Multiple sequence alignment - TraesCS4D01G297100

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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 TraesCS4D01G297100 chr4D 100.000 2290 0 0 1 2290 466289357 466291646 0.000000e+00 4229.0
1 TraesCS4D01G297100 chr4D 95.708 1724 53 8 1 1716 504270327 504272037 0.000000e+00 2754.0
2 TraesCS4D01G297100 chr4D 97.260 73 2 0 1708 1780 466331584 466331656 8.590000e-25 124.0
3 TraesCS4D01G297100 chr4D 93.103 58 4 0 1722 1779 466733200 466733143 4.050000e-13 86.1
4 TraesCS4D01G297100 chr7D 96.294 1727 49 10 1 1717 98406312 98404591 0.000000e+00 2820.0
5 TraesCS4D01G297100 chr1D 95.338 1716 56 11 1 1708 421086766 421085067 0.000000e+00 2704.0
6 TraesCS4D01G297100 chr2A 95.169 1718 71 8 1 1711 165347582 165345870 0.000000e+00 2702.0
7 TraesCS4D01G297100 chr2A 94.988 1716 68 8 3 1707 68890365 68888657 0.000000e+00 2676.0
8 TraesCS4D01G297100 chr3D 95.058 1720 62 10 1 1712 479622715 479624419 0.000000e+00 2684.0
9 TraesCS4D01G297100 chr1A 95.044 1715 64 8 1 1707 493296191 493294490 0.000000e+00 2676.0
10 TraesCS4D01G297100 chr6A 94.289 1716 84 9 1 1708 479912673 479910964 0.000000e+00 2614.0
11 TraesCS4D01G297100 chr4A 94.234 1717 83 10 1 1707 619180412 619182122 0.000000e+00 2608.0
12 TraesCS4D01G297100 chr4A 90.566 424 25 3 1882 2290 4476487 4476064 4.300000e-152 547.0
13 TraesCS4D01G297100 chr4A 83.649 422 42 11 1885 2289 4242714 4242303 2.780000e-99 372.0
14 TraesCS4D01G297100 chr4A 95.283 106 5 0 1708 1813 4477009 4476904 3.910000e-38 169.0
15 TraesCS4D01G297100 chr4A 93.860 114 2 3 1708 1817 4243364 4243252 1.410000e-37 167.0
16 TraesCS4D01G297100 chr4A 95.775 71 3 0 1709 1779 4198877 4198807 5.170000e-22 115.0
17 TraesCS4D01G297100 chr4A 96.296 54 2 0 1722 1775 4155316 4155369 3.130000e-14 89.8
18 TraesCS4D01G297100 chr2B 92.343 1737 89 20 1 1709 643125120 643126840 0.000000e+00 2431.0
19 TraesCS4D01G297100 chr2B 91.624 1743 83 25 1 1711 23892255 23890544 0.000000e+00 2351.0
20 TraesCS4D01G297100 chr6B 91.155 1741 104 23 5 1713 567281092 567282814 0.000000e+00 2316.0
21 TraesCS4D01G297100 chr3B 91.837 490 21 8 1 486 79286371 79286845 0.000000e+00 665.0
22 TraesCS4D01G297100 chr4B 85.849 424 37 7 1882 2289 583764331 583764747 1.630000e-116 429.0
23 TraesCS4D01G297100 chr4B 92.982 114 2 2 1708 1817 583763809 583763920 6.550000e-36 161.0
24 TraesCS4D01G297100 chr4B 94.521 73 4 0 1708 1780 584123434 584123506 1.860000e-21 113.0
25 TraesCS4D01G297100 chr4B 96.296 54 2 0 1722 1775 584531062 584531009 3.130000e-14 89.8


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 TraesCS4D01G297100 chr4D 466289357 466291646 2289 False 4229.0 4229 100.0000 1 2290 1 chr4D.!!$F1 2289
1 TraesCS4D01G297100 chr4D 504270327 504272037 1710 False 2754.0 2754 95.7080 1 1716 1 chr4D.!!$F3 1715
