Multiple sequence alignment - TraesCS2B01G014800

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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 TraesCS2B01G014800 chr2B 100.000 2864 0 0 1 2864 7044934 7042071 0.000000e+00 5289.0
1 TraesCS2B01G014800 chr2B 98.464 2864 39 1 1 2864 454723911 454726769 0.000000e+00 5040.0
2 TraesCS2B01G014800 chr2B 98.394 2865 39 3 1 2864 7157991 7155133 0.000000e+00 5029.0
3 TraesCS2B01G014800 chr2B 98.254 2864 43 3 1 2864 7083743 7080887 0.000000e+00 5005.0
4 TraesCS2B01G014800 chr2B 98.080 2864 39 2 1 2864 454788046 454790893 0.000000e+00 4970.0
5 TraesCS2B01G014800 chr2B 98.229 2258 34 2 607 2864 7124820 7122569 0.000000e+00 3943.0
6 TraesCS2B01G014800 chr2B 96.267 2304 78 4 562 2864 6960612 6962908 0.000000e+00 3771.0
7 TraesCS2B01G014800 chr2B 96.245 2104 71 4 562 2664 6874654 6876750 0.000000e+00 3441.0
8 TraesCS2B01G014800 chr2B 96.884 353 11 0 34 386 454694954 454695306 2.460000e-165 592.0
9 TraesCS2B01G014800 chr2B 96.429 112 4 0 467 578 6877791 6877902 4.870000e-43 185.0
10 TraesCS2B01G014800 chr2B 96.429 112 4 0 467 578 6960422 6960533 4.870000e-43 185.0
11 TraesCS2B01G014800 chr2B 96.429 84 3 0 442 525 454695768 454695851 3.850000e-29 139.0
12 TraesCS2B01G014800 chr2B 96.970 66 2 0 383 448 454695651 454695716 8.390000e-21 111.0
13 TraesCS2B01G014800 chrUn 98.801 1918 23 0 1 1918 268874773 268876690 0.000000e+00 3415.0
14 TraesCS2B01G014800 chrUn 99.092 661 6 0 1 661 360049446 360050106 0.000000e+00 1188.0
15 TraesCS2B01G014800 chrUn 100.000 35 0 0 1 35 100309659 100309625 6.620000e-07 65.8
16 TraesCS2B01G014800 chr2D 91.721 2295 143 22 577 2864 3973253 3975507 0.000000e+00 3142.0
17 TraesCS2B01G014800 chr2D 91.835 2082 144 12 789 2864 4030763 4032824 0.000000e+00 2880.0
18 TraesCS2B01G014800 chr2D 95.854 410 15 2 34 442 3972505 3972913 0.000000e+00 662.0
19 TraesCS2B01G014800 chr2D 95.610 410 17 1 34 442 4030103 4030512 0.000000e+00 656.0


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 TraesCS2B01G014800 chr2B 7042071 7044934 2863 True 5289.000000 5289 100.0000 1 2864 1 chr2B.!!$R1 2863
1 TraesCS2B01G014800 chr2B 454723911 454726769 2858 False 5040.000000 5040 98.4640 1 2864 1 chr2B.!!$F1 2863
2 TraesCS2B01G014800 chr2B 7155133 7157991 2858 True 5029.000000 5029 98.3940 1 2864 1 chr2B.!!$R4 2863
3 TraesCS2B01G014800 chr2B 7080887 7083743 2856 True 5005.000000 5005 98.2540 1 2864 1 chr2B.!!$R2 2863
4 TraesCS2B01G014800 chr2B 454788046 454790893 2847 False 4970.000000 4970 98.0800 1 2864 1 chr2B.!!$F2 2863
5 TraesCS2B01G014800 chr2B 7122569 7124820 2251 True 3943.000000 3943 98.2290 607 2864 1 chr2B.!!$R3 2257
6 TraesCS2B01G014800 chr2B 6960422 6962908 2486 False 1978.000000 3771 96.3480 467 2864 2 chr2B.!!$F4 2397
7 TraesCS2B01G014800 chr2B 6874654 6877902 3248 False 1813.000000 3441 96.3370 467 2664 2 chr2B.!!$F3 2197
8 TraesCS2B01G014800 chr2B 454694954 454695851 897 False 280.666667 592 96.7610 34 525 3 chr2B.!!$F5 491
9 TraesCS2B01G014800 chrUn 268874773 268876690 1917 False 3415.000000 3415 98.8010 1 1918 1 chrUn.!!$F1 1917
10 TraesCS2B01G014800 chrUn 360049446 360050106 660 False 1188.000000 1188 99.0920 1 661 1 chrUn.!!$F2 660
11 TraesCS2B01G014800 chr2D 3972505 3975507 3002 False 1902.000000 3142 93.7875 34 2864 2 chr2D.!!$F1 2830
12 TraesCS2B01G014800 chr2D 4030103 4032824 2721 False 1768.000000 2880 93.7225 34 2864 2 chr2D.!!$F2 2830

