Multiple sequence alignment - TraesCS4D01G199000

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 TraesCS4D01G199000 chr4D 100.000 2234 0 0 1 2234 345428736 345430969 0.000000e+00 4126
1 TraesCS4D01G199000 chr4A 94.016 2256 77 21 1 2234 120143307 120141088 0.000000e+00 3365
2 TraesCS4D01G199000 chr4B 94.552 1854 52 10 78 1909 427068580 427070406 0.000000e+00 2819
3 TraesCS4D01G199000 chr4B 96.073 331 10 1 1904 2234 427070491 427070818 9.080000e-149 536
4 TraesCS4D01G199000 chr7B 91.811 635 43 7 655 1281 486675355 486675988 0.000000e+00 876
5 TraesCS4D01G199000 chr5B 91.866 627 45 5 655 1275 237113741 237114367 0.000000e+00 870
6 TraesCS4D01G199000 chr2B 91.892 629 42 8 655 1275 51990482 51991109 0.000000e+00 870
7 TraesCS4D01G199000 chr1A 91.733 629 41 9 655 1275 453783256 453782631 0.000000e+00 863
8 TraesCS4D01G199000 chr5A 91.415 629 45 8 655 1275 603009450 603010077 0.000000e+00 854
9 TraesCS4D01G199000 chr3B 91.181 635 38 8 658 1275 188240159 188239526 0.000000e+00 846
10 TraesCS4D01G199000 chr1B 88.889 630 41 14 655 1275 216530918 216531527 0.000000e+00 749
11 TraesCS4D01G199000 chr7D 87.302 630 45 12 655 1275 70124957 70124354 0.000000e+00 688


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 TraesCS4D01G199000 chr4D 345428736 345430969 2233 False 4126.0 4126 100.0000 1 2234 1 chr4D.!!$F1 2233
1 TraesCS4D01G199000 chr4A 120141088 120143307 2219 True 3365.0 3365 94.0160 1 2234 1 chr4A.!!$R1 2233
2 TraesCS4D01G199000 chr4B 427068580 427070818 2238 False 1677.5 2819 95.3125 78 2234 2 chr4B.!!$F1 2156
3 TraesCS4D01G199000 chr7B 486675355 486675988 633 False 876.0 876 91.8110 655 1281 1 chr7B.!!$F1 626
4 TraesCS4D01G199000 chr5B 237113741 237114367 626 False 870.0 870 91.8660 655 1275 1 chr5B.!!$F1 620
5 TraesCS4D01G199000 chr2B 51990482 51991109 627 False 870.0 870 91.8920 655 1275 1 chr2B.!!$F1 620
6 TraesCS4D01G199000 chr1A 453782631 453783256 625 True 863.0 863 91.7330 655 1275 1 chr1A.!!$R1 620
7 TraesCS4D01G199000 chr5A 603009450 603010077 627 False 854.0 854 91.4150 655 1275 1 chr5A.!!$F1 620
8 TraesCS4D01G199000 chr3B 188239526 188240159 633 True 846.0 846 91.1810 658 1275 1 chr3B.!!$R1 617
9 TraesCS4D01G199000 chr1B 216530918 216531527 609 False 749.0 749 88.8890 655 1275 1 chr1B.!!$F1 620
10 TraesCS4D01G199000 chr7D 70124354 70124957 603 True 688.0 688 87.3020 655 1275 1 chr7D.!!$R1 620

