Multiple sequence alignment - TraesCS6D01G376200

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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 TraesCS6D01G376200 chr6D 100.000 2524 0 0 1 2524 459057238 459059761 0.000000e+00 4662
1 TraesCS6D01G376200 chr6D 98.470 915 14 0 1 915 266787897 266786983 0.000000e+00 1613
2 TraesCS6D01G376200 chr6D 91.708 1001 58 7 909 1908 458976850 458977826 0.000000e+00 1365
3 TraesCS6D01G376200 chr6D 86.617 934 87 18 909 1835 459247702 459248604 0.000000e+00 998
4 TraesCS6D01G376200 chr6D 84.903 828 84 20 909 1709 459264873 459265686 0.000000e+00 798
5 TraesCS6D01G376200 chr6D 89.394 528 43 3 1950 2469 458977831 458978353 0.000000e+00 652
6 TraesCS6D01G376200 chr6D 78.683 319 38 23 1789 2085 459266113 459266423 4.290000e-43 185
7 TraesCS6D01G376200 chr6D 78.295 258 19 23 2295 2524 459248700 459248948 5.670000e-27 132
8 TraesCS6D01G376200 chr6D 95.652 46 2 0 2295 2340 459266605 459266650 9.680000e-10 75
9 TraesCS6D01G376200 chr2D 99.339 908 6 0 1 908 381302693 381301786 0.000000e+00 1644
10 TraesCS6D01G376200 chr2D 99.119 908 8 0 1 908 86504305 86505212 0.000000e+00 1633
11 TraesCS6D01G376200 chr5D 99.120 909 8 0 1 909 463023443 463024351 0.000000e+00 1635
12 TraesCS6D01G376200 chr5D 98.686 913 8 1 1 909 95267167 95268079 0.000000e+00 1616
13 TraesCS6D01G376200 chr1D 99.010 909 8 1 1 908 85934070 85934978 0.000000e+00 1628
14 TraesCS6D01G376200 chr7D 99.009 908 8 1 1 908 32629016 32629922 0.000000e+00 1626
15 TraesCS6D01G376200 chr3D 99.009 908 8 1 1 908 132868240 132869146 0.000000e+00 1626
16 TraesCS6D01G376200 chr4D 98.791 910 11 0 1 910 62776255 62777164 0.000000e+00 1620
17 TraesCS6D01G376200 chr6A 91.833 1004 57 11 909 1909 605338836 605339817 0.000000e+00 1376
18 TraesCS6D01G376200 chr6A 86.188 934 91 18 909 1835 605362801 605363703 0.000000e+00 976
19 TraesCS6D01G376200 chr6A 85.749 814 93 16 985 1792 605369940 605370736 0.000000e+00 839
20 TraesCS6D01G376200 chr6A 88.645 502 36 8 1950 2450 605339821 605340302 2.160000e-165 592
21 TraesCS6D01G376200 chr6A 85.149 202 18 5 1914 2103 605371584 605371785 1.980000e-46 196
22 TraesCS6D01G376200 chr6A 86.441 118 4 6 2412 2524 605363935 605364045 4.410000e-23 119
23 TraesCS6D01G376200 chr6B 86.495 933 89 20 909 1834 698977594 698978496 0.000000e+00 990
24 TraesCS6D01G376200 chr6B 86.075 912 83 24 909 1792 698990532 698991427 0.000000e+00 941
25 TraesCS6D01G376200 chr6B 83.748 763 100 14 1213 1968 698106292 698107037 0.000000e+00 701
