Multiple sequence alignment - TraesCS5A01G079500

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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 TraesCS5A01G079500 chr5A 100.000 5140 0 0 1 5140 98977691 98982830 0.000000e+00 9492.0
1 TraesCS5A01G079500 chr5A 84.161 322 36 6 3290 3597 324967038 324967358 1.080000e-76 298.0
2 TraesCS5A01G079500 chr5A 78.868 265 44 6 950 1213 98453605 98453352 8.850000e-38 169.0
3 TraesCS5A01G079500 chr5D 97.525 5010 101 11 1 4998 101461582 101456584 0.000000e+00 8543.0
4 TraesCS5A01G079500 chr5D 84.699 549 58 12 3063 3597 35871877 35871341 4.560000e-145 525.0
5 TraesCS5A01G079500 chr5D 78.868 265 46 6 950 1213 101698395 101698650 2.460000e-38 171.0
6 TraesCS5A01G079500 chr5D 95.122 41 2 0 5098 5138 101456417 101456377 1.190000e-06 65.8
7 TraesCS5A01G079500 chr5B 96.745 4086 85 9 1 4085 109889998 109885960 0.000000e+00 6765.0
8 TraesCS5A01G079500 chr5B 85.103 678 28 15 4358 4999 109885602 109884962 4.370000e-175 625.0
9 TraesCS5A01G079500 chr5B 92.623 244 8 3 4084 4318 109885836 109885594 4.930000e-90 342.0
10 TraesCS5A01G079500 chr5B 82.803 314 40 6 3068 3380 311042350 311042050 8.480000e-68 268.0
11 TraesCS5A01G079500 chr5B 78.491 265 45 8 950 1213 110113544 110113797 4.120000e-36 163.0


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 TraesCS5A01G079500 chr5A 98977691 98982830 5139 False 9492.000000 9492 100.000000 1 5140 1 chr5A.!!$F1 5139
1 TraesCS5A01G079500 chr5D 101456377 101461582 5205 True 4304.400000 8543 96.323500 1 5138 2 chr5D.!!$R2 5137
2 TraesCS5A01G079500 chr5D 35871341 35871877 536 True 525.000000 525 84.699000 3063 3597 1 chr5D.!!$R1 534
3 TraesCS5A01G079500 chr5B 109884962 109889998 5036 True 2577.333333 6765 91.490333 1 4999 3 chr5B.!!$R2 4998

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
39 40 0.959867 GGGCGCCCAATTGCATTTTT 60.960 50.000 40.73 0.0 35.81 1.94 F
908 910 1.288633 TCTAACCCCTGACCACGGATA 59.711 52.381 0.00 0.0 0.00 2.59 F
1394 1396 3.474600 GACATGGTCTCTGCTATGCAAT 58.525 45.455 0.00 0.0 38.41 3.56 F
2777 2780 1.039856 ATGGCTTGTTTGGTCACACC 58.960 50.000 0.00 0.0 39.22 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1152 1154 4.623932 ACCATTCTGTTGTAGCTCAAGA 57.376 40.909 0.0 0.0 36.66 3.02 R
1769 1771 4.644234 TCATTCCTTGTTTTCAGTTCAGCA 59.356 37.500 0.0 0.0 0.00 4.41 R
3330 3333 0.804989 GTCCTGTCCGCCTTTTGATG 59.195 55.000 0.0 0.0 0.00 3.07 R
4160 4325 1.780309 ACCTCCATGTTCTTCCACCAA 59.220 47.619 0.0 0.0 0.00 3.67 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
39 40 0.959867 GGGCGCCCAATTGCATTTTT 60.960 50.000 40.73 0.00 35.81 1.94
