Multiple sequence alignment - TraesCS4A01G444400

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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 TraesCS4A01G444400 chr4A 100.000 2264 0 0 1 2264 712877478 712879741 0.000000e+00 4181
1 TraesCS4A01G444400 chr2B 94.711 2269 90 12 1 2264 138731809 138734052 0.000000e+00 3498
2 TraesCS4A01G444400 chr2B 93.962 2269 103 16 1 2264 563917140 563914901 0.000000e+00 3400
3 TraesCS4A01G444400 chr2B 95.174 2155 79 15 1 2149 42193403 42195538 0.000000e+00 3380
4 TraesCS4A01G444400 chr2B 95.859 483 20 0 1782 2264 717653799 717654281 0.000000e+00 782
5 TraesCS4A01G444400 chr2B 93.582 483 21 1 1782 2264 153866850 153867322 0.000000e+00 712
6 TraesCS4A01G444400 chr2B 92.402 487 26 2 1779 2264 45597732 45598208 0.000000e+00 684
7 TraesCS4A01G444400 chr3B 94.182 2269 102 13 1 2264 16124436 16122193 0.000000e+00 3432
8 TraesCS4A01G444400 chr3B 93.556 1707 89 15 565 2264 28617489 28619181 0.000000e+00 2523
9 TraesCS4A01G444400 chr3B 93.782 193 12 0 2072 2264 803582822 803582630 7.910000e-75 291
10 TraesCS4A01G444400 chr5B 94.888 2191 77 15 1 2185 464634106 464636267 0.000000e+00 3393
11 TraesCS4A01G444400 chr5B 96.826 1733 51 3 1 1730 530940831 530939100 0.000000e+00 2892
12 TraesCS4A01G444400 chr5B 95.445 483 21 1 1782 2264 530939084 530938603 0.000000e+00 769
13 TraesCS4A01G444400 chr4B 95.486 1994 62 11 1 1989 402787203 402785233 0.000000e+00 3158
14 TraesCS4A01G444400 chr7B 96.546 1882 49 10 1 1877 687040622 687042492 0.000000e+00 3101
15 TraesCS4A01G444400 chr7B 97.171 1732 47 1 1 1730 235458094 235456363 0.000000e+00 2926
16 TraesCS4A01G444400 chr1B 96.176 1883 55 11 1 1877 38183391 38185262 0.000000e+00 3062
17 TraesCS4A01G444400 chr1B 96.273 483 18 0 1782 2264 550438351 550437869 0.000000e+00 793
18 TraesCS4A01G444400 chr7A 96.859 1719 53 1 1 1719 7487849 7486132 0.000000e+00 2874
19 TraesCS4A01G444400 chr6B 94.203 483 28 0 1782 2264 114143087 114142605 0.000000e+00 737


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 TraesCS4A01G444400 chr4A 712877478 712879741 2263 False 4181.0 4181 100.0000 1 2264 1 chr4A.!!$F1 2263
1 TraesCS4A01G444400 chr2B 138731809 138734052 2243 False 3498.0 3498 94.7110 1 2264 1 chr2B.!!$F3 2263
2 TraesCS4A01G444400 chr2B 563914901 563917140 2239 True 3400.0 3400 93.9620 1 2264 1 chr2B.!!$R1 2263
3 TraesCS4A01G444400 chr2B 42193403 42195538 2135 False 3380.0 3380 95.1740 1 2149 1 chr2B.!!$F1 2148
4 TraesCS4A01G444400 chr3B 16122193 16124436 2243 True 3432.0 3432 94.1820 1 2264 1 chr3B.!!$R1 2263
5 TraesCS4A01G444400 chr3B 28617489 28619181 1692 False 2523.0 2523 93.5560 565 2264 1 chr3B.!!$F1 1699
