Multiple sequence alignment - TraesCS5D01G095100

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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 TraesCS5D01G095100 chr5D 100.000 5864 0 0 1 5864 104474742 104468879 0.000000e+00 10829.0
1 TraesCS5D01G095100 chr5D 92.182 2699 182 18 932 3612 104157600 104154913 0.000000e+00 3788.0
2 TraesCS5D01G095100 chr5D 87.746 457 43 8 4627 5081 104153818 104153373 6.730000e-144 521.0
3 TraesCS5D01G095100 chr5D 86.500 200 24 3 4623 4821 450611540 450611343 3.560000e-52 217.0
4 TraesCS5D01G095100 chr5D 80.476 210 27 9 5096 5299 104153334 104153133 1.320000e-31 148.0
5 TraesCS5D01G095100 chr5A 98.114 5248 77 12 627 5864 107392617 107387382 0.000000e+00 9123.0
6 TraesCS5D01G095100 chr5A 92.145 2699 185 19 932 3612 94083195 94085884 0.000000e+00 3784.0
7 TraesCS5D01G095100 chr5A 96.960 625 12 2 7 629 107393262 107392643 0.000000e+00 1042.0
8 TraesCS5D01G095100 chr5A 87.939 456 49 6 4628 5081 94087949 94088400 3.110000e-147 532.0
9 TraesCS5D01G095100 chr5A 80.476 210 27 9 5096 5299 94088439 94088640 1.320000e-31 148.0
10 TraesCS5D01G095100 chr5B 97.926 3519 60 6 1 3518 113877549 113874043 0.000000e+00 6082.0
11 TraesCS5D01G095100 chr5B 91.775 2699 193 23 932 3612 113559959 113557272 0.000000e+00 3727.0
12 TraesCS5D01G095100 chr5B 96.782 2144 49 10 3723 5864 113874043 113871918 0.000000e+00 3559.0
13 TraesCS5D01G095100 chr5B 88.377 456 47 6 4628 5081 113556194 113555743 1.440000e-150 544.0
14 TraesCS5D01G095100 chr5B 83.986 281 43 2 3032 3311 119392257 119391978 9.690000e-68 268.0
15 TraesCS5D01G095100 chr5B 78.098 347 56 12 2967 3312 320823491 320823818 9.960000e-48 202.0
16 TraesCS5D01G095100 chr4D 84.351 262 40 1 3058 3318 304184272 304184533 7.540000e-64 255.0
17 TraesCS5D01G095100 chr4D 87.000 200 21 5 4623 4821 465418402 465418207 2.750000e-53 220.0
18 TraesCS5D01G095100 chr4D 93.590 78 5 0 1624 1701 178522915 178522838 3.710000e-22 117.0
19 TraesCS5D01G095100 chr7D 87.500 200 22 3 4623 4821 65501908 65502105 1.640000e-55 228.0
20 TraesCS5D01G095100 chr3B 89.130 138 15 0 1564 1701 522886039 522886176 7.810000e-39 172.0
21 TraesCS5D01G095100 chr3B 94.382 89 5 0 2274 2362 522886170 522886258 2.850000e-28 137.0
22 TraesCS5D01G095100 chr1A 95.294 85 4 0 1617 1701 532211265 532211181 1.030000e-27 135.0
23 TraesCS5D01G095100 chr1A 93.590 78 4 1 1624 1701 233202843 233202919 1.340000e-21 115.0
24 TraesCS5D01G095100 chr1A 88.764 89 10 0 2274 2362 233202913 233203001 6.210000e-20 110.0
25 TraesCS5D01G095100 chr7B 84.259 108 5 5 2255 2362 279198500 279198405 1.740000e-15 95.3


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 TraesCS5D01G095100 chr5D 104468879 104474742 5863 True 10829.000000 10829 100.000000 1 5864 1 chr5D.!!$R1 5863
1 TraesCS5D01G095100 chr5D 104153133 104157600 4467 True 1485.666667 3788 86.801333 932 5299 3 chr5D.!!$R3 4367
2 TraesCS5D01G095100 chr5A 107387382 107393262 5880 True 5082.500000 9123 97.537000 7 5864 2 chr5A.!!$R1 5857
3 TraesCS5D01G095100 chr5A 94083195 94088640 5445 False 1488.000000 3784 86.853333 932 5299 3 chr5A.!!$F1 4367
4 TraesCS5D01G095100 chr5B 113871918 113877549 5631 True 4820.500000 6082 97.354000 1 5864 2 chr5B.!!$R3 5863
5 TraesCS5D01G095100 chr5B 113555743 113559959 4216 True 2135.500000 3727 90.076000 932 5081 2 chr5B.!!$R2 4149


