Multiple sequence alignment - TraesCS1A01G321400

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 TraesCS1A01G321400 chr1A 100.000 3081 0 0 1 3081 511637236 511634156 0.000000e+00 5690.0
1 TraesCS1A01G321400 chr1A 87.791 1548 85 38 864 2363 512040399 512038908 0.000000e+00 1716.0
2 TraesCS1A01G321400 chr1A 91.098 865 69 5 1 865 512041304 512040448 0.000000e+00 1164.0
3 TraesCS1A01G321400 chr1A 90.603 862 79 2 4 865 512019497 512018638 0.000000e+00 1142.0
4 TraesCS1A01G321400 chr1A 89.177 887 72 14 1 865 511791647 511790763 0.000000e+00 1085.0
5 TraesCS1A01G321400 chr1A 84.917 663 59 28 1516 2174 512461280 512460655 1.560000e-177 632.0
6 TraesCS1A01G321400 chr1A 85.041 488 37 5 1152 1606 512018426 512017942 6.020000e-127 464.0
7 TraesCS1A01G321400 chr1A 90.055 362 12 7 859 1219 511790719 511790381 6.060000e-122 448.0
8 TraesCS1A01G321400 chr1A 90.311 289 18 8 2049 2332 511784853 511784570 1.350000e-98 370.0
9 TraesCS1A01G321400 chr1A 85.926 270 13 6 1082 1335 512462033 512461773 6.550000e-67 265.0
10 TraesCS1A01G321400 chr1A 93.636 110 7 0 1330 1439 512461850 512461741 6.830000e-37 165.0
11 TraesCS1A01G321400 chr1A 92.793 111 5 1 1430 1540 511789786 511789679 1.140000e-34 158.0
12 TraesCS1A01G321400 chr1A 91.743 109 8 1 1009 1116 512018530 512018422 1.910000e-32 150.0
13 TraesCS1A01G321400 chr1D 89.455 2532 169 50 1 2449 415054925 415052409 0.000000e+00 3107.0
14 TraesCS1A01G321400 chr1D 91.040 1663 74 38 859 2460 414942003 414940355 0.000000e+00 2176.0
15 TraesCS1A01G321400 chr1D 86.963 721 80 8 1 720 415039979 415039272 0.000000e+00 798.0
16 TraesCS1A01G321400 chr1D 86.078 668 53 16 1511 2174 415145634 415145003 0.000000e+00 682.0
17 TraesCS1A01G321400 chr1D 83.288 730 89 19 42 766 414942988 414942287 2.590000e-180 641.0
18 TraesCS1A01G321400 chr1D 85.350 628 56 14 855 1468 415059116 415058511 4.360000e-173 617.0
19 TraesCS1A01G321400 chr1D 84.954 545 47 14 1605 2149 416986038 416986547 1.270000e-143 520.0
20 TraesCS1A01G321400 chr1D 92.742 248 9 4 1088 1335 415146343 415146105 1.760000e-92 350.0
21 TraesCS1A01G321400 chr1D 87.500 232 25 2 635 862 416931092 416931323 6.550000e-67 265.0
22 TraesCS1A01G321400 chr1D 92.727 110 8 0 1330 1439 415146182 415146073 3.180000e-35 159.0
23 TraesCS1A01G321400 chr1D 74.083 436 66 23 257 688 415158459 415158067 5.360000e-28 135.0
24 TraesCS1A01G321400 chr1B 91.067 1500 92 20 859 2339 560789409 560787933 0.000000e+00 1989.0
25 TraesCS1A01G321400 chr1B 86.203 848 109 6 23 865 560790297 560789453 0.000000e+00 911.0
26 TraesCS1A01G321400 chr1B 83.165 790 69 29 1511 2282 561157088 561156345 0.000000e+00 664.0
27 TraesCS1A01G321400 chr1B 84.771 545 55 14 1605 2149 563847816 563848332 3.520000e-144 521.0
28 TraesCS1A01G321400 chr1B 80.079 763 77 37 1516 2268 561256458 561255761 5.930000e-137 497.0
29 TraesCS1A01G321400 chr1B 88.987 227 24 1 2712 2937 560786591 560786365 2.340000e-71 279.0
30 TraesCS1A01G321400 chr1B 79.684 443 44 15 1015 1425 563847319 563847747 8.410000e-71 278.0
31 TraesCS1A01G321400 chr1B 85.211 284 13 4 1072 1335 561257224 561256950 6.550000e-67 265.0
32 TraesCS1A01G321400 chr1B 84.588 279 21 7 1079 1335 561157849 561157571 1.100000e-64 257.0
33 TraesCS1A01G321400 chr1B 84.082 245 28 7 2719 2954 47204933 47204691 3.090000e-55 226.0
34 TraesCS1A01G321400 chr1B 94.615 130 1 3 2343 2470 560787711 560787586 2.420000e-46 196.0
35 TraesCS1A01G321400 chr1B 91.367 139 5 3 2584 2715 560787531 560787393 1.890000e-42 183.0
36 TraesCS1A01G321400 chr1B 97.059 34 0 1 904 936 563787164 563787197 4.290000e-04 56.5
37 TraesCS1A01G321400 chr1B 97.059 34 0 1 904 936 563847189 563847222 4.290000e-04 56.5
38 TraesCS1A01G321400 chrUn 90.404 198 19 0 634 831 305657929 305658126 8.470000e-66 261.0
39 TraesCS1A01G321400 chrUn 90.404 198 19 0 634 831 394107049 394106852 8.470000e-66 261.0
40 TraesCS1A01G321400 chr3D 85.333 225 31 2 2713 2937 559226479 559226257 6.640000e-57 231.0
41 TraesCS1A01G321400 chr6D 83.843 229 31 6 2715 2937 4238927 4239155 2.410000e-51 213.0
42 TraesCS1A01G321400 chr6D 81.070 243 28 8 2713 2938 467161057 467161298 8.780000e-41 178.0
43 TraesCS1A01G321400 chr6D 85.714 91 10 3 2709 2798 25727458 25727370 3.270000e-15 93.5
44 TraesCS1A01G321400 chr7A 82.128 235 30 8 2713 2937 19165412 19165644 1.130000e-44 191.0
45 TraesCS1A01G321400 chr7A 90.541 74 5 2 2508 2581 722599694 722599623 2.530000e-16 97.1
46 TraesCS1A01G321400 chr7A 90.411 73 3 3 2510 2581 106813350 106813281 3.270000e-15 93.5
47 TraesCS1A01G321400 chr5D 80.827 266 24 12 2713 2953 548292498 548292761 1.890000e-42 183.0
48 TraesCS1A01G321400 chr5D 91.071 56 5 0 2768 2823 66298719 66298664 3.290000e-10 76.8
49 TraesCS1A01G321400 chr5D 93.478 46 2 1 2885 2929 481641618 481641663 1.980000e-07 67.6
50 TraesCS1A01G321400 chr5D 91.304 46 4 0 2885 2930 498184903 498184858 2.560000e-06 63.9
51 TraesCS1A01G321400 chr2B 79.848 263 25 15 2714 2952 109211256 109210998 1.900000e-37 167.0
52 TraesCS1A01G321400 chr2B 90.667 75 5 2 2507 2581 376149172 376149244 7.030000e-17 99.0
53 TraesCS1A01G321400 chr3A 78.017 232 31 11 2713 2926 94185951 94185722 8.970000e-26 128.0
54 TraesCS1A01G321400 chr3A 91.781 73 5 1 2510 2581 141041325 141041253 1.950000e-17 100.0
55 TraesCS1A01G321400 chr2A 92.000 75 4 2 2508 2581 89486322 89486249 1.510000e-18 104.0
56 TraesCS1A01G321400 chr6A 88.372 86 8 2 2713 2798 23849249 23849166 5.440000e-18 102.0
57 TraesCS1A01G321400 chr7B 91.667 72 4 2 2510 2581 589938038 589938107 7.030000e-17 99.0
58 TraesCS1A01G321400 chr6B 91.549 71 4 2 2511 2581 22733668 22733736 2.530000e-16 97.1
59 TraesCS1A01G321400 chr5A 91.549 71 5 1 2512 2581 532036113 532036043 2.530000e-16 97.1
60 TraesCS1A01G321400 chr2D 89.333 75 6 2 2507 2581 199881331 199881403 3.270000e-15 93.5
61 TraesCS1A01G321400 chr7D 93.333 45 3 0 2885 2929 12386923 12386967 1.980000e-07 67.6


