Multiple sequence alignment - TraesCS1D01G188300

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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 TraesCS1D01G188300 chr1D 100.000 2186 0 0 1 2186 260891267 260893452 0 4037
1 TraesCS1D01G188300 chr1D 95.664 2145 76 8 1 2139 254416224 254418357 0 3430
2 TraesCS1D01G188300 chr1D 95.196 2144 95 6 1 2139 51878912 51876772 0 3382
3 TraesCS1D01G188300 chr5D 95.812 2149 79 9 1 2139 503286460 503288607 0 3459
4 TraesCS1D01G188300 chr5D 95.711 2145 81 11 1 2139 120799030 120801169 0 3441
5 TraesCS1D01G188300 chr5D 95.203 2147 81 15 1 2139 6181784 6179652 0 3374
6 TraesCS1D01G188300 chr5D 94.406 2145 107 13 1 2139 167071093 167073230 0 3284
7 TraesCS1D01G188300 chr6D 95.573 2146 75 14 1 2139 45512404 45510272 0 3419
8 TraesCS1D01G188300 chr2A 95.463 1631 70 4 1 1630 335831468 335829841 0 2599
9 TraesCS1D01G188300 chr2A 94.843 1144 42 8 1003 2139 334595896 334594763 0 1770
10 TraesCS1D01G188300 chr4A 93.667 1737 99 9 1 1735 310731434 310729707 0 2588


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 TraesCS1D01G188300 chr1D 260891267 260893452 2185 False 4037 4037 100.000 1 2186 1 chr1D.!!$F2 2185
1 TraesCS1D01G188300 chr1D 254416224 254418357 2133 False 3430 3430 95.664 1 2139 1 chr1D.!!$F1 2138
2 TraesCS1D01G188300 chr1D 51876772 51878912 2140 True 3382 3382 95.196 1 2139 1 chr1D.!!$R1 2138
3 TraesCS1D01G188300 chr5D 503286460 503288607 2147 False 3459 3459 95.812 1 2139 1 chr5D.!!$F3 2138
4 TraesCS1D01G188300 chr5D 120799030 120801169 2139 False 3441 3441 95.711 1 2139 1 chr5D.!!$F1 2138
5 TraesCS1D01G188300 chr5D 6179652 6181784 2132 True 3374 3374 95.203 1 2139 1 chr5D.!!$R1 2138
6 TraesCS1D01G188300 chr5D 167071093 167073230 2137 False 3284 3284 94.406 1 2139 1 chr5D.!!$F2 2138
7 TraesCS1D01G188300 chr6D 45510272 45512404 2132 True 3419 3419 95.573 1 2139 1 chr6D.!!$R1 2138
8 TraesCS1D01G188300 chr2A 335829841 335831468 1627 True 2599 2599 95.463 1 1630 1 chr2A.!!$R2 1629
9 TraesCS1D01G188300 chr2A 334594763 334595896 1133 True 1770 1770 94.843 1003 2139 1 chr2A.!!$R1 1136
10 TraesCS1D01G188300 chr4A 310729707 310731434 1727 True 2588 2588 93.667 1 1735 1 chr4A.!!$R1 1734

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
880 885 2.093973 AGAGTGCGAATACAAGGAGGTG 60.094 50.0 0.0 0.0 0.0 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1798 1819 1.13467 CGAATCCCTCTCTTTCCGCTT 60.135 52.381 0.0 0.0 0.0 4.68 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