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
269 270 1.076350 CCTCCGTCTCTCCCCATCTAT 59.924 57.143 0.00 0.0 0.00 1.98 F
1167 1201 0.543174 AGAAACCTGAGGAGAGCCGT 60.543 55.000 4.99 0.0 39.96 5.68 F
2924 2958 0.585357 GCATATGCAGCTGGTTCGAG 59.415 55.000 22.84 0.0 41.59 4.04 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1755 1789 0.101759 GCATGTATGTGGCCAGCTTG 59.898 55.000 5.11 6.86 0.00 4.01 R
3649 3705 9.797642 ATTCAGTATCACATAAGCAATTATCCA 57.202 29.630 0.00 0.00 0.00 3.41 R
5303 6647 1.271926 GCCCCCACATAGTGAAGTTGT 60.272 52.381 0.00 0.00 35.23 3.32 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
269 270 1.076350 CCTCCGTCTCTCCCCATCTAT 59.924 57.143 0.00 0.00 0.00 1.98
480 483 2.027192 TCACTGGGTAATCACTGGAAGC 60.027 50.000 0.00 0.00 37.60 3.86
573 576 3.330701 TCATTGGTAGAGGGAAGCAGTTT 59.669 43.478 0.00 0.00 0.00 2.66
709 741 4.993029 AGTAGTATGTTGTCCTGCTCTC 57.007 45.455 0.00 0.00 0.00 3.20
723 755 5.918011 GTCCTGCTCTCGTCAGATTTTATAG 59.082 44.000 0.00 0.00 33.54 1.31
917 949 6.944234 AAAGAGGACTTTACTTTGTCAAGG 57.056 37.500 0.00 0.00 43.44 3.61
1167 1201 0.543174 AGAAACCTGAGGAGAGCCGT 60.543 55.000 4.99 0.00 39.96 5.68
1527 1561 5.409826 CCAAGACCAAGTCAACAAGATACTC 59.590 44.000 0.00 0.00 34.60 2.59
1755 1789 8.062448 GTGGCTATTTCATCAACTTATTACGAC 58.938 37.037 0.00 0.00 0.00 4.34
1788 1822 8.184192 GCCACATACATGCAGGATATATTTAAC 58.816 37.037 4.84 0.00 0.00 2.01
1962 1996 2.045131 GCAAGCTCTTCCTGCCCTG 61.045 63.158 0.00 0.00 0.00 4.45
2924 2958 0.585357 GCATATGCAGCTGGTTCGAG 59.415 55.000 22.84 0.00 41.59 4.04
3511 3558 4.854399 TCAAGGAAACTAATGCAAACACG 58.146 39.130 0.00 0.00 42.68 4.49
3782 3968 7.358830 GCCTTGCTCTTCTGAATTATATGAAC 58.641 38.462 0.00 0.00 0.00 3.18
3808 3994 1.251251 AAAGCTGCAACTGGTGGATC 58.749 50.000 1.02 0.00 0.00 3.36
4045 5281 5.046950 ACTCCTAGCTAACACTGAAGGAAAG 60.047 44.000 0.00 0.00 32.94 2.62
4059 5295 9.793252 CACTGAAGGAAAGTATGAATATTTTGG 57.207 33.333 0.00 0.00 0.00 3.28
4494 5782 5.880332 ACTTACATACACCTTGCACTATTGG 59.120 40.000 0.00 0.00 0.00 3.16
4543 5832 0.887933 CAGCCAACCAATACCACACC 59.112 55.000 0.00 0.00 0.00 4.16
4544 5833 0.251608 AGCCAACCAATACCACACCC 60.252 55.000 0.00 0.00 0.00 4.61
4546 5835 1.544724 CCAACCAATACCACACCCTG 58.455 55.000 0.00 0.00 0.00 4.45
4547 5836 1.074727 CCAACCAATACCACACCCTGA 59.925 52.381 0.00 0.00 0.00 3.86
4548 5837 2.159382 CAACCAATACCACACCCTGAC 58.841 52.381 0.00 0.00 0.00 3.51
4549 5838 1.440618 ACCAATACCACACCCTGACA 58.559 50.000 0.00 0.00 0.00 3.58
4550 5839 1.073284 ACCAATACCACACCCTGACAC 59.927 52.381 0.00 0.00 0.00 3.67
4867 6179 2.946752 GCGGTTTCGGGTTGACGTC 61.947 63.158 9.11 9.11 36.79 4.34
5036 6350 3.572255 GTCAACCCAGCCTTTTTCACATA 59.428 43.478 0.00 0.00 0.00 2.29
5080 6394 3.824443 GGCCACCTGCTAACTTTTCTAAA 59.176 43.478 0.00 0.00 40.92 1.85
5303 6647 4.425180 TTTTTGTACTGCTCAGGGTGTA 57.575 40.909 1.66 0.00 0.00 2.90
5335 6679 4.083155 GGGGGCATGTTCCTCCTA 57.917 61.111 1.08 0.00 43.73 2.94
5610 6954 3.998341 GGGCAGTTGTCGAGTTGTATTTA 59.002 43.478 0.00 0.00 0.00 1.40
