Multiple sequence alignment - TraesCS5A01G162500

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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 TraesCS5A01G162500 chr5A 100.000 3652 0 0 1 3652 346305662 346309313 0.000000e+00 6745
1 TraesCS5A01G162500 chr5A 96.855 636 20 0 1 636 346285374 346286009 0.000000e+00 1064
2 TraesCS5A01G162500 chr5A 94.828 638 32 1 1 637 390336202 390336839 0.000000e+00 994
3 TraesCS5A01G162500 chr4B 99.172 3020 25 0 633 3652 139742621 139745640 0.000000e+00 5439
4 TraesCS5A01G162500 chr4B 97.439 2577 54 2 636 3201 2598690 2601265 0.000000e+00 4383
5 TraesCS5A01G162500 chr3A 99.105 3016 27 0 637 3652 199412059 199415074 0.000000e+00 5421
6 TraesCS5A01G162500 chr3A 94.969 636 32 0 1 636 563811654 563811019 0.000000e+00 998
7 TraesCS5A01G162500 chr7B 98.471 2944 31 3 634 3566 554160474 554163414 0.000000e+00 5175
8 TraesCS5A01G162500 chr1A 99.026 2568 25 0 636 3203 63763700 63761133 0.000000e+00 4604
9 TraesCS5A01G162500 chr1A 98.927 559 5 1 3095 3652 320477403 320476845 0.000000e+00 998
10 TraesCS5A01G162500 chr1B 99.100 2556 23 0 635 3190 167930127 167927572 0.000000e+00 4593
11 TraesCS5A01G162500 chr1B 99.107 560 3 2 3095 3652 167927765 167927206 0.000000e+00 1005
12 TraesCS5A01G162500 chr3B 98.346 2600 42 1 634 3233 681202911 681200313 0.000000e+00 4562
13 TraesCS5A01G162500 chr3B 98.084 2609 37 3 637 3233 731127043 731129650 0.000000e+00 4529
14 TraesCS5A01G162500 chr2A 98.785 2387 29 0 636 3022 672536852 672539238 0.000000e+00 4248
15 TraesCS5A01G162500 chr2A 93.885 278 3 8 636 899 672544098 672543821 1.220000e-109 407
16 TraesCS5A01G162500 chr2A 90.706 269 21 4 634 899 628686509 628686242 4.490000e-94 355
17 TraesCS5A01G162500 chr2A 90.530 264 22 2 636 896 5490841 5491104 2.700000e-91 346
18 TraesCS5A01G162500 chr7A 95.618 639 24 4 1 636 706527923 706527286 0.000000e+00 1022
19 TraesCS5A01G162500 chr7A 95.390 629 29 0 8 636 250146949 250146321 0.000000e+00 1002
20 TraesCS5A01G162500 chr7A 94.969 636 32 0 1 636 416739734 416740369 0.000000e+00 998
21 TraesCS5A01G162500 chr6A 95.298 638 27 3 1 636 64230026 64230662 0.000000e+00 1009
22 TraesCS5A01G162500 chr6A 94.984 638 29 3 1 636 64238314 64238950 0.000000e+00 998
23 TraesCS5A01G162500 chr5B 100.000 546 0 0 3107 3652 56908667 56909212 0.000000e+00 1009
24 TraesCS5A01G162500 chr4A 99.284 559 3 1 3095 3652 683249681 683249123 0.000000e+00 1009
25 TraesCS5A01G162500 chr4A 95.126 636 29 2 2 636 498977560 498976926 0.000000e+00 1002
26 TraesCS5A01G162500 chr2B 98.927 559 5 1 3095 3652 652847488 652846930 0.000000e+00 998
27 TraesCS5A01G162500 chr2B 83.951 405 24 21 3285 3652 679637428 679637828 2.090000e-92 350
28 TraesCS5A01G162500 chr2B 92.500 120 6 3 3285 3402 366914371 366914253 6.270000e-38 169
29 TraesCS5A01G162500 chr2B 94.845 97 4 1 3192 3287 652847488 652847392 2.270000e-32 150


