Multiple sequence alignment - TraesCS2A01G576000

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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 TraesCS2A01G576000 chr2A 100.000 2444 0 0 1 2444 770254753 770257196 0.000000e+00 4514
1 TraesCS2A01G576000 chr2B 89.436 1808 110 36 5 1804 790647326 790645592 0.000000e+00 2206
2 TraesCS2A01G576000 chr2B 89.039 1478 97 32 5 1474 790657845 790656425 0.000000e+00 1772
3 TraesCS2A01G576000 chr2B 89.129 1389 94 26 99 1474 790668270 790666926 0.000000e+00 1676
4 TraesCS2A01G576000 chr2B 91.632 478 28 1 1906 2371 790653804 790653327 0.000000e+00 651
5 TraesCS2A01G576000 chr2B 91.423 478 29 4 1906 2371 790664305 790663828 0.000000e+00 645
6 TraesCS2A01G576000 chr2B 95.430 372 17 0 1906 2277 790645476 790645105 5.820000e-166 593
7 TraesCS2A01G576000 chr2B 82.759 551 83 3 1906 2444 796084004 796083454 4.730000e-132 481
8 TraesCS2A01G576000 chr2B 83.696 460 22 15 1470 1905 790664765 790664335 3.810000e-103 385
9 TraesCS2A01G576000 chr2B 83.660 459 22 15 1471 1905 790654263 790653834 1.370000e-102 383
10 TraesCS2A01G576000 chr2B 92.857 168 12 0 2277 2444 790644930 790644763 6.750000e-61 244
11 TraesCS2A01G576000 chr2D 93.581 1480 67 18 435 1905 644896580 644898040 0.000000e+00 2182
12 TraesCS2A01G576000 chr2D 97.959 539 11 0 1906 2444 644898070 644898608 0.000000e+00 935
13 TraesCS2A01G576000 chr6A 83.303 551 80 3 1906 2444 6430725 6431275 4.690000e-137 497
14 TraesCS2A01G576000 chr5D 76.174 298 68 3 1962 2258 55959334 55959039 1.170000e-33 154
15 TraesCS2A01G576000 chr5A 74.257 303 72 6 1952 2251 378279844 378280143 3.300000e-24 122
16 TraesCS2A01G576000 chr3B 73.030 330 80 9 1925 2250 773846752 773847076 9.240000e-20 108


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 TraesCS2A01G576000 chr2A 770254753 770257196 2443 False 4514.000000 4514 100.000000 1 2444 1 chr2A.!!$F1 2443
1 TraesCS2A01G576000 chr2B 790644763 790647326 2563 True 1014.333333 2206 92.574333 5 2444 3 chr2B.!!$R2 2439
2 TraesCS2A01G576000 chr2B 790653327 790657845 4518 True 935.333333 1772 88.110333 5 2371 3 chr2B.!!$R3 2366
3 TraesCS2A01G576000 chr2B 790663828 790668270 4442 True 902.000000 1676 88.082667 99 2371 3 chr2B.!!$R4 2272
4 TraesCS2A01G576000 chr2B 796083454 796084004 550 True 481.000000 481 82.759000 1906 2444 1 chr2B.!!$R1 538
5 TraesCS2A01G576000 chr2D 644896580 644898608 2028 False 1558.500000 2182 95.770000 435 2444 2 chr2D.!!$F1 2009
6 TraesCS2A01G576000 chr6A 6430725 6431275 550 False 497.000000 497 83.303000 1906 2444 1 chr6A.!!$F1 538

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
