Multiple sequence alignment - TraesCS4A01G244100

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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 TraesCS4A01G244100 chr4A 100.000 2801 0 0 1 2801 554698174 554700974 0.000000e+00 5173
1 TraesCS4A01G244100 chr4A 97.858 2801 59 1 1 2801 557664145 557661346 0.000000e+00 4839
2 TraesCS4A01G244100 chr1D 92.582 2858 133 28 1 2801 96036115 96033280 0.000000e+00 4030
3 TraesCS4A01G244100 chr1D 91.259 2860 142 41 1 2801 64335920 64338730 0.000000e+00 3797
4 TraesCS4A01G244100 chr1D 92.450 2331 113 18 524 2801 439404020 439406340 0.000000e+00 3271
5 TraesCS4A01G244100 chr7D 91.215 2857 151 24 1 2801 600062939 600065751 0.000000e+00 3794
6 TraesCS4A01G244100 chr6A 90.954 2852 174 23 4 2801 121725555 121722734 0.000000e+00 3760
7 TraesCS4A01G244100 chr3B 90.359 2510 157 34 341 2801 734914114 734911641 0.000000e+00 3216
8 TraesCS4A01G244100 chr3B 86.995 2399 184 41 368 2682 774402758 774405112 0.000000e+00 2584
9 TraesCS4A01G244100 chr3A 88.386 2385 159 31 486 2801 714788242 714790577 0.000000e+00 2761
10 TraesCS4A01G244100 chr3A 89.704 2030 119 28 280 2242 638855302 638853296 0.000000e+00 2508
11 TraesCS4A01G244100 chr3A 88.374 1987 118 28 883 2801 607845898 607847839 0.000000e+00 2285
12 TraesCS4A01G244100 chr1B 91.254 2058 106 19 524 2529 596176023 596178058 0.000000e+00 2736
13 TraesCS4A01G244100 chr1B 93.602 422 22 2 1 418 596175558 596175978 2.370000e-175 625
14 TraesCS4A01G244100 chr4D 94.431 1634 60 13 1 1607 42333873 42335502 0.000000e+00 2484
15 TraesCS4A01G244100 chr7B 93.691 1474 72 5 1 1455 6998569 7000040 0.000000e+00 2187
16 TraesCS4A01G244100 chr7B 89.614 1348 104 12 1487 2801 7000041 7001385 0.000000e+00 1681
17 TraesCS4A01G244100 chr2B 86.839 1740 126 36 526 2216 755329850 755331535 0.000000e+00 1849
18 TraesCS4A01G244100 chr3D 90.313 1373 53 18 857 2166 579688196 579689551 0.000000e+00 1725
19 TraesCS4A01G244100 chr2A 85.236 1673 153 39 1163 2801 749651367 749652979 0.000000e+00 1635
20 TraesCS4A01G244100 chr6D 92.145 1133 69 6 1 1129 68973814 68974930 0.000000e+00 1581


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 TraesCS4A01G244100 chr4A 554698174 554700974 2800 False 5173.0 5173 100.0000 1 2801 1 chr4A.!!$F1 2800
1 TraesCS4A01G244100 chr4A 557661346 557664145 2799 True 4839.0 4839 97.8580 1 2801 1 chr4A.!!$R1 2800
2 TraesCS4A01G244100 chr1D 96033280 96036115 2835 True 4030.0 4030 92.5820 1 2801 1 chr1D.!!$R1 2800
3 TraesCS4A01G244100 chr1D 64335920 64338730 2810 False 3797.0 3797 91.2590 1 2801 1 chr1D.!!$F1 2800
4 TraesCS4A01G244100 chr1D 439404020 439406340 2320 False 3271.0 3271 92.4500 524 2801 1 chr1D.!!$F2 2277
5 TraesCS4A01G244100 chr7D 600062939 600065751 2812 False 3794.0 3794 91.2150 1 2801 1 chr7D.!!$F1 2800
6 TraesCS4A01G244100 chr6A 121722734 121725555 2821 True 3760.0 3760 90.9540 4 2801 1 chr6A.!!$R1 2797
7 TraesCS4A01G244100 chr3B 734911641 734914114 2473 True 3216.0 3216 90.3590 341 2801 1 chr3B.!!$R1 2460
8 TraesCS4A01G244100 chr3B 774402758 774405112 2354 False 2584.0 2584 86.9950 368 2682 1 chr3B.!!$F1 2314
9 TraesCS4A01G244100 chr3A 714788242 714790577 2335 False 2761.0 2761 88.3860 486 2801 1 chr3A.!!$F2 2315
10 TraesCS4A01G244100 chr3A 638853296 638855302 2006 True 2508.0 2508 89.7040 280 2242 1 chr3A.!!$R1 1962
11 TraesCS4A01G244100 chr3A 607845898 607847839 1941 False 2285.0 2285 88.3740 883 2801 1 chr3A.!!$F1 1918
12 TraesCS4A01G244100 chr1B 596175558 596178058 2500 False 1680.5 2736 92.4280 1 2529 2 chr1B.!!$F1 2528
13 TraesCS4A01G244100 chr4D 42333873 42335502 1629 False 2484.0 2484 94.4310 1 1607 1 chr4D.!!$F1 1606
14 TraesCS4A01G244100 chr7B 6998569 7001385 2816 False 1934.0 2187 91.6525 1 2801 2 chr7B.!!$F1 2800
15 TraesCS4A01G244100 chr2B 755329850 755331535 1685 False 1849.0 1849 86.8390 526 2216 1 chr2B.!!$F1 1690
16 TraesCS4A01G244100 chr3D 579688196 579689551 1355 False 1725.0 1725 90.3130 857 2166 1 chr3D.!!$F1 1309
17 TraesCS4A01G244100 chr2A 749651367 749652979 1612 False 1635.0 1635 85.2360 1163 2801 1 chr2A.!!$F1 1638
18 TraesCS4A01G244100 chr6D 68973814 68974930 1116 False 1581.0 1581 92.1450 1 1129 1 chr6D.!!$F1 1128

