Multiple sequence alignment - TraesCS7A01G028200

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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 TraesCS7A01G028200 chr7A 100.000 2642 0 0 1 2642 11312661 11310020 0.000000e+00 4879.0
1 TraesCS7A01G028200 chr7A 77.909 1014 168 28 835 1830 11229917 11228942 4.900000e-162 580.0
2 TraesCS7A01G028200 chr7A 79.970 674 108 17 1152 1818 11345592 11344939 3.080000e-129 472.0
3 TraesCS7A01G028200 chr7A 81.250 384 41 14 1998 2353 11228646 11228266 5.570000e-72 281.0
4 TraesCS7A01G028200 chr7A 87.342 79 10 0 172 250 31115481 31115559 1.010000e-14 91.6
5 TraesCS7A01G028200 chr4A 94.448 1657 64 6 433 2075 726072940 726074582 0.000000e+00 2525.0
6 TraesCS7A01G028200 chr4A 79.562 822 133 23 851 1650 726107980 726108788 2.970000e-154 555.0
7 TraesCS7A01G028200 chr4A 83.582 402 46 12 1424 1823 726064695 726065078 2.500000e-95 359.0
8 TraesCS7A01G028200 chr4A 78.585 509 84 21 1169 1661 725864887 725865386 1.970000e-81 313.0
9 TraesCS7A01G028200 chr4A 80.447 358 58 10 2000 2350 726065477 726065829 2.020000e-66 263.0
10 TraesCS7A01G028200 chr4A 95.370 108 4 1 291 397 726072837 726072944 1.260000e-38 171.0
11 TraesCS7A01G028200 chr4A 96.296 81 2 1 1 81 726072759 726072838 5.930000e-27 132.0
12 TraesCS7A01G028200 chr7D 96.729 1131 26 9 1515 2642 11705742 11704620 0.000000e+00 1873.0
13 TraesCS7A01G028200 chr7D 93.393 999 49 8 8 995 11706763 11705771 0.000000e+00 1463.0
14 TraesCS7A01G028200 chr7D 81.096 365 39 13 2016 2353 11693584 11693223 5.610000e-67 265.0
15 TraesCS7A01G028200 chr7D 80.208 384 44 12 1998 2353 11725465 11725086 2.610000e-65 259.0
16 TraesCS7A01G028200 chr3A 77.628 1189 196 43 522 1665 731844234 731843071 0.000000e+00 658.0
17 TraesCS7A01G028200 chr3A 75.878 854 145 35 843 1665 731893954 731893131 1.920000e-101 379.0
18 TraesCS7A01G028200 chr7B 78.431 867 147 20 852 1702 750116196 750115354 1.800000e-146 529.0
19 TraesCS7A01G028200 chr7B 79.837 367 60 12 475 838 750116613 750116258 3.370000e-64 255.0
20 TraesCS7A01G028200 chr7B 77.852 149 23 8 46 189 732636956 732636813 1.690000e-12 84.2
21 TraesCS7A01G028200 chr3B 81.319 182 22 2 8 177 512518251 512518432 1.280000e-28 137.0
22 TraesCS7A01G028200 chr1A 81.548 168 23 6 15 176 479858017 479857852 5.930000e-27 132.0
23 TraesCS7A01G028200 chr6B 83.969 131 17 3 123 250 633895059 633895188 3.570000e-24 122.0
24 TraesCS7A01G028200 chr1D 78.882 161 25 9 22 177 384847842 384847998 1.670000e-17 100.0
