Multiple sequence alignment - TraesCS3A01G487400

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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 TraesCS3A01G487400 chr3A 100.000 2591 0 0 1 2591 715213653 715216243 0.000000e+00 4785
1 TraesCS3A01G487400 chr3A 95.127 2606 63 10 1 2591 27908550 27905994 0.000000e+00 4050
2 TraesCS3A01G487400 chr3A 94.960 2599 85 8 1 2591 37633070 37635630 0.000000e+00 4032
3 TraesCS3A01G487400 chr3A 94.473 1158 27 6 1 1158 547977019 547975899 0.000000e+00 1749
4 TraesCS3A01G487400 chr2A 96.800 2594 52 6 1 2591 461392451 461395016 0.000000e+00 4301
5 TraesCS3A01G487400 chr1A 95.889 2603 67 15 1 2591 302911999 302914573 0.000000e+00 4178
6 TraesCS3A01G487400 chr5D 92.969 2617 115 23 1 2591 408555174 408552601 0.000000e+00 3749
7 TraesCS3A01G487400 chr5D 94.734 1728 74 11 874 2591 545534111 545535831 0.000000e+00 2671
8 TraesCS3A01G487400 chr7A 94.998 2419 64 9 1 2390 147920292 147917902 0.000000e+00 3744
9 TraesCS3A01G487400 chr7D 92.784 2619 119 22 1 2591 92234381 92231805 0.000000e+00 3725
10 TraesCS3A01G487400 chr7D 92.467 2615 121 29 1 2591 631818418 631815856 0.000000e+00 3668
11 TraesCS3A01G487400 chr4A 93.944 2444 112 15 1 2434 521945348 521947765 0.000000e+00 3661
12 TraesCS3A01G487400 chr6A 95.778 2037 55 9 559 2591 608061677 608063686 0.000000e+00 3256
13 TraesCS3A01G487400 chr6A 96.286 1858 40 6 1 1847 428285755 428287594 0.000000e+00 3022
14 TraesCS3A01G487400 chr5A 96.663 1828 39 3 1 1826 680753338 680755145 0.000000e+00 3018
15 TraesCS3A01G487400 chr5A 94.309 1810 80 5 1 1810 647551295 647553081 0.000000e+00 2750
16 TraesCS3A01G487400 chr2D 94.801 1731 71 12 874 2591 624288122 624289846 0.000000e+00 2680
17 TraesCS3A01G487400 chr1D 94.789 1727 74 10 874 2590 444899318 444901038 0.000000e+00 2676
18 TraesCS3A01G487400 chr1D 80.344 524 74 17 2092 2591 843678 844196 1.130000e-98 370


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 TraesCS3A01G487400 chr3A 715213653 715216243 2590 False 4785 4785 100.000 1 2591 1 chr3A.!!$F2 2590
1 TraesCS3A01G487400 chr3A 27905994 27908550 2556 True 4050 4050 95.127 1 2591 1 chr3A.!!$R1 2590
2 TraesCS3A01G487400 chr3A 37633070 37635630 2560 False 4032 4032 94.960 1 2591 1 chr3A.!!$F1 2590
3 TraesCS3A01G487400 chr3A 547975899 547977019 1120 True 1749 1749 94.473 1 1158 1 chr3A.!!$R2 1157
4 TraesCS3A01G487400 chr2A 461392451 461395016 2565 False 4301 4301 96.800 1 2591 1 chr2A.!!$F1 2590
5 TraesCS3A01G487400 chr1A 302911999 302914573 2574 False 4178 4178 95.889 1 2591 1 chr1A.!!$F1 2590
6 TraesCS3A01G487400 chr5D 408552601 408555174 2573 True 3749 3749 92.969 1 2591 1 chr5D.!!$R1 2590
7 TraesCS3A01G487400 chr5D 545534111 545535831 1720 False 2671 2671 94.734 874 2591 1 chr5D.!!$F1 1717
8 TraesCS3A01G487400 chr7A 147917902 147920292 2390 True 3744 3744 94.998 1 2390 1 chr7A.!!$R1 2389
9 TraesCS3A01G487400 chr7D 92231805 92234381 2576 True 3725 3725 92.784 1 2591 1 chr7D.!!$R1 2590
10 TraesCS3A01G487400 chr7D 631815856 631818418 2562 True 3668 3668 92.467 1 2591 1 chr7D.!!$R2 2590
11 TraesCS3A01G487400 chr4A 521945348 521947765 2417 False 3661 3661 93.944 1 2434 1 chr4A.!!$F1 2433
12 TraesCS3A01G487400 chr6A 608061677 608063686 2009 False 3256 3256 95.778 559 2591 1 chr6A.!!$F2 2032
13 TraesCS3A01G487400 chr6A 428285755 428287594 1839 False 3022 3022 96.286 1 1847 1 chr6A.!!$F1 1846
14 TraesCS3A01G487400 chr5A 680753338 680755145 1807 False 3018 3018 96.663 1 1826 1 chr5A.!!$F2 1825
15 TraesCS3A01G487400 chr5A 647551295 647553081 1786 False 2750 2750 94.309 1 1810 1 chr5A.!!$F1 1809
16 TraesCS3A01G487400 chr2D 624288122 624289846 1724 False 2680 2680 94.801 874 2591 1 chr2D.!!$F1 1717
17 TraesCS3A01G487400 chr1D 444899318 444901038 1720 False 2676 2676 94.789 874 2590 1 chr1D.!!$F2 1716
18 TraesCS3A01G487400 chr1D 843678 844196 518 False 370 370 80.344 2092 2591 1 chr1D.!!$F1 499

