Multiple sequence alignment - TraesCS6D01G209800

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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 TraesCS6D01G209800 chr6D 100.000 3865 0 0 1 3865 296393482 296389618 0 7138
1 TraesCS6D01G209800 chr6D 97.060 3878 88 15 1 3865 340966958 340963094 0 6506
2 TraesCS6D01G209800 chr6D 96.208 3877 122 17 1 3865 176853542 176857405 0 6322
3 TraesCS6D01G209800 chr4D 97.184 3871 83 15 1 3865 444110620 444106770 0 6521
4 TraesCS6D01G209800 chr4D 93.771 3901 186 41 4 3865 178593039 178589157 0 5805
5 TraesCS6D01G209800 chr4D 96.894 3123 77 11 747 3865 173594958 173591852 0 5212
6 TraesCS6D01G209800 chr7D 97.059 3876 91 15 1 3865 535911808 535915671 0 6505
7 TraesCS6D01G209800 chr7D 96.025 3874 126 22 4 3865 564196104 564192247 0 6276
8 TraesCS6D01G209800 chr7D 94.259 3588 160 33 4 3562 420897481 420893911 0 5443
9 TraesCS6D01G209800 chr7D 95.483 952 34 3 1 951 394988556 394987613 0 1511
10 TraesCS6D01G209800 chr3D 95.733 3890 124 22 4 3865 468650505 468646630 0 6226
11 TraesCS6D01G209800 chr2D 93.318 3891 173 46 4 3865 610030236 610026404 0 5664
12 TraesCS6D01G209800 chr5D 91.426 1143 80 13 4 1140 168016161 168017291 0 1552


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 TraesCS6D01G209800 chr6D 296389618 296393482 3864 True 7138 7138 100.000 1 3865 1 chr6D.!!$R1 3864
1 TraesCS6D01G209800 chr6D 340963094 340966958 3864 True 6506 6506 97.060 1 3865 1 chr6D.!!$R2 3864
2 TraesCS6D01G209800 chr6D 176853542 176857405 3863 False 6322 6322 96.208 1 3865 1 chr6D.!!$F1 3864
3 TraesCS6D01G209800 chr4D 444106770 444110620 3850 True 6521 6521 97.184 1 3865 1 chr4D.!!$R3 3864
4 TraesCS6D01G209800 chr4D 178589157 178593039 3882 True 5805 5805 93.771 4 3865 1 chr4D.!!$R2 3861
5 TraesCS6D01G209800 chr4D 173591852 173594958 3106 True 5212 5212 96.894 747 3865 1 chr4D.!!$R1 3118
6 TraesCS6D01G209800 chr7D 535911808 535915671 3863 False 6505 6505 97.059 1 3865 1 chr7D.!!$F1 3864
7 TraesCS6D01G209800 chr7D 564192247 564196104 3857 True 6276 6276 96.025 4 3865 1 chr7D.!!$R3 3861
8 TraesCS6D01G209800 chr7D 420893911 420897481 3570 True 5443 5443 94.259 4 3562 1 chr7D.!!$R2 3558
9 TraesCS6D01G209800 chr7D 394987613 394988556 943 True 1511 1511 95.483 1 951 1 chr7D.!!$R1 950
10 TraesCS6D01G209800 chr3D 468646630 468650505 3875 True 6226 6226 95.733 4 3865 1 chr3D.!!$R1 3861
11 TraesCS6D01G209800 chr2D 610026404 610030236 3832 True 5664 5664 93.318 4 3865 1 chr2D.!!$R1 3861
12 TraesCS6D01G209800 chr5D 168016161 168017291 1130 False 1552 1552 91.426 4 1140 1 chr5D.!!$F1 1136

