Multiple sequence alignment - TraesCS3D01G483100

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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 TraesCS3D01G483100 chr3D 100.000 2570 0 0 1 2570 580652165 580649596 0 4747
1 TraesCS3D01G483100 chr3D 95.458 2598 70 5 1 2570 374010842 374008265 0 4100
2 TraesCS3D01G483100 chr3D 96.306 1895 51 3 676 2570 155676585 155678460 0 3094
3 TraesCS3D01G483100 chr2D 95.379 2597 74 4 1 2570 535662354 535664931 0 4089
4 TraesCS3D01G483100 chr2D 96.322 1903 55 4 676 2570 77210318 77212213 0 3112
5 TraesCS3D01G483100 chr2D 96.359 1895 49 3 676 2570 207005497 207003623 0 3099
6 TraesCS3D01G483100 chr1D 95.189 2598 80 11 1 2570 422850759 422848179 0 4063
7 TraesCS3D01G483100 chr6D 95.185 2596 79 4 1 2569 445278065 445275489 0 4060
8 TraesCS3D01G483100 chr6D 96.024 2188 66 5 386 2570 445209561 445207392 0 3539
9 TraesCS3D01G483100 chr6D 95.712 1889 42 4 682 2570 387623954 387622105 0 3003
10 TraesCS3D01G483100 chr5D 94.686 2597 89 6 2 2570 504761451 504764026 0 3986
11 TraesCS3D01G483100 chr2A 93.869 1941 98 11 1 1925 721575191 721577126 0 2905
12 TraesCS3D01G483100 chr6A 93.244 1939 109 12 3 1925 615748495 615750427 0 2835
13 TraesCS3D01G483100 chr3A 92.787 1941 120 12 1 1925 721545966 721547902 0 2791


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 TraesCS3D01G483100 chr3D 580649596 580652165 2569 True 4747 4747 100.000 1 2570 1 chr3D.!!$R2 2569
1 TraesCS3D01G483100 chr3D 374008265 374010842 2577 True 4100 4100 95.458 1 2570 1 chr3D.!!$R1 2569
2 TraesCS3D01G483100 chr3D 155676585 155678460 1875 False 3094 3094 96.306 676 2570 1 chr3D.!!$F1 1894
3 TraesCS3D01G483100 chr2D 535662354 535664931 2577 False 4089 4089 95.379 1 2570 1 chr2D.!!$F2 2569
4 TraesCS3D01G483100 chr2D 77210318 77212213 1895 False 3112 3112 96.322 676 2570 1 chr2D.!!$F1 1894
5 TraesCS3D01G483100 chr2D 207003623 207005497 1874 True 3099 3099 96.359 676 2570 1 chr2D.!!$R1 1894
6 TraesCS3D01G483100 chr1D 422848179 422850759 2580 True 4063 4063 95.189 1 2570 1 chr1D.!!$R1 2569
7 TraesCS3D01G483100 chr6D 445275489 445278065 2576 True 4060 4060 95.185 1 2569 1 chr6D.!!$R3 2568
8 TraesCS3D01G483100 chr6D 445207392 445209561 2169 True 3539 3539 96.024 386 2570 1 chr6D.!!$R2 2184
9 TraesCS3D01G483100 chr6D 387622105 387623954 1849 True 3003 3003 95.712 682 2570 1 chr6D.!!$R1 1888
10 TraesCS3D01G483100 chr5D 504761451 504764026 2575 False 3986 3986 94.686 2 2570 1 chr5D.!!$F1 2568
11 TraesCS3D01G483100 chr2A 721575191 721577126 1935 False 2905 2905 93.869 1 1925 1 chr2A.!!$F1 1924
12 TraesCS3D01G483100 chr6A 615748495 615750427 1932 False 2835 2835 93.244 3 1925 1 chr6A.!!$F1 1922
13 TraesCS3D01G483100 chr3A 721545966 721547902 1936 False 2791 2791 92.787 1 1925 1 chr3A.!!$F1 1924

