Multiple sequence alignment - TraesCS4A01G425900

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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 TraesCS4A01G425900 chr4A 100.000 2902 0 0 1 2902 697749799 697746898 0.000000e+00 5360
1 TraesCS4A01G425900 chr4A 97.185 1883 40 5 1 1872 697734718 697732838 0.000000e+00 3171
2 TraesCS4A01G425900 chr4A 97.182 1029 28 1 1875 2902 697732785 697731757 0.000000e+00 1738
3 TraesCS4A01G425900 chr5B 95.069 1886 75 11 1 1873 239173265 239175145 0.000000e+00 2952
4 TraesCS4A01G425900 chr5B 94.592 1886 89 7 1 1873 42677608 42679493 0.000000e+00 2905
5 TraesCS4A01G425900 chr5B 94.023 1857 76 12 34 1876 538735695 538733860 0.000000e+00 2782
6 TraesCS4A01G425900 chr5B 93.171 1889 104 18 1 1873 419833036 419834915 0.000000e+00 2750
7 TraesCS4A01G425900 chr5B 89.933 1927 132 35 1 1876 511467983 511466068 0.000000e+00 2427
8 TraesCS4A01G425900 chr5B 95.574 723 31 1 2178 2900 42681631 42682352 0.000000e+00 1157
9 TraesCS4A01G425900 chr5B 95.149 268 12 1 1875 2141 42679546 42679813 3.460000e-114 422
10 TraesCS4A01G425900 chr5B 94.403 268 14 1 1875 2141 511466018 511465751 7.480000e-111 411
11 TraesCS4A01G425900 chr5B 94.403 268 14 1 1875 2141 538733810 538733543 7.480000e-111 411
12 TraesCS4A01G425900 chr5B 81.373 306 37 8 1877 2181 377898943 377899229 6.250000e-57 231
13 TraesCS4A01G425900 chr7B 94.544 1888 85 8 1 1876 143198360 143196479 0.000000e+00 2900
14 TraesCS4A01G425900 chr7B 96.680 723 24 0 2178 2900 679983481 679984203 0.000000e+00 1203
15 TraesCS4A01G425900 chr7B 95.694 720 31 0 2181 2900 143192273 143191554 0.000000e+00 1158
16 TraesCS4A01G425900 chr7B 94.776 268 13 1 1875 2141 39610588 39610321 1.610000e-112 416
17 TraesCS4A01G425900 chr7B 94.776 268 13 1 1875 2141 679962505 679962772 1.610000e-112 416
18 TraesCS4A01G425900 chr7B 91.558 308 14 3 1875 2181 143196429 143196133 5.790000e-112 414
19 TraesCS4A01G425900 chr3B 95.060 1842 74 7 47 1873 478315345 478317184 0.000000e+00 2881
20 TraesCS4A01G425900 chr3B 93.818 275 14 3 1875 2147 786521640 786521913 7.480000e-111 411
21 TraesCS4A01G425900 chr4B 94.233 1890 92 10 1 1876 609363164 609365050 0.000000e+00 2870
22 TraesCS4A01G425900 chr4B 93.443 1891 102 14 1 1876 474332733 474330850 0.000000e+00 2785
23 TraesCS4A01G425900 chr4B 92.438 1891 113 21 1 1873 581846649 581848527 0.000000e+00 2673
24 TraesCS4A01G425900 chr4B 91.163 860 58 14 9 856 493786265 493787118 0.000000e+00 1151
25 TraesCS4A01G425900 chr2B 93.140 1895 105 15 2 1876 22542991 22541102 0.000000e+00 2756
26 TraesCS4A01G425900 chr2B 95.989 723 29 0 2178 2900 215485535 215484813 0.000000e+00 1175
27 TraesCS4A01G425900 chr2B 94.355 372 20 1 2175 2545 772673297 772673668 1.170000e-158 569
28 TraesCS4A01G425900 chr2B 95.896 268 10 1 1875 2141 215499024 215498757 1.600000e-117 433
29 TraesCS4A01G425900 chr1B 92.589 1889 109 20 9 1873 37703384 37705265 0.000000e+00 2684
30 TraesCS4A01G425900 chr1B 92.577 1428 81 15 37 1443 331124942 331123519 0.000000e+00 2026
