Multiple sequence alignment - TraesCS5A01G497900

Loading Multiple Alignment...

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 TraesCS5A01G497900 chr5A 100.000 3107 0 0 1 3107 665442564 665445670 0.000000e+00 5738.0
1 TraesCS5A01G497900 chr5A 97.605 167 4 0 2165 2331 675526887 675527053 1.410000e-73 287.0
2 TraesCS5A01G497900 chr5A 96.532 173 5 1 2162 2333 690959228 690959400 5.070000e-73 285.0
3 TraesCS5A01G497900 chr5A 91.096 146 13 0 595 740 238837450 238837305 6.800000e-47 198.0
4 TraesCS5A01G497900 chr4B 95.256 1328 58 3 800 2126 616967225 616968548 0.000000e+00 2098.0
5 TraesCS5A01G497900 chr4B 89.130 460 28 11 2582 3025 616969034 616969487 1.260000e-153 553.0
6 TraesCS5A01G497900 chr4B 86.290 372 38 5 223 583 616957632 616958001 2.900000e-105 392.0
7 TraesCS5A01G497900 chr4B 83.986 281 8 7 2329 2585 616968700 616968967 5.180000e-58 235.0
8 TraesCS5A01G497900 chr4B 97.778 90 2 0 3018 3107 567354287 567354198 4.150000e-34 156.0
9 TraesCS5A01G497900 chr4B 100.000 34 0 0 2131 2164 616968663 616968696 2.590000e-06 63.9
10 TraesCS5A01G497900 chr4D 94.626 1135 43 3 995 2126 484620688 484621807 0.000000e+00 1742.0
11 TraesCS5A01G497900 chr4D 91.031 446 20 10 2598 3025 484624751 484625194 4.460000e-163 584.0
12 TraesCS5A01G497900 chr4D 85.533 394 35 14 223 596 484616528 484616919 2.900000e-105 392.0
13 TraesCS5A01G497900 chr4D 91.765 255 8 5 2330 2584 484624436 484624677 2.970000e-90 342.0
14 TraesCS5A01G497900 chr4D 90.588 255 11 3 2329 2583 250701551 250701792 2.990000e-85 326.0
15 TraesCS5A01G497900 chr4D 89.453 256 14 3 2329 2584 250766546 250766788 8.370000e-81 311.0
16 TraesCS5A01G497900 chr4D 93.011 186 12 1 800 985 484620055 484620239 1.420000e-68 270.0
17 TraesCS5A01G497900 chr4D 89.209 139 14 1 90 227 484616310 484616448 4.120000e-39 172.0
18 TraesCS5A01G497900 chr3D 86.584 1051 115 15 1069 2100 21793036 21794079 0.000000e+00 1136.0
19 TraesCS5A01G497900 chr3D 85.742 1017 134 6 1068 2081 21888415 21889423 0.000000e+00 1064.0
20 TraesCS5A01G497900 chr3D 89.844 256 13 3 2329 2584 245677536 245677294 1.800000e-82 316.0
21 TraesCS5A01G497900 chr3D 88.716 257 15 4 2329 2585 499434958 499434716 5.040000e-78 302.0
22 TraesCS5A01G497900 chr3D 90.972 144 13 0 595 738 478082939 478083082 8.790000e-46 195.0
23 TraesCS5A01G497900 chr3D 88.710 62 4 3 2598 2658 245677220 245677161 4.300000e-09 73.1
24 TraesCS5A01G497900 chr3B 86.122 1052 120 15 1068 2100 37970718 37971762 0.000000e+00 1110.0
25 TraesCS5A01G497900 chr3B 97.674 172 2 2 2156 2327 520150016 520149847 8.430000e-76 294.0
26 TraesCS5A01G497900 chr3B 98.204 167 2 1 2163 2329 486371126 486371291 1.090000e-74 291.0
27 TraesCS5A01G497900 chr3B 97.647 170 3 1 2158 2327 731267208 731267040 1.090000e-74 291.0
28 TraesCS5A01G497900 chr3B 97.605 167 4 0 2165 2331 256781474 256781308 1.410000e-73 287.0
29 TraesCS5A01G497900 chr3B 85.714 175 22 2 424 596 720955068 720955241 6.840000e-42 182.0
30 TraesCS5A01G497900 chr3B 98.876 89 1 0 3019 3107 433645586 433645498 3.210000e-35 159.0
31 TraesCS5A01G497900 chr3A 86.174 1056 112 23 1068 2100 31559186 31560230 0.000000e+00 1110.0
32 TraesCS5A01G497900 chr3A 85.644 1010 135 5 1068 2075 31603483 31604484 0.000000e+00 1053.0
33 TraesCS5A01G497900 chr3A 96.023 176 6 1 2164 2338 618872386 618872561 5.070000e-73 285.0
34 TraesCS5A01G497900 chr3A 98.990 99 1 0 1 99 43450176 43450274 8.850000e-41 178.0
35 TraesCS5A01G497900 chr3A 98.990 99 1 0 1 99 44034459 44034557 8.850000e-41 178.0
