Multiple sequence alignment - TraesCS4A01G201100

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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 TraesCS4A01G201100 chr4A 100.000 2964 0 0 1 2964 490340785 490343748 0.000000e+00 5474.0
1 TraesCS4A01G201100 chr4A 95.884 2964 70 13 42 2964 429488002 429490954 0.000000e+00 4750.0
2 TraesCS4A01G201100 chr4A 95.527 2012 79 7 963 2964 523832642 523834652 0.000000e+00 3206.0
3 TraesCS4A01G201100 chr4A 97.561 41 1 0 1 41 429487932 429487972 1.470000e-08 71.3
4 TraesCS4A01G201100 chr6A 96.318 2933 94 7 42 2964 401364309 401367237 0.000000e+00 4806.0
5 TraesCS4A01G201100 chr6A 97.561 41 1 0 1 41 136655384 136655424 1.470000e-08 71.3
6 TraesCS4A01G201100 chr6A 97.561 41 1 0 1 41 529359905 529359945 1.470000e-08 71.3
7 TraesCS4A01G201100 chr6A 95.122 41 2 0 1 41 401364239 401364279 6.860000e-07 65.8
8 TraesCS4A01G201100 chr5A 96.201 2869 84 5 42 2907 133817615 133820461 0.000000e+00 4671.0
9 TraesCS4A01G201100 chr5A 95.423 2316 60 6 1 2315 345673015 345670745 0.000000e+00 3648.0
10 TraesCS4A01G201100 chr5A 94.770 2046 75 16 929 2964 501869175 501871198 0.000000e+00 3157.0
11 TraesCS4A01G201100 chr5A 93.587 1653 81 15 121 1766 168400319 168398685 0.000000e+00 2442.0
12 TraesCS4A01G201100 chr5A 98.000 50 1 0 1 50 168400371 168400322 1.460000e-13 87.9
13 TraesCS4A01G201100 chr5A 97.561 41 1 0 1 41 133817545 133817585 1.470000e-08 71.3
14 TraesCS4A01G201100 chr3A 95.600 2932 90 21 42 2964 513294830 513297731 0.000000e+00 4663.0
15 TraesCS4A01G201100 chr3A 93.893 1703 79 11 42 1739 733887536 733885854 0.000000e+00 2545.0
16 TraesCS4A01G201100 chr1A 96.751 2647 78 4 326 2964 575419163 575421809 0.000000e+00 4405.0
17 TraesCS4A01G201100 chr1A 95.553 2406 79 10 568 2964 580783461 580785847 0.000000e+00 3825.0
18 TraesCS4A01G201100 chr1A 93.437 1676 90 14 121 1792 443853300 443854959 0.000000e+00 2468.0
19 TraesCS4A01G201100 chr1A 98.294 586 9 1 123 708 497975155 497975739 0.000000e+00 1026.0
20 TraesCS4A01G201100 chr1A 98.737 475 5 1 42 516 580782981 580783454 0.000000e+00 843.0
21 TraesCS4A01G201100 chr1A 98.000 50 1 0 1 50 443853248 443853297 1.460000e-13 87.9
22 TraesCS4A01G201100 chr1A 98.000 50 1 0 1 50 497975101 497975150 1.460000e-13 87.9
23 TraesCS4A01G201100 chr1A 97.561 41 1 0 1 41 575418889 575418929 1.470000e-08 71.3
24 TraesCS4A01G201100 chr7B 95.940 1995 52 11 978 2964 471054623 471056596 0.000000e+00 3208.0
25 TraesCS4A01G201100 chr2B 95.169 2008 68 8 965 2964 131501159 131499173 0.000000e+00 3144.0
