Multiple sequence alignment - TraesCS7B01G213900

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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 TraesCS7B01G213900 chr7B 100.000 2044 0 0 501 2544 392804664 392802621 0.000000e+00 3775
1 TraesCS7B01G213900 chr7B 100.000 265 0 0 1 265 392805164 392804900 8.180000e-135 490
2 TraesCS7B01G213900 chr7B 95.865 266 10 1 1 265 540335199 540335464 1.810000e-116 429
3 TraesCS7B01G213900 chr7B 94.737 266 12 2 1 265 540424644 540424908 1.820000e-111 412
4 TraesCS7B01G213900 chr7B 95.547 247 10 1 1 246 540381380 540381626 6.600000e-106 394
5 TraesCS7B01G213900 chr7A 90.270 2076 123 36 503 2544 445483112 445481082 0.000000e+00 2641
6 TraesCS7B01G213900 chr7D 94.851 1107 23 9 505 1588 393103045 393101950 0.000000e+00 1698
7 TraesCS7B01G213900 chr7D 96.178 942 26 6 1610 2544 393101753 393100815 0.000000e+00 1531
8 TraesCS7B01G213900 chr1B 87.319 552 53 10 1996 2544 375359595 375360132 1.290000e-172 616
9 TraesCS7B01G213900 chr6B 96.241 266 9 1 1 265 31471224 31471489 3.890000e-118 435
10 TraesCS7B01G213900 chr5B 95.865 266 10 1 1 265 704832110 704831845 1.810000e-116 429
11 TraesCS7B01G213900 chr4A 89.270 233 20 4 2315 2543 624470042 624470273 1.150000e-73 287
12 TraesCS7B01G213900 chr1A 89.868 227 18 4 2321 2543 569672295 569672070 1.150000e-73 287
13 TraesCS7B01G213900 chr1A 89.868 227 18 4 2321 2543 569723206 569722981 1.150000e-73 287
14 TraesCS7B01G213900 chr4B 90.955 199 17 1 68 265 668756919 668756721 1.500000e-67 267
15 TraesCS7B01G213900 chr4B 90.452 199 18 1 68 265 668658139 668657941 6.980000e-66 261
16 TraesCS7B01G213900 chr4B 94.667 75 3 1 1845 1918 642426335 642426261 5.750000e-22 115
17 TraesCS7B01G213900 chr5A 92.941 170 10 2 98 265 707991157 707990988 1.950000e-61 246


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 TraesCS7B01G213900 chr7B 392802621 392805164 2543 True 2132.5 3775 100.0000 1 2544 2 chr7B.!!$R1 2543
1 TraesCS7B01G213900 chr7A 445481082 445483112 2030 True 2641.0 2641 90.2700 503 2544 1 chr7A.!!$R1 2041
2 TraesCS7B01G213900 chr7D 393100815 393103045 2230 True 1614.5 1698 95.5145 505 2544 2 chr7D.!!$R1 2039
3 TraesCS7B01G213900 chr1B 375359595 375360132 537 False 616.0 616 87.3190 1996 2544 1 chr1B.!!$F1 548

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
253 254 1.064946 CTCAGATCCACCGCGAGTC 59.935 63.158 8.23 0.00 0.0 3.36 F
256 257 1.078759 CAGATCCACCGCGAGTCAAC 61.079 60.000 8.23 0.00 0.0 3.18 F
257 258 2.126071 ATCCACCGCGAGTCAACG 60.126 61.111 8.23 0.00 0.0 4.10 F