310 311 0.17691 TATTGGATTCGCAGCGACCA 59.823 50.0 19.37 19.94 34.89 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1735 6124 0.391793 CGAGAGGAGGAAAACCCAGC 60.392 60.0 0.0 0.0 37.41 4.85 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
82 83 9.706846 CAAATTTTTGGTGAAAAGCTAAGAAAG 57.293 29.630 0.00 0.00 40.35 2.62
87 88 4.821805 TGGTGAAAAGCTAAGAAAGACTGG 59.178 41.667 0.00 0.00 0.00 4.00
108 109 7.153315 ACTGGTGAAAACCGAAAAGTTAAAAA 58.847 30.769 0.00 0.00 0.00 1.94
148 149 7.074507 TCTAAAAAGTAGAAAACGTGTGCAA 57.925 32.000 0.00 0.00 0.00 4.08
180 181 1.852157 AATCCAGAGGAAGCGCCCAA 61.852 55.000 2.29 0.00 34.34 4.12
185 186 1.078143 GAGGAAGCGCCCAAGATGT 60.078 57.895 2.29 0.00 37.37 3.06
194 195 2.562912 CCAAGATGTGGCACGTGC 59.437 61.111 32.15 32.15 41.72 5.34
260 261 1.169577 AGTGATCGTTGCGAGACTCT 58.830 50.000 0.03 0.00 39.91 3.24
266 267 1.607148 TCGTTGCGAGACTCTTGAAGA 59.393 47.619 0.03 0.00 0.00 2.87
285 286 5.526111 TGAAGAAGCGCTTGTTAACTAGTTT 59.474 36.000 29.83 7.28 36.83 2.66
288 289 5.758784 AGAAGCGCTTGTTAACTAGTTTCTT 59.241 36.000 30.47 15.49 0.00 2.52
295 296 8.169268 CGCTTGTTAACTAGTTTCTTCCTATTG 58.831 37.037 14.49 0.00 0.00 1.90
310 311 0.176910 TATTGGATTCGCAGCGACCA 59.823 50.000 19.37 19.94 34.89 4.02
322 323 2.393764 CAGCGACCACCATTGTTTTTC 58.606 47.619 0.00 0.00 0.00 2.29
325 326 3.132111 AGCGACCACCATTGTTTTTCTTT 59.868 39.130 0.00 0.00 0.00 2.52
326 327 3.868661 GCGACCACCATTGTTTTTCTTTT 59.131 39.130 0.00 0.00 0.00 2.27
327 328 4.331443 GCGACCACCATTGTTTTTCTTTTT 59.669 37.500 0.00 0.00 0.00 1.94
375 376 1.709760 CGCCTGCAACGTCACATAG 59.290 57.895 0.00 0.00 0.00 2.23
376 377 0.735978 CGCCTGCAACGTCACATAGA 60.736 55.000 0.00 0.00 0.00 1.98
386 387 3.620488 ACGTCACATAGAATTTGCCCAT 58.380 40.909 0.00 0.00 0.00 4.00
431 432 1.839994 CCTGGGCCATTTCTAGTCTGA 59.160 52.381 6.72 0.00 0.00 3.27
600 601 6.292381 CGAAAATCAAAGGATCTAGCGGTTAG 60.292 42.308 0.00 0.00 31.88 2.34
814 816 6.581712 TCTGGCAATAATCCTTAATTTTGGC 58.418 36.000 0.00 0.00 39.09 4.52
815 817 6.155910 TCTGGCAATAATCCTTAATTTTGGCA 59.844 34.615 10.04 10.04 42.05 4.92
816 818 6.897986 TGGCAATAATCCTTAATTTTGGCAT 58.102 32.000 7.23 0.00 40.96 4.40
817 819 6.766944 TGGCAATAATCCTTAATTTTGGCATG 59.233 34.615 7.23 0.00 40.96 4.06
881 908 1.235724 GTGTGTTGTCCTGCCTAACC 58.764 55.000 0.00 0.00 0.00 2.85
899 926 5.238432 CCTAACCGATTAATTAGTGCATGCA 59.762 40.000 18.46 18.46 0.00 3.96
900 927 5.772825 AACCGATTAATTAGTGCATGCAT 57.227 34.783 25.64 15.04 0.00 3.96
901 928 5.112220 ACCGATTAATTAGTGCATGCATG 57.888 39.130 25.64 22.70 0.00 4.06
924 951 9.605955 CATGCTGAAGTATATATATCTACGCTC 57.394 37.037 0.00 5.17 0.00 5.03
925 952 8.732746 TGCTGAAGTATATATATCTACGCTCA 57.267 34.615 0.00 11.86 0.00 4.26
