Multiple sequence alignment - TraesCS5D01G541800

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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 TraesCS5D01G541800 chr5D 100.000 3968 0 0 1 3968 552445237 552441270 0.000000e+00 7328.0
1 TraesCS5D01G541800 chr5D 86.777 242 28 4 3089 3327 552420419 552420179 2.350000e-67 267.0
2 TraesCS5D01G541800 chr5D 77.184 412 81 12 1973 2374 537216839 537217247 1.110000e-55 228.0
3 TraesCS5D01G541800 chr5D 87.179 195 21 3 2827 3018 552420821 552420628 6.680000e-53 219.0
4 TraesCS5D01G541800 chr5D 97.059 102 1 1 3326 3427 30613906 30614005 1.900000e-38 171.0
5 TraesCS5D01G541800 chr5D 75.487 359 73 11 1077 1429 552422797 552422448 1.140000e-35 161.0
6 TraesCS5D01G541800 chr5D 86.466 133 12 3 3428 3555 478461247 478461116 1.490000e-29 141.0
7 TraesCS5D01G541800 chr5D 80.851 141 23 3 1043 1182 543503748 543503611 1.510000e-19 108.0
8 TraesCS5D01G541800 chr1B 85.097 2429 306 35 779 3174 327487059 327489464 0.000000e+00 2429.0
9 TraesCS5D01G541800 chr1B 83.542 559 72 12 3 553 327486154 327486700 4.580000e-139 505.0
10 TraesCS5D01G541800 chr1D 86.000 1950 240 20 779 2708 227867094 227869030 0.000000e+00 2058.0
11 TraesCS5D01G541800 chr1D 86.727 1213 156 4 779 1988 208239528 208238318 0.000000e+00 1343.0
12 TraesCS5D01G541800 chr1D 82.988 1205 164 25 1993 3174 208202660 208201474 0.000000e+00 1051.0
13 TraesCS5D01G541800 chr1D 84.838 554 66 11 6 553 208240169 208239628 3.490000e-150 542.0
14 TraesCS5D01G541800 chr1D 84.324 555 62 14 7 553 227866171 227866708 1.630000e-143 520.0
15 TraesCS5D01G541800 chr1D 95.238 105 5 0 2747 2851 227869032 227869136 2.450000e-37 167.0
16 TraesCS5D01G541800 chr1A 87.411 1676 207 4 779 2453 295465840 295467512 0.000000e+00 1923.0
17 TraesCS5D01G541800 chr1A 85.766 555 64 9 3 553 295464912 295465455 1.240000e-159 573.0
18 TraesCS5D01G541800 chr1A 79.238 761 110 28 2443 3174 295517172 295517913 1.660000e-133 486.0
19 TraesCS5D01G541800 chr1A 100.000 94 0 0 3335 3428 445930225 445930132 1.470000e-39 174.0
20 TraesCS5D01G541800 chr1A 97.959 98 2 0 3330 3427 549119553 549119650 1.900000e-38 171.0
21 TraesCS5D01G541800 chr5A 94.343 548 24 3 3428 3968 536286492 536287039 0.000000e+00 833.0
22 TraesCS5D01G541800 chr5A 91.058 548 35 7 3431 3968 534584427 534584970 0.000000e+00 728.0
23 TraesCS5D01G541800 chr3A 91.978 536 36 3 3440 3968 158167026 158166491 0.000000e+00 745.0
24 TraesCS5D01G541800 chr4D 91.408 547 40 4 3428 3968 251423489 251424034 0.000000e+00 743.0
25 TraesCS5D01G541800 chr4D 81.921 354 51 9 3428 3773 440385381 440385033 1.800000e-73 287.0
26 TraesCS5D01G541800 chr4D 85.075 67 9 1 473 538 506346931 506346997 2.560000e-07 67.6
27 TraesCS5D01G541800 chr3B 93.439 503 27 5 3468 3968 810545350 810544852 0.000000e+00 741.0