26 TraesCS6D01G376200 chr6B 88.450 329 28 3 909 1227 698105780 698106108 3.040000e-104 388
27 TraesCS6D01G376200 chr6B 79.027 329 35 20 1789 2090 698991589 698991910 7.120000e-46 195
28 TraesCS6D01G376200 chr6B 87.000 100 4 3 2419 2513 698978760 698978855 1.240000e-18 104


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 TraesCS6D01G376200 chr6D 459057238 459059761 2523 False 4662.000000 4662 100.000000 1 2524 1 chr6D.!!$F1 2523
1 TraesCS6D01G376200 chr6D 266786983 266787897 914 True 1613.000000 1613 98.470000 1 915 1 chr6D.!!$R1 914
2 TraesCS6D01G376200 chr6D 458976850 458978353 1503 False 1008.500000 1365 90.551000 909 2469 2 chr6D.!!$F2 1560
3 TraesCS6D01G376200 chr6D 459247702 459248948 1246 False 565.000000 998 82.456000 909 2524 2 chr6D.!!$F3 1615
4 TraesCS6D01G376200 chr6D 459264873 459266650 1777 False 352.666667 798 86.412667 909 2340 3 chr6D.!!$F4 1431
5 TraesCS6D01G376200 chr2D 381301786 381302693 907 True 1644.000000 1644 99.339000 1 908 1 chr2D.!!$R1 907
6 TraesCS6D01G376200 chr2D 86504305 86505212 907 False 1633.000000 1633 99.119000 1 908 1 chr2D.!!$F1 907
7 TraesCS6D01G376200 chr5D 463023443 463024351 908 False 1635.000000 1635 99.120000 1 909 1 chr5D.!!$F2 908
8 TraesCS6D01G376200 chr5D 95267167 95268079 912 False 1616.000000 1616 98.686000 1 909 1 chr5D.!!$F1 908
9 TraesCS6D01G376200 chr1D 85934070 85934978 908 False 1628.000000 1628 99.010000 1 908 1 chr1D.!!$F1 907
10 TraesCS6D01G376200 chr7D 32629016 32629922 906 False 1626.000000 1626 99.009000 1 908 1 chr7D.!!$F1 907
11 TraesCS6D01G376200 chr3D 132868240 132869146 906 False 1626.000000 1626 99.009000 1 908 1 chr3D.!!$F1 907
12 TraesCS6D01G376200 chr4D 62776255 62777164 909 False 1620.000000 1620 98.791000 1 910 1 chr4D.!!$F1 909
13 TraesCS6D01G376200 chr6A 605338836 605340302 1466 False 984.000000 1376 90.239000 909 2450 2 chr6A.!!$F1 1541
14 TraesCS6D01G376200 chr6A 605362801 605364045 1244 False 547.500000 976 86.314500 909 2524 2 chr6A.!!$F2 1615
15 TraesCS6D01G376200 chr6A 605369940 605371785 1845 False 517.500000 839 85.449000 985 2103 2 chr6A.!!$F3 1118
16 TraesCS6D01G376200 chr6B 698990532 698991910 1378 False 568.000000 941 82.551000 909 2090 2 chr6B.!!$F3 1181
17 TraesCS6D01G376200 chr6B 698977594 698978855 1261 False 547.000000 990 86.747500 909 2513 2 chr6B.!!$F2 1604
18 TraesCS6D01G376200 chr6B 698105780 698107037 1257 False 544.500000 701 86.099000 909 1968 2 chr6B.!!$F1 1059

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
