Multiple sequence alignment - TraesCS4D01G087000

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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 TraesCS4D01G087000 chr4D 100.000 2558 0 0 1 2558 62302754 62305311 0.000000e+00 4724
1 TraesCS4D01G087000 chr4D 81.366 161 25 5 163 322 421534413 421534257 2.670000e-25 126
2 TraesCS4D01G087000 chr4B 92.681 2596 138 33 1 2556 89928072 89930655 0.000000e+00 3694
3 TraesCS4D01G087000 chr4B 83.735 166 22 2 162 322 639141342 639141177 4.410000e-33 152
4 TraesCS4D01G087000 chr4A 91.775 2614 141 18 3 2556 535818006 535820605 0.000000e+00 3568
5 TraesCS4D01G087000 chr7D 79.755 326 52 9 1 322 632785027 632784712 9.210000e-55 224
6 TraesCS4D01G087000 chr7D 83.425 181 27 3 144 321 413110211 413110391 5.660000e-37 165
7 TraesCS4D01G087000 chr7D 77.622 286 54 9 2 285 523044705 523044982 5.660000e-37 165
8 TraesCS4D01G087000 chr7A 79.094 287 44 13 4 285 603290612 603290887 1.560000e-42 183
9 TraesCS4D01G087000 chr7A 76.780 323 64 6 4 322 96829235 96828920 1.220000e-38 171
10 TraesCS4D01G087000 chr2A 77.652 264 48 9 2 261 61775133 61775389 1.590000e-32 150
11 TraesCS4D01G087000 chr1D 85.315 143 19 1 1 143 216730561 216730701 2.050000e-31 147
12 TraesCS4D01G087000 chr7B 81.977 172 23 7 152 319 289195301 289195468 3.430000e-29 139
13 TraesCS4D01G087000 chr2D 75.000 284 53 12 42 319 61301269 61301540 5.780000e-22 115


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 TraesCS4D01G087000 chr4D 62302754 62305311 2557 False 4724 4724 100.000 1 2558 1 chr4D.!!$F1 2557
1 TraesCS4D01G087000 chr4B 89928072 89930655 2583 False 3694 3694 92.681 1 2556 1 chr4B.!!$F1 2555
2 TraesCS4D01G087000 chr4A 535818006 535820605 2599 False 3568 3568 91.775 3 2556 1 chr4A.!!$F1 2553

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
297 299 0.246086 GATGCGGGTGGAAATTTGCA 59.754 50.0 8.47 8.47 36.69 4.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2038 2087 0.390866 AGCTCTGTTCTGGCATGACG 60.391 55.0 0.0 0.0 0.0 4.35 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
57 58 2.545742 CGTGAGAATGGATATGTGCCGA 60.546 50.000 0.00 0.00 0.00 5.54
89 90 7.618512 AGCATAGACTAGTTTTACCTTAGTCCA 59.381 37.037 0.00 0.00 38.24 4.02
160 161 5.604650 TGGTTTGGGTTTGTATGAAATCCTT 59.395 36.000 0.00 0.00 31.72 3.36
212 214 9.651913 AGTTCAAAAAGTTGTTGAAATGTATGT 57.348 25.926 20.38 0.61 44.35 2.29
216 218 9.044150 CAAAAAGTTGTTGAAATGTATGTGGAT 57.956 29.630 0.00 0.00 0.00 3.41
