Multiple sequence alignment - TraesCS2A01G049100

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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 TraesCS2A01G049100 chr2A 100.000 3767 0 0 1 3767 19031629 19027863 0.000000e+00 6957
1 TraesCS2A01G049100 chr2D 96.903 3778 82 9 1 3767 17609399 17605646 0.000000e+00 6296
2 TraesCS2A01G049100 chr2D 97.692 3596 70 8 183 3767 17634990 17631397 0.000000e+00 6168
3 TraesCS2A01G049100 chr2D 97.872 141 3 0 1 141 17635138 17634998 1.050000e-60 244
4 TraesCS2A01G049100 chr2D 80.503 159 19 7 1328 1479 274856568 274856415 1.110000e-20 111
5 TraesCS2A01G049100 chr2D 82.540 126 14 5 1364 1482 234759883 234759759 1.850000e-18 104
6 TraesCS2A01G049100 chr2B 95.439 2960 103 13 185 3131 29552845 29555785 0.000000e+00 4689
7 TraesCS2A01G049100 chr2B 95.644 528 22 1 3240 3767 29555805 29556331 0.000000e+00 846
8 TraesCS2A01G049100 chr2B 78.121 713 102 37 2381 3080 29263993 29264664 1.630000e-108 403
9 TraesCS2A01G049100 chr2B 78.121 713 102 37 2381 3080 29319230 29319901 1.630000e-108 403
10 TraesCS2A01G049100 chr2B 77.980 713 104 34 2381 3080 29350348 29351020 7.580000e-107 398
11 TraesCS2A01G049100 chr2B 94.326 141 6 1 1 139 29552705 29552845 8.200000e-52 215
12 TraesCS2A01G049100 chr1D 79.605 304 53 8 1801 2099 110589309 110589010 3.810000e-50 209
13 TraesCS2A01G049100 chr7A 78.438 320 62 7 1784 2099 38518617 38518933 6.380000e-48 202
14 TraesCS2A01G049100 chr7A 77.707 314 65 5 1787 2097 38515928 38516239 1.790000e-43 187
15 TraesCS2A01G049100 chr1A 78.302 318 59 10 1787 2099 351866401 351866089 2.970000e-46 196
16 TraesCS2A01G049100 chr1A 77.019 322 68 6 1780 2099 6207600 6207283 2.990000e-41 180
17 TraesCS2A01G049100 chr6B 77.961 304 58 8 1801 2099 533280329 533280628 8.310000e-42 182
18 TraesCS2A01G049100 chr3D 83.125 160 17 5 1327 1479 609076898 609076742 1.820000e-28 137
19 TraesCS2A01G049100 chr6D 83.226 155 17 3 1328 1475 392273074 392273226 2.360000e-27 134
20 TraesCS2A01G049100 chr7B 81.169 154 21 2 1328 1475 78546813 78546964 2.380000e-22 117
21 TraesCS2A01G049100 chr5A 80.645 155 21 5 1328 1475 277726088 277725936 1.110000e-20 111


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 TraesCS2A01G049100 chr2A 19027863 19031629 3766 True 6957.000000 6957 100.000000 1 3767 1 chr2A.!!$R1 3766
1 TraesCS2A01G049100 chr2D 17605646 17609399 3753 True 6296.000000 6296 96.903000 1 3767 1 chr2D.!!$R1 3766
2 TraesCS2A01G049100 chr2D 17631397 17635138 3741 True 3206.000000 6168 97.782000 1 3767 2 chr2D.!!$R4 3766
3 TraesCS2A01G049100 chr2B 29552705 29556331 3626 False 1916.666667 4689 95.136333 1 3767 3 chr2B.!!$F4 3766
4 TraesCS2A01G049100 chr2B 29263993 29264664 671 False 403.000000 403 78.121000 2381 3080 1 chr2B.!!$F1 699
5 TraesCS2A01G049100 chr2B 29319230 29319901 671 False 403.000000 403 78.121000 2381 3080 1 chr2B.!!$F2 699
6 TraesCS2A01G049100 chr2B 29350348 29351020 672 False 398.000000 398 77.980000 2381 3080 1 chr2B.!!$F3 699

