Multiple sequence alignment - TraesCS5B01G477100

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 TraesCS5B01G477100 chr5B 100.000 3266 0 0 1 3266 649452942 649456207 0.000000e+00 6032.0
1 TraesCS5B01G477100 chr5B 78.404 1278 223 31 953 2214 651211059 651212299 0.000000e+00 782.0
2 TraesCS5B01G477100 chr5B 78.228 1185 207 29 953 2122 650983115 650984263 0.000000e+00 712.0
3 TraesCS5B01G477100 chr5B 83.884 726 70 23 1 691 148882943 148883656 0.000000e+00 649.0
4 TraesCS5B01G477100 chr5B 83.707 669 81 19 71 729 293250065 293249415 1.000000e-169 606.0
5 TraesCS5B01G477100 chr5B 78.484 818 135 25 1413 2214 652375835 652376627 6.290000e-137 497.0
6 TraesCS5B01G477100 chr5B 82.569 109 19 0 2772 2880 709330998 709330890 2.680000e-16 97.1
7 TraesCS5B01G477100 chr5B 83.871 93 15 0 2656 2748 684625614 684625522 4.490000e-14 89.8
8 TraesCS5B01G477100 chr5B 97.297 37 1 0 2770 2806 137049692 137049728 2.720000e-06 63.9
9 TraesCS5B01G477100 chr5D 95.625 1440 51 3 883 2319 517046053 517047483 0.000000e+00 2300.0
10 TraesCS5B01G477100 chr5D 78.201 1312 224 36 921 2214 517976283 517975016 0.000000e+00 782.0
11 TraesCS5B01G477100 chr5D 78.092 1310 230 33 921 2214 518755457 518756725 0.000000e+00 776.0
12 TraesCS5B01G477100 chr5D 88.839 448 25 7 2301 2748 517047494 517047916 8.030000e-146 527.0
13 TraesCS5B01G477100 chr5D 83.936 498 63 3 2769 3266 517048169 517048649 8.260000e-126 460.0
14 TraesCS5B01G477100 chr5D 82.051 117 21 0 2769 2885 28996692 28996576 2.070000e-17 100.0
15 TraesCS5B01G477100 chr5A 88.788 1106 78 20 1650 2751 644208727 644209790 0.000000e+00 1314.0
16 TraesCS5B01G477100 chr5A 90.704 753 63 3 906 1652 644176880 644177631 0.000000e+00 996.0
17 TraesCS5B01G477100 chr5A 79.848 526 92 8 1530 2048 644330000 644330518 3.980000e-99 372.0
18 TraesCS5B01G477100 chr6B 86.658 742 76 18 1 728 476337828 476337096 0.000000e+00 800.0
19 TraesCS5B01G477100 chr6B 83.158 95 14 2 2655 2748 562544240 562544333 5.810000e-13 86.1
20 TraesCS5B01G477100 chr6B 75.497 151 28 7 2599 2748 661913191 661913049 7.560000e-07 65.8
21 TraesCS5B01G477100 chr1B 86.912 680 64 15 70 729 268395526 268394852 0.000000e+00 739.0
22 TraesCS5B01G477100 chr1B 83.752 757 90 21 1 728 684622866 684623618 0.000000e+00 686.0
23 TraesCS5B01G477100 chr1B 77.551 196 32 7 2552 2746 681057244 681057428 1.240000e-19 108.0
24 TraesCS5B01G477100 chr2B 84.768 755 72 19 1 734 642971274 642972006 0.000000e+00 717.0
25 TraesCS5B01G477100 chr2B 84.211 114 14 3 2774 2885 18022383 18022494 1.240000e-19 108.0
26 TraesCS5B01G477100 chr1A 83.735 664 80 20 70 716 557944907 557944255 1.300000e-168 603.0
27 TraesCS5B01G477100 chr1A 81.897 116 12 6 2633 2748 404559590 404559696 4.490000e-14 89.8
28 TraesCS5B01G477100 chr1A 87.143 70 9 0 2910 2979 263155392 263155461 2.700000e-11 80.5
29 TraesCS5B01G477100 chr1A 83.333 90 11 4 2660 2748 299179439 299179353 2.700000e-11 80.5
30 TraesCS5B01G477100 chr1A 86.364 66 9 0 2882 2947 121558849 121558914 4.520000e-09 73.1
31 TraesCS5B01G477100 chr1A 93.023 43 3 0 2712 2754 463035586 463035544 2.720000e-06 63.9
32 TraesCS5B01G477100 chr7D 84.603 630 67 20 121 729 204444318 204444938 1.680000e-167 599.0
