Multiple sequence alignment - TraesCS2D01G551400

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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 TraesCS2D01G551400 chr2D 100.000 4178 0 0 1 4178 627144807 627148984 0.000000e+00 7716
1 TraesCS2D01G551400 chr6D 98.289 3097 52 1 1 3096 380491692 380488596 0.000000e+00 5424
2 TraesCS2D01G551400 chr6D 97.940 728 11 3 3094 3821 379328310 379329033 0.000000e+00 1258
3 TraesCS2D01G551400 chr6D 97.778 360 7 1 3819 4178 379331163 379331521 1.650000e-173 619
4 TraesCS2D01G551400 chr5D 98.002 3103 52 8 1 3096 512437805 512434706 0.000000e+00 5378
5 TraesCS2D01G551400 chr5D 98.224 732 11 2 3094 3824 512424042 512423312 0.000000e+00 1279
6 TraesCS2D01G551400 chr5D 97.500 360 9 0 3819 4178 512421214 512420855 2.130000e-172 616
7 TraesCS2D01G551400 chr7A 94.084 2265 119 9 839 3096 83229236 83231492 0.000000e+00 3426
8 TraesCS2D01G551400 chr7A 93.681 728 42 3 3094 3821 83256994 83257717 0.000000e+00 1086
9 TraesCS2D01G551400 chr7A 96.522 575 19 1 238 811 83228661 83229235 0.000000e+00 950
10 TraesCS2D01G551400 chr7A 93.889 360 22 0 3819 4178 83268152 83268511 1.020000e-150 544
11 TraesCS2D01G551400 chr3B 78.855 1589 285 35 1548 3103 65315963 65314393 0.000000e+00 1026
12 TraesCS2D01G551400 chr3B 82.087 1083 173 13 51 1126 65329062 65327994 0.000000e+00 905
13 TraesCS2D01G551400 chr5B 89.726 730 69 5 3094 3821 677706441 677707166 0.000000e+00 928
14 TraesCS2D01G551400 chr5B 90.909 187 16 1 3819 4004 677709107 677709293 2.490000e-62 250
15 TraesCS2D01G551400 chr7B 98.056 360 7 0 3819 4178 612899783 612900142 9.860000e-176 627
16 TraesCS2D01G551400 chr2B 97.222 360 9 1 3819 4178 747859585 747859227 3.570000e-170 608


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 TraesCS2D01G551400 chr2D 627144807 627148984 4177 False 7716.0 7716 100.0000 1 4178 1 chr2D.!!$F1 4177
1 TraesCS2D01G551400 chr6D 380488596 380491692 3096 True 5424.0 5424 98.2890 1 3096 1 chr6D.!!$R1 3095
2 TraesCS2D01G551400 chr6D 379328310 379331521 3211 False 938.5 1258 97.8590 3094 4178 2 chr6D.!!$F1 1084
3 TraesCS2D01G551400 chr5D 512434706 512437805 3099 True 5378.0 5378 98.0020 1 3096 1 chr5D.!!$R1 3095
4 TraesCS2D01G551400 chr5D 512420855 512424042 3187 True 947.5 1279 97.8620 3094 4178 2 chr5D.!!$R2 1084
5 TraesCS2D01G551400 chr7A 83228661 83231492 2831 False 2188.0 3426 95.3030 238 3096 2 chr7A.!!$F3 2858
6 TraesCS2D01G551400 chr7A 83256994 83257717 723 False 1086.0 1086 93.6810 3094 3821 1 chr7A.!!$F1 727
7 TraesCS2D01G551400 chr3B 65314393 65315963 1570 True 1026.0 1026 78.8550 1548 3103 1 chr3B.!!$R1 1555
8 TraesCS2D01G551400 chr3B 65327994 65329062 1068 True 905.0 905 82.0870 51 1126 1 chr3B.!!$R2 1075
9 TraesCS2D01G551400 chr5B 677706441 677709293 2852 False 589.0 928 90.3175 3094 4004 2 chr5B.!!$F1 910