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
533 540 4.175962 TCTTGGGTTCCCTCAGATTACTT 58.824 43.478 9.43 0.0 0.0 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1822 1875 1.680314 CTGCCCTTTCCCTGGAAGC 60.68 63.158 0.0 0.61 35.38 3.86 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
50 52 6.884280 AAACCAATTGTAGAAACTCTGGAG 57.116 37.500 4.43 0.00 0.00 3.86
55 57 7.725844 ACCAATTGTAGAAACTCTGGAGATTTT 59.274 33.333 4.43 0.00 30.96 1.82
86 88 7.645058 TGTCTTGAGGAATGATAATTTTCCC 57.355 36.000 3.47 0.00 41.99 3.97
88 90 5.299279 TCTTGAGGAATGATAATTTTCCCGC 59.701 40.000 3.47 0.00 41.99 6.13
185 187 4.916183 AGAAGTCCAATTTTCAGAGGGAG 58.084 43.478 0.00 0.00 0.00 4.30
347 350 5.912892 TGTAGACACACTCTGTTTTGATGA 58.087 37.500 0.00 0.00 31.03 2.92
533 540 4.175962 TCTTGGGTTCCCTCAGATTACTT 58.824 43.478 9.43 0.00 0.00 2.24
602 616 8.714906 ACAAGCTACCCATCACTAAATAATACT 58.285 33.333 0.00 0.00 0.00 2.12
603 617 9.209175 CAAGCTACCCATCACTAAATAATACTC 57.791 37.037 0.00 0.00 0.00 2.59
604 618 7.908453 AGCTACCCATCACTAAATAATACTCC 58.092 38.462 0.00 0.00 0.00 3.85
605 619 7.735321 AGCTACCCATCACTAAATAATACTCCT 59.265 37.037 0.00 0.00 0.00 3.69
606 620 9.032624 GCTACCCATCACTAAATAATACTCCTA 57.967 37.037 0.00 0.00 0.00 2.94
672 686 8.108551 TGAAGTTACTAGGAAGTGAGAACTAC 57.891 38.462 0.00 0.00 33.07 2.73
714 733 4.700692 GCATAATCATGGATGCTGATCAGT 59.299 41.667 23.38 4.98 44.15 3.41
718 737 9.043079 CATAATCATGGATGCTGATCAGTATAC 57.957 37.037 24.81 24.81 35.27 1.47
742 764 6.901300 ACTATTCTAGGTGACCCAGTATTTCA 59.099 38.462 0.00 0.00 0.00 2.69
1155 1189 3.644884 TTCGGTGAGAACTCTGAGAAC 57.355 47.619 12.44 4.83 33.14 3.01
1496 1545 2.360475 GTGGCTTGGGAGTCTGCC 60.360 66.667 2.82 2.82 45.10 4.85
1534 1583 2.098934 ACATGCTCTGAGATCGACTGAC 59.901 50.000 9.28 0.00 0.00 3.51
1549 1598 5.228665 TCGACTGACTACTAGGATCATACG 58.771 45.833 0.00 4.28 0.00 3.06
1655 1704 5.431179 GAACTGGAGTTCCATAAGGGTAA 57.569 43.478 8.14 0.00 46.42 2.85
1656 1705 6.002653 GAACTGGAGTTCCATAAGGGTAAT 57.997 41.667 8.14 0.00 46.42 1.89
1657 1706 7.133133 GAACTGGAGTTCCATAAGGGTAATA 57.867 40.000 8.14 0.00 46.42 0.98
1658 1707 6.749036 ACTGGAGTTCCATAAGGGTAATAG 57.251 41.667 0.48 0.00 46.46 1.73
1659 1708 5.071923 ACTGGAGTTCCATAAGGGTAATAGC 59.928 44.000 0.48 0.00 46.46 2.97
1660 1709 5.224441 TGGAGTTCCATAAGGGTAATAGCT 58.776 41.667 0.00 0.00 42.01 3.32
1661 1710 5.670361 TGGAGTTCCATAAGGGTAATAGCTT 59.330 40.000 0.00 0.00 42.01 3.74
1662 1711 6.159751 TGGAGTTCCATAAGGGTAATAGCTTT 59.840 38.462 0.00 0.00 42.01 3.51
1663 1712 7.348801 TGGAGTTCCATAAGGGTAATAGCTTTA 59.651 37.037 0.00 0.00 42.01 1.85