33 TraesCS5B01G477100 chr7D 81.525 682 89 21 73 726 31600247 31599575 8.030000e-146 527.0
34 TraesCS5B01G477100 chr7D 83.713 571 55 23 180 728 422340446 422339892 3.760000e-139 505.0
35 TraesCS5B01G477100 chr7D 82.456 114 18 2 2773 2885 287897457 287897569 7.460000e-17 99.0
36 TraesCS5B01G477100 chr6A 82.448 678 89 22 70 728 387874941 387875607 1.700000e-157 566.0
37 TraesCS5B01G477100 chr6A 83.636 110 18 0 2769 2878 374426322 374426213 1.600000e-18 104.0
38 TraesCS5B01G477100 chr6A 79.310 145 20 5 2605 2748 16340922 16341057 3.470000e-15 93.5
39 TraesCS5B01G477100 chr3D 78.696 859 131 24 1465 2295 597867947 597868781 2.890000e-145 525.0
40 TraesCS5B01G477100 chr3D 80.242 496 69 19 875 1351 597863791 597864276 2.410000e-91 346.0
41 TraesCS5B01G477100 chr3D 84.444 270 41 1 2880 3148 423849703 423849972 6.950000e-67 265.0
42 TraesCS5B01G477100 chr3D 86.000 100 13 1 2882 2980 449202300 449202399 4.460000e-19 106.0
43 TraesCS5B01G477100 chr3D 84.270 89 12 2 2660 2748 563842219 563842305 5.810000e-13 86.1
44 TraesCS5B01G477100 chr2D 81.669 671 82 29 70 728 426918170 426917529 1.340000e-143 520.0
45 TraesCS5B01G477100 chr2D 84.043 94 15 0 2655 2748 71849295 71849202 1.250000e-14 91.6
46 TraesCS5B01G477100 chr4B 84.018 438 47 13 290 722 14540840 14540421 1.830000e-107 399.0
47 TraesCS5B01G477100 chr4B 75.532 188 35 7 2562 2748 571903926 571904103 7.510000e-12 82.4
48 TraesCS5B01G477100 chr4B 97.297 37 1 0 2712 2748 495353806 495353842 2.720000e-06 63.9
49 TraesCS5B01G477100 chr4D 88.043 92 11 0 2657 2748 495111336 495111427 3.450000e-20 110.0
50 TraesCS5B01G477100 chr4D 81.915 94 17 0 2655 2748 3776946 3777039 2.700000e-11 80.5
51 TraesCS5B01G477100 chr2A 83.621 116 18 1 2769 2884 94203286 94203172 1.240000e-19 108.0
52 TraesCS5B01G477100 chr1D 77.436 195 34 7 2552 2746 488609867 488609683 1.240000e-19 108.0
53 TraesCS5B01G477100 chr1D 83.036 112 19 0 2769 2880 2122459 2122348 5.770000e-18 102.0
54 TraesCS5B01G477100 chr1D 81.416 113 19 2 2769 2880 270024598 270024487 1.250000e-14 91.6
55 TraesCS5B01G477100 chr1D 81.481 108 20 0 2778 2885 445998806 445998913 4.490000e-14 89.8
56 TraesCS5B01G477100 chr1D 92.982 57 4 0 2689 2745 307665387 307665443 2.090000e-12 84.2
57 TraesCS5B01G477100 chr3A 82.677 127 15 5 2882 3005 591600604 591600726 4.460000e-19 106.0
58 TraesCS5B01G477100 chr7A 82.759 116 20 0 2766 2881 393325549 393325664 1.600000e-18 104.0
59 TraesCS5B01G477100 chr7A 81.553 103 19 0 2769 2871 558758275 558758173 5.810000e-13 86.1
60 TraesCS5B01G477100 chr7B 90.541 74 7 0 2675 2748 687299919 687299992 7.460000e-17 99.0
61 TraesCS5B01G477100 chr7B 87.500 80 8 1 2669 2748 424011724 424011647 1.250000e-14 91.6
62 TraesCS5B01G477100 chr7B 76.923 182 29 6 2570 2748 687678294 687678123 1.250000e-14 91.6
63 TraesCS5B01G477100 chr7B 78.261 115 24 1 2771 2885 513819862 513819975 4.520000e-09 73.1
64 TraesCS5B01G477100 chrUn 87.838 74 7 2 2673 2745 62652877 62652949 5.810000e-13 86.1
65 TraesCS5B01G477100 chr4A 82.979 94 15 1 2655 2748 628628601 628628693 2.090000e-12 84.2
66 TraesCS5B01G477100 chr3B 82.796 93 14 2 2884 2974 624809009 624809101 7.510000e-12 82.4
