Multiple sequence alignment - TraesCS6D01G156100

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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 TraesCS6D01G156100 chr6D 100.000 2966 0 0 1 2966 132289158 132292123 0.000000e+00 5478
1 TraesCS6D01G156100 chr6D 92.877 716 35 5 1 700 132408654 132409369 0.000000e+00 1026
2 TraesCS6D01G156100 chr5B 95.297 2275 101 6 694 2964 138152398 138154670 0.000000e+00 3603
3 TraesCS6D01G156100 chr5B 95.343 1546 69 3 704 2248 442824892 442826435 0.000000e+00 2453
4 TraesCS6D01G156100 chr5B 80.981 1977 339 32 999 2962 612506681 612504729 0.000000e+00 1533
5 TraesCS6D01G156100 chr5B 90.659 1092 86 6 1080 2171 12259723 12258648 0.000000e+00 1437
6 TraesCS6D01G156100 chr5B 96.122 722 28 0 2243 2964 442835174 442835895 0.000000e+00 1179
7 TraesCS6D01G156100 chr5B 89.524 630 53 6 2347 2964 12258159 12257531 0.000000e+00 785
8 TraesCS6D01G156100 chr6A 94.652 1496 51 9 1472 2965 373095853 373094385 0.000000e+00 2292
9 TraesCS6D01G156100 chr6A 94.645 691 33 4 784 1474 373100062 373099376 0.000000e+00 1068
10 TraesCS6D01G156100 chr6A 91.004 667 46 5 1 656 171454594 171455257 0.000000e+00 887
11 TraesCS6D01G156100 chr6A 93.258 89 5 1 706 794 373109134 373109047 2.400000e-26 130
12 TraesCS6D01G156100 chr1D 80.678 797 134 20 696 1482 29586399 29585613 4.230000e-168 601
13 TraesCS6D01G156100 chr5D 74.229 551 127 11 2421 2964 496539064 496538522 1.790000e-52 217
14 TraesCS6D01G156100 chr2D 73.996 523 129 4 2421 2941 76928250 76927733 3.880000e-49 206
15 TraesCS6D01G156100 chr2D 73.588 549 140 5 2418 2964 557645293 557645838 3.880000e-49 206
16 TraesCS6D01G156100 chr7A 73.201 556 143 5 2409 2962 149265799 149265248 2.330000e-46 196


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 TraesCS6D01G156100 chr6D 132289158 132292123 2965 False 5478 5478 100.0000 1 2966 1 chr6D.!!$F1 2965
1 TraesCS6D01G156100 chr6D 132408654 132409369 715 False 1026 1026 92.8770 1 700 1 chr6D.!!$F2 699
2 TraesCS6D01G156100 chr5B 138152398 138154670 2272 False 3603 3603 95.2970 694 2964 1 chr5B.!!$F1 2270
3 TraesCS6D01G156100 chr5B 442824892 442826435 1543 False 2453 2453 95.3430 704 2248 1 chr5B.!!$F2 1544
4 TraesCS6D01G156100 chr5B 612504729 612506681 1952 True 1533 1533 80.9810 999 2962 1 chr5B.!!$R1 1963
5 TraesCS6D01G156100 chr5B 442835174 442835895 721 False 1179 1179 96.1220 2243 2964 1 chr5B.!!$F3 721
6 TraesCS6D01G156100 chr5B 12257531 12259723 2192 True 1111 1437 90.0915 1080 2964 2 chr5B.!!$R2 1884
7 TraesCS6D01G156100 chr6A 373094385 373100062 5677 True 1680 2292 94.6485 784 2965 2 chr6A.!!$R2 2181
8 TraesCS6D01G156100 chr6A 171454594 171455257 663 False 887 887 91.0040 1 656 1 chr6A.!!$F1 655
9 TraesCS6D01G156100 chr1D 29585613 29586399 786 True 601 601 80.6780 696 1482 1 chr1D.!!$R1 786
10 TraesCS6D01G156100 chr5D 496538522 496539064 542 True 217 217 74.2290 2421 2964 1 chr5D.!!$R1 543
11 TraesCS6D01G156100 chr2D 76927733 76928250 517 True 206 206 73.9960 2421 2941 1 chr2D.!!$R1 520
12 TraesCS6D01G156100 chr2D 557645293 557645838 545 False 206 206 73.5880 2418 2964 1 chr2D.!!$F1 546