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
158 192 1.001503 CCTCTCACTCCCCTGCTCT 59.998 63.158 0.0 0.0 0.0 4.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1955 2015 1.49091 AGTAGGCCTAGGGTTGCATTC 59.509 52.381 14.38 0.0 0.0 2.67 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
140 174 3.071206 TGCTCGCTCACTCCCCTC 61.071 66.667 0.00 0.00 0.00 4.30
158 192 1.001503 CCTCTCACTCCCCTGCTCT 59.998 63.158 0.00 0.00 0.00 4.09
370 416 3.019564 GCCATGGATCTTGCTAAGTGTT 58.980 45.455 18.40 0.00 0.00 3.32
407 455 6.380079 AGGATTCTTGTTCAATAGTGAGGT 57.620 37.500 0.00 0.00 34.49 3.85
536 586 6.816640 GTGCAAGTATATTCTGGTGTTGAGTA 59.183 38.462 0.00 0.00 0.00 2.59
1122 1179 1.882623 GAGCAGAACTTTGGAAGGGTG 59.117 52.381 0.00 0.00 0.00 4.61
1336 1396 6.239458 GGAGGAAGAACTTGAGAAGAAGAAGA 60.239 42.308 0.00 0.00 0.00 2.87
1339 1399 6.073276 GGAAGAACTTGAGAAGAAGAAGAAGC 60.073 42.308 0.00 0.00 0.00 3.86
1340 1400 5.923204 AGAACTTGAGAAGAAGAAGAAGCA 58.077 37.500 0.00 0.00 0.00 3.91
1341 1401 6.352516 AGAACTTGAGAAGAAGAAGAAGCAA 58.647 36.000 0.00 0.00 0.00 3.91
1493 1553 6.042638 TGACAGAGATGTTCTTAAGAAGGG 57.957 41.667 18.22 5.81 34.27 3.95
1606 1666 4.946157 AGTCTTGAAGTGGCTTTGATATGG 59.054 41.667 0.00 0.00 0.00 2.74
1647 1707 6.010219 TCCAAAGGCCTTTATATAAGGATGC 58.990 40.000 29.94 2.40 39.81 3.91
1784 1844 8.486210 TGCTATTAAGTGTTGTAATGGATCTCT 58.514 33.333 0.00 0.00 0.00 3.10
1955 2015 0.105039 GGCCCACTATTCTCTGACCG 59.895 60.000 0.00 0.00 0.00 4.79
2013 2074 5.911178 TCCATCTGTCAATATAAACCCCTCT 59.089 40.000 0.00 0.00 0.00 3.69
2014 2075 7.079700 TCCATCTGTCAATATAAACCCCTCTA 58.920 38.462 0.00 0.00 0.00 2.43
2151 2221 2.215625 AGCAGCAGCACAGAGGAGT 61.216 57.895 3.17 0.00 45.49 3.85
2254 2336 3.498397 GGAGAAGTGCAATGACGAAGAAA 59.502 43.478 0.00 0.00 0.00 2.52
2393 2475 7.219484 TCTTTGAGCGATATGACTGATATGA 57.781 36.000 0.00 0.00 0.00 2.15
2512 2642 6.371548 GTGTTTGATGCTACTCTGAACCAATA 59.628 38.462 0.00 0.00 0.00 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
111 128 0.465460 AGCGAGCAGGGAGAGAGTAG 60.465 60.000 0.00 0.0 0.00 2.57
112 129 0.464735 GAGCGAGCAGGGAGAGAGTA 60.465 60.000 0.00 0.0 0.00 2.59
140 174 0.260230 TAGAGCAGGGGAGTGAGAGG 59.740 60.000 0.00 0.0 0.00 3.69
370 416 4.085357 AGAATCCTACAACAGCAACACA 57.915 40.909 0.00 0.0 0.00 3.72
407 455 5.004361 TCAATCCTACAATCAAACCCCAA 57.996 39.130 0.00 0.0 0.00 4.12
536 586 5.009010 CCAGCAAACACTAGTTTCAATCTGT 59.991 40.000 0.00 0.0 45.80 3.41
944 998 5.189180 AGGAGCTTATTTCAGTTCCATGAC 58.811 41.667 6.39 0.0 44.64 3.06
1122 1179 2.810852 CTCAAACTTCTCCTTGTCCTGC 59.189 50.000 0.00 0.0 0.00 4.85
1336 1396 5.188751 ACATAGCTTTCTCCTCTAGTTGCTT 59.811 40.000 0.00 0.0 32.03 3.91
1339 1399 5.814705 CCAACATAGCTTTCTCCTCTAGTTG 59.185 44.000 0.00 0.0 34.16 3.16
1340 1400 5.721960 TCCAACATAGCTTTCTCCTCTAGTT 59.278 40.000 0.00 0.0 0.00 2.24
1341 1401 5.273208 TCCAACATAGCTTTCTCCTCTAGT 58.727 41.667 0.00 0.0 0.00 2.57
1606 1666 5.411669 CCTTTGGATGTACTTACTTCACCAC 59.588 44.000 0.00 0.0 33.47 4.16
1955 2015 1.490910 AGTAGGCCTAGGGTTGCATTC 59.509 52.381 14.38 0.0 0.00 2.67
2013 2074 1.853565 GGGAAAGGGTGGGGGTGTA 60.854 63.158 0.00 0.0 0.00 2.90
2014 2075 3.190391 GGGAAAGGGTGGGGGTGT 61.190 66.667 0.00 0.0 0.00 4.16
2151 2221 3.402681 GCCCTCTGCCTGTGCCTA 61.403 66.667 0.00 0.0 36.33 3.93
2254 2336 1.145738 ACCAGTGAAAACCAGCTCCAT 59.854 47.619 0.00 0.0 0.00 3.41


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

AutoCloner maintained by Alex Coulton.