1126 1181 1.377856 GAAGGTGAAGAGGCTGCCC 60.378 63.158 16.57 7.08 0.0 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1126 1181 0.621571 TTCCTCCCCTCCATGGTGAG 60.622 60.000 15.47 14.02 0.0 3.51 R
1127 1182 0.621571 CTTCCTCCCCTCCATGGTGA 60.622 60.000 15.47 5.73 0.0 4.02 R
1133 1188 1.866997 TCCCTCTTCCTCCCCTCCA 60.867 63.158 0.00 0.00 0.0 3.86 R
2179 2423 2.230266 TCTAGCATACAACTCACACGCA 59.770 45.455 0.00 0.00 0.0 5.24 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
71 72 4.108299 CCGCACCACAGGGCCATA 62.108 66.667 6.18 0.00 37.90 2.74
72 73 2.514592 CGCACCACAGGGCCATAG 60.515 66.667 6.18 0.00 37.90 2.23
73 74 2.124151 GCACCACAGGGCCATAGG 60.124 66.667 6.18 5.68 37.90 2.57
149 150 3.745803 GCCAGGAAGCAGCAGCAC 61.746 66.667 3.17 0.00 45.49 4.40
150 151 3.060615 CCAGGAAGCAGCAGCACC 61.061 66.667 3.17 6.55 45.49 5.01
151 152 2.033757 CAGGAAGCAGCAGCACCT 59.966 61.111 12.53 12.53 45.74 4.00
152 153 2.033757 AGGAAGCAGCAGCACCTG 59.966 61.111 16.30 0.00 44.12 4.00
153 154 3.060615 GGAAGCAGCAGCACCTGG 61.061 66.667 3.17 0.00 45.49 4.45
154 155 3.060615 GAAGCAGCAGCACCTGGG 61.061 66.667 3.17 0.00 45.49 4.45
155 156 3.557903 GAAGCAGCAGCACCTGGGA 62.558 63.158 3.17 0.00 45.49 4.37
156 157 3.564345 AAGCAGCAGCACCTGGGAG 62.564 63.158 3.17 0.00 45.49 4.30
157 158 4.025858 GCAGCAGCACCTGGGAGA 62.026 66.667 0.00 0.00 41.58 3.71
158 159 2.046507 CAGCAGCACCTGGGAGAC 60.047 66.667 0.00 0.00 31.21 3.36
159 160 3.699894 AGCAGCACCTGGGAGACG 61.700 66.667 0.00 0.00 31.21 4.18
161 162 4.767255 CAGCACCTGGGAGACGCC 62.767 72.222 0.00 0.00 0.00 5.68
164 165 3.314331 CACCTGGGAGACGCCACT 61.314 66.667 0.00 0.00 38.95 4.00
165 166 2.997897 ACCTGGGAGACGCCACTC 60.998 66.667 0.00 0.00 38.95 3.51
166 167 2.681778 CCTGGGAGACGCCACTCT 60.682 66.667 0.00 0.00 38.95 3.24
167 168 2.575993 CTGGGAGACGCCACTCTG 59.424 66.667 0.00 0.00 38.95 3.35
168 169 3.655810 CTGGGAGACGCCACTCTGC 62.656 68.421 0.00 0.00 38.95 4.26
195 196 4.838152 CCGGCCACCATCTCCACG 62.838 72.222 2.24 0.00 0.00 4.94
199 200 3.770040 CCACCATCTCCACGCCGA 61.770 66.667 0.00 0.00 0.00 5.54
200 201 2.509336 CACCATCTCCACGCCGAC 60.509 66.667 0.00 0.00 0.00 4.79
202 203 4.873129 CCATCTCCACGCCGACGG 62.873 72.222 10.29 10.29 46.04 4.79
203 204 4.873129 CATCTCCACGCCGACGGG 62.873 72.222 17.22 8.43 46.04 5.28
241 242 3.222855 CGAGCTCGGCCCTCAGAT 61.223 66.667 28.40 0.00 35.37 2.90
242 243 2.733945 GAGCTCGGCCCTCAGATC 59.266 66.667 0.00 0.00 0.00 2.75
243 244 2.841988 AGCTCGGCCCTCAGATCC 60.842 66.667 0.00 0.00 0.00 3.36
