Multiple sequence alignment - TraesCS4D01G172200

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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 TraesCS4D01G172200 chr4D 100.000 3120 0 0 1 3120 299450118 299446999 0.000000e+00 5762.0
1 TraesCS4D01G172200 chr4B 95.698 1604 37 9 1544 3120 372252584 372250986 0.000000e+00 2551.0
2 TraesCS4D01G172200 chr4B 94.832 1161 37 6 413 1554 372253800 372252644 0.000000e+00 1790.0
3 TraesCS4D01G172200 chr4B 94.231 312 7 2 109 419 372264562 372264261 1.690000e-127 466.0
4 TraesCS4D01G172200 chr4A 91.957 920 23 18 1544 2435 185179178 185180074 0.000000e+00 1242.0
5 TraesCS4D01G172200 chr4A 95.113 798 16 6 778 1554 185178323 185179118 0.000000e+00 1236.0
6 TraesCS4D01G172200 chr4A 97.800 591 10 2 183 773 185177645 185178232 0.000000e+00 1016.0
7 TraesCS4D01G172200 chr4A 94.646 635 25 6 2490 3120 185180093 185180722 0.000000e+00 976.0
8 TraesCS4D01G172200 chr4A 94.074 135 5 2 1 133 185177512 185177645 5.280000e-48 202.0
9 TraesCS4D01G172200 chr1B 89.189 74 7 1 3026 3099 398382719 398382791 1.190000e-14 91.6
10 TraesCS4D01G172200 chr1B 100.000 28 0 0 2508 2535 652927280 652927253 6.000000e-03 52.8
11 TraesCS4D01G172200 chr2B 85.455 55 8 0 3028 3082 159979325 159979379 1.210000e-04 58.4
12 TraesCS4D01G172200 chr2A 85.455 55 8 0 3028 3082 107188177 107188231 1.210000e-04 58.4


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 TraesCS4D01G172200 chr4D 299446999 299450118 3119 True 5762.0 5762 100.000 1 3120 1 chr4D.!!$R1 3119
1 TraesCS4D01G172200 chr4B 372250986 372253800 2814 True 2170.5 2551 95.265 413 3120 2 chr4B.!!$R2 2707
2 TraesCS4D01G172200 chr4A 185177512 185180722 3210 False 934.4 1242 94.718 1 3120 5 chr4A.!!$F1 3119

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
169 172 0.837272 ATCCGTCCATTTCCCGATGT 59.163 50.000 0.00 0.00 0.00 3.06 F
409 412 0.874390 TGCCAAGAACAGCGATGTTC 59.126 50.000 33.25 33.25 46.11 3.18 F
971 1062 1.269998 CACAGTAGCTAGCGGGGTATC 59.730 57.143 9.55 0.00 0.00 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1461 1570 0.792640 CATCAACCAGCGTGTCAGTC 59.207 55.000 0.00 0.00 0.0 3.51 R
1549 1727 1.885887 CCTCCAGTTTCCATCGCAAAA 59.114 47.619 0.00 0.00 0.0 2.44 R
2219 2422 2.615447 CACTGGTTAGATTCATGCGCAT 59.385 45.455 19.28 19.28 0.0 4.73 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
99 102 8.786826 TTTATGGAGTTAGACCAAATACACAG 57.213 34.615 0.00 0.00 40.93 3.66
124 127 2.570415 TAGGCCAAATCACACGGAAA 57.430 45.000 5.01 0.00 0.00 3.13
133 136 6.183360 GCCAAATCACACGGAAATACTGAATA 60.183 38.462 0.00 0.00 0.00 1.75
134 137 7.186804 CCAAATCACACGGAAATACTGAATAC 58.813 38.462 0.00 0.00 0.00 1.89
136 139 5.063180 TCACACGGAAATACTGAATACGT 57.937 39.130 0.00 0.00 0.00 3.57
