Multiple sequence alignment - TraesCS5D01G007300

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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 TraesCS5D01G007300 chr5D 100.000 3876 0 0 1 3876 6088831 6084956 0.000000e+00 7158.0
1 TraesCS5D01G007300 chr5D 98.144 3556 63 3 324 3876 6101376 6097821 0.000000e+00 6198.0
2 TraesCS5D01G007300 chr5D 100.000 52 0 0 1 52 6101442 6101391 3.190000e-16 97.1
3 TraesCS5D01G007300 chr5A 93.780 2540 97 26 709 3201 3348638 3351163 0.000000e+00 3759.0
4 TraesCS5D01G007300 chr5A 93.324 704 34 8 1 695 3347956 3348655 0.000000e+00 1027.0
5 TraesCS5D01G007300 chr5A 87.500 416 33 8 3197 3602 3352308 3352714 2.730000e-126 462.0
6 TraesCS5D01G007300 chr5A 76.425 386 83 7 1843 2224 442282991 442283372 6.570000e-48 202.0
7 TraesCS5D01G007300 chr5A 93.939 66 4 0 3736 3801 3352764 3352829 2.460000e-17 100.0
8 TraesCS5D01G007300 chr5B 93.643 1573 63 13 801 2341 6215927 6217494 0.000000e+00 2316.0
9 TraesCS5D01G007300 chr5B 88.589 333 35 3 3336 3667 6217503 6217833 6.030000e-108 401.0
10 TraesCS5D01G007300 chr5B 74.936 391 90 7 1843 2230 400522817 400523202 5.150000e-39 172.0
11 TraesCS5D01G007300 chr5B 80.631 222 38 3 3395 3616 6208071 6208287 2.400000e-37 167.0
12 TraesCS5D01G007300 chr5B 94.495 109 4 2 1 109 6215791 6215897 2.400000e-37 167.0
13 TraesCS5D01G007300 chr5B 87.952 83 9 1 3737 3819 6217835 6217916 3.190000e-16 97.1
14 TraesCS5D01G007300 chr5B 74.059 239 53 8 1844 2078 400467840 400468073 5.330000e-14 89.8
15 TraesCS5D01G007300 chr6D 87.313 134 16 1 1066 1199 816329 816197 6.710000e-33 152.0
16 TraesCS5D01G007300 chr7D 87.121 132 17 0 1068 1199 632121134 632121003 2.410000e-32 150.0
17 TraesCS5D01G007300 chr2B 88.000 125 15 0 1068 1192 162860511 162860635 8.680000e-32 148.0
18 TraesCS5D01G007300 chr2B 95.652 46 2 0 3670 3715 755584174 755584219 1.490000e-09 75.0
19 TraesCS5D01G007300 chr2D 86.822 129 17 0 1068 1196 112538491 112538619 1.120000e-30 145.0
20 TraesCS5D01G007300 chr2D 91.489 47 4 0 3669 3715 639728504 639728458 8.990000e-07 65.8
21 TraesCS5D01G007300 chr2A 86.822 129 17 0 1068 1196 55953014 55953142 1.120000e-30 145.0
22 TraesCS5D01G007300 chr4D 85.294 136 18 2 1063 1196 3306148 3306283 5.220000e-29 139.0
23 TraesCS5D01G007300 chr4B 88.710 62 5 2 3666 3727 222545905 222545846 1.490000e-09 75.0
24 TraesCS5D01G007300 chr4B 88.710 62 5 2 3666 3727 222561214 222561155 1.490000e-09 75.0
25 TraesCS5D01G007300 chr4B 95.652 46 2 0 3670 3715 661648346 661648301 1.490000e-09 75.0
26 TraesCS5D01G007300 chr4B 89.796 49 5 0 3667 3715 466787730 466787778 3.230000e-06 63.9
27 TraesCS5D01G007300 chr1A 93.478 46 3 0 3670 3715 20890135 20890180 6.950000e-08 69.4
28 TraesCS5D01G007300 chr1A 84.746 59 7 2 3657 3715 13940179 13940235 1.500000e-04 58.4