926 953 9.343539 TGCTGAAGTATATATATCTACGCTCAT 57.656 33.333 0.00 0.00 0.00 2.90
945 976 6.615088 GCTCATAATTTGCCATACATACAGG 58.385 40.000 0.00 0.00 0.00 4.00
971 1002 2.507944 CTGCCAAGCCCTAGCGAT 59.492 61.111 0.00 0.00 46.67 4.58
981 1017 4.623932 AGCCCTAGCGATTGATTTGATA 57.376 40.909 0.00 0.00 46.67 2.15
982 1018 4.319177 AGCCCTAGCGATTGATTTGATAC 58.681 43.478 0.00 0.00 46.67 2.24
1031 1067 2.708051 ACTCGTTCACCTCGATCTACA 58.292 47.619 0.00 0.00 36.73 2.74
1032 1068 3.079578 ACTCGTTCACCTCGATCTACAA 58.920 45.455 0.00 0.00 36.73 2.41
1033 1069 3.695060 ACTCGTTCACCTCGATCTACAAT 59.305 43.478 0.00 0.00 36.73 2.71
1037 1075 4.499865 CGTTCACCTCGATCTACAATCCAT 60.500 45.833 0.00 0.00 0.00 3.41
1051 1097 1.139498 ATCCATGACCACCACCACCA 61.139 55.000 0.00 0.00 0.00 4.17
1068 1114 3.009026 CACCATCACCAATTCGATGACA 58.991 45.455 9.56 0.00 41.28 3.58
1092 1138 1.372683 GACCAGCCAGCAGAGACAA 59.627 57.895 0.00 0.00 0.00 3.18
1157 1203 4.178214 CGCCGCCGTTGATTGCAT 62.178 61.111 0.00 0.00 0.00 3.96
1194 1240 3.276091 CACACGCCGTTCAAGCCA 61.276 61.111 0.00 0.00 0.00 4.75
1206 1252 1.750399 CAAGCCAATCCCGGACCTG 60.750 63.158 0.73 0.00 0.00 4.00
1446 1492 3.367910 GGCTCGACTCTTTCAACTGATCT 60.368 47.826 0.00 0.00 0.00 2.75
1548 5924 8.723311 TCGATTTCCAGTTTTGAATTTATACGT 58.277 29.630 0.00 0.00 0.00 3.57
1611 5987 7.259882 CAAGTATGCATGCTTTCTTTTGGATA 58.740 34.615 25.19 1.01 30.06 2.59
1644 6021 6.966632 TGCTTGTTTTCATATCACGAAATAGC 59.033 34.615 0.00 0.00 35.01 2.97
1678 6055 2.158928 ACCCGTACAAGCACACACTAAA 60.159 45.455 0.00 0.00 0.00 1.85
1736 6125 4.261801 TGGAGTTGCCATAGAAAACTAGC 58.738 43.478 0.00 0.00 43.33 3.42
1737 6126 4.019321 TGGAGTTGCCATAGAAAACTAGCT 60.019 41.667 0.00 0.00 43.33 3.32
1738 6127 4.333926 GGAGTTGCCATAGAAAACTAGCTG 59.666 45.833 0.00 0.00 34.37 4.24
1739 6128 4.265073 AGTTGCCATAGAAAACTAGCTGG 58.735 43.478 0.00 0.00 32.48 4.85
1740 6129 3.281727 TGCCATAGAAAACTAGCTGGG 57.718 47.619 0.85 0.00 0.00 4.45
1741 6130 2.576191 TGCCATAGAAAACTAGCTGGGT 59.424 45.455 0.85 0.00 0.00 4.51
1742 6131 3.010138 TGCCATAGAAAACTAGCTGGGTT 59.990 43.478 0.85 0.00 0.00 4.11
1816 6229 0.474184 CCCCAGGTGATCCGCTAATT 59.526 55.000 0.00 0.00 39.05 1.40
1830 6243 1.801178 GCTAATTAGTCTGGATGGCGC 59.199 52.381 13.91 0.00 0.00 6.53
1894 6307 3.706373 ATCTGCCGCCAAGTCCGT 61.706 61.111 0.00 0.00 0.00 4.69
2121 6563 1.311059 GTGCTTGGGGGATTGGGAT 59.689 57.895 0.00 0.00 0.00 3.85
2355 6972 7.407393 AGACTATGTAAGAGTCAGGGTTAAC 57.593 40.000 4.98 0.00 44.86 2.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 4.857588 TGCGTCAAAATACACGTTTTTGTT 59.142 33.333 18.51 0.00 42.16 2.83