31 TraesCS4A01G425900 chr1B 94.228 745 40 2 1 743 40383102 40383845 0.000000e+00 1134
32 TraesCS4A01G425900 chr1D 90.236 1905 144 28 1 1876 79046237 79044346 0.000000e+00 2449
33 TraesCS4A01G425900 chr1D 89.595 1903 154 30 1 1873 74252563 74254451 0.000000e+00 2377
34 TraesCS4A01G425900 chr1D 89.562 1897 160 24 1 1873 398922736 398924618 0.000000e+00 2372
35 TraesCS4A01G425900 chr1D 89.443 1904 158 28 1 1876 467310782 467308894 0.000000e+00 2362
36 TraesCS4A01G425900 chr3D 89.868 1895 148 30 9 1873 274369805 274371685 0.000000e+00 2396
37 TraesCS4A01G425900 chr3D 90.794 1738 132 19 156 1873 82111880 82113609 0.000000e+00 2298
38 TraesCS4A01G425900 chr5D 89.826 1897 149 30 9 1876 239957821 239955940 0.000000e+00 2394
39 TraesCS4A01G425900 chr5D 87.507 1881 181 27 9 1856 440708508 440706649 0.000000e+00 2122
40 TraesCS4A01G425900 chr5D 95.436 723 33 0 2178 2900 13780414 13781136 0.000000e+00 1153
41 TraesCS4A01G425900 chr5D 95.436 723 33 0 2178 2900 559011412 559012134 0.000000e+00 1153
42 TraesCS4A01G425900 chr6D 89.648 1903 152 31 1 1873 340209326 340207439 0.000000e+00 2381
43 TraesCS4A01G425900 chr6D 89.626 1899 155 27 1 1873 51478013 51479895 0.000000e+00 2377
44 TraesCS4A01G425900 chr6D 89.368 1900 162 26 1 1876 365439542 365437659 0.000000e+00 2353
45 TraesCS4A01G425900 chr6D 89.128 1904 165 29 1 1876 237094156 237092267 0.000000e+00 2331
46 TraesCS4A01G425900 chr6D 89.823 1808 147 29 91 1873 139921993 139923788 0.000000e+00 2285
47 TraesCS4A01G425900 chr6D 91.348 1676 126 13 215 1873 293098511 293100184 0.000000e+00 2274
48 TraesCS4A01G425900 chr6D 90.654 1712 113 20 191 1873 23532548 23534241 0.000000e+00 2231
49 TraesCS4A01G425900 chr6D 88.133 1896 159 46 10 1876 338195704 338193846 0.000000e+00 2194
50 TraesCS4A01G425900 chr6D 87.376 1909 179 40 9 1876 460235678 460233791 0.000000e+00 2134
51 TraesCS4A01G425900 chr6D 91.610 1466 102 14 425 1873 256717421 256718882 0.000000e+00 2006
52 TraesCS4A01G425900 chr6D 83.051 1003 109 40 9 965 80749932 80750919 0.000000e+00 854
53 TraesCS4A01G425900 chr6D 81.468 804 96 34 10 782 384279401 384278620 6.880000e-171 610
54 TraesCS4A01G425900 chr4D 89.526 1900 160 25 1 1873 297889401 297891288 0.000000e+00 2370
55 TraesCS4A01G425900 chr4D 89.840 1811 145 29 91 1876 234398926 234397130 0.000000e+00 2289
56 TraesCS4A01G425900 chr4D 88.889 1755 151 29 1 1731 346281269 346283003 0.000000e+00 2121
57 TraesCS4A01G425900 chr4D 95.417 720 33 0 2181 2900 460573595 460572876 0.000000e+00 1147
58 TraesCS4A01G425900 chr7D 89.357 1898 164 25 1 1873 106887156 106889040 0.000000e+00 2351
59 TraesCS4A01G425900 chr7D 91.452 1743 95 28 166 1876 546788754 546787034 0.000000e+00 2344
60 TraesCS4A01G425900 chr2D 89.185 1914 150 36 1 1873 138164860 138166757 0.000000e+00 2335
61 TraesCS4A01G425900 chr2D 95.851 723 30 0 2178 2900 192144333 192145055 0.000000e+00 1170


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 TraesCS4A01G425900 chr4A 697746898 697749799 2901 True 5360.000000 5360 100.0000 1 2902 1 chr4A.!!$R1 2901
