Multiple sequence alignment - TraesCS5D01G159200

Loading Multiple Alignment...

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 TraesCS5D01G159200 chr5D 100.000 3526 0 0 1547 5072 247617189 247613664 0.000000e+00 6512
1 TraesCS5D01G159200 chr5D 100.000 1269 0 0 1 1269 247618735 247617467 0.000000e+00 2344
2 TraesCS5D01G159200 chr5B 97.134 3524 62 4 1571 5056 281843608 281840086 0.000000e+00 5912
3 TraesCS5D01G159200 chr5B 94.113 1274 65 6 1 1269 281845107 281843839 0.000000e+00 1929
4 TraesCS5D01G159200 chr5B 81.851 281 45 3 533 812 696159317 696159592 1.100000e-56 231
5 TraesCS5D01G159200 chr5A 96.386 1660 39 8 3428 5072 331404586 331402933 0.000000e+00 2713
6 TraesCS5D01G159200 chr5A 91.857 921 55 9 319 1234 331407786 331406881 0.000000e+00 1267
7 TraesCS5D01G159200 chr5A 96.006 701 14 3 1640 2329 331406416 331405719 0.000000e+00 1127
8 TraesCS5D01G159200 chr5A 95.042 706 26 5 2321 3026 331405676 331404980 0.000000e+00 1101
9 TraesCS5D01G159200 chr5A 94.207 328 14 2 3052 3374 331404907 331404580 3.530000e-136 496
10 TraesCS5D01G159200 chr5A 91.843 331 24 2 1 330 331408286 331407958 4.630000e-125 459


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 TraesCS5D01G159200 chr5D 247613664 247618735 5071 True 4428.000000 6512 100.0000 1 5072 2 chr5D.!!$R1 5071
1 TraesCS5D01G159200 chr5B 281840086 281845107 5021 True 3920.500000 5912 95.6235 1 5056 2 chr5B.!!$R1 5055
2 TraesCS5D01G159200 chr5A 331402933 331408286 5353 True 1193.833333 2713 94.2235 1 5072 6 chr5A.!!$R1 5071

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
522 708 0.464036 AGGCACTCACACTCACGAAA 59.536 50.000 0.00 0.00 0.00 3.46 F
608 794 1.521141 GTTCCGGGGGCTCTTACTC 59.479 63.158 0.00 0.00 0.00 2.59 F
733 919 1.533625 TGCCGCTTTGCTTGATTAGT 58.466 45.000 0.00 0.00 0.00 2.24 F
739 925 3.187227 CGCTTTGCTTGATTAGTGTCACT 59.813 43.478 10.99 10.99 0.00 3.41 F
2557 2869 0.033894 ACAAGTCCGGTGGTTTGGTT 60.034 50.000 0.00 0.00 0.00 3.67 F
2701 3013 1.145900 TGGGGTGGGTTGGATGTCAT 61.146 55.000 0.00 0.00 0.00 3.06 F
3407 3771 2.047844 CAGGCTCCACAGGACGTG 60.048 66.667 0.00 0.00 45.92 4.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1567 1759 0.108019 GTATCGCTAGGGTTTGGGGG 59.892 60.000 6.70 0.00 0.00 5.40 R
1569 1761 0.834612 TGGTATCGCTAGGGTTTGGG 59.165 55.000 6.70 0.00 0.00 4.12 R
1638 1830 2.026879 GAGATGACGCCGGAGAGC 59.973 66.667 13.83 3.86 0.00 4.09 R