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
812 829 5.419788 ACGCGTATATGATGGATAACCCTTA 59.58 40.0 11.67 0.0 35.38 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2060 2220 1.59626 CTTACATCATCAGCAGCACCG 59.404 52.381 0.0 0.0 0.0 4.94 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
812 829 5.419788 ACGCGTATATGATGGATAACCCTTA 59.580 40.000 11.67 0.00 35.38 2.69
944 961 6.092670 GCTTCATACAAATGCTTGTCTGACTA 59.907 38.462 9.51 0.09 44.06 2.59
1457 1552 7.950512 TCCTTCAGCAAATTAATCTCACAAAA 58.049 30.769 0.00 0.00 0.00 2.44
1572 1667 1.280133 TCCTCTGGTGCCTGAGATTTG 59.720 52.381 21.70 8.92 42.28 2.32
2060 2220 5.653507 TCTTCATTTGCAAATATGACTGCC 58.346 37.500 23.69 0.00 37.79 4.85
2155 2316 8.767085 CACATTTTAAGTTGCTCATGTCATTTT 58.233 29.630 0.00 0.00 0.00 1.82
2182 2343 2.923121 GCCATCTGCTTGGAACTGATA 58.077 47.619 5.26 0.00 39.25 2.15
2347 2548 0.694783 TCCCTCTCCTCTCGCCTCTA 60.695 60.000 0.00 0.00 0.00 2.43
2522 2724 6.877611 AATCGTGTCTGGTTTGATTTACTT 57.122 33.333 0.00 0.00 0.00 2.24
2613 2816 2.144078 TGTTCTTGGGGCCGTCTCA 61.144 57.895 0.00 0.00 0.00 3.27
2737 2948 2.011222 ACGTTTTGTGTTCACGGTGAT 58.989 42.857 12.26 0.00 38.26 3.06
2739 2951 2.031068 CGTTTTGTGTTCACGGTGATCA 59.969 45.455 15.90 15.90 0.00 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
357 364 5.935206 TGATCATTGCAACCTACTAAAACGA 59.065 36.000 0.00 0.00 0.00 3.85
358 365 6.021596 GTGATCATTGCAACCTACTAAAACG 58.978 40.000 0.00 0.00 0.00 3.60
429 436 6.861055 ACATTAACAATGGTAAAGTTGCTTCG 59.139 34.615 0.00 0.00 43.21 3.79
645 653 6.568869 CCACTTATTCTCCACAAAAACACAA 58.431 36.000 0.00 0.00 0.00 3.33
838 855 7.915397 CAGCTTTAGTTATGTGTGAACAAGTTT 59.085 33.333 0.00 0.00 0.00 2.66
1416 1510 5.590259 GCTGAAGGAACCAAGCTTATATCAA 59.410 40.000 0.00 0.00 0.00 2.57
1572 1667 4.393062 CCCAATCAGTCTTGTACATGTGAC 59.607 45.833 9.11 7.28 0.00 3.67
2060 2220 1.596260 CTTACATCATCAGCAGCACCG 59.404 52.381 0.00 0.00 0.00 4.94
2126 2286 6.017400 ACATGAGCAACTTAAAATGTGAGG 57.983 37.500 0.00 0.00 0.00 3.86
2347 2548 3.074412 CAGGGACGAGCAACATAAAGTT 58.926 45.455 0.00 0.00 42.42 2.66
2522 2724 3.008157 ACTCTAGACTGACGAGGAGAACA 59.992 47.826 0.00 0.00 0.00 3.18
2613 2816 2.122369 GGGATGGAGACCCCCGAT 60.122 66.667 0.00 0.00 41.38 4.18
2737 2948 4.832266 ACAAGTAAATGCAGGAACCATTGA 59.168 37.500 0.00 0.00 33.48 2.57
2739 2951 4.561326 GCACAAGTAAATGCAGGAACCATT 60.561 41.667 0.00 0.00 41.65 3.16


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

AutoCloner maintained by Alex Coulton.