25 TraesCS7A01G028200 chr3D 87.342 79 10 0 172 250 420484337 420484415 1.010000e-14 91.6
26 TraesCS7A01G028200 chr3D 86.250 80 11 0 98 177 564925540 564925619 1.300000e-13 87.9
27 TraesCS7A01G028200 chr3D 90.323 62 6 0 127 188 122585671 122585610 6.060000e-12 82.4
28 TraesCS7A01G028200 chr3D 85.507 69 10 0 107 175 531377301 531377369 3.650000e-09 73.1
29 TraesCS7A01G028200 chr2B 85.882 85 12 0 172 256 676486113 676486029 1.010000e-14 91.6
30 TraesCS7A01G028200 chr6A 86.076 79 11 0 172 250 14658127 14658049 4.690000e-13 86.1
31 TraesCS7A01G028200 chr4D 86.076 79 11 0 172 250 488687503 488687425 4.690000e-13 86.1
32 TraesCS7A01G028200 chr4B 86.076 79 11 0 172 250 455976717 455976795 4.690000e-13 86.1
33 TraesCS7A01G028200 chr2A 84.706 85 13 0 172 256 256585176 256585092 4.690000e-13 86.1


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 TraesCS7A01G028200 chr7A 11310020 11312661 2641 True 4879.000000 4879 100.000000 1 2642 1 chr7A.!!$R1 2641
1 TraesCS7A01G028200 chr7A 11344939 11345592 653 True 472.000000 472 79.970000 1152 1818 1 chr7A.!!$R2 666
2 TraesCS7A01G028200 chr7A 11228266 11229917 1651 True 430.500000 580 79.579500 835 2353 2 chr7A.!!$R3 1518
3 TraesCS7A01G028200 chr4A 726072759 726074582 1823 False 942.666667 2525 95.371333 1 2075 3 chr4A.!!$F4 2074
4 TraesCS7A01G028200 chr4A 726107980 726108788 808 False 555.000000 555 79.562000 851 1650 1 chr4A.!!$F2 799
5 TraesCS7A01G028200 chr4A 726064695 726065829 1134 False 311.000000 359 82.014500 1424 2350 2 chr4A.!!$F3 926
6 TraesCS7A01G028200 chr7D 11704620 11706763 2143 True 1668.000000 1873 95.061000 8 2642 2 chr7D.!!$R3 2634
7 TraesCS7A01G028200 chr3A 731843071 731844234 1163 True 658.000000 658 77.628000 522 1665 1 chr3A.!!$R1 1143
8 TraesCS7A01G028200 chr3A 731893131 731893954 823 True 379.000000 379 75.878000 843 1665 1 chr3A.!!$R2 822
9 TraesCS7A01G028200 chr7B 750115354 750116613 1259 True 392.000000 529 79.134000 475 1702 2 chr7B.!!$R2 1227

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
983 1049 0.548031 CCTTGCTCCTGGCCAGAATA 59.452 55.0 34.91 17.41 40.92 1.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2350 2737 0.179171 CTCCTGCAGCATGAAAAGCG 60.179 55.0 8.66 0.0 39.69 4.68 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
257 269 2.754552 CCACTTAGCCAGCTTTGCATAA 59.245 45.455 7.67 3.34 0.00 1.90
279 291 0.696501 TTGAACCCTAGGCAGTTCCC 59.303 55.000 21.41 5.83 41.36 3.97
335 347 2.415983 TCCTTGTCCCTTCTCTTCCA 57.584 50.000 0.00 0.00 0.00 3.53