5816 7166 2.650608 CAACTCTTTTACGCAGTTGGC 58.349 47.619 3.56 0.00 37.78 4.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
96 97 2.965999 GCAGCTCTGCGATGCGAT 60.966 61.111 6.08 0.00 45.98 4.58
269 270 2.011122 AGAGGAGAACGGAACAAGGA 57.989 50.000 0.00 0.00 0.00 3.36
544 547 2.693591 TCCCTCTACCAATGAACTAGCG 59.306 50.000 0.00 0.00 0.00 4.26
723 755 9.245962 CATGAATGGCAAAATTCTAAAGAGATC 57.754 33.333 0.00 0.00 37.44 2.75
875 907 2.214376 TTGGGTAGAGCCAAACCATG 57.786 50.000 10.70 0.00 39.65 3.66
956 988 3.499338 AGGAGAGTCAGATAGCTCATGG 58.501 50.000 0.00 0.00 34.39 3.66
1167 1201 2.968574 GAGGATCAGACCAGCCAATCTA 59.031 50.000 0.00 0.00 33.17 1.98
1527 1561 2.254546 TACCCTGAACAACAGCTGTG 57.745 50.000 22.49 16.62 44.52 3.66
1755 1789 0.101759 GCATGTATGTGGCCAGCTTG 59.898 55.000 5.11 6.86 0.00 4.01
1962 1996 2.677524 TCCAGCAGCATTGGCACC 60.678 61.111 0.00 0.00 44.61 5.01
3649 3705 9.797642 ATTCAGTATCACATAAGCAATTATCCA 57.202 29.630 0.00 0.00 0.00 3.41
3782 3968 1.728971 CCAGTTGCAGCTTTAGACTCG 59.271 52.381 0.00 0.00 0.00 4.18
3808 3994 6.721571 TCGAAAGTAGCTATGAAAAAGTGG 57.278 37.500 0.00 0.00 0.00 4.00
4045 5281 6.317893 ACGACCCACTTCCAAAATATTCATAC 59.682 38.462 0.00 0.00 0.00 2.39
4059 5295 9.408069 CACTATTTATTCTATACGACCCACTTC 57.592 37.037 0.00 0.00 0.00 3.01
4152 5391 8.158132 TGGATTTAACACCTGTCAACTATACAA 58.842 33.333 0.00 0.00 0.00 2.41
4153 5392 7.681679 TGGATTTAACACCTGTCAACTATACA 58.318 34.615 0.00 0.00 0.00 2.29
4183 5442 2.814805 AGTAGGCCTGTAACGGACTA 57.185 50.000 17.99 0.00 41.89 2.59
4184 5443 1.934410 AAGTAGGCCTGTAACGGACT 58.066 50.000 17.99 5.78 46.60 3.85
4229 5507 1.538687 GCCAGGCTGCTTGACCAAAT 61.539 55.000 13.84 0.00 0.00 2.32
4494 5782 5.543507 TTGGGAGAGAGATTCTATTCTGC 57.456 43.478 9.40 9.40 35.87 4.26
4543 5832 4.103153 ACTGGTCATTATATGGGTGTCAGG 59.897 45.833 0.00 0.00 0.00 3.86
4544 5833 5.070981 AGACTGGTCATTATATGGGTGTCAG 59.929 44.000 3.51 0.00 0.00 3.51
4546 5835 5.070446 TGAGACTGGTCATTATATGGGTGTC 59.930 44.000 3.51 0.00 0.00 3.67
4547 5836 4.968719 TGAGACTGGTCATTATATGGGTGT 59.031 41.667 3.51 0.00 0.00 4.16
4548 5837 5.551305 TGAGACTGGTCATTATATGGGTG 57.449 43.478 3.51 0.00 0.00 4.61
4549 5838 6.770286 AATGAGACTGGTCATTATATGGGT 57.230 37.500 5.90 0.00 43.85 4.51
4550 5839 8.355169 CAAAAATGAGACTGGTCATTATATGGG 58.645 37.037 7.64 0.00 44.72 4.00
4650 5962 6.261826 CAGAATCATCCCTGAAATGGTAAGAC 59.738 42.308 0.00 0.00 34.37 3.01
4867 6179 3.313249 TGTGCAGACTCAAGACAAATGTG 59.687 43.478 0.00 0.00 0.00 3.21
5036 6350 3.434940 ACTTAACCCTCTTTTCCGCAT 57.565 42.857 0.00 0.00 0.00 4.73
5303 6647 1.271926 GCCCCCACATAGTGAAGTTGT 60.272 52.381 0.00 0.00 35.23 3.32
5491 6835 2.216898 GAACAGCAGCATAGATGACCC 58.783 52.381 0.00 0.00 0.00 4.46
5542 6886 5.562635 ACCTATAATTGTTCGTTTCCACCA 58.437 37.500 0.00 0.00 0.00 4.17
5816 7166 3.325293 TCTGCTCAAAGCCTTCTACTG 57.675 47.619 0.00 0.00 41.51 2.74



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

AutoCloner maintained by Alex Coulton.