Multiple sequence alignment - TraesCS5A01G175800

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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 TraesCS5A01G175800 chr5A 100.000 2231 0 0 1 2231 370095565 370097795 0.000000e+00 4120.0
1 TraesCS5A01G175800 chr5A 94.079 1824 83 4 1 1809 370044218 370042405 0.000000e+00 2747.0
2 TraesCS5A01G175800 chr5A 95.354 861 40 0 1 861 650586541 650585681 0.000000e+00 1369.0
3 TraesCS5A01G175800 chr5A 95.046 868 40 3 1 867 650584781 650583916 0.000000e+00 1362.0
4 TraesCS5A01G175800 chr5A 95.444 856 34 3 1 856 35092966 35093816 0.000000e+00 1360.0
5 TraesCS5A01G175800 chr5A 94.451 865 34 4 1 856 35088358 35089217 0.000000e+00 1321.0
6 TraesCS5A01G175800 chr5A 92.601 865 54 3 1 864 686762843 686761988 0.000000e+00 1234.0
7 TraesCS5A01G175800 chr5A 98.792 414 5 0 1818 2231 370037021 370036608 0.000000e+00 737.0
8 TraesCS5A01G175800 chr5D 95.562 1352 36 10 899 2231 278468318 278466972 0.000000e+00 2143.0
9 TraesCS5A01G175800 chr5B 94.624 1358 48 7 899 2231 316624144 316622787 0.000000e+00 2080.0
10 TraesCS5A01G175800 chr3D 95.470 861 38 1 1 861 505951579 505952438 0.000000e+00 1373.0
11 TraesCS5A01G175800 chr3A 93.792 902 51 2 1 902 198171198 198170302 0.000000e+00 1351.0
12 TraesCS5A01G175800 chr2A 93.456 871 48 2 1 864 645906471 645905603 0.000000e+00 1284.0
13 TraesCS5A01G175800 chr4A 91.219 763 49 4 1 763 139129819 139130563 0.000000e+00 1022.0
14 TraesCS5A01G175800 chr4A 95.579 475 21 0 1 475 601209527 601210001 0.000000e+00 761.0
15 TraesCS5A01G175800 chr6A 80.672 238 38 7 1410 1646 510865535 510865765 6.330000e-41 178.0
16 TraesCS5A01G175800 chr6D 79.412 238 41 7 1410 1646 369661721 369661951 6.380000e-36 161.0
17 TraesCS5A01G175800 chr6B 78.151 238 44 6 1410 1646 555293861 555294091 6.420000e-31 145.0
18 TraesCS5A01G175800 chr7B 90.196 51 5 0 849 899 91263689 91263739 1.430000e-07 67.6


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 TraesCS5A01G175800 chr5A 370095565 370097795 2230 False 4120.0 4120 100.0000 1 2231 1 chr5A.!!$F1 2230
1 TraesCS5A01G175800 chr5A 370042405 370044218 1813 True 2747.0 2747 94.0790 1 1809 1 chr5A.!!$R2 1808
2 TraesCS5A01G175800 chr5A 650583916 650586541 2625 True 1365.5 1369 95.2000 1 867 2 chr5A.!!$R4 866
3 TraesCS5A01G175800 chr5A 35088358 35093816 5458 False 1340.5 1360 94.9475 1 856 2 chr5A.!!$F2 855
4 TraesCS5A01G175800 chr5A 686761988 686762843 855 True 1234.0 1234 92.6010 1 864 1 chr5A.!!$R3 863
5 TraesCS5A01G175800 chr5D 278466972 278468318 1346 True 2143.0 2143 95.5620 899 2231 1 chr5D.!!$R1 1332
6 TraesCS5A01G175800 chr5B 316622787 316624144 1357 True 2080.0 2080 94.6240 899 2231 1 chr5B.!!$R1 1332
7 TraesCS5A01G175800 chr3D 505951579 505952438 859 False 1373.0 1373 95.4700 1 861 1 chr3D.!!$F1 860
8 TraesCS5A01G175800 chr3A 198170302 198171198 896 True 1351.0 1351 93.7920 1 902 1 chr3A.!!$R1 901
9 TraesCS5A01G175800 chr2A 645905603 645906471 868 True 1284.0 1284 93.4560 1 864 1 chr2A.!!$R1 863
10 TraesCS5A01G175800 chr4A 139129819 139130563 744 False 1022.0 1022 91.2190 1 763 1 chr4A.!!$F1 762