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
853 858 0.107456 CGGCTGCCATCTGTTCCTAT 59.893 55.000 20.29 0.00 0.00 2.57 F
2131 2185 1.100510 TACTATGCCGAGCAACGACT 58.899 50.000 2.68 0.00 43.62 4.18 F
2872 2939 1.140852 TGTGGCAGTGGCATATACCTC 59.859 52.381 23.48 8.41 43.71 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2172 2226 1.488390 ATCCGAATTTTGGCTGGCAT 58.512 45.000 4.22 0.0 0.0 4.40 R
3006 3073 0.104855 TGAAGAGTGCAGCGTGAAGT 59.895 50.000 0.00 0.0 0.0 3.01 R
4040 6264 1.964223 TCTGTCCAGCTCGTCTTCTTT 59.036 47.619 0.00 0.0 0.0 2.52 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
25 26 5.766670 AGCTGTTCTTCATCAATCTGAACAA 59.233 36.000 0.00 0.00 43.85 2.83
324 326 6.071221 TGCTTCAGATTAAGTCATGGCAAAAT 60.071 34.615 0.00 0.00 0.00 1.82
599 603 2.746277 GGACATCGCCGCCAACTT 60.746 61.111 0.00 0.00 0.00 2.66
781 786 8.143193 ACATTTTGAAACATCTGTTCAATGCTA 58.857 29.630 0.81 0.00 37.25 3.49
812 817 9.897744 GAAATTCAAGTCAGATGTCATTAAACA 57.102 29.630 0.00 0.00 0.00 2.83
853 858 0.107456 CGGCTGCCATCTGTTCCTAT 59.893 55.000 20.29 0.00 0.00 2.57
875 880 3.735591 AGGTACAAATGTTACGCACAGT 58.264 40.909 0.00 0.00 39.40 3.55
1316 1330 3.499918 CCATCTGCGCCTATTTTAAGAGG 59.500 47.826 4.18 0.00 40.37 3.69
1361 1375 6.016360 CCACAAGATTTCTCAAACCACATACA 60.016 38.462 0.00 0.00 0.00 2.29
2131 2185 1.100510 TACTATGCCGAGCAACGACT 58.899 50.000 2.68 0.00 43.62 4.18
2172 2226 1.408340 TCGGAACTACAAACGACACCA 59.592 47.619 0.00 0.00 0.00 4.17
2474 2531 7.639113 ACAACAACTATCAGGAAAAGAACAA 57.361 32.000 0.00 0.00 0.00 2.83
2684 2743 3.186909 GTTTCTTGTGTTTTGCAGACCC 58.813 45.455 0.00 0.00 0.00 4.46
2695 2754 3.806949 TTGCAGACCCCAGTTTTATCT 57.193 42.857 0.00 0.00 0.00 1.98
2872 2939 1.140852 TGTGGCAGTGGCATATACCTC 59.859 52.381 23.48 8.41 43.71 3.85
3111 3178 1.072331 GTGATATCACGGGCATCCCTT 59.928 52.381 19.63 0.00 42.67 3.95
3312 3380 3.065371 CACTCGCAGTTGAAAAAGGTCTT 59.935 43.478 0.00 0.00 0.00 3.01
3337 3405 7.655521 ATCATCATCAACATCAACCTTGAAT 57.344 32.000 0.00 0.00 41.13 2.57
3610 3680 7.050377 TGCATTTTGTTTTACTGGATGGAAAA 58.950 30.769 0.00 0.00 0.00 2.29
4153 6377 2.507407 ACAGTTTGGTGTGGACAAGT 57.493 45.000 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 5.599656 AGCCATTACCTATTTGCATGAACAT 59.400 36.000 0.00 0.0 0.00 2.71
341 343 3.567397 ACTCTATCCATGAGGTAAGCGT 58.433 45.455 0.00 0.0 35.98 5.07
781 786 9.471702 AATGACATCTGACTTGAATTTCCTTAT 57.528 29.630 0.00 0.0 0.00 1.73
853 858 4.687018 CACTGTGCGTAACATTTGTACCTA 59.313 41.667 0.00 0.0 38.39 3.08
875 880 4.202461 ACCAACTTAATGACAGAGGCTTCA 60.202 41.667 0.00 0.0 0.00 3.02
907 915 4.141733 ACAACTGTTAGCTTGGGCAAAAAT 60.142 37.500 0.00 0.0 41.70 1.82
1033 1041 7.601508 TGTGATATCAATCATCTTCTTCATCGG 59.398 37.037 7.07 0.0 43.87 4.18
1187 1201 1.269051 CGTTTTGTTCAGCCTTGACCC 60.269 52.381 0.00 0.0 31.71 4.46
1316 1330 9.620660 CTTGTGGACCAATTTTATTGTAAGTAC 57.379 33.333 0.00 0.0 31.20 2.73
1728 1744 3.037549 TGGGAGAAACCTTGTTGCAAAT 58.962 40.909 0.00 0.0 38.98 2.32
1960 2012 2.722201 GGGTCGTCCAGCCGAAGAT 61.722 63.158 0.04 0.0 38.80 2.40
2131 2185 5.509670 CCGAATGTAACATATCCAGAGCTCA 60.510 44.000 17.77 0.0 0.00 4.26
2172 2226 1.488390 ATCCGAATTTTGGCTGGCAT 58.512 45.000 4.22 0.0 0.00 4.40
2474 2531 4.020751 ACAGCACACATCTCATGACTAAGT 60.021 41.667 0.00 0.0 0.00 2.24
2684 2743 5.063204 TGGATCGGCATTAGATAAAACTGG 58.937 41.667 0.00 0.0 0.00 4.00
2695 2754 3.411446 GATGGTCAATGGATCGGCATTA 58.589 45.455 0.00 0.0 0.00 1.90
3006 3073 0.104855 TGAAGAGTGCAGCGTGAAGT 59.895 50.000 0.00 0.0 0.00 3.01
3111 3178 2.613595 GCACATATTGAAGCGATGGACA 59.386 45.455 0.00 0.0 0.00 4.02
3161 3228 3.979101 TGTGTCAGCAGGTTATGATCA 57.021 42.857 0.00 0.0 0.00 2.92
3312 3380 8.756486 ATTCAAGGTTGATGTTGATGATGATA 57.244 30.769 0.00 0.0 37.00 2.15
3610 3680 5.474876 CCAGCCTTCAAGAAGATAGTGTTTT 59.525 40.000 11.25 0.0 40.79 2.43
4040 6264 1.964223 TCTGTCCAGCTCGTCTTCTTT 59.036 47.619 0.00 0.0 0.00 2.52


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

AutoCloner maintained by Alex Coulton.