Multiple sequence alignment - TraesCS4D01G223400

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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 TraesCS4D01G223400 chr4D 100.000 2729 0 0 1 2729 380294336 380297064 0.000000 5040.0
1 TraesCS4D01G223400 chr4D 93.095 811 39 14 1934 2729 145940342 145939534 0.000000 1171.0
2 TraesCS4D01G223400 chr4A 93.832 1978 52 24 1 1933 83573130 83571178 0.000000 2913.0
3 TraesCS4D01G223400 chr4B 93.834 1946 67 22 1 1927 467716886 467718797 0.000000 2880.0
4 TraesCS4D01G223400 chr2D 93.276 818 38 13 1927 2728 398508844 398509660 0.000000 1190.0
5 TraesCS4D01G223400 chr2D 92.743 813 38 17 1932 2729 367590310 367589504 0.000000 1155.0
6 TraesCS4D01G223400 chr2D 92.402 816 46 10 1929 2729 604068494 604069308 0.000000 1149.0
7 TraesCS4D01G223400 chr6D 93.252 815 38 13 1932 2729 58444215 58443401 0.000000 1184.0
8 TraesCS4D01G223400 chr1D 93.112 813 34 14 1931 2728 387956370 387955565 0.000000 1171.0
9 TraesCS4D01G223400 chr1D 100.000 34 0 0 1204 1237 439511293 439511326 0.000002 63.9
10 TraesCS4D01G223400 chr1D 100.000 34 0 0 1204 1237 439557432 439557465 0.000002 63.9
11 TraesCS4D01G223400 chr1D 100.000 33 0 0 1205 1237 440049337 440049305 0.000008 62.1
12 TraesCS4D01G223400 chr7D 92.883 815 40 14 1932 2729 97945137 97944324 0.000000 1168.0
13 TraesCS4D01G223400 chr5B 92.866 813 40 14 1933 2729 448102975 448102165 0.000000 1164.0
14 TraesCS4D01G223400 chr3D 92.752 814 43 12 1932 2729 608917425 608916612 0.000000 1162.0
15 TraesCS4D01G223400 chr1B 100.000 34 0 0 1204 1237 596316608 596316641 0.000002 63.9
16 TraesCS4D01G223400 chr1B 100.000 34 0 0 1204 1237 597558140 597558107 0.000002 63.9
17 TraesCS4D01G223400 chr1A 100.000 34 0 0 1204 1237 537821370 537821403 0.000002 63.9


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 TraesCS4D01G223400 chr4D 380294336 380297064 2728 False 5040 5040 100.000 1 2729 1 chr4D.!!$F1 2728
1 TraesCS4D01G223400 chr4D 145939534 145940342 808 True 1171 1171 93.095 1934 2729 1 chr4D.!!$R1 795
2 TraesCS4D01G223400 chr4A 83571178 83573130 1952 True 2913 2913 93.832 1 1933 1 chr4A.!!$R1 1932
3 TraesCS4D01G223400 chr4B 467716886 467718797 1911 False 2880 2880 93.834 1 1927 1 chr4B.!!$F1 1926
4 TraesCS4D01G223400 chr2D 398508844 398509660 816 False 1190 1190 93.276 1927 2728 1 chr2D.!!$F1 801
5 TraesCS4D01G223400 chr2D 367589504 367590310 806 True 1155 1155 92.743 1932 2729 1 chr2D.!!$R1 797
6 TraesCS4D01G223400 chr2D 604068494 604069308 814 False 1149 1149 92.402 1929 2729 1 chr2D.!!$F2 800
7 TraesCS4D01G223400 chr6D 58443401 58444215 814 True 1184 1184 93.252 1932 2729 1 chr6D.!!$R1 797
8 TraesCS4D01G223400 chr1D 387955565 387956370 805 True 1171 1171 93.112 1931 2728 1 chr1D.!!$R1 797
9 TraesCS4D01G223400 chr7D 97944324 97945137 813 True 1168 1168 92.883 1932 2729 1 chr7D.!!$R1 797
10 TraesCS4D01G223400 chr5B 448102165 448102975 810 True 1164 1164 92.866 1933 2729 1 chr5B.!!$R1 796
11 TraesCS4D01G223400 chr3D 608916612 608917425 813 True 1162 1162 92.752 1932 2729 1 chr3D.!!$R1 797

