Multiple sequence alignment - TraesCS7B01G231100

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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 TraesCS7B01G231100 chr7B 100.000 2273 0 0 1 2273 433797545 433795273 0.000000e+00 4198
1 TraesCS7B01G231100 chr7B 98.067 1293 25 0 11 1303 740171966 740173258 0.000000e+00 2250
2 TraesCS7B01G231100 chr4A 98.081 1303 25 0 1 1303 19527828 19526526 0.000000e+00 2268
3 TraesCS7B01G231100 chr3A 97.650 1319 30 1 1 1319 171251160 171249843 0.000000e+00 2263
4 TraesCS7B01G231100 chr6D 94.500 1309 66 4 1 1303 121292811 121291503 0.000000e+00 2013
5 TraesCS7B01G231100 chr1A 96.749 1138 37 0 166 1303 29199046 29197909 0.000000e+00 1897
6 TraesCS7B01G231100 chr6B 91.667 1308 102 7 1 1307 665099341 665098040 0.000000e+00 1805
7 TraesCS7B01G231100 chr6B 91.839 968 73 4 1310 2273 552128370 552129335 0.000000e+00 1345
8 TraesCS7B01G231100 chr4B 92.850 1049 66 6 257 1303 42140145 42141186 0.000000e+00 1513
9 TraesCS7B01G231100 chr4B 92.260 969 70 3 1310 2273 92608364 92609332 0.000000e+00 1369
10 TraesCS7B01G231100 chr4B 91.718 966 73 5 1313 2273 90541193 90540230 0.000000e+00 1334
11 TraesCS7B01G231100 chr1B 92.539 965 68 2 1313 2273 353873597 353872633 0.000000e+00 1380
12 TraesCS7B01G231100 chr1B 98.467 522 8 0 782 1303 86748592 86749113 0.000000e+00 920
13 TraesCS7B01G231100 chr3B 91.641 969 76 3 1310 2273 322766252 322767220 0.000000e+00 1336
14 TraesCS7B01G231100 chr3B 91.710 965 72 7 1313 2273 371917426 371916466 0.000000e+00 1332
15 TraesCS7B01G231100 chr3B 91.399 965 79 2 1313 2273 63779910 63778946 0.000000e+00 1319
16 TraesCS7B01G231100 chr3B 91.201 966 80 3 1313 2273 371853477 371852512 0.000000e+00 1308
17 TraesCS7B01G231100 chr2B 91.649 970 71 8 1310 2272 253901565 253902531 0.000000e+00 1334
18 TraesCS7B01G231100 chr7A 98.164 708 12 1 601 1308 85340421 85339715 0.000000e+00 1234
19 TraesCS7B01G231100 chr2A 82.323 775 127 8 222 995 674196068 674195303 0.000000e+00 664
20 TraesCS7B01G231100 chr3D 77.259 343 66 12 64 400 133998539 133998875 8.290000e-45 191