137 140 5.472148 TCACACGGAAATACTGAATACGTT 58.528 37.500 0.00 0.00 0.00 3.99
138 141 5.574055 TCACACGGAAATACTGAATACGTTC 59.426 40.000 0.00 0.00 34.85 3.95
139 142 5.575606 CACACGGAAATACTGAATACGTTCT 59.424 40.000 0.00 0.00 35.33 3.01
140 143 5.803967 ACACGGAAATACTGAATACGTTCTC 59.196 40.000 0.00 0.00 35.33 2.87
141 144 5.803461 CACGGAAATACTGAATACGTTCTCA 59.197 40.000 0.00 0.00 35.33 3.27
142 145 6.309494 CACGGAAATACTGAATACGTTCTCAA 59.691 38.462 0.00 0.00 35.33 3.02
143 146 6.530534 ACGGAAATACTGAATACGTTCTCAAG 59.469 38.462 0.00 0.00 35.33 3.02
144 147 6.750501 CGGAAATACTGAATACGTTCTCAAGA 59.249 38.462 0.00 0.00 35.33 3.02
145 148 7.043986 CGGAAATACTGAATACGTTCTCAAGAG 60.044 40.741 0.00 0.00 35.33 2.85
146 149 7.974501 GGAAATACTGAATACGTTCTCAAGAGA 59.025 37.037 0.00 0.00 35.33 3.10
147 150 8.690680 AAATACTGAATACGTTCTCAAGAGAC 57.309 34.615 0.00 0.00 37.14 3.36
148 151 5.707242 ACTGAATACGTTCTCAAGAGACA 57.293 39.130 0.00 0.00 37.14 3.41
149 152 6.274157 ACTGAATACGTTCTCAAGAGACAT 57.726 37.500 0.00 0.00 37.14 3.06
150 153 7.392494 ACTGAATACGTTCTCAAGAGACATA 57.608 36.000 0.00 0.00 37.14 2.29
151 154 8.001881 ACTGAATACGTTCTCAAGAGACATAT 57.998 34.615 0.00 0.00 37.14 1.78
152 155 8.132362 ACTGAATACGTTCTCAAGAGACATATC 58.868 37.037 0.00 0.00 37.14 1.63
153 156 7.426410 TGAATACGTTCTCAAGAGACATATCC 58.574 38.462 0.00 0.00 37.14 2.59
154 157 4.294416 ACGTTCTCAAGAGACATATCCG 57.706 45.455 0.00 0.00 37.14 4.18
155 158 3.695060 ACGTTCTCAAGAGACATATCCGT 59.305 43.478 0.00 0.00 37.14 4.69
156 159 4.201930 ACGTTCTCAAGAGACATATCCGTC 60.202 45.833 0.00 0.00 37.14 4.79
157 160 4.612943 GTTCTCAAGAGACATATCCGTCC 58.387 47.826 0.00 0.00 37.14 4.79
158 161 3.898482 TCTCAAGAGACATATCCGTCCA 58.102 45.455 0.00 0.00 36.52 4.02
159 162 4.474394 TCTCAAGAGACATATCCGTCCAT 58.526 43.478 0.00 0.00 36.52 3.41
160 163 4.895889 TCTCAAGAGACATATCCGTCCATT 59.104 41.667 0.00 0.00 36.52 3.16
161 164 5.363868 TCTCAAGAGACATATCCGTCCATTT 59.636 40.000 0.00 0.00 36.52 2.32
162 165 5.601662 TCAAGAGACATATCCGTCCATTTC 58.398 41.667 0.00 0.00 36.52 2.17
163 166 4.608948 AGAGACATATCCGTCCATTTCC 57.391 45.455 0.00 0.00 36.52 3.13
164 167 3.325135 AGAGACATATCCGTCCATTTCCC 59.675 47.826 0.00 0.00 36.52 3.97
165 168 2.037251 AGACATATCCGTCCATTTCCCG 59.963 50.000 0.00 0.00 36.52 5.14
166 169 2.036733 GACATATCCGTCCATTTCCCGA 59.963 50.000 0.00 0.00 0.00 5.14
167 170 2.637872 ACATATCCGTCCATTTCCCGAT 59.362 45.455 0.00 0.00 0.00 4.18
168 171 2.831685 TATCCGTCCATTTCCCGATG 57.168 50.000 0.00 0.00 0.00 3.84
169 172 0.837272 ATCCGTCCATTTCCCGATGT 59.163 50.000 0.00 0.00 0.00 3.06
170 173 1.487300 TCCGTCCATTTCCCGATGTA 58.513 50.000 0.00 0.00 0.00 2.29
171 174 1.832366 TCCGTCCATTTCCCGATGTAA 59.168 47.619 0.00 0.00 0.00 2.41
