Multiple sequence alignment - TraesCS5A01G109700

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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 TraesCS5A01G109700 chr5A 100.000 3309 0 0 1 3309 204996528 204999836 0.000000e+00 6111.0
1 TraesCS5A01G109700 chr5A 94.231 52 2 1 21 71 679753327 679753276 9.840000e-11 78.7
2 TraesCS5A01G109700 chr7A 97.596 2662 46 6 656 3309 723922254 723924905 0.000000e+00 4545.0
3 TraesCS5A01G109700 chr7A 90.465 860 55 10 1021 1876 27314213 27313377 0.000000e+00 1109.0
4 TraesCS5A01G109700 chr7A 95.090 387 14 3 2924 3309 27313397 27313015 3.650000e-169 604.0
5 TraesCS5A01G109700 chr7A 90.691 333 25 3 659 987 27315028 27314698 3.920000e-119 438.0
6 TraesCS5A01G109700 chr7A 93.750 48 2 1 15 62 560588186 560588232 1.650000e-08 71.3
7 TraesCS5A01G109700 chrUn 84.335 1564 160 39 790 2334 206982772 206984269 0.000000e+00 1452.0
8 TraesCS5A01G109700 chrUn 96.043 657 20 3 1 657 67782769 67783419 0.000000e+00 1064.0
9 TraesCS5A01G109700 chrUn 87.500 264 25 6 2951 3212 206985171 206985428 6.940000e-77 298.0
10 TraesCS5A01G109700 chrUn 87.008 254 26 4 2331 2579 206984327 206984578 2.510000e-71 279.0
11 TraesCS5A01G109700 chrUn 87.692 130 15 1 663 792 206982408 206982536 2.060000e-32 150.0
12 TraesCS5A01G109700 chr5B 93.514 663 22 10 1 659 174866994 174867639 0.000000e+00 966.0
13 TraesCS5A01G109700 chr5B 89.474 57 3 3 11 67 615614774 615614721 5.930000e-08 69.4
14 TraesCS5A01G109700 chr6B 93.220 236 14 2 660 895 15707824 15707591 2.440000e-91 346.0
15 TraesCS5A01G109700 chr6B 92.742 124 6 1 3186 3309 15707585 15707465 3.390000e-40 176.0
16 TraesCS5A01G109700 chr6D 87.008 254 26 4 2331 2579 443961640 443961891 2.510000e-71 279.0
17 TraesCS5A01G109700 chr6D 95.745 47 1 1 16 61 249956876 249956922 1.270000e-09 75.0
18 TraesCS5A01G109700 chr1D 96.078 102 3 1 1021 1122 62568760 62568860 7.350000e-37 165.0
19 TraesCS5A01G109700 chr1D 89.431 123 12 1 819 941 62568507 62568628 1.590000e-33 154.0
20 TraesCS5A01G109700 chr5D 95.745 47 2 0 21 67 408541214 408541260 3.540000e-10 76.8
21 TraesCS5A01G109700 chr5D 93.750 48 3 0 20 67 6347814 6347767 4.580000e-09 73.1
22 TraesCS5A01G109700 chr2A 95.745 47 2 0 21 67 771527337 771527291 3.540000e-10 76.8
23 TraesCS5A01G109700 chr2D 91.837 49 4 0 13 61 465862887 465862935 5.930000e-08 69.4
24 TraesCS5A01G109700 chr3D 79.518 83 16 1 674 756 116009067 116008986 1.280000e-04 58.4
25 TraesCS5A01G109700 chr3A 96.875 32 1 0 671 702 112298832 112298863 2.000000e-03 54.7


