Multiple sequence alignment - TraesCS4A01G016300

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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 TraesCS4A01G016300 chr4A 100.000 2605 0 0 1 2605 10937614 10940218 0.000000e+00 4811.0
1 TraesCS4A01G016300 chr4D 94.533 2140 64 14 64 2157 458092620 458090488 0.000000e+00 3254.0
2 TraesCS4A01G016300 chr4D 91.499 447 23 4 2171 2605 458090443 458090000 3.710000e-168 601.0
3 TraesCS4A01G016300 chr4D 97.826 46 1 0 1 46 458092655 458092610 2.150000e-11 80.5
4 TraesCS4A01G016300 chr4B 94.805 1155 42 6 64 1205 572158587 572157438 0.000000e+00 1784.0
5 TraesCS4A01G016300 chr4B 88.536 881 59 20 1292 2163 572157394 572156547 0.000000e+00 1029.0
6 TraesCS4A01G016300 chr4B 88.822 331 13 11 2171 2494 572156501 572156188 4.070000e-103 385.0
7 TraesCS4A01G016300 chr4B 87.805 123 4 2 2494 2605 572156086 572155964 1.630000e-27 134.0
8 TraesCS4A01G016300 chr4B 97.826 46 1 0 1 46 572158622 572158577 2.150000e-11 80.5
9 TraesCS4A01G016300 chr2B 91.566 83 7 0 1465 1547 746680788 746680870 5.890000e-22 115.0
10 TraesCS4A01G016300 chr2A 92.958 71 5 0 1465 1535 744408905 744408975 1.280000e-18 104.0


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 TraesCS4A01G016300 chr4A 10937614 10940218 2604 False 4811.000000 4811 100.000000 1 2605 1 chr4A.!!$F1 2604
1 TraesCS4A01G016300 chr4D 458090000 458092655 2655 True 1311.833333 3254 94.619333 1 2605 3 chr4D.!!$R1 2604
2 TraesCS4A01G016300 chr4B 572155964 572158622 2658 True 682.500000 1784 91.558800 1 2605 5 chr4B.!!$R1 2604

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
240 241 0.102481 CCCGGTATCACTGTTCCTCG 59.898 60.0 0.0 0.0 0.0 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1865 1915 0.165295 CGAAGCAGCACATCACACAG 59.835 55.0 0.0 0.0 0.0 3.66 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
115 116 8.267183 TGCTAAAATTTCTGATCTGACAGGATA 58.733 33.333 1.81 0.00 38.31 2.59
194 195 0.585357 GAGGCACTTGCGCATCTATG 59.415 55.000 12.75 8.68 41.55 2.23
219 220 6.404954 GGAGTAGTGAGTAGTGACTGGAATTC 60.405 46.154 0.00 0.00 35.45 2.17
230 231 2.169769 GACTGGAATTCACCCGGTATCA 59.830 50.000 7.93 0.00 42.99 2.15
238 239 0.902531 CACCCGGTATCACTGTTCCT 59.097 55.000 0.00 0.00 0.00 3.36
240 241 0.102481 CCCGGTATCACTGTTCCTCG 59.898 60.000 0.00 0.00 0.00 4.63
244 245 1.481871 GTATCACTGTTCCTCGGGGA 58.518 55.000 0.00 0.00 39.39 4.81
419 421 3.554129 GGGCAAGAACAATAAACCCACAC 60.554 47.826 0.00 0.00 35.84 3.82
614 624 3.054434 TCCCTCTCTCTGTCTCTCTCTTG 60.054 52.174 0.00 0.00 0.00 3.02
701 723 3.047695 CCCTATAGGTCAGGGTCTTGT 57.952 52.381 17.72 0.00 46.77 3.16
854 876 1.056660 TCCCTCTCTTCCAACACCAC 58.943 55.000 0.00 0.00 0.00 4.16
1216 1238 7.287927 TGGTTAGACTCTTCTTCTTCTTCTTCA 59.712 37.037 0.00 0.00 32.75 3.02
1217 1239 7.597369 GGTTAGACTCTTCTTCTTCTTCTTCAC 59.403 40.741 0.00 0.00 32.75 3.18
