Multiple sequence alignment - TraesCS5B01G161300

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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 TraesCS5B01G161300 chr5B 100.000 2264 0 0 1 2264 297110492 297112755 0.000000e+00 4181
1 TraesCS5B01G161300 chr5B 98.970 1942 20 0 1 1942 436476554 436478495 0.000000e+00 3476
2 TraesCS5B01G161300 chr5B 98.869 1946 21 1 1 1945 351469616 351467671 0.000000e+00 3470
3 TraesCS5B01G161300 chr5B 92.676 355 25 1 1827 2180 454662700 454663054 5.580000e-141 510
4 TraesCS5B01G161300 chr5B 99.107 112 1 0 2153 2264 297107692 297107581 3.810000e-48 202
5 TraesCS5B01G161300 chr5A 99.128 2180 19 0 1 2180 591473726 591475905 0.000000e+00 3921
6 TraesCS5B01G161300 chr5A 98.214 112 2 0 2153 2264 591470986 591470875 1.770000e-46 196
7 TraesCS5B01G161300 chr1B 98.499 2198 30 3 1 2196 649301320 649299124 0.000000e+00 3873
8 TraesCS5B01G161300 chr1B 94.558 294 15 1 1887 2180 357900324 357900032 9.530000e-124 453
9 TraesCS5B01G161300 chr1B 98.214 112 2 0 2153 2264 649304457 649304568 1.770000e-46 196
10 TraesCS5B01G161300 chr7A 98.317 2198 34 3 1 2196 497719530 497717334 0.000000e+00 3851
11 TraesCS5B01G161300 chr7A 98.919 1943 19 2 1 1942 16005011 16006952 0.000000e+00 3470
12 TraesCS5B01G161300 chr7A 99.091 110 1 0 2155 2264 497712219 497712110 4.930000e-47 198
13 TraesCS5B01G161300 chr6A 98.258 2182 34 4 1 2180 466678913 466681092 0.000000e+00 3816
14 TraesCS5B01G161300 chr6A 99.107 112 1 0 2153 2264 137869686 137869575 3.810000e-48 202
15 TraesCS5B01G161300 chr6A 99.107 112 1 0 2153 2264 600293969 600293858 3.810000e-48 202
16 TraesCS5B01G161300 chr2A 98.920 1945 21 0 1 1945 148615284 148613340 0.000000e+00 3476
17 TraesCS5B01G161300 chr2A 98.970 1942 20 0 1 1942 728933672 728935613 0.000000e+00 3476
18 TraesCS5B01G161300 chr2B 90.812 468 32 7 1742 2199 138733566 138734032 1.150000e-172 616
19 TraesCS5B01G161300 chr2B 88.488 443 39 9 1738 2179 563915374 563914943 1.990000e-145 525
20 TraesCS5B01G161300 chr2B 97.368 114 3 0 2149 2262 440606013 440606126 6.380000e-46 195
21 TraesCS5B01G161300 chr2B 97.321 112 3 0 2153 2264 364340185 364340296 8.250000e-45 191
22 TraesCS5B01G161300 chr3B 89.616 443 38 7 1738 2179 16122670 16122235 7.060000e-155 556