244 245 3.157252 GCTCGGCCCTCAGATCCA 61.157 66.667 0.00 0.00 0.00 3.41
245 246 2.818132 CTCGGCCCTCAGATCCAC 59.182 66.667 0.00 0.00 0.00 4.02
246 247 2.764128 TCGGCCCTCAGATCCACC 60.764 66.667 0.00 0.00 0.00 4.61
247 248 4.227134 CGGCCCTCAGATCCACCG 62.227 72.222 0.00 0.00 0.00 4.94
248 249 4.554036 GGCCCTCAGATCCACCGC 62.554 72.222 0.00 0.00 0.00 5.68
249 250 4.899239 GCCCTCAGATCCACCGCG 62.899 72.222 0.00 0.00 0.00 6.46
250 251 3.147595 CCCTCAGATCCACCGCGA 61.148 66.667 8.23 0.00 0.00 5.87
251 252 2.415010 CCTCAGATCCACCGCGAG 59.585 66.667 8.23 0.00 0.00 5.03
252 253 2.418910 CCTCAGATCCACCGCGAGT 61.419 63.158 8.23 0.00 0.00 4.18
253 254 1.064946 CTCAGATCCACCGCGAGTC 59.935 63.158 8.23 0.00 0.00 3.36
254 255 1.657751 CTCAGATCCACCGCGAGTCA 61.658 60.000 8.23 0.00 0.00 3.41
255 256 1.215382 CAGATCCACCGCGAGTCAA 59.785 57.895 8.23 0.00 0.00 3.18
256 257 1.078759 CAGATCCACCGCGAGTCAAC 61.079 60.000 8.23 0.00 0.00 3.18
257 258 2.126071 ATCCACCGCGAGTCAACG 60.126 61.111 8.23 0.00 0.00 4.10
584 585 2.766263 TCTCTCAAGGTCAACACAGTGT 59.234 45.455 0.00 0.00 0.00 3.55
588 589 4.161565 TCTCAAGGTCAACACAGTGTTAGT 59.838 41.667 18.74 1.27 38.77 2.24
606 607 5.163237 TGTTAGTTTAACTGTCAGCTTCCCT 60.163 40.000 8.00 0.00 39.38 4.20
1056 1106 2.986413 AGCGACAGAGTGAGGCGT 60.986 61.111 0.00 0.00 0.00 5.68
1076 1126 4.737946 GCGTTCAGCTAATAGACTCCACAT 60.738 45.833 0.00 0.00 44.04 3.21
1126 1181 1.377856 GAAGGTGAAGAGGCTGCCC 60.378 63.158 16.57 7.08 0.00 5.36
1127 1182 1.846712 GAAGGTGAAGAGGCTGCCCT 61.847 60.000 16.57 9.52 46.74 5.19
1153 1208 1.707200 GAGGGGAGGAAGAGGGAGT 59.293 63.158 0.00 0.00 0.00 3.85
1175 1230 2.896443 GGCGACAAGGAGGAGGAG 59.104 66.667 0.00 0.00 0.00 3.69
1230 1285 1.220206 CAAGAGGAGGATGCTGCGT 59.780 57.895 0.00 0.00 36.27 5.24
1501 1562 7.909267 TGAGATGCTCTTGTCGTAAATATTTG 58.091 34.615 11.05 0.00 0.00 2.32
1852 2091 1.035923 TCTTCATAGCTCTGCCCTCG 58.964 55.000 0.00 0.00 0.00 4.63
1928 2167 4.339247 CCTGCCAAATTATAGTGAACTGGG 59.661 45.833 0.00 0.00 0.00 4.45
2161 2405 5.552178 ACCTTCAAACTGAGACTATGAACC 58.448 41.667 0.00 0.00 0.00 3.62
2380 2624 3.756933 AAATGTGCTTGCAGATTTGGT 57.243 38.095 23.54 6.22 28.71 3.67
2395 2639 6.144402 GCAGATTTGGTACATTCTTGTTGTTG 59.856 38.462 0.00 0.00 39.30 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
54 55 4.108299 TATGGCCCTGTGGTGCGG 62.108 66.667 0.00 0.00 0.00 5.69
55 56 2.514592 CTATGGCCCTGTGGTGCG 60.515 66.667 0.00 0.00 0.00 5.34
56 57 2.124151 CCTATGGCCCTGTGGTGC 60.124 66.667 0.00 0.00 0.00 5.01
