Multiple sequence alignment - TraesCS1D01G275300

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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 TraesCS1D01G275300 chr1D 100.000 2402 0 0 1 2402 371185350 371187751 0.000000e+00 4436
1 TraesCS1D01G275300 chr1A 96.472 2069 37 12 352 2402 470299844 470301894 0.000000e+00 3384
2 TraesCS1D01G275300 chr1B 95.762 2100 39 14 325 2402 495094230 495096301 0.000000e+00 3339
3 TraesCS1D01G275300 chr1B 91.525 177 15 0 6 182 495092796 495092972 6.630000e-61 244
4 TraesCS1D01G275300 chr1B 89.441 161 12 2 173 333 495094035 495094190 5.240000e-47 198
5 TraesCS1D01G275300 chr3B 82.353 221 30 5 1117 1337 643266347 643266558 1.470000e-42 183
6 TraesCS1D01G275300 chr3D 76.731 361 53 21 997 1337 481711078 481711427 3.170000e-39 172
7 TraesCS1D01G275300 chr3A 81.776 214 30 7 1124 1337 624859039 624859243 1.140000e-38 171


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 TraesCS1D01G275300 chr1D 371185350 371187751 2401 False 4436.000000 4436 100.000000 1 2402 1 chr1D.!!$F1 2401
1 TraesCS1D01G275300 chr1A 470299844 470301894 2050 False 3384.000000 3384 96.472000 352 2402 1 chr1A.!!$F1 2050
2 TraesCS1D01G275300 chr1B 495092796 495096301 3505 False 1260.333333 3339 92.242667 6 2402 3 chr1B.!!$F1 2396