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
937 966 1.133668 GCAATAGGGCCTCACAGGAAT 60.134 52.381 10.74 0.0 37.67 3.01 F
2531 2646 0.172352 CTCAGCTCCGTCTTGTCCTC 59.828 60.000 0.00 0.0 0.00 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2723 2846 2.158696 GCTGTCAGAGCCATTAAGGGAT 60.159 50.00 11.08 2.46 42.54 3.85 R
3662 3801 4.929479 AGTTGCCATGTAGGTGGAATAAA 58.071 39.13 0.00 0.00 42.02 1.40 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
105 107 2.961062 AGGCAGGATAATGTGGCAAATC 59.039 45.455 0.00 0.00 41.59 2.17
172 175 6.363882 TGTGATATCTGAACATATTTGGCCA 58.636 36.000 0.00 0.00 0.00 5.36
236 239 3.704061 AGTTGCCACATTACAGGTTGTTT 59.296 39.130 0.00 0.00 0.00 2.83
678 699 1.449070 CTCAGCAGAATGGCTCGCA 60.449 57.895 0.00 0.00 43.68 5.10
718 739 6.849588 TGATGATGATTTCATGGAGTTACG 57.150 37.500 0.00 0.00 45.29 3.18
731 752 1.808390 GTTACGGCGGCAGAATCGT 60.808 57.895 13.24 6.79 39.30 3.73
751 772 1.270094 TGCAACTAGACGGACAACAGG 60.270 52.381 0.00 0.00 0.00 4.00
778 799 3.910039 GGTAACTGTCCACCCCCA 58.090 61.111 1.11 0.00 0.00 4.96
779 800 1.683441 GGTAACTGTCCACCCCCAG 59.317 63.158 1.11 0.00 34.82 4.45
814 842 4.443315 CCTTCCCCCATATGTTTTGAATGC 60.443 45.833 1.24 0.00 0.00 3.56
843 871 4.081697 TGAGTTTGCAATCGTCTGATAGGA 60.082 41.667 0.00 0.00 33.40 2.94
927 956 1.589803 AACGTAATCGCAATAGGGCC 58.410 50.000 0.00 0.00 41.18 5.80
937 966 1.133668 GCAATAGGGCCTCACAGGAAT 60.134 52.381 10.74 0.00 37.67 3.01
956 987 3.685139 ATGCCTGACTATATTGACCGG 57.315 47.619 0.00 0.00 0.00 5.28
1076 1108 1.467875 CTCGGTGAGATTTACGAGCG 58.532 55.000 0.00 0.00 44.90 5.03
1818 1915 4.606457 GCAACTGCCAACATAACTAGAG 57.394 45.455 0.00 0.00 34.31 2.43
1819 1916 3.375299 GCAACTGCCAACATAACTAGAGG 59.625 47.826 0.00 0.00 34.31 3.69
1820 1917 3.914426 ACTGCCAACATAACTAGAGGG 57.086 47.619 0.00 0.00 0.00 4.30
1821 1918 2.092914 ACTGCCAACATAACTAGAGGGC 60.093 50.000 0.00 0.00 40.29 5.19
1822 1919 1.912731 TGCCAACATAACTAGAGGGCA 59.087 47.619 0.00 0.00 46.74 5.36
1823 1920 2.307392 TGCCAACATAACTAGAGGGCAA 59.693 45.455 0.00 0.00 46.01 4.52
1824 1921 2.683362 GCCAACATAACTAGAGGGCAAC 59.317 50.000 0.00 0.00 39.66 4.17
1825 1922 3.622455 GCCAACATAACTAGAGGGCAACT 60.622 47.826 0.00 0.00 39.66 3.16
1826 1923 4.383770 GCCAACATAACTAGAGGGCAACTA 60.384 45.833 0.00 0.00 39.66 2.24
1827 1924 5.741011 CCAACATAACTAGAGGGCAACTAA 58.259 41.667 0.00 0.00 0.00 2.24
1828 1925 5.585047 CCAACATAACTAGAGGGCAACTAAC 59.415 44.000 0.00 0.00 0.00 2.34
1829 1926 6.170506 CAACATAACTAGAGGGCAACTAACA 58.829 40.000 0.00 0.00 0.00 2.41
1830 1927 5.731591 ACATAACTAGAGGGCAACTAACAC 58.268 41.667 0.00 0.00 0.00 3.32
1831 1928 5.247564 ACATAACTAGAGGGCAACTAACACA 59.752 40.000 0.00 0.00 0.00 3.72
1832 1929 4.910458 AACTAGAGGGCAACTAACACAT 57.090 40.909 0.00 0.00 0.00 3.21
1833 1930 4.207891 ACTAGAGGGCAACTAACACATG 57.792 45.455 0.00 0.00 0.00 3.21
2015 2118 2.969628 ATCGTCTTGATCTGTCCACC 57.030 50.000 0.00 0.00 28.49 4.61
2160 2263 1.271379 TGCAGGTTAGTTCTGGCTTCC 60.271 52.381 0.00 0.00 33.16 3.46
2166 2269 4.004314 GGTTAGTTCTGGCTTCCTTCTTC 58.996 47.826 0.00 0.00 0.00 2.87
2227 2334 2.525105 AAAATCCCCATACGGCAACT 57.475 45.000 0.00 0.00 0.00 3.16
2531 2646 0.172352 CTCAGCTCCGTCTTGTCCTC 59.828 60.000 0.00 0.00 0.00 3.71
2723 2846 0.923358 AGTTGGTTGAGGGTTGGACA 59.077 50.000 0.00 0.00 0.00 4.02
