Multiple sequence alignment - TraesCS3A01G471700

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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 TraesCS3A01G471700 chr3A 100.000 3286 0 0 1 3286 703169734 703173019 0.000000e+00 6069.0
1 TraesCS3A01G471700 chr3A 91.743 1308 79 13 1037 2320 703203807 703205109 0.000000e+00 1790.0
2 TraesCS3A01G471700 chr3A 92.009 851 51 5 2450 3286 595118045 595117198 0.000000e+00 1179.0
3 TraesCS3A01G471700 chr3A 80.033 1227 187 41 1052 2238 703304297 703303089 0.000000e+00 856.0
4 TraesCS3A01G471700 chr3A 78.536 1216 183 48 1069 2237 655637061 655635877 0.000000e+00 728.0
5 TraesCS3A01G471700 chr3D 95.758 1556 51 9 896 2443 570280876 570282424 0.000000e+00 2494.0
6 TraesCS3A01G471700 chr3D 94.922 1418 54 10 1038 2448 570328415 570329821 0.000000e+00 2204.0
7 TraesCS3A01G471700 chr3D 92.616 1246 83 7 1012 2253 570379544 570380784 0.000000e+00 1783.0
8 TraesCS3A01G471700 chr3D 90.827 1101 91 5 1142 2236 570311115 570312211 0.000000e+00 1465.0
9 TraesCS3A01G471700 chr3D 83.990 1218 147 28 1046 2225 570393676 570394883 0.000000e+00 1125.0
10 TraesCS3A01G471700 chr3D 79.542 1222 208 31 1046 2238 570496394 570495186 0.000000e+00 833.0
11 TraesCS3A01G471700 chr3D 78.485 1241 184 51 1048 2237 520191927 520190719 0.000000e+00 736.0
12 TraesCS3A01G471700 chr3D 78.739 555 93 18 1697 2238 570400497 570399955 6.750000e-92 348.0
13 TraesCS3A01G471700 chr3D 82.748 313 23 8 444 753 570280539 570280823 1.960000e-62 250.0
14 TraesCS3A01G471700 chr3D 82.584 178 8 13 856 1028 570305509 570305668 5.720000e-28 135.0
15 TraesCS3A01G471700 chr3D 100.000 42 0 0 840 881 570280837 570280878 9.780000e-11 78.7
16 TraesCS3A01G471700 chr3B 93.665 1547 76 12 910 2448 757472725 757474257 0.000000e+00 2294.0
17 TraesCS3A01G471700 chr3B 92.471 1222 84 6 1037 2253 757708069 757709287 0.000000e+00 1740.0
18 TraesCS3A01G471700 chr3B 88.490 1338 122 15 930 2253 757498177 757499496 0.000000e+00 1589.0
19 TraesCS3A01G471700 chr3B 83.990 1218 146 29 1046 2225 757734142 757735348 0.000000e+00 1123.0
20 TraesCS3A01G471700 chr3B 86.311 862 84 20 2450 3286 572803951 572803099 0.000000e+00 907.0
21 TraesCS3A01G471700 chr3B 88.780 205 18 5 512 712 757472440 757472643 2.530000e-61 246.0
22 TraesCS3A01G471700 chr3B 100.000 40 0 0 840 879 757472683 757472722 1.260000e-09 75.0
23 TraesCS3A01G471700 chr2A 92.488 852 46 5 2450 3286 678613102 678612254 0.000000e+00 1203.0
24 TraesCS3A01G471700 chr2A 86.070 804 75 21 2447 3225 485039704 485038913 0.000000e+00 830.0
25 TraesCS3A01G471700 chr5A 92.299 844 54 5 2450 3286 549582745 549583584 0.000000e+00 1188.0
26 TraesCS3A01G471700 chr5A 86.605 754 67 19 2560 3286 548773727 548772981 0.000000e+00 802.0
27 TraesCS3A01G471700 chr4D 87.791 860 77 13 2450 3286 478228505 478229359 0.000000e+00 981.0
28 TraesCS3A01G471700 chr1B 86.621 867 78 21 2447 3286 629109688 629108833 0.000000e+00 924.0
29 TraesCS3A01G471700 chr1B 84.088 861 73 29 2450 3286 401157104 401156284 0.000000e+00 773.0
30 TraesCS3A01G471700 chr1B 89.340 197 21 0 2446 2642 611129357 611129553 7.040000e-62 248.0
31 TraesCS3A01G471700 chr7A 92.369 629 44 4 2450 3075 244498326 244497699 0.000000e+00 893.0
32 TraesCS3A01G471700 chr6B 86.033 852 88 18 2461 3286 57155135 57155981 0.000000e+00 885.0
33 TraesCS3A01G471700 chr4A 85.012 854 80 22 2457 3286 102440622 102441451 0.000000e+00 824.0
34 TraesCS3A01G471700 chr7B 84.859 852 89 18 2450 3286 28934211 28933385 0.000000e+00 822.0


