Multiple sequence alignment - TraesCS5D01G003300

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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 TraesCS5D01G003300 chr5D 100.000 2832 0 0 1 2832 3134889 3137720 0 5230
1 TraesCS5D01G003300 chrUn 97.783 2842 49 5 1 2832 223706933 223704096 0 4887
2 TraesCS5D01G003300 chrUn 97.327 2843 60 6 1 2832 40085860 40088697 0 4815
3 TraesCS5D01G003300 chr1B 97.643 2842 51 5 1 2832 683734141 683731306 0 4863
4 TraesCS5D01G003300 chr7B 97.607 2842 53 5 1 2832 698140161 698142997 0 4857
5 TraesCS5D01G003300 chr2A 97.738 2829 49 6 1 2819 605912876 605910053 0 4855
6 TraesCS5D01G003300 chr6D 97.603 2837 57 5 1 2832 430481762 430484592 0 4852
7 TraesCS5D01G003300 chr1A 97.392 2837 62 4 1 2832 278500836 278503665 0 4819
8 TraesCS5D01G003300 chr3B 97.291 2842 61 8 1 2832 92261857 92264692 0 4807
9 TraesCS5D01G003300 chr2D 97.321 2837 58 5 1 2832 634995177 634998000 0 4802


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 TraesCS5D01G003300 chr5D 3134889 3137720 2831 False 5230 5230 100.000 1 2832 1 chr5D.!!$F1 2831
1 TraesCS5D01G003300 chrUn 223704096 223706933 2837 True 4887 4887 97.783 1 2832 1 chrUn.!!$R1 2831
2 TraesCS5D01G003300 chrUn 40085860 40088697 2837 False 4815 4815 97.327 1 2832 1 chrUn.!!$F1 2831
3 TraesCS5D01G003300 chr1B 683731306 683734141 2835 True 4863 4863 97.643 1 2832 1 chr1B.!!$R1 2831
4 TraesCS5D01G003300 chr7B 698140161 698142997 2836 False 4857 4857 97.607 1 2832 1 chr7B.!!$F1 2831
5 TraesCS5D01G003300 chr2A 605910053 605912876 2823 True 4855 4855 97.738 1 2819 1 chr2A.!!$R1 2818
6 TraesCS5D01G003300 chr6D 430481762 430484592 2830 False 4852 4852 97.603 1 2832 1 chr6D.!!$F1 2831
7 TraesCS5D01G003300 chr1A 278500836 278503665 2829 False 4819 4819 97.392 1 2832 1 chr1A.!!$F1 2831
8 TraesCS5D01G003300 chr3B 92261857 92264692 2835 False 4807 4807 97.291 1 2832 1 chr3B.!!$F1 2831
9 TraesCS5D01G003300 chr2D 634995177 634998000 2823 False 4802 4802 97.321 1 2832 1 chr2D.!!$F1 2831

