Multiple sequence alignment - TraesCS2A01G292200

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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 TraesCS2A01G292200 chr2A 100.000 2513 0 0 1 2513 503207190 503209702 0 4641
1 TraesCS2A01G292200 chr2A 95.117 2519 104 12 1 2513 677262026 677264531 0 3952
2 TraesCS2A01G292200 chr4A 95.547 2515 94 10 4 2513 45631403 45633904 0 4008
3 TraesCS2A01G292200 chr4A 94.780 613 21 5 1901 2513 246821249 246820648 0 944
4 TraesCS2A01G292200 chr6D 95.193 2538 84 13 1 2513 451600145 451597621 0 3976
5 TraesCS2A01G292200 chr6D 94.805 2541 81 14 1 2513 397854468 397851951 0 3914
6 TraesCS2A01G292200 chr6D 95.673 1687 56 9 1 1678 451143989 451145667 0 2695
7 TraesCS2A01G292200 chr6A 95.276 2519 99 12 1 2513 484784649 484782145 0 3975
8 TraesCS2A01G292200 chr6A 94.919 2519 103 10 1 2513 176534597 176532098 0 3919
9 TraesCS2A01G292200 chr6A 94.617 613 23 5 1901 2513 357524783 357524181 0 941
10 TraesCS2A01G292200 chr3D 94.957 2538 82 17 1 2513 337615078 337617594 0 3936
11 TraesCS2A01G292200 chr3D 94.604 2539 99 13 1 2513 533780637 533783163 0 3895
12 TraesCS2A01G292200 chr7D 94.729 2542 93 15 1 2513 417527680 417530209 0 3914
13 TraesCS2A01G292200 chr7D 94.749 2533 96 13 4 2513 403016543 403014025 0 3906
14 TraesCS2A01G292200 chr1A 94.636 2517 102 14 1 2513 519376699 519374212 0 3869
15 TraesCS2A01G292200 chr1A 94.943 613 21 5 1901 2513 517445084 517444482 0 952
16 TraesCS2A01G292200 chr5B 93.607 1877 99 12 1 1866 469762800 469764666 0 2782
17 TraesCS2A01G292200 chr5A 93.262 1870 99 15 4 1866 673332407 673330558 0 2730


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 TraesCS2A01G292200 chr2A 503207190 503209702 2512 False 4641 4641 100.000 1 2513 1 chr2A.!!$F1 2512
1 TraesCS2A01G292200 chr2A 677262026 677264531 2505 False 3952 3952 95.117 1 2513 1 chr2A.!!$F2 2512
2 TraesCS2A01G292200 chr4A 45631403 45633904 2501 False 4008 4008 95.547 4 2513 1 chr4A.!!$F1 2509
3 TraesCS2A01G292200 chr4A 246820648 246821249 601 True 944 944 94.780 1901 2513 1 chr4A.!!$R1 612
4 TraesCS2A01G292200 chr6D 451597621 451600145 2524 True 3976 3976 95.193 1 2513 1 chr6D.!!$R2 2512
5 TraesCS2A01G292200 chr6D 397851951 397854468 2517 True 3914 3914 94.805 1 2513 1 chr6D.!!$R1 2512
6 TraesCS2A01G292200 chr6D 451143989 451145667 1678 False 2695 2695 95.673 1 1678 1 chr6D.!!$F1 1677
7 TraesCS2A01G292200 chr6A 484782145 484784649 2504 True 3975 3975 95.276 1 2513 1 chr6A.!!$R3 2512
8 TraesCS2A01G292200 chr6A 176532098 176534597 2499 True 3919 3919 94.919 1 2513 1 chr6A.!!$R1 2512
9 TraesCS2A01G292200 chr6A 357524181 357524783 602 True 941 941 94.617 1901 2513 1 chr6A.!!$R2 612