28 TraesCS5D01G541800 chr3B 91.650 503 41 1 3464 3965 734477930 734477428 0.000000e+00 695.0
29 TraesCS5D01G541800 chr3B 84.746 59 9 0 476 534 477364270 477364328 4.280000e-05 60.2
30 TraesCS5D01G541800 chr6A 91.865 504 38 1 3468 3968 234173142 234172639 0.000000e+00 701.0
31 TraesCS5D01G541800 chr4A 76.857 579 114 14 1809 2374 616839988 616839417 3.850000e-80 309.0
32 TraesCS5D01G541800 chr4A 75.891 589 118 18 1803 2374 616885286 616884705 3.020000e-71 279.0
33 TraesCS5D01G541800 chr4A 74.727 550 120 17 1748 2286 616229932 616229391 1.110000e-55 228.0
34 TraesCS5D01G541800 chr4A 80.214 187 37 0 1093 1279 616897505 616897319 1.490000e-29 141.0
35 TraesCS5D01G541800 chr5B 76.967 521 108 11 1864 2374 677812796 677813314 1.800000e-73 287.0
36 TraesCS5D01G541800 chr5B 76.259 556 107 19 1791 2340 685504419 685504955 5.050000e-69 272.0
37 TraesCS5D01G541800 chr5B 75.507 592 114 22 1803 2374 699354723 699355303 1.090000e-65 261.0
38 TraesCS5D01G541800 chr5B 76.626 492 104 9 1799 2286 703716856 703717340 1.090000e-65 261.0
39 TraesCS5D01G541800 chr5B 76.096 502 105 12 1791 2286 685322424 685321932 8.510000e-62 248.0
40 TraesCS5D01G541800 chr5B 75.233 537 108 20 1748 2270 700229028 700228503 8.580000e-57 231.0
41 TraesCS5D01G541800 chr5B 76.038 313 60 9 1042 1352 685323111 685322812 8.880000e-32 148.0
42 TraesCS5D01G541800 chr5B 78.333 240 40 7 1042 1279 685503732 685503961 1.150000e-30 145.0
43 TraesCS5D01G541800 chr2D 89.831 177 17 1 3661 3836 2567158 2566982 3.990000e-55 226.0
44 TraesCS5D01G541800 chr6B 100.000 94 0 0 3334 3427 706995395 706995302 1.470000e-39 174.0
45 TraesCS5D01G541800 chr6B 93.103 58 4 0 3911 3968 719748492 719748549 7.070000e-13 86.1
46 TraesCS5D01G541800 chr2B 98.980 98 0 1 3331 3427 57884578 57884481 1.470000e-39 174.0
47 TraesCS5D01G541800 chr2B 98.958 96 1 0 3332 3427 653671191 653671286 5.270000e-39 172.0
48 TraesCS5D01G541800 chrUn 98.958 96 1 0 3332 3427 79765330 79765425 5.270000e-39 172.0
49 TraesCS5D01G541800 chrUn 96.970 33 1 0 503 535 282486920 282486888 5.540000e-04 56.5
50 TraesCS5D01G541800 chrUn 96.970 33 1 0 503 535 307153120 307153088 5.540000e-04 56.5
51 TraesCS5D01G541800 chr7B 98.969 97 0 1 3332 3427 704405836 704405740 5.270000e-39 172.0
52 TraesCS5D01G541800 chr7B 78.912 147 19 7 475 612 186819135 186819278 5.460000e-14 89.8
53 TraesCS5D01G541800 chr7D 93.578 109 5 2 3318 3426 561540616 561540722 1.140000e-35 161.0
54 TraesCS5D01G541800 chr3D 93.103 58 4 0 3911 3968 601183283 601183226 7.070000e-13 86.1
55 TraesCS5D01G541800 chr6D 89.655 58 5 1 479 535 450126285 450126342 5.500000e-09 73.1


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 TraesCS5D01G541800 chr5D 552441270 552445237 3967 True 7328.000000 7328 100.000000 1 3968 1 chr5D.!!$R3 3967