2701 3013 2.550606 GACCAGAAACACCAAATACGCA 59.449 45.455 0.00 0.00 0.00 5.24 R
3407 3771 1.745489 CAAAGCGGGCCTAGTGGAC 60.745 63.158 0.84 0.00 41.93 4.02 R
4012 4383 2.420058 ATAGGTGCACTTTGGCCTAC 57.580 50.000 17.98 0.00 36.54 3.18 R
4602 4981 5.342433 GTGAATTTCATGCATTCCGAATGA 58.658 37.500 22.76 9.76 41.46 2.57 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
60 61 4.263018 TGGATGAAGATCTAATGGAGCG 57.737 45.455 0.00 0.00 35.20 5.03
80 81 2.606725 CGGATTGTTGACATCAGAGAGC 59.393 50.000 0.00 0.00 0.00 4.09
103 104 5.400703 CCAAGTGCAAAACATTTGCTTTTT 58.599 33.333 23.49 14.24 42.88 1.94
253 255 5.516090 TGTTCAACGTTTTATTTCTGAGCC 58.484 37.500 0.00 0.00 0.00 4.70
281 283 1.064003 TGAAACCCCTAGAAGCTGCA 58.936 50.000 1.02 0.00 0.00 4.41
332 334 5.192927 CCATCTATAACTGTTGGAAGCCAA 58.807 41.667 2.69 0.00 41.69 4.52
354 539 6.183360 CCAACCCTAGTCGATCATGTTAAAAC 60.183 42.308 0.00 0.00 0.00 2.43
481 667 3.062763 GGCATGAAGTATCCGACATCAG 58.937 50.000 0.00 0.00 39.05 2.90
522 708 0.464036 AGGCACTCACACTCACGAAA 59.536 50.000 0.00 0.00 0.00 3.46
552 738 7.573710 TGATAATGACTAAGGTGGTTATTGCT 58.426 34.615 0.00 0.00 0.00 3.91
574 760 4.056092 TGTGATTGCAAGCAAAACATGA 57.944 36.364 20.56 0.00 39.55 3.07
577 763 3.490155 TGATTGCAAGCAAAACATGAACG 59.510 39.130 16.30 0.00 39.55 3.95
608 794 1.521141 GTTCCGGGGGCTCTTACTC 59.479 63.158 0.00 0.00 0.00 2.59
621 807 4.451435 GGCTCTTACTCGCCCATTATTAAC 59.549 45.833 0.00 0.00 40.43 2.01
669 855 3.822940 TGATAGTTGTTCGGTTGGGTTT 58.177 40.909 0.00 0.00 0.00 3.27
733 919 1.533625 TGCCGCTTTGCTTGATTAGT 58.466 45.000 0.00 0.00 0.00 2.24
738 924 3.482786 CGCTTTGCTTGATTAGTGTCAC 58.517 45.455 0.00 0.00 0.00 3.67
739 925 3.187227 CGCTTTGCTTGATTAGTGTCACT 59.813 43.478 10.99 10.99 0.00 3.41
772 959 6.569127 TTGCTAATCCTATGACCCAACTTA 57.431 37.500 0.00 0.00 0.00 2.24
777 964 9.740710 GCTAATCCTATGACCCAACTTATATTT 57.259 33.333 0.00 0.00 0.00 1.40
779 966 8.848474 AATCCTATGACCCAACTTATATTTCG 57.152 34.615 0.00 0.00 0.00 3.46
806 993 6.075280 GGACGTTTATATCGCGCAATAAAAT 58.925 36.000 20.19 14.38 31.30 1.82
824 1013 8.558700 CAATAAAATTGTTGAACCCCTCAAAAG 58.441 33.333 0.00 0.00 45.67 2.27
2164 2415 1.860950 CATCCAGTAAGTCCGCATTCG 59.139 52.381 0.00 0.00 0.00 3.34
2223 2474 2.160822 ATACGTGCTCAGATCATGGC 57.839 50.000 0.00 0.00 0.00 4.40
