Multiple sequence alignment - TraesCS7A01G307500

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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 TraesCS7A01G307500 chr7A 100.000 2995 0 0 1 2995 434741319 434738325 0.000000e+00 5531
1 TraesCS7A01G307500 chr7D 96.272 3031 73 8 1 2995 386360423 386357397 0.000000e+00 4935
2 TraesCS7A01G307500 chr7B 93.225 1963 83 11 402 2331 380538653 380536708 0.000000e+00 2843
3 TraesCS7A01G307500 chr7B 94.141 495 23 3 2500 2994 380511800 380511312 0.000000e+00 749
4 TraesCS7A01G307500 chr7B 95.238 357 12 3 1 354 380538996 380538642 7.250000e-156 560
5 TraesCS7A01G307500 chr7B 85.965 171 16 4 2335 2504 380511991 380511828 3.070000e-40 176


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 TraesCS7A01G307500 chr7A 434738325 434741319 2994 True 5531.0 5531 100.0000 1 2995 1 chr7A.!!$R1 2994
1 TraesCS7A01G307500 chr7D 386357397 386360423 3026 True 4935.0 4935 96.2720 1 2995 1 chr7D.!!$R1 2994
2 TraesCS7A01G307500 chr7B 380536708 380538996 2288 True 1701.5 2843 94.2315 1 2331 2 chr7B.!!$R2 2330
3 TraesCS7A01G307500 chr7B 380511312 380511991 679 True 462.5 749 90.0530 2335 2994 2 chr7B.!!$R1 659