401 413 5.523588 AGAGAGAGAGAGAGAGAAGAGAGA 58.476 45.833 0.00 0.00 0.00 3.10
625 637 3.426117 CTTCCTGCGCCGATACCGT 62.426 63.158 4.18 0.00 0.00 4.83
760 778 0.621571 CATCCTTCCTCCCCTCCACA 60.622 60.000 0.00 0.00 0.00 4.17
802 820 3.247648 CAGTTGATTTCTTTGACGGACGT 59.752 43.478 0.00 0.00 0.00 4.34
804 822 2.828877 TGATTTCTTTGACGGACGTGT 58.171 42.857 0.53 0.00 0.00 4.49
814 832 3.063084 GGACGTGTCCTCCTCGCT 61.063 66.667 11.81 0.00 46.16 4.93
840 906 1.291877 CCGGACAAAGAAGACAGCCG 61.292 60.000 0.00 0.00 37.20 5.52
983 1049 0.548031 CCTTGCTCCTGGCCAGAATA 59.452 55.000 34.91 17.41 40.92 1.75
989 1055 2.568546 TCCTGGCCAGAATAAGGAGA 57.431 50.000 34.91 16.81 33.85 3.71
1080 1158 1.915614 GACAAGGACAGTGGCATGCG 61.916 60.000 12.44 0.00 0.00 4.73
1323 1415 1.748591 GCAGAAGGGATGCTCGGAATT 60.749 52.381 0.00 0.00 40.59 2.17
1348 1443 1.069935 GAAGGCTATGGCGAGGACC 59.930 63.158 0.00 0.00 39.81 4.46
1380 1475 3.016736 CCCATTTTGGCTCACGTATTCT 58.983 45.455 0.00 0.00 35.79 2.40
1406 1501 4.701651 TCTGAGAAATAACCAATGGCACTG 59.298 41.667 0.00 0.00 0.00 3.66
1581 1679 0.034756 TCGCTGAGCTTAGCAAACCA 59.965 50.000 27.73 5.31 43.87 3.67
1582 1680 1.089920 CGCTGAGCTTAGCAAACCAT 58.910 50.000 27.73 0.00 43.87 3.55
2024 2363 2.479275 GGTAGTTCTGCCAGTTCGTTTC 59.521 50.000 2.21 0.00 0.00 2.78
2039 2379 6.202188 CAGTTCGTTTCTACATGGTTACAACT 59.798 38.462 0.00 0.00 0.00 3.16
2071 2411 8.161699 TGTTTACAAAACCCTTGAATCTCTAC 57.838 34.615 0.41 0.00 0.00 2.59
2197 2583 4.520492 AGATTGGTTTCAAGTCACCATGTC 59.480 41.667 0.00 0.00 42.81 3.06
2213 2599 4.279169 ACCATGTCTTGTGGATGTGAAAAG 59.721 41.667 0.00 0.00 39.12 2.27
2414 2801 0.511653 GGCGTCAGAAAGAAACGACC 59.488 55.000 0.00 0.00 38.48 4.79
2503 2890 7.985634 TTTTCTGATGCTAGTTTTCACAAAC 57.014 32.000 0.00 0.00 42.48 2.93
2613 3000 0.529992 CGAATACCACCTCTTCGGGC 60.530 60.000 0.00 0.00 38.41 6.13
2632 3019 3.629855 GGGCTTTTTCTCCTCTGAATAGC 59.370 47.826 0.00 0.00 35.30 2.97
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
102 103 7.282224 GCACAACACATCCCAGTTATCTTTATA 59.718 37.037 0.00 0.00 0.00 0.98
104 105 5.414454 GCACAACACATCCCAGTTATCTTTA 59.586 40.000 0.00 0.00 0.00 1.85
111 123 1.172180 CGGCACAACACATCCCAGTT 61.172 55.000 0.00 0.00 0.00 3.16
113 125 2.334946 CCGGCACAACACATCCCAG 61.335 63.158 0.00 0.00 0.00 4.45
143 155 1.743252 GTGCTTTCGCTGCTAGGCT 60.743 57.895 0.00 0.00 36.97 4.58
239 251 3.075866 GCTTATGCAAAGCTGGCTAAG 57.924 47.619 19.77 14.65 40.01 2.18