3524 3656 2.443887 TTTGCCTTTCAATGCAGCTC 57.556 45.000 0.00 0.00 38.95 4.09
3529 3663 2.165845 GCCTTTCAATGCAGCTCTTCAT 59.834 45.455 0.00 0.00 0.00 2.57
3618 3757 4.093743 TCTTACTACATGGCAACTCCTGA 58.906 43.478 0.00 0.00 35.26 3.86
3662 3801 0.971386 CCAGGCAAAATGGCAACTCT 59.029 50.000 6.68 0.00 46.46 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
718 739 3.430862 TTGCACGATTCTGCCGCC 61.431 61.111 0.00 0.00 36.21 6.13
731 752 1.270094 CCTGTTGTCCGTCTAGTTGCA 60.270 52.381 0.00 0.00 0.00 4.08
751 772 1.146358 GACAGTTACCTCATCGCCGC 61.146 60.000 0.00 0.00 0.00 6.53
814 842 3.058016 AGACGATTGCAAACTCAACATGG 60.058 43.478 1.71 0.00 0.00 3.66
843 871 9.911788 ATGTTTCACTATCATGAAGGTTTAGAT 57.088 29.630 0.00 0.00 39.68 1.98
937 966 1.691976 CCCGGTCAATATAGTCAGGCA 59.308 52.381 0.00 0.00 0.00 4.75
956 987 2.186125 GGTCGTCGGTGAATCCCC 59.814 66.667 0.00 0.00 0.00 4.81
1076 1108 1.678970 ACAAATTCCCTGGAGGCGC 60.679 57.895 0.00 0.00 34.51 6.53
1495 1548 5.474532 ACAAGAAGTTGCTGCATCAGAAATA 59.525 36.000 12.76 0.00 37.14 1.40
1814 1911 5.020795 TCTACATGTGTTAGTTGCCCTCTA 58.979 41.667 9.11 0.00 0.00 2.43
1815 1912 3.838317 TCTACATGTGTTAGTTGCCCTCT 59.162 43.478 9.11 0.00 0.00 3.69
1816 1913 4.202245 TCTACATGTGTTAGTTGCCCTC 57.798 45.455 9.11 0.00 0.00 4.30
1817 1914 4.517285 CATCTACATGTGTTAGTTGCCCT 58.483 43.478 9.11 0.00 0.00 5.19
1818 1915 3.627577 CCATCTACATGTGTTAGTTGCCC 59.372 47.826 9.11 0.00 0.00 5.36
1819 1916 3.065371 GCCATCTACATGTGTTAGTTGCC 59.935 47.826 9.11 0.00 0.00 4.52
1820 1917 3.689161 TGCCATCTACATGTGTTAGTTGC 59.311 43.478 9.11 3.32 0.00 4.17
1821 1918 5.412594 AGTTGCCATCTACATGTGTTAGTTG 59.587 40.000 9.11 3.54 0.00 3.16
1822 1919 5.560724 AGTTGCCATCTACATGTGTTAGTT 58.439 37.500 9.11 0.00 0.00 2.24
1823 1920 5.165961 AGTTGCCATCTACATGTGTTAGT 57.834 39.130 9.11 0.00 0.00 2.24
1824 1921 6.593770 TGTTAGTTGCCATCTACATGTGTTAG 59.406 38.462 9.11 0.00 0.00 2.34
1825 1922 6.468543 TGTTAGTTGCCATCTACATGTGTTA 58.531 36.000 9.11 0.00 0.00 2.41
1826 1923 5.312895 TGTTAGTTGCCATCTACATGTGTT 58.687 37.500 9.11 0.00 0.00 3.32
1827 1924 4.905429 TGTTAGTTGCCATCTACATGTGT 58.095 39.130 9.11 0.00 0.00 3.72
1828 1925 5.178061 TCTGTTAGTTGCCATCTACATGTG 58.822 41.667 9.11 0.00 0.00 3.21
1829 1926 5.420725 TCTGTTAGTTGCCATCTACATGT 57.579 39.130 2.69 2.69 0.00 3.21
1830 1927 6.741992 TTTCTGTTAGTTGCCATCTACATG 57.258 37.500 0.00 0.00 0.00 3.21
1831 1928 8.046708 TGTATTTCTGTTAGTTGCCATCTACAT 58.953 33.333 0.00 0.00 0.00 2.29
1832 1929 7.390823 TGTATTTCTGTTAGTTGCCATCTACA 58.609 34.615 0.00 0.00 0.00 2.74
1833 1930 7.843490 TGTATTTCTGTTAGTTGCCATCTAC 57.157 36.000 0.00 0.00 0.00 2.59
2015 2118 3.028850 TCCTATCCCTGTAAAGTCCACG 58.971 50.000 0.00 0.00 0.00 4.94
2027 2130 4.964241 GGCGGGCCTCCTATCCCT 62.964 72.222 4.98 0.00 40.41 4.20
2160 2263 3.795561 AAAGAATGTCGTGCGAAGAAG 57.204 42.857 0.00 0.00 0.00 2.85
2166 2269 6.504821 GTCAAAATTAAAAGAATGTCGTGCG 58.495 36.000 0.00 0.00 0.00 5.34
2227 2334 3.578282 TCATCTCTTGTTAGCCACAGACA 59.422 43.478 0.00 0.00 36.48 3.41
2723 2846 2.158696 GCTGTCAGAGCCATTAAGGGAT 60.159 50.000 11.08 2.46 42.54 3.85
3257 3386 2.350522 CCTCGCTGCACATAAGAAAGT 58.649 47.619 0.00 0.00 0.00 2.66
3662 3801 4.929479 AGTTGCCATGTAGGTGGAATAAA 58.071 39.130 0.00 0.00 42.02 1.40


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

AutoCloner maintained by Alex Coulton.