148 149 8.792633 AGAAATCGACATGATGTTTTCCTTTTA 58.207 29.630 14.33 0.00 37.39 1.52
154 155 7.095229 CGACATGATGTTTTCCTTTTACTCTGA 60.095 37.037 0.00 0.00 0.00 3.27
223 224 2.438021 TGGTGTCTCCAGTTAGCACTTT 59.562 45.455 0.00 0.00 41.93 2.66
537 539 9.651913 TTTAATTCTCAGAACATTTATTTGGGC 57.348 29.630 0.00 0.00 0.00 5.36
693 695 8.877864 AAATGACACCTTGGATAATACTTCAA 57.122 30.769 0.00 0.00 0.00 2.69
839 841 8.193438 AGAAAGTGCCATCTCATTAAATTTAGC 58.807 33.333 0.00 0.00 0.00 3.09
908 910 1.288633 TCTAACCCCTGACCACGGATA 59.711 52.381 0.00 0.00 0.00 2.59
1152 1154 4.344679 TGTGTCATGGAGGAAAAAGCAAAT 59.655 37.500 0.00 0.00 0.00 2.32
1156 1158 5.636543 GTCATGGAGGAAAAAGCAAATCTTG 59.363 40.000 0.00 0.00 34.67 3.02
1356 1358 7.228706 ACAGTACTCCCATCTGTTTGTTAAAAG 59.771 37.037 0.00 0.00 39.00 2.27
1394 1396 3.474600 GACATGGTCTCTGCTATGCAAT 58.525 45.455 0.00 0.00 38.41 3.56
1404 1406 7.137426 GTCTCTGCTATGCAATTTTTCTATGG 58.863 38.462 0.00 0.00 38.41 2.74
1769 1771 6.547141 TGATCACTGAAAAGGACAAACTGATT 59.453 34.615 0.00 0.00 0.00 2.57
1936 1938 5.565455 TTTCCTTGGAGCAATTGGAAATT 57.435 34.783 7.72 0.00 40.52 1.82
2109 2111 7.944729 ATGTGGATCTTTATTTGCAGTAGTT 57.055 32.000 0.00 0.00 0.00 2.24
2201 2203 8.548025 TCTTATTTGGAGTCATTGATCTTGGTA 58.452 33.333 0.00 0.00 0.00 3.25
2777 2780 1.039856 ATGGCTTGTTTGGTCACACC 58.960 50.000 0.00 0.00 39.22 4.16
2803 2806 9.919348 CATTTTAACTGTTCTGTTGAAAAATGG 57.081 29.630 18.58 7.97 39.34 3.16
2978 2981 4.024472 GCTTCGAAGAAAGCTTCTGAGTTT 60.024 41.667 28.95 0.00 46.64 2.66
3054 3057 3.009033 TGTCATGGAGAAAGGTAACCCTG 59.991 47.826 0.00 0.00 41.56 4.45
3085 3088 3.276857 TCTCTAAGGTACTACTGCACCG 58.723 50.000 0.00 0.00 38.49 4.94
3201 3204 5.674525 TGTGTGATTAGGAGATTGATGTCC 58.325 41.667 0.00 0.00 40.35 4.02
3330 3333 1.608590 CCATCATACCCGTGATTTGGC 59.391 52.381 0.00 0.00 36.72 4.52
3340 3343 1.994779 CGTGATTTGGCATCAAAAGGC 59.005 47.619 0.00 0.00 44.83 4.35
3467 3484 9.778741 TTCAAGTAAGAATCTTCTGCTTCTTAA 57.221 29.630 0.00 0.00 42.51 1.85
3775 3815 4.405116 TTGTGCTTCCAGAAATTTTGCT 57.595 36.364 0.00 0.00 0.00 3.91
3915 3955 4.529716 TTTGGTACCTCCTGTTTCCTTT 57.470 40.909 14.36 0.00 37.07 3.11
3956 3996 9.986833 TCACATTCTTCAATGAATATTTGTACG 57.013 29.630 0.00 0.00 41.97 3.67
3970 4010 9.429600 GAATATTTGTACGTGCACCTAAATTAC 57.570 33.333 12.15 4.15 0.00 1.89
4238 4403 9.095700 AGATCCTAGAAATTCTGGACCTTATAC 57.904 37.037 7.98 0.83 30.44 1.47
4290 4464 5.186409 ACCTAGCTGATGTTGCATGAAAAAT 59.814 36.000 0.00 0.00 0.00 1.82
4520 4696 2.679336 TGGCAGAACATTGTCATGATCG 59.321 45.455 0.00 0.00 37.30 3.69
