Multiple sequence alignment - TraesCS5A01G484500

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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 TraesCS5A01G484500 chr5A 100.000 2678 0 0 1 2678 655800346 655797669 0.000000e+00 4946
1 TraesCS5A01G484500 chr5A 98.367 2694 28 3 1 2678 655729253 655726560 0.000000e+00 4717
2 TraesCS5A01G484500 chr5A 98.093 2097 18 6 590 2678 655871947 655869865 0.000000e+00 3631
3 TraesCS5A01G484500 chr5A 96.769 1919 35 8 1 1893 655646690 655644773 0.000000e+00 3175
4 TraesCS5A01G484500 chr5A 79.119 795 102 33 1062 1843 655924906 655924163 8.620000e-135 490
5 TraesCS5A01G484500 chr5A 84.346 428 43 8 935 1358 655717865 655717458 5.370000e-107 398
6 TraesCS5A01G484500 chr5A 84.346 428 43 8 935 1358 655790431 655790024 5.370000e-107 398
7 TraesCS5A01G484500 chr5A 84.346 428 43 8 935 1358 655862983 655862576 5.370000e-107 398
8 TraesCS5A01G484500 chr5A 85.751 393 27 15 1536 1905 655644763 655644377 3.230000e-104 388
9 TraesCS5A01G484500 chr5A 86.486 296 19 10 318 592 655872382 655872087 3.350000e-79 305
10 TraesCS5A01G484500 chr5A 82.456 228 18 14 312 520 655718455 655718231 2.120000e-41 180
11 TraesCS5A01G484500 chr5A 82.456 228 18 14 312 520 655863573 655863349 2.120000e-41 180
12 TraesCS5A01G484500 chr5A 81.579 228 20 14 312 520 655791021 655790797 4.590000e-38 169
13 TraesCS5A01G484500 chr5A 84.270 178 14 8 694 870 655718045 655717881 7.670000e-36 161
14 TraesCS5A01G484500 chr5A 84.270 178 14 8 694 870 655790611 655790447 7.670000e-36 161
15 TraesCS5A01G484500 chrUn 87.935 1177 71 35 753 1905 405885818 405886947 0.000000e+00 1321
16 TraesCS5A01G484500 chrUn 86.187 695 46 23 692 1383 268244249 268243602 0.000000e+00 706
17 TraesCS5A01G484500 chrUn 92.016 501 23 9 1422 1905 68358647 68358147 0.000000e+00 688
18 TraesCS5A01G484500 chr5B 85.164 1247 100 44 701 1898 664727802 664726592 0.000000e+00 1199
19 TraesCS5A01G484500 chr5B 82.962 628 55 26 692 1308 664805931 664805345 1.100000e-143 520
20 TraesCS5A01G484500 chr5B 82.962 628 55 26 692 1308 664940280 664939694 1.100000e-143 520
21 TraesCS5A01G484500 chr5B 90.741 108 10 0 1911 2018 664908571 664908464 7.730000e-31 145
22 TraesCS5A01G484500 chr5D 82.152 790 83 29 541 1308 528121593 528120840 2.260000e-175 625
23 TraesCS5A01G484500 chr5D 85.839 459 54 6 2065 2522 520111705 520111257 6.710000e-131 477
24 TraesCS5A01G484500 chr5D 91.749 303 20 4 1 300 505398712 505398412 1.480000e-112 416
25 TraesCS5A01G484500 chr5D 91.118 304 23 3 1 301 179972656 179972958 2.480000e-110 409
26 TraesCS5A01G484500 chr5D 94.558 147 7 1 1917 2063 528120419 528120274 2.680000e-55 226
27 TraesCS5A01G484500 chr6D 88.791 455 39 3 2065 2518 121158386 121158829 5.040000e-152 547
28 TraesCS5A01G484500 chr6D 90.683 161 15 0 2516 2676 382343698 382343538 5.810000e-52 215
29 TraesCS5A01G484500 chr1D 88.132 455 41 6 2066 2519 418404815 418405257 1.830000e-146 529
30 TraesCS5A01G484500 chr1D 87.033 455 47 3 2066 2519 389330473 389330916 1.110000e-138 503
31 TraesCS5A01G484500 chr1D 85.312 320 34 7 2201 2519 307210287 307210594 4.300000e-83 318
32 TraesCS5A01G484500 chr1D 90.062 161 16 0 2516 2676 375353184 375353344 2.700000e-50 209
33 TraesCS5A01G484500 chr1D 89.441 161 15 1 2516 2676 469610633 469610791 4.520000e-48 202
34 TraesCS5A01G484500 chr4D 87.124 466 45 6 2060 2522 99207623 99207170 5.110000e-142 514
35 TraesCS5A01G484500 chr4D 91.419 303 21 4 1 300 486565484 486565784 6.900000e-111 411
36 TraesCS5A01G484500 chr4D 91.333 300 22 3 1 297 481887324 481887026 8.930000e-110 407
37 TraesCS5A01G484500 chr2B 86.928 459 46 5 2062 2518 589530384 589529938 1.110000e-138 503
38 TraesCS5A01G484500 chr2B 86.784 454 49 6 2065 2517 681736176 681736619 1.850000e-136 496
39 TraesCS5A01G484500 chr2B 85.590 458 48 5 2064 2519 752824470 752824911 5.220000e-127 464
40 TraesCS5A01G484500 chr2B 90.062 161 16 0 2516 2676 708303664 708303504 2.700000e-50 209
41 TraesCS5A01G484500 chr2B 88.820 161 18 0 2516 2676 210461460 210461300 5.850000e-47 198
42 TraesCS5A01G484500 chr2A 86.057 459 47 8 2067 2522 449263819 449263375 6.710000e-131 477
43 TraesCS5A01G484500 chr2A 84.340 447 57 7 2078 2522 105681966 105681531 2.460000e-115 425
44 TraesCS5A01G484500 chr6B 85.321 436 45 9 1425 1847 644446539 644446110 1.470000e-117 433
45 TraesCS5A01G484500 chr6B 89.516 124 13 0 1721 1844 644421547 644421424 9.920000e-35 158
46 TraesCS5A01G484500 chr7D 91.447 304 23 2 1 301 18553932 18554235 5.330000e-112 414
47 TraesCS5A01G484500 chr3D 91.060 302 23 3 1 299 376916711 376916411 3.210000e-109 405
48 TraesCS5A01G484500 chr3D 91.060 302 24 2 3 301 562635077 562634776 3.210000e-109 405
49 TraesCS5A01G484500 chr2D 83.007 459 47 14 2066 2522 100958481 100958052 1.160000e-103 387
50 TraesCS5A01G484500 chr2D 86.378 323 30 4 2201 2522 596576140 596575831 9.180000e-90 340
51 TraesCS5A01G484500 chr2D 90.683 161 15 0 2516 2676 596575781 596575621 5.810000e-52 215
52 TraesCS5A01G484500 chr2D 85.859 198 16 5 2323 2519 408343535 408343721 1.630000e-47 200
53 TraesCS5A01G484500 chr7A 90.062 161 16 0 2516 2676 562174201 562174041 2.700000e-50 209


