Multiple sequence alignment - TraesCS7D01G323600

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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 TraesCS7D01G323600 chr7D 100.000 3280 0 0 1 3280 413249287 413246008 0 6058
1 TraesCS7D01G323600 chr7A 94.181 2526 83 11 808 3280 474790503 474787989 0 3792
2 TraesCS7D01G323600 chr7A 92.545 778 44 9 37 809 474791308 474790540 0 1103
3 TraesCS7D01G323600 chr7B 95.637 1719 43 12 1590 3280 427711631 427709917 0 2730
4 TraesCS7D01G323600 chr7B 93.432 746 35 10 808 1549 427712363 427711628 0 1094
5 TraesCS7D01G323600 chr7B 92.154 752 43 10 15 755 427713185 427712439 0 1048


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 TraesCS7D01G323600 chr7D 413246008 413249287 3279 True 6058.0 6058 100.000 1 3280 1 chr7D.!!$R1 3279
1 TraesCS7D01G323600 chr7A 474787989 474791308 3319 True 2447.5 3792 93.363 37 3280 2 chr7A.!!$R1 3243
2 TraesCS7D01G323600 chr7B 427709917 427713185 3268 True 1624.0 2730 93.741 15 3280 3 chr7B.!!$R1 3265

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
195 198 0.388649 TCTCCTCGTCTCGCAAAAGC 60.389 55.0 0.00 0.00 0.0 3.51 F
1724 1788 0.250295 TTGACAAGTTCTCTGGCCGG 60.250 55.0 4.71 4.71 0.0 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1949 2013 0.732571 ATTTGTAGCAATCACCGCCG 59.267 50.000 0.00 0.00 0.00 6.46 R
3097 3182 1.407025 GGACTTTCTTAAGGGCCCTCG 60.407 57.143 28.84 17.09 35.61 4.63 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
81 82 1.802636 CAAAGGGCGCACGATCAAT 59.197 52.632 10.83 0.00 0.00 2.57
131 133 2.386661 TTTTCTCAGATCGGCTGGAC 57.613 50.000 6.41 0.00 44.98 4.02
169 172 2.525592 CCCACCCTTGGCTTCCAA 59.474 61.111 0.00 0.00 42.35 3.53
195 198 0.388649 TCTCCTCGTCTCGCAAAAGC 60.389 55.000 0.00 0.00 0.00 3.51
196 199 0.667487 CTCCTCGTCTCGCAAAAGCA 60.667 55.000 0.00 0.00 0.00 3.91
299 303 2.119655 TTCCTCCTCCTCGCTACGC 61.120 63.158 0.00 0.00 0.00 4.42
357 361 6.777213 TCTTTCTAGGTTTAGATCTTCGCT 57.223 37.500 0.00 0.00 35.88 4.93
431 443 3.378959 AATTCGATCGCCGTTTGTTAC 57.621 42.857 11.09 0.00 39.75 2.50
436 448 3.304026 TCGATCGCCGTTTGTTACAATAC 59.696 43.478 11.09 0.00 39.75 1.89
508 520 6.979238 TCGTTTCAATTTCACCGGTTAATTTT 59.021 30.769 17.63 6.56 0.00 1.82
510 522 7.043325 CGTTTCAATTTCACCGGTTAATTTTCA 60.043 33.333 17.63 6.39 0.00 2.69
551 565 1.137872 CTCGTGGCTTGCCTCTATTCT 59.862 52.381 13.18 0.00 0.00 2.40
655 669 7.929245 GGGTAAGAAGAATAATCTCCTTCAGAC 59.071 40.741 0.00 0.00 38.89 3.51
672 686 3.627577 TCAGACACCAAAAGCAAGAAGAC 59.372 43.478 0.00 0.00 0.00 3.01
687 701 1.278127 GAAGACCGACCCAATTCCAGA 59.722 52.381 0.00 0.00 0.00 3.86
745 761 2.928731 GCTAAGTGCTTCTGCTCGTTCT 60.929 50.000 0.00 0.00 40.48 3.01
815 869 3.633986 CCTCCCAACTGATGCCTTTTATC 59.366 47.826 0.00 0.00 0.00 1.75