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 TraesCS5B01G161300 chr5B 297110492 297112755 2263 False 4181 4181 100.000 1 2264 1 chr5B.!!$F1 2263
1 TraesCS5B01G161300 chr5B 436476554 436478495 1941 False 3476 3476 98.970 1 1942 1 chr5B.!!$F2 1941
2 TraesCS5B01G161300 chr5B 351467671 351469616 1945 True 3470 3470 98.869 1 1945 1 chr5B.!!$R2 1944
3 TraesCS5B01G161300 chr5A 591473726 591475905 2179 False 3921 3921 99.128 1 2180 1 chr5A.!!$F1 2179
4 TraesCS5B01G161300 chr1B 649299124 649301320 2196 True 3873 3873 98.499 1 2196 1 chr1B.!!$R2 2195
5 TraesCS5B01G161300 chr7A 497717334 497719530 2196 True 3851 3851 98.317 1 2196 1 chr7A.!!$R2 2195
6 TraesCS5B01G161300 chr7A 16005011 16006952 1941 False 3470 3470 98.919 1 1942 1 chr7A.!!$F1 1941
7 TraesCS5B01G161300 chr6A 466678913 466681092 2179 False 3816 3816 98.258 1 2180 1 chr6A.!!$F1 2179
8 TraesCS5B01G161300 chr2A 148613340 148615284 1944 True 3476 3476 98.920 1 1945 1 chr2A.!!$R1 1944
9 TraesCS5B01G161300 chr2A 728933672 728935613 1941 False 3476 3476 98.970 1 1942 1 chr2A.!!$F1 1941