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 TraesCS5A01G109700 chr5A 204996528 204999836 3308 False 6111.00 6111 100.00000 1 3309 1 chr5A.!!$F1 3308
1 TraesCS5A01G109700 chr7A 723922254 723924905 2651 False 4545.00 4545 97.59600 656 3309 1 chr7A.!!$F2 2653
2 TraesCS5A01G109700 chr7A 27313015 27315028 2013 True 717.00 1109 92.08200 659 3309 3 chr7A.!!$R1 2650
3 TraesCS5A01G109700 chrUn 67782769 67783419 650 False 1064.00 1064 96.04300 1 657 1 chrUn.!!$F1 656
4 TraesCS5A01G109700 chrUn 206982408 206985428 3020 False 544.75 1452 86.63375 663 3212 4 chrUn.!!$F2 2549
5 TraesCS5A01G109700 chr5B 174866994 174867639 645 False 966.00 966 93.51400 1 659 1 chr5B.!!$F1 658

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
495 497 1.063867 GCCTGGGAGTAGAGTAGGTGA 60.064 57.143 0.0 0.0 0.00 4.02 F
920 1165 1.140589 CGATGGTCGAAGCTGAGCT 59.859 57.895 0.0 0.0 43.74 4.09 F
2105 2841 2.342650 GGCCGGTCGTGTAGGTGTA 61.343 63.158 1.9 0.0 0.00 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1827 2562 0.668096 GTCATACGCGTCACCCAACA 60.668 55.000 18.63 0.0 0.00 3.33 R
2179 2917 2.290367 TGTCAATGACAAAGAGCGGTTG 59.710 45.455 14.37 0.0 39.78 3.77 R
3279 4422 2.175202 ACCAACAAGCCTGTTCAAACA 58.825 42.857 0.00 0.0 44.15 2.83 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
47 48 8.013667 ACTTCCTCTGTCCCATAATATAAGAGT 58.986 37.037 0.00 0.00 0.00 3.24
71 72 9.640963 AGTATTTTTGACACTAGTGTAGATCAC 57.359 33.333 27.98 18.08 45.05 3.06
205 206 3.708563 ACACAGTGCAACACAAATACC 57.291 42.857 0.00 0.00 41.43 2.73
404 406 8.850454 TGTGCACTTATTCTTTTAGTTGAAAC 57.150 30.769 19.41 0.00 0.00 2.78
420 422 1.564348 GAAACCCATAGAGGAAGCCCA 59.436 52.381 0.00 0.00 41.22 5.36
495 497 1.063867 GCCTGGGAGTAGAGTAGGTGA 60.064 57.143 0.00 0.00 0.00 4.02
496 498 2.425102 GCCTGGGAGTAGAGTAGGTGAT 60.425 54.545 0.00 0.00 0.00 3.06
521 523 3.270027 CCTCCAAACGACTCATGCATTA 58.730 45.455 0.00 0.00 0.00 1.90
599 604 6.965866 TGCTTGGGGACATTAGTAGGATATAT 59.034 38.462 0.00 0.00 42.32 0.86
600 605 8.126385 TGCTTGGGGACATTAGTAGGATATATA 58.874 37.037 0.00 0.00 42.32 0.86
703 708 2.867251 GCTCAGCTGCACCTGATATCTC 60.867 54.545 12.07 0.00 40.77 2.75
733 738 4.779475 GTGCATAGGGATGGACGG 57.221 61.111 0.00 0.00 43.43 4.79
920 1165 1.140589 CGATGGTCGAAGCTGAGCT 59.859 57.895 0.00 0.00 43.74 4.09
1700 2435 3.181434 TGGGTAATTCAGGTTGTGCTTCT 60.181 43.478 0.00 0.00 0.00 2.85
1794 2529 4.202010 TGCAGAAGAACCTACAAAAAGTGC 60.202 41.667 0.00 0.00 0.00 4.40