26 TraesCS4A01G201100 chr7A 95.048 1878 77 4 1094 2964 153039565 153037697 0.000000e+00 2939.0
27 TraesCS4A01G201100 chr7A 94.873 1697 59 9 121 1814 644066816 644065145 0.000000e+00 2627.0
28 TraesCS4A01G201100 chr7A 93.867 1663 77 16 110 1766 49623241 49621598 0.000000e+00 2483.0
29 TraesCS4A01G201100 chr7A 86.792 1060 102 16 929 1957 220993534 220994586 0.000000e+00 1147.0
30 TraesCS4A01G201100 chr7A 98.000 50 1 0 1 50 633712665 633712616 1.460000e-13 87.9
31 TraesCS4A01G201100 chr7A 98.000 50 1 0 1 50 644066868 644066819 1.460000e-13 87.9
32 TraesCS4A01G201100 chr4D 87.901 2025 149 55 323 2311 261239527 261237563 0.000000e+00 2294.0
33 TraesCS4A01G201100 chr4D 91.503 153 13 0 171 323 480889845 480889693 8.320000e-51 211.0
34 TraesCS4A01G201100 chr4D 95.192 104 3 2 74 176 480889985 480889883 2.360000e-36 163.0
35 TraesCS4A01G201100 chr4D 96.970 33 1 0 9 41 480890066 480890034 4.130000e-04 56.5
36 TraesCS4A01G201100 chr2A 97.466 947 23 1 301 1247 605761987 605762932 0.000000e+00 1615.0
37 TraesCS4A01G201100 chr2A 98.000 50 1 0 1 50 655909959 655909910 1.460000e-13 87.9
38 TraesCS4A01G201100 chr6D 97.624 505 12 0 320 824 297179389 297178885 0.000000e+00 867.0
39 TraesCS4A01G201100 chr4B 93.548 155 8 2 171 323 608980300 608980146 2.300000e-56 230.0
40 TraesCS4A01G201100 chr4B 91.837 98 7 1 76 173 608980438 608980342 5.150000e-28 135.0


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 TraesCS4A01G201100 chr4A 490340785 490343748 2963 False 5474.00 5474 100.0000 1 2964 1 chr4A.!!$F1 2963
1 TraesCS4A01G201100 chr4A 523832642 523834652 2010 False 3206.00 3206 95.5270 963 2964 1 chr4A.!!$F2 2001
2 TraesCS4A01G201100 chr4A 429487932 429490954 3022 False 2410.65 4750 96.7225 1 2964 2 chr4A.!!$F3 2963
3 TraesCS4A01G201100 chr6A 401364239 401367237 2998 False 2435.90 4806 95.7200 1 2964 2 chr6A.!!$F3 2963
4 TraesCS4A01G201100 chr5A 345670745 345673015 2270 True 3648.00 3648 95.4230 1 2315 1 chr5A.!!$R1 2314
5 TraesCS4A01G201100 chr5A 501869175 501871198 2023 False 3157.00 3157 94.7700 929 2964 1 chr5A.!!$F1 2035
6 TraesCS4A01G201100 chr5A 133817545 133820461 2916 False 2371.15 4671 96.8810 1 2907 2 chr5A.!!$F2 2906
7 TraesCS4A01G201100 chr5A 168398685 168400371 1686 True 1264.95 2442 95.7935 1 1766 2 chr5A.!!$R2 1765
8 TraesCS4A01G201100 chr3A 513294830 513297731 2901 False 4663.00 4663 95.6000 42 2964 1 chr3A.!!$F1 2922
9 TraesCS4A01G201100 chr3A 733885854 733887536 1682 True 2545.00 2545 93.8930 42 1739 1 chr3A.!!$R1 1697
