Multiple sequence alignment - TraesCS2A01G501500

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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 TraesCS2A01G501500 chr2A 100.000 2839 0 0 458 3296 729778472 729775634 0.000000e+00 5243.0
1 TraesCS2A01G501500 chr2A 100.000 301 0 0 1 301 729778929 729778629 1.030000e-154 556.0
2 TraesCS2A01G501500 chr2D 96.291 2858 75 9 458 3296 596125528 596122683 0.000000e+00 4662.0
3 TraesCS2A01G501500 chr2D 96.057 279 6 5 27 301 596125798 596125521 1.800000e-122 449.0
4 TraesCS2A01G501500 chr2B 96.714 2739 79 4 558 3296 724554423 724551696 0.000000e+00 4549.0
5 TraesCS2A01G501500 chr2B 86.147 231 5 5 15 218 724554954 724554724 1.190000e-54 224.0
6 TraesCS2A01G501500 chr3A 82.367 431 54 14 1872 2298 501487287 501487699 4.050000e-94 355.0
7 TraesCS2A01G501500 chr7B 89.474 209 20 2 2281 2488 361656455 361656662 2.520000e-66 263.0
8 TraesCS2A01G501500 chr7B 85.841 113 16 0 1792 1904 598301599 598301487 1.610000e-23 121.0
9 TraesCS2A01G501500 chr6D 95.238 42 2 0 1900 1941 221565580 221565621 2.120000e-07 67.6


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 TraesCS2A01G501500 chr2A 729775634 729778929 3295 True 2899.5 5243 100.0000 1 3296 2 chr2A.!!$R1 3295
1 TraesCS2A01G501500 chr2D 596122683 596125798 3115 True 2555.5 4662 96.1740 27 3296 2 chr2D.!!$R1 3269
2 TraesCS2A01G501500 chr2B 724551696 724554954 3258 True 2386.5 4549 91.4305 15 3296 2 chr2B.!!$R1 3281