1827 2562 6.265422 CCAGATCTTGGGTTGAGTTTTTACTT 59.735 38.462 0.00 0.00 43.75 2.24
2105 2841 2.342650 GGCCGGTCGTGTAGGTGTA 61.343 63.158 1.90 0.00 0.00 2.90
2179 2917 3.495670 ACTGAGTACAGCGAGAATCAC 57.504 47.619 0.00 0.00 46.95 3.06
2180 2918 2.820197 ACTGAGTACAGCGAGAATCACA 59.180 45.455 0.00 0.00 46.95 3.58
2337 3136 3.463944 GGAAGTTTCTTCAGGTCGTGAA 58.536 45.455 7.68 7.68 43.26 3.18
2889 4022 6.308566 AGAGTCTAGGGCCATAAACTAGTAG 58.691 44.000 2.79 0.00 36.47 2.57
2890 4023 6.028258 AGTCTAGGGCCATAAACTAGTAGT 57.972 41.667 0.46 0.00 36.47 2.73
2891 4024 6.069994 AGTCTAGGGCCATAAACTAGTAGTC 58.930 44.000 0.46 0.00 36.47 2.59
2892 4025 6.069994 GTCTAGGGCCATAAACTAGTAGTCT 58.930 44.000 6.18 0.00 36.47 3.24
2893 4026 7.073470 AGTCTAGGGCCATAAACTAGTAGTCTA 59.927 40.741 0.46 0.00 36.47 2.59
2894 4027 7.391275 GTCTAGGGCCATAAACTAGTAGTCTAG 59.609 44.444 6.18 7.52 46.43 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
71 72 4.782156 CTGCTGTATCTATGTCTCTCGTG 58.218 47.826 0.00 0.00 0.00 4.35
72 73 3.252215 GCTGCTGTATCTATGTCTCTCGT 59.748 47.826 0.00 0.00 0.00 4.18
388 390 8.390921 TCCTCTATGGGTTTCAACTAAAAGAAT 58.609 33.333 0.00 0.00 36.20 2.40
404 406 0.918983 TGTTGGGCTTCCTCTATGGG 59.081 55.000 0.00 0.00 36.20 4.00
420 422 8.852135 TCTCTGTTTCCGGTAAAATTTATTGTT 58.148 29.630 0.00 0.00 0.00 2.83
495 497 3.470709 CATGAGTCGTTTGGAGGCATAT 58.529 45.455 0.00 0.00 0.00 1.78
496 498 2.905075 CATGAGTCGTTTGGAGGCATA 58.095 47.619 0.00 0.00 0.00 3.14
521 523 4.677832 GCGTGAACCGATAAACACAAAAAT 59.322 37.500 0.00 0.00 39.56 1.82
546 548 3.001330 CCATTCGTTCGCTCCTTGAATAC 59.999 47.826 0.00 0.00 0.00 1.89
733 738 0.594028 TGACGCGTCTGACACACTTC 60.594 55.000 36.27 9.92 0.00 3.01
920 1165 1.532604 CCCACGCAGTAGACAGGACA 61.533 60.000 0.00 0.00 41.61 4.02
1143 1872 2.047655 GGACGACGGCAATCCACA 60.048 61.111 1.63 0.00 32.35 4.17
1794 2529 1.271379 ACCCAAGATCTGGTTTCACCG 60.271 52.381 0.00 0.00 44.76 4.94
1827 2562 0.668096 GTCATACGCGTCACCCAACA 60.668 55.000 18.63 0.00 0.00 3.33
2105 2841 2.497273 GCCTAATCAACACAGGGCATTT 59.503 45.455 0.00 0.00 39.38 2.32
2161 2897 3.575630 GTTGTGATTCTCGCTGTACTCA 58.424 45.455 0.00 0.00 0.00 3.41
2179 2917 2.290367 TGTCAATGACAAAGAGCGGTTG 59.710 45.455 14.37 0.00 39.78 3.77
2180 2918 2.571212 TGTCAATGACAAAGAGCGGTT 58.429 42.857 14.37 0.00 39.78 4.44
3279 4422 2.175202 ACCAACAAGCCTGTTCAAACA 58.825 42.857 0.00 0.00 44.15 2.83


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

AutoCloner maintained by Alex Coulton.