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 TraesCS5D01G007300 chr5D 6084956 6088831 3875 True 7158.000 7158 100.00000 1 3876 1 chr5D.!!$R1 3875
1 TraesCS5D01G007300 chr5D 6097821 6101442 3621 True 3147.550 6198 99.07200 1 3876 2 chr5D.!!$R2 3875
2 TraesCS5D01G007300 chr5A 3347956 3352829 4873 False 1337.000 3759 92.13575 1 3801 4 chr5A.!!$F2 3800
3 TraesCS5D01G007300 chr5B 6215791 6217916 2125 False 745.275 2316 91.16975 1 3819 4 chr5B.!!$F4 3818

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
367 376 0.395311 AGCCATCAACTCATGCCAGG 60.395 55.000 0.0 0.0 0.0 4.45 F
1603 1634 0.325671 GTGGGGAGTGAGAGGATGGA 60.326 60.000 0.0 0.0 0.0 3.41 F
1775 1806 4.290093 TGACATGAGACTACCCTAAGCAT 58.710 43.478 0.0 0.0 0.0 3.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1932 1974 0.033699 AGAAGATTTGCCAGGGCTCC 60.034 55.000 12.19 0.00 42.51 4.70 R
2590 2635 0.181350 CCCTATGTGGTGGGCTCTTC 59.819 60.000 0.00 0.00 36.61 2.87 R
3496 4719 2.582436 CACCGCGGGTCCAGTAAT 59.418 61.111 31.76 0.57 31.02 1.89 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
186 194 8.519526 AGAAAATAATGCGGTAAAGATGTTTGA 58.480 29.630 0.00 0.00 0.00 2.69
295 303 7.790782 ATGGCTCAAAATTTTAGTCCCTTTA 57.209 32.000 2.44 0.00 0.00 1.85
367 376 0.395311 AGCCATCAACTCATGCCAGG 60.395 55.000 0.00 0.00 0.00 4.45
600 610 2.826128 GTGGGTTGAGGATTCCCTTTTC 59.174 50.000 0.00 0.00 44.53 2.29
610 620 1.828979 TTCCCTTTTCGGTACATGGC 58.171 50.000 0.00 0.00 0.00 4.40
877 888 6.099269 AGTGGAACGGGACAACTATTATGTAT 59.901 38.462 0.00 0.00 45.86 2.29
1238 1267 7.622893 TGATGATGAATTTTTCACACGGATA 57.377 32.000 0.00 0.00 43.48 2.59
1603 1634 0.325671 GTGGGGAGTGAGAGGATGGA 60.326 60.000 0.00 0.00 0.00 3.41
1775 1806 4.290093 TGACATGAGACTACCCTAAGCAT 58.710 43.478 0.00 0.00 0.00 3.79
2444 2487 7.565323 AATGCTTTGCTTATTTTGTCCAAAA 57.435 28.000 7.58 7.58 43.48 2.44
2445 2488 6.992063 TGCTTTGCTTATTTTGTCCAAAAA 57.008 29.167 9.06 0.00 42.71 1.94
2483 2526 8.141909 TGAATTATTGAGATACGAAGGGTGTAG 58.858 37.037 0.00 0.00 0.00 2.74
2590 2635 5.391310 GCGGATAATGAGTAATGGCATCTTG 60.391 44.000 0.00 0.00 0.00 3.02
2795 2840 2.491693 CGCCAAGGAAAAAGGCTTATCA 59.508 45.455 0.00 0.00 46.14 2.15
3121 3178 1.141053 AGTCTTCGCACTTCCTTTGGT 59.859 47.619 0.00 0.00 0.00 3.67
3125 3182 0.250295 TCGCACTTCCTTTGGTCCTG 60.250 55.000 0.00 0.00 0.00 3.86
3144 3201 8.998814 TGGTCCTGATTGGTTTTAATATCTCTA 58.001 33.333 0.00 0.00 37.07 2.43