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
153 156 0.239613 TGCAACACACACACACACAC 59.760 50.0 0.0 0.0 0.0 3.82 F
160 163 0.871057 CACACACACACACACACACA 59.129 50.0 0.0 0.0 0.0 3.72 F
172 175 0.871057 CACACACACACACACACACA 59.129 50.0 0.0 0.0 0.0 3.72 F
174 177 0.871057 CACACACACACACACACACA 59.129 50.0 0.0 0.0 0.0 3.72 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1522 1532 2.766828 AGGTGCTAGTGGGAATACTGTC 59.233 50.0 0.00 0.0 32.19 3.51 R
1691 1704 5.876357 TCTAGGGCAGTAACAAGTGAAAAT 58.124 37.5 0.00 0.0 0.00 1.82 R
2378 2399 7.932120 ATGTACATGTAACGAAGCTAGAATC 57.068 36.0 7.78 0.0 0.00 2.52 R
3256 3285 1.398692 AATTTGTGGTTGGTCGTGCT 58.601 45.0 0.00 0.0 0.00 4.40 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
118 121 5.469084 ACTGAAAACGAGGGAGTAACATTTC 59.531 40.000 0.00 0.00 0.00 2.17
141 144 2.618241 TCTTTGTCACTGGATGCAACAC 59.382 45.455 0.00 0.00 0.00 3.32
143 146 1.308047 TGTCACTGGATGCAACACAC 58.692 50.000 0.00 0.00 0.00 3.82
145 148 1.002468 GTCACTGGATGCAACACACAC 60.002 52.381 0.00 0.00 0.00 3.82
147 150 1.024271 ACTGGATGCAACACACACAC 58.976 50.000 0.00 0.00 0.00 3.82
149 152 0.737804 TGGATGCAACACACACACAC 59.262 50.000 0.00 0.00 0.00 3.82
151 154 1.533756 GGATGCAACACACACACACAC 60.534 52.381 0.00 0.00 0.00 3.82
153 156 0.239613 TGCAACACACACACACACAC 59.760 50.000 0.00 0.00 0.00 3.82
155 158 1.962412 CAACACACACACACACACAC 58.038 50.000 0.00 0.00 0.00 3.82
157 160 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
159 162 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
160 163 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
161 164 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
162 165 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
163 166 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
164 167 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
165 168 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
166 169 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
167 170 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
168 171 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
169 172 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
170 173 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
171 174 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
172 175 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
173 176 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
174 177 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
175 178 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
176 179 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
177 180 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
178 181 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
179 182 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
180 183 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
181 184 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
219 222 5.523588 AGAGAGAGAGAGAGAGAGAGAGAA 58.476 45.833 0.00 0.00 0.00 2.87
256 259 6.710744 TCTTTTCAGAGATTGGTAGGTTGAAC 59.289 38.462 0.00 0.00 0.00 3.18
406 412 7.280876 GTGTACAATGGTGTGAACATCTATGAT 59.719 37.037 0.00 0.00 38.82 2.45
415 421 4.747108 GTGAACATCTATGATCAAGGACGG 59.253 45.833 0.00 0.52 40.52 4.79
432 438 4.652421 AGGACGGCATATTACAAGAACCTA 59.348 41.667 0.00 0.00 0.00 3.08
524 531 9.081997 TGAAAGCTGTTTAATACAACAACAAAG 57.918 29.630 0.00 0.00 36.22 2.77
525 532 8.996024 AAAGCTGTTTAATACAACAACAAAGT 57.004 26.923 0.00 0.00 36.22 2.66
816 823 3.815401 GCTTTCCACTTCAGCTTCAGTTA 59.185 43.478 0.00 0.00 0.00 2.24
1089 1098 3.694566 GTGGTGTCCAATCCCTTGTAATC 59.305 47.826 0.00 0.00 34.18 1.75
1280 1289 2.505628 AATTGTGCGCATCAACAACA 57.494 40.000 15.91 0.85 0.00 3.33
1293 1302 6.527372 CGCATCAACAACATGTAAATCAATGA 59.473 34.615 0.00 0.00 0.00 2.57
1490 1500 6.126883 TGGGGGAGTACTTAATTGTATGTCAG 60.127 42.308 0.00 0.00 0.00 3.51
1691 1704 5.598417 TCTTATCGGATCCTTTGTGAGATCA 59.402 40.000 10.75 0.00 40.59 2.92
2284 2304 5.977725 ACTATGTGCACACGTATAATCTGAC 59.022 40.000 24.37 0.00 32.87 3.51
3256 3285 4.692041 TGACCATGGCCCTCCCCA 62.692 66.667 13.04 0.00 39.65 4.96
3453 3482 0.803380 TGAGATGCTCATGTCGTGCG 60.803 55.000 0.00 0.00 35.39 5.34