1 TraesCS4A01G425900 chr4A 697731757 697734718 2961 True 2454.500000 3171 97.1835 1 2902 2 chr4A.!!$R2 2901
2 TraesCS4A01G425900 chr5B 239173265 239175145 1880 False 2952.000000 2952 95.0690 1 1873 1 chr5B.!!$F1 1872
3 TraesCS4A01G425900 chr5B 419833036 419834915 1879 False 2750.000000 2750 93.1710 1 1873 1 chr5B.!!$F3 1872
4 TraesCS4A01G425900 chr5B 538733543 538735695 2152 True 1596.500000 2782 94.2130 34 2141 2 chr5B.!!$R2 2107
5 TraesCS4A01G425900 chr5B 42677608 42682352 4744 False 1494.666667 2905 95.1050 1 2900 3 chr5B.!!$F4 2899
6 TraesCS4A01G425900 chr5B 511465751 511467983 2232 True 1419.000000 2427 92.1680 1 2141 2 chr5B.!!$R1 2140
7 TraesCS4A01G425900 chr7B 143191554 143198360 6806 True 1490.666667 2900 93.9320 1 2900 3 chr7B.!!$R2 2899
8 TraesCS4A01G425900 chr7B 679983481 679984203 722 False 1203.000000 1203 96.6800 2178 2900 1 chr7B.!!$F2 722
9 TraesCS4A01G425900 chr3B 478315345 478317184 1839 False 2881.000000 2881 95.0600 47 1873 1 chr3B.!!$F1 1826
10 TraesCS4A01G425900 chr4B 609363164 609365050 1886 False 2870.000000 2870 94.2330 1 1876 1 chr4B.!!$F3 1875
11 TraesCS4A01G425900 chr4B 474330850 474332733 1883 True 2785.000000 2785 93.4430 1 1876 1 chr4B.!!$R1 1875
12 TraesCS4A01G425900 chr4B 581846649 581848527 1878 False 2673.000000 2673 92.4380 1 1873 1 chr4B.!!$F2 1872
13 TraesCS4A01G425900 chr4B 493786265 493787118 853 False 1151.000000 1151 91.1630 9 856 1 chr4B.!!$F1 847
14 TraesCS4A01G425900 chr2B 22541102 22542991 1889 True 2756.000000 2756 93.1400 2 1876 1 chr2B.!!$R1 1874
15 TraesCS4A01G425900 chr2B 215484813 215485535 722 True 1175.000000 1175 95.9890 2178 2900 1 chr2B.!!$R2 722
16 TraesCS4A01G425900 chr1B 37703384 37705265 1881 False 2684.000000 2684 92.5890 9 1873 1 chr1B.!!$F1 1864
17 TraesCS4A01G425900 chr1B 331123519 331124942 1423 True 2026.000000 2026 92.5770 37 1443 1 chr1B.!!$R1 1406
18 TraesCS4A01G425900 chr1B 40383102 40383845 743 False 1134.000000 1134 94.2280 1 743 1 chr1B.!!$F2 742
19 TraesCS4A01G425900 chr1D 79044346 79046237 1891 True 2449.000000 2449 90.2360 1 1876 1 chr1D.!!$R1 1875
20 TraesCS4A01G425900 chr1D 74252563 74254451 1888 False 2377.000000 2377 89.5950 1 1873 1 chr1D.!!$F1 1872
21 TraesCS4A01G425900 chr1D 398922736 398924618 1882 False 2372.000000 2372 89.5620 1 1873 1 chr1D.!!$F2 1872
22 TraesCS4A01G425900 chr1D 467308894 467310782 1888 True 2362.000000 2362 89.4430 1 1876 1 chr1D.!!$R2 1875
23 TraesCS4A01G425900 chr3D 274369805 274371685 1880 False 2396.000000 2396 89.8680 9 1873 1 chr3D.!!$F2 1864
24 TraesCS4A01G425900 chr3D 82111880 82113609 1729 False 2298.000000 2298 90.7940 156 1873 1 chr3D.!!$F1 1717
25 TraesCS4A01G425900 chr5D 239955940 239957821 1881 True 2394.000000 2394 89.8260 9 1876 1 chr5D.!!$R1 1867
26 TraesCS4A01G425900 chr5D 440706649 440708508 1859 True 2122.000000 2122 87.5070 9 1856 1 chr5D.!!$R2 1847
27 TraesCS4A01G425900 chr5D 13780414 13781136 722 False 1153.000000 1153 95.4360 2178 2900 1 chr5D.!!$F1 722
28 TraesCS4A01G425900 chr5D 559011412 559012134 722 False 1153.000000 1153 95.4360 2178 2900 1 chr5D.!!$F2 722