21 22 4.413087 TGCGTCAAAATACACGTTTTTGT 58.587 34.783 18.51 3.21 42.16 2.83
22 23 5.362987 TTGCGTCAAAATACACGTTTTTG 57.637 34.783 14.83 14.83 42.63 2.44
38 39 4.866682 TTTGGAAAACCAATTTTGCGTC 57.133 36.364 0.00 0.00 46.15 5.19
59 60 8.478066 AGTCTTTCTTAGCTTTTCACCAAAAAT 58.522 29.630 0.00 0.00 36.30 1.82
61 62 7.257722 CAGTCTTTCTTAGCTTTTCACCAAAA 58.742 34.615 0.00 0.00 0.00 2.44
63 64 5.299279 CCAGTCTTTCTTAGCTTTTCACCAA 59.701 40.000 0.00 0.00 0.00 3.67
64 65 4.821805 CCAGTCTTTCTTAGCTTTTCACCA 59.178 41.667 0.00 0.00 0.00 4.17
65 66 4.822350 ACCAGTCTTTCTTAGCTTTTCACC 59.178 41.667 0.00 0.00 0.00 4.02
66 67 5.527582 TCACCAGTCTTTCTTAGCTTTTCAC 59.472 40.000 0.00 0.00 0.00 3.18
67 68 5.680619 TCACCAGTCTTTCTTAGCTTTTCA 58.319 37.500 0.00 0.00 0.00 2.69
82 83 4.365899 AACTTTTCGGTTTTCACCAGTC 57.634 40.909 0.00 0.00 44.53 3.51
120 121 8.277713 GCACACGTTTTCTACTTTTTAGATGTA 58.722 33.333 0.00 0.00 0.00 2.29
133 134 8.462143 TTTTATTTGTTTGCACACGTTTTCTA 57.538 26.923 0.00 0.00 30.32 2.10
160 161 1.077429 GGGCGCTTCCTCTGGATTT 60.077 57.895 7.64 0.00 34.39 2.17
194 195 4.504916 CGTCCTCTCAGCTGCCGG 62.505 72.222 9.47 9.09 0.00 6.13
208 209 2.658707 GAGCGTGCCACTTGACGTC 61.659 63.158 9.11 9.11 37.89 4.34
260 261 5.054477 ACTAGTTAACAAGCGCTTCTTCAA 58.946 37.500 22.21 9.21 31.27 2.69
266 267 5.049612 GGAAGAAACTAGTTAACAAGCGCTT 60.050 40.000 18.98 18.98 0.00 4.68
295 296 3.195698 GGTGGTCGCTGCGAATCC 61.196 66.667 27.68 23.74 37.72 3.01
331 332 8.670135 GCCCGTTATTGTGTATATTAATATGCA 58.330 33.333 18.83 18.83 33.83 3.96
332 333 7.849026 CGCCCGTTATTGTGTATATTAATATGC 59.151 37.037 16.72 15.63 0.00 3.14
333 334 7.849026 GCGCCCGTTATTGTGTATATTAATATG 59.151 37.037 16.72 0.00 0.00 1.78
334 335 7.011669 GGCGCCCGTTATTGTGTATATTAATAT 59.988 37.037 18.11 12.51 0.00 1.28
349 350 3.131478 GTTGCAGGCGCCCGTTAT 61.131 61.111 26.15 0.00 37.32 1.89
371 372 6.299141 AGTACTACCATGGGCAAATTCTATG 58.701 40.000 18.09 0.00 0.00 2.23
375 376 5.914898 AAAGTACTACCATGGGCAAATTC 57.085 39.130 18.09 0.24 0.00 2.17
376 377 6.680148 AAAAAGTACTACCATGGGCAAATT 57.320 33.333 18.09 1.07 0.00 1.82
408 409 2.649816 AGACTAGAAATGGCCCAGGTTT 59.350 45.455 0.00 0.00 0.00 3.27
431 432 8.088365 GTCAATTTTGTAGCCTCCTTGTAAAAT 58.912 33.333 0.00 0.00 0.00 1.82
580 581 3.996480 GCTAACCGCTAGATCCTTTGAT 58.004 45.455 0.00 0.00 35.14 2.57
600 601 0.733150 GGCGTGGATTAGTTTCCAGC 59.267 55.000 0.00 0.78 46.31 4.85
705 707 2.487934 CACTAATCAATCCTGAGGCGG 58.512 52.381 0.00 0.00 34.23 6.13
814 816 5.220739 GCATGAGTAGTTTCCTAACTGCATG 60.221 44.000 16.86 16.86 45.92 4.06
815 817 4.878397 GCATGAGTAGTTTCCTAACTGCAT 59.122 41.667 0.00 3.97 45.92 3.96
816 818 4.253685 GCATGAGTAGTTTCCTAACTGCA 58.746 43.478 0.00 0.00 45.92 4.41