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 TraesCS5A01G484500 chr5A 655797669 655800346 2677 True 4946.000000 4946 100.000000 1 2678 1 chr5A.!!$R2 2677
1 TraesCS5A01G484500 chr5A 655726560 655729253 2693 True 4717.000000 4717 98.367000 1 2678 1 chr5A.!!$R1 2677
2 TraesCS5A01G484500 chr5A 655869865 655872382 2517 True 1968.000000 3631 92.289500 318 2678 2 chr5A.!!$R8 2360
3 TraesCS5A01G484500 chr5A 655644377 655646690 2313 True 1781.500000 3175 91.260000 1 1905 2 chr5A.!!$R4 1904
4 TraesCS5A01G484500 chr5A 655924163 655924906 743 True 490.000000 490 79.119000 1062 1843 1 chr5A.!!$R3 781
5 TraesCS5A01G484500 chr5A 655862576 655863573 997 True 289.000000 398 83.401000 312 1358 2 chr5A.!!$R7 1046
6 TraesCS5A01G484500 chr5A 655717458 655718455 997 True 246.333333 398 83.690667 312 1358 3 chr5A.!!$R5 1046
7 TraesCS5A01G484500 chr5A 655790024 655791021 997 True 242.666667 398 83.398333 312 1358 3 chr5A.!!$R6 1046
8 TraesCS5A01G484500 chrUn 405885818 405886947 1129 False 1321.000000 1321 87.935000 753 1905 1 chrUn.!!$F1 1152
9 TraesCS5A01G484500 chrUn 268243602 268244249 647 True 706.000000 706 86.187000 692 1383 1 chrUn.!!$R2 691
10 TraesCS5A01G484500 chrUn 68358147 68358647 500 True 688.000000 688 92.016000 1422 1905 1 chrUn.!!$R1 483
11 TraesCS5A01G484500 chr5B 664726592 664727802 1210 True 1199.000000 1199 85.164000 701 1898 1 chr5B.!!$R1 1197
12 TraesCS5A01G484500 chr5B 664805345 664805931 586 True 520.000000 520 82.962000 692 1308 1 chr5B.!!$R2 616
13 TraesCS5A01G484500 chr5B 664939694 664940280 586 True 520.000000 520 82.962000 692 1308 1 chr5B.!!$R4 616
14 TraesCS5A01G484500 chr5D 528120274 528121593 1319 True 425.500000 625 88.355000 541 2063 2 chr5D.!!$R3 1522
15 TraesCS5A01G484500 chr2D 596575621 596576140 519 True 277.500000 340 88.530500 2201 2676 2 chr2D.!!$R2 475