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
934 1591 2.544726 GCGAACAGCTTGTAGCCTT 58.455 52.632 0.0 0.0 43.77 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2472 3136 1.004918 CTCCGACCAACACCCAGTC 60.005 63.158 0.0 0.0 0.0 3.51 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
311 313 5.531634 TGTGATTGCATCTTCCTTCAAAAC 58.468 37.500 0.00 0.00 0.00 2.43
488 954 6.206829 GGGTTAGTGCAAAAGTCATTAGAAGT 59.793 38.462 0.00 0.00 0.00 3.01
934 1591 2.544726 GCGAACAGCTTGTAGCCTT 58.455 52.632 0.00 0.00 43.77 4.35
1001 1658 2.044946 GGCCCTCTGGTTTCGCAT 60.045 61.111 0.00 0.00 0.00 4.73
1024 1681 0.987294 CTCTGGGGGCAAGAGAAAGA 59.013 55.000 5.44 0.00 43.27 2.52
1131 1790 4.552365 ATGTCTCGCCGGCATGGG 62.552 66.667 28.98 11.64 38.63 4.00
1229 1888 1.963515 GACCAATGACCTTGCCTTTGT 59.036 47.619 0.00 0.00 33.20 2.83
2023 2687 6.745116 TGCGTACTACTACATATGCAGAAAT 58.255 36.000 10.02 0.00 38.18 2.17
2244 2908 7.064866 ACTCCATTACATGTGGATGATCATTT 58.935 34.615 19.71 0.00 44.34 2.32
2416 3080 5.049336 GTCCTGAAGAGTTTAAGCCTGAAAC 60.049 44.000 0.00 0.00 37.11 2.78
2442 3106 7.696453 CGTTTGAGAACAATAACATGGATTACC 59.304 37.037 0.00 0.00 35.44 2.85
2468 3132 4.340617 GGACATACTTTGAATTCACCCCA 58.659 43.478 7.89 0.00 0.00 4.96
2472 3136 5.125417 ACATACTTTGAATTCACCCCATTCG 59.875 40.000 7.89 0.00 33.91 3.34
2473 3137 3.761897 ACTTTGAATTCACCCCATTCGA 58.238 40.909 7.89 0.00 33.91 3.71
2474 3138 3.506067 ACTTTGAATTCACCCCATTCGAC 59.494 43.478 7.89 0.00 33.91 4.20
2475 3139 3.433306 TTGAATTCACCCCATTCGACT 57.567 42.857 7.89 0.00 33.91 4.18
2476 3140 2.710377 TGAATTCACCCCATTCGACTG 58.290 47.619 3.38 0.00 33.91 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
488 954 5.677319 AATGGAGAAAGTGGAGTTCGATA 57.323 39.130 0.00 0.00 0.00 2.92
619 1271 4.040461 TCCTAGGTTTGCTATCAGGCATAC 59.960 45.833 9.08 0.00 42.09 2.39
934 1591 0.918983 CTTAACCAGCCCTCCATGGA 59.081 55.000 15.27 15.27 39.02 3.41
1001 1658 2.203983 TCTTGCCCCCAGAGAGCA 60.204 61.111 0.00 0.00 33.97 4.26
1024 1681 3.644606 CCCAGGAGGCAGCTGTGT 61.645 66.667 16.64 2.11 0.00 3.72
1131 1790 1.650912 CATAAGGTGCATCAGCGGC 59.349 57.895 0.00 0.00 46.23 6.53
1701 2360 4.908687 TGTGTGGCAGCTCGCGTT 62.909 61.111 5.77 0.00 43.84 4.84
2244 2908 3.961408 GGATGCAGTCTAAGAACCTCCTA 59.039 47.826 0.00 0.00 0.00 2.94
2416 3080 7.696453 GGTAATCCATGTTATTGTTCTCAAACG 59.304 37.037 0.00 0.00 38.28 3.60
2442 3106 5.163519 GGGTGAATTCAAAGTATGTCCCATG 60.164 44.000 17.38 0.00 0.00 3.66
2468 3132 3.625745 GACCAACACCCAGTCGAAT 57.374 52.632 0.00 0.00 0.00 3.34
2472 3136 1.004918 CTCCGACCAACACCCAGTC 60.005 63.158 0.00 0.00 0.00 3.51
2473 3137 2.516888 CCTCCGACCAACACCCAGT 61.517 63.158 0.00 0.00 0.00 4.00
2474 3138 2.347490 CCTCCGACCAACACCCAG 59.653 66.667 0.00 0.00 0.00 4.45
2475 3139 3.948719 GCCTCCGACCAACACCCA 61.949 66.667 0.00 0.00 0.00 4.51
2476 3140 3.901797 CTGCCTCCGACCAACACCC 62.902 68.421 0.00 0.00 0.00 4.61


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

AutoCloner maintained by Alex Coulton.