3614 3643 2.251040 CGCGCGTATATAAGCATGTCT 58.749 47.619 24.19 0.00 0.00 3.41
3649 3678 7.496529 TCCTAACTTGTCATTCAGAGTTTTG 57.503 36.000 0.00 0.00 33.27 2.44
3656 3685 4.583907 TGTCATTCAGAGTTTTGCAATCCA 59.416 37.500 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
118 121 2.189594 TGCATCCAGTGACAAAGAGG 57.810 50.000 0.00 0.00 0.00 3.69
141 144 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
143 146 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
145 148 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
147 150 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
149 152 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
151 154 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
153 156 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
155 158 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
157 160 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
159 162 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
160 163 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
161 164 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
162 165 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
163 166 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
164 167 1.155889 CTGTGTGTGTGTGTGTGTGT 58.844 50.000 0.00 0.00 0.00 3.72
165 168 1.394572 CTCTGTGTGTGTGTGTGTGTG 59.605 52.381 0.00 0.00 0.00 3.82
166 169 1.275010 TCTCTGTGTGTGTGTGTGTGT 59.725 47.619 0.00 0.00 0.00 3.72
167 170 1.929169 CTCTCTGTGTGTGTGTGTGTG 59.071 52.381 0.00 0.00 0.00 3.82
168 171 1.824852 TCTCTCTGTGTGTGTGTGTGT 59.175 47.619 0.00 0.00 0.00 3.72
169 172 2.099756 TCTCTCTCTGTGTGTGTGTGTG 59.900 50.000 0.00 0.00 0.00 3.82
170 173 2.360483 CTCTCTCTCTGTGTGTGTGTGT 59.640 50.000 0.00 0.00 0.00 3.72
171 174 2.620585 TCTCTCTCTCTGTGTGTGTGTG 59.379 50.000 0.00 0.00 0.00 3.82
172 175 2.884012 CTCTCTCTCTCTGTGTGTGTGT 59.116 50.000 0.00 0.00 0.00 3.72
173 176 3.145286 TCTCTCTCTCTCTGTGTGTGTG 58.855 50.000 0.00 0.00 0.00 3.82
174 177 3.072330 TCTCTCTCTCTCTCTGTGTGTGT 59.928 47.826 0.00 0.00 0.00 3.72
175 178 3.673902 TCTCTCTCTCTCTCTGTGTGTG 58.326 50.000 0.00 0.00 0.00 3.82
176 179 3.582647 TCTCTCTCTCTCTCTCTGTGTGT 59.417 47.826 0.00 0.00 0.00 3.72
177 180 4.081476 TCTCTCTCTCTCTCTCTCTGTGTG 60.081 50.000 0.00 0.00 0.00 3.82
178 181 4.096681 TCTCTCTCTCTCTCTCTCTGTGT 58.903 47.826 0.00 0.00 0.00 3.72
179 182 4.403752 TCTCTCTCTCTCTCTCTCTCTGTG 59.596 50.000 0.00 0.00 0.00 3.66
180 183 4.614475 TCTCTCTCTCTCTCTCTCTCTGT 58.386 47.826 0.00 0.00 0.00 3.41
181 184 4.892345 TCTCTCTCTCTCTCTCTCTCTCTG 59.108 50.000 0.00 0.00 0.00 3.35
406 412 4.746535 TCTTGTAATATGCCGTCCTTGA 57.253 40.909 0.00 0.00 0.00 3.02
415 421 9.765795 AACATAGTCTAGGTTCTTGTAATATGC 57.234 33.333 4.08 0.00 0.00 3.14
496 502 9.593134 TTGTTGTTGTATTAAACAGCTTTCAAT 57.407 25.926 5.68 0.00 40.93 2.57
524 531 3.558418 TGCGTCACTCAAAAGGTAAAGAC 59.442 43.478 0.00 0.00 0.00 3.01
525 532 3.799366 TGCGTCACTCAAAAGGTAAAGA 58.201 40.909 0.00 0.00 0.00 2.52
665 672 5.244178 GGTTTTACATTTCCCCACACACATA 59.756 40.000 0.00 0.00 0.00 2.29
673 680 5.482175 CCTTGTATGGTTTTACATTTCCCCA 59.518 40.000 0.00 0.00 32.39 4.96
816 823 4.889409 AGTTGTGTCATTTCCAACATGTCT 59.111 37.500 0.00 0.00 40.64 3.41
1280 1289 9.866655 ACATATTACCCTGTCATTGATTTACAT 57.133 29.630 0.00 0.00 0.00 2.29
1293 1302 7.001674 TGTCAGTTTCAAACATATTACCCTGT 58.998 34.615 2.41 0.00 0.00 4.00
1465 1475 5.727279 TGACATACAATTAAGTACTCCCCCA 59.273 40.000 0.00 0.00 0.00 4.96
1490 1500 6.985645 TGCTATTTATTCAAAATCCCATGTGC 59.014 34.615 0.00 0.00 0.00 4.57
1522 1532 2.766828 AGGTGCTAGTGGGAATACTGTC 59.233 50.000 0.00 0.00 32.19 3.51
1691 1704 5.876357 TCTAGGGCAGTAACAAGTGAAAAT 58.124 37.500 0.00 0.00 0.00 1.82
2378 2399 7.932120 ATGTACATGTAACGAAGCTAGAATC 57.068 36.000 7.78 0.00 0.00 2.52
3256 3285 1.398692 AATTTGTGGTTGGTCGTGCT 58.601 45.000 0.00 0.00 0.00 4.40
3614 3643 4.081697 TGACAAGTTAGGATCGATGCTTGA 60.082 41.667 25.06 11.33 37.39 3.02
3649 3678 9.503427 GTAAAATGTACACTTATCTTGGATTGC 57.497 33.333 0.00 0.00 0.00 3.56
3656 3685 6.315393 CGCCCTGTAAAATGTACACTTATCTT 59.685 38.462 0.00 0.00 0.00 2.40


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

AutoCloner maintained by Alex Coulton.