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
550 551 0.237235 GTTTTTGGTGCGATCGCTCA 59.763 50.0 37.01 30.27 42.51 4.26 F
1599 1607 1.592400 CCCTCGTCGAGTGGTGCTTA 61.592 60.0 20.37 0.00 0.00 3.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1762 1770 0.463654 GCACATAAGCCATCGGGTCA 60.464 55.0 0.0 0.0 36.17 4.02 R
2541 2554 1.187087 AAACAAACCGACCCAGCAAA 58.813 45.0 0.0 0.0 0.00 3.68 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
82 83 3.737559 AGCCCAATATTGAGACCACAA 57.262 42.857 17.23 0.00 0.00 3.33
176 177 1.076841 TCCTTTCCATGGCCATTCACA 59.923 47.619 17.92 0.00 0.00 3.58
186 187 2.480555 CATTCACAGCCCGCGAAC 59.519 61.111 8.23 0.00 0.00 3.95
416 417 5.105554 TGCCTCTAGAAAGATCAGACAGAAC 60.106 44.000 0.00 0.00 0.00 3.01
550 551 0.237235 GTTTTTGGTGCGATCGCTCA 59.763 50.000 37.01 30.27 42.51 4.26
771 773 8.596781 AGGGTTCGAATAGCATCTACTAATAT 57.403 34.615 0.00 0.00 0.00 1.28
903 905 7.259161 GTCTTCGAACTAGTCATTAATGGTCT 58.741 38.462 15.36 15.02 0.00 3.85
956 958 4.926244 TGCGAACACTTTCATTTTTAGCA 58.074 34.783 0.00 0.00 0.00 3.49
960 962 7.021196 GCGAACACTTTCATTTTTAGCATCTA 58.979 34.615 0.00 0.00 0.00 1.98
1111 1113 4.023980 CAGTAGAGATGTTCCCACTGGTA 58.976 47.826 0.00 0.00 36.46 3.25
1112 1114 4.651503 CAGTAGAGATGTTCCCACTGGTAT 59.348 45.833 0.00 0.00 36.46 2.73
1275 1277 4.713792 ACCAGACAAAATGGAGAGAAGT 57.286 40.909 0.00 0.00 40.51 3.01
1282 1284 5.634118 ACAAAATGGAGAGAAGTTCATCCA 58.366 37.500 24.18 24.18 45.48 3.41
1504 1506 4.151157 GGAATGAGCAACAAAATGACAAGC 59.849 41.667 0.00 0.00 0.00 4.01
1516 1518 3.177884 ACAAGCTGAGGTGCCCCA 61.178 61.111 0.00 0.00 0.00 4.96
1550 1552 7.201974 CCATATAGAAAGAAGGGTCGAAGGTTA 60.202 40.741 0.00 0.00 0.00 2.85
1571 1573 2.824489 GCCTGTAGCTTTCCCCGC 60.824 66.667 0.00 0.00 38.99 6.13
1572 1574 2.124695 CCTGTAGCTTTCCCCGCC 60.125 66.667 0.00 0.00 0.00 6.13
1599 1607 1.592400 CCCTCGTCGAGTGGTGCTTA 61.592 60.000 20.37 0.00 0.00 3.09
1762 1770 0.828022 TGGGTGTTCTTCTGTCGTGT 59.172 50.000 0.00 0.00 0.00 4.49
1841 1849 1.298859 GGCGGCGTGAACTCTGATTT 61.299 55.000 9.37 0.00 0.00 2.17
1872 1880 1.524621 CAATCCCGCCGCTGAGATT 60.525 57.895 0.00 0.00 0.00 2.40
2116 2124 2.520465 TACGTCCGTACCGCTCCTCA 62.520 60.000 0.00 0.00 0.00 3.86
2217 2225 4.980805 GTGAGCGCGGTGGGAACA 62.981 66.667 18.92 3.48 38.70 3.18
2263 2271 0.758734 CGGGTCAGCATAGAATGGGA 59.241 55.000 0.00 0.00 0.00 4.37
2289 2297 1.884497 CGGCCCTAATGTTGTGTTGGA 60.884 52.381 0.00 0.00 0.00 3.53
2350 2358 1.366854 GGGGCACAGCGTAACTAAGC 61.367 60.000 0.00 0.00 0.00 3.09
2357 2365 0.458025 AGCGTAACTAAGCGAGCCAC 60.458 55.000 0.00 0.00 38.61 5.01
2386 2394 2.892640 CGAGACAGAATGGGCGGA 59.107 61.111 0.00 0.00 43.62 5.54
2425 2433 0.103208 GAGCCGATTGGTCAGACGAT 59.897 55.000 0.00 0.00 41.24 3.73
2459 2472 8.432805 GCACATATTATATTAGCCACCTATCCT 58.567 37.037 0.00 0.00 0.00 3.24
2541 2554 1.154301 CGCCTGCGCATACGTTTTT 60.154 52.632 12.24 0.00 42.83 1.94
2615 2633 3.979497 CCCGCCCCCTTTCCTGTT 61.979 66.667 0.00 0.00 0.00 3.16
2620 2638 2.067197 CCCCCTTTCCTGTTCGTCT 58.933 57.895 0.00 0.00 0.00 4.18
2706 2724 1.671379 GGCAGAAACTCGTCCCACC 60.671 63.158 0.00 0.00 0.00 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
82 83 7.342026 GGATCCTTTGTGGTTTGAATAATAGGT 59.658 37.037 3.84 0.0 37.07 3.08
176 177 2.746277 GGTTGATGTTCGCGGGCT 60.746 61.111 6.13 0.0 0.00 5.19
186 187 2.390599 CGGGCACGAGTGGTTGATG 61.391 63.158 0.00 0.0 44.60 3.07
416 417 5.330295 ACGTACAATTACAGCTCGTCTTAG 58.670 41.667 0.00 0.0 0.00 2.18
550 551 7.230027 AGTGAAATTCAGAAGTCTCAATTCCT 58.770 34.615 0.00 0.0 0.00 3.36
564 565 9.212641 TCATGAGACTCTTTTAGTGAAATTCAG 57.787 33.333 3.68 0.0 39.07 3.02
620 621 9.483916 CTGATACCCTACTATATCATAGTCTCG 57.516 40.741 2.19 0.0 37.23 4.04
771 773 9.857957 AAGTATTTTCACAAAGTTTTCGGTAAA 57.142 25.926 0.00 0.0 0.00 2.01
1059 1061 1.191535 TCAATAGTACGGGTGCTGCT 58.808 50.000 0.00 0.0 0.00 4.24
1371 1373 4.973168 AGAATTGTAAACAGAGCAGACCA 58.027 39.130 0.00 0.0 0.00 4.02
1516 1518 3.074857 TCTTTCTATATGGGGGTGCCT 57.925 47.619 0.00 0.0 0.00 4.75
1550 1552 1.615262 GGGAAAGCTACAGGCCCAT 59.385 57.895 0.00 0.0 43.05 4.00
1762 1770 0.463654 GCACATAAGCCATCGGGTCA 60.464 55.000 0.00 0.0 36.17 4.02
1872 1880 4.899457 TCAAGGTTAAGGAGTCAACTGAGA 59.101 41.667 0.00 0.0 0.00 3.27
2116 2124 1.270907 GGATGCGGGATCTACTCCAT 58.729 55.000 9.42 0.0 46.98 3.41
2350 2358 0.815615 GCCCTAAATGGAGTGGCTCG 60.816 60.000 0.00 0.0 39.05 5.03
2357 2365 1.757118 TCTGTCTCGCCCTAAATGGAG 59.243 52.381 0.00 0.0 38.35 3.86
2425 2433 8.811994 TGGCTAATATAATATGTGCAGTAGTCA 58.188 33.333 0.00 0.0 0.00 3.41
2459 2472 1.679981 TTCCATCCCAGTCCATTCCA 58.320 50.000 0.00 0.0 0.00 3.53
2541 2554 1.187087 AAACAAACCGACCCAGCAAA 58.813 45.000 0.00 0.0 0.00 3.68
2620 2638 4.680237 CCAACTGCTGCCGGTCGA 62.680 66.667 1.90 0.0 0.00 4.20
2789 2807 2.770130 GGGACCCAAGGGCAATCA 59.230 61.111 5.33 0.0 39.32 2.57


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

AutoCloner maintained by Alex Coulton.