4546 4748 7.970061 GGTGTGTTATGTGATCGTTTAGTACTA 59.030 37.037 0.00 0.00 0.00 1.82
4556 4758 8.338986 GTGATCGTTTAGTACTACCTAACTACC 58.661 40.741 0.91 0.00 0.00 3.18
4557 4759 8.267894 TGATCGTTTAGTACTACCTAACTACCT 58.732 37.037 0.91 0.00 0.00 3.08
4558 4760 7.849804 TCGTTTAGTACTACCTAACTACCTG 57.150 40.000 0.91 0.00 0.00 4.00
4595 4797 2.735857 CGCAAGCAGCCCTTTTGC 60.736 61.111 6.96 6.96 42.75 3.68
4634 4836 6.235231 TGTCCTCTTAGTTTCAGTGTTCTT 57.765 37.500 0.00 0.00 0.00 2.52
4787 4989 9.528018 TTTTAAATTGTCTCTTGCCTGTTTTAG 57.472 29.630 0.00 0.00 0.00 1.85
4872 5083 0.806884 AGTTTTTGACCGCGACGACA 60.807 50.000 8.23 0.00 0.00 4.35
4877 5088 3.456039 GACCGCGACGACAACGAC 61.456 66.667 8.23 0.00 42.66 4.34
4990 5201 7.908193 TCGCAAGTTTCAAAGATTAAAACTC 57.092 32.000 0.69 0.00 41.17 3.01
4991 5202 6.631238 TCGCAAGTTTCAAAGATTAAAACTCG 59.369 34.615 0.69 2.23 41.17 4.18
4992 5203 6.631238 CGCAAGTTTCAAAGATTAAAACTCGA 59.369 34.615 0.69 0.00 41.17 4.04
4993 5204 7.165154 CGCAAGTTTCAAAGATTAAAACTCGAA 59.835 33.333 0.69 0.00 41.17 3.71
4994 5205 8.803799 GCAAGTTTCAAAGATTAAAACTCGAAA 58.196 29.630 0.69 0.00 41.17 3.46
5000 5211 9.640974 TTCAAAGATTAAAACTCGAAACTTACG 57.359 29.630 0.00 0.00 0.00 3.18
5001 5212 9.033481 TCAAAGATTAAAACTCGAAACTTACGA 57.967 29.630 0.00 0.00 38.11 3.43
5002 5213 9.640974 CAAAGATTAAAACTCGAAACTTACGAA 57.359 29.630 0.00 0.00 39.23 3.85
5004 5215 9.859692 AAGATTAAAACTCGAAACTTACGAAAG 57.140 29.630 0.00 0.00 39.23 2.62
5005 5216 9.252962 AGATTAAAACTCGAAACTTACGAAAGA 57.747 29.630 0.00 0.00 39.23 2.52
5012 5223 9.642312 AACTCGAAACTTACGAAAGATTAAAAC 57.358 29.630 0.00 0.00 39.23 2.43
5013 5224 9.038803 ACTCGAAACTTACGAAAGATTAAAACT 57.961 29.630 0.00 0.00 39.23 2.66
5014 5225 9.859692 CTCGAAACTTACGAAAGATTAAAACTT 57.140 29.630 0.00 0.00 39.23 2.66
5015 5226 9.853921 TCGAAACTTACGAAAGATTAAAACTTC 57.146 29.630 0.00 0.00 36.84 3.01
5016 5227 9.640974 CGAAACTTACGAAAGATTAAAACTTCA 57.359 29.630 0.00 0.00 36.50 3.02
5024 5235 9.849166 ACGAAAGATTAAAACTTCAAACAAAGA 57.151 25.926 0.00 0.00 0.00 2.52
5078 5289 6.646267 ACTTGAAACTTACTGTGTCCTTGTA 58.354 36.000 0.00 0.00 31.90 2.41
5090 5301 4.532126 TGTGTCCTTGTATGAGATCCAACT 59.468 41.667 0.00 0.00 0.00 3.16
5094 5305 6.127338 TGTCCTTGTATGAGATCCAACTACTG 60.127 42.308 0.00 0.00 0.00 2.74
5103 5448 0.685097 TCCAACTACTGTGTGCTCCC 59.315 55.000 0.00 0.00 0.00 4.30
5104 5449 0.396435 CCAACTACTGTGTGCTCCCA 59.604 55.000 0.00 0.00 0.00 4.37
5138 5483 7.063780 GTGCCCATATGAATTTTTGAGAACTTG 59.936 37.037 3.65 0.00 0.00 3.16
5139 5484 6.536224 GCCCATATGAATTTTTGAGAACTTGG 59.464 38.462 3.65 0.00 0.00 3.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