172 175 1.937899 CCGTCCATTTCCCGATGTAAC 59.062 52.381 0.00 0.00 0.00 2.50
173 176 1.937899 CGTCCATTTCCCGATGTAACC 59.062 52.381 0.00 0.00 0.00 2.85
174 177 2.419574 CGTCCATTTCCCGATGTAACCT 60.420 50.000 0.00 0.00 0.00 3.50
175 178 3.617284 GTCCATTTCCCGATGTAACCTT 58.383 45.455 0.00 0.00 0.00 3.50
176 179 4.014406 GTCCATTTCCCGATGTAACCTTT 58.986 43.478 0.00 0.00 0.00 3.11
177 180 4.095932 GTCCATTTCCCGATGTAACCTTTC 59.904 45.833 0.00 0.00 0.00 2.62
178 181 4.018779 TCCATTTCCCGATGTAACCTTTCT 60.019 41.667 0.00 0.00 0.00 2.52
179 182 4.096382 CCATTTCCCGATGTAACCTTTCTG 59.904 45.833 0.00 0.00 0.00 3.02
180 183 4.360951 TTTCCCGATGTAACCTTTCTGT 57.639 40.909 0.00 0.00 0.00 3.41
181 184 4.360951 TTCCCGATGTAACCTTTCTGTT 57.639 40.909 0.00 0.00 0.00 3.16
182 185 4.360951 TCCCGATGTAACCTTTCTGTTT 57.639 40.909 0.00 0.00 0.00 2.83
183 186 4.721132 TCCCGATGTAACCTTTCTGTTTT 58.279 39.130 0.00 0.00 0.00 2.43
184 187 4.517453 TCCCGATGTAACCTTTCTGTTTTG 59.483 41.667 0.00 0.00 0.00 2.44
185 188 4.320935 CCCGATGTAACCTTTCTGTTTTGG 60.321 45.833 0.00 0.00 0.00 3.28
186 189 4.226761 CGATGTAACCTTTCTGTTTTGGC 58.773 43.478 0.00 0.00 0.00 4.52
187 190 4.261405 CGATGTAACCTTTCTGTTTTGGCA 60.261 41.667 0.00 0.00 0.00 4.92
188 191 4.379339 TGTAACCTTTCTGTTTTGGCAC 57.621 40.909 0.00 0.00 0.00 5.01
351 354 7.754851 TGGAGAAAGGTTCCAGTATAAAAAC 57.245 36.000 0.00 0.00 39.74 2.43
409 412 0.874390 TGCCAAGAACAGCGATGTTC 59.126 50.000 33.25 33.25 46.11 3.18
633 636 1.462616 GCATTGCCTGTGACCATACA 58.537 50.000 0.00 0.00 0.00 2.29
634 637 1.402968 GCATTGCCTGTGACCATACAG 59.597 52.381 0.00 0.00 45.93 2.74
635 638 2.715046 CATTGCCTGTGACCATACAGT 58.285 47.619 0.00 0.00 45.12 3.55
870 961 2.213499 CGATAAGAATGGGAGTGGCAC 58.787 52.381 10.29 10.29 0.00 5.01
904 995 8.827677 CCTCAACTTAATTAATTAGAGAACCCG 58.172 37.037 17.51 3.89 0.00 5.28
938 1029 2.739292 CGCCTACGCTGAAGCTTATAA 58.261 47.619 0.00 0.00 39.32 0.98
971 1062 1.269998 CACAGTAGCTAGCGGGGTATC 59.730 57.143 9.55 0.00 0.00 2.24
1309 1409 6.889019 GGTTAATAACCGAACTCTCTTCAG 57.111 41.667 6.41 0.00 42.62 3.02
1458 1567 3.130160 GGCTTCTCTGGCAAGCGG 61.130 66.667 3.04 0.00 46.21 5.52
1461 1570 2.032528 TTCTCTGGCAAGCGGGTG 59.967 61.111 0.00 0.00 0.00 4.61
1549 1727 1.896220 TCCGAGGTACGTACACTTGT 58.104 50.000 26.02 5.84 40.78 3.16
1891 2069 1.153997 GTTCAGCTCCTCGTCCGAC 60.154 63.158 0.00 0.00 0.00 4.79
2504 2718 5.585390 GGCTTGAAATGTTGATGTATGAGG 58.415 41.667 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
124 127 7.392494 TGTCTCTTGAGAACGTATTCAGTAT 57.608 36.000 1.51 0.00 37.29 2.12
133 136 3.695060 ACGGATATGTCTCTTGAGAACGT 59.305 43.478 1.51 4.49 0.00 3.99
134 137 4.283678 GACGGATATGTCTCTTGAGAACG 58.716 47.826 1.51 3.96 35.95 3.95