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 TraesCS1A01G321400 chr1A 511634156 511637236 3080 True 5690.000000 5690 100.000000 1 3081 1 chr1A.!!$R1 3080
1 TraesCS1A01G321400 chr1A 512038908 512041304 2396 True 1440.000000 1716 89.444500 1 2363 2 chr1A.!!$R5 2362
2 TraesCS1A01G321400 chr1A 512017942 512019497 1555 True 585.333333 1142 89.129000 4 1606 3 chr1A.!!$R4 1602
3 TraesCS1A01G321400 chr1A 511789679 511791647 1968 True 563.666667 1085 90.675000 1 1540 3 chr1A.!!$R3 1539
4 TraesCS1A01G321400 chr1A 512460655 512462033 1378 True 354.000000 632 88.159667 1082 2174 3 chr1A.!!$R6 1092
5 TraesCS1A01G321400 chr1D 415052409 415059116 6707 True 1862.000000 3107 87.402500 1 2449 2 chr1D.!!$R4 2448
6 TraesCS1A01G321400 chr1D 414940355 414942988 2633 True 1408.500000 2176 87.164000 42 2460 2 chr1D.!!$R3 2418
7 TraesCS1A01G321400 chr1D 415039272 415039979 707 True 798.000000 798 86.963000 1 720 1 chr1D.!!$R1 719
8 TraesCS1A01G321400 chr1D 416986038 416986547 509 False 520.000000 520 84.954000 1605 2149 1 chr1D.!!$F2 544
9 TraesCS1A01G321400 chr1D 415145003 415146343 1340 True 397.000000 682 90.515667 1088 2174 3 chr1D.!!$R5 1086
10 TraesCS1A01G321400 chr1B 560786365 560790297 3932 True 711.600000 1989 90.447800 23 2937 5 chr1B.!!$R2 2914
11 TraesCS1A01G321400 chr1B 561156345 561157849 1504 True 460.500000 664 83.876500 1079 2282 2 chr1B.!!$R3 1203
12 TraesCS1A01G321400 chr1B 561255761 561257224 1463 True 381.000000 497 82.645000 1072 2268 2 chr1B.!!$R4 1196
13 TraesCS1A01G321400 chr1B 563847189 563848332 1143 False 285.166667 521 87.171333 904 2149 3 chr1B.!!$F2 1245


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
471 4669 0.038251 TCTCTTCTGATGCGCAACGT 60.038 50.0 17.11 0.0 0.0 3.99 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2428 8043 0.031585 CCGGATCGACGAGGCAATTA 59.968 55.0 3.01 0.0 35.47 1.4 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.