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 TraesCS5A01G162500 chr5A 346305662 346309313 3651 False 6745 6745 100.0000 1 3652 1 chr5A.!!$F2 3651
1 TraesCS5A01G162500 chr5A 346285374 346286009 635 False 1064 1064 96.8550 1 636 1 chr5A.!!$F1 635
2 TraesCS5A01G162500 chr5A 390336202 390336839 637 False 994 994 94.8280 1 637 1 chr5A.!!$F3 636
3 TraesCS5A01G162500 chr4B 139742621 139745640 3019 False 5439 5439 99.1720 633 3652 1 chr4B.!!$F2 3019
4 TraesCS5A01G162500 chr4B 2598690 2601265 2575 False 4383 4383 97.4390 636 3201 1 chr4B.!!$F1 2565
5 TraesCS5A01G162500 chr3A 199412059 199415074 3015 False 5421 5421 99.1050 637 3652 1 chr3A.!!$F1 3015
6 TraesCS5A01G162500 chr3A 563811019 563811654 635 True 998 998 94.9690 1 636 1 chr3A.!!$R1 635
7 TraesCS5A01G162500 chr7B 554160474 554163414 2940 False 5175 5175 98.4710 634 3566 1 chr7B.!!$F1 2932
8 TraesCS5A01G162500 chr1A 63761133 63763700 2567 True 4604 4604 99.0260 636 3203 1 chr1A.!!$R1 2567
9 TraesCS5A01G162500 chr1A 320476845 320477403 558 True 998 998 98.9270 3095 3652 1 chr1A.!!$R2 557
10 TraesCS5A01G162500 chr1B 167927206 167930127 2921 True 2799 4593 99.1035 635 3652 2 chr1B.!!$R1 3017
11 TraesCS5A01G162500 chr3B 681200313 681202911 2598 True 4562 4562 98.3460 634 3233 1 chr3B.!!$R1 2599
12 TraesCS5A01G162500 chr3B 731127043 731129650 2607 False 4529 4529 98.0840 637 3233 1 chr3B.!!$F1 2596
13 TraesCS5A01G162500 chr2A 672536852 672539238 2386 False 4248 4248 98.7850 636 3022 1 chr2A.!!$F2 2386
14 TraesCS5A01G162500 chr7A 706527286 706527923 637 True 1022 1022 95.6180 1 636 1 chr7A.!!$R2 635
15 TraesCS5A01G162500 chr7A 250146321 250146949 628 True 1002 1002 95.3900 8 636 1 chr7A.!!$R1 628
16 TraesCS5A01G162500 chr7A 416739734 416740369 635 False 998 998 94.9690 1 636 1 chr7A.!!$F1 635
17 TraesCS5A01G162500 chr6A 64230026 64230662 636 False 1009 1009 95.2980 1 636 1 chr6A.!!$F1 635
18 TraesCS5A01G162500 chr6A 64238314 64238950 636 False 998 998 94.9840 1 636 1 chr6A.!!$F2 635
19 TraesCS5A01G162500 chr5B 56908667 56909212 545 False 1009 1009 100.0000 3107 3652 1 chr5B.!!$F1 545
20 TraesCS5A01G162500 chr4A 683249123 683249681 558 True 1009 1009 99.2840 3095 3652 1 chr4A.!!$R2 557
21 TraesCS5A01G162500 chr4A 498976926 498977560 634 True 1002 1002 95.1260 2 636 1 chr4A.!!$R1 634
22 TraesCS5A01G162500 chr2B 652846930 652847488 558 True 574 998 96.8860 3095 3652 2 chr2B.!!$R2 557