817 819 4.253685 TGCATGAGTAGTTTCCTAACTGC 58.746 43.478 0.00 0.00 44.22 4.40
859 861 0.107831 TAGGCAGGACAACACACACC 59.892 55.000 0.00 0.00 0.00 4.16
860 862 1.602377 GTTAGGCAGGACAACACACAC 59.398 52.381 0.00 0.00 0.00 3.82
861 863 1.476110 GGTTAGGCAGGACAACACACA 60.476 52.381 0.00 0.00 0.00 3.72
899 926 9.343539 TGAGCGTAGATATATATACTTCAGCAT 57.656 33.333 14.02 2.92 0.00 3.79
900 927 8.732746 TGAGCGTAGATATATATACTTCAGCA 57.267 34.615 14.02 6.89 0.00 4.41
920 947 6.239908 TGTATGTATGGCAAATTATGAGCG 57.760 37.500 0.00 0.00 0.00 5.03
954 985 1.153086 AATCGCTAGGGCTTGGCAG 60.153 57.895 5.70 0.00 36.09 4.85
1031 1067 0.039618 GGTGGTGGTGGTCATGGATT 59.960 55.000 0.00 0.00 0.00 3.01
1032 1068 1.139498 TGGTGGTGGTGGTCATGGAT 61.139 55.000 0.00 0.00 0.00 3.41
1033 1069 1.139498 ATGGTGGTGGTGGTCATGGA 61.139 55.000 0.00 0.00 0.00 3.41
1037 1075 1.454104 GTGATGGTGGTGGTGGTCA 59.546 57.895 0.00 0.00 0.00 4.02
1051 1097 3.370978 GTCGTTGTCATCGAATTGGTGAT 59.629 43.478 7.55 0.00 39.01 3.06
1068 1114 3.865929 CTGCTGGCTGGTCGTCGTT 62.866 63.158 0.00 0.00 0.00 3.85
1092 1138 4.790962 CTGCAGGTCGCCATGGCT 62.791 66.667 33.07 13.08 41.33 4.75
1157 1203 2.535485 ATCCTGATCAAACGCCGCCA 62.535 55.000 0.00 0.00 0.00 5.69
1446 1492 5.123344 CGATCGGTACATATGTCACTGGATA 59.877 44.000 12.68 0.29 0.00 2.59
1548 5924 7.701539 AATGCCTGTGATGTAGAAACAAATA 57.298 32.000 0.00 0.00 39.58 1.40
1611 5987 9.935682 CGTGATATGAAAACAAGCATATACTTT 57.064 29.630 0.00 0.00 37.71 2.66
1644 6021 5.006358 GCTTGTACGGGTTCAATACTATGTG 59.994 44.000 0.00 0.00 0.00 3.21
1732 6121 2.169561 GAGAGGAGGAAAACCCAGCTAG 59.830 54.545 0.00 0.00 37.41 3.42
1733 6122 2.188817 GAGAGGAGGAAAACCCAGCTA 58.811 52.381 0.00 0.00 37.41 3.32
1734 6123 0.988063 GAGAGGAGGAAAACCCAGCT 59.012 55.000 0.00 0.00 37.41 4.24
1735 6124 0.391793 CGAGAGGAGGAAAACCCAGC 60.392 60.000 0.00 0.00 37.41 4.85
1736 6125 3.842869 CGAGAGGAGGAAAACCCAG 57.157 57.895 0.00 0.00 37.41 4.45
1816 6229 3.161450 GGGGCGCCATCCAGACTA 61.161 66.667 30.85 0.00 0.00 2.59
1877 6290 3.254024 AACGGACTTGGCGGCAGAT 62.254 57.895 12.87 3.94 0.00 2.90
1894 6307 2.646175 CGAACTCCGCCCTCCAGAA 61.646 63.158 0.00 0.00 0.00 3.02
2085 6527 2.778679 GATGCCTGCACGACGAAC 59.221 61.111 0.00 0.00 0.00 3.95
2100 6542 1.076777 CCAATCCCCCAAGCACGAT 60.077 57.895 0.00 0.00 0.00 3.73
2121 6563 2.035449 CGGTCCCTGTAGCATAATTCGA 59.965 50.000 0.00 0.00 0.00 3.71
2227 6669 2.931969 GCTTATGGATTTGCAGCCAAAC 59.068 45.455 8.78 0.00 43.20 2.93
2355 6972 1.133575 AGGGGCATTCTGATGTCATGG 60.134 52.381 0.00 0.00 39.68 3.66


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

AutoCloner maintained by Alex Coulton.