979 994 5.542616 TGTGCTTGACCAAAATTTTGTTG 57.457 34.783 25.25 15.5 36.45 3.33 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2106 3310 0.310854 CCCAAAAAGAGGCGACACAC 59.689 55.0 0.0 0.0 0.0 3.82 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
739 740 6.348050 GCTTTTATCTCTCCAAACTCAGTGTG 60.348 42.308 0.00 0.00 0.00 3.82
979 994 5.542616 TGTGCTTGACCAAAATTTTGTTG 57.457 34.783 25.25 15.50 36.45 3.33
1079 1112 5.408909 GCTTTGGAGTTTTACTACTGGAGAC 59.591 44.000 0.00 0.00 27.92 3.36
1098 1131 3.072184 AGACTGTGAGTGGCTCAAAGATT 59.928 43.478 19.71 7.21 45.87 2.40
1161 1194 7.264373 AGCCTATGTAAGTAAAATGACATGC 57.736 36.000 0.00 0.00 34.46 4.06
1285 1525 0.400213 TCGTCAATTGTGGGGAGCTT 59.600 50.000 5.13 0.00 0.00 3.74
1490 1734 6.634436 CAGAAAATACTGTGAAGTCTGCAAAC 59.366 38.462 0.00 0.00 33.73 2.93
1514 1758 7.611770 ACAACATGAGCATTACAGTACTAGAA 58.388 34.615 0.00 0.00 0.00 2.10
1602 1866 8.342634 CCGGATAAGAAACTGGTATTTGTATTG 58.657 37.037 0.00 0.00 0.00 1.90
1603 1867 9.104965 CGGATAAGAAACTGGTATTTGTATTGA 57.895 33.333 0.00 0.00 0.00 2.57
1609 1873 9.793259 AGAAACTGGTATTTGTATTGAAGAAGA 57.207 29.630 0.00 0.00 0.00 2.87
1612 1876 9.793259 AACTGGTATTTGTATTGAAGAAGAAGA 57.207 29.630 0.00 0.00 0.00 2.87
1613 1877 9.793259 ACTGGTATTTGTATTGAAGAAGAAGAA 57.207 29.630 0.00 0.00 0.00 2.52
1711 2158 7.668492 AGGTCGAAATGTTCTTACTAAAGACT 58.332 34.615 0.00 0.00 41.48 3.24
1720 2167 7.361127 TGTTCTTACTAAAGACTCTTCTCACG 58.639 38.462 0.00 0.00 41.48 4.35
1721 2168 7.228108 TGTTCTTACTAAAGACTCTTCTCACGA 59.772 37.037 0.00 0.00 41.48 4.35
1744 2191 7.331687 ACGAAAGAATTTTGGATGCATAAAAGG 59.668 33.333 11.82 1.13 43.86 3.11
1749 2196 1.679139 TGGATGCATAAAAGGAGGCG 58.321 50.000 0.00 0.00 0.00 5.52
1757 2204 4.189231 GCATAAAAGGAGGCGAGTTAAGA 58.811 43.478 0.00 0.00 0.00 2.10
1762 2214 3.320673 AGGAGGCGAGTTAAGAAGTTG 57.679 47.619 0.00 0.00 0.00 3.16
1771 2223 6.142320 GGCGAGTTAAGAAGTTGAATTTTGTG 59.858 38.462 0.00 0.00 0.00 3.33
1838 2992 6.030228 GCATGCAATTTGTCTCTTAGTTACC 58.970 40.000 14.21 0.00 0.00 2.85
1896 3053 8.693120 AGAAATAGTCAGAGTTATCGGATACA 57.307 34.615 0.00 0.00 32.08 2.29
1910 3067 5.984233 TCGGATACATCACTTTATTGTGC 57.016 39.130 0.00 0.00 37.81 4.57
1912 3069 4.318760 CGGATACATCACTTTATTGTGCCG 60.319 45.833 0.00 0.00 37.81 5.69
1941 3126 9.768662 AATCATGTAGAAAAGCAACTTCAAATT 57.231 25.926 0.00 0.00 0.00 1.82
1986 3177 5.186198 GCTTACCTAGAAGAAAAGGCATCA 58.814 41.667 0.00 0.00 36.24 3.07
2069 3268 4.065088 TCGGTCCAGAAATGAGAAACTTG 58.935 43.478 0.00 0.00 0.00 3.16
2106 3310 5.536916 TGAACCCTTAACAATACCAAGGTTG 59.463 40.000 0.00 0.00 37.69 3.77