10 TraesCS4A01G201100 chr1A 580782981 580785847 2866 False 2334.00 3825 97.1450 42 2964 2 chr1A.!!$F4 2922
11 TraesCS4A01G201100 chr1A 575418889 575421809 2920 False 2238.15 4405 97.1560 1 2964 2 chr1A.!!$F3 2963
12 TraesCS4A01G201100 chr1A 443853248 443854959 1711 False 1277.95 2468 95.7185 1 1792 2 chr1A.!!$F1 1791
13 TraesCS4A01G201100 chr1A 497975101 497975739 638 False 556.95 1026 98.1470 1 708 2 chr1A.!!$F2 707
14 TraesCS4A01G201100 chr7B 471054623 471056596 1973 False 3208.00 3208 95.9400 978 2964 1 chr7B.!!$F1 1986
15 TraesCS4A01G201100 chr2B 131499173 131501159 1986 True 3144.00 3144 95.1690 965 2964 1 chr2B.!!$R1 1999
16 TraesCS4A01G201100 chr7A 153037697 153039565 1868 True 2939.00 2939 95.0480 1094 2964 1 chr7A.!!$R2 1870
17 TraesCS4A01G201100 chr7A 49621598 49623241 1643 True 2483.00 2483 93.8670 110 1766 1 chr7A.!!$R1 1656
18 TraesCS4A01G201100 chr7A 644065145 644066868 1723 True 1357.45 2627 96.4365 1 1814 2 chr7A.!!$R4 1813
19 TraesCS4A01G201100 chr7A 220993534 220994586 1052 False 1147.00 1147 86.7920 929 1957 1 chr7A.!!$F1 1028
20 TraesCS4A01G201100 chr4D 261237563 261239527 1964 True 2294.00 2294 87.9010 323 2311 1 chr4D.!!$R1 1988
21 TraesCS4A01G201100 chr2A 605761987 605762932 945 False 1615.00 1615 97.4660 301 1247 1 chr2A.!!$F1 946
22 TraesCS4A01G201100 chr6D 297178885 297179389 504 True 867.00 867 97.6240 320 824 1 chr6D.!!$R1 504

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
217 247 4.811498 TGCTAGGTATGCTAGTTTCCCTA 58.189 43.478 0.00 0.0 0.0 3.53 F
1252 1342 1.149174 ACAGGCTGTGGGAAGTGTG 59.851 57.895 21.37 0.0 0.0 3.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1389 1479 1.462731 ATGCGGCACATGGTGTTGTT 61.463 50.0 4.03 0.0 37.70 2.83 R
2668 3175 2.303163 GGTGTTTTCAAAAACCGGCT 57.697 45.0 14.07 0.0 45.82 5.52 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
217 247 4.811498 TGCTAGGTATGCTAGTTTCCCTA 58.189 43.478 0.00 0.00 0.00 3.53
902 975 7.543172 GTGCATTGCTCTTCTCATTTTTATCAA 59.457 33.333 10.49 0.00 0.00 2.57
1252 1342 1.149174 ACAGGCTGTGGGAAGTGTG 59.851 57.895 21.37 0.00 0.00 3.82
1389 1479 3.186702 TGTTCACCGTGAAGATGTTCA 57.813 42.857 14.35 0.23 37.00 3.18
1597 1822 2.515071 GGAGCAGAGCGGGGATGAT 61.515 63.158 0.00 0.00 0.00 2.45
1598 1823 1.301558 GAGCAGAGCGGGGATGATG 60.302 63.158 0.00 0.00 0.00 3.07
1603 1828 1.301558 GAGCGGGGATGATGAGCAG 60.302 63.158 0.00 0.00 0.00 4.24
1625 1886 1.758514 GGGGATGACGAGGAGCAGA 60.759 63.158 0.00 0.00 0.00 4.26