1245 1294 2.435437 AGAAATTGGCCACTGCTTTGTT 59.565 40.909 3.88 0.00 37.74 2.83
1254 1303 3.606153 GCCACTGCTTTGTTGTAGTTACG 60.606 47.826 0.00 0.00 30.70 3.18
1256 1305 4.318546 CCACTGCTTTGTTGTAGTTACGAC 60.319 45.833 0.00 3.22 40.29 4.34
1260 1310 5.786311 TGCTTTGTTGTAGTTACGACCTAT 58.214 37.500 7.11 0.00 39.36 2.57
1265 1315 5.786311 TGTTGTAGTTACGACCTATTGCTT 58.214 37.500 7.11 0.00 39.36 3.91
1276 1326 4.331717 CGACCTATTGCTTACCGTTCAATT 59.668 41.667 0.00 0.00 33.13 2.32
1283 1333 2.163613 GCTTACCGTTCAATTCCTTGGG 59.836 50.000 0.00 0.00 32.95 4.12
1286 1336 3.732048 ACCGTTCAATTCCTTGGGTAT 57.268 42.857 0.00 0.00 32.95 2.73
1291 1341 7.523415 ACCGTTCAATTCCTTGGGTATATTAT 58.477 34.615 0.00 0.00 32.95 1.28
1292 1342 8.662255 ACCGTTCAATTCCTTGGGTATATTATA 58.338 33.333 0.00 0.00 32.95 0.98
1293 1343 9.509956 CCGTTCAATTCCTTGGGTATATTATAA 57.490 33.333 0.00 0.00 32.95 0.98
1329 1379 8.830201 ATGATGAACTAATCAGCTATGTCTTC 57.170 34.615 0.00 0.00 44.84 2.87
1574 1624 3.792047 GACATGAGCAGCGCGCAA 61.792 61.111 35.10 13.41 42.18 4.85
1843 1893 3.977244 GCCCGTGGTTGGTGCAAG 61.977 66.667 0.00 0.00 0.00 4.01
1858 1908 1.202568 CAAGTTGTGCTCTCGCGTG 59.797 57.895 5.77 3.13 39.65 5.34
1865 1915 2.014554 TGCTCTCGCGTGTCGTTTC 61.015 57.895 5.77 0.00 39.65 2.78
1884 1934 0.165295 CTGTGTGATGTGCTGCTTCG 59.835 55.000 0.00 0.00 0.00 3.79
1978 2038 0.329596 ACAAGAGGGTTCATGGGAGC 59.670 55.000 0.00 0.00 0.00 4.70
1983 2043 1.077429 GGGTTCATGGGAGCTGTCC 60.077 63.158 0.00 0.00 43.05 4.02
1988 2048 1.198713 TCATGGGAGCTGTCCTCTTC 58.801 55.000 0.00 0.00 43.36 2.87
2020 2080 2.660064 GGTGGTCGCTGATGAGGGT 61.660 63.158 0.00 0.00 33.81 4.34
2079 2139 3.002042 CAGCTGCAATTATCAGGACTTCG 59.998 47.826 0.00 0.00 32.41 3.79
2097 2157 4.072088 CAACCGACAGTTCCGCGC 62.072 66.667 0.00 0.00 36.18 6.86
2102 2162 2.774951 CGACAGTTCCGCGCTAACG 61.775 63.158 5.56 8.89 44.07 3.18
2142 2202 1.758440 GCCCGGCCTGATGACTGATA 61.758 60.000 0.00 0.00 0.00 2.15
2143 2203 0.979665 CCCGGCCTGATGACTGATAT 59.020 55.000 0.00 0.00 0.00 1.63
2144 2204 1.338484 CCCGGCCTGATGACTGATATG 60.338 57.143 0.00 0.00 0.00 1.78
2165 2225 1.151668 CAACGTCTGCTTCCTGAAGG 58.848 55.000 8.85 0.00 38.80 3.46
2166 2226 0.603975 AACGTCTGCTTCCTGAAGGC 60.604 55.000 8.85 2.50 38.80 4.35
2168 2228 0.603707 CGTCTGCTTCCTGAAGGCAA 60.604 55.000 8.85 0.00 38.80 4.52
2172 2232 2.025605 TCTGCTTCCTGAAGGCAATGAT 60.026 45.455 8.85 0.00 38.80 2.45
2259 2361 0.889186 ACTGGCCGTGTGAATGAACC 60.889 55.000 0.00 0.00 0.00 3.62
2271 2373 3.125316 GTGAATGAACCTGTCGATTGACC 59.875 47.826 10.69 0.00 44.86 4.02
2278 2380 1.406219 CTGTCGATTGACCGCAGACG 61.406 60.000 10.69 0.00 44.86 4.18
2295 2397 1.060122 GACGGACGCGATAACCTTTTG 59.940 52.381 15.93 0.73 0.00 2.44
2434 2536 1.521681 GTCGTCCCATGCCTAGCAC 60.522 63.158 0.00 0.00 43.04 4.40