6 TraesCS4A01G444400 chr5B 464634106 464636267 2161 False 3393.0 3393 94.8880 1 2185 1 chr5B.!!$F1 2184
7 TraesCS4A01G444400 chr5B 530938603 530940831 2228 True 1830.5 2892 96.1355 1 2264 2 chr5B.!!$R1 2263
8 TraesCS4A01G444400 chr4B 402785233 402787203 1970 True 3158.0 3158 95.4860 1 1989 1 chr4B.!!$R1 1988
9 TraesCS4A01G444400 chr7B 687040622 687042492 1870 False 3101.0 3101 96.5460 1 1877 1 chr7B.!!$F1 1876
10 TraesCS4A01G444400 chr7B 235456363 235458094 1731 True 2926.0 2926 97.1710 1 1730 1 chr7B.!!$R1 1729
11 TraesCS4A01G444400 chr1B 38183391 38185262 1871 False 3062.0 3062 96.1760 1 1877 1 chr1B.!!$F1 1876
12 TraesCS4A01G444400 chr7A 7486132 7487849 1717 True 2874.0 2874 96.8590 1 1719 1 chr7A.!!$R1 1718

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
823 824 0.977395 AAGTGCTAGAGGTGGTGGTC 59.023 55.0 0.0 0.0 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2118 2144 0.107456 CAGCTTGTCTGGTCACCTGT 59.893 55.0 0.0 0.0 39.15 4.0 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
253 254 1.926426 GCCTGAGTACCATGGCCCTT 61.926 60.000 13.04 0.00 39.49 3.95
542 543 1.070786 GTGGTGGTCGAGGAAGCAA 59.929 57.895 0.00 0.00 0.00 3.91
561 562 2.808543 CAAAAGTGTCAGAGGTGGTAGC 59.191 50.000 0.00 0.00 0.00 3.58
823 824 0.977395 AAGTGCTAGAGGTGGTGGTC 59.023 55.000 0.00 0.00 0.00 4.02
852 853 6.520021 AGAGGAATGGTTGATAATGGATCA 57.480 37.500 0.00 0.00 43.11 2.92
1158 1159 1.356124 AGCTGAAGGTGTCCACTGAT 58.644 50.000 0.00 0.00 0.00 2.90
1212 1213 0.389296 TCGTGTGTCCCAACTATGCG 60.389 55.000 0.00 0.00 0.00 4.73
1342 1343 2.606751 ATATGTAGTCCCCTCCTCCG 57.393 55.000 0.00 0.00 0.00 4.63
1565 1566 4.797743 AGAAGAGAGGGCAAGAAAACTTT 58.202 39.130 0.00 0.00 0.00 2.66
1721 1722 6.619801 ACTTGTTATTTGAGACCTTGTGTC 57.380 37.500 0.00 0.00 44.82 3.67
1722 1723 5.531287 ACTTGTTATTTGAGACCTTGTGTCC 59.469 40.000 0.00 0.00 45.68 4.02
1723 1724 5.042463 TGTTATTTGAGACCTTGTGTCCA 57.958 39.130 0.00 0.00 45.68 4.02
1724 1725 5.630121 TGTTATTTGAGACCTTGTGTCCAT 58.370 37.500 0.00 0.00 45.68 3.41
1725 1726 5.473162 TGTTATTTGAGACCTTGTGTCCATG 59.527 40.000 0.00 0.00 45.68 3.66
1726 1727 3.855255 TTTGAGACCTTGTGTCCATGA 57.145 42.857 0.00 0.00 45.68 3.07
1727 1728 3.855255 TTGAGACCTTGTGTCCATGAA 57.145 42.857 0.00 0.00 45.68 2.57
1728 1729 3.126001 TGAGACCTTGTGTCCATGAAC 57.874 47.619 0.00 0.00 45.68 3.18
1729 1730 2.705658 TGAGACCTTGTGTCCATGAACT 59.294 45.455 0.00 0.00 45.68 3.01
1730 1731 3.070018 GAGACCTTGTGTCCATGAACTG 58.930 50.000 0.00 0.00 45.68 3.16
1738 1751 2.029828 GTGTCCATGAACTGTCGAGACT 60.030 50.000 4.78 0.00 0.00 3.24