2123 3327 2.450160 GTTGTGTGTCGCCTCTTTTTG 58.550 47.619 0.00 0.00 0.00 2.44
2131 3335 2.112190 TCGCCTCTTTTTGGGGTTTTT 58.888 42.857 0.00 0.00 38.47 1.94
2138 3342 6.017440 GCCTCTTTTTGGGGTTTTTGATAAAC 60.017 38.462 0.00 0.00 0.00 2.01
2146 3350 4.373527 GGGTTTTTGATAAACACCACACC 58.626 43.478 10.67 0.00 31.57 4.16
2172 3376 5.334337 CGCTTGAAAGAGTCATTGATCAACA 60.334 40.000 11.07 0.00 35.70 3.33
2174 3379 6.581542 GCTTGAAAGAGTCATTGATCAACAAG 59.418 38.462 11.07 15.81 42.02 3.16
2181 3386 6.094603 AGAGTCATTGATCAACAAGGTAATGC 59.905 38.462 11.07 0.00 42.02 3.56
2182 3387 5.948162 AGTCATTGATCAACAAGGTAATGCT 59.052 36.000 11.07 2.13 42.02 3.79
2183 3388 7.112122 AGTCATTGATCAACAAGGTAATGCTA 58.888 34.615 11.07 0.00 42.02 3.49
2190 3395 5.739959 TCAACAAGGTAATGCTATGCTACA 58.260 37.500 0.00 0.00 0.00 2.74
2225 3430 4.126520 TGAAATAAGCTTTTGGGGGAGT 57.873 40.909 3.20 0.00 0.00 3.85
2226 3431 3.831911 TGAAATAAGCTTTTGGGGGAGTG 59.168 43.478 3.20 0.00 0.00 3.51
2229 3434 0.178924 AAGCTTTTGGGGGAGTGCAT 60.179 50.000 0.00 0.00 0.00 3.96
2387 3636 3.081804 AGATTCCGTAACAAAGGCCAAG 58.918 45.455 5.01 0.00 0.00 3.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
739 740 2.162681 CAAACTCATGGTGGAGGAACC 58.837 52.381 0.00 0.00 39.27 3.62
979 994 2.096174 TGTAACCGCTGTTTGAACACAC 59.904 45.455 0.00 0.00 35.87 3.82
1079 1112 3.373439 GCTAATCTTTGAGCCACTCACAG 59.627 47.826 4.71 4.71 40.46 3.66
1098 1131 2.038426 TGCTTTTAGGTGCACAGAGCTA 59.962 45.455 20.43 7.82 45.94 3.32
1285 1525 6.073440 GCACCGTAAAGTTTCATTAAGTGAGA 60.073 38.462 0.00 0.00 38.29 3.27
1490 1734 7.223582 CCTTCTAGTACTGTAATGCTCATGTTG 59.776 40.741 5.39 0.00 0.00 3.33
1538 1797 5.133221 AGGTACCCATGAATATGCAGAAAC 58.867 41.667 8.74 0.00 32.79 2.78
1552 1811 7.341030 GGTATACAGTTGTAAAAGGTACCCAT 58.659 38.462 8.74 0.00 33.76 4.00
1560 1820 9.590451 TTCTTATCCGGTATACAGTTGTAAAAG 57.410 33.333 0.00 0.00 33.76 2.27
1602 1866 7.657354 AGCTTCTTCTTCTTCTTCTTCTTCTTC 59.343 37.037 0.00 0.00 0.00 2.87
1603 1867 7.508687 AGCTTCTTCTTCTTCTTCTTCTTCTT 58.491 34.615 0.00 0.00 0.00 2.52
1604 1868 7.066307 AGCTTCTTCTTCTTCTTCTTCTTCT 57.934 36.000 0.00 0.00 0.00 2.85
1605 1869 7.728847 AAGCTTCTTCTTCTTCTTCTTCTTC 57.271 36.000 0.00 0.00 0.00 2.87
1606 1870 7.555914 ACAAAGCTTCTTCTTCTTCTTCTTCTT 59.444 33.333 0.00 0.00 0.00 2.52
1607 1871 7.053498 ACAAAGCTTCTTCTTCTTCTTCTTCT 58.947 34.615 0.00 0.00 0.00 2.85
1608 1872 7.258022 ACAAAGCTTCTTCTTCTTCTTCTTC 57.742 36.000 0.00 0.00 0.00 2.87
