Multiple sequence alignment - TraesCS7B01G096300

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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 TraesCS7B01G096300 chr7B 100.000 2951 0 0 1 2951 111316287 111319237 0.000000e+00 5450.0
1 TraesCS7B01G096300 chr7D 90.642 1464 93 20 801 2241 148160592 148162034 0.000000e+00 1905.0
2 TraesCS7B01G096300 chr7D 93.836 146 7 2 2598 2743 141292834 141292691 4.950000e-53 219.0
3 TraesCS7B01G096300 chr7A 89.835 846 68 10 1405 2240 149315987 149316824 0.000000e+00 1070.0
4 TraesCS7B01G096300 chr7A 85.370 663 95 2 143 804 601999840 601999179 0.000000e+00 686.0
5 TraesCS7B01G096300 chr7A 91.697 277 17 4 882 1157 149313052 149313323 2.150000e-101 379.0
6 TraesCS7B01G096300 chr7A 86.859 312 25 6 860 1171 149315535 149315830 4.710000e-88 335.0
7 TraesCS7B01G096300 chr7A 91.216 148 11 2 1 147 149315325 149315471 1.790000e-47 200.0
8 TraesCS7B01G096300 chr7A 89.394 132 14 0 1183 1314 149313321 149313452 1.820000e-37 167.0
9 TraesCS7B01G096300 chr7A 93.617 47 2 1 1320 1365 149315949 149315995 5.280000e-08 69.4
10 TraesCS7B01G096300 chrUn 94.246 643 35 1 144 784 93008452 93009094 0.000000e+00 981.0
11 TraesCS7B01G096300 chr3D 94.629 633 33 1 172 804 7162934 7162303 0.000000e+00 979.0
12 TraesCS7B01G096300 chr3D 93.506 154 8 2 2590 2743 397162536 397162687 8.230000e-56 228.0
13 TraesCS7B01G096300 chr3D 92.949 156 6 4 2591 2743 486424777 486424930 3.830000e-54 222.0
14 TraesCS7B01G096300 chr1D 93.202 662 43 2 144 804 413664130 413664790 0.000000e+00 972.0
15 TraesCS7B01G096300 chr1D 86.099 669 90 3 135 801 401161900 401162567 0.000000e+00 717.0
16 TraesCS7B01G096300 chr1D 95.139 144 6 1 2600 2743 37884065 37883923 2.960000e-55 226.0
17 TraesCS7B01G096300 chr2B 93.395 651 43 0 154 804 145434711 145434061 0.000000e+00 965.0
18 TraesCS7B01G096300 chr2A 92.273 660 47 2 145 804 159193959 159193304 0.000000e+00 933.0
19 TraesCS7B01G096300 chr2A 85.758 660 91 3 144 801 579864226 579864884 0.000000e+00 695.0
20 TraesCS7B01G096300 chr3A 85.520 663 93 3 144 804 90374113 90373452 0.000000e+00 689.0
21 TraesCS7B01G096300 chr6B 95.238 147 6 1 2597 2743 601199431 601199576 6.360000e-57 231.0
22 TraesCS7B01G096300 chr3B 94.667 150 7 1 2594 2743 540175096 540174948 6.360000e-57 231.0
23 TraesCS7B01G096300 chr3B 95.139 144 6 1 2600 2743 697395158 697395016 2.960000e-55 226.0
24 TraesCS7B01G096300 chr1B 95.139 144 6 1 2600 2743 183877200 183877342 2.960000e-55 226.0
25 TraesCS7B01G096300 chr4A 93.960 149 7 2 2596 2743 199801276 199801129 1.060000e-54 224.0
26 TraesCS7B01G096300 chr5D 87.963 108 13 0 1005 1112 480155382 480155275 8.580000e-26 128.0
27 TraesCS7B01G096300 chr5B 86.111 108 10 1 1005 1112 588156782 588156680 8.650000e-21 111.0
28 TraesCS7B01G096300 chr4B 81.416 113 18 3 998 1108 50400338 50400227 4.050000e-14 89.8
29 TraesCS7B01G096300 chr4B 81.416 113 18 3 998 1108 50443293 50443404 4.050000e-14 89.8


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 TraesCS7B01G096300 chr7B 111316287 111319237 2950 False 5450.000000 5450 100.000000 1 2951 1 chr7B.!!$F1 2950
1 TraesCS7B01G096300 chr7D 148160592 148162034 1442 False 1905.000000 1905 90.642000 801 2241 1 chr7D.!!$F1 1440
2 TraesCS7B01G096300 chr7A 601999179 601999840 661 True 686.000000 686 85.370000 143 804 1 chr7A.!!$R1 661
3 TraesCS7B01G096300 chr7A 149313052 149316824 3772 False 370.066667 1070 90.436333 1 2240 6 chr7A.!!$F1 2239
4 TraesCS7B01G096300 chrUn 93008452 93009094 642 False 981.000000 981 94.246000 144 784 1 chrUn.!!$F1 640
5 TraesCS7B01G096300 chr3D 7162303 7162934 631 True 979.000000 979 94.629000 172 804 1 chr3D.!!$R1 632
6 TraesCS7B01G096300 chr1D 413664130 413664790 660 False 972.000000 972 93.202000 144 804 1 chr1D.!!$F2 660
7 TraesCS7B01G096300 chr1D 401161900 401162567 667 False 717.000000 717 86.099000 135 801 1 chr1D.!!$F1 666
8 TraesCS7B01G096300 chr2B 145434061 145434711 650 True 965.000000 965 93.395000 154 804 1 chr2B.!!$R1 650
9 TraesCS7B01G096300 chr2A 159193304 159193959 655 True 933.000000 933 92.273000 145 804 1 chr2A.!!$R1 659
10 TraesCS7B01G096300 chr2A 579864226 579864884 658 False 695.000000 695 85.758000 144 801 1 chr2A.!!$F1 657
11 TraesCS7B01G096300 chr3A 90373452 90374113 661 True 689.000000 689 85.520000 144 804 1 chr3A.!!$R1 660


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
943 951 0.034337 ATTGCCTTTTGCCTGCACAG 59.966 50.0 0.0 0.0 40.16 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2545 5063 0.030101 GCAAACGCAACTGTTAGGCA 59.97 50.0 0.0 0.0 34.36 4.75 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)



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AutoCloner maintained by Alex Coulton.