148 149 5.421056 TCTGTCATTACCGGTTAATCAGAGT 59.579 40.000 15.04 0.00 31.03 3.24
154 155 6.938030 TGAAAACTCTGTCATTACCGGTTAAT 59.062 34.615 15.04 7.97 0.00 1.40
223 224 9.647797 AACTCGAATCTGTATTTGTGTTGTATA 57.352 29.630 5.45 0.00 39.79 1.47
240 241 8.396390 GGAACCTAGGAAAATAAAACTCGAATC 58.604 37.037 17.98 0.00 0.00 2.52
537 539 8.061857 ACATACTTGTAAATCGATAAATGTGCG 58.938 33.333 0.00 0.00 33.16 5.34
908 910 4.829872 TGTGGAAACCAGTAACCGATAT 57.170 40.909 0.00 0.00 32.34 1.63
1152 1154 4.623932 ACCATTCTGTTGTAGCTCAAGA 57.376 40.909 0.00 0.00 36.66 3.02
1156 1158 7.173390 AGAGTTTTTACCATTCTGTTGTAGCTC 59.827 37.037 0.00 0.00 0.00 4.09
1305 1307 9.330063 GTGTTTCTGATGATCCTATTATGTCAA 57.670 33.333 0.00 0.00 0.00 3.18
1356 1358 5.045215 CCATGTCCATGCACAAAACATATC 58.955 41.667 0.00 0.00 37.49 1.63
1394 1396 9.258826 CAAATTCATGTGACAACCATAGAAAAA 57.741 29.630 0.00 0.00 0.00 1.94
1449 1451 8.897752 AGACCAGTAAGAGAAAATGCATTTATC 58.102 33.333 24.35 22.57 39.11 1.75
1627 1629 7.967854 TGACAATAAAAGTTCAAGTGTGAAGTG 59.032 33.333 0.00 0.00 44.98 3.16
1769 1771 4.644234 TCATTCCTTGTTTTCAGTTCAGCA 59.356 37.500 0.00 0.00 0.00 4.41
1936 1938 4.871557 GCAAGGATTAGCAATCAAAATGCA 59.128 37.500 9.92 0.00 46.22 3.96
2050 2052 8.424133 TGCAGCTAATAAACTGAAGATCTGATA 58.576 33.333 0.00 0.00 35.90 2.15
2109 2111 6.811665 CCAATGAAATGTAACTACTCGACAGA 59.188 38.462 0.00 0.00 0.00 3.41
2222 2224 5.302360 ACACACGTACACAATAAAGTGGAT 58.698 37.500 0.00 0.00 43.72 3.41
2566 2568 5.399858 TCTGCTTATCGTCTTGTACACTTC 58.600 41.667 0.00 0.00 0.00 3.01
2681 2684 8.912988 TGAGTAACTTCAACAAGGATTTTCAAT 58.087 29.630 0.00 0.00 33.37 2.57
2682 2685 8.287439 TGAGTAACTTCAACAAGGATTTTCAA 57.713 30.769 0.00 0.00 33.37 2.69
2777 2780 9.919348 CCATTTTTCAACAGAACAGTTAAAATG 57.081 29.630 15.40 15.40 41.48 2.32
2803 2806 5.873179 TTTTCAATATTCCACCTCGTGTC 57.127 39.130 0.00 0.00 0.00 3.67
2978 2981 3.490761 GCTGCTTCTGCCAAAAGTTGTAA 60.491 43.478 0.00 0.00 38.71 2.41
3054 3057 7.662669 CAGTAGTACCTTAGAGATACCTTCCTC 59.337 44.444 0.00 0.00 0.00 3.71
3085 3088 5.119694 AGAACTTTGAGGTTCAGACAAGAC 58.880 41.667 8.43 0.00 45.52 3.01
3201 3204 2.095869 GCTTTAGCAGATCGGCATCATG 60.096 50.000 20.15 6.99 41.59 3.07
3330 3333 0.804989 GTCCTGTCCGCCTTTTGATG 59.195 55.000 0.00 0.00 0.00 3.07
3340 3343 2.262915 GAGTGGCTGTCCTGTCCG 59.737 66.667 0.00 0.00 0.00 4.79
3467 3484 8.055181 TCTAGCCAAATATCAAAGGACAATCTT 58.945 33.333 0.00 0.00 0.00 2.40
3527 3566 2.093306 TGGCGTTCCAATCAGTACTG 57.907 50.000 17.17 17.17 39.99 2.74
3834 3874 6.237901 TGTACAGAGCACATATGGTTCTTTT 58.762 36.000 7.80 2.11 36.44 2.27