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
627 630 1.428912 TGATCCCTTTTGGCTCAAGGT 59.571 47.619 12.52 0.0 39.50 3.50 F
1381 1396 0.614812 TCTTAGCATGTGCAGAGCCA 59.385 50.000 7.83 0.0 45.16 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1569 1584 0.109873 GCACACAACAGAGCATGCTC 60.110 55.000 35.57 35.57 43.03 4.26 R
2820 2839 4.082081 GGAGTTCAAATGCACAATCCATCA 60.082 41.667 0.00 0.00 0.00 3.07 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
235 238 7.489574 CTCTTTTGAGGATGATTAGTAAGGC 57.510 40.000 0.00 0.00 42.66 4.35
237 240 7.633789 TCTTTTGAGGATGATTAGTAAGGCTT 58.366 34.615 4.58 4.58 0.00 4.35
391 394 2.000447 GCCGAGGATGTTGTAGTTGAC 59.000 52.381 0.00 0.00 0.00 3.18
442 445 6.317088 CCATGTCTAGCTTGTATTTTGTGTG 58.683 40.000 0.00 0.00 0.00 3.82
478 481 6.798959 GTGCATTCTTAGTTTGTCATGACTTC 59.201 38.462 25.55 15.30 0.00 3.01
481 484 7.334421 GCATTCTTAGTTTGTCATGACTTCCTA 59.666 37.037 25.55 17.78 0.00 2.94
526 529 8.173542 TCGTAAACATGCCTACTTGATATCTA 57.826 34.615 3.98 0.00 0.00 1.98
553 556 3.503748 AGCATGCTCCAGTTTTCACTAAC 59.496 43.478 16.30 0.00 0.00 2.34
611 614 7.277098 ACATGCTTGCAAATGTATTTTCTGATC 59.723 33.333 13.80 0.00 35.28 2.92
627 630 1.428912 TGATCCCTTTTGGCTCAAGGT 59.571 47.619 12.52 0.00 39.50 3.50
948 963 3.515562 TCTTCTTCCTTCTCTCTGCCTT 58.484 45.455 0.00 0.00 0.00 4.35
1381 1396 0.614812 TCTTAGCATGTGCAGAGCCA 59.385 50.000 7.83 0.00 45.16 4.75
1667 1682 9.319143 GCTGATGTGTGACTCTTAATAAGTAAT 57.681 33.333 0.00 0.00 0.00 1.89
1819 1834 7.929245 TGCAAAGTTGAATGTAGTGTTACTCTA 59.071 33.333 0.00 0.00 0.00 2.43
2278 2294 0.403271 AGAGCTGAATTGGTGGCTGT 59.597 50.000 0.00 0.00 35.01 4.40
2820 2839 8.125978 TGCTATTCATCCTTTTGTGAGAAAAT 57.874 30.769 0.00 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
442 445 4.702131 ACTAAGAATGCACCCATCAAGAAC 59.298 41.667 0.00 0.00 0.00 3.01
478 481 3.738282 GCTCGATGCACTCACTAAATAGG 59.262 47.826 0.00 0.00 42.31 2.57
481 484 3.452474 GAGCTCGATGCACTCACTAAAT 58.548 45.455 0.00 0.00 45.94 1.40
526 529 3.575256 TGAAAACTGGAGCATGCTGAAAT 59.425 39.130 28.27 4.99 0.00 2.17
553 556 7.025963 GGCAAAAACATAATCAGTTCTCAGAG 58.974 38.462 0.00 0.00 0.00 3.35
627 630 6.109156 TCTGTGCAATTTACTCCTTAGTGA 57.891 37.500 0.00 0.00 36.36 3.41
723 726 4.947147 TTTGCAACGGCTCGCCCT 62.947 61.111 0.00 0.00 41.91 5.19
1569 1584 0.109873 GCACACAACAGAGCATGCTC 60.110 55.000 35.57 35.57 43.03 4.26
2278 2294 7.741027 TTCTTTGCCATTTTTGCATTCATAA 57.259 28.000 0.00 0.00 38.76 1.90
2820 2839 4.082081 GGAGTTCAAATGCACAATCCATCA 60.082 41.667 0.00 0.00 0.00 3.07


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

AutoCloner maintained by Alex Coulton.