1 TraesCS5D01G541800 chr5D 552420179 552422797 2618 True 215.666667 267 83.147667 1077 3327 3 chr5D.!!$R4 2250
2 TraesCS5D01G541800 chr1B 327486154 327489464 3310 False 1467.000000 2429 84.319500 3 3174 2 chr1B.!!$F1 3171
3 TraesCS5D01G541800 chr1D 208201474 208202660 1186 True 1051.000000 1051 82.988000 1993 3174 1 chr1D.!!$R1 1181
4 TraesCS5D01G541800 chr1D 208238318 208240169 1851 True 942.500000 1343 85.782500 6 1988 2 chr1D.!!$R2 1982
5 TraesCS5D01G541800 chr1D 227866171 227869136 2965 False 915.000000 2058 88.520667 7 2851 3 chr1D.!!$F1 2844
6 TraesCS5D01G541800 chr1A 295464912 295467512 2600 False 1248.000000 1923 86.588500 3 2453 2 chr1A.!!$F3 2450
7 TraesCS5D01G541800 chr1A 295517172 295517913 741 False 486.000000 486 79.238000 2443 3174 1 chr1A.!!$F1 731
8 TraesCS5D01G541800 chr5A 536286492 536287039 547 False 833.000000 833 94.343000 3428 3968 1 chr5A.!!$F2 540
9 TraesCS5D01G541800 chr5A 534584427 534584970 543 False 728.000000 728 91.058000 3431 3968 1 chr5A.!!$F1 537
10 TraesCS5D01G541800 chr3A 158166491 158167026 535 True 745.000000 745 91.978000 3440 3968 1 chr3A.!!$R1 528
11 TraesCS5D01G541800 chr4D 251423489 251424034 545 False 743.000000 743 91.408000 3428 3968 1 chr4D.!!$F1 540
12 TraesCS5D01G541800 chr3B 734477428 734477930 502 True 695.000000 695 91.650000 3464 3965 1 chr3B.!!$R1 501
13 TraesCS5D01G541800 chr6A 234172639 234173142 503 True 701.000000 701 91.865000 3468 3968 1 chr6A.!!$R1 500
14 TraesCS5D01G541800 chr4A 616839417 616839988 571 True 309.000000 309 76.857000 1809 2374 1 chr4A.!!$R2 565
15 TraesCS5D01G541800 chr4A 616884705 616885286 581 True 279.000000 279 75.891000 1803 2374 1 chr4A.!!$R3 571
16 TraesCS5D01G541800 chr4A 616229391 616229932 541 True 228.000000 228 74.727000 1748 2286 1 chr4A.!!$R1 538
17 TraesCS5D01G541800 chr5B 677812796 677813314 518 False 287.000000 287 76.967000 1864 2374 1 chr5B.!!$F1 510
18 TraesCS5D01G541800 chr5B 699354723 699355303 580 False 261.000000 261 75.507000 1803 2374 1 chr5B.!!$F2 571
19 TraesCS5D01G541800 chr5B 700228503 700229028 525 True 231.000000 231 75.233000 1748 2270 1 chr5B.!!$R1 522
20 TraesCS5D01G541800 chr5B 685503732 685504955 1223 False 208.500000 272 77.296000 1042 2340 2 chr5B.!!$F4 1298


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
758 940 0.108804 GAGTCGAATGCGGTGGAGAA 60.109 55.0 0.0 0.0 38.28 2.87 F
1465 1656 0.109458 CCACGGAGTTCATCGTTCGA 60.109 55.0 0.0 0.0 41.61 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1653 1844 0.173935 CAAGGACACACCCGCGTATA 59.826 55.0 4.92 0.0 40.05 1.47 R
3417 4201 0.107654 CTCCGCCCCTCTTTGTAAGG 60.108 60.0 0.00 0.0 0.00 2.69 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.