Multiple sequence alignment - TraesCS4A01G493700

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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 TraesCS4A01G493700 chr4A 100.000 3653 0 0 1 3653 742073717 742077369 0.000000e+00 6746.0
1 TraesCS4A01G493700 chr4A 99.153 3661 20 5 1 3652 739679729 739683387 0.000000e+00 6578.0
2 TraesCS4A01G493700 chr4A 85.686 2564 290 42 628 3140 740604876 740602339 0.000000e+00 2630.0
3 TraesCS4A01G493700 chr4A 92.728 1829 119 9 679 2503 741780955 741779137 0.000000e+00 2628.0
4 TraesCS4A01G493700 chr4A 85.693 1978 258 17 876 2843 740156289 740158251 0.000000e+00 2061.0
5 TraesCS4A01G493700 chr4A 88.624 1679 168 10 1480 3140 740000020 739998347 0.000000e+00 2021.0
6 TraesCS4A01G493700 chr4A 87.408 1493 144 24 693 2170 741045121 741046584 0.000000e+00 1676.0
7 TraesCS4A01G493700 chr4A 85.450 1189 160 10 1859 3041 740157124 740158305 0.000000e+00 1225.0
8 TraesCS4A01G493700 chr4A 81.393 1134 200 10 1859 2987 739999789 739998662 0.000000e+00 915.0
9 TraesCS4A01G493700 chr4A 84.197 791 99 13 2375 3143 741778833 741778047 0.000000e+00 745.0
10 TraesCS4A01G493700 chr4A 79.700 1000 176 23 2003 2989 740603637 740602652 0.000000e+00 697.0
11 TraesCS4A01G493700 chr4A 85.822 663 84 8 2003 2661 741779780 741779124 0.000000e+00 695.0
12 TraesCS4A01G493700 chr4A 83.908 609 92 6 1555 2160 739740558 739741163 8.800000e-161 577.0
13 TraesCS4A01G493700 chr4A 90.417 240 12 6 571 809 740000249 740000020 4.580000e-79 305.0
14 TraesCS4A01G493700 chr4A 81.290 310 37 11 2852 3140 526608946 526609255 7.890000e-57 231.0
15 TraesCS4A01G493700 chr4A 90.789 152 9 1 525 676 741781348 741781202 8.000000e-47 198.0
16 TraesCS4A01G493700 chr4A 77.627 295 30 23 3380 3652 741777335 741777055 2.940000e-31 147.0
17 TraesCS4A01G493700 chr4A 80.814 172 25 3 3186 3357 739741740 739741903 1.060000e-25 128.0
18 TraesCS4A01G493700 chr4A 83.607 122 11 7 3466 3587 739836555 739836443 4.990000e-19 106.0
19 TraesCS4A01G493700 chr4A 88.372 86 6 3 3569 3652 739997752 739997669 2.320000e-17 100.0
20 TraesCS4A01G493700 chr4A 79.762 168 11 10 3449 3613 740159277 740159424 2.320000e-17 100.0
21 TraesCS4A01G493700 chr4A 88.372 86 6 3 3569 3652 741047321 741047404 2.320000e-17 100.0
22 TraesCS4A01G493700 chr4A 81.818 110 9 8 3487 3596 733922704 733922802 8.410000e-12 82.4
23 TraesCS4A01G493700 chr4A 80.000 115 12 9 3485 3598 740863807 740863911 1.410000e-09 75.0
24 TraesCS4A01G493700 chr4A 100.000 34 0 0 521 554 740000280 740000247 3.050000e-06 63.9
25 TraesCS4A01G493700 chr7D 89.576 1650 116 16 521 2160 2885791 2884188 0.000000e+00 2043.0
26 TraesCS4A01G493700 chr7D 85.373 964 116 16 2183 3125 2883673 2882714 0.000000e+00 976.0
27 TraesCS4A01G493700 chr7D 78.241 216 14 17 3449 3652 2880714 2880520 1.390000e-19 108.0
28 TraesCS4A01G493700 chr7D 88.608 79 5 3 3569 3645 2882112 2882036 3.880000e-15 93.5
29 TraesCS4A01G493700 chr7A 76.409 2395 483 55 692 3041 2742100 2744457 0.000000e+00 1218.0
30 TraesCS4A01G493700 chr7A 76.417 1976 417 33 868 2823 3029337 3031283 0.000000e+00 1022.0
31 TraesCS4A01G493700 chr7A 83.841 984 122 17 692 1652 2762871 2763840 0.000000e+00 902.0
32 TraesCS4A01G493700 chr7A 91.650 515 39 3 1 511 666559166 666558652 0.000000e+00 710.0
33 TraesCS4A01G493700 chr7A 78.362 989 207 7 1918 2903 2662890 2661906 5.150000e-178 634.0
34 TraesCS4A01G493700 chr7A 89.130 276 22 4 917 1191 2664255 2663987 1.630000e-88 337.0
35 TraesCS4A01G493700 chr7A 87.660 235 24 3 582 816 2605897 2605668 6.010000e-68 268.0
36 TraesCS4A01G493700 chr7A 87.624 202 23 2 562 762 2664492 2664292 2.190000e-57 233.0
37 TraesCS4A01G493700 chr7A 84.236 203 13 8 3186 3381 2660902 2660712 2.900000e-41 180.0
38 TraesCS4A01G493700 chr7A 89.831 118 12 0 582 699 2741953 2742070 6.320000e-33 152.0
39 TraesCS4A01G493700 chr7A 89.831 118 12 0 582 699 2762724 2762841 6.320000e-33 152.0
40 TraesCS4A01G493700 chr7A 81.373 204 19 6 3449 3652 3031859 3032043 8.170000e-32 148.0
41 TraesCS4A01G493700 chr7A 92.222 90 4 1 683 769 2939451 2939540 1.380000e-24 124.0
42 TraesCS4A01G493700 chr7A 76.733 202 25 11 3457 3652 2947065 2947250 3.880000e-15 93.5
43 TraesCS4A01G493700 chr5B 98.848 521 5 1 1 520 657879608 657880128 0.000000e+00 928.0
44 TraesCS4A01G493700 chr5B 98.095 525 9 1 1 524 55543140 55543664 0.000000e+00 913.0
45 TraesCS4A01G493700 chr5B 92.829 516 31 5 1 511 84670014 84669500 0.000000e+00 743.0
46 TraesCS4A01G493700 chr3B 97.552 531 10 3 1 529 823010794 823010265 0.000000e+00 905.0
47 TraesCS4A01G493700 chr4B 97.714 525 8 2 1 521 515116931 515116407 0.000000e+00 900.0
48 TraesCS4A01G493700 chr6B 95.247 526 19 3 1 520 11726543 11727068 0.000000e+00 828.0
49 TraesCS4A01G493700 chr2A 92.000 525 35 5 1 520 312713852 312713330 0.000000e+00 730.0