2 TraesCS4D01G297100 chr7D 98404591 98406312 1721 True 2820.0 2820 96.2940 1 1717 1 chr7D.!!$R1 1716
3 TraesCS4D01G297100 chr1D 421085067 421086766 1699 True 2704.0 2704 95.3380 1 1708 1 chr1D.!!$R1 1707
4 TraesCS4D01G297100 chr2A 165345870 165347582 1712 True 2702.0 2702 95.1690 1 1711 1 chr2A.!!$R2 1710
5 TraesCS4D01G297100 chr2A 68888657 68890365 1708 True 2676.0 2676 94.9880 3 1707 1 chr2A.!!$R1 1704
6 TraesCS4D01G297100 chr3D 479622715 479624419 1704 False 2684.0 2684 95.0580 1 1712 1 chr3D.!!$F1 1711
7 TraesCS4D01G297100 chr1A 493294490 493296191 1701 True 2676.0 2676 95.0440 1 1707 1 chr1A.!!$R1 1706
8 TraesCS4D01G297100 chr6A 479910964 479912673 1709 True 2614.0 2614 94.2890 1 1708 1 chr6A.!!$R1 1707
9 TraesCS4D01G297100 chr4A 619180412 619182122 1710 False 2608.0 2608 94.2340 1 1707 1 chr4A.!!$F2 1706
10 TraesCS4D01G297100 chr4A 4476064 4477009 945 True 358.0 547 92.9245 1708 2290 2 chr4A.!!$R3 582
11 TraesCS4D01G297100 chr4A 4242303 4243364 1061 True 269.5 372 88.7545 1708 2289 2 chr4A.!!$R2 581
12 TraesCS4D01G297100 chr2B 643125120 643126840 1720 False 2431.0 2431 92.3430 1 1709 1 chr2B.!!$F1 1708
13 TraesCS4D01G297100 chr2B 23890544 23892255 1711 True 2351.0 2351 91.6240 1 1711 1 chr2B.!!$R1 1710
14 TraesCS4D01G297100 chr6B 567281092 567282814 1722 False 2316.0 2316 91.1550 5 1713 1 chr6B.!!$F1 1708
15 TraesCS4D01G297100 chr4B 583763809 583764747 938 False 295.0 429 89.4155 1708 2289 2 chr4B.!!$F2 581

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
533 552 0.395724 CCTCCAGCCAATACCCCAAC 60.396 60.0 0.0 0.0 0.0 3.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1875 2023 0.028374 ACAACGTGGCTTGCGTAAAC 59.972 50.0 0.0 0.0 42.1 2.01 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
121 138 0.671251 GTCGATCTGCCAGGTAGGAG 59.329 60.000 4.47 0.00 41.22 3.69
287 304 2.173569 ACTTGCACCACTTCTTCCTCTT 59.826 45.455 0.00 0.00 0.00 2.85
533 552 0.395724 CCTCCAGCCAATACCCCAAC 60.396 60.000 0.00 0.00 0.00 3.77
685 709 3.513515 GGAGGAGAAGAGTGACAGTCATT 59.486 47.826 6.51 1.51 0.00 2.57
789 843 4.778143 GTGCTCCCGGCCGTTGAT 62.778 66.667 26.12 0.00 40.92 2.57
802 856 1.453155 CGTTGATAGCAAGGGCAAGT 58.547 50.000 5.52 0.00 44.61 3.16
1157 1218 1.372582 GCAGCCGTTCATCAGATCAA 58.627 50.000 0.00 0.00 0.00 2.57
1158 1219 1.329906 GCAGCCGTTCATCAGATCAAG 59.670 52.381 0.00 0.00 0.00 3.02
1359 1426 5.933790 TGGTTTATGCGTTGAACTGTTATC 58.066 37.500 0.00 0.00 0.00 1.75
1362 1430 6.248631 GTTTATGCGTTGAACTGTTATCTCC 58.751 40.000 0.00 0.00 0.00 3.71
1366 1434 3.571571 CGTTGAACTGTTATCTCCGTGA 58.428 45.455 0.00 0.00 0.00 4.35
1433 1506 4.452114 GTCTGTTGTGCTTATGATGTGTGA 59.548 41.667 0.00 0.00 0.00 3.58
1496 1569 1.303888 CCACACATCAGGCCTTGCT 60.304 57.895 0.00 0.00 0.00 3.91