36 TraesCS5A01G497900 chr3A 100.000 87 0 0 3021 3107 342978284 342978370 8.920000e-36 161.0
37 TraesCS5A01G497900 chrUn 84.372 1011 134 12 1071 2078 336370761 336369772 0.000000e+00 970.0
38 TraesCS5A01G497900 chrUn 84.273 1011 135 12 1071 2078 336373427 336372438 0.000000e+00 965.0
39 TraesCS5A01G497900 chrUn 90.411 146 14 0 595 740 45126974 45127119 3.160000e-45 193.0
40 TraesCS5A01G497900 chrUn 90.411 146 14 0 595 740 86494169 86494314 3.160000e-45 193.0
41 TraesCS5A01G497900 chrUn 90.411 146 14 0 595 740 186175302 186175157 3.160000e-45 193.0
42 TraesCS5A01G497900 chrUn 97.087 103 1 2 1 102 151418327 151418428 4.120000e-39 172.0
43 TraesCS5A01G497900 chrUn 98.876 89 1 0 3019 3107 71293455 71293543 3.210000e-35 159.0
44 TraesCS5A01G497900 chr2D 90.588 255 11 5 2329 2583 330426909 330427150 2.990000e-85 326.0
45 TraesCS5A01G497900 chr2D 88.710 62 4 3 2598 2658 330427225 330427284 4.300000e-09 73.1
46 TraesCS5A01G497900 chr2A 98.788 165 2 0 2163 2327 632622110 632622274 8.430000e-76 294.0
47 TraesCS5A01G497900 chr2A 98.193 166 3 0 2166 2331 113822458 113822293 1.090000e-74 291.0
48 TraesCS5A01G497900 chr2A 95.495 111 2 3 1 108 31808134 31808244 1.150000e-39 174.0
49 TraesCS5A01G497900 chr2A 94.690 113 3 3 1 111 721939481 721939370 4.120000e-39 172.0
50 TraesCS5A01G497900 chr2A 98.876 89 1 0 3019 3107 175227671 175227583 3.210000e-35 159.0
51 TraesCS5A01G497900 chr2A 98.876 89 1 0 3019 3107 206444152 206444064 3.210000e-35 159.0
52 TraesCS5A01G497900 chr2A 98.876 89 1 0 3019 3107 477947459 477947371 3.210000e-35 159.0
53 TraesCS5A01G497900 chr1B 97.110 173 4 1 2155 2327 67053875 67054046 1.090000e-74 291.0
54 TraesCS5A01G497900 chr1B 94.944 178 7 2 2155 2331 481299534 481299710 8.490000e-71 278.0
55 TraesCS5A01G497900 chr1B 98.913 92 1 0 3016 3107 297475507 297475598 6.890000e-37 165.0
56 TraesCS5A01G497900 chr7B 96.045 177 5 2 2158 2333 657551554 657551379 1.410000e-73 287.0
57 TraesCS5A01G497900 chr7B 90.972 144 13 0 597 740 115174241 115174098 8.790000e-46 195.0
58 TraesCS5A01G497900 chr5B 96.023 176 7 0 2156 2331 709856462 709856637 1.410000e-73 287.0
59 TraesCS5A01G497900 chr5B 97.059 170 4 1 2162 2331 578078559 578078727 5.070000e-73 285.0
60 TraesCS5A01G497900 chr5B 91.096 146 13 0 595 740 130625883 130625738 6.800000e-47 198.0
61 TraesCS5A01G497900 chr1A 92.466 146 11 0 595 740 94698885 94698740 3.140000e-50 209.0
62 TraesCS5A01G497900 chr1A 95.413 109 5 0 1 109 11368381 11368273 1.150000e-39 174.0
63 TraesCS5A01G497900 chr1D 91.096 146 13 0 595 740 351095703 351095558 6.800000e-47 198.0
64 TraesCS5A01G497900 chr4A 96.190 105 4 0 1 105 428394193 428394297 4.120000e-39 172.0
65 TraesCS5A01G497900 chr4A 95.370 108 4 1 1 108 584906897 584906791 1.480000e-38 171.0
66 TraesCS5A01G497900 chr4A 80.282 142 26 2 882 1021 426335270 426335411 4.240000e-19 106.0
67 TraesCS5A01G497900 chr7A 93.860 114 3 4 1 111 521985727 521985839 5.330000e-38 169.0
68 TraesCS5A01G497900 chr7A 88.028 142 14 2 429 568 116004282 116004422 6.890000e-37 165.0
69 TraesCS5A01G497900 chr6A 98.876 89 1 0 3019 3107 510214465 510214553 3.210000e-35 159.0
70 TraesCS5A01G497900 chr6A 77.348 181 23 12 220 385 26720328 26720505 1.190000e-14 91.6
71 TraesCS5A01G497900 chr6A 96.226 53 2 0 223 275 40220988 40220936 1.530000e-13 87.9
72 TraesCS5A01G497900 chr6A 100.000 28 0 0 744 771 1029130 1029157 6.000000e-03 52.8
73 TraesCS5A01G497900 chr6A 96.774 31 1 0 744 774 40220334 40220304 6.000000e-03 52.8
74 TraesCS5A01G497900 chr6D 100.000 28 0 0 744 771 1589742 1589715 6.000000e-03 52.8