876 930 3.009115 GGGGTGCTGGCACTAGGA 61.009 66.667 22.32 0.00 45.52 2.94
896 951 7.873505 ACTAGGATATCCTTTCGCAAATAACTC 59.126 37.037 29.06 0.00 46.09 3.01
926 981 3.259902 ACGCTAGTACTTTTTGCTAGGC 58.740 45.455 0.00 0.00 40.11 3.93
981 1037 2.300437 CCCCCTTATAGCTACTGACAGC 59.700 54.545 1.25 0.00 42.12 4.40
1115 1171 5.014858 TCGAGTTACTGAGACCAAGGTATT 58.985 41.667 0.00 0.00 0.00 1.89
1192 1249 7.715657 ACACATGATTTTCTTAGTCAAGCAAA 58.284 30.769 0.00 0.00 32.60 3.68
1258 1315 4.963276 TGCCACTAAACACTTATGATGC 57.037 40.909 0.00 0.00 0.00 3.91
1330 1387 5.649395 TCATTCTGTCCATTTGGTGAATCTC 59.351 40.000 0.00 0.00 32.89 2.75
1351 1408 6.873997 TCTCTCCATGAATTTTACGCTTAGA 58.126 36.000 0.00 0.00 0.00 2.10
1357 1414 9.725019 TCCATGAATTTTACGCTTAGATATGAT 57.275 29.630 0.00 0.00 0.00 2.45
1365 1422 4.810790 ACGCTTAGATATGATACTGCACC 58.189 43.478 0.00 0.00 0.00 5.01
1562 1619 7.710907 TGCTACTGATTTGTATCCTACATCAAC 59.289 37.037 0.00 0.00 38.68 3.18
1724 1788 0.250295 TTGACAAGTTCTCTGGCCGG 60.250 55.000 4.71 4.71 0.00 6.13
2616 2701 3.417101 TCGCTGTGGTTATTGGAATTGT 58.583 40.909 0.00 0.00 0.00 2.71
2741 2826 8.633561 CCTCCTTAAAATATTCCATCAGAAACC 58.366 37.037 0.00 0.00 38.21 3.27
2792 2877 9.764363 AACCTTTTGTTTCAATTATTCCTTCTC 57.236 29.630 0.00 0.00 31.47 2.87
3010 3095 5.724854 ACTTCTTTGGGCTCCTAGTATAACA 59.275 40.000 0.00 0.00 0.00 2.41
3097 3182 2.270986 CCTGCTGCAACCCAAGTCC 61.271 63.158 3.02 0.00 0.00 3.85
3162 3260 3.460340 TGTGTTTCTCAAAGGGGGAACTA 59.540 43.478 0.00 0.00 0.00 2.24
3167 3265 6.266786 TGTTTCTCAAAGGGGGAACTATTTTC 59.733 38.462 0.00 0.00 0.00 2.29
3276 3386 4.623932 TTTGACAGTAGTGAGCTCCAAT 57.376 40.909 12.15 1.21 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 2.044946 ATTCCTCGGCAAGTGGGC 60.045 61.111 0.00 0.00 34.38 5.36
4 5 0.462759 GAGATTCCTCGGCAAGTGGG 60.463 60.000 0.00 0.00 34.38 4.61
5 6 0.250234 TGAGATTCCTCGGCAAGTGG 59.750 55.000 0.00 0.00 42.33 4.00
6 7 1.649664 CTGAGATTCCTCGGCAAGTG 58.350 55.000 0.00 0.00 42.33 3.16
12 13 0.962489 ATACGGCTGAGATTCCTCGG 59.038 55.000 0.00 0.00 46.27 4.63
13 14 2.398498 CAATACGGCTGAGATTCCTCG 58.602 52.381 0.00 0.00 42.33 4.63
81 82 7.426410 GTCTGATCATAGATCAACGGTTCTTA 58.574 38.462 10.54 0.00 0.00 2.10
131 133 5.091261 GGGGGTCAATATATACTGCAGAG 57.909 47.826 23.35 0.00 0.00 3.35
164 167 2.431057 GACGAGGAGATAAGGCTTGGAA 59.569 50.000 10.69 0.00 0.00 3.53
169 172 1.600023 CGAGACGAGGAGATAAGGCT 58.400 55.000 0.00 0.00 0.00 4.58
195 198 5.277974 GGAATCGATCTCTCTTCTGTCTCTG 60.278 48.000 0.00 0.00 0.00 3.35
196 199 4.821805 GGAATCGATCTCTCTTCTGTCTCT 59.178 45.833 0.00 0.00 0.00 3.10
299 303 3.490078 GGACAGCTAGACGAAGAGATTGG 60.490 52.174 0.00 0.00 0.00 3.16