1626 1887 1.739049 GGGATGACGAGGAGCAGAG 59.261 63.158 0.00 0.00 0.00 3.35
1627 1888 1.067250 GGATGACGAGGAGCAGAGC 59.933 63.158 0.00 0.00 0.00 4.09
1628 1889 1.299014 GATGACGAGGAGCAGAGCG 60.299 63.158 0.00 0.00 0.00 5.03
1629 1890 2.676016 GATGACGAGGAGCAGAGCGG 62.676 65.000 0.00 0.00 0.00 5.52
1630 1891 4.200283 GACGAGGAGCAGAGCGGG 62.200 72.222 0.00 0.00 0.00 6.13
1633 1894 2.841988 GAGGAGCAGAGCGGGGAT 60.842 66.667 0.00 0.00 0.00 3.85
1634 1895 3.160047 AGGAGCAGAGCGGGGATG 61.160 66.667 0.00 0.00 0.00 3.51
1635 1896 3.157252 GGAGCAGAGCGGGGATGA 61.157 66.667 0.00 0.00 0.00 2.92
1636 1897 2.515071 GGAGCAGAGCGGGGATGAT 61.515 63.158 0.00 0.00 0.00 2.45
1637 1898 1.301558 GAGCAGAGCGGGGATGATG 60.302 63.158 0.00 0.00 0.00 3.07
1638 1899 1.752358 GAGCAGAGCGGGGATGATGA 61.752 60.000 0.00 0.00 0.00 2.92
1639 1900 1.301558 GCAGAGCGGGGATGATGAG 60.302 63.158 0.00 0.00 0.00 2.90
1640 1901 1.370437 CAGAGCGGGGATGATGAGG 59.630 63.158 0.00 0.00 0.00 3.86
1641 1902 1.117749 CAGAGCGGGGATGATGAGGA 61.118 60.000 0.00 0.00 0.00 3.71
1642 1903 0.831288 AGAGCGGGGATGATGAGGAG 60.831 60.000 0.00 0.00 0.00 3.69
1643 1904 2.031768 GCGGGGATGATGAGGAGC 59.968 66.667 0.00 0.00 0.00 4.70
1644 1905 2.811514 GCGGGGATGATGAGGAGCA 61.812 63.158 0.00 0.00 0.00 4.26
1645 1906 2.064628 CGGGGATGATGAGGAGCAT 58.935 57.895 0.00 0.00 40.77 3.79
1715 2003 1.051556 TGCTATGGTGGTGGCGGATA 61.052 55.000 0.00 0.00 0.00 2.59
1814 2288 1.421410 CGACGACCTTGCTATGGTGC 61.421 60.000 0.00 0.00 38.03 5.01
1841 2315 3.047718 GACGACCTCGCGATGGTGA 62.048 63.158 27.44 0.00 44.43 4.02
1957 2431 4.787534 AGGTTGATGAAGGAGAAGAAGGAT 59.212 41.667 0.00 0.00 0.00 3.24
2171 2674 6.413783 TTTATGCATGCTCATGGATGAAAT 57.586 33.333 21.83 1.50 46.94 2.17
2288 2793 1.448893 GCCGTGACTAAATCCGCCA 60.449 57.895 0.00 0.00 0.00 5.69
2315 2820 9.042632 GTTTTTGAAAACACCGTAAAAATTCAC 57.957 29.630 13.00 0.00 45.72 3.18
2481 2988 1.153005 CCTCGTAGCTACTCCCGGT 60.153 63.158 21.20 0.00 0.00 5.28
2668 3175 3.176578 GTCGCCGCGACGAAATCA 61.177 61.111 28.44 0.00 46.56 2.57
2787 3297 2.785562 ACTAAACTTGCAATACCGGCA 58.214 42.857 0.00 0.00 40.00 5.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 7.277098 GCACAATACGAGTAACTCCTAAATCAA 59.723 37.037 0.00 0.00 0.00 2.57
217 247 2.365617 ACGTCACTGTGAAGAGAACCAT 59.634 45.455 26.45 3.24 30.40 3.55
433 464 5.946377 GCTTTGCTAGGGTTTATATAGCCAT 59.054 40.000 13.02 3.70 40.97 4.40
902 975 6.875195 CAGAACCAAGTTTATGATGGCAAAAT 59.125 34.615 0.00 0.00 37.77 1.82
1252 1342 1.613437 CTTCACCATCAAACACCACCC 59.387 52.381 0.00 0.00 0.00 4.61