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 TraesCS7B01G231100 chr7B 433795273 433797545 2272 True 4198 4198 100.000 1 2273 1 chr7B.!!$R1 2272
1 TraesCS7B01G231100 chr7B 740171966 740173258 1292 False 2250 2250 98.067 11 1303 1 chr7B.!!$F1 1292
2 TraesCS7B01G231100 chr4A 19526526 19527828 1302 True 2268 2268 98.081 1 1303 1 chr4A.!!$R1 1302
3 TraesCS7B01G231100 chr3A 171249843 171251160 1317 True 2263 2263 97.650 1 1319 1 chr3A.!!$R1 1318
4 TraesCS7B01G231100 chr6D 121291503 121292811 1308 True 2013 2013 94.500 1 1303 1 chr6D.!!$R1 1302
5 TraesCS7B01G231100 chr1A 29197909 29199046 1137 True 1897 1897 96.749 166 1303 1 chr1A.!!$R1 1137
6 TraesCS7B01G231100 chr6B 665098040 665099341 1301 True 1805 1805 91.667 1 1307 1 chr6B.!!$R1 1306
7 TraesCS7B01G231100 chr6B 552128370 552129335 965 False 1345 1345 91.839 1310 2273 1 chr6B.!!$F1 963
8 TraesCS7B01G231100 chr4B 42140145 42141186 1041 False 1513 1513 92.850 257 1303 1 chr4B.!!$F1 1046
9 TraesCS7B01G231100 chr4B 92608364 92609332 968 False 1369 1369 92.260 1310 2273 1 chr4B.!!$F2 963
10 TraesCS7B01G231100 chr4B 90540230 90541193 963 True 1334 1334 91.718 1313 2273 1 chr4B.!!$R1 960
11 TraesCS7B01G231100 chr1B 353872633 353873597 964 True 1380 1380 92.539 1313 2273 1 chr1B.!!$R1 960
12 TraesCS7B01G231100 chr1B 86748592 86749113 521 False 920 920 98.467 782 1303 1 chr1B.!!$F1 521
13 TraesCS7B01G231100 chr3B 322766252 322767220 968 False 1336 1336 91.641 1310 2273 1 chr3B.!!$F1 963
14 TraesCS7B01G231100 chr3B 371916466 371917426 960 True 1332 1332 91.710 1313 2273 1 chr3B.!!$R3 960
15 TraesCS7B01G231100 chr3B 63778946 63779910 964 True 1319 1319 91.399 1313 2273 1 chr3B.!!$R1 960
16 TraesCS7B01G231100 chr3B 371852512 371853477 965 True 1308 1308 91.201 1313 2273 1 chr3B.!!$R2 960
17 TraesCS7B01G231100 chr2B 253901565 253902531 966 False 1334 1334 91.649 1310 2272 1 chr2B.!!$F1 962
18 TraesCS7B01G231100 chr7A 85339715 85340421 706 True 1234 1234 98.164 601 1308 1 chr7A.!!$R1 707
19 TraesCS7B01G231100 chr2A 674195303 674196068 765 True 664 664 82.323 222 995 1 chr2A.!!$R1 773