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
396 397 0.029567 CAGTACATCTCCTCCGACGC 59.97 60.0 0.0 0.0 0.0 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2133 2226 1.207085 GAGCTCGTCGTCGTGAAGT 59.793 57.895 8.24 0.0 38.33 3.01 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
39 40 5.046376 CCTGGTCCCTAATCTTTTGCAAAAT 60.046 40.000 24.06 12.77 0.00 1.82
52 53 1.889170 TGCAAAATCCACCGCACATTA 59.111 42.857 0.00 0.00 0.00 1.90
142 143 1.522668 CCAAAATCTCTGACGTGGCA 58.477 50.000 0.00 0.00 0.00 4.92
240 241 0.524392 ACATCTCGCTCGCTCTTTCG 60.524 55.000 0.00 0.00 0.00 3.46
276 277 2.917227 TCTGCTCCCACACTCGCA 60.917 61.111 0.00 0.00 0.00 5.10
396 397 0.029567 CAGTACATCTCCTCCGACGC 59.970 60.000 0.00 0.00 0.00 5.19
609 610 3.364549 TGTTGCATTTGAGGGGATAAGG 58.635 45.455 0.00 0.00 0.00 2.69
624 625 4.038633 GGATAAGGACTGGTAGGAGGTTT 58.961 47.826 0.00 0.00 0.00 3.27
678 706 3.069872 TGTGTTTGCAGCATTCCAATTCT 59.930 39.130 0.00 0.00 0.00 2.40
691 719 6.295292 GCATTCCAATTCTTGTTCTAGGGTTT 60.295 38.462 0.00 0.00 0.00 3.27
692 720 6.648879 TTCCAATTCTTGTTCTAGGGTTTG 57.351 37.500 0.00 0.00 0.00 2.93
738 766 5.294552 GGTTCATAGTTACTGCTCATGTTCC 59.705 44.000 0.00 0.00 0.00 3.62
1023 1053 2.881111 ATGAGCATAGCCAGCATGAT 57.119 45.000 0.00 0.00 39.69 2.45
1069 1099 3.317150 TCAAGCACTGTACACAATCTCG 58.683 45.455 0.00 0.00 0.00 4.04
1078 1108 0.033920 ACACAATCTCGCACAGCAGA 59.966 50.000 0.00 0.00 0.00 4.26
1511 1545 2.551459 GCATTGTTGAGCTCAAGACAGT 59.449 45.455 29.13 18.61 36.39 3.55
1555 1589 5.372373 AGCTTCACCAGATTAAGGCTATTC 58.628 41.667 0.00 0.00 0.00 1.75
1556 1590 5.104360 AGCTTCACCAGATTAAGGCTATTCA 60.104 40.000 0.00 0.00 0.00 2.57
1706 1740 7.118496 TGAACCTTGGATTGTATGTTGTTTT 57.882 32.000 0.00 0.00 0.00 2.43
1738 1772 9.371136 GTACTCTGTTTGTGATGAATTATCAGA 57.629 33.333 0.00 0.00 46.09 3.27
1742 1776 8.680001 TCTGTTTGTGATGAATTATCAGATTGG 58.320 33.333 0.00 0.00 46.09 3.16
1837 1872 8.303156 GTTCATACTGCATAGATAGTCTGACAT 58.697 37.037 10.88 1.68 32.13 3.06
1838 1873 9.520515 TTCATACTGCATAGATAGTCTGACATA 57.479 33.333 10.88 0.37 32.13 2.29
1839 1874 9.520515 TCATACTGCATAGATAGTCTGACATAA 57.479 33.333 10.88 0.00 28.80 1.90
1921 2013 6.582677 ACCTGCATAGATAGTCTGACATAC 57.417 41.667 10.88 0.66 0.00 2.39
1932 2024 9.360901 AGATAGTCTGACATACATACAACTGAT 57.639 33.333 10.88 0.00 0.00 2.90
2133 2226 2.423898 CGCCGCCCTCCTCTTCTTA 61.424 63.158 0.00 0.00 0.00 2.10
2143 2236 3.426426 CCTCCTCTTCTTACTTCACGACG 60.426 52.174 0.00 0.00 0.00 5.12
2322 2415 0.400594 TCAGAGGAGTGGTCGTCAGA 59.599 55.000 0.00 0.00 39.62 3.27
2563 2657 1.507140 TCGCCCATAGGAGAATGGTT 58.493 50.000 2.43 0.00 44.29 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 6.509386 AGATTAGGGACCAGGTAGTTTTCTA 58.491 40.000 0.00 0.00 0.00 2.10
39 40 5.347620 ACTATTACTTAATGTGCGGTGGA 57.652 39.130 0.00 0.00 0.00 4.02
142 143 2.657296 CGTCCGCGCATCCGTTAT 60.657 61.111 8.75 0.00 36.67 1.89