2454 2560 0.034896 AGCACCGGTTCCACTACTTG 59.965 55.000 2.97 0.00 0.00 3.16
2508 2719 3.328637 AGGTACTAGTAGGAGCTAGGAGC 59.671 52.174 12.58 6.46 45.80 4.70
2604 2825 2.504920 TCCACCTGGAGTAGCATCG 58.495 57.895 0.00 0.00 39.78 3.84
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
53 54 5.732810 GCTCCTTATGAAAATCTGCTCTTGC 60.733 44.000 0.00 0.00 40.20 4.01
54 55 5.356190 TGCTCCTTATGAAAATCTGCTCTTG 59.644 40.000 0.00 0.00 0.00 3.02
55 56 5.503927 TGCTCCTTATGAAAATCTGCTCTT 58.496 37.500 0.00 0.00 0.00 2.85
56 57 5.108187 TGCTCCTTATGAAAATCTGCTCT 57.892 39.130 0.00 0.00 0.00 4.09
57 58 5.824904 TTGCTCCTTATGAAAATCTGCTC 57.175 39.130 0.00 0.00 0.00 4.26
58 59 5.393896 GCTTTGCTCCTTATGAAAATCTGCT 60.394 40.000 0.00 0.00 0.00 4.24
59 60 4.802563 GCTTTGCTCCTTATGAAAATCTGC 59.197 41.667 0.00 0.00 0.00 4.26
60 61 6.034591 CAGCTTTGCTCCTTATGAAAATCTG 58.965 40.000 0.00 0.00 36.40 2.90
61 62 5.948162 TCAGCTTTGCTCCTTATGAAAATCT 59.052 36.000 0.00 0.00 36.40 2.40
62 63 6.094603 TCTCAGCTTTGCTCCTTATGAAAATC 59.905 38.462 0.00 0.00 36.40 2.17
63 64 5.948162 TCTCAGCTTTGCTCCTTATGAAAAT 59.052 36.000 0.00 0.00 36.40 1.82
64 65 5.316167 TCTCAGCTTTGCTCCTTATGAAAA 58.684 37.500 0.00 0.00 36.40 2.29
65 66 4.910195 TCTCAGCTTTGCTCCTTATGAAA 58.090 39.130 0.00 0.00 36.40 2.69
66 67 4.558226 TCTCAGCTTTGCTCCTTATGAA 57.442 40.909 0.00 0.00 36.40 2.57
67 68 4.767578 ATCTCAGCTTTGCTCCTTATGA 57.232 40.909 0.00 0.00 36.40 2.15
68 69 4.497674 GCAATCTCAGCTTTGCTCCTTATG 60.498 45.833 12.56 0.00 43.75 1.90
194 195 3.952931 TCCAGTCACTACTCACTACTCC 58.047 50.000 0.00 0.00 31.97 3.85
219 220 0.902531 AGGAACAGTGATACCGGGTG 59.097 55.000 10.66 0.00 0.00 4.61
238 239 1.675219 GCAAACACTAGGTCCCCGA 59.325 57.895 0.00 0.00 0.00 5.14
240 241 1.376812 CCGCAAACACTAGGTCCCC 60.377 63.158 0.00 0.00 0.00 4.81
244 245 1.045407 TGTCTCCGCAAACACTAGGT 58.955 50.000 0.00 0.00 0.00 3.08
256 257 2.693069 AGCACAAATCTCTTGTCTCCG 58.307 47.619 0.00 0.00 0.00 4.63
284 285 4.687464 GGGTTCAGTGTACACCCG 57.313 61.111 22.28 13.95 41.00 5.28
419 421 7.276218 CCATGTTACTTGAACTGCCAAAATATG 59.724 37.037 0.00 0.00 38.98 1.78
566 568 1.065854 ACCATACTGAGGAGCTTGTGC 60.066 52.381 0.00 0.00 40.05 4.57
614 624 0.668535 AAACTGAAAGCGGAACTGCC 59.331 50.000 1.77 0.00 37.60 4.85
701 723 1.121407 ACACAGTGCTCAGCCCAGTA 61.121 55.000 0.00 0.00 0.00 2.74
854 876 4.142337 GGACGGAGAGGAACTAAGAAGAAG 60.142 50.000 0.00 0.00 41.55 2.85
958 980 5.853936 TCGGATGTACTTAGGAATTGGATG 58.146 41.667 0.00 0.00 0.00 3.51
1216 1238 2.765699 AGTGGCCAATTTCTTTGTGTGT 59.234 40.909 7.24 0.00 33.15 3.72
1217 1239 3.125316 CAGTGGCCAATTTCTTTGTGTG 58.875 45.455 7.24 0.00 33.15 3.82
1245 1294 5.449041 CGGTAAGCAATAGGTCGTAACTACA 60.449 44.000 0.00 0.00 0.00 2.74
1254 1303 5.220796 GGAATTGAACGGTAAGCAATAGGTC 60.221 44.000 0.00 0.00 32.39 3.85
1256 1305 4.881850 AGGAATTGAACGGTAAGCAATAGG 59.118 41.667 0.00 0.00 32.39 2.57