2294 2556 0.896923 TGATGCTGAAATTGTGCCCC 59.103 50.000 0.00 0.00 0.00 5.80
2295 2557 0.176449 GATGCTGAAATTGTGCCCCC 59.824 55.000 0.00 0.00 0.00 5.40
2557 2869 0.033894 ACAAGTCCGGTGGTTTGGTT 60.034 50.000 0.00 0.00 0.00 3.67
2701 3013 1.145900 TGGGGTGGGTTGGATGTCAT 61.146 55.000 0.00 0.00 0.00 3.06
2906 3218 9.236006 ACATCTGTTCACTTGCTTAATCTTAAT 57.764 29.630 0.00 0.00 0.00 1.40
2932 3244 9.936759 TTTTTGAATAACTGTTCCTTGAAGTTT 57.063 25.926 0.00 0.00 35.77 2.66
3193 3557 2.102084 CAGCTTGTATCTAGCTCCTGCA 59.898 50.000 0.00 0.00 45.52 4.41
3214 3578 2.826725 AGTTAGAGTTGCCGACTAGCTT 59.173 45.455 0.00 0.00 39.19 3.74
3407 3771 2.047844 CAGGCTCCACAGGACGTG 60.048 66.667 0.00 0.00 45.92 4.49
3725 4092 7.282675 TGAGTGGAAGTGTATTAGTAGCTCTAC 59.717 40.741 0.00 0.00 36.35 2.59
3962 4329 6.040166 CCATTGAGTTGCCTTTAGATGCTAAT 59.960 38.462 0.00 0.00 0.00 1.73
3963 4330 7.417116 CCATTGAGTTGCCTTTAGATGCTAATT 60.417 37.037 0.00 0.00 0.00 1.40
4012 4383 0.320771 AAGCTGCGAACCAGTACCAG 60.321 55.000 0.00 0.00 43.71 4.00
4892 5271 8.050778 TCATACCGCTTTGTATTCAGAAAAAT 57.949 30.769 0.00 0.00 28.98 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
53 54 2.292267 GATGTCAACAATCCGCTCCAT 58.708 47.619 0.00 0.00 0.00 3.41
60 61 2.941720 GGCTCTCTGATGTCAACAATCC 59.058 50.000 0.00 0.00 0.00 3.01
103 104 7.175467 GCATGTGATAATGATTCCAACATCCTA 59.825 37.037 0.00 0.00 0.00 2.94
186 188 5.866092 GGCTCTGAAAATTTTCTTCATGGAC 59.134 40.000 26.73 12.45 38.02 4.02
253 255 4.286297 TCTAGGGGTTTCATGTTGTCAG 57.714 45.455 0.00 0.00 0.00 3.51
332 334 6.295719 AGTTTTAACATGATCGACTAGGGT 57.704 37.500 0.00 0.00 0.00 4.34
333 335 8.765219 CATAAGTTTTAACATGATCGACTAGGG 58.235 37.037 0.00 0.00 0.00 3.53
334 336 9.314321 ACATAAGTTTTAACATGATCGACTAGG 57.686 33.333 0.00 0.00 0.00 3.02
354 539 4.130118 GGCTAGACCACCATCAACATAAG 58.870 47.826 0.00 0.00 38.86 1.73
541 727 3.911868 TGCAATCACAAGCAATAACCAC 58.088 40.909 0.00 0.00 37.90 4.16
552 738 4.439968 TCATGTTTTGCTTGCAATCACAA 58.560 34.783 18.44 0.00 0.00 3.33
574 760 4.127171 CCGGAACCATCTTTGATATCGTT 58.873 43.478 0.00 0.00 0.00 3.85
577 763 3.412386 CCCCGGAACCATCTTTGATATC 58.588 50.000 0.73 0.00 0.00 1.63
608 794 7.186021 AGAATAAACTCGTTAATAATGGGCG 57.814 36.000 0.00 0.00 0.00 6.13
621 807 9.968870 AAATAGCTAGACCTAAGAATAAACTCG 57.031 33.333 0.00 0.00 0.00 4.18
669 855 4.634004 TCAAAACTTGAAGCTCGACTTTCA 59.366 37.500 0.00 3.39 39.29 2.69