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
79 80 0.620556 ACCATTCAGATGCGGGTTCT 59.379 50.0 0.00 0.0 31.67 3.01 F
1569 5125 0.540365 ACCTAGACGTGGAACCGGAA 60.540 55.0 9.46 0.0 0.00 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1579 5135 0.178891 ACCTCCATGTCACTCCCTGT 60.179 55.0 0.0 0.0 0.0 4.00 R
2556 6481 1.238439 CACGCACCATCCTTGTTTCT 58.762 50.0 0.0 0.0 0.0 2.52 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
70 71 1.707427 GGCCTCCCATACCATTCAGAT 59.293 52.381 0.00 0.00 0.00 2.90
79 80 0.620556 ACCATTCAGATGCGGGTTCT 59.379 50.000 0.00 0.00 31.67 3.01
117 118 1.388837 AAAACCAAAGGAGCGGCGTT 61.389 50.000 9.37 0.48 0.00 4.84
429 430 2.818274 GGAATCGCCTCGCCGTTT 60.818 61.111 0.00 0.00 0.00 3.60
515 516 3.740141 CGACTGGGTGATTAAACGGCTAT 60.740 47.826 0.00 0.00 0.00 2.97
580 581 3.294493 GCAAGGCAAGCGGTGGAA 61.294 61.111 0.00 0.00 0.00 3.53
690 705 9.788960 GGTTGTTAAATGGTAAAAATTGCAAAA 57.211 25.926 1.71 0.00 0.00 2.44
732 747 2.775219 ACGGTGGGGTCCCTGTTT 60.775 61.111 8.15 0.00 36.94 2.83
827 842 4.172232 CCCCTCCGATCCCCTCCA 62.172 72.222 0.00 0.00 0.00 3.86
864 880 1.072331 GTTGTCCCCTTGCTTCTCTCA 59.928 52.381 0.00 0.00 0.00 3.27
896 915 3.072468 CCGGTCAGCCTTCGGGTA 61.072 66.667 0.00 0.00 40.07 3.69
906 925 0.806102 CCTTCGGGTATCAGTGCACG 60.806 60.000 12.01 6.78 38.28 5.34
929 949 1.993391 CGTACACCCCCACCATCCT 60.993 63.158 0.00 0.00 0.00 3.24
984 1004 3.953775 AAGGTGTGGGGAGCACGG 61.954 66.667 0.00 0.00 37.70 4.94
1006 1026 4.530857 GGTCGGGAGCCATGGACG 62.531 72.222 18.40 13.77 0.00 4.79
1132 1152 3.330701 AGCAATGGGGAAGTTGTTCTCTA 59.669 43.478 0.00 0.00 33.12 2.43
1443 1474 3.502303 GGGAAGACTTGGGGGAAGAAATT 60.502 47.826 0.00 0.00 35.42 1.82
1569 5125 0.540365 ACCTAGACGTGGAACCGGAA 60.540 55.000 9.46 0.00 0.00 4.30
1579 5135 1.494716 GGAACCGGAAGAGGGGGAAA 61.495 60.000 9.46 0.00 35.02 3.13
1957 5514 3.685139 AGGAAAAGAAGAGCACGATCA 57.315 42.857 0.00 0.00 0.00 2.92
1963 5520 5.757850 AAAGAAGAGCACGATCAAAACTT 57.242 34.783 0.00 0.00 0.00 2.66
2081 5663 0.105778 GAGGAAGCGGAAGGATCAGG 59.894 60.000 0.00 0.00 0.00 3.86
2098 5680 4.025401 GGAGTGCGGCCACAAACG 62.025 66.667 2.24 0.00 44.53 3.60
2199 5781 4.137543 GTGATATAAAGGGGGAACTGCAG 58.862 47.826 13.48 13.48 0.00 4.41
2200 5782 2.729028 TATAAAGGGGGAACTGCAGC 57.271 50.000 15.27 0.00 0.00 5.25
2248 5832 4.936685 AAAGAGTAAGAAGGGCAGGAAT 57.063 40.909 0.00 0.00 0.00 3.01
2400 6325 1.950973 GACAAGGAGGGAGACGGAGC 61.951 65.000 0.00 0.00 0.00 4.70
2402 6327 4.824515 AGGAGGGAGACGGAGCCG 62.825 72.222 7.48 7.48 46.03 5.52
2668 6593 1.480545 GTGGACTGGCTTTGTTTTGGT 59.519 47.619 0.00 0.00 0.00 3.67
2676 6601 5.539955 ACTGGCTTTGTTTTGGTAGAATCAT 59.460 36.000 0.00 0.00 0.00 2.45
2697 6633 8.757982 ATCATGTTAATCTCAAGCTAATTGGT 57.242 30.769 0.00 0.00 39.54 3.67
2710 6646 3.426292 GCTAATTGGTTTTGTCTCTCGGC 60.426 47.826 0.00 0.00 0.00 5.54
2965 6901 2.098443 GCTCTAGAGGTGTGTGAGCTAC 59.902 54.545 21.23 0.00 44.52 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 49 0.986019 TGAATGGTATGGGAGGCCGT 60.986 55.000 0.00 0.00 0.00 5.68
70 71 1.002624 GTTCCATGGAGAACCCGCA 60.003 57.895 15.53 0.00 40.25 5.69
105 106 4.314440 TGCTCAACGCCGCTCCTT 62.314 61.111 0.00 0.00 38.05 3.36