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
885 888 1.002792 GATCGGCCTTCGGTTATTTGC 60.003 52.381 0.0 0.0 39.77 3.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2055 2058 1.500844 CGAGCAAAGCAAGCCAGAG 59.499 57.895 0.0 0.0 0.0 3.35 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
649 652 3.299977 CGGTGGTGGTGGTCGAGA 61.300 66.667 0.00 0.00 0.00 4.04
725 728 2.089980 GGTGCTAGTGTTCGTAGAGGA 58.910 52.381 0.00 0.00 38.43 3.71
885 888 1.002792 GATCGGCCTTCGGTTATTTGC 60.003 52.381 0.00 0.00 39.77 3.68
1659 1662 0.469144 ACAAATGGAAAGGCACCGGT 60.469 50.000 0.00 0.00 0.00 5.28
2046 2049 3.625897 CACACCCAGACGCCAGGA 61.626 66.667 0.00 0.00 0.00 3.86
2047 2050 2.847234 ACACCCAGACGCCAGGAA 60.847 61.111 0.00 0.00 0.00 3.36
2195 2198 3.365265 GCCCCTTTGCCACGTCAG 61.365 66.667 0.00 0.00 0.00 3.51
2196 2199 3.365265 CCCCTTTGCCACGTCAGC 61.365 66.667 0.04 0.04 0.00 4.26
2197 2200 2.594303 CCCTTTGCCACGTCAGCA 60.594 61.111 5.70 5.70 38.81 4.41
2198 2201 2.620112 CCCTTTGCCACGTCAGCAG 61.620 63.158 9.53 0.58 42.17 4.24
2199 2202 2.620112 CCTTTGCCACGTCAGCAGG 61.620 63.158 9.53 5.63 42.17 4.85
2200 2203 1.893808 CTTTGCCACGTCAGCAGGT 60.894 57.895 9.53 0.00 42.17 4.00
2201 2204 1.845809 CTTTGCCACGTCAGCAGGTC 61.846 60.000 9.53 0.00 42.17 3.85
2202 2205 2.601194 TTTGCCACGTCAGCAGGTCA 62.601 55.000 9.53 0.00 42.17 4.02
2203 2206 2.046892 GCCACGTCAGCAGGTCAT 60.047 61.111 2.25 0.00 0.00 3.06
2204 2207 2.103042 GCCACGTCAGCAGGTCATC 61.103 63.158 2.25 0.00 0.00 2.92
2205 2208 1.807165 CCACGTCAGCAGGTCATCG 60.807 63.158 0.00 0.00 0.00 3.84
2206 2209 1.807165 CACGTCAGCAGGTCATCGG 60.807 63.158 0.00 0.00 0.00 4.18
2207 2210 2.202797 CGTCAGCAGGTCATCGGG 60.203 66.667 0.00 0.00 0.00 5.14
2208 2211 2.512515 GTCAGCAGGTCATCGGGC 60.513 66.667 0.00 0.00 0.00 6.13
2209 2212 3.002583 TCAGCAGGTCATCGGGCA 61.003 61.111 0.00 0.00 0.00 5.36
2210 2213 2.513204 CAGCAGGTCATCGGGCAG 60.513 66.667 0.00 0.00 0.00 4.85
2211 2214 3.790437 AGCAGGTCATCGGGCAGG 61.790 66.667 0.00 0.00 0.00 4.85
2250 2253 4.742201 CAGACGCCAGGGACCGTG 62.742 72.222 7.23 7.23 37.87 4.94
2257 2260 4.742201 CAGGGACCGTGGCGTCTG 62.742 72.222 6.27 0.00 33.07 3.51
2260 2263 4.681978 GGACCGTGGCGTCTGCTT 62.682 66.667 0.00 0.00 42.25 3.91
2261 2264 3.112709 GACCGTGGCGTCTGCTTC 61.113 66.667 0.00 0.00 42.25 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
261 262 0.036010 AACTCTTGCATCCTCACGGG 60.036 55.000 0.00 0.00 0.00 5.28
649 652 2.224066 CCACCTCTGACACTCGTTCTTT 60.224 50.000 0.00 0.00 0.00 2.52
725 728 1.271054 CCACCTCTAGCACTTGTGCTT 60.271 52.381 29.37 15.68 43.52 3.91
1087 1090 1.134250 GGGCACATCCTTCTCCTTCTC 60.134 57.143 0.00 0.00 34.39 2.87
1327 1330 2.482494 CAAAGTGGAGGAGGGGACTAT 58.518 52.381 0.00 0.00 44.43 2.12
1659 1662 2.747446 TCTCGACAGTTCATCATCGACA 59.253 45.455 0.00 0.00 38.59 4.35
2055 2058 1.500844 CGAGCAAAGCAAGCCAGAG 59.499 57.895 0.00 0.00 0.00 3.35
2180 2183 2.594303 TGCTGACGTGGCAAAGGG 60.594 61.111 9.89 0.00 36.71 3.95
2181 2184 2.620112 CCTGCTGACGTGGCAAAGG 61.620 63.158 12.75 8.52 39.30 3.11
2182 2185 1.845809 GACCTGCTGACGTGGCAAAG 61.846 60.000 12.75 9.98 39.30 2.77
2183 2186 1.891919 GACCTGCTGACGTGGCAAA 60.892 57.895 12.75 0.00 39.30 3.68
2186 2189 2.046892 ATGACCTGCTGACGTGGC 60.047 61.111 0.00 0.00 0.00 5.01
2187 2190 1.807165 CGATGACCTGCTGACGTGG 60.807 63.158 0.00 0.00 0.00 4.94
2189 2192 2.573869 CCGATGACCTGCTGACGT 59.426 61.111 0.00 0.00 0.00 4.34
2191 2194 2.512515 GCCCGATGACCTGCTGAC 60.513 66.667 0.00 0.00 0.00 3.51
2192 2195 3.002583 TGCCCGATGACCTGCTGA 61.003 61.111 0.00 0.00 0.00 4.26
2193 2196 2.513204 CTGCCCGATGACCTGCTG 60.513 66.667 0.00 0.00 0.00 4.41
2194 2197 3.790437 CCTGCCCGATGACCTGCT 61.790 66.667 0.00 0.00 0.00 4.24
2233 2236 4.742201 CACGGTCCCTGGCGTCTG 62.742 72.222 0.00 0.00 0.00 3.51
2240 2243 4.742201 CAGACGCCACGGTCCCTG 62.742 72.222 0.00 0.00 37.66 4.45
2243 2246 4.681978 AAGCAGACGCCACGGTCC 62.682 66.667 0.00 0.00 39.83 4.46
2244 2247 3.112709 GAAGCAGACGCCACGGTC 61.113 66.667 0.00 0.00 39.83 4.79


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

AutoCloner maintained by Alex Coulton.