701 887 1.538047 AGCGGCATGTTTGACAAGAT 58.462 45.000 1.45 0.00 0.00 2.40
738 924 6.712095 TCATAGGATTAGCAAGCCACAAATAG 59.288 38.462 6.07 0.00 40.13 1.73
739 925 6.486657 GTCATAGGATTAGCAAGCCACAAATA 59.513 38.462 6.07 0.00 40.13 1.40
772 959 5.284660 GCGATATAAACGTCCGTCGAAATAT 59.715 40.000 11.27 4.64 42.86 1.28
777 964 1.657260 CGCGATATAAACGTCCGTCGA 60.657 52.381 0.00 0.00 42.86 4.20
779 966 0.428618 GCGCGATATAAACGTCCGTC 59.571 55.000 12.10 0.00 0.00 4.79
806 993 5.659079 ACAATACTTTTGAGGGGTTCAACAA 59.341 36.000 0.00 0.00 45.22 2.83
889 1078 4.618965 GGATGTCCGTTTCATACTCCTAC 58.381 47.826 0.00 0.00 0.00 3.18
1567 1759 0.108019 GTATCGCTAGGGTTTGGGGG 59.892 60.000 6.70 0.00 0.00 5.40
1568 1760 0.108019 GGTATCGCTAGGGTTTGGGG 59.892 60.000 6.70 0.00 0.00 4.96
1569 1761 0.834612 TGGTATCGCTAGGGTTTGGG 59.165 55.000 6.70 0.00 0.00 4.12
1638 1830 2.026879 GAGATGACGCCGGAGAGC 59.973 66.667 13.83 3.86 0.00 4.09
2194 2445 5.847111 TCTGAGCACGTATATAGTTTGGT 57.153 39.130 0.00 0.00 0.00 3.67
2223 2474 8.581263 CGCAAATTTTCTGAACATGAATAGAAG 58.419 33.333 0.00 0.00 31.52 2.85
2294 2556 7.178274 ACTGAATCTGCCATCTCTAACTATAGG 59.822 40.741 4.43 0.00 0.00 2.57
2295 2557 8.121305 ACTGAATCTGCCATCTCTAACTATAG 57.879 38.462 0.00 0.00 0.00 1.31
2340 2652 5.351465 CAGCGGCATTAGAACTTTAGAAGAA 59.649 40.000 1.45 0.00 0.00 2.52
2342 2654 4.631813 ACAGCGGCATTAGAACTTTAGAAG 59.368 41.667 1.45 0.00 0.00 2.85
2557 2869 5.027460 TGCCCTTGAAGTAGGATAGTAACA 58.973 41.667 0.00 0.00 37.50 2.41
2619 2931 2.871096 TCTTTGCCCACCGAAATACT 57.129 45.000 0.00 0.00 0.00 2.12
2701 3013 2.550606 GACCAGAAACACCAAATACGCA 59.449 45.455 0.00 0.00 0.00 5.24
2906 3218 9.936759 AAACTTCAAGGAACAGTTATTCAAAAA 57.063 25.926 0.00 0.00 0.00 1.94
3084 3448 0.179018 AAAACTGAAGGACGCAGGCT 60.179 50.000 0.00 0.00 37.69 4.58
3193 3557 2.448453 AGCTAGTCGGCAACTCTAACT 58.552 47.619 0.00 0.00 39.55 2.24
3214 3578 9.431887 CCTGTATGTTTACTTGAGTTAAGCTTA 57.568 33.333 0.86 0.86 40.16 3.09
3407 3771 1.745489 CAAAGCGGGCCTAGTGGAC 60.745 63.158 0.84 0.00 41.93 4.02
3702 4069 6.259608 TCGTAGAGCTACTAATACACTTCCAC 59.740 42.308 6.14 0.00 34.04 4.02
4012 4383 2.420058 ATAGGTGCACTTTGGCCTAC 57.580 50.000 17.98 0.00 36.54 3.18
4602 4981 5.342433 GTGAATTTCATGCATTCCGAATGA 58.658 37.500 22.76 9.76 41.46 2.57


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

AutoCloner maintained by Alex Coulton.