Multiple sequence alignment - TraesCS2B01G509900

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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 TraesCS2B01G509900 chr2B 100.000 2999 0 0 1 2999 705902890 705899892 0.000000e+00 5539
1 TraesCS2B01G509900 chr2B 92.530 589 34 4 2411 2998 75624780 75624201 0.000000e+00 835
2 TraesCS2B01G509900 chr3B 97.676 2410 56 0 1 2410 373191733 373194142 0.000000e+00 4141
3 TraesCS2B01G509900 chr3B 97.796 2042 45 0 1 2042 373196184 373194143 0.000000e+00 3522
4 TraesCS2B01G509900 chr3B 92.190 589 34 6 2411 2998 615587703 615587126 0.000000e+00 822
5 TraesCS2B01G509900 chr3B 92.061 592 32 6 2411 2998 79092151 79092731 0.000000e+00 819
6 TraesCS2B01G509900 chr3B 91.851 589 35 6 2411 2998 726089190 726089766 0.000000e+00 809
7 TraesCS2B01G509900 chr3D 96.845 1680 49 4 735 2410 429608339 429610018 0.000000e+00 2806
8 TraesCS2B01G509900 chr3D 96.365 1678 59 2 735 2410 489594414 489596091 0.000000e+00 2760
9 TraesCS2B01G509900 chr3D 92.505 507 16 4 1 507 429607421 429607905 0.000000e+00 706
10 TraesCS2B01G509900 chr6D 96.367 1679 58 3 735 2410 148847366 148845688 0.000000e+00 2760
11 TraesCS2B01G509900 chr6D 96.147 1687 60 5 735 2418 329379837 329381521 0.000000e+00 2750
12 TraesCS2B01G509900 chr6D 92.547 738 36 4 1 738 329378956 329379674 0.000000e+00 1040
13 TraesCS2B01G509900 chr6D 92.702 507 19 3 1 507 148848286 148847798 0.000000e+00 715
14 TraesCS2B01G509900 chr6D 92.415 501 20 3 7 507 385336419 385336901 0.000000e+00 699
15 TraesCS2B01G509900 chr6D 93.388 242 8 1 505 738 385336929 385337170 4.760000e-93 351
16 TraesCS2B01G509900 chr5D 96.307 1679 58 4 735 2411 468506037 468507713 0.000000e+00 2754
17 TraesCS2B01G509900 chr5D 92.110 507 22 3 1 507 468505117 468505605 0.000000e+00 699
18 TraesCS2B01G509900 chr6A 96.195 1682 55 6 736 2410 35314949 35313270 0.000000e+00 2743
19 TraesCS2B01G509900 chr6A 96.154 234 9 0 505 738 35315346 35315113 1.690000e-102 383
20 TraesCS2B01G509900 chr6A 94.872 234 12 0 505 738 395601350 395601583 1.700000e-97 366
21 TraesCS2B01G509900 chr2D 96.081 1684 61 5 735 2414 607746168 607744486 0.000000e+00 2739
22 TraesCS2B01G509900 chr2D 92.505 507 20 3 1 507 607747086 607746598 0.000000e+00 710
23 TraesCS2B01G509900 chr3A 91.734 738 41 3 1 738 736999147 736998430 0.000000e+00 1007
24 TraesCS2B01G509900 chr1B 92.530 589 29 9 2411 2998 436276688 436276114 0.000000e+00 830
25 TraesCS2B01G509900 chr1B 92.347 588 34 4 2411 2998 61519312 61518736 0.000000e+00 826
26 TraesCS2B01G509900 chr1B 92.020 589 30 10 2411 2998 61512297 61511725 0.000000e+00 811
27 TraesCS2B01G509900 chr4B 92.020 589 35 6 2411 2998 116533754 116534331 0.000000e+00 817
28 TraesCS2B01G509900 chr5B 91.554 592 38 5 2411 2998 401039325 401039908 0.000000e+00 806
29 TraesCS2B01G509900 chr7D 93.491 507 15 3 1 507 1786313 1786801 0.000000e+00 737
30 TraesCS2B01G509900 chr7D 92.505 507 28 8 1 507 285355487 285354991 0.000000e+00 717
31 TraesCS2B01G509900 chr2A 96.154 234 9 0 505 738 351179018 351179251 1.690000e-102 383
32 TraesCS2B01G509900 chr2A 95.726 234 10 0 505 738 315571568 315571801 7.850000e-101 377