126 128 2.281484 ACACGCAACGGATGGCTT 60.281 55.556 0.00 0.00 0.00 4.35
148 150 6.458478 GCTTGAGATGATCAATCTTGAAGTGG 60.458 42.308 0.00 0.00 46.12 4.00
684 689 6.744082 GGTTTTATGCGACACTAATAAACACC 59.256 38.462 0.00 0.00 0.00 4.16
880 885 2.093973 AGAGTGCGAATACAAGGAGGTG 60.094 50.000 0.00 0.00 0.00 4.00
916 921 6.150318 GGAAAGTCCGAAGAAAAAGGATTTC 58.850 40.000 0.00 0.00 37.28 2.17
924 929 7.335924 TCCGAAGAAAAAGGATTTCGAATATGT 59.664 33.333 0.00 0.00 43.60 2.29
1091 1098 3.380320 GCCAAATTACCCGAAGCTTATGT 59.620 43.478 0.00 0.00 0.00 2.29
1331 1344 7.432148 TCTTCTACATTGAATGGGTAGCTAA 57.568 36.000 10.27 0.00 35.58 3.09
1364 1377 2.119495 GGATCAGCCTTTCTACTCCCA 58.881 52.381 0.00 0.00 0.00 4.37
1426 1439 7.290714 CACAATACCTAACCACCTAACCCTATA 59.709 40.741 0.00 0.00 0.00 1.31
1549 1564 2.287368 CGTGTGGTAAGGAAAAACTGGC 60.287 50.000 0.00 0.00 0.00 4.85
1672 1690 7.028131 AGGATTCTTATCTAATGACCCAGGAT 58.972 38.462 0.00 0.00 0.00 3.24
1760 1781 3.778075 TCTATGAGAAAATCCGGGGTCAA 59.222 43.478 0.00 0.00 0.00 3.18
1798 1819 4.344104 GAAAGTCCCAAATGATCCAAGGA 58.656 43.478 0.00 0.00 0.00 3.36
1893 1915 0.976641 TCAGCCATCTCTCCACGTTT 59.023 50.000 0.00 0.00 0.00 3.60
2086 2116 7.873719 TCTTTCTAAAAATCGATATTGGCCA 57.126 32.000 0.00 0.00 0.00 5.36
2126 2156 3.350219 TTCTCTTTAGCGGGCATTTCT 57.650 42.857 0.00 0.00 0.00 2.52
2139 2169 5.568825 GCGGGCATTTCTATATAGGACTTGA 60.569 44.000 9.89 0.00 0.00 3.02
2140 2170 6.464222 CGGGCATTTCTATATAGGACTTGAA 58.536 40.000 9.89 0.00 0.00 2.69
2141 2171 7.106239 CGGGCATTTCTATATAGGACTTGAAT 58.894 38.462 9.89 0.00 0.00 2.57
2142 2172 8.258007 CGGGCATTTCTATATAGGACTTGAATA 58.742 37.037 9.89 0.00 0.00 1.75
2143 2173 9.959721 GGGCATTTCTATATAGGACTTGAATAA 57.040 33.333 9.89 0.00 0.00 1.40
2157 2187 9.533831 AGGACTTGAATAAATAGTTCACCAATT 57.466 29.630 0.00 0.00 35.47 2.32
2158 2188 9.573133 GGACTTGAATAAATAGTTCACCAATTG 57.427 33.333 0.00 0.00 35.47 2.32
2159 2189 9.573133 GACTTGAATAAATAGTTCACCAATTGG 57.427 33.333 23.31 23.31 35.47 3.16
2160 2190 8.531146 ACTTGAATAAATAGTTCACCAATTGGG 58.469 33.333 27.89 16.62 44.81 4.12
2161 2191 8.657387 TTGAATAAATAGTTCACCAATTGGGA 57.343 30.769 27.89 18.56 41.15 4.37
2162 2192 8.657387 TGAATAAATAGTTCACCAATTGGGAA 57.343 30.769 27.89 22.70 41.15 3.97
2163 2193 9.094578 TGAATAAATAGTTCACCAATTGGGAAA 57.905 29.630 27.89 17.88 41.15 3.13
2164 2194 9.936759 GAATAAATAGTTCACCAATTGGGAAAA 57.063 29.630 27.89 15.48 41.15 2.29