1260 1310 3.254657 CCAAGGAATTGAACGGTAAGCAA 59.745 43.478 0.00 0.00 0.00 3.91
1265 1315 4.847990 ATACCCAAGGAATTGAACGGTA 57.152 40.909 0.00 0.00 0.00 4.02
1276 1326 8.984112 ACTAGGCTTTATAATATACCCAAGGA 57.016 34.615 0.00 0.00 0.00 3.36
1292 1342 8.928448 TGATTAGTTCATCATCTACTAGGCTTT 58.072 33.333 0.00 0.00 0.00 3.51
1293 1343 8.484214 TGATTAGTTCATCATCTACTAGGCTT 57.516 34.615 0.00 0.00 0.00 4.35
1294 1344 7.309744 GCTGATTAGTTCATCATCTACTAGGCT 60.310 40.741 0.00 0.00 32.59 4.58
1300 1350 9.352784 GACATAGCTGATTAGTTCATCATCTAC 57.647 37.037 0.00 0.00 35.64 2.59
1329 1379 3.065786 AGCATGCAATTGTAGGATTGTCG 59.934 43.478 21.98 0.00 38.86 4.35
1849 1899 0.660595 ACAGAAACGACACGCGAGAG 60.661 55.000 15.93 7.72 44.57 3.20
1850 1900 0.933047 CACAGAAACGACACGCGAGA 60.933 55.000 15.93 0.00 44.57 4.04
1858 1908 1.867233 AGCACATCACACAGAAACGAC 59.133 47.619 0.00 0.00 0.00 4.34
1865 1915 0.165295 CGAAGCAGCACATCACACAG 59.835 55.000 0.00 0.00 0.00 3.66
1884 1934 3.044305 ACTTCGAGTTGGCGCTGC 61.044 61.111 7.64 0.00 0.00 5.25
1923 1983 1.664965 GCAACGCTTCCGAGTGTCT 60.665 57.895 0.00 0.00 45.51 3.41
1978 2038 1.078567 GCTGCCCAGAAGAGGACAG 60.079 63.158 0.00 0.00 33.97 3.51
1983 2043 2.818714 CGCTGCTGCCCAGAAGAG 60.819 66.667 10.24 0.00 44.64 2.85
2020 2080 1.777878 AGGGAGAGCGAGAGGAATCTA 59.222 52.381 0.00 0.00 0.00 1.98
2079 2139 4.072088 CGCGGAACTGTCGGTTGC 62.072 66.667 0.56 3.61 41.83 4.17
2097 2157 2.673368 GACCTGTGCTTGGATTCGTTAG 59.327 50.000 0.00 0.00 0.00 2.34
2102 2162 1.523758 AACGACCTGTGCTTGGATTC 58.476 50.000 0.00 0.00 0.00 2.52
2166 2226 5.548406 TCATGTCTCCTAGATGCATCATTG 58.452 41.667 27.81 16.16 0.00 2.82
2168 2228 4.322877 GCTCATGTCTCCTAGATGCATCAT 60.323 45.833 27.81 15.23 0.00 2.45
2172 2232 2.364647 CTGCTCATGTCTCCTAGATGCA 59.635 50.000 0.00 0.00 0.00 3.96
2175 2235 3.636300 GTCACTGCTCATGTCTCCTAGAT 59.364 47.826 0.00 0.00 0.00 1.98
2177 2237 2.757314 TGTCACTGCTCATGTCTCCTAG 59.243 50.000 0.00 0.00 0.00 3.02
2259 2361 1.406219 CGTCTGCGGTCAATCGACAG 61.406 60.000 0.00 0.00 44.54 3.51
2278 2380 3.372822 TCATTCAAAAGGTTATCGCGTCC 59.627 43.478 5.77 5.14 0.00 4.79
2295 2397 5.867716 ACTACTGTGGTTTATCGTGTCATTC 59.132 40.000 0.00 0.00 0.00 2.67
2359 2461 5.335191 GGCTCCCATTGAAAATGATATCGAC 60.335 44.000 1.54 0.00 0.00 4.20
2434 2536 0.034896 AAGTAGTGGAACCGGTGCTG 59.965 55.000 13.69 0.00 37.80 4.41
2495 2706 1.004511 GGATACCGCTCCTAGCTCCTA 59.995 57.143 0.00 0.00 39.60 2.94
2496 2707 0.251430 GGATACCGCTCCTAGCTCCT 60.251 60.000 0.00 0.00 39.60 3.69
2497 2708 0.251430 AGGATACCGCTCCTAGCTCC 60.251 60.000 0.00 0.00 44.04 4.70
2508 2719 3.641906 ACTGGGAGTTTCATAGGATACCG 59.358 47.826 0.00 0.00 37.17 4.02
2509 2720 5.454897 GGAACTGGGAGTTTCATAGGATACC 60.455 48.000 0.00 0.00 38.80 2.73


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

AutoCloner maintained by Alex Coulton.