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 TraesCS2B01G509900 chr2B 705899892 705902890 2998 True 5539.0 5539 100.0000 1 2999 1 chr2B.!!$R2 2998
1 TraesCS2B01G509900 chr2B 75624201 75624780 579 True 835.0 835 92.5300 2411 2998 1 chr2B.!!$R1 587
2 TraesCS2B01G509900 chr3B 373191733 373194142 2409 False 4141.0 4141 97.6760 1 2410 1 chr3B.!!$F2 2409
3 TraesCS2B01G509900 chr3B 373194143 373196184 2041 True 3522.0 3522 97.7960 1 2042 1 chr3B.!!$R1 2041
4 TraesCS2B01G509900 chr3B 615587126 615587703 577 True 822.0 822 92.1900 2411 2998 1 chr3B.!!$R2 587
5 TraesCS2B01G509900 chr3B 79092151 79092731 580 False 819.0 819 92.0610 2411 2998 1 chr3B.!!$F1 587
6 TraesCS2B01G509900 chr3B 726089190 726089766 576 False 809.0 809 91.8510 2411 2998 1 chr3B.!!$F3 587
7 TraesCS2B01G509900 chr3D 489594414 489596091 1677 False 2760.0 2760 96.3650 735 2410 1 chr3D.!!$F1 1675
8 TraesCS2B01G509900 chr3D 429607421 429610018 2597 False 1756.0 2806 94.6750 1 2410 2 chr3D.!!$F2 2409
9 TraesCS2B01G509900 chr6D 329378956 329381521 2565 False 1895.0 2750 94.3470 1 2418 2 chr6D.!!$F1 2417
10 TraesCS2B01G509900 chr6D 148845688 148848286 2598 True 1737.5 2760 94.5345 1 2410 2 chr6D.!!$R1 2409
11 TraesCS2B01G509900 chr6D 385336419 385337170 751 False 525.0 699 92.9015 7 738 2 chr6D.!!$F2 731
12 TraesCS2B01G509900 chr5D 468505117 468507713 2596 False 1726.5 2754 94.2085 1 2411 2 chr5D.!!$F1 2410
13 TraesCS2B01G509900 chr6A 35313270 35315346 2076 True 1563.0 2743 96.1745 505 2410 2 chr6A.!!$R1 1905
14 TraesCS2B01G509900 chr2D 607744486 607747086 2600 True 1724.5 2739 94.2930 1 2414 2 chr2D.!!$R1 2413
15 TraesCS2B01G509900 chr3A 736998430 736999147 717 True 1007.0 1007 91.7340 1 738 1 chr3A.!!$R1 737
16 TraesCS2B01G509900 chr1B 436276114 436276688 574 True 830.0 830 92.5300 2411 2998 1 chr1B.!!$R3 587
17 TraesCS2B01G509900 chr1B 61518736 61519312 576 True 826.0 826 92.3470 2411 2998 1 chr1B.!!$R2 587
18 TraesCS2B01G509900 chr1B 61511725 61512297 572 True 811.0 811 92.0200 2411 2998 1 chr1B.!!$R1 587
19 TraesCS2B01G509900 chr4B 116533754 116534331 577 False 817.0 817 92.0200 2411 2998 1 chr4B.!!$F1 587
20 TraesCS2B01G509900 chr5B 401039325 401039908 583 False 806.0 806 91.5540 2411 2998 1 chr5B.!!$F1 587