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
950 998 0.674895 ATTCGTGGCTTCTGTGCTCC 60.675 55.0 0.0 0.0 0.0 4.7 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2813 2861 0.322816 CCCCTGAACAGACACATGGG 60.323 60.0 0.0 0.0 36.11 4.0 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
805 853 2.481471 GGCGGCTGGTAGGCAATTC 61.481 63.158 0.00 0.00 41.44 2.17
950 998 0.674895 ATTCGTGGCTTCTGTGCTCC 60.675 55.000 0.00 0.00 0.00 4.70
1029 1077 0.976073 TTAGAGGGGAGGCTTGGTCG 60.976 60.000 0.00 0.00 0.00 4.79
1385 1433 3.001406 ACCGTCGGGGAAGAAGGG 61.001 66.667 17.28 0.00 42.79 3.95
1419 1467 6.620678 TGCTGGATTGCTTAATTCTTGTAAC 58.379 36.000 0.00 0.00 0.00 2.50
1614 1662 6.166984 AGTTCACTTGAGTTGAAGAGATCA 57.833 37.500 0.00 0.00 35.85 2.92
1615 1663 6.767456 AGTTCACTTGAGTTGAAGAGATCAT 58.233 36.000 0.00 0.00 38.03 2.45
1711 1759 3.174375 GCGCTTAGGCAAAGAAGAATTG 58.826 45.455 0.00 0.00 37.38 2.32
1744 1792 3.777465 CAGGTCATTCTGCTCAAATGG 57.223 47.619 6.48 0.00 35.32 3.16
1827 1875 1.838077 AGGAAATTACTACCGCCAGCT 59.162 47.619 0.00 0.00 0.00 4.24
2381 2429 6.785488 TGTACATTCAAGCTGAAGTAACAG 57.215 37.500 0.00 0.00 40.05 3.16
2448 2496 4.461781 CAGAATTCTGCTCCCAGATTTGTT 59.538 41.667 21.96 0.00 46.84 2.83
2528 2576 1.561076 TCTGTTCATGCTGCATAGGGT 59.439 47.619 15.78 0.00 0.00 4.34
2529 2577 2.025981 TCTGTTCATGCTGCATAGGGTT 60.026 45.455 15.78 0.00 0.00 4.11
2813 2861 0.034896 TCTCTTTTCACCCTCGGCAC 59.965 55.000 0.00 0.00 0.00 5.01
2832 2880 0.322816 CCCATGTGTCTGTTCAGGGG 60.323 60.000 0.66 0.66 46.56 4.79
2855 2903 1.331756 GCTGGTGTGTTGTCTCAAGTG 59.668 52.381 0.00 0.00 0.00 3.16
2866 2914 4.782019 TGTCTCAAGTGCTTGTGTTTTT 57.218 36.364 11.17 0.00 41.16 1.94
2870 2918 5.739161 GTCTCAAGTGCTTGTGTTTTTACTG 59.261 40.000 11.17 0.00 41.16 2.74
2876 2924 6.113411 AGTGCTTGTGTTTTTACTGTAGAGT 58.887 36.000 0.00 0.00 36.07 3.24
2877 2925 6.258068 AGTGCTTGTGTTTTTACTGTAGAGTC 59.742 38.462 0.00 0.00 33.21 3.36
2878 2926 5.526111 TGCTTGTGTTTTTACTGTAGAGTCC 59.474 40.000 0.00 0.00 33.21 3.85
2916 2964 9.730705 AATGGTAGATGTATCCATAATTGAGTG 57.269 33.333 5.00 0.00 40.52 3.51
3090 3139 4.594062 TGTAGGGACTTTGCTAGTTTACCA 59.406 41.667 0.00 0.00 41.75 3.25
3127 3176 1.090052 GCTGACGGTACCTGAATGGC 61.090 60.000 10.90 3.22 40.22 4.40
3245 3294 1.356624 GTGCACTTGTGTGGTCTGC 59.643 57.895 10.32 0.00 43.97 4.26
3246 3295 2.179547 TGCACTTGTGTGGTCTGCG 61.180 57.895 2.61 0.00 43.97 5.18
3261 3310 1.205485 CTGCGTCAGTGAGCTATCGC 61.205 60.000 15.78 15.78 42.11 4.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 3.935872 CGTGGGTGTGTGTGTGCG 61.936 66.667 0.00 0.00 0.00 5.34
13 14 4.250431 GCGTGGGTGTGTGTGTGC 62.250 66.667 0.00 0.00 0.00 4.57
14 15 2.821810 TGCGTGGGTGTGTGTGTG 60.822 61.111 0.00 0.00 0.00 3.82
15 16 2.822255 GTGCGTGGGTGTGTGTGT 60.822 61.111 0.00 0.00 0.00 3.72
16 17 3.935872 CGTGCGTGGGTGTGTGTG 61.936 66.667 0.00 0.00 0.00 3.82
37 38 1.019805 GGCCCTTCTTGTAGTCGTGC 61.020 60.000 0.00 0.00 0.00 5.34
84 90 3.006728 CCAGCGGGTGGGGACTAA 61.007 66.667 18.37 0.00 43.63 2.24
975 1023 3.400054 CCACCCCTCCCTCGGAAC 61.400 72.222 0.00 0.00 0.00 3.62
1029 1077 1.153208 CTGCTGAGGTGGAGCCATC 60.153 63.158 0.00 0.00 40.61 3.51
1403 1451 4.289238 TCCCCGTTACAAGAATTAAGCA 57.711 40.909 0.00 0.00 0.00 3.91
1419 1467 3.042733 TAACAGCCTGGCATCCCCG 62.043 63.158 22.65 4.17 35.87 5.73
1581 1629 1.463056 TCAAGTGAACTTAATGCGCCG 59.537 47.619 4.18 0.00 34.28 6.46
1614 1662 6.477688 CAGCTTCACATTGTTGAAAAGACAAT 59.522 34.615 0.00 0.00 45.80 2.71
1615 1663 5.806502 CAGCTTCACATTGTTGAAAAGACAA 59.193 36.000 0.00 0.00 40.86 3.18
1711 1759 2.435586 ACCTGCAGCATCGCTCAC 60.436 61.111 8.66 0.00 36.40 3.51
1744 1792 1.493311 CTCGCACAGGACTTTTCGC 59.507 57.895 0.00 0.00 0.00 4.70
1827 1875 3.266772 AGTGATCTTCCCCTGCATTAACA 59.733 43.478 0.00 0.00 0.00 2.41
2289 2337 1.638133 CAAGCTCCATCTGTCAGTCG 58.362 55.000 0.00 0.00 0.00 4.18
2381 2429 5.895928 TCTTCTATGATGTGACTGCAGTAC 58.104 41.667 21.73 17.71 0.00 2.73
2481 2529 4.023291 GACTTCCTTTATTGGGGCATCAA 58.977 43.478 0.00 0.00 0.00 2.57
2528 2576 1.153449 CCGCGGGAGTGCTAATGAA 60.153 57.895 20.10 0.00 39.52 2.57
2529 2577 2.355986 ACCGCGGGAGTGCTAATGA 61.356 57.895 31.76 0.00 39.52 2.57
2803 2851 4.033776 CACATGGGTGCCGAGGGT 62.034 66.667 0.00 0.00 38.37 4.34
2813 2861 0.322816 CCCCTGAACAGACACATGGG 60.323 60.000 0.00 0.00 36.11 4.00
2832 2880 2.591715 AGACAACACACCAGCCGC 60.592 61.111 0.00 0.00 0.00 6.53
2855 2903 5.758784 AGGACTCTACAGTAAAAACACAAGC 59.241 40.000 0.00 0.00 30.63 4.01
2870 2918 5.423886 CATTTCCTTTCTGGAGGACTCTAC 58.576 45.833 0.00 0.00 45.30 2.59
2916 2964 1.792949 GAACCGCGATCATGATACACC 59.207 52.381 8.23 0.00 0.00 4.16
3030 3079 6.320418 GGAACTGGAATTGTACCGGATATTTT 59.680 38.462 9.46 0.00 37.25 1.82
3035 3084 2.574369 TGGAACTGGAATTGTACCGGAT 59.426 45.455 9.46 0.00 37.25 4.18
3090 3139 4.504097 GTCAGCGTTGCTTCTTCAAAATTT 59.496 37.500 0.00 0.00 36.40 1.82
3127 3176 3.270027 TCTATCAACACAGGAAATGCGG 58.730 45.455 0.00 0.00 0.00 5.69
3261 3310 6.857964 GGATATGAAACGATTGTAAATGGCAG 59.142 38.462 0.00 0.00 0.00 4.85


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

AutoCloner maintained by Alex Coulton.