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
48 49 0.107654 GGTGAGGCTAGATTTGGCGT 60.108 55.0 0.0 0.0 35.01 5.68 F
626 821 0.898320 AGTACGCAGTTGGAGATGCT 59.102 50.0 0.0 0.0 37.78 3.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1675 2050 3.266510 AGTTGATGAGCCAAGCGATTA 57.733 42.857 0.00 0.0 0.0 1.75 R
2646 3502 0.611062 AAAAGGCGGCTAGGGTTTCC 60.611 55.000 13.71 0.0 0.0 3.13 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)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 49 0.107654 GGTGAGGCTAGATTTGGCGT 60.108 55.000 0.00 0.00 35.01 5.68
287 288 1.675310 TTTGACTGGATGCGGGCAG 60.675 57.895 0.38 0.00 0.00 4.85
395 408 3.221771 TCAAAAGGAACAGTGTGGATGG 58.778 45.455 0.00 0.00 0.00 3.51
523 553 7.566760 TCTGTAATTCTTTTGAGTGCTTCAA 57.433 32.000 0.87 0.87 43.92 2.69
626 821 0.898320 AGTACGCAGTTGGAGATGCT 59.102 50.000 0.00 0.00 37.78 3.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
57 58 0.179034 GGAGATGGAAATCTGGCGCT 60.179 55.000 7.64 0.0 0.00 5.92
287 288 0.107848 ATACAGTAAGGGCGTGTGGC 60.108 55.000 0.00 0.0 42.51 5.01
395 408 2.778299 TGTAGGGCATGAAGTGTTGTC 58.222 47.619 0.00 0.0 0.00 3.18
1675 2050 3.266510 AGTTGATGAGCCAAGCGATTA 57.733 42.857 0.00 0.0 0.00 1.75
2646 3502 0.611062 AAAAGGCGGCTAGGGTTTCC 60.611 55.000 13.71 0.0 0.00 3.13


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

AutoCloner maintained by Alex Coulton.