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 TraesCS5A01G497900 chr5A 665442564 665445670 3106 False 5738.000000 5738 100.0000 1 3107 1 chr5A.!!$F1 3106
1 TraesCS5A01G497900 chr4B 616967225 616969487 2262 False 737.475000 2098 92.0930 800 3025 4 chr4B.!!$F2 2225
2 TraesCS5A01G497900 chr4D 484616310 484625194 8884 False 583.666667 1742 90.8625 90 3025 6 chr4D.!!$F3 2935
3 TraesCS5A01G497900 chr3D 21793036 21794079 1043 False 1136.000000 1136 86.5840 1069 2100 1 chr3D.!!$F1 1031
4 TraesCS5A01G497900 chr3D 21888415 21889423 1008 False 1064.000000 1064 85.7420 1068 2081 1 chr3D.!!$F2 1013
5 TraesCS5A01G497900 chr3B 37970718 37971762 1044 False 1110.000000 1110 86.1220 1068 2100 1 chr3B.!!$F1 1032
6 TraesCS5A01G497900 chr3A 31559186 31560230 1044 False 1110.000000 1110 86.1740 1068 2100 1 chr3A.!!$F1 1032
7 TraesCS5A01G497900 chr3A 31603483 31604484 1001 False 1053.000000 1053 85.6440 1068 2075 1 chr3A.!!$F2 1007
8 TraesCS5A01G497900 chrUn 336369772 336373427 3655 True 967.500000 970 84.3225 1071 2078 2 chrUn.!!$R2 1007


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
722 828 0.036671 AGGTTTTAGCCCTCCGTTCG 60.037 55.0 0.0 0.0 0.0 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2314 11200 0.322546 AACATTGCTCCCTCCGTTCC 60.323 55.0 0.0 0.0 0.0 3.62 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)



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

AutoCloner maintained by Alex Coulton.