10 TraesCS2A01G292200 chr3D 337615078 337617594 2516 False 3936 3936 94.957 1 2513 1 chr3D.!!$F1 2512
11 TraesCS2A01G292200 chr3D 533780637 533783163 2526 False 3895 3895 94.604 1 2513 1 chr3D.!!$F2 2512
12 TraesCS2A01G292200 chr7D 417527680 417530209 2529 False 3914 3914 94.729 1 2513 1 chr7D.!!$F1 2512
13 TraesCS2A01G292200 chr7D 403014025 403016543 2518 True 3906 3906 94.749 4 2513 1 chr7D.!!$R1 2509
14 TraesCS2A01G292200 chr1A 519374212 519376699 2487 True 3869 3869 94.636 1 2513 1 chr1A.!!$R2 2512
15 TraesCS2A01G292200 chr1A 517444482 517445084 602 True 952 952 94.943 1901 2513 1 chr1A.!!$R1 612
16 TraesCS2A01G292200 chr5B 469762800 469764666 1866 False 2782 2782 93.607 1 1866 1 chr5B.!!$F1 1865
17 TraesCS2A01G292200 chr5A 673330558 673332407 1849 True 2730 2730 93.262 4 1866 1 chr5A.!!$R1 1862

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
704 725 0.108329 ACGATCTGCCCCACTTTACG 60.108 55.0 0.0 0.0 0.0 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2387 2466 4.873746 TTGTGTTTTGTTTGTCCCAAGA 57.126 36.364 0.0 0.0 0.0 3.02 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)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
123 125 9.649167 AAGCTATGGAGATTTTTCTGATTTTTG 57.351 29.630 0.00 0.00 0.00 2.44
166 172 1.008571 ACCCTAAACCCTCTCTCCCTC 59.991 57.143 0.00 0.00 0.00 4.30
169 175 3.052033 CCCTAAACCCTCTCTCCCTCTTA 60.052 52.174 0.00 0.00 0.00 2.10
200 206 6.127168 ACTCCGAACATGTTCATAGGTGATAA 60.127 38.462 32.06 12.31 39.46 1.75
222 229 6.463995 AACTCATTTGTGTGAAGCCTTTTA 57.536 33.333 0.00 0.00 0.00 1.52
301 312 1.132834 TGGCTATGTGCGCAAGAATTG 59.867 47.619 14.00 8.81 43.75 2.32
355 368 7.449934 AAACATTTGAACTTGATTTCGACAC 57.550 32.000 0.00 0.00 0.00 3.67
358 371 7.870826 ACATTTGAACTTGATTTCGACACATA 58.129 30.769 0.00 0.00 0.00 2.29
447 465 4.206609 GTCTCATAAACGGATGAACTACGC 59.793 45.833 0.00 0.00 35.44 4.42
593 612 1.518774 GCCGTCGGATCCTACCAAA 59.481 57.895 17.49 0.00 0.00 3.28
619 638 1.371183 CACCACCCGTCAGATGTGT 59.629 57.895 0.00 0.00 0.00 3.72
704 725 0.108329 ACGATCTGCCCCACTTTACG 60.108 55.000 0.00 0.00 0.00 3.18
1084 1112 1.353022 AGAATGGGAACTTTGGGCGTA 59.647 47.619 0.00 0.00 0.00 4.42
1127 1155 3.143010 CGGAGGGGCAGGTTAGATA 57.857 57.895 0.00 0.00 0.00 1.98
1137 1165 5.437060 GGGCAGGTTAGATATGAGTTTTCA 58.563 41.667 0.00 0.00 37.81 2.69
1351 1379 4.694233 CTCCGGCAGCAGCAGTGT 62.694 66.667 2.65 0.00 44.61 3.55
1380 1408 0.901580 ACCCGACGGTGGTAGATGTT 60.902 55.000 13.94 0.00 42.48 2.71
1387 1415 2.289444 ACGGTGGTAGATGTTGAACTGG 60.289 50.000 0.00 0.00 0.00 4.00
1403 1431 3.601443 ACTGGAGACGGAATTGAAGAG 57.399 47.619 0.00 0.00 41.09 2.85
1442 1470 3.336468 AGCAGCTGATTGAGTTGAAGAG 58.664 45.455 20.43 0.00 34.91 2.85