2166 2196 9.942850 ATAAATAGTTCACCAATTGGGAAAAAG 57.057 29.630 27.89 10.51 41.15 2.27
2167 2197 6.994421 ATAGTTCACCAATTGGGAAAAAGT 57.006 33.333 27.89 18.64 41.15 2.66
2168 2198 5.692115 AGTTCACCAATTGGGAAAAAGTT 57.308 34.783 27.89 1.53 41.15 2.66
2169 2199 5.427378 AGTTCACCAATTGGGAAAAAGTTG 58.573 37.500 27.89 14.32 41.15 3.16
2170 2200 5.188751 AGTTCACCAATTGGGAAAAAGTTGA 59.811 36.000 27.89 16.33 41.15 3.18
2171 2201 5.017294 TCACCAATTGGGAAAAAGTTGAC 57.983 39.130 27.89 0.00 41.15 3.18
2172 2202 4.714308 TCACCAATTGGGAAAAAGTTGACT 59.286 37.500 27.89 0.00 41.15 3.41
2173 2203 4.810491 CACCAATTGGGAAAAAGTTGACTG 59.190 41.667 27.89 8.77 41.15 3.51
2174 2204 4.141733 ACCAATTGGGAAAAAGTTGACTGG 60.142 41.667 27.89 0.00 41.15 4.00
2175 2205 4.100808 CCAATTGGGAAAAAGTTGACTGGA 59.899 41.667 17.36 0.00 40.01 3.86
2176 2206 5.221702 CCAATTGGGAAAAAGTTGACTGGAT 60.222 40.000 17.36 0.00 40.01 3.41
2177 2207 6.290605 CAATTGGGAAAAAGTTGACTGGATT 58.709 36.000 0.00 0.00 0.00 3.01
2178 2208 5.948742 TTGGGAAAAAGTTGACTGGATTT 57.051 34.783 0.00 0.00 0.00 2.17
2179 2209 5.275067 TGGGAAAAAGTTGACTGGATTTG 57.725 39.130 0.00 0.00 0.00 2.32
2180 2210 4.714308 TGGGAAAAAGTTGACTGGATTTGT 59.286 37.500 0.00 0.00 0.00 2.83
2181 2211 5.188751 TGGGAAAAAGTTGACTGGATTTGTT 59.811 36.000 0.00 0.00 0.00 2.83
2182 2212 6.112734 GGGAAAAAGTTGACTGGATTTGTTT 58.887 36.000 0.00 0.00 0.00 2.83
2183 2213 6.597672 GGGAAAAAGTTGACTGGATTTGTTTT 59.402 34.615 0.00 0.00 0.00 2.43
2184 2214 7.120579 GGGAAAAAGTTGACTGGATTTGTTTTT 59.879 33.333 0.00 0.00 0.00 1.94
2185 2215 8.175069 GGAAAAAGTTGACTGGATTTGTTTTTC 58.825 33.333 0.00 0.00 39.91 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
92 94 8.635124 CGTTGCGTGTGAAAATTTAAGAATAAT 58.365 29.630 0.00 0.00 0.00 1.28
107 109 3.047280 GCCATCCGTTGCGTGTGA 61.047 61.111 0.00 0.00 0.00 3.58
111 113 2.031919 TCAAGCCATCCGTTGCGT 59.968 55.556 0.00 0.00 0.00 5.24
113 115 0.379669 CATCTCAAGCCATCCGTTGC 59.620 55.000 0.00 0.00 0.00 4.17
126 128 5.190330 TCCCACTTCAAGATTGATCATCTCA 59.810 40.000 0.00 0.00 41.93 3.27
331 335 7.820044 ATTCGAGTTGAAGAAGTATGAGAAC 57.180 36.000 0.00 0.00 40.65 3.01
384 389 8.687242 TCAGGATATGCCTCTACTATAAAATCG 58.313 37.037 0.00 0.00 46.97 3.34
616 621 0.400975 TAAGGCAGCGGGTTTTGGTA 59.599 50.000 0.00 0.00 0.00 3.25
741 746 7.043059 GCATGTGTAGAATACTAGCAAGAGAAC 60.043 40.741 0.00 0.00 43.54 3.01
880 885 3.119424 TCGGACTTTCCCAAACACAAAAC 60.119 43.478 0.00 0.00 31.13 2.43
