Multiple sequence alignment - TraesCS5B01G477100
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 pairsThese primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible. |
---|
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 primersListed 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. |
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Based at the University of Bristol with support from BBSRC.
AutoCloner maintained by Alex Coulton.