATTTTGTATGGACAGTTTATTTCGTC 57.379 29.630 0.00 0.00 36.76 4.20
1791 3315 8.565896 TCAGAATAATTAGCATGACAGTGTTT 57.434 30.769 0.00 0.00 0.00 2.83
1927 3451 5.447818 GCTGATCATTTTGGGTAAGTTCGAG 60.448 44.000 0.00 0.00 0.00 4.04
1928 3452 4.394920 GCTGATCATTTTGGGTAAGTTCGA 59.605 41.667 0.00 0.00 0.00 3.71
1929 3453 4.662145 GCTGATCATTTTGGGTAAGTTCG 58.338 43.478 0.00 0.00 0.00 3.95
1930 3454 4.156008 ACGCTGATCATTTTGGGTAAGTTC 59.844 41.667 0.00 0.00 0.00 3.01
2065 3591 6.674278 GCGAAATTCAAAAGTTTCTGCCAAAA 60.674 34.615 0.00 0.00 33.32 2.44
2073 3599 5.710613 TTGTGGCGAAATTCAAAAGTTTC 57.289 34.783 0.00 0.00 0.00 2.78
2081 3607 3.427909 GCTGATCATTGTGGCGAAATTCA 60.428 43.478 0.00 0.00 0.00 2.57
2085 3611 1.532523 TGCTGATCATTGTGGCGAAA 58.467 45.000 0.00 0.00 0.00 3.46
2217 3743 3.932545 TGCGGACATTATTGTTTTGCT 57.067 38.095 9.60 0.00 35.79 3.91
2357 3884 2.810852 CTCTGAACTCCAACTTTCTGGC 59.189 50.000 0.00 0.00 36.32 4.85


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

AutoCloner maintained by Alex Coulton.