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
281 290 0.671472 TGCCTTGTCATGTCTGCTCG 60.671 55.000 0.0 0.0 0.0 5.03 F
1038 1075 1.798223 GCTGTCATTGTCTGCGTGTTA 59.202 47.619 0.0 0.0 0.0 2.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1083 1120 0.249573 CCTTGTTTTGTGCAGCCTGG 60.250 55.0 0.00 0.00 0.00 4.45 R
2925 3004 2.105993 CAGGAATCATCATGGCAGGAGA 59.894 50.0 8.21 5.92 33.78 3.71 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
106 107 2.833794 TCTACACCAGAGTTGTTGCAC 58.166 47.619 0.00 0.00 0.00 4.57
142 143 9.454859 AAGTTATTTCCTAGATGTTCTTTCTGG 57.545 33.333 0.00 0.00 0.00 3.86
241 250 8.931775 GTTAATCAAAGCATATTTTCCGGTTTT 58.068 29.630 0.00 0.00 0.00 2.43
256 265 5.878627 TCCGGTTTTATGAGGTTTCCTTAA 58.121 37.500 0.00 0.00 31.76 1.85
281 290 0.671472 TGCCTTGTCATGTCTGCTCG 60.671 55.000 0.00 0.00 0.00 5.03
517 529 8.350722 AGTTTGATTCTCATTGATATGCATGTC 58.649 33.333 15.93 15.93 0.00 3.06
1008 1045 3.813443 ACAGCTATACAAGATGGCCAAG 58.187 45.455 10.96 0.00 46.23 3.61
1017 1054 3.137913 ACAAGATGGCCAAGATGATAGCT 59.862 43.478 10.96 0.00 0.00 3.32
1038 1075 1.798223 GCTGTCATTGTCTGCGTGTTA 59.202 47.619 0.00 0.00 0.00 2.41
1083 1120 1.070914 GGCATACTAGGACTTCAGGCC 59.929 57.143 0.00 0.00 0.00 5.19
1202 1239 6.003326 TGTTTCAGCTATTTCTTCATGGACA 58.997 36.000 0.00 0.00 0.00 4.02
1212 1249 9.653287 CTATTTCTTCATGGACAGTTGTTACTA 57.347 33.333 0.00 0.00 31.96 1.82
1314 1351 2.089980 ACAGTGCTCTTCATCCAATGC 58.910 47.619 0.00 0.00 0.00 3.56
1323 1360 2.787473 TCATCCAATGCGAGAAACCT 57.213 45.000 0.00 0.00 0.00 3.50
1401 1438 0.535102 CAGTGGCCAACTTTCTCGGT 60.535 55.000 7.24 0.00 36.83 4.69
1434 1471 0.894141 TCTGCTCTCAGCTGGAGTTC 59.106 55.000 24.26 14.31 44.40 3.01
1639 1681 2.094234 AGAACACACAAAAGGGTTGCAC 60.094 45.455 0.00 0.00 0.00 4.57
1803 1845 7.257722 GGTAATAACCATTGTTGGATGTTCTG 58.742 38.462 0.00 0.00 46.92 3.02
1811 1853 6.548622 CCATTGTTGGATGTTCTGATAGGATT 59.451 38.462 0.00 0.00 46.92 3.01
1835 1877 1.063616 CTCATCGTCGGCTTCTCGTTA 59.936 52.381 0.00 0.00 0.00 3.18
2122 2167 1.104577 TTCAGTTTGTGGTTCGGCCC 61.105 55.000 0.00 0.00 36.04 5.80
2213 2258 8.418662 AGGAATATGATTGTGGTTTGATTGATG 58.581 33.333 0.00 0.00 0.00 3.07
2331 2376 6.640518 TCAAATAGCTCAAAGTAGTCCGAAT 58.359 36.000 0.00 0.00 0.00 3.34
2394 2441 9.651913 AAGCACCGAATCAAAATTATAAACATT 57.348 25.926 0.00 0.00 0.00 2.71
2461 2508 6.206243 CACTGATCTGTGATTCAACCTTCTTT 59.794 38.462 24.09 0.00 40.12 2.52
2513 2592 3.119708 GCAAGGCAGTTGTATGAAAGGAG 60.120 47.826 0.54 0.00 38.55 3.69
2714 2793 3.264193 AGTTCCATGCTTGATCAGGTACA 59.736 43.478 6.70 0.00 0.00 2.90
2874 2953 2.040939 CCAGAGGCAGATGACTGATCT 58.959 52.381 0.00 0.00 46.03 2.75
2925 3004 3.637273 GTCCTGCCCGGTGGAAGT 61.637 66.667 9.27 0.00 35.14 3.01
2965 3044 1.727511 GCTGCTGTGGCTGTGTTTCA 61.728 55.000 0.00 0.00 39.19 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
241 250 7.182060 AGGCAAAGATTTAAGGAAACCTCATA 58.818 34.615 0.00 0.00 30.89 2.15
256 265 3.057033 GCAGACATGACAAGGCAAAGATT 60.057 43.478 0.00 0.00 0.00 2.40
392 404 6.131544 TGTTTAGCTTCAGAACCTTCAAAC 57.868 37.500 0.00 0.00 0.00 2.93
517 529 5.695851 AATAACAAGGAAAGACACAGCAG 57.304 39.130 0.00 0.00 0.00 4.24
1008 1045 4.211584 CAGACAATGACAGCAGCTATCATC 59.788 45.833 16.67 5.69 31.84 2.92
1017 1054 0.532640 ACACGCAGACAATGACAGCA 60.533 50.000 1.26 0.00 0.00 4.41
1038 1075 4.687219 GCAGTGATATCCAGGGCTAAAACT 60.687 45.833 0.00 0.00 0.00 2.66
1083 1120 0.249573 CCTTGTTTTGTGCAGCCTGG 60.250 55.000 0.00 0.00 0.00 4.45
1190 1227 9.031537 TCTATAGTAACAACTGTCCATGAAGAA 57.968 33.333 0.00 0.00 0.00 2.52
1212 1249 8.656849 CGTTTGAAGCACATTTAACTACTCTAT 58.343 33.333 0.00 0.00 0.00 1.98
1226 1263 5.758296 AGAAAGAACTATCGTTTGAAGCACA 59.242 36.000 0.00 0.00 32.39 4.57
1247 1284 3.014623 CAAATGAGAGCAGGCATCAGAA 58.985 45.455 5.62 0.00 0.00 3.02
1253 1290 3.054582 AGAAGATCAAATGAGAGCAGGCA 60.055 43.478 0.00 0.00 0.00 4.75
1255 1292 4.335874 CCAAGAAGATCAAATGAGAGCAGG 59.664 45.833 0.00 0.00 0.00 4.85
1314 1351 6.018994 GGTATGCTTTATACACAGGTTTCTCG 60.019 42.308 0.00 0.00 42.85 4.04
1323 1360 5.221641 CCCTAGCTGGTATGCTTTATACACA 60.222 44.000 0.00 0.00 42.85 3.72
1413 1450 2.450867 ACTCCAGCTGAGAGCAGATA 57.549 50.000 23.94 0.00 45.56 1.98
1434 1471 0.466007 TGTTGATGGATGCCCGGATG 60.466 55.000 0.73 0.00 34.29 3.51
1545 1585 3.576078 TGAAGTGACACTTTCCCACAT 57.424 42.857 21.42 0.00 38.80 3.21
1639 1681 2.945008 TCTCTGGCTTAATGAAATGGCG 59.055 45.455 0.00 0.00 0.00 5.69
1803 1845 3.497118 CGACGATGAGAGCAATCCTATC 58.503 50.000 0.00 0.00 32.38 2.08
1811 1853 1.139734 GAAGCCGACGATGAGAGCA 59.860 57.895 0.00 0.00 0.00 4.26
1835 1877 3.988678 ATGGCCCCAGCAAGCAGT 61.989 61.111 0.00 0.00 42.56 4.40
2164 2209 2.330231 TGCGCAACTTTGATACAAGC 57.670 45.000 8.16 0.00 0.00 4.01
2213 2258 4.318263 GCATTCACAACAAAACAGTGATGC 60.318 41.667 0.00 0.00 41.42 3.91
2299 2344 7.982354 ACTACTTTGAGCTATTTGATACCACTC 59.018 37.037 0.00 0.00 0.00 3.51
2331 2376 5.929992 ACTATCAGACAAAATTCGTTCGGAA 59.070 36.000 0.00 0.00 39.42 4.30
2394 2441 3.119209 TGCATAGCGAAAATGGAAATGCA 60.119 39.130 3.15 3.15 44.16 3.96
2461 2508 3.225104 AGCAAAGATCTTCTGTTTGGCA 58.775 40.909 8.78 0.00 38.29 4.92
2513 2592 5.725110 CACTAGATGATGTGCTGGTTTAC 57.275 43.478 0.00 0.00 0.00 2.01
2783 2862 6.801862 CGTCTGATGGAAACTAACCAAAATTC 59.198 38.462 0.00 0.00 40.93 2.17
2874 2953 2.106338 TGTTGACCTTGAGGCATCAGAA 59.894 45.455 0.00 0.00 39.32 3.02
2925 3004 2.105993 CAGGAATCATCATGGCAGGAGA 59.894 50.000 8.21 5.92 33.78 3.71
2965 3044 3.717294 GGCACTGATCCGGGTGGT 61.717 66.667 0.00 0.00 36.30 4.16



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

AutoCloner maintained by Alex Coulton.