57 58 2.124151 GCCTATGGCCCTGTGGTG 60.124 66.667 0.00 0.00 44.06 4.17
132 133 3.745803 GTGCTGCTGCTTCCTGGC 61.746 66.667 17.00 0.00 40.48 4.85
133 134 3.060615 GGTGCTGCTGCTTCCTGG 61.061 66.667 17.00 0.00 40.48 4.45
134 135 2.033757 AGGTGCTGCTGCTTCCTG 59.966 61.111 23.34 0.00 40.45 3.86
135 136 2.033757 CAGGTGCTGCTGCTTCCT 59.966 61.111 20.32 20.32 41.73 3.36
136 137 3.060615 CCAGGTGCTGCTGCTTCC 61.061 66.667 17.00 17.23 40.48 3.46
137 138 3.060615 CCCAGGTGCTGCTGCTTC 61.061 66.667 17.00 9.53 40.48 3.86
138 139 3.564345 CTCCCAGGTGCTGCTGCTT 62.564 63.158 17.00 0.00 40.48 3.91
139 140 4.031129 CTCCCAGGTGCTGCTGCT 62.031 66.667 17.00 0.00 40.48 4.24
140 141 4.025858 TCTCCCAGGTGCTGCTGC 62.026 66.667 8.89 8.89 40.20 5.25
141 142 2.046507 GTCTCCCAGGTGCTGCTG 60.047 66.667 0.00 0.00 0.00 4.41
142 143 3.699894 CGTCTCCCAGGTGCTGCT 61.700 66.667 0.00 0.00 0.00 4.24
144 145 4.767255 GGCGTCTCCCAGGTGCTG 62.767 72.222 0.00 0.00 0.00 4.41
147 148 3.302347 GAGTGGCGTCTCCCAGGTG 62.302 68.421 0.00 0.00 35.05 4.00
148 149 2.997897 GAGTGGCGTCTCCCAGGT 60.998 66.667 0.00 0.00 35.05 4.00
149 150 2.681778 AGAGTGGCGTCTCCCAGG 60.682 66.667 6.01 0.00 35.05 4.45
150 151 2.575993 CAGAGTGGCGTCTCCCAG 59.424 66.667 6.01 0.00 35.05 4.45
151 152 3.695606 GCAGAGTGGCGTCTCCCA 61.696 66.667 6.01 0.00 35.28 4.37
178 179 4.838152 CGTGGAGATGGTGGCCGG 62.838 72.222 0.00 0.00 0.00 6.13
182 183 3.770040 TCGGCGTGGAGATGGTGG 61.770 66.667 6.85 0.00 0.00 4.61
183 184 2.509336 GTCGGCGTGGAGATGGTG 60.509 66.667 6.85 0.00 0.00 4.17
184 185 4.129737 CGTCGGCGTGGAGATGGT 62.130 66.667 6.85 0.00 0.00 3.55
185 186 4.873129 CCGTCGGCGTGGAGATGG 62.873 72.222 9.28 2.35 37.22 3.51
186 187 4.873129 CCCGTCGGCGTGGAGATG 62.873 72.222 19.62 0.42 36.15 2.90
224 225 3.206211 GATCTGAGGGCCGAGCTCG 62.206 68.421 29.06 29.06 32.17 5.03
225 226 2.733945 GATCTGAGGGCCGAGCTC 59.266 66.667 2.73 2.73 0.00 4.09
226 227 2.841988 GGATCTGAGGGCCGAGCT 60.842 66.667 0.00 0.00 0.00 4.09
227 228 3.157252 TGGATCTGAGGGCCGAGC 61.157 66.667 0.00 0.00 0.00 5.03
228 229 2.801631 GGTGGATCTGAGGGCCGAG 61.802 68.421 0.00 0.00 0.00 4.63
229 230 2.764128 GGTGGATCTGAGGGCCGA 60.764 66.667 0.00 0.00 0.00 5.54
230 231 4.227134 CGGTGGATCTGAGGGCCG 62.227 72.222 0.00 0.00 0.00 6.13
231 232 4.554036 GCGGTGGATCTGAGGGCC 62.554 72.222 0.00 0.00 0.00 5.80
232 233 4.899239 CGCGGTGGATCTGAGGGC 62.899 72.222 0.00 0.00 0.00 5.19
233 234 3.144120 CTCGCGGTGGATCTGAGGG 62.144 68.421 6.13 0.00 0.00 4.30
234 235 2.343163 GACTCGCGGTGGATCTGAGG 62.343 65.000 6.13 0.00 0.00 3.86