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 TraesCS3A01G471700 chr3A 703169734 703173019 3285 False 6069.000000 6069 100.000000 1 3286 1 chr3A.!!$F1 3285
1 TraesCS3A01G471700 chr3A 703203807 703205109 1302 False 1790.000000 1790 91.743000 1037 2320 1 chr3A.!!$F2 1283
2 TraesCS3A01G471700 chr3A 595117198 595118045 847 True 1179.000000 1179 92.009000 2450 3286 1 chr3A.!!$R1 836
3 TraesCS3A01G471700 chr3A 703303089 703304297 1208 True 856.000000 856 80.033000 1052 2238 1 chr3A.!!$R3 1186
4 TraesCS3A01G471700 chr3A 655635877 655637061 1184 True 728.000000 728 78.536000 1069 2237 1 chr3A.!!$R2 1168
5 TraesCS3A01G471700 chr3D 570328415 570329821 1406 False 2204.000000 2204 94.922000 1038 2448 1 chr3D.!!$F3 1410
6 TraesCS3A01G471700 chr3D 570379544 570380784 1240 False 1783.000000 1783 92.616000 1012 2253 1 chr3D.!!$F4 1241
7 TraesCS3A01G471700 chr3D 570311115 570312211 1096 False 1465.000000 1465 90.827000 1142 2236 1 chr3D.!!$F2 1094
8 TraesCS3A01G471700 chr3D 570393676 570394883 1207 False 1125.000000 1125 83.990000 1046 2225 1 chr3D.!!$F5 1179
9 TraesCS3A01G471700 chr3D 570280539 570282424 1885 False 940.900000 2494 92.835333 444 2443 3 chr3D.!!$F6 1999
10 TraesCS3A01G471700 chr3D 570495186 570496394 1208 True 833.000000 833 79.542000 1046 2238 1 chr3D.!!$R3 1192
11 TraesCS3A01G471700 chr3D 520190719 520191927 1208 True 736.000000 736 78.485000 1048 2237 1 chr3D.!!$R1 1189
12 TraesCS3A01G471700 chr3D 570399955 570400497 542 True 348.000000 348 78.739000 1697 2238 1 chr3D.!!$R2 541
13 TraesCS3A01G471700 chr3B 757708069 757709287 1218 False 1740.000000 1740 92.471000 1037 2253 1 chr3B.!!$F2 1216
14 TraesCS3A01G471700 chr3B 757498177 757499496 1319 False 1589.000000 1589 88.490000 930 2253 1 chr3B.!!$F1 1323
15 TraesCS3A01G471700 chr3B 757734142 757735348 1206 False 1123.000000 1123 83.990000 1046 2225 1 chr3B.!!$F3 1179
16 TraesCS3A01G471700 chr3B 572803099 572803951 852 True 907.000000 907 86.311000 2450 3286 1 chr3B.!!$R1 836
17 TraesCS3A01G471700 chr3B 757472440 757474257 1817 False 871.666667 2294 94.148333 512 2448 3 chr3B.!!$F4 1936
18 TraesCS3A01G471700 chr2A 678612254 678613102 848 True 1203.000000 1203 92.488000 2450 3286 1 chr2A.!!$R2 836
19 TraesCS3A01G471700 chr2A 485038913 485039704 791 True 830.000000 830 86.070000 2447 3225 1 chr2A.!!$R1 778
20 TraesCS3A01G471700 chr5A 549582745 549583584 839 False 1188.000000 1188 92.299000 2450 3286 1 chr5A.!!$F1 836
21 TraesCS3A01G471700 chr5A 548772981 548773727 746 True 802.000000 802 86.605000 2560 3286 1 chr5A.!!$R1 726
22 TraesCS3A01G471700 chr4D 478228505 478229359 854 False 981.000000 981 87.791000 2450 3286 1 chr4D.!!$F1 836
23 TraesCS3A01G471700 chr1B 629108833 629109688 855 True 924.000000 924 86.621000 2447 3286 1 chr1B.!!$R2 839
24 TraesCS3A01G471700 chr1B 401156284 401157104 820 True 773.000000 773 84.088000 2450 3286 1 chr1B.!!$R1 836
25 TraesCS3A01G471700 chr7A 244497699 244498326 627 True 893.000000 893 92.369000 2450 3075 1 chr7A.!!$R1 625
26 TraesCS3A01G471700 chr6B 57155135 57155981 846 False 885.000000 885 86.033000 2461 3286 1 chr6B.!!$F1 825
27 TraesCS3A01G471700 chr4A 102440622 102441451 829 False 824.000000 824 85.012000 2457 3286 1 chr4A.!!$F1 829
28 TraesCS3A01G471700 chr7B 28933385 28934211 826 True 822.000000 822 84.859000 2450 3286 1 chr7B.!!$R1 836


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
805 815 0.095245 CACGTAGAGCCATTTGTGCG 59.905 55.0 0.0 0.0 0.0 5.34 F
881 891 0.168128 GGCATGGTTTGTCTACGCAC 59.832 55.0 0.0 0.0 0.0 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2104 2208 0.613260 CCCCTTCATCTCCACGAACA 59.387 55.000 0.0 0.0 0.00 3.18 R
2539 2664 1.065709 ACCGTATTTGAACGCCCAGAT 60.066 47.619 0.0 0.0 41.51 2.90 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.