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
375 380 0.388659 GCTGTTGCACCAAATGACCA 59.611 50.0 0.0 0.0 39.41 4.02 F
899 1145 1.530013 GCCAAGATGCAACACCAGCT 61.530 55.0 0.0 0.0 31.86 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1543 1793 3.518590 ACTTTATCTTACGGGCGTTCTG 58.481 45.455 0.0 0.0 0.0 3.02 R
2872 3134 0.912006 AGCAAGGGGAAGGAGAGGTC 60.912 60.000 0.0 0.0 0.0 3.85 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
83 84 7.501892 TGCAACTGATTTATACATGCCTTGATA 59.498 33.333 0.00 0.0 0.00 2.15
266 271 2.376109 CCTTTGGTCTCGCCTAGTCTA 58.624 52.381 0.00 0.0 38.35 2.59
375 380 0.388659 GCTGTTGCACCAAATGACCA 59.611 50.000 0.00 0.0 39.41 4.02
549 614 6.435277 AGTCTGAAGGTAATCATTTTGTGCAT 59.565 34.615 0.00 0.0 0.00 3.96
899 1145 1.530013 GCCAAGATGCAACACCAGCT 61.530 55.000 0.00 0.0 31.86 4.24
954 1201 3.555956 CGTATGTGGTTGCTGGTAATCTC 59.444 47.826 0.00 0.0 0.00 2.75
1005 1252 5.895534 TCAGAGGGTTGTTTAGTCGGTATAT 59.104 40.000 0.00 0.0 0.00 0.86
1041 1288 3.891366 TCTGGATCTGTATCGAGCATTGA 59.109 43.478 0.00 0.0 37.74 2.57
1274 1522 3.077359 GCTTTGCTTCTGCCTTCTTCTA 58.923 45.455 0.00 0.0 38.71 2.10
1283 1531 7.128976 GCTTCTGCCTTCTTCTATAAAAATCG 58.871 38.462 0.00 0.0 0.00 3.34
1792 2042 4.901197 AAGAAGAGGAGGGAAAAGACTC 57.099 45.455 0.00 0.0 0.00 3.36
2434 2688 1.143277 TCAGCCACCGGGAAAGTTTTA 59.857 47.619 6.32 0.0 35.59 1.52
2809 3071 2.354401 CCCTCTCGCTGAGCTTGGA 61.354 63.158 1.78 0.0 41.35 3.53
2872 3134 1.339291 TGTGCTGCTAGATCTCCATCG 59.661 52.381 0.00 0.0 33.75 3.84
2899 3163 1.063417 CCTTCCCCTTGCTGGATCAAT 60.063 52.381 0.00 0.0 38.35 2.57
2998 3262 0.448990 TTGGATCACGACGAGTACGG 59.551 55.000 0.00 0.0 44.46 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
266 271 2.188829 CATGCCGGATTGCGGTGAT 61.189 57.895 18.23 7.84 0.00 3.06
358 363 1.680735 GTCTGGTCATTTGGTGCAACA 59.319 47.619 0.00 0.00 39.98 3.33
375 380 0.113776 TTCGGTGTCTAGGGTGGTCT 59.886 55.000 0.00 0.00 0.00 3.85
899 1145 9.678260 CCTACTTTTACACTAGGACTAGTTCTA 57.322 37.037 10.59 10.59 43.35 2.10
932 1178 3.531538 AGATTACCAGCAACCACATACG 58.468 45.455 0.00 0.00 0.00 3.06
954 1201 9.575868 TTAATGAACCTCTAGTCTCCATAGTAG 57.424 37.037 0.00 0.00 0.00 2.57
1041 1288 7.610692 GGAAACTTATTTAGTCCTACAAGGCTT 59.389 37.037 0.00 0.00 35.54 4.35
1543 1793 3.518590 ACTTTATCTTACGGGCGTTCTG 58.481 45.455 0.00 0.00 0.00 3.02
1689 1939 5.698545 GCATTTAGCCACAAAATTACCAACA 59.301 36.000 0.00 0.00 37.23 3.33
2434 2688 2.044758 GATACAATACCGGTGACCCCT 58.955 52.381 19.93 0.00 0.00 4.79
2703 2964 3.116174 CTCCTCTTTATATAGGGGCCCC 58.884 54.545 35.90 35.90 35.61 5.80
2809 3071 1.222936 CAATCTCGGCAGGGCTTCT 59.777 57.895 0.00 0.00 0.00 2.85
2872 3134 0.912006 AGCAAGGGGAAGGAGAGGTC 60.912 60.000 0.00 0.00 0.00 3.85
2899 3163 1.341778 GGGGAAGACGTCTCCTCCTTA 60.342 57.143 27.43 0.00 44.68 2.69


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

AutoCloner maintained by Alex Coulton.