1536 1609 4.658063 CCTTGGGTTTGTGGACTAACATA 58.342 43.478 6.47 0.00 34.16 2.29
1549 1622 4.521256 GGACTAACATACAGGCAACCAAAA 59.479 41.667 0.00 0.00 37.17 2.44
1550 1623 5.010213 GGACTAACATACAGGCAACCAAAAA 59.990 40.000 0.00 0.00 37.17 1.94
1579 1653 1.152589 TGTGGTTCAGCCCATGCAA 60.153 52.632 0.00 0.00 41.13 4.08
1586 1660 2.819608 GTTCAGCCCATGCAAGTAAGAA 59.180 45.455 0.00 0.00 41.13 2.52
1823 1900 3.196648 CCATGTGGCCGGCTTAAC 58.803 61.111 28.56 21.76 0.00 2.01
1824 1901 2.760159 CCATGTGGCCGGCTTAACG 61.760 63.158 28.56 12.45 0.00 3.18
1825 1902 3.131478 ATGTGGCCGGCTTAACGC 61.131 61.111 28.56 16.70 38.13 4.84
1826 1903 3.910914 ATGTGGCCGGCTTAACGCA 62.911 57.895 28.56 22.07 41.67 5.24
1827 1904 4.097863 GTGGCCGGCTTAACGCAC 62.098 66.667 28.56 20.41 41.67 5.34
1830 1907 2.810458 GCCGGCTTAACGCACGTA 60.810 61.111 22.15 0.00 41.67 3.57
1831 1908 3.075085 GCCGGCTTAACGCACGTAC 62.075 63.158 22.15 0.00 41.67 3.67
1833 1910 1.797143 CGGCTTAACGCACGTACGA 60.797 57.895 24.41 0.00 41.67 3.43
1835 1912 1.826327 GGCTTAACGCACGTACGATA 58.174 50.000 24.41 4.37 41.67 2.92
1836 1913 1.514402 GGCTTAACGCACGTACGATAC 59.486 52.381 24.41 9.49 41.67 2.24
1837 1914 3.950952 GGCTTAACGCACGTACGATACG 61.951 54.545 24.41 22.38 46.02 3.06
1848 1925 4.119334 CGTACGATACGTATGTGCTACA 57.881 45.455 13.97 0.00 44.12 2.74
1851 1928 4.627611 ACGATACGTATGTGCTACACTT 57.372 40.909 13.97 0.00 38.73 3.16
1852 1929 4.990257 ACGATACGTATGTGCTACACTTT 58.010 39.130 13.97 0.00 38.73 2.66
1853 1930 6.122850 ACGATACGTATGTGCTACACTTTA 57.877 37.500 13.97 0.00 38.73 1.85
1854 1931 5.967674 ACGATACGTATGTGCTACACTTTAC 59.032 40.000 13.97 1.39 38.73 2.01
1855 1932 5.113084 CGATACGTATGTGCTACACTTTACG 59.887 44.000 13.97 21.22 44.31 3.18
1862 2010 6.864360 ATGTGCTACACTTTACGGTAAAAA 57.136 33.333 13.78 0.00 35.11 1.94
1890 2461 0.094730 GCTAGTTTACGCAAGCCACG 59.905 55.000 0.00 0.00 45.62 4.94
1901 2472 1.469079 GCAAGCCACGTTGTTTCTGTT 60.469 47.619 0.00 0.00 0.00 3.16
1995 2566 1.270826 CCTGTCCTATGCGATCGATGT 59.729 52.381 21.57 5.91 0.00 3.06
2022 2593 0.419865 TCCCCAATCAGGTCCTGGTA 59.580 55.000 19.11 0.37 34.66 3.25
2057 2629 4.228567 TGCGGCCAGACGTGTCAA 62.229 61.111 2.24 0.00 35.98 3.18
2062 2634 1.669440 GCCAGACGTGTCAACCCTA 59.331 57.895 0.00 0.00 0.00 3.53
2138 2710 2.600470 GCGCCACCCCCTTTCTTT 60.600 61.111 0.00 0.00 0.00 2.52
2165 2737 7.254137 TCATGAAAAATGACTTCGACAAAACA 58.746 30.769 0.00 0.00 0.00 2.83
2168 2740 7.893824 TGAAAAATGACTTCGACAAAACATTG 58.106 30.769 0.00 0.00 29.99 2.82
2189 2776 9.550406 ACATTGAAATAGCCCATGATTAATTTG 57.450 29.630 0.00 0.00 0.00 2.32
2237 2825 5.412904 TGCATGTGTGATTTTATACGGACAA 59.587 36.000 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
81 88 3.210528 GACTCCGCCGAGGACGAT 61.211 66.667 7.01 0.00 45.98 3.73