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
21 22 0.534203 CGCACAACTGTTACCCCTGT 60.534 55.0 0.00 0.0 0.00 4.00 F
97 98 0.742281 GGTCGTGCTGCATGTCATCT 60.742 55.0 20.33 0.0 0.00 2.90 F
356 364 0.961857 TACCACGCTCGTTGCCTCTA 60.962 55.0 0.00 0.0 38.78 2.43 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1142 1215 1.228337 TTCCTCACGTGGGACGAGA 60.228 57.895 19.37 1.83 46.05 4.04 R
1147 1221 2.099652 CTGCACTTCCTCACGTGGGA 62.100 60.000 19.37 18.75 0.00 4.37 R
2058 4277 2.234661 CAGCTGGTTCTATCTGTCACCA 59.765 50.000 5.57 0.00 36.94 4.17 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
21 22 0.534203 CGCACAACTGTTACCCCTGT 60.534 55.000 0.00 0.00 0.00 4.00
40 41 2.105821 TGTCCTCGACCAAACCTCATTT 59.894 45.455 0.00 0.00 0.00 2.32
97 98 0.742281 GGTCGTGCTGCATGTCATCT 60.742 55.000 20.33 0.00 0.00 2.90
295 296 2.037772 GGATTATGCAGGGACGACATCT 59.962 50.000 0.00 0.00 31.64 2.90
356 364 0.961857 TACCACGCTCGTTGCCTCTA 60.962 55.000 0.00 0.00 38.78 2.43
404 412 1.024579 GCAAGGGAGAAAATCGGCGA 61.025 55.000 13.87 13.87 0.00 5.54
454 464 1.139853 AGAGATGAAGGGGATTGACGC 59.860 52.381 0.00 0.00 0.00 5.19
477 487 4.443315 CCCATGCATATGTTTCCTTTTCCC 60.443 45.833 0.00 0.00 32.21 3.97
829 850 2.204090 GGAAGGGGTGGTGGGAGA 60.204 66.667 0.00 0.00 0.00 3.71
883 946 3.000727 GGGACTATTCAACCAACTCGTG 58.999 50.000 0.00 0.00 0.00 4.35
884 947 3.556423 GGGACTATTCAACCAACTCGTGT 60.556 47.826 0.00 0.00 0.00 4.49
990 1053 2.229675 TCATTCACAGCCAGCTATCG 57.770 50.000 0.00 0.00 0.00 2.92
1964 3117 9.065871 CGTCATCAAATCTTTCCAAAGTTAATC 57.934 33.333 0.00 0.00 37.31 1.75
2037 4256 7.566858 AATGTAAATTCGATTCAAACAGTGC 57.433 32.000 0.00 0.00 0.00 4.40
2058 4277 4.823442 TGCAAATCTGACAGAAGAATGTGT 59.177 37.500 9.70 0.00 35.42 3.72
2098 4317 0.826062 GCCCAAATGGACCCAGAATG 59.174 55.000 0.00 0.00 37.39 2.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 2.290071 GGAAATGAGGTTTGGTCGAGGA 60.290 50.000 0.00 0.00 0.00 3.71
40 41 2.058595 GCCGCTCCTTCCAGTAGGA 61.059 63.158 0.00 0.00 43.93 2.94
80 81 1.803998 GCTAGATGACATGCAGCACGA 60.804 52.381 0.00 0.00 34.69 4.35
97 98 4.266070 GCCGTCGCCGATCTGCTA 62.266 66.667 7.56 0.00 35.63 3.49
295 296 1.345741 CTGACCTTGCAGTCCTTCTCA 59.654 52.381 3.85 0.00 35.83 3.27
356 364 5.843019 TCTCCTTAAAGAGGTGGACATTT 57.157 39.130 1.25 0.00 46.39 2.32
454 464 4.443315 GGGAAAAGGAAACATATGCATGGG 60.443 45.833 10.16 3.48 36.39 4.00
477 487 9.811655 GAAGAAAAGAAAAAGGAAAACAAACTG 57.188 29.630 0.00 0.00 0.00 3.16
782 803 1.264557 CCGAATCGCGTCTGATACTCT 59.735 52.381 5.77 0.00 38.67 3.24
883 946 8.960075 GCATCTCGTTTTCTCTACTTCTAATAC 58.040 37.037 0.00 0.00 0.00 1.89
884 947 8.683615 TGCATCTCGTTTTCTCTACTTCTAATA 58.316 33.333 0.00 0.00 0.00 0.98
990 1053 0.976073 TCCAGAACATCGGACTCCCC 60.976 60.000 0.00 0.00 0.00 4.81
1142 1215 1.228337 TTCCTCACGTGGGACGAGA 60.228 57.895 19.37 1.83 46.05 4.04
1147 1221 2.099652 CTGCACTTCCTCACGTGGGA 62.100 60.000 19.37 18.75 0.00 4.37
1150 1224 2.661566 CGCTGCACTTCCTCACGTG 61.662 63.158 9.94 9.94 0.00 4.49
1964 3117 7.158021 TGAAAGTAAATTGGGGTGCAAATTAG 58.842 34.615 0.00 0.00 0.00 1.73
2011 3164 9.123709 GCACTGTTTGAATCGAATTTACATTTA 57.876 29.630 0.00 0.00 0.00 1.40
2015 3168 6.066054 TGCACTGTTTGAATCGAATTTACA 57.934 33.333 0.00 0.00 0.00 2.41
2037 4256 5.240183 ACCACACATTCTTCTGTCAGATTTG 59.760 40.000 2.68 2.36 0.00 2.32
2058 4277 2.234661 CAGCTGGTTCTATCTGTCACCA 59.765 50.000 5.57 0.00 36.94 4.17
2098 4317 6.505044 AAATAAATACCACGGAACTGTTCC 57.495 37.500 26.14 26.14 46.62 3.62
2107 4326 9.627395 TGATTGTTTGTTAAATAAATACCACGG 57.373 29.630 0.00 0.00 0.00 4.94


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

AutoCloner maintained by Alex Coulton.