136 139 4.278310 TGGACGGATATGTCTCTTGAGAA 58.722 43.478 1.51 0.00 38.91 2.87
137 140 3.898482 TGGACGGATATGTCTCTTGAGA 58.102 45.455 0.00 0.00 38.91 3.27
138 141 4.862902 ATGGACGGATATGTCTCTTGAG 57.137 45.455 0.00 0.00 38.91 3.02
139 142 5.453339 GGAAATGGACGGATATGTCTCTTGA 60.453 44.000 0.00 0.00 38.91 3.02
140 143 4.752101 GGAAATGGACGGATATGTCTCTTG 59.248 45.833 0.00 0.00 38.91 3.02
141 144 4.202367 GGGAAATGGACGGATATGTCTCTT 60.202 45.833 0.00 0.00 38.91 2.85
142 145 3.325135 GGGAAATGGACGGATATGTCTCT 59.675 47.826 0.00 0.00 38.91 3.10
143 146 3.665190 GGGAAATGGACGGATATGTCTC 58.335 50.000 0.00 0.00 38.91 3.36
144 147 2.037251 CGGGAAATGGACGGATATGTCT 59.963 50.000 0.00 0.00 38.91 3.41
145 148 2.036733 TCGGGAAATGGACGGATATGTC 59.963 50.000 0.00 0.00 38.17 3.06
146 149 2.043992 TCGGGAAATGGACGGATATGT 58.956 47.619 0.00 0.00 0.00 2.29
147 150 2.831685 TCGGGAAATGGACGGATATG 57.168 50.000 0.00 0.00 0.00 1.78
148 151 2.637872 ACATCGGGAAATGGACGGATAT 59.362 45.455 0.00 0.00 0.00 1.63
149 152 2.043992 ACATCGGGAAATGGACGGATA 58.956 47.619 0.00 0.00 0.00 2.59
150 153 0.837272 ACATCGGGAAATGGACGGAT 59.163 50.000 0.00 0.00 0.00 4.18
151 154 1.487300 TACATCGGGAAATGGACGGA 58.513 50.000 0.00 0.00 0.00 4.69
152 155 1.937899 GTTACATCGGGAAATGGACGG 59.062 52.381 0.00 0.00 0.00 4.79
153 156 1.937899 GGTTACATCGGGAAATGGACG 59.062 52.381 0.00 0.00 0.00 4.79
154 157 3.277142 AGGTTACATCGGGAAATGGAC 57.723 47.619 0.00 0.00 0.00 4.02
155 158 4.018779 AGAAAGGTTACATCGGGAAATGGA 60.019 41.667 0.00 0.00 0.00 3.41
156 159 4.096382 CAGAAAGGTTACATCGGGAAATGG 59.904 45.833 0.00 0.00 0.00 3.16
157 160 4.700213 ACAGAAAGGTTACATCGGGAAATG 59.300 41.667 0.00 0.00 0.00 2.32
158 161 4.918588 ACAGAAAGGTTACATCGGGAAAT 58.081 39.130 0.00 0.00 0.00 2.17
159 162 4.360951 ACAGAAAGGTTACATCGGGAAA 57.639 40.909 0.00 0.00 0.00 3.13
160 163 4.360951 AACAGAAAGGTTACATCGGGAA 57.639 40.909 0.00 0.00 0.00 3.97
161 164 4.360951 AAACAGAAAGGTTACATCGGGA 57.639 40.909 0.00 0.00 0.00 5.14
162 165 4.320935 CCAAAACAGAAAGGTTACATCGGG 60.321 45.833 0.00 0.00 0.00 5.14
163 166 4.794169 CCAAAACAGAAAGGTTACATCGG 58.206 43.478 0.00 0.00 0.00 4.18
164 167 4.226761 GCCAAAACAGAAAGGTTACATCG 58.773 43.478 0.00 0.00 0.00 3.84
165 168 4.982295 GTGCCAAAACAGAAAGGTTACATC 59.018 41.667 0.00 0.00 0.00 3.06
166 169 4.404073 TGTGCCAAAACAGAAAGGTTACAT 59.596 37.500 0.00 0.00 0.00 2.29
167 170 3.764434 TGTGCCAAAACAGAAAGGTTACA 59.236 39.130 0.00 0.00 0.00 2.41
168 171 4.379339 TGTGCCAAAACAGAAAGGTTAC 57.621 40.909 0.00 0.00 0.00 2.50
178 181 1.308783 TGACACGCTGTGCCAAAACA 61.309 50.000 8.31 0.00 36.98 2.83
179 182 0.865639 GTGACACGCTGTGCCAAAAC 60.866 55.000 8.31 0.00 36.98 2.43
180 183 1.029408 AGTGACACGCTGTGCCAAAA 61.029 50.000 8.31 0.00 36.98 2.44
181 184 1.436195 GAGTGACACGCTGTGCCAAA 61.436 55.000 1.62 0.00 36.98 3.28