3474 4697 2.577700 TCTCGGTCTCTAAGAGATGGC 58.422 52.381 0.00 0.00 40.98 4.40
3543 4766 4.689612 TGAGCAAGTCAAGGTAGAACTT 57.310 40.909 0.00 0.00 29.64 2.66
3575 4798 2.743928 CGCTCTGGGAGTGGTTGC 60.744 66.667 0.68 0.00 36.63 4.17
3755 4991 6.487331 AGAGTAGAAGAATGATGGGTACGTAG 59.513 42.308 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
76 77 9.103861 GCCTTATTATTTAGCTATCTGGATGAC 57.896 37.037 0.00 0.00 0.00 3.06
101 102 1.067425 TGAATGCATTGGCTCAACAGC 60.067 47.619 18.59 0.00 46.06 4.40
148 155 8.668353 ACCGCATTATTTTCTATGCACATATAG 58.332 33.333 0.00 0.00 45.73 1.31
152 159 5.772825 ACCGCATTATTTTCTATGCACAT 57.227 34.783 0.00 0.00 45.73 3.21
171 179 5.121768 CCTACAGGTTCAAACATCTTTACCG 59.878 44.000 0.00 0.00 0.00 4.02
270 278 6.686484 AAGGGACTAAAATTTTGAGCCATT 57.314 33.333 13.76 11.53 38.49 3.16
295 303 1.958288 ACCACCAGATGCCTAAGTCT 58.042 50.000 0.00 0.00 0.00 3.24
367 376 8.271012 TTTTTATAAAAATAACTGGCCCGTGCC 61.271 37.037 17.45 0.23 44.06 5.01
600 610 8.241367 AGAAAATAAGTAAAAAGCCATGTACCG 58.759 33.333 0.00 0.00 0.00 4.02
702 713 3.562141 CACCACACGTAAGAAAATGGACA 59.438 43.478 0.00 0.00 43.62 4.02
706 717 3.896648 AGCACCACACGTAAGAAAATG 57.103 42.857 0.00 0.00 43.62 2.32
806 817 7.112122 TGAGTTAGTATTCATGATGCCAAACT 58.888 34.615 11.05 11.05 33.09 2.66
1238 1267 6.623549 GCAACTGCAATGTTATGTACATGACT 60.624 38.462 25.70 12.57 46.75 3.41
1495 1524 4.700213 GGTCATGCCACATACTGTTACTTT 59.300 41.667 1.78 0.00 37.17 2.66
1510 1539 1.137479 CCCATGTTCATTGGTCATGCC 59.863 52.381 12.88 0.00 37.99 4.40
1652 1683 6.286758 AGCTATCACTGATGTAAATGTCCTG 58.713 40.000 1.42 0.00 0.00 3.86
1775 1806 5.534278 TGTTTCACATGGAACTATTGCTTGA 59.466 36.000 4.70 0.00 34.56 3.02
1932 1974 0.033699 AGAAGATTTGCCAGGGCTCC 60.034 55.000 12.19 0.00 42.51 4.70
2154 2196 6.605119 ACAATGTATAAGGCTTGGCTAGAAT 58.395 36.000 10.69 0.00 0.00 2.40
2568 2613 7.663081 TCTTCAAGATGCCATTACTCATTATCC 59.337 37.037 0.00 0.00 0.00 2.59
2590 2635 0.181350 CCCTATGTGGTGGGCTCTTC 59.819 60.000 0.00 0.00 36.61 2.87
2795 2840 8.133024 TGATTTGCTTAAATTATCAGGGTGTT 57.867 30.769 0.00 0.00 0.00 3.32
3414 4636 7.436376 GGTCGCCTAGTTTTTAGTTTATATCGT 59.564 37.037 0.00 0.00 0.00 3.73
3496 4719 2.582436 CACCGCGGGTCCAGTAAT 59.418 61.111 31.76 0.57 31.02 1.89


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

AutoCloner maintained by Alex Coulton.