1664 1713 7.660617 GGAGTTCCATAAGGGTAATAGCTTTAC 59.339 40.741 0.00 0.68 38.11 2.01
1665 1714 8.097791 AGTTCCATAAGGGTAATAGCTTTACA 57.902 34.615 15.81 2.20 38.11 2.41
1666 1715 8.554011 AGTTCCATAAGGGTAATAGCTTTACAA 58.446 33.333 15.81 4.35 38.11 2.41
1667 1716 9.350951 GTTCCATAAGGGTAATAGCTTTACAAT 57.649 33.333 15.81 7.63 38.11 2.71
1723 1772 8.078596 ACTCTTCAATTTTGTCAATCTAGTTGC 58.921 33.333 0.00 0.00 37.74 4.17
2082 2225 5.792741 TCTTCCTTTGGTGCCAAATTAATG 58.207 37.500 15.75 5.16 43.78 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
61 63 7.148086 CGGGAAAATTATCATTCCTCAAGACAA 60.148 37.037 6.60 0.00 43.75 3.18
69 71 3.551846 ACGCGGGAAAATTATCATTCCT 58.448 40.909 12.47 0.00 43.75 3.36
76 78 7.281549 AGTCTACAATTAACGCGGGAAAATTAT 59.718 33.333 12.47 2.53 0.00 1.28
86 88 4.143803 CGATGCTAGTCTACAATTAACGCG 60.144 45.833 3.53 3.53 0.00 6.01
88 90 4.148348 GGCGATGCTAGTCTACAATTAACG 59.852 45.833 0.00 0.00 0.00 3.18
185 187 4.012374 TCAGACAAAGGCATTTCCATCTC 58.988 43.478 0.00 0.00 37.29 2.75
347 350 1.812571 CTTTGCCGCTTACATTGGAGT 59.187 47.619 0.00 0.00 0.00 3.85
533 540 0.325602 TGGACATGTGCAGAGCATCA 59.674 50.000 16.89 0.00 41.91 3.07
602 616 8.162085 ACGGATCATCTAATAGTAGTTGTAGGA 58.838 37.037 7.85 0.00 31.51 2.94
603 617 8.338072 ACGGATCATCTAATAGTAGTTGTAGG 57.662 38.462 7.85 1.27 31.51 3.18
604 618 9.613957 CAACGGATCATCTAATAGTAGTTGTAG 57.386 37.037 7.85 2.63 33.00 2.74
605 619 8.573885 CCAACGGATCATCTAATAGTAGTTGTA 58.426 37.037 7.85 0.00 35.03 2.41
606 620 7.069578 ACCAACGGATCATCTAATAGTAGTTGT 59.930 37.037 7.85 0.00 35.03 3.32
607 621 7.434492 ACCAACGGATCATCTAATAGTAGTTG 58.566 38.462 2.52 2.52 36.13 3.16
613 627 5.692204 GTGTGACCAACGGATCATCTAATAG 59.308 44.000 0.00 0.00 0.00 1.73
672 686 4.424061 TGCTCCTGATGTGAATTTTTCG 57.576 40.909 0.00 0.00 0.00 3.46
718 737 7.361457 TGAAATACTGGGTCACCTAGAATAG 57.639 40.000 15.44 0.00 38.80 1.73
880 914 8.997621 TGGAAGTCTGTATTGTACATTTAGTC 57.002 34.615 0.00 0.00 38.15 2.59
1285 1321 5.697633 GTGAAAACATCCACATTTGATTGCT 59.302 36.000 0.00 0.00 33.72 3.91
1534 1583 7.481642 ACTTTGTTGACGTATGATCCTAGTAG 58.518 38.462 0.00 0.00 0.00 2.57
1723 1772 4.404507 AAAATCGACGAAACATCCAGTG 57.595 40.909 0.00 0.00 0.00 3.66
1822 1875 1.680314 CTGCCCTTTCCCTGGAAGC 60.680 63.158 0.00 0.61 35.38 3.86
1978 2121 8.861086 CAGTAACCTATGACATCCTACTGTTAT 58.139 37.037 13.14 0.00 33.33 1.89
2082 2225 1.755179 ATGTGCACCTTGTGATAGGC 58.245 50.000 15.69 0.00 38.99 3.93
2132 2275 9.498176 GAGTTAGATTAAAAAGGTCCTGTTACA 57.502 33.333 0.00 0.00 0.00 2.41


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

AutoCloner maintained by Alex Coulton.