67 TraesCS5B01G477100 chr6D 78.761 113 23 1 2769 2881 380821043 380820932 1.260000e-09 75.0
68 TraesCS5B01G477100 chr6D 79.439 107 16 2 2778 2884 156427086 156426986 1.630000e-08 71.3
69 TraesCS5B01G477100 chr6D 78.723 94 20 0 2655 2748 57878017 57878110 2.720000e-06 63.9


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 TraesCS5B01G477100 chr5B 649452942 649456207 3265 False 6032.000000 6032 100.000000 1 3266 1 chr5B.!!$F3 3265
1 TraesCS5B01G477100 chr5B 651211059 651212299 1240 False 782.000000 782 78.404000 953 2214 1 chr5B.!!$F5 1261
2 TraesCS5B01G477100 chr5B 650983115 650984263 1148 False 712.000000 712 78.228000 953 2122 1 chr5B.!!$F4 1169
3 TraesCS5B01G477100 chr5B 148882943 148883656 713 False 649.000000 649 83.884000 1 691 1 chr5B.!!$F2 690
4 TraesCS5B01G477100 chr5B 293249415 293250065 650 True 606.000000 606 83.707000 71 729 1 chr5B.!!$R1 658
5 TraesCS5B01G477100 chr5B 652375835 652376627 792 False 497.000000 497 78.484000 1413 2214 1 chr5B.!!$F6 801
6 TraesCS5B01G477100 chr5D 517046053 517048649 2596 False 1095.666667 2300 89.466667 883 3266 3 chr5D.!!$F2 2383
7 TraesCS5B01G477100 chr5D 517975016 517976283 1267 True 782.000000 782 78.201000 921 2214 1 chr5D.!!$R2 1293
8 TraesCS5B01G477100 chr5D 518755457 518756725 1268 False 776.000000 776 78.092000 921 2214 1 chr5D.!!$F1 1293
9 TraesCS5B01G477100 chr5A 644208727 644209790 1063 False 1314.000000 1314 88.788000 1650 2751 1 chr5A.!!$F2 1101
10 TraesCS5B01G477100 chr5A 644176880 644177631 751 False 996.000000 996 90.704000 906 1652 1 chr5A.!!$F1 746
11 TraesCS5B01G477100 chr5A 644330000 644330518 518 False 372.000000 372 79.848000 1530 2048 1 chr5A.!!$F3 518
12 TraesCS5B01G477100 chr6B 476337096 476337828 732 True 800.000000 800 86.658000 1 728 1 chr6B.!!$R1 727
13 TraesCS5B01G477100 chr1B 268394852 268395526 674 True 739.000000 739 86.912000 70 729 1 chr1B.!!$R1 659
14 TraesCS5B01G477100 chr1B 684622866 684623618 752 False 686.000000 686 83.752000 1 728 1 chr1B.!!$F2 727
15 TraesCS5B01G477100 chr2B 642971274 642972006 732 False 717.000000 717 84.768000 1 734 1 chr2B.!!$F2 733
16 TraesCS5B01G477100 chr1A 557944255 557944907 652 True 603.000000 603 83.735000 70 716 1 chr1A.!!$R3 646
17 TraesCS5B01G477100 chr7D 204444318 204444938 620 False 599.000000 599 84.603000 121 729 1 chr7D.!!$F1 608
18 TraesCS5B01G477100 chr7D 31599575 31600247 672 True 527.000000 527 81.525000 73 726 1 chr7D.!!$R1 653
19 TraesCS5B01G477100 chr7D 422339892 422340446 554 True 505.000000 505 83.713000 180 728 1 chr7D.!!$R2 548
20 TraesCS5B01G477100 chr6A 387874941 387875607 666 False 566.000000 566 82.448000 70 728 1 chr6A.!!$F2 658
21 TraesCS5B01G477100 chr3D 597863791 597868781 4990 False 435.500000 525 79.469000 875 2295 2 chr3D.!!$F4 1420
22 TraesCS5B01G477100 chr2D 426917529 426918170 641 True 520.000000 520 81.669000 70 728 1 chr2D.!!$R2 658


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
821 1023 0.026803 GCGACCATTGAGCGCTTAAG 59.973 55.0 19.88 9.89 46.53 1.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2807 6905 0.106894 CTTATCGCCCCTTCCTCACC 59.893 60.0 0.0 0.0 0.0 4.02 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.