29 TraesCS4A01G425900 chr6D 340207439 340209326 1887 True 2381.000000 2381 89.6480 1 1873 1 chr6D.!!$R3 1872
30 TraesCS4A01G425900 chr6D 51478013 51479895 1882 False 2377.000000 2377 89.6260 1 1873 1 chr6D.!!$F2 1872
31 TraesCS4A01G425900 chr6D 365437659 365439542 1883 True 2353.000000 2353 89.3680 1 1876 1 chr6D.!!$R4 1875
32 TraesCS4A01G425900 chr6D 237092267 237094156 1889 True 2331.000000 2331 89.1280 1 1876 1 chr6D.!!$R1 1875
33 TraesCS4A01G425900 chr6D 139921993 139923788 1795 False 2285.000000 2285 89.8230 91 1873 1 chr6D.!!$F4 1782
34 TraesCS4A01G425900 chr6D 293098511 293100184 1673 False 2274.000000 2274 91.3480 215 1873 1 chr6D.!!$F6 1658
35 TraesCS4A01G425900 chr6D 23532548 23534241 1693 False 2231.000000 2231 90.6540 191 1873 1 chr6D.!!$F1 1682
36 TraesCS4A01G425900 chr6D 338193846 338195704 1858 True 2194.000000 2194 88.1330 10 1876 1 chr6D.!!$R2 1866
37 TraesCS4A01G425900 chr6D 460233791 460235678 1887 True 2134.000000 2134 87.3760 9 1876 1 chr6D.!!$R6 1867
38 TraesCS4A01G425900 chr6D 256717421 256718882 1461 False 2006.000000 2006 91.6100 425 1873 1 chr6D.!!$F5 1448
39 TraesCS4A01G425900 chr6D 80749932 80750919 987 False 854.000000 854 83.0510 9 965 1 chr6D.!!$F3 956
40 TraesCS4A01G425900 chr6D 384278620 384279401 781 True 610.000000 610 81.4680 10 782 1 chr6D.!!$R5 772
41 TraesCS4A01G425900 chr4D 297889401 297891288 1887 False 2370.000000 2370 89.5260 1 1873 1 chr4D.!!$F1 1872
42 TraesCS4A01G425900 chr4D 234397130 234398926 1796 True 2289.000000 2289 89.8400 91 1876 1 chr4D.!!$R1 1785
43 TraesCS4A01G425900 chr4D 346281269 346283003 1734 False 2121.000000 2121 88.8890 1 1731 1 chr4D.!!$F2 1730
44 TraesCS4A01G425900 chr4D 460572876 460573595 719 True 1147.000000 1147 95.4170 2181 2900 1 chr4D.!!$R2 719
45 TraesCS4A01G425900 chr7D 106887156 106889040 1884 False 2351.000000 2351 89.3570 1 1873 1 chr7D.!!$F1 1872
46 TraesCS4A01G425900 chr7D 546787034 546788754 1720 True 2344.000000 2344 91.4520 166 1876 1 chr7D.!!$R1 1710
47 TraesCS4A01G425900 chr2D 138164860 138166757 1897 False 2335.000000 2335 89.1850 1 1873 1 chr2D.!!$F1 1872
48 TraesCS4A01G425900 chr2D 192144333 192145055 722 False 1170.000000 1170 95.8510 2178 2900 1 chr2D.!!$F2 722

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
900 1126 1.339438 GGGTGGATGCGCTATGATGAT 60.339 52.381 9.73 0.0 0.0 2.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2176 6362 0.323725 GGACACCAATCACCCATGCT 60.324 55.0 0.0 0.0 0.0 3.79 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
616 802 4.845621 ACATATGCTTTGAATTTTGCGC 57.154 36.364 0.00 0.00 0.00 6.09
766 959 1.819632 GGTGGAGCAGCGGGTAATG 60.820 63.158 0.00 0.00 0.00 1.90
852 1055 7.831753 TGATTTGTTTGTTTGTTTGTAGGAGA 58.168 30.769 0.00 0.00 0.00 3.71
900 1126 1.339438 GGGTGGATGCGCTATGATGAT 60.339 52.381 9.73 0.00 0.00 2.45
934 1160 6.844388 ACCATATGTAAGGGAGACATGACTTA 59.156 38.462 0.00 0.00 38.03 2.24
1002 1228 1.811266 AGCACTCACCGCGCTTATG 60.811 57.895 5.56 0.25 29.87 1.90