916 921 6.599638 AGGGAAAGAAGGAAAAGACATATTCG 59.400 38.462 0.00 0.00 0.00 3.34
963 969 9.120538 TCATTCTTGTAGAGTAAATAATTGGGC 57.879 33.333 0.00 0.00 0.00 5.36
1331 1344 5.945144 AGGCTGATCCAAATTTATTGCTT 57.055 34.783 0.00 0.00 37.29 3.91
1364 1377 0.254178 CCTGCTCAACCTAGGTGCAT 59.746 55.000 21.88 2.32 33.02 3.96
1647 1665 6.393897 TCCTGGGTCATTAGATAAGAATCCT 58.606 40.000 0.00 0.00 31.98 3.24
1672 1690 2.721167 CCTCGCGTCCAGGATTCCA 61.721 63.158 5.77 0.00 31.91 3.53
1798 1819 1.134670 CGAATCCCTCTCTTTCCGCTT 60.135 52.381 0.00 0.00 0.00 4.68
1860 1881 1.592223 GCTGAGTGGACTAAGCGGT 59.408 57.895 0.16 0.00 40.40 5.68
1893 1915 1.332375 CACGGAAACCTTTCGCTTTGA 59.668 47.619 0.00 0.00 38.06 2.69
2140 2170 9.942850 CTTTTTCCCAATTGGTGAACTATTTAT 57.057 29.630 22.91 0.00 34.77 1.40
2141 2171 8.929487 ACTTTTTCCCAATTGGTGAACTATTTA 58.071 29.630 22.91 7.39 34.77 1.40
2142 2172 7.801104 ACTTTTTCCCAATTGGTGAACTATTT 58.199 30.769 22.91 6.87 34.77 1.40
2143 2173 7.373617 ACTTTTTCCCAATTGGTGAACTATT 57.626 32.000 22.91 8.02 34.77 1.73
2144 2174 6.994421 ACTTTTTCCCAATTGGTGAACTAT 57.006 33.333 22.91 8.71 34.77 2.12
2145 2175 6.381420 TCAACTTTTTCCCAATTGGTGAACTA 59.619 34.615 22.91 12.61 34.77 2.24
2146 2176 5.188751 TCAACTTTTTCCCAATTGGTGAACT 59.811 36.000 22.91 6.25 34.77 3.01
2147 2177 5.293324 GTCAACTTTTTCCCAATTGGTGAAC 59.707 40.000 22.91 8.54 34.77 3.18
2148 2178 5.188751 AGTCAACTTTTTCCCAATTGGTGAA 59.811 36.000 22.91 20.56 34.77 3.18
2149 2179 4.714308 AGTCAACTTTTTCCCAATTGGTGA 59.286 37.500 22.91 16.20 34.77 4.02
2150 2180 4.810491 CAGTCAACTTTTTCCCAATTGGTG 59.190 41.667 22.91 14.20 34.77 4.17
2151 2181 4.141733 CCAGTCAACTTTTTCCCAATTGGT 60.142 41.667 22.91 0.00 34.77 3.67
2152 2182 4.100808 TCCAGTCAACTTTTTCCCAATTGG 59.899 41.667 18.21 18.21 0.00 3.16
2153 2183 5.275067 TCCAGTCAACTTTTTCCCAATTG 57.725 39.130 0.00 0.00 0.00 2.32
2154 2184 6.499106 AATCCAGTCAACTTTTTCCCAATT 57.501 33.333 0.00 0.00 0.00 2.32
2155 2185 6.126796 ACAAATCCAGTCAACTTTTTCCCAAT 60.127 34.615 0.00 0.00 0.00 3.16
2156 2186 5.188751 ACAAATCCAGTCAACTTTTTCCCAA 59.811 36.000 0.00 0.00 0.00 4.12
2157 2187 4.714308 ACAAATCCAGTCAACTTTTTCCCA 59.286 37.500 0.00 0.00 0.00 4.37
2158 2188 5.276461 ACAAATCCAGTCAACTTTTTCCC 57.724 39.130 0.00 0.00 0.00 3.97
2159 2189 7.609760 AAAACAAATCCAGTCAACTTTTTCC 57.390 32.000 0.00 0.00 0.00 3.13


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

AutoCloner maintained by Alex Coulton.