240 241 3.749735 GAGAGCGAGCGTGAGAGCC 62.750 68.421 0.00 0.00 38.01 4.70
276 277 2.677228 CAAATGGGAGGGGAGCGT 59.323 61.111 0.00 0.00 0.00 5.07
330 331 3.680786 CGCTCCAGGACACCGTGA 61.681 66.667 5.28 0.00 0.00 4.35
333 334 3.633094 CTGTCGCTCCAGGACACCG 62.633 68.421 0.00 0.00 39.36 4.94
609 610 3.200165 AGGCAATAAACCTCCTACCAGTC 59.800 47.826 0.00 0.00 28.76 3.51
624 625 1.073763 ACTTCAGTGGCACAGGCAATA 59.926 47.619 21.41 0.00 41.80 1.90
678 706 7.128234 ACAGTAACTACAAACCCTAGAACAA 57.872 36.000 0.00 0.00 0.00 2.83
691 719 6.495872 ACCCTAGAACATGAACAGTAACTACA 59.504 38.462 0.00 0.00 0.00 2.74
692 720 6.932947 ACCCTAGAACATGAACAGTAACTAC 58.067 40.000 0.00 0.00 0.00 2.73
738 766 9.449719 AACTAAATTCAGTAACTATGAACCCTG 57.550 33.333 0.00 0.00 39.36 4.45
901 930 6.215495 TCCAACACCCTACAAAAGAAAAAG 57.785 37.500 0.00 0.00 0.00 2.27
902 931 6.607004 TTCCAACACCCTACAAAAGAAAAA 57.393 33.333 0.00 0.00 0.00 1.94
903 932 6.607004 TTTCCAACACCCTACAAAAGAAAA 57.393 33.333 0.00 0.00 0.00 2.29
1023 1053 1.284491 TCCAGGCATGCCATCTTGTTA 59.716 47.619 37.18 14.43 38.92 2.41
1511 1545 4.383118 GCTTCCTCTTGTTGCTATCACCTA 60.383 45.833 0.00 0.00 0.00 3.08
1555 1589 5.702670 ACAACACAACTTAGTCCTCATCATG 59.297 40.000 0.00 0.00 0.00 3.07
1556 1590 5.869579 ACAACACAACTTAGTCCTCATCAT 58.130 37.500 0.00 0.00 0.00 2.45
1706 1740 6.405278 TCATCACAAACAGAGTACTCTCAA 57.595 37.500 22.76 3.96 42.66 3.02
1738 1772 8.408043 TCATCACAAACTGAACTTAATCCAAT 57.592 30.769 0.00 0.00 30.60 3.16
1768 1802 6.731292 TCTACTTGCTATAATCCAAGCTGA 57.269 37.500 0.00 0.00 41.56 4.26
1840 1875 9.634021 TGTCAGTTCTATCTATGTCAGTTCTAT 57.366 33.333 0.00 0.00 0.00 1.98
1841 1876 9.634021 ATGTCAGTTCTATCTATGTCAGTTCTA 57.366 33.333 0.00 0.00 0.00 2.10
1842 1877 7.946381 TGTCAGTTCTATCTATGTCAGTTCT 57.054 36.000 0.00 0.00 0.00 3.01
1843 1878 9.891828 CTATGTCAGTTCTATCTATGTCAGTTC 57.108 37.037 0.00 0.00 0.00 3.01
1844 1879 9.634021 TCTATGTCAGTTCTATCTATGTCAGTT 57.366 33.333 0.00 0.00 0.00 3.16
1845 1880 9.806448 ATCTATGTCAGTTCTATCTATGTCAGT 57.194 33.333 0.00 0.00 0.00 3.41
1892 1984 7.945109 TGTCAGACTATCTATGCAGGTACTATT 59.055 37.037 1.31 0.00 36.02 1.73
1899 1991 6.581171 TGTATGTCAGACTATCTATGCAGG 57.419 41.667 1.31 0.00 0.00 4.85
1943 2035 5.585820 TCGTCAGTATGTTAGTATGCCAA 57.414 39.130 0.00 0.00 37.40 4.52
1949 2041 7.879070 AGTTCAGTTTCGTCAGTATGTTAGTA 58.121 34.615 0.00 0.00 37.40 1.82
2133 2226 1.207085 GAGCTCGTCGTCGTGAAGT 59.793 57.895 8.24 0.00 38.33 3.01
2143 2236 1.444553 CGACAACCCAGAGCTCGTC 60.445 63.158 8.37 7.55 0.00 4.20
2313 2406 1.469308 ACTCTGACGAATCTGACGACC 59.531 52.381 0.00 0.00 34.70 4.79
2322 2415 5.009710 TCTGACAACTACAACTCTGACGAAT 59.990 40.000 0.00 0.00 0.00 3.34
2518 2612 4.521062 GTGCAGCGCTCTCCCGAT 62.521 66.667 7.13 0.00 0.00 4.18


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

AutoCloner maintained by Alex Coulton.