235 236 1.064946 GACTCGCGGTGGATCTGAG 59.935 63.158 6.13 0.00 0.00 3.35
236 237 1.248101 TTGACTCGCGGTGGATCTGA 61.248 55.000 6.13 0.00 0.00 3.27
237 238 1.078759 GTTGACTCGCGGTGGATCTG 61.079 60.000 6.13 0.00 0.00 2.90
238 239 1.215647 GTTGACTCGCGGTGGATCT 59.784 57.895 6.13 0.00 0.00 2.75
239 240 2.158959 CGTTGACTCGCGGTGGATC 61.159 63.158 6.13 0.00 0.00 3.36
240 241 2.126071 CGTTGACTCGCGGTGGAT 60.126 61.111 6.13 0.00 0.00 3.41
535 536 9.866655 TTAAAGATGGGATATTGTTAAGCTCAT 57.133 29.630 0.00 0.00 0.00 2.90
584 585 5.305585 CAGGGAAGCTGACAGTTAAACTAA 58.694 41.667 3.99 0.00 0.00 2.24
588 589 2.158682 TGCAGGGAAGCTGACAGTTAAA 60.159 45.455 3.99 0.00 34.99 1.52
606 607 0.608856 ATGTGGATCCAAGCGTTGCA 60.609 50.000 18.20 8.83 0.00 4.08
961 1007 1.587876 GTCGCGTCGTGCATCCATA 60.588 57.895 5.77 0.00 46.97 2.74
1056 1106 6.833933 TCTGTATGTGGAGTCTATTAGCTGAA 59.166 38.462 0.00 0.00 0.00 3.02
1062 1112 7.450903 TCTCGATCTGTATGTGGAGTCTATTA 58.549 38.462 0.00 0.00 0.00 0.98
1076 1126 2.099405 TGTGCACCATCTCGATCTGTA 58.901 47.619 15.69 0.00 0.00 2.74
1116 1171 2.285969 ATGGTGAGGGCAGCCTCT 60.286 61.111 12.43 6.78 41.74 3.69
1126 1181 0.621571 TTCCTCCCCTCCATGGTGAG 60.622 60.000 15.47 14.02 0.00 3.51
1127 1182 0.621571 CTTCCTCCCCTCCATGGTGA 60.622 60.000 15.47 5.73 0.00 4.02
1133 1188 1.866997 TCCCTCTTCCTCCCCTCCA 60.867 63.158 0.00 0.00 0.00 3.86
1153 1208 3.744719 CCTCCTTGTCGCCGTCGA 61.745 66.667 0.00 0.00 43.28 4.20
1175 1230 2.747855 CGCCACCTTGCCTCCTTC 60.748 66.667 0.00 0.00 0.00 3.46
1553 1615 7.839200 AGCTTAATCCTTCTTTGCCCTATTTTA 59.161 33.333 0.00 0.00 0.00 1.52
1852 2091 2.730550 CAAAAGTGGACATTGGCCTC 57.269 50.000 10.60 6.26 0.00 4.70
1948 2187 5.324784 AGTTTGGGACTTGACAAAAAGAC 57.675 39.130 0.00 0.00 38.20 3.01
1949 2188 4.401202 GGAGTTTGGGACTTGACAAAAAGA 59.599 41.667 0.00 0.00 39.19 2.52
1950 2189 4.159506 TGGAGTTTGGGACTTGACAAAAAG 59.840 41.667 0.00 0.00 39.19 2.27
2074 2316 5.694006 TCATTTGGCCGTTTTACAATTTCAG 59.306 36.000 0.00 0.00 0.00 3.02
2161 2405 6.303970 CACACGCAATGAAAGACATCTTTAAG 59.696 38.462 6.85 0.05 45.37 1.85
2179 2423 2.230266 TCTAGCATACAACTCACACGCA 59.770 45.455 0.00 0.00 0.00 5.24
2343 2587 8.801715 AGCACATTTTGTAAGTGTATCTTTTG 57.198 30.769 0.00 0.00 37.56 2.44
2380 2624 5.650266 ACACCAGTTCAACAACAAGAATGTA 59.350 36.000 0.00 0.00 39.40 2.29
2455 2699 6.659668 GGCATTTCTTTCCCTCTAAAGTTAGT 59.340 38.462 0.00 0.00 37.65 2.24


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

AutoCloner maintained by Alex Coulton.