257 269 1.003696 GAACTGCCTAGGGTTCAAGCT 59.996 52.381 20.14 0.00 40.79 3.74
401 413 0.037790 GTGGCGCTTCTCTTCTCACT 60.038 55.000 7.64 0.00 0.00 3.41
437 449 2.348104 GGTGGGGATTCGGTTTGGC 61.348 63.158 0.00 0.00 0.00 4.52
619 631 2.423898 CGGGTGGAGAGCACGGTAT 61.424 63.158 0.00 0.00 0.00 2.73
647 659 2.125350 GTCTTGGAGCAGGCCGAG 60.125 66.667 0.00 0.00 40.28 4.63
814 832 3.758973 TTCTTTGTCCGGTGCGCCA 62.759 57.895 18.18 0.00 34.09 5.69
820 838 0.250338 GGCTGTCTTCTTTGTCCGGT 60.250 55.000 0.00 0.00 0.00 5.28
859 925 2.996168 GAACAGGGTCGCACACAGCT 62.996 60.000 0.00 0.00 42.61 4.24
874 940 0.036765 GGACATAGCGGTGGTGAACA 60.037 55.000 0.00 0.00 0.00 3.18
960 1026 1.845627 CTGGCCAGGAGCAAGGAAGA 61.846 60.000 26.14 0.00 46.50 2.87
983 1049 0.995024 CATCACCCAGGGTTCTCCTT 59.005 55.000 9.12 0.00 45.47 3.36
989 1055 2.034066 CGCACATCACCCAGGGTT 59.966 61.111 9.12 0.00 31.02 4.11
1023 1101 5.392767 AGAAGACGAGAATGAGCAGTTTA 57.607 39.130 0.00 0.00 0.00 2.01
1080 1158 5.068198 ACCACTCCATTGATCAAATGTATGC 59.932 40.000 13.09 0.00 43.66 3.14
1323 1415 0.461548 CGCCATAGCCTTCAGTGAGA 59.538 55.000 0.00 0.00 34.57 3.27
1348 1443 2.097466 GCCAAAATGGGTCACTATCGTG 59.903 50.000 0.00 0.00 39.17 4.35
1380 1475 7.067372 CAGTGCCATTGGTTATTTCTCAGAATA 59.933 37.037 4.26 0.00 0.00 1.75
1406 1501 2.094026 GGCAATTGGATGACCTTGTTCC 60.094 50.000 7.72 0.00 37.04 3.62
1581 1679 6.755607 CAGCATATAGTCGAGCATACATGAAT 59.244 38.462 0.00 0.00 0.00 2.57
1582 1680 6.095377 CAGCATATAGTCGAGCATACATGAA 58.905 40.000 0.00 0.00 0.00 2.57
1703 1802 8.861033 CAACACATTGCTATTTGCTGTATAAT 57.139 30.769 0.00 0.00 43.37 1.28
1870 1972 6.228258 TGTCTTACATTTTGGTACAGAGGTC 58.772 40.000 0.00 0.00 42.39 3.85
1950 2280 1.221021 GGGTTTGCTACTCCCTCCG 59.779 63.158 0.00 0.00 38.29 4.63
2024 2363 4.870426 CAGCCAGTAGTTGTAACCATGTAG 59.130 45.833 0.00 0.00 0.00 2.74
2039 2379 4.173290 AGGGTTTTGTAAACAGCCAGTA 57.827 40.909 4.85 0.00 0.00 2.74
2197 2583 6.086222 CGTAAATCCTTTTCACATCCACAAG 58.914 40.000 0.00 0.00 0.00 3.16
2213 2599 0.831307 AGGTCTCCTGCCGTAAATCC 59.169 55.000 0.00 0.00 29.57 3.01
2350 2737 0.179171 CTCCTGCAGCATGAAAAGCG 60.179 55.000 8.66 0.00 39.69 4.68
2414 2801 4.623932 TCATAATACCCTTGCTAGCCTG 57.376 45.455 13.29 4.61 0.00 4.85
2602 2989 1.271434 GGAGAAAAAGCCCGAAGAGGT 60.271 52.381 0.00 0.00 38.74 3.85
2613 3000 7.446001 AAACTGCTATTCAGAGGAGAAAAAG 57.554 36.000 0.00 0.00 45.72 2.27


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

AutoCloner maintained by Alex Coulton.