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 TraesCS4A01G493700 chr4A 742073717 742077369 3652 False 6746.000000 6746 100.0000 1 3653 1 chr4A.!!$F5 3652
1 TraesCS4A01G493700 chr4A 739679729 739683387 3658 False 6578.000000 6578 99.1530 1 3652 1 chr4A.!!$F3 3651
2 TraesCS4A01G493700 chr4A 740602339 740604876 2537 True 1663.500000 2630 82.6930 628 3140 2 chr4A.!!$R3 2512
3 TraesCS4A01G493700 chr4A 740156289 740159424 3135 False 1128.666667 2061 83.6350 876 3613 3 chr4A.!!$F7 2737
4 TraesCS4A01G493700 chr4A 741045121 741047404 2283 False 888.000000 1676 87.8900 693 3652 2 chr4A.!!$F8 2959
5 TraesCS4A01G493700 chr4A 741777055 741781348 4293 True 882.600000 2628 86.2326 525 3652 5 chr4A.!!$R4 3127
6 TraesCS4A01G493700 chr4A 739997669 740000280 2611 True 680.980000 2021 89.7612 521 3652 5 chr4A.!!$R2 3131
7 TraesCS4A01G493700 chr4A 739740558 739741903 1345 False 352.500000 577 82.3610 1555 3357 2 chr4A.!!$F6 1802
8 TraesCS4A01G493700 chr7D 2880520 2885791 5271 True 805.125000 2043 85.4495 521 3652 4 chr7D.!!$R1 3131
9 TraesCS4A01G493700 chr7A 666558652 666559166 514 True 710.000000 710 91.6500 1 511 1 chr7A.!!$R2 510
10 TraesCS4A01G493700 chr7A 2741953 2744457 2504 False 685.000000 1218 83.1200 582 3041 2 chr7A.!!$F3 2459
11 TraesCS4A01G493700 chr7A 3029337 3032043 2706 False 585.000000 1022 78.8950 868 3652 2 chr7A.!!$F5 2784
12 TraesCS4A01G493700 chr7A 2762724 2763840 1116 False 527.000000 902 86.8360 582 1652 2 chr7A.!!$F4 1070
13 TraesCS4A01G493700 chr7A 2660712 2664492 3780 True 346.000000 634 84.8380 562 3381 4 chr7A.!!$R3 2819
14 TraesCS4A01G493700 chr5B 657879608 657880128 520 False 928.000000 928 98.8480 1 520 1 chr5B.!!$F2 519
15 TraesCS4A01G493700 chr5B 55543140 55543664 524 False 913.000000 913 98.0950 1 524 1 chr5B.!!$F1 523
16 TraesCS4A01G493700 chr5B 84669500 84670014 514 True 743.000000 743 92.8290 1 511 1 chr5B.!!$R1 510
17 TraesCS4A01G493700 chr3B 823010265 823010794 529 True 905.000000 905 97.5520 1 529 1 chr3B.!!$R1 528
18 TraesCS4A01G493700 chr4B 515116407 515116931 524 True 900.000000 900 97.7140 1 521 1 chr4B.!!$R1 520
19 TraesCS4A01G493700 chr6B 11726543 11727068 525 False 828.000000 828 95.2470 1 520 1 chr6B.!!$F1 519
20 TraesCS4A01G493700 chr2A 312713330 312713852 522 True 730.000000 730 92.0000 1 520 1 chr2A.!!$R1 519