357 361 2.034999 ATCTGCCGCGGGGAAAAA 59.965 55.556 29.38 2.78 34.06 1.94
431 443 5.629435 TGAGCATCGCTATCTAAACGTATTG 59.371 40.000 0.00 0.00 39.88 1.90
436 448 4.045104 AGTTGAGCATCGCTATCTAAACG 58.955 43.478 0.00 0.00 39.88 3.60
551 565 2.734606 CGCCGTGACTAATCAGAACAAA 59.265 45.455 0.00 0.00 34.75 2.83
647 661 2.951642 TCTTGCTTTTGGTGTCTGAAGG 59.048 45.455 0.00 0.00 0.00 3.46
655 669 1.946768 TCGGTCTTCTTGCTTTTGGTG 59.053 47.619 0.00 0.00 0.00 4.17
672 686 1.812571 CTTGTTCTGGAATTGGGTCGG 59.187 52.381 0.00 0.00 0.00 4.79
687 701 8.196378 AGTAGACAACCTAGAAGAATCTTGTT 57.804 34.615 0.00 0.00 37.10 2.83
745 761 8.450578 AACATCTCAAGTTGACAACTGATTTA 57.549 30.769 21.24 7.26 41.91 1.40
843 897 3.244422 GCACCCCGGATTGATTAGTCATA 60.244 47.826 0.73 0.00 33.56 2.15
876 930 7.011482 GTGAGTGAGTTATTTGCGAAAGGATAT 59.989 37.037 0.00 0.00 0.00 1.63
896 951 5.652744 AAAAGTACTAGCGTTTGTGAGTG 57.347 39.130 0.00 0.00 0.00 3.51
926 981 4.275936 CACAAAGTACAAGGGGTTCTTCAG 59.724 45.833 0.00 0.00 36.26 3.02
1115 1171 6.295802 CCAGGCCCATATGAAAAGAAGAAAAA 60.296 38.462 3.65 0.00 0.00 1.94
1120 1176 3.902218 TCCAGGCCCATATGAAAAGAAG 58.098 45.455 3.65 0.00 0.00 2.85
1209 1266 5.826643 TGTAATTATTGGTGAGGGAAAGCT 58.173 37.500 0.00 0.00 0.00 3.74
1252 1309 8.627403 CCAGTTGTTAAAATATCTCAGCATCAT 58.373 33.333 0.00 0.00 0.00 2.45
1330 1387 9.208022 TCATATCTAAGCGTAAAATTCATGGAG 57.792 33.333 0.00 0.00 0.00 3.86
1351 1408 4.889409 CCAAAACCTGGTGCAGTATCATAT 59.111 41.667 0.00 0.00 40.78 1.78
1357 1414 2.107378 TCATCCAAAACCTGGTGCAGTA 59.893 45.455 0.00 0.00 46.51 2.74
1358 1415 1.133513 TCATCCAAAACCTGGTGCAGT 60.134 47.619 0.00 0.00 46.51 4.40
1464 1521 7.429340 GCAATGTTTACAGATTCCTTATTCACG 59.571 37.037 0.00 0.00 0.00 4.35
1562 1619 5.695851 AGAAATGGCTAAGACAACAACTG 57.304 39.130 0.00 0.00 0.00 3.16
1575 1632 5.532557 GACTTGCAAAAGTTAGAAATGGCT 58.467 37.500 0.00 0.00 32.22 4.75
1579 1636 5.507315 CCACCGACTTGCAAAAGTTAGAAAT 60.507 40.000 0.00 0.00 32.22 2.17
1685 1747 3.719268 AGAACCACCTGCACATTGATA 57.281 42.857 0.00 0.00 0.00 2.15
1686 1748 2.559668 CAAGAACCACCTGCACATTGAT 59.440 45.455 0.00 0.00 0.00 2.57
1724 1788 1.336755 ACAAATCCAAAGCCACGTGAC 59.663 47.619 19.30 5.07 0.00 3.67
1949 2013 0.732571 ATTTGTAGCAATCACCGCCG 59.267 50.000 0.00 0.00 0.00 6.46
2447 2532 1.472480 CGGTTACAAGCCAAATCCAGG 59.528 52.381 0.00 0.00 0.00 4.45
2741 2826 3.181491 ACCATTTGTTTCGTTGGTCACAG 60.181 43.478 0.00 0.00 38.00 3.66
3097 3182 1.407025 GGACTTTCTTAAGGGCCCTCG 60.407 57.143 28.84 17.09 35.61 4.63
3162 3260 3.433615 CGACCTTCGCTGAGAAAGAAAAT 59.566 43.478 0.00 0.00 38.57 1.82
3227 3335 4.572909 AGACACCGAACCCTACAAATAAC 58.427 43.478 0.00 0.00 0.00 1.89


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

AutoCloner maintained by Alex Coulton.