1740 1753 3.069586 TGTCCATGAACTGTCGAGACTTT 59.930 43.478 4.78 0.00 0.00 2.66
1743 1756 3.809832 CCATGAACTGTCGAGACTTTGTT 59.190 43.478 4.78 7.06 0.00 2.83
1747 1760 7.307989 CCATGAACTGTCGAGACTTTGTTTATT 60.308 37.037 4.78 0.00 0.00 1.40
1748 1761 6.943981 TGAACTGTCGAGACTTTGTTTATTG 58.056 36.000 4.78 0.00 0.00 1.90
1749 1762 6.537301 TGAACTGTCGAGACTTTGTTTATTGT 59.463 34.615 4.78 0.00 0.00 2.71
1757 1770 8.922676 TCGAGACTTTGTTTATTGTATGAACTC 58.077 33.333 0.00 0.00 30.85 3.01
1760 1773 8.495949 AGACTTTGTTTATTGTATGAACTCGTG 58.504 33.333 0.00 0.00 30.85 4.35
1775 1788 2.347697 TCGTGATTCGAGACCTTGTG 57.652 50.000 0.00 0.00 44.01 3.33
1776 1789 1.611977 TCGTGATTCGAGACCTTGTGT 59.388 47.619 0.00 0.00 44.01 3.72
1777 1790 1.986378 CGTGATTCGAGACCTTGTGTC 59.014 52.381 0.00 0.00 44.82 3.67
1778 1791 2.338500 GTGATTCGAGACCTTGTGTCC 58.662 52.381 0.00 0.00 45.68 4.02
1779 1792 1.967779 TGATTCGAGACCTTGTGTCCA 59.032 47.619 0.00 0.00 45.68 4.02
1780 1793 2.567169 TGATTCGAGACCTTGTGTCCAT 59.433 45.455 0.00 0.00 45.68 3.41
1781 1794 2.455674 TTCGAGACCTTGTGTCCATG 57.544 50.000 0.00 0.00 45.68 3.66
1908 1922 3.629855 TGTTTGCTACAAGTTGCTAAGCA 59.370 39.130 18.88 18.88 41.19 3.91
2106 2132 2.586792 GATCCTGGCGTCTGGCTT 59.413 61.111 8.27 0.00 42.94 4.35
2118 2144 2.906388 TGGCTTGCTTTGCTCGCA 60.906 55.556 0.00 0.00 35.22 5.10
2155 2181 0.035317 TGTCTGGTGTGTCTGATGGC 59.965 55.000 0.00 0.00 0.00 4.40
2198 2225 2.449518 TCTGCCTCCCACACCCAA 60.450 61.111 0.00 0.00 0.00 4.12
2253 2280 1.069765 CGCAGGTGACCAGACAAGT 59.930 57.895 3.63 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
253 254 5.087323 CAGAAGAGGGTCTGGCCTAATATA 58.913 45.833 3.32 0.00 41.21 0.86
542 543 1.000955 CGCTACCACCTCTGACACTTT 59.999 52.381 0.00 0.00 0.00 2.66
561 562 1.218316 GCTCCCTCTACAACCACCG 59.782 63.158 0.00 0.00 0.00 4.94
717 718 2.280552 GGTAGCTCGACCACCACCA 61.281 63.158 0.45 0.00 39.51 4.17
823 824 2.933495 TCAACCATTCCTCTACGACG 57.067 50.000 0.00 0.00 0.00 5.12
1111 1112 2.565046 TCAGCACACCAACATGATGA 57.435 45.000 4.25 0.00 38.84 2.92
1158 1159 1.069978 TCTGTCCATGACTTGTTGCGA 59.930 47.619 0.00 0.00 33.15 5.10
1212 1213 1.089481 TTGGCCTTCGACGATCATGC 61.089 55.000 3.32 0.00 0.00 4.06
1505 1506 1.140312 TTGTGTGCCCTCTCTTCCTT 58.860 50.000 0.00 0.00 0.00 3.36
1565 1566 2.033911 TGCATTGCGAGCCCTTGA 59.966 55.556 3.84 0.00 0.00 3.02
1656 1657 0.246360 ACAGTTCATCATCGACGCCA 59.754 50.000 0.00 0.00 0.00 5.69
1708 1709 2.705658 AGTTCATGGACACAAGGTCTCA 59.294 45.455 6.96 0.00 46.16 3.27
1721 1722 3.393800 ACAAAGTCTCGACAGTTCATGG 58.606 45.455 0.00 0.00 0.00 3.66
1722 1723 5.409643 AAACAAAGTCTCGACAGTTCATG 57.590 39.130 0.00 0.00 0.00 3.07