297 299 0.246086 GATGCGGGTGGAAATTTGCA 59.754 50.000 8.47 8.47 36.69 4.08
301 303 0.678950 CGGGTGGAAATTTGCAGGTT 59.321 50.000 13.15 0.00 0.00 3.50
370 372 8.134895 TCATAAAAGTTGAAACTAGCCACTTTG 58.865 33.333 0.00 0.00 38.57 2.77
421 444 4.701956 AAATTCGTGGTTGAGCTATTGG 57.298 40.909 0.00 0.00 0.00 3.16
556 579 1.686052 TCCAAAACCATTGCACTGTCC 59.314 47.619 3.14 0.00 0.00 4.02
659 682 4.944930 TCTTTTTATATCCCAACACACCCG 59.055 41.667 0.00 0.00 0.00 5.28
746 769 1.903404 CCCAGCTCAAACACCACCC 60.903 63.158 0.00 0.00 0.00 4.61
921 961 3.857157 TCCAACACCAACTTAGAGCTT 57.143 42.857 0.00 0.00 0.00 3.74
1143 1183 2.394563 GCTTGGCAGCTTCGAGTCC 61.395 63.158 0.00 0.00 43.51 3.85
1605 1645 9.418045 GAGGTCGAAATTAATCAAAATTTTCCA 57.582 29.630 0.00 0.00 38.77 3.53
1636 1676 5.515106 ACGGAAAATTTAGGGATTCCATCA 58.485 37.500 4.80 0.00 41.11 3.07
1732 1773 5.468746 GTGTGGCATTTCTTTGTACTACAGA 59.531 40.000 0.00 0.00 0.00 3.41
1784 1825 8.883731 ACAATAATTAAGTTCCACTGAGAATCG 58.116 33.333 0.00 0.00 38.61 3.34
1798 1839 5.126384 ACTGAGAATCGAACCTCCTTTCTAG 59.874 44.000 12.88 6.75 38.61 2.43
1806 1847 4.220163 CGAACCTCCTTTCTAGTTACTGGT 59.780 45.833 0.00 0.00 0.00 4.00
1807 1848 5.279356 CGAACCTCCTTTCTAGTTACTGGTT 60.279 44.000 0.00 0.00 37.89 3.67
1864 1905 1.306397 TCCCTCGGGAAGGTAACCC 60.306 63.158 1.21 0.00 44.56 4.11
1906 1947 3.881780 ATAGAGAGGATCGAACGAACG 57.118 47.619 0.12 0.00 42.67 3.95
1907 1948 0.099082 AGAGAGGATCGAACGAACGC 59.901 55.000 0.12 0.07 42.67 4.84
1908 1949 0.179171 GAGAGGATCGAACGAACGCA 60.179 55.000 0.12 0.00 42.67 5.24
1909 1950 0.242825 AGAGGATCGAACGAACGCAA 59.757 50.000 0.12 0.00 42.67 4.85
1910 1951 1.065358 GAGGATCGAACGAACGCAAA 58.935 50.000 0.12 0.00 0.00 3.68
1911 1952 1.458064 GAGGATCGAACGAACGCAAAA 59.542 47.619 0.12 0.00 0.00 2.44
1953 2002 1.949525 CCCTCCAGAATTGTTATGCGG 59.050 52.381 0.00 0.00 0.00 5.69
2046 2095 3.829886 TTGTCAGAAAATCGTCATGCC 57.170 42.857 0.00 0.00 0.00 4.40
2048 2097 2.743664 TGTCAGAAAATCGTCATGCCAG 59.256 45.455 0.00 0.00 0.00 4.85
2063 2112 0.519077 GCCAGAACAGAGCTTTTCCG 59.481 55.000 0.00 0.00 0.00 4.30
2111 2161 2.024590 GCATGGAGATTTGCCAGCCC 62.025 60.000 0.00 0.00 39.11 5.19
2140 2191 8.624367 AAAAGAAATGATGAAAATTGCCATGA 57.376 26.923 0.00 0.00 0.00 3.07
2145 2196 8.568676 AAATGATGAAAATTGCCATGATCAAA 57.431 26.923 0.00 0.00 0.00 2.69
2168 2219 4.990543 TTTGTCGTCTTGCTACATCAAG 57.009 40.909 0.00 0.00 43.53 3.02