1365 1455 2.038426 ACATCTTCACGGTGAACATGGA 59.962 45.455 29.86 21.55 37.17 3.41
1389 1479 1.462731 ATGCGGCACATGGTGTTGTT 61.463 50.000 4.03 0.00 37.70 2.83
1597 1822 2.364186 TCATCCCCGCTCTGCTCA 60.364 61.111 0.00 0.00 0.00 4.26
1598 1823 2.107953 GTCATCCCCGCTCTGCTC 59.892 66.667 0.00 0.00 0.00 4.26
1603 1828 2.833582 TCCTCGTCATCCCCGCTC 60.834 66.667 0.00 0.00 0.00 5.03
1625 1886 2.515071 GCTCCTCATCATCCCCGCT 61.515 63.158 0.00 0.00 0.00 5.52
1626 1887 2.031768 GCTCCTCATCATCCCCGC 59.968 66.667 0.00 0.00 0.00 6.13
1627 1888 2.064628 ATGCTCCTCATCATCCCCG 58.935 57.895 0.00 0.00 0.00 5.73
1630 1891 4.470664 AGAATAGGATGCTCCTCATCATCC 59.529 45.833 12.06 12.06 45.66 3.51
1631 1892 5.421277 CAGAATAGGATGCTCCTCATCATC 58.579 45.833 7.85 0.00 45.66 2.92
1632 1893 4.225492 CCAGAATAGGATGCTCCTCATCAT 59.775 45.833 7.85 2.75 45.66 2.45
1633 1894 3.581770 CCAGAATAGGATGCTCCTCATCA 59.418 47.826 7.85 0.00 45.66 3.07
1634 1895 3.619487 GCCAGAATAGGATGCTCCTCATC 60.619 52.174 7.85 8.01 45.66 2.92
1635 1896 2.305343 GCCAGAATAGGATGCTCCTCAT 59.695 50.000 7.85 0.06 45.66 2.90
1636 1897 1.696336 GCCAGAATAGGATGCTCCTCA 59.304 52.381 7.85 0.00 45.66 3.86
1637 1898 1.977129 AGCCAGAATAGGATGCTCCTC 59.023 52.381 7.85 0.00 45.66 3.71
1639 1900 1.696336 TCAGCCAGAATAGGATGCTCC 59.304 52.381 0.00 0.00 44.55 4.70
1640 1901 3.007723 TCATCAGCCAGAATAGGATGCTC 59.992 47.826 0.00 0.00 44.55 4.26
1641 1902 2.977580 TCATCAGCCAGAATAGGATGCT 59.022 45.455 0.00 0.00 44.55 3.79
1642 1903 3.072944 GTCATCAGCCAGAATAGGATGC 58.927 50.000 0.00 0.00 44.55 3.91
1643 1904 3.006217 TCGTCATCAGCCAGAATAGGATG 59.994 47.826 0.00 0.00 46.23 3.51
1644 1905 3.234353 TCGTCATCAGCCAGAATAGGAT 58.766 45.455 0.00 0.00 0.00 3.24
1645 1906 2.666317 TCGTCATCAGCCAGAATAGGA 58.334 47.619 0.00 0.00 0.00 2.94
1715 2003 2.235402 CCACCACCATAGTAAGGTCGTT 59.765 50.000 0.00 0.00 37.23 3.85
1724 2012 2.987125 GTCCGCCACCACCATAGT 59.013 61.111 0.00 0.00 0.00 2.12
1779 2202 4.386951 CGTCCGCCACCACCATCA 62.387 66.667 0.00 0.00 0.00 3.07
1814 2288 4.477975 GAGGTCGTCGTCCGCCAG 62.478 72.222 2.81 0.00 35.87 4.85
1957 2431 6.174720 ACACCTTCTTAACATCTTCACTCA 57.825 37.500 0.00 0.00 0.00 3.41
2171 2674 8.887717 GCATGCACAAAAACCCATAATTTTATA 58.112 29.630 14.21 0.00 0.00 0.98
2288 2793 8.989980 TGAATTTTTACGGTGTTTTCAAAAACT 58.010 25.926 16.77 2.55 46.37 2.66
2668 3175 2.303163 GGTGTTTTCAAAAACCGGCT 57.697 45.000 14.07 0.00 45.82 5.52


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

AutoCloner maintained by Alex Coulton.