117 118 1.202188 CGCGAGAATACTCACTGCTCA 60.202 52.381 0.00 0.00 42.72 4.26
134 135 4.758251 TCCACCCACAGCATCGCG 62.758 66.667 0.00 0.00 0.00 5.87
139 140 2.431683 GAAGCTCCACCCACAGCA 59.568 61.111 0.00 0.00 38.18 4.41
159 160 0.889186 GCAGTTGACATTCCACCCGT 60.889 55.000 0.00 0.00 0.00 5.28
213 214 1.509923 GGATCTCGTTTCCCGTCGT 59.490 57.895 0.00 0.00 37.94 4.34
386 387 0.822532 ACTCTCCGTGGAAGTGTCGT 60.823 55.000 3.84 0.00 0.00 4.34
429 430 1.988293 TCTTCGTGGCAATTTTGGGA 58.012 45.000 0.00 0.00 0.00 4.37
515 516 0.318360 CTCGCGGTTATATCGGCACA 60.318 55.000 6.13 0.10 34.15 4.57
614 622 4.101585 TCGAATCTTACATCATTGCTCCCT 59.898 41.667 0.00 0.00 0.00 4.20
690 705 2.509964 ACAGGGGACAGACTTGACTTTT 59.490 45.455 0.00 0.00 0.00 2.27
691 706 2.127708 ACAGGGGACAGACTTGACTTT 58.872 47.619 0.00 0.00 0.00 2.66
692 707 1.417890 CACAGGGGACAGACTTGACTT 59.582 52.381 0.00 0.00 0.00 3.01
693 708 1.051812 CACAGGGGACAGACTTGACT 58.948 55.000 0.00 0.00 0.00 3.41
694 709 0.759346 ACACAGGGGACAGACTTGAC 59.241 55.000 0.00 0.00 0.00 3.18
695 710 0.758734 CACACAGGGGACAGACTTGA 59.241 55.000 0.00 0.00 0.00 3.02
696 711 0.758734 TCACACAGGGGACAGACTTG 59.241 55.000 0.00 0.00 0.00 3.16
697 712 0.759346 GTCACACAGGGGACAGACTT 59.241 55.000 0.00 0.00 34.22 3.01
698 713 1.464376 CGTCACACAGGGGACAGACT 61.464 60.000 0.00 0.00 33.66 3.24
702 717 2.445085 ACCGTCACACAGGGGACA 60.445 61.111 0.00 0.00 33.89 4.02
732 747 2.786539 AATCGCTCTGCTTGTCGCCA 62.787 55.000 0.00 0.00 38.05 5.69
827 842 0.252284 AACCACCTCGATGGGAGACT 60.252 55.000 9.79 0.00 46.23 3.24
940 960 7.039644 GGAGATGGAAGAAATCGAACTATCCTA 60.040 40.741 0.00 0.00 0.00 2.94
984 1004 3.728373 ATGGCTCCCGACCAACCC 61.728 66.667 0.00 0.00 41.49 4.11
1006 1026 2.854805 GCTTCAACTTGTCTTCAACGCC 60.855 50.000 0.00 0.00 0.00 5.68
1132 1152 3.135895 CCTCCTACATGTCCCGGTTTATT 59.864 47.826 0.00 0.00 0.00 1.40
1376 1407 3.243877 CAGCGGAACATTGTAGATTCTCG 59.756 47.826 0.00 0.00 0.00 4.04
1443 1474 4.402155 GCATCAACCTCCATCAATTTACCA 59.598 41.667 0.00 0.00 0.00 3.25
1569 5125 0.842467 CACTCCCTGTTTCCCCCTCT 60.842 60.000 0.00 0.00 0.00 3.69
1579 5135 0.178891 ACCTCCATGTCACTCCCTGT 60.179 55.000 0.00 0.00 0.00 4.00
1963 5520 9.085645 TGTGATCTTTAGAGGACTTGTAACTTA 57.914 33.333 0.00 0.00 0.00 2.24
2081 5663 4.025401 CGTTTGTGGCCGCACTCC 62.025 66.667 21.09 8.74 0.00 3.85
2098 5680 0.823356 TGCTTGTTTGGGACTGCCTC 60.823 55.000 0.00 0.00 0.00 4.70
2199 5781 2.216898 GTATGAGCCTTCACATCTGGC 58.783 52.381 0.00 0.00 46.42 4.85
2200 5782 2.437281 AGGTATGAGCCTTCACATCTGG 59.563 50.000 0.00 0.00 34.71 3.86
2228 5812 3.054065 CCATTCCTGCCCTTCTTACTCTT 60.054 47.826 0.00 0.00 0.00 2.85
2400 6325 3.242413 CGCATCCTCACATTTCTTTACGG 60.242 47.826 0.00 0.00 0.00 4.02
2402 6327 3.065371 CCCGCATCCTCACATTTCTTTAC 59.935 47.826 0.00 0.00 0.00 2.01
2556 6481 1.238439 CACGCACCATCCTTGTTTCT 58.762 50.000 0.00 0.00 0.00 2.52
2676 6601 8.637986 ACAAAACCAATTAGCTTGAGATTAACA 58.362 29.630 0.00 0.00 36.97 2.41
2697 6633 3.627395 ATATGGTGCCGAGAGACAAAA 57.373 42.857 0.00 0.00 0.00 2.44
2710 6646 8.601845 TCAGTTATTTCCGTATCAATATGGTG 57.398 34.615 7.89 0.00 39.82 4.17


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

AutoCloner maintained by Alex Coulton.