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
892 915 1.821216 AGCCATTGTTACTTCCGGTG 58.179 50.0 0.0 0.0 0.0 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2377 2456 0.984995 ACGGAAAGGGAAGGGAAGAG 59.015 55.0 0.0 0.0 0.0 2.85 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
79 84 4.400961 GGCAGCAGGAGCCGTTCT 62.401 66.667 0.00 0.00 43.15 3.01
277 284 3.525619 TCGCCTGCGACTGTAATTT 57.474 47.368 10.61 0.00 44.01 1.82
298 305 8.457238 AATTTGTACTGCTTCTTTCTCTTCTT 57.543 30.769 0.00 0.00 0.00 2.52
331 341 2.167487 ACCGAAGCAGATTCTCTTCTCC 59.833 50.000 16.72 1.65 37.22 3.71
332 342 2.430332 CCGAAGCAGATTCTCTTCTCCT 59.570 50.000 16.72 0.00 37.22 3.69
333 343 3.490761 CCGAAGCAGATTCTCTTCTCCTC 60.491 52.174 16.72 1.16 37.22 3.71
763 786 7.064609 CGAATGGCTAACATCTTGTTTCTCTAA 59.935 37.037 0.00 0.00 41.45 2.10
820 843 5.595885 TCTTTGACATCTTGATCGATCTCC 58.404 41.667 25.02 1.09 0.00 3.71
855 878 4.783450 GCATCATCTACGCTTTGCAAGTAC 60.783 45.833 0.00 0.00 0.00 2.73
887 910 6.403878 TGAACTAGGTAGCCATTGTTACTTC 58.596 40.000 0.00 0.00 0.00 3.01
891 914 2.355412 GGTAGCCATTGTTACTTCCGGT 60.355 50.000 0.00 0.00 0.00 5.28
892 915 1.821216 AGCCATTGTTACTTCCGGTG 58.179 50.000 0.00 0.00 0.00 4.94
918 941 6.433716 TGGTGCACAGATCATTCATTTCTAAA 59.566 34.615 20.43 0.00 0.00 1.85
920 943 7.977853 GGTGCACAGATCATTCATTTCTAAATT 59.022 33.333 20.43 0.00 0.00 1.82
921 944 9.017669 GTGCACAGATCATTCATTTCTAAATTC 57.982 33.333 13.17 0.00 0.00 2.17
1359 1386 2.815647 GAGGAGAACAAGCGCCGG 60.816 66.667 2.29 0.00 32.50 6.13
1670 1697 2.666098 GCGAGGAAGGGCAAGGGTA 61.666 63.158 0.00 0.00 0.00 3.69
1698 1725 2.353958 CATGGTGGCTCAGCTGGT 59.646 61.111 15.13 0.00 32.61 4.00
1757 1784 2.404789 GCTGTATGCGCGCATTGT 59.595 55.556 46.64 29.72 37.82 2.71
1865 1922 7.962441 ACAACAAGCAGTTATTTATCCCTTTT 58.038 30.769 0.00 0.00 38.74 2.27
1867 1924 6.935167 ACAAGCAGTTATTTATCCCTTTTGG 58.065 36.000 0.00 0.00 39.97 3.28
1903 1969 2.955614 ACTACCGTGAGTTTGAATCCG 58.044 47.619 0.00 0.00 0.00 4.18
1964 2030 1.267121 TGGAGCAGTTGGTAGTCTCC 58.733 55.000 0.00 0.00 42.67 3.71
2027 2099 3.322466 CTCCCCCACCTTCGCTGT 61.322 66.667 0.00 0.00 0.00 4.40
2104 2181 2.940410 GTCACCCTCTCAACAACGAAAA 59.060 45.455 0.00 0.00 0.00 2.29
2332 2411 7.038154 TCTCCAAACAAAGGAAACAATACAG 57.962 36.000 0.00 0.00 34.08 2.74
2337 2416 3.058224 ACAAAGGAAACAATACAGCGAGC 60.058 43.478 0.00 0.00 0.00 5.03
2377 2456 7.880195 ACTCCCTTTCTTATGACATGTATATGC 59.120 37.037 0.00 0.00 37.85 3.14
2440 2519 3.434319 CGATGCTTGGGCTGCGTT 61.434 61.111 0.00 0.00 39.59 4.84
2479 2558 1.824329 GAGGACGAGGATGGCGAGA 60.824 63.158 0.00 0.00 0.00 4.04
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
79 84 2.231380 GGGGAGGGAAGGTGAGCAA 61.231 63.158 0.00 0.00 0.00 3.91
85 90 1.641192 GATTTCAAGGGGAGGGAAGGT 59.359 52.381 0.00 0.00 0.00 3.50