2188 2240 6.985117 TCAAGGAAAGAAATGTGAGAATTGG 58.015 36.000 0.00 0.00 0.00 3.16
2211 2263 7.095910 TGGCATGTTGTACAAAGATAAATTGG 58.904 34.615 10.51 0.00 32.02 3.16
2212 2264 7.096551 GGCATGTTGTACAAAGATAAATTGGT 58.903 34.615 10.51 0.00 32.02 3.67
2243 2316 2.736721 TGTGTTCGCTCTCAAATACTGC 59.263 45.455 0.00 0.00 0.00 4.40
2249 2322 2.281762 CGCTCTCAAATACTGCCGTTAC 59.718 50.000 0.00 0.00 0.00 2.50
2259 2332 0.658897 CTGCCGTTACCACGTTGTTT 59.341 50.000 0.00 0.00 45.62 2.83
2262 2335 0.317186 CCGTTACCACGTTGTTTGCC 60.317 55.000 0.00 0.00 45.62 4.52
2300 2373 1.599797 GGCGGCGCATAGGGTATTT 60.600 57.895 34.36 0.00 0.00 1.40
2383 2457 7.283127 TGCCATGAGAATTTGTAGGATTAACTC 59.717 37.037 0.00 0.00 0.00 3.01
2458 2532 0.110238 CATGGAACTTTGTGACGCGG 60.110 55.000 12.47 0.00 0.00 6.46
2486 2560 2.218953 TTCCGTAGAATGACGATGCC 57.781 50.000 0.00 0.00 45.82 4.40
2511 2585 1.753930 TACTACCGCGACAAGATGGA 58.246 50.000 8.23 0.00 0.00 3.41
2550 2624 4.371417 TCCTCGCCCGTACCACCT 62.371 66.667 0.00 0.00 0.00 4.00
2556 2630 2.934570 GCCCGTACCACCTTGACGA 61.935 63.158 0.00 0.00 38.88 4.20
2557 2631 1.667151 CCCGTACCACCTTGACGAA 59.333 57.895 0.00 0.00 38.88 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 1.341531 CCCTTGACTAGTCTATGGCCG 59.658 57.143 23.01 4.25 0.00 6.13
7 8 2.399580 ACCCTTGACTAGTCTATGGCC 58.600 52.381 23.01 0.00 0.00 5.36
57 58 1.390565 AACTAGTCTATGCTCGGCGT 58.609 50.000 6.85 0.00 0.00 5.68
160 161 3.801050 CGGACAAATTCATGCAAACACAA 59.199 39.130 0.00 0.00 0.00 3.33
212 214 0.180171 CCGCCATCCAACACTATCCA 59.820 55.000 0.00 0.00 0.00 3.41
216 218 2.252072 GAGGCCGCCATCCAACACTA 62.252 60.000 13.15 0.00 0.00 2.74
286 288 0.033228 CGCCAACCTGCAAATTTCCA 59.967 50.000 0.00 0.00 0.00 3.53
297 299 1.675641 GCATCTCCAACGCCAACCT 60.676 57.895 0.00 0.00 0.00 3.50
393 395 8.902540 ATAGCTCAACCACGAATTTTGATATA 57.097 30.769 0.00 0.00 0.00 0.86
395 397 7.415095 CCAATAGCTCAACCACGAATTTTGATA 60.415 37.037 0.00 0.00 0.00 2.15
397 399 5.335583 CCAATAGCTCAACCACGAATTTTGA 60.336 40.000 0.00 0.00 0.00 2.69
421 444 2.679450 ACATCAATGTTGTGTGCATGC 58.321 42.857 11.82 11.82 37.90 4.06
455 478 7.231317 TGGCTTTGTGACTTCTTTTATCTTCAT 59.769 33.333 0.00 0.00 0.00 2.57
460 483 5.631096 GCTTGGCTTTGTGACTTCTTTTATC 59.369 40.000 0.00 0.00 0.00 1.75
472 495 2.409975 CTTCAATGGCTTGGCTTTGTG 58.590 47.619 17.54 10.92 32.95 3.33
477 500 1.604593 ACGCTTCAATGGCTTGGCT 60.605 52.632 0.00 0.00 32.95 4.75