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
970 979 0.310543 GCGTGATGGTGTGCTTTTCA 59.689 50.0 0.0 0.0 0.0 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2115 2129 3.513912 ACACACTGCCTACTGTAGCATAA 59.486 43.478 9.35 0.0 38.56 1.9 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
263 266 2.096268 TCGTGAATCAAAAAGAGCGCAG 60.096 45.455 11.47 0.00 0.00 5.18
410 414 2.901192 TCCCGGATGAACAAACTCTACA 59.099 45.455 0.73 0.00 0.00 2.74
502 507 2.081462 TGATTCACTGTGCTCATGCTG 58.919 47.619 2.12 0.00 40.48 4.41
723 728 2.352032 GCGTGTGACTAGGGAGGCT 61.352 63.158 0.00 0.00 0.00 4.58
970 979 0.310543 GCGTGATGGTGTGCTTTTCA 59.689 50.000 0.00 0.00 0.00 2.69
1067 1076 2.035449 ACAACTCTCGTTCGATTGTGGA 59.965 45.455 10.45 0.00 32.42 4.02
1332 1341 8.568617 AAAAATCTAGGTAGTAGTGATCCCAT 57.431 34.615 0.00 0.00 0.00 4.00
1339 1348 6.790319 AGGTAGTAGTGATCCCATTGTTTTT 58.210 36.000 0.00 0.00 0.00 1.94
1544 1556 6.753744 GGACCATGAAAAGAATGCTTTATGTC 59.246 38.462 0.00 2.67 43.32 3.06
1663 1675 5.413969 TCTTTTATGCGAGCATCATTGAG 57.586 39.130 14.35 7.07 37.82 3.02
1741 1753 9.865152 ACCCAACACTTTTACCTACTATTTTTA 57.135 29.630 0.00 0.00 0.00 1.52
1876 1889 1.111277 AACAGAAACTTTTGCGCCCT 58.889 45.000 4.18 0.00 0.00 5.19
1914 1927 8.855110 TCTAAAATTCACTGGAATGTGCTTTTA 58.145 29.630 0.00 0.00 42.87 1.52
1934 1948 9.628746 GCTTTTAATCTGAAATTTTTACGGGTA 57.371 29.630 0.00 0.00 0.00 3.69
2095 2109 7.388776 TGCTAGTTTCTATGGCTTATATTGCTG 59.611 37.037 0.00 0.00 0.00 4.41
2132 2146 8.499162 GTTGAAATATTATGCTACAGTAGGCAG 58.501 37.037 9.74 0.00 41.88 4.85
2179 2195 4.873827 TGTCTTTGACAGTACCAAAGTGAC 59.126 41.667 17.32 12.32 46.30 3.67
2183 2199 4.681074 TGACAGTACCAAAGTGACATGA 57.319 40.909 0.00 0.00 29.84 3.07
2215 2231 9.011095 TCTTTATCATACTAACCTATCTCACGG 57.989 37.037 0.00 0.00 0.00 4.94
2239 2255 6.056428 AGTTCCGTTAAGTTTTGTGTGATC 57.944 37.500 0.00 0.00 0.00 2.92
2268 2285 6.957920 TTTCAAGTTTTGGATGAGATGTCA 57.042 33.333 0.00 0.00 37.02 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
84 85 2.821378 CAACTGCTGATTCCATGTCCAA 59.179 45.455 0.00 0.00 0.00 3.53
263 266 1.611491 CCGTCCCTTCATCTAGAGCTC 59.389 57.143 5.27 5.27 0.00 4.09
410 414 3.386768 AATCGCTAATATGCCGTGACT 57.613 42.857 0.00 0.00 0.00 3.41
454 459 3.245016 TGCTTGAGGTCTTTGTCCATGAT 60.245 43.478 0.00 0.00 0.00 2.45
456 461 2.507484 TGCTTGAGGTCTTTGTCCATG 58.493 47.619 0.00 0.00 0.00 3.66
463 468 1.891150 CAAGGCATGCTTGAGGTCTTT 59.109 47.619 18.92 0.00 33.98 2.52
502 507 3.658757 AGCCTCATTCTAGAATCGAGC 57.341 47.619 24.70 21.14 31.09 5.03
723 728 4.127171 GTGGTAACTCAAGAAGTGCAAGA 58.873 43.478 0.00 0.00 38.58 3.02
970 979 3.200483 GTGTGTAACCTCGAAGTTTGGT 58.800 45.455 4.45 0.00 34.36 3.67
1067 1076 7.936301 GCTCTCCAATTTCAACTAAGATAGGAT 59.064 37.037 0.00 0.00 0.00 3.24
1308 1317 8.432805 CAATGGGATCACTACTACCTAGATTTT 58.567 37.037 0.00 0.00 0.00 1.82
1311 1320 6.625267 ACAATGGGATCACTACTACCTAGAT 58.375 40.000 0.00 0.00 0.00 1.98
1332 1341 4.204012 AGATTCGACACCCTCAAAAACAA 58.796 39.130 0.00 0.00 0.00 2.83
1339 1348 5.925506 TGTAATAAGATTCGACACCCTCA 57.074 39.130 0.00 0.00 0.00 3.86
1382 1391 8.367660 TCACTAAATAAAGTCATGACCTCTCT 57.632 34.615 22.21 0.00 0.00 3.10
1663 1675 3.501445 CCTTTTAGCTAGGCATGATGAGC 59.499 47.826 0.00 0.42 35.07 4.26
1971 1985 8.734386 CATACTTCTGCTACTCCAAAAATTCTT 58.266 33.333 0.00 0.00 0.00 2.52
2070 2084 7.604164 TCAGCAATATAAGCCATAGAAACTAGC 59.396 37.037 0.00 0.00 0.00 3.42
2108 2122 7.657354 CACTGCCTACTGTAGCATAATATTTCA 59.343 37.037 9.35 0.00 38.56 2.69
2114 2128 4.162320 ACACACTGCCTACTGTAGCATAAT 59.838 41.667 9.35 0.00 38.56 1.28
2115 2129 3.513912 ACACACTGCCTACTGTAGCATAA 59.486 43.478 9.35 0.00 38.56 1.90
2132 2146 7.867403 ACAAGATTCATAATTGTTTCCACACAC 59.133 33.333 0.00 0.00 33.49 3.82
2215 2231 5.473796 TCACACAAAACTTAACGGAACTC 57.526 39.130 0.00 0.00 0.00 3.01
2239 2255 6.494842 TCTCATCCAAAACTTGAAAACTTCG 58.505 36.000 0.00 0.00 0.00 3.79


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

AutoCloner maintained by Alex Coulton.