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
198 1270 0.035458 CCGCCTCACTGAAGAAAGGT 59.965 55.0 0.0 0.0 0.0 3.5 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1655 2804 0.237498 CGCAGTCACGACTCACACTA 59.763 55.0 0.0 0.0 40.2 2.74 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
22 23 2.428890 CAGACAGTAGTAGCCTTCCTGG 59.571 54.545 0.00 0.00 39.35 4.45
43 44 2.747855 CAGAGCTTGCCGGGGAAC 60.748 66.667 2.18 0.00 0.00 3.62
45 46 2.282180 GAGCTTGCCGGGGAACAA 60.282 61.111 2.18 0.00 0.00 2.83
82 83 4.359706 CAAGACTTGGCTTACAAAACCAC 58.640 43.478 7.35 0.00 38.91 4.16
124 125 4.993584 AGTCGTCGAGAAGTACTAAGTCAA 59.006 41.667 0.00 0.00 0.00 3.18
182 183 3.423154 CGGCAAGTGAAGACCCGC 61.423 66.667 0.00 0.00 31.87 6.13
188 1260 1.122019 AAGTGAAGACCCGCCTCACT 61.122 55.000 0.00 0.00 42.62 3.41
198 1270 0.035458 CCGCCTCACTGAAGAAAGGT 59.965 55.000 0.00 0.00 0.00 3.50
201 1273 2.618709 CGCCTCACTGAAGAAAGGTTTT 59.381 45.455 0.00 0.00 0.00 2.43
223 1295 4.344978 TCCAAAGTCTCTTCTAGCAGCTA 58.655 43.478 1.13 1.13 0.00 3.32
239 1311 3.063725 GCAGCTAGCACAAATTCTCTCTG 59.936 47.826 18.83 2.33 44.79 3.35
270 1342 0.462047 GTGACCGGCCAATCGATCTT 60.462 55.000 0.00 0.00 0.00 2.40
283 1355 9.490663 GGCCAATCGATCTTTAAATAATAATCG 57.509 33.333 0.00 9.59 37.83 3.34
346 1466 4.717280 AGATCAGAAATTACGGACCTTCCT 59.283 41.667 0.00 0.00 33.30 3.36
361 1481 2.619646 CCTTCCTAGACCTCTTAGCGAC 59.380 54.545 0.00 0.00 0.00 5.19
435 1563 4.020543 ACCTGACCTTTACTTGCAAAACA 58.979 39.130 0.00 0.00 0.00 2.83
645 1773 1.995626 GGCAGGGGGCTCTCACTTA 60.996 63.158 0.00 0.00 44.01 2.24
733 1866 2.780010 CTCCAAACCACCCTATCTCCAT 59.220 50.000 0.00 0.00 0.00 3.41
738 1871 1.869648 ACCACCCTATCTCCATCTCCT 59.130 52.381 0.00 0.00 0.00 3.69
741 1874 2.156425 ACCCTATCTCCATCTCCTCCA 58.844 52.381 0.00 0.00 0.00 3.86
744 1877 2.111613 CCTATCTCCATCTCCTCCACCT 59.888 54.545 0.00 0.00 0.00 4.00
745 1878 2.397044 ATCTCCATCTCCTCCACCTC 57.603 55.000 0.00 0.00 0.00 3.85
746 1879 0.263172 TCTCCATCTCCTCCACCTCC 59.737 60.000 0.00 0.00 0.00 4.30
1017 2150 3.245016 TGAAGATGAGCAGGAACAATGGT 60.245 43.478 0.00 0.00 0.00 3.55
1050 2183 1.130054 TGGACCTGAGGCTGAGCTTT 61.130 55.000 3.72 0.00 0.00 3.51
1158 2297 1.811359 TCTTCGTCGTCTTCTTCCTCC 59.189 52.381 0.00 0.00 0.00 4.30
1465 2604 2.413351 GTCGATCGCCTAGCTGCA 59.587 61.111 11.09 0.00 0.00 4.41
1531 2680 1.226547 GTTGGTGTTGGTGTGTGCG 60.227 57.895 0.00 0.00 0.00 5.34
1532 2681 1.675972 TTGGTGTTGGTGTGTGCGT 60.676 52.632 0.00 0.00 0.00 5.24
1533 2682 1.927608 TTGGTGTTGGTGTGTGCGTG 61.928 55.000 0.00 0.00 0.00 5.34
1534 2683 2.277884 GTGTTGGTGTGTGCGTGC 60.278 61.111 0.00 0.00 0.00 5.34
1655 2804 9.614792 GGTCTAGGTAATAATTTCATCTGTTGT 57.385 33.333 0.00 0.00 0.00 3.32
1758 2907 2.113860 GCAGTAATGCCCTTGTCTCA 57.886 50.000 3.16 0.00 0.00 3.27
2011 3168 9.826574 ATGCGTAATAACCTTTTCTGAATACTA 57.173 29.630 0.00 0.00 0.00 1.82
2104 3267 1.556911 ACATGAATGAAGACTCGGGCT 59.443 47.619 0.00 0.00 0.00 5.19