182 185 1.887242 GAGTGACACGCTGTGCCAA 60.887 57.895 1.62 0.00 36.98 4.52
183 186 2.280119 GAGTGACACGCTGTGCCA 60.280 61.111 1.62 1.70 36.98 4.92
184 187 1.595382 AAGAGTGACACGCTGTGCC 60.595 57.895 12.88 0.00 36.98 5.01
185 188 0.875908 TCAAGAGTGACACGCTGTGC 60.876 55.000 12.88 3.39 36.98 4.57
186 189 1.135046 CTCAAGAGTGACACGCTGTG 58.865 55.000 12.88 12.40 39.75 3.66
187 190 0.598680 GCTCAAGAGTGACACGCTGT 60.599 55.000 12.88 0.88 0.00 4.40
188 191 0.598419 TGCTCAAGAGTGACACGCTG 60.598 55.000 12.88 7.40 0.00 5.18
351 354 7.118680 CCTTTTGAAAATTGGAGACATGAATGG 59.881 37.037 0.00 0.00 42.32 3.16
574 577 3.053828 CCAGGCCTTGGTGCAAAG 58.946 61.111 0.00 0.00 42.41 2.77
626 629 2.602878 CGCGTTTGACTACTGTATGGT 58.397 47.619 0.00 0.00 0.00 3.55
633 636 3.467119 CGCGCGCGTTTGACTACT 61.467 61.111 42.49 0.00 34.35 2.57
769 772 1.675641 GCATGGAAGCACGGGAGTT 60.676 57.895 0.00 0.00 44.67 3.01
870 961 7.867445 AATTAATTAAGTTGAGGTGTTTGCG 57.133 32.000 0.00 0.00 0.00 4.85
904 995 1.610554 TAGGCGCAGGTAGGGTGAAC 61.611 60.000 10.83 0.00 0.00 3.18
928 1019 2.928116 AGCGTTCACCGTTATAAGCTTC 59.072 45.455 0.00 0.00 39.32 3.86
938 1029 2.358193 TACTGTGCAGCGTTCACCGT 62.358 55.000 0.00 7.80 39.32 4.83
971 1062 2.928301 CAGCAGTGCTACACCACTAGTG 60.928 54.545 19.26 16.34 43.85 2.74
1251 1351 1.980772 TTTCCTCGTCCTCCCGGTC 60.981 63.158 0.00 0.00 0.00 4.79
1292 1392 2.492484 GCTCCTGAAGAGAGTTCGGTTA 59.508 50.000 0.00 0.00 46.50 2.85
1295 1395 0.891373 TGCTCCTGAAGAGAGTTCGG 59.109 55.000 0.00 0.00 46.50 4.30
1309 1409 1.517257 CAGATCGACCGTGTGCTCC 60.517 63.158 0.00 0.00 0.00 4.70
1458 1567 1.227556 AACCAGCGTGTCAGTCACC 60.228 57.895 0.00 0.00 43.51 4.02
1461 1570 0.792640 CATCAACCAGCGTGTCAGTC 59.207 55.000 0.00 0.00 0.00 3.51
1549 1727 1.885887 CCTCCAGTTTCCATCGCAAAA 59.114 47.619 0.00 0.00 0.00 2.44
2219 2422 2.615447 CACTGGTTAGATTCATGCGCAT 59.385 45.455 19.28 19.28 0.00 4.73
2251 2454 8.730680 AGTTGTGCACTGGTTATTATCTAAAAG 58.269 33.333 19.41 0.00 32.83 2.27
2256 2459 6.418101 ATCAGTTGTGCACTGGTTATTATCT 58.582 36.000 19.41 0.00 45.46 1.98
2257 2460 6.683974 ATCAGTTGTGCACTGGTTATTATC 57.316 37.500 19.41 0.00 45.46 1.75
2258 2461 8.752005 AATATCAGTTGTGCACTGGTTATTAT 57.248 30.769 19.41 4.85 45.46 1.28
2483 2697 8.267620 TGTACCTCATACATCAACATTTCAAG 57.732 34.615 0.00 0.00 38.95 3.02
2824 3039 3.369451 GCCTTTTTGAGCGAAACAAACAA 59.631 39.130 0.00 0.00 37.05 2.83
2825 3040 2.926838 GCCTTTTTGAGCGAAACAAACA 59.073 40.909 0.00 0.00 37.05 2.83
2826 3041 3.569304 GCCTTTTTGAGCGAAACAAAC 57.431 42.857 0.00 0.00 37.05 2.93
3009 3225 2.918712 AGGTAAGCCTCATTCCATCG 57.081 50.000 0.00 0.00 42.67 3.84


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

AutoCloner maintained by Alex Coulton.