1053 1279 0.398664 ATCTTCGGACCGGGGAGATT 60.399 55.000 15.25 3.70 0.00 2.40
1193 1420 2.282958 TCCGGAGCCTCGTGAACT 60.283 61.111 0.00 0.00 0.00 3.01
1351 1579 8.355169 GGTACGTGATATCCAAGACTATGTTTA 58.645 37.037 0.00 0.00 0.00 2.01
1860 2091 8.714179 TCGTAACTCGATATCAATTTTGTGTTT 58.286 29.630 3.12 0.00 44.01 2.83
1889 2171 6.656693 CCCATTTTGTAGTTCAGTCTGAATCT 59.343 38.462 18.08 17.23 38.79 2.40
1934 2216 2.828095 GCATATGCGGTGCCCACA 60.828 61.111 12.82 0.00 36.61 4.17
1935 2217 2.413963 GCATATGCGGTGCCCACAA 61.414 57.895 12.82 0.00 36.61 3.33
2043 2325 0.685097 ACACGGACAAGGTGCTACAT 59.315 50.000 0.00 0.00 38.98 2.29
2084 2366 2.561419 ACTAGCACTTAACGGCTTCTCA 59.439 45.455 1.78 0.00 41.41 3.27
2405 6591 1.609320 GCTTCTTCTGAGTCCGCCTTT 60.609 52.381 0.00 0.00 0.00 3.11
2412 6598 1.134367 CTGAGTCCGCCTTTCGTGATA 59.866 52.381 0.00 0.00 36.19 2.15
2473 6659 1.531149 CTTGTACTTGTGCGGGTTCTG 59.469 52.381 0.00 0.00 0.00 3.02
2488 6674 1.476891 GTTCTGACCCGCTATCTGTGA 59.523 52.381 0.00 0.00 0.00 3.58
2684 6870 4.215399 CACTTGTTCCGGTATTGAATGTGT 59.785 41.667 0.00 0.00 0.00 3.72
2758 6944 5.968528 TTGTTGTACAAAGTGGTGAAACT 57.031 34.783 10.51 0.00 34.76 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
355 371 4.415881 AATCAAACAAAGGTTCCCCAAC 57.584 40.909 0.00 0.00 35.82 3.77
766 959 3.438781 TCATAACACCGGCAACTTTCATC 59.561 43.478 0.00 0.00 0.00 2.92
934 1160 4.338879 CTGACCAACTGAATGAAAGGGAT 58.661 43.478 0.00 0.00 0.00 3.85
1002 1228 1.072159 CTCCGGCCTCCAATGATCC 59.928 63.158 0.00 0.00 0.00 3.36
1053 1279 0.107066 TATCCTGGAGCGTCACGGTA 60.107 55.000 0.00 0.00 37.83 4.02
1193 1420 9.793259 TTTCCTTCTTCTTATCTTTTGCTTCTA 57.207 29.630 0.00 0.00 0.00 2.10
1351 1579 2.360350 CTTGCCTGTGCCATCGGT 60.360 61.111 0.00 0.00 36.33 4.69
1856 2087 8.472007 ACTGAACTACAAAATGGGATAAAACA 57.528 30.769 0.00 0.00 0.00 2.83
1860 2091 7.685481 TCAGACTGAACTACAAAATGGGATAA 58.315 34.615 1.64 0.00 0.00 1.75
1889 2171 2.090775 TCCCTATCCCTAGTGCACATCA 60.091 50.000 21.04 2.40 0.00 3.07
1934 2216 1.204467 CAACCGCCCAGTTGCATATTT 59.796 47.619 0.00 0.00 40.60 1.40
1935 2217 0.817013 CAACCGCCCAGTTGCATATT 59.183 50.000 0.00 0.00 40.60 1.28
2043 2325 6.932960 GCTAGTTAGAAACAGAAACTTACCCA 59.067 38.462 0.00 0.00 35.23 4.51
2084 2366 7.175990 ACAGAATATTACCACCATTGAAACGTT 59.824 33.333 0.00 0.00 0.00 3.99
2176 6362 0.323725 GGACACCAATCACCCATGCT 60.324 55.000 0.00 0.00 0.00 3.79
2405 6591 6.645306 TGAATGGTTGGTATTTCTATCACGA 58.355 36.000 0.00 0.00 0.00 4.35
2412 6598 6.256053 AGGTTGATGAATGGTTGGTATTTCT 58.744 36.000 0.00 0.00 0.00 2.52
2473 6659 2.101582 ACAGATTCACAGATAGCGGGTC 59.898 50.000 0.00 0.00 0.00 4.46
2638 6824 3.126858 GGCACGTGCTTTTGATGAAGATA 59.873 43.478 36.84 0.00 41.70 1.98
2684 6870 3.775316 GGGGTCAAGACTTTCTCCATAGA 59.225 47.826 0.00 0.00 0.00 1.98
2758 6944 1.068472 GTCTCGCTTTCTCCGACAAGA 60.068 52.381 0.00 0.00 0.00 3.02
2881 7067 3.354948 CAGTGGAGATTGACATTCCCA 57.645 47.619 4.42 4.42 0.00 4.37


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

AutoCloner maintained by Alex Coulton.