2235 3400 1.071471 GACCACACCACACCAGAGG 59.929 63.158 0.00 0.00 0.00 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.093057 CAGGAAGGCTACTACTGTCTGT 58.907 50.000 0.00 0.00 31.12 3.41
1 2 2.428890 CCAGGAAGGCTACTACTGTCTG 59.571 54.545 0.00 0.00 32.80 3.51
2 3 2.741145 CCAGGAAGGCTACTACTGTCT 58.259 52.381 0.00 0.00 32.80 3.41
27 28 2.829384 TTGTTCCCCGGCAAGCTCT 61.829 57.895 0.00 0.00 0.00 4.09
29 30 2.597510 GTTGTTCCCCGGCAAGCT 60.598 61.111 0.00 0.00 0.00 3.74
36 37 3.735591 TCTTGTTTAGAGTTGTTCCCCG 58.264 45.455 0.00 0.00 0.00 5.73
59 60 3.181480 TGGTTTTGTAAGCCAAGTCTTGC 60.181 43.478 7.09 3.26 33.75 4.01
82 83 2.072298 CTTGCCTTGAGGTCTTCTTCG 58.928 52.381 0.00 0.00 37.57 3.79
124 125 3.525199 ACCAAGGCCTTGATCTTCAGTAT 59.475 43.478 41.10 13.69 42.93 2.12
165 166 3.423154 GCGGGTCTTCACTTGCCG 61.423 66.667 0.00 0.00 0.00 5.69
182 183 4.207165 TGGAAAACCTTTCTTCAGTGAGG 58.793 43.478 0.00 0.00 35.39 3.86
188 1260 6.187682 AGAGACTTTGGAAAACCTTTCTTCA 58.812 36.000 0.00 0.00 0.00 3.02
198 1270 4.757149 GCTGCTAGAAGAGACTTTGGAAAA 59.243 41.667 0.27 0.00 0.00 2.29
201 1273 3.169099 AGCTGCTAGAAGAGACTTTGGA 58.831 45.455 0.27 0.00 0.00 3.53
223 1295 2.373169 TGGACCAGAGAGAATTTGTGCT 59.627 45.455 0.00 0.00 0.00 4.40
257 1329 9.490663 CGATTATTATTTAAAGATCGATTGGCC 57.509 33.333 0.00 0.00 36.77 5.36
292 1364 9.288124 CGATGATAGTTGATGAATAGATCAGAC 57.712 37.037 0.00 0.00 42.53 3.51
301 1373 9.096160 GATCTATTGCGATGATAGTTGATGAAT 57.904 33.333 0.00 0.00 0.00 2.57
346 1466 2.687700 AGTCGTCGCTAAGAGGTCTA 57.312 50.000 0.00 0.00 32.89 2.59
361 1481 7.410800 TGTGTGTTAGGTTAAATTGTAGTCG 57.589 36.000 0.00 0.00 0.00 4.18
435 1563 1.732259 CACGATGCTAGCTCCGTTTTT 59.268 47.619 24.74 7.88 32.50 1.94
733 1866 1.229209 GGTGTGGAGGTGGAGGAGA 60.229 63.158 0.00 0.00 0.00 3.71
738 1871 1.065410 AATGTGGGTGTGGAGGTGGA 61.065 55.000 0.00 0.00 0.00 4.02
741 1874 0.991920 CCTAATGTGGGTGTGGAGGT 59.008 55.000 0.00 0.00 0.00 3.85
744 1877 1.074727 CCAACCTAATGTGGGTGTGGA 59.925 52.381 0.00 0.00 43.01 4.02
745 1878 1.544724 CCAACCTAATGTGGGTGTGG 58.455 55.000 0.00 0.00 43.01 4.17
973 2106 3.229156 TAACTCCGCACACCACCGG 62.229 63.158 0.00 0.00 45.64 5.28
1017 2150 2.285069 TCCAGCTTCGGCCCCTTA 60.285 61.111 0.00 0.00 43.01 2.69
1465 2604 0.886563 ACGAAAGAGGACGGTCGATT 59.113 50.000 1.43 0.00 36.98 3.34
1531 2680 4.993945 CAACTCGCACGCACGCAC 62.994 66.667 0.00 0.00 0.00 5.34
1655 2804 0.237498 CGCAGTCACGACTCACACTA 59.763 55.000 0.00 0.00 40.20 2.74
1656 2805 1.008424 CGCAGTCACGACTCACACT 60.008 57.895 0.00 0.00 40.20 3.55
1657 2806 1.299165 ACGCAGTCACGACTCACAC 60.299 57.895 0.00 0.00 40.20 3.82
1749 2898 1.481056 AAGGACGGGGTGAGACAAGG 61.481 60.000 0.00 0.00 0.00 3.61
1984 3133 9.826574 AGTATTCAGAAAAGGTTATTACGCATA 57.173 29.630 0.00 0.00 0.00 3.14
2104 3267 8.055279 AGACTTTTCTCAACTTTGATTTGACA 57.945 30.769 0.00 0.00 36.46 3.58
2235 3400 2.441410 CCTCTTCCCTTGCTTCTTTCC 58.559 52.381 0.00 0.00 0.00 3.13


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

AutoCloner maintained by Alex Coulton.