277 284 5.511545 GGGAAGAAGAGAAAGAAGCAGTACA 60.512 44.000 0.00 0.00 0.00 2.90
298 305 0.035439 GCTTCGGTTTCATCCAGGGA 60.035 55.000 0.00 0.00 0.00 4.20
331 341 3.911964 CCAAAAGCCAAAACGATAACGAG 59.088 43.478 0.00 0.00 42.66 4.18
332 342 3.854045 GCCAAAAGCCAAAACGATAACGA 60.854 43.478 0.00 0.00 38.09 3.85
333 343 2.407026 GCCAAAAGCCAAAACGATAACG 59.593 45.455 0.00 0.00 39.71 3.18
541 551 6.016860 TGTGAACAATCTCTCACAAAATGGAG 60.017 38.462 2.54 0.00 46.74 3.86
763 786 6.968263 CCATCAGATCGAGGGTATATACAT 57.032 41.667 14.70 2.54 40.88 2.29
820 843 0.588233 GATGATGCGACGCTTGCAAG 60.588 55.000 22.44 22.44 46.87 4.01
855 878 9.561069 ACAATGGCTACCTAGTTCAAAATATAG 57.439 33.333 0.00 0.00 0.00 1.31
891 914 2.565046 TGAATGATCTGTGCACCACA 57.435 45.000 15.69 9.41 42.45 4.17
892 915 4.157289 AGAAATGAATGATCTGTGCACCAC 59.843 41.667 15.69 3.63 34.56 4.16
918 941 7.876068 TCAAGATGGTTCTTTACGTGTTAGAAT 59.124 33.333 0.00 0.00 40.28 2.40
920 943 6.751157 TCAAGATGGTTCTTTACGTGTTAGA 58.249 36.000 0.00 0.00 40.28 2.10
921 944 7.596749 ATCAAGATGGTTCTTTACGTGTTAG 57.403 36.000 0.00 0.00 40.28 2.34
925 948 7.584987 AGAAAATCAAGATGGTTCTTTACGTG 58.415 34.615 0.00 0.00 40.28 4.49
926 949 7.094762 GGAGAAAATCAAGATGGTTCTTTACGT 60.095 37.037 0.00 0.00 40.28 3.57
927 950 7.094805 TGGAGAAAATCAAGATGGTTCTTTACG 60.095 37.037 9.39 0.00 40.28 3.18
928 951 8.110860 TGGAGAAAATCAAGATGGTTCTTTAC 57.889 34.615 9.39 5.89 40.28 2.01
929 952 8.742777 CATGGAGAAAATCAAGATGGTTCTTTA 58.257 33.333 9.39 4.69 40.28 1.85
930 953 7.609056 CATGGAGAAAATCAAGATGGTTCTTT 58.391 34.615 9.39 0.00 40.28 2.52
931 954 6.350780 GCATGGAGAAAATCAAGATGGTTCTT 60.351 38.462 9.39 0.00 43.09 2.52
932 955 5.126707 GCATGGAGAAAATCAAGATGGTTCT 59.873 40.000 8.29 8.29 32.11 3.01
996 1023 1.926511 GCTGGTGGTTCTCCATTGCG 61.927 60.000 0.00 0.00 46.20 4.85
1757 1784 5.929992 GCCGTGGTAAATAGCATTGAGTATA 59.070 40.000 0.00 0.00 35.99 1.47
1873 1932 4.803098 ACTCACGGTAGTTATCTGCTTT 57.197 40.909 0.00 0.00 0.00 3.51
1889 1948 1.133025 CATGCCCGGATTCAAACTCAC 59.867 52.381 0.73 0.00 0.00 3.51
1938 2004 6.303839 AGACTACCAACTGCTCCATTAAAAA 58.696 36.000 0.00 0.00 0.00 1.94
2006 2073 2.070650 GCGAAGGTGGGGGAGGTAT 61.071 63.158 0.00 0.00 0.00 2.73
2258 2337 5.883661 AGGTTAATGTGATTGAGCGATTTG 58.116 37.500 0.00 0.00 32.35 2.32
2332 2411 2.603560 AGTTTATTTACTGCTCGCTCGC 59.396 45.455 0.00 0.00 0.00 5.03
2337 2416 5.875359 AGAAAGGGAGTTTATTTACTGCTCG 59.125 40.000 0.00 0.00 36.78 5.03
2377 2456 0.984995 ACGGAAAGGGAAGGGAAGAG 59.015 55.000 0.00 0.00 0.00 2.85
2440 2519 3.740397 CACCGTCGCGACCCAGTA 61.740 66.667 31.84 0.00 0.00 2.74
2628 2707 4.660938 GGGCCCGCTTCCAAGTGT 62.661 66.667 5.69 0.00 34.79 3.55


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

AutoCloner maintained by Alex Coulton.