1723 1724 7.226720 ACAATAAACAAAGTCTCGACAGTTCAT 59.773 33.333 0.00 0.00 0.00 2.57
1724 1725 6.537301 ACAATAAACAAAGTCTCGACAGTTCA 59.463 34.615 0.00 0.00 0.00 3.18
1725 1726 6.945072 ACAATAAACAAAGTCTCGACAGTTC 58.055 36.000 0.00 0.00 0.00 3.01
1726 1727 6.920569 ACAATAAACAAAGTCTCGACAGTT 57.079 33.333 0.00 0.00 0.00 3.16
1727 1728 7.870954 TCATACAATAAACAAAGTCTCGACAGT 59.129 33.333 0.00 0.00 0.00 3.55
1728 1729 8.239681 TCATACAATAAACAAAGTCTCGACAG 57.760 34.615 0.00 0.00 0.00 3.51
1729 1730 8.492748 GTTCATACAATAAACAAAGTCTCGACA 58.507 33.333 0.00 0.00 0.00 4.35
1730 1731 8.709646 AGTTCATACAATAAACAAAGTCTCGAC 58.290 33.333 0.00 0.00 0.00 4.20
1738 1751 9.820229 GAATCACGAGTTCATACAATAAACAAA 57.180 29.630 0.00 0.00 0.00 2.83
1740 1753 7.542824 TCGAATCACGAGTTCATACAATAAACA 59.457 33.333 0.00 0.00 46.45 2.83
1757 1770 1.986378 GACACAAGGTCTCGAATCACG 59.014 52.381 0.00 0.00 43.46 4.35
1760 1773 2.743636 TGGACACAAGGTCTCGAATC 57.256 50.000 0.00 0.00 46.16 2.52
1768 1781 5.013079 TCTCAAATAGTCATGGACACAAGGT 59.987 40.000 0.00 0.00 34.60 3.50
1769 1782 5.491070 TCTCAAATAGTCATGGACACAAGG 58.509 41.667 0.00 0.00 34.60 3.61
1770 1783 7.621428 AATCTCAAATAGTCATGGACACAAG 57.379 36.000 0.00 0.00 34.60 3.16
1771 1784 9.112725 CATAATCTCAAATAGTCATGGACACAA 57.887 33.333 0.00 0.00 34.60 3.33
1772 1785 8.267183 ACATAATCTCAAATAGTCATGGACACA 58.733 33.333 0.00 0.00 34.60 3.72
1773 1786 8.554528 CACATAATCTCAAATAGTCATGGACAC 58.445 37.037 0.00 0.00 34.60 3.67
1774 1787 7.227314 GCACATAATCTCAAATAGTCATGGACA 59.773 37.037 0.00 0.00 34.60 4.02
1775 1788 7.227314 TGCACATAATCTCAAATAGTCATGGAC 59.773 37.037 0.00 0.00 0.00 4.02
1776 1789 7.281841 TGCACATAATCTCAAATAGTCATGGA 58.718 34.615 0.00 0.00 0.00 3.41
1777 1790 7.500720 TGCACATAATCTCAAATAGTCATGG 57.499 36.000 0.00 0.00 0.00 3.66
1778 1791 9.229784 GTTTGCACATAATCTCAAATAGTCATG 57.770 33.333 0.00 0.00 32.07 3.07
1779 1792 9.182214 AGTTTGCACATAATCTCAAATAGTCAT 57.818 29.630 0.00 0.00 32.07 3.06
1780 1793 8.565896 AGTTTGCACATAATCTCAAATAGTCA 57.434 30.769 0.00 0.00 32.07 3.41
1908 1922 9.573133 CACTTCTGTCTTTTGTTAATGTCTTTT 57.427 29.630 0.00 0.00 0.00 2.27
1912 1937 7.429340 CACACACTTCTGTCTTTTGTTAATGTC 59.571 37.037 0.00 0.00 0.00 3.06
2091 2117 4.704833 GCAAGCCAGACGCCAGGA 62.705 66.667 0.00 0.00 38.78 3.86
2106 2132 2.203195 ACCTGTGCGAGCAAAGCA 60.203 55.556 9.67 0.00 42.99 3.91
2118 2144 0.107456 CAGCTTGTCTGGTCACCTGT 59.893 55.000 0.00 0.00 39.15 4.00
2155 2181 0.108138 GGACCTTGACGTCTGGATGG 60.108 60.000 26.66 16.54 33.07 3.51
2166 2193 1.296392 CAGACGCCATGGACCTTGA 59.704 57.895 18.40 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.