556 579 1.492133 TTGTGGGAGGGAGCTTCCTG 61.492 60.000 21.72 0.00 37.25 3.86
921 961 1.289066 GCAGGAGTGTCGCAGTGTA 59.711 57.895 0.00 0.00 0.00 2.90
1605 1645 6.718522 TCCCTAAATTTTCCGTTGTCTTTT 57.281 33.333 0.00 0.00 0.00 2.27
1615 1655 6.098838 AGCTTGATGGAATCCCTAAATTTTCC 59.901 38.462 0.00 0.00 44.73 3.13
1636 1676 9.758651 ACTTAAATTTGTTCGGAAATTAAGCTT 57.241 25.926 3.48 3.48 35.01 3.74
1784 1825 5.741962 ACCAGTAACTAGAAAGGAGGTTC 57.258 43.478 0.00 0.00 0.00 3.62
1864 1905 3.266510 TGGGGAATGATTGTTCTCTCG 57.733 47.619 0.00 0.00 0.00 4.04
1918 1967 0.546598 GAGGGTTCGGTGGGAATGAT 59.453 55.000 0.00 0.00 36.92 2.45
1922 1971 2.122324 TGGAGGGTTCGGTGGGAA 60.122 61.111 0.00 0.00 0.00 3.97
1928 1977 2.200373 AACAATTCTGGAGGGTTCGG 57.800 50.000 0.00 0.00 0.00 4.30
1929 1978 3.065371 GCATAACAATTCTGGAGGGTTCG 59.935 47.826 0.00 0.00 0.00 3.95
1967 2016 7.201688 GGCAAATCCTTTACAACAAACACAATT 60.202 33.333 0.00 0.00 0.00 2.32
1974 2023 7.731054 ACATTAGGCAAATCCTTTACAACAAA 58.269 30.769 0.00 0.00 44.75 2.83
2038 2087 0.390866 AGCTCTGTTCTGGCATGACG 60.391 55.000 0.00 0.00 0.00 4.35
2046 2095 1.532868 CCACGGAAAAGCTCTGTTCTG 59.467 52.381 7.01 7.01 41.13 3.02
2048 2097 0.875059 CCCACGGAAAAGCTCTGTTC 59.125 55.000 0.00 0.00 41.13 3.18
2140 2191 6.312399 TGTAGCAAGACGACAAATTTTGAT 57.688 33.333 15.81 0.50 30.19 2.57
2145 2196 5.106555 CCTTGATGTAGCAAGACGACAAATT 60.107 40.000 11.14 0.00 46.31 1.82
2168 2219 5.138125 TGCCAATTCTCACATTTCTTTCC 57.862 39.130 0.00 0.00 0.00 3.13
2188 2240 9.801873 ATACCAATTTATCTTTGTACAACATGC 57.198 29.630 8.07 0.00 0.00 4.06
2249 2322 1.156736 CCTCTAGGCAAACAACGTGG 58.843 55.000 0.00 0.00 0.00 4.94
2259 2332 3.390521 CCGTGCACCCTCTAGGCA 61.391 66.667 12.15 0.00 40.58 4.75
2262 2335 0.757188 AGATCCCGTGCACCCTCTAG 60.757 60.000 12.15 0.00 0.00 2.43
2300 2373 6.347563 CGTTAGTTTTATAGGTTTTCCGCACA 60.348 38.462 0.00 0.00 46.35 4.57
2433 2507 4.083003 GCGTCACAAAGTTCCATGGAAATA 60.083 41.667 28.64 9.50 35.75 1.40
2435 2509 2.034053 GCGTCACAAAGTTCCATGGAAA 59.966 45.455 28.64 8.75 35.75 3.13
2446 2520 0.882927 TTTCCTCCCGCGTCACAAAG 60.883 55.000 4.92 0.00 0.00 2.77
2458 2532 4.270325 CGTCATTCTACGGAAATTTCCTCC 59.730 45.833 29.85 9.87 45.33 4.30
2486 2560 4.744136 TCTTGTCGCGGTAGTATATCTG 57.256 45.455 6.13 0.00 0.00 2.90
2511 2585 1.802365 GAAACAGTGGGATAACGCGTT 59.198 47.619 29.27 29.27 0.00 4.84


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

AutoCloner maintained by Alex Coulton.