1609 1873 7.637631 AACAAAGCTTCTTCTTCTTCTTCTT 57.362 32.000 0.00 0.00 0.00 2.52
1610 1874 7.637631 AAACAAAGCTTCTTCTTCTTCTTCT 57.362 32.000 0.00 0.00 0.00 2.85
1611 1875 9.788960 TTAAAACAAAGCTTCTTCTTCTTCTTC 57.211 29.630 0.00 0.00 0.00 2.87
1720 2167 8.776376 TCCTTTTATGCATCCAAAATTCTTTC 57.224 30.769 0.19 0.00 0.00 2.62
1721 2168 7.825761 CCTCCTTTTATGCATCCAAAATTCTTT 59.174 33.333 0.19 0.00 0.00 2.52
1744 2191 5.864628 AATTCAACTTCTTAACTCGCCTC 57.135 39.130 0.00 0.00 0.00 4.70
1749 2196 8.406297 AGGACACAAAATTCAACTTCTTAACTC 58.594 33.333 0.00 0.00 0.00 3.01
1809 2957 5.662211 AAGAGACAAATTGCATGCAAAAC 57.338 34.783 34.84 22.29 39.55 2.43
1859 3015 7.550906 ACTCTGACTATTTCTTACTTTCATGCC 59.449 37.037 0.00 0.00 0.00 4.40
1865 3021 9.804758 CCGATAACTCTGACTATTTCTTACTTT 57.195 33.333 0.00 0.00 0.00 2.66
1896 3053 4.704540 TGATTTCCGGCACAATAAAGTGAT 59.295 37.500 0.00 0.00 42.05 3.06
1910 3067 4.963276 TGCTTTTCTACATGATTTCCGG 57.037 40.909 0.00 0.00 0.00 5.14
1912 3069 7.370383 TGAAGTTGCTTTTCTACATGATTTCC 58.630 34.615 0.00 0.00 0.00 3.13
1941 3126 8.861033 AAGCGTCGTGTATATTTTCTAATGTA 57.139 30.769 0.00 0.00 0.00 2.29
1960 3145 3.617706 GCCTTTTCTTCTAGGTAAGCGTC 59.382 47.826 0.00 0.00 33.91 5.19
1986 3177 2.558378 CACTCTGGATCAATGCGACAT 58.442 47.619 0.00 0.00 0.00 3.06
2069 3268 3.983044 AGGGTTCACATTCTCCTACAC 57.017 47.619 0.00 0.00 0.00 2.90
2106 3310 0.310854 CCCAAAAAGAGGCGACACAC 59.689 55.000 0.00 0.00 0.00 3.82
2123 3327 4.373527 GTGTGGTGTTTATCAAAAACCCC 58.626 43.478 8.22 0.00 30.77 4.95
2131 3335 0.606944 GCGGGGTGTGGTGTTTATCA 60.607 55.000 0.00 0.00 0.00 2.15
2138 3342 1.795170 CTTTCAAGCGGGGTGTGGTG 61.795 60.000 0.00 0.00 0.00 4.17
2146 3350 2.426522 TCAATGACTCTTTCAAGCGGG 58.573 47.619 0.00 0.00 37.92 6.13
2172 3376 6.414732 TCAAAGTGTAGCATAGCATTACCTT 58.585 36.000 0.00 0.00 0.00 3.50
2174 3379 6.677781 TTCAAAGTGTAGCATAGCATTACC 57.322 37.500 0.00 0.00 0.00 2.85
2181 3386 8.032952 TCAACAGATTTCAAAGTGTAGCATAG 57.967 34.615 0.00 0.00 0.00 2.23
2182 3387 7.977789 TCAACAGATTTCAAAGTGTAGCATA 57.022 32.000 0.00 0.00 0.00 3.14
2183 3388 6.882610 TCAACAGATTTCAAAGTGTAGCAT 57.117 33.333 0.00 0.00 0.00 3.79
2190 3395 9.822185 AAAGCTTATTTCAACAGATTTCAAAGT 57.178 25.926 0.00 0.00 0.00 2.66
2225 3430 5.045234 AGGAAACTTTACGGTGCTTATGCA 61.045 41.667 0.00 0.00 43.11 3.96
2226 3431 3.439129 AGGAAACTTTACGGTGCTTATGC 59.561 43.478 0.00 0.00 37.44 3.14
2387 3636 0.478507 AGCCATACAACCTATGCCCC 59.521 55.000 0.00 0.00 0.00 5.80


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

AutoCloner maintained by Alex Coulton.