1453 1481 5.178096 TGAGTTGAAGAGGCAATCCAATA 57.822 39.130 0.00 0.00 33.74 1.90
1566 1594 9.162764 GTTTAGCAATCCAAGTCTGTTTATCTA 57.837 33.333 0.00 0.00 0.00 1.98
1611 1639 6.865726 GCAACTATCGATCTCTGAATGTATGT 59.134 38.462 0.00 0.00 0.00 2.29
1647 1675 2.589798 TCGACACTTTCAGTTTCGGT 57.410 45.000 11.43 0.00 45.44 4.69
1767 1795 6.412362 ACTTGAGTAGCACAAGGGATATAG 57.588 41.667 0.00 0.00 45.92 1.31
2387 2466 2.210116 CGCCAATTAGCCGTGTCTAAT 58.790 47.619 0.00 0.00 40.05 1.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
54 56 9.225436 AGAAGGATCTGAACTTACTTTTTCATC 57.775 33.333 0.00 0.00 33.59 2.92
166 172 5.803461 TGAACATGTTCGGAGTTCGTATAAG 59.197 40.000 28.55 0.00 43.36 1.73
169 175 4.182693 TGAACATGTTCGGAGTTCGTAT 57.817 40.909 28.55 0.00 43.36 3.06
200 206 6.265196 TGATAAAAGGCTTCACACAAATGAGT 59.735 34.615 0.00 0.00 0.00 3.41
222 229 6.248433 ACTTGGTGTAGGTCATTTTCATGAT 58.752 36.000 0.00 0.00 41.64 2.45
593 612 4.493049 ACGGGTGGTGTTTGGCGT 62.493 61.111 0.00 0.00 0.00 5.68
704 725 9.071221 TCATGTGCGAAAAATACAATTTCATAC 57.929 29.630 0.00 0.00 36.75 2.39
980 1008 1.682849 GGCACTGGACCATACACCA 59.317 57.895 0.00 0.00 34.81 4.17
1084 1112 1.461127 GCTCTCGCATTTGACGAACTT 59.539 47.619 0.00 0.00 39.39 2.66
1127 1155 6.769822 AGATAAAGGATGCGATGAAAACTCAT 59.230 34.615 0.00 0.00 0.00 2.90
1137 1165 8.370940 TGAGAAATTAGAGATAAAGGATGCGAT 58.629 33.333 0.00 0.00 0.00 4.58
1201 1229 6.015265 TGGCATTTCTTCATGATCTGAAAACA 60.015 34.615 17.11 14.37 43.20 2.83
1380 1408 3.323691 TCTTCAATTCCGTCTCCAGTTCA 59.676 43.478 0.00 0.00 0.00 3.18
1387 1415 4.392921 TCATCCTCTTCAATTCCGTCTC 57.607 45.455 0.00 0.00 0.00 3.36
1403 1431 4.791974 CTGCTTGAAGTTCTTGTTCATCC 58.208 43.478 4.17 0.00 33.95 3.51
1442 1470 6.886459 TCCTAAAGCTATCATATTGGATTGCC 59.114 38.462 6.09 0.00 43.86 4.52
1453 1481 7.972301 AGAGCAAGTATTCCTAAAGCTATCAT 58.028 34.615 0.00 0.00 0.00 2.45
1566 1594 5.261209 TGCACTAAACAGAGTTGCATTTT 57.739 34.783 0.00 0.00 32.33 1.82
1611 1639 8.931385 AAGTGTCGAAACTTAACAGTAAACTA 57.069 30.769 19.55 0.00 38.62 2.24
1647 1675 5.831525 TCACTGAACTGGTAGTTGTCTTCTA 59.168 40.000 0.00 0.00 38.80 2.10
1767 1795 6.201517 CGAGAGAGAAGAGATGAACTTGATC 58.798 44.000 0.00 0.00 0.00 2.92
1992 2027 6.269538 CCTCAATGAGATAGAAGAGATTGGGA 59.730 42.308 12.53 0.00 0.00 4.37
2168 2226 7.254852 TGGCTTTAGTCAAAAGTGTAGTTTTG 58.745 34.615 15.43 15.43 45.46 2.44
2387 2466 4.873746 TTGTGTTTTGTTTGTCCCAAGA 57.126 36.364 0.00 0.00 0.00 3.02
2431 2510 7.783042 ACCCTATCTAAGTTAAGTCATGTGTC 58.217 38.462 0.00 0.00 0.00 3.67
2438 2517 7.435305 CCTAGCAACCCTATCTAAGTTAAGTC 58.565 42.308 0.00 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.