3915 3955 9.936759 TGAAGAATGTGATTATGTGTACTGTAA 57.063 29.630 0.00 0.00 0.00 2.41
3956 3996 3.187637 TGCACGAAGTAATTTAGGTGCAC 59.812 43.478 19.40 8.80 46.08 4.57
3970 4010 3.002791 ACATTCATGGTACTGCACGAAG 58.997 45.455 0.00 0.00 0.00 3.79
4160 4325 1.780309 ACCTCCATGTTCTTCCACCAA 59.220 47.619 0.00 0.00 0.00 3.67
4264 4438 3.689347 TCATGCAACATCAGCTAGGTTT 58.311 40.909 0.00 0.00 27.18 3.27
4520 4696 6.810182 AGTACTAAACGATCACATAACACACC 59.190 38.462 0.00 0.00 0.00 4.16
4546 4748 6.768641 TTTTAAGGTTCCAGGTAGTTAGGT 57.231 37.500 0.00 0.00 0.00 3.08
4556 4758 7.981142 TGCGTTAATCTATTTTAAGGTTCCAG 58.019 34.615 0.00 0.00 32.32 3.86
4557 4759 7.925043 TGCGTTAATCTATTTTAAGGTTCCA 57.075 32.000 0.00 0.00 32.32 3.53
4558 4760 7.431376 GCTTGCGTTAATCTATTTTAAGGTTCC 59.569 37.037 0.00 0.00 32.32 3.62
4595 4797 4.058817 GAGGACAGCTAAAATACGATGGG 58.941 47.826 0.00 0.00 0.00 4.00
4634 4836 3.071206 GCTGCCGGAGAGTCCAGA 61.071 66.667 5.05 0.00 35.91 3.86
4787 4989 1.975660 TGGCCAGGTTAGACAAACAC 58.024 50.000 0.00 0.00 40.08 3.32
4872 5083 0.250793 TGGGCCATCATAACGTCGTT 59.749 50.000 15.97 15.97 0.00 3.85
4877 5088 3.130164 TGATTTTGTGGGCCATCATAACG 59.870 43.478 10.70 0.00 0.00 3.18
4933 5144 2.816087 GCTTGCTCATCCAGTTTCAGAA 59.184 45.455 0.00 0.00 0.00 3.02
4990 5201 9.640974 TGAAGTTTTAATCTTTCGTAAGTTTCG 57.359 29.630 1.51 0.00 39.48 3.46
4998 5209 9.849166 TCTTTGTTTGAAGTTTTAATCTTTCGT 57.151 25.926 0.00 0.00 0.00 3.85
5047 5258 9.447040 GGACACAGTAAGTTTCAAGTTTTAATC 57.553 33.333 0.00 0.00 0.00 1.75
5048 5259 9.185680 AGGACACAGTAAGTTTCAAGTTTTAAT 57.814 29.630 0.00 0.00 0.00 1.40
5049 5260 8.570068 AGGACACAGTAAGTTTCAAGTTTTAA 57.430 30.769 0.00 0.00 0.00 1.52
5050 5261 8.455682 CAAGGACACAGTAAGTTTCAAGTTTTA 58.544 33.333 0.00 0.00 0.00 1.52
5051 5262 7.039993 ACAAGGACACAGTAAGTTTCAAGTTTT 60.040 33.333 0.00 0.00 0.00 2.43
5052 5263 6.433093 ACAAGGACACAGTAAGTTTCAAGTTT 59.567 34.615 0.00 0.00 0.00 2.66
5053 5264 5.944007 ACAAGGACACAGTAAGTTTCAAGTT 59.056 36.000 0.00 0.00 0.00 2.66
5054 5265 5.497474 ACAAGGACACAGTAAGTTTCAAGT 58.503 37.500 0.00 0.00 0.00 3.16
5055 5266 7.441157 TCATACAAGGACACAGTAAGTTTCAAG 59.559 37.037 0.00 0.00 0.00 3.02
5056 5267 7.276658 TCATACAAGGACACAGTAAGTTTCAA 58.723 34.615 0.00 0.00 0.00 2.69
5078 5289 3.517100 AGCACACAGTAGTTGGATCTCAT 59.483 43.478 0.00 0.00 0.00 2.90
5103 5448 1.451927 ATATGGGCACGCAGGTGTG 60.452 57.895 8.55 8.55 46.13 3.82
5104 5449 1.451927 CATATGGGCACGCAGGTGT 60.452 57.895 0.00 0.00 46.13 4.16


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

AutoCloner maintained by Alex Coulton.