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
458 470 1.451936 GATATGGGAGTTGCGCCCT 59.548 57.895 4.18 0.0 44.04 5.19 F
1764 2385 9.857957 CGAGAACTAGGTTATCTTCTAAACTTT 57.142 33.333 0.00 0.0 32.41 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1764 2385 0.476338 TGCCAAGTTGCAGGTCCTTA 59.524 50.000 0.0 0.0 36.04 2.69 R
3487 7626 4.222124 TGGGAACTTTAGGCAATCTCTC 57.778 45.455 0.0 0.0 0.00 3.20 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
443 455 6.674066 TGTAATCTCAATCATGTACGCGATA 58.326 36.000 15.93 0.00 0.00 2.92
458 470 1.451936 GATATGGGAGTTGCGCCCT 59.548 57.895 4.18 0.00 44.04 5.19
1764 2385 9.857957 CGAGAACTAGGTTATCTTCTAAACTTT 57.142 33.333 0.00 0.00 32.41 2.66
2192 3882 5.051891 CAAGAATTGGAGTACCTTGCAAG 57.948 43.478 19.93 19.93 43.94 4.01
2963 5950 0.620556 ACTAACAGGTGCCATCCCAG 59.379 55.000 0.00 0.00 0.00 4.45
3418 7540 1.527793 GCTATCGCTGTTGTTTGCTCG 60.528 52.381 0.00 0.00 0.00 5.03
3487 7626 3.320541 AGTGAATTAGCGAGGAGGAGATG 59.679 47.826 0.00 0.00 0.00 2.90
3488 7627 3.319405 GTGAATTAGCGAGGAGGAGATGA 59.681 47.826 0.00 0.00 0.00 2.92
3537 7689 2.645730 TTAATGAACCATTGCGCACC 57.354 45.000 11.12 0.00 35.54 5.01
3647 7801 5.529060 CCTGCCTGAATGTTTATCCTTACTC 59.471 44.000 0.00 0.00 0.00 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
443 455 0.689745 TACTAGGGCGCAACTCCCAT 60.690 55.000 10.83 0.0 46.36 4.00
458 470 4.539870 GACGGCTGCGTGTTTATATACTA 58.460 43.478 0.00 0.0 0.00 1.82
1764 2385 0.476338 TGCCAAGTTGCAGGTCCTTA 59.524 50.000 0.00 0.0 36.04 2.69
2192 3882 8.680039 TTCACTAAGATCTAGGTACTCTAAGC 57.320 38.462 0.00 0.0 41.75 3.09
2963 5950 5.643379 TTTGTCAGATTGCCAAGGTTATC 57.357 39.130 0.00 0.0 0.00 1.75
3418 7540 4.246458 CTCCAGTTTAGGACAACTACAGC 58.754 47.826 0.00 0.0 35.10 4.40
3487 7626 4.222124 TGGGAACTTTAGGCAATCTCTC 57.778 45.455 0.00 0.0 0.00 3.20
3488 7627 4.568592 CCTTGGGAACTTTAGGCAATCTCT 60.569 45.833 0.00 0.0 0.00 3.10


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

AutoCloner maintained by Alex Coulton.