138 155 1.078214 GGTGCACATGCCAGCTAGA 60.078 57.895 20.43 0.00 41.18 2.43
533 552 2.350458 CCAATGCCAACCCCTTCCG 61.350 63.158 0.00 0.00 0.00 4.30
685 709 5.603596 TCAAGAGCTTGTAGTTAAAACGGA 58.396 37.500 9.79 0.00 41.16 4.69
802 856 2.595095 CATTGGGCGAAGGGGCTA 59.405 61.111 0.00 0.00 41.87 3.93
812 866 3.957535 CCTCATCGCGCATTGGGC 61.958 66.667 15.19 15.19 38.15 5.36
821 875 2.467826 GGCAGCTCAACCTCATCGC 61.468 63.158 0.00 0.00 0.00 4.58
1056 1117 1.302192 GGAGCAGCCGGTGTTGTTA 60.302 57.895 1.90 0.00 0.00 2.41
1157 1218 1.683917 GTCACCATGTAGCCGATCTCT 59.316 52.381 0.00 0.00 0.00 3.10
1158 1219 1.600663 CGTCACCATGTAGCCGATCTC 60.601 57.143 0.00 0.00 0.00 2.75
1359 1426 6.502136 TCAGATATAAGCAGTATCACGGAG 57.498 41.667 6.01 0.00 32.26 4.63
1433 1506 0.398696 TTACCACCACACTTCGGCAT 59.601 50.000 0.00 0.00 0.00 4.40
1496 1569 2.672098 AGGCATGGTGTTTGGTTGTAA 58.328 42.857 0.00 0.00 0.00 2.41
1536 1609 1.206849 CTGGTGTTTTTGGTTGCCTGT 59.793 47.619 0.00 0.00 0.00 4.00
1549 1622 1.841277 TGAACCACACTACCTGGTGTT 59.159 47.619 10.23 3.48 46.71 3.32
1579 1653 0.329261 TGCCTGCATGCCTTCTTACT 59.671 50.000 16.68 0.00 0.00 2.24
1586 1660 1.837947 TTTGGTTGCCTGCATGCCT 60.838 52.632 16.68 0.00 0.00 4.75
1817 1894 1.183631 CGTATCGTACGTGCGTTAAGC 59.816 52.381 24.94 9.71 46.41 3.09
1827 1904 3.896612 GTGTAGCACATACGTATCGTACG 59.103 47.826 9.53 9.53 45.07 3.67
1829 1906 5.739752 AAGTGTAGCACATACGTATCGTA 57.260 39.130 4.74 4.56 37.82 3.43
1830 1907 4.627611 AAGTGTAGCACATACGTATCGT 57.372 40.909 4.74 5.05 39.26 3.73
1831 1908 5.113084 CGTAAAGTGTAGCACATACGTATCG 59.887 44.000 19.63 4.41 42.09 2.92
1833 1910 5.163622 ACCGTAAAGTGTAGCACATACGTAT 60.164 40.000 22.86 1.14 43.70 3.06
1835 1912 3.057315 ACCGTAAAGTGTAGCACATACGT 60.057 43.478 22.86 0.00 43.70 3.57
1836 1913 3.504863 ACCGTAAAGTGTAGCACATACG 58.495 45.455 20.33 20.33 44.22 3.06
1837 1914 6.949578 TTTACCGTAAAGTGTAGCACATAC 57.050 37.500 0.00 4.21 36.74 2.39
1839 1916 6.864360 TTTTTACCGTAAAGTGTAGCACAT 57.136 33.333 4.00 0.00 36.74 3.21
1862 2010 6.458342 GGCTTGCGTAAACTAGCATAATTCTT 60.458 38.462 0.00 0.00 43.42 2.52
1868 2016 2.933906 GTGGCTTGCGTAAACTAGCATA 59.066 45.455 0.00 0.00 43.42 3.14
1872 2020 1.425412 ACGTGGCTTGCGTAAACTAG 58.575 50.000 0.00 0.00 41.06 2.57
1873 2021 1.527736 CAACGTGGCTTGCGTAAACTA 59.472 47.619 0.00 0.00 42.10 2.24
1874 2022 0.306533 CAACGTGGCTTGCGTAAACT 59.693 50.000 0.00 0.00 42.10 2.66
1875 2023 0.028374 ACAACGTGGCTTGCGTAAAC 59.972 50.000 0.00 0.00 42.10 2.01
1876 2024 0.733729 AACAACGTGGCTTGCGTAAA 59.266 45.000 0.00 0.00 42.10 2.01
1877 2025 0.733729 AAACAACGTGGCTTGCGTAA 59.266 45.000 0.00 0.00 42.10 3.18
1878 2026 0.305313 GAAACAACGTGGCTTGCGTA 59.695 50.000 0.00 0.00 42.10 4.42
1879 2027 1.063488 GAAACAACGTGGCTTGCGT 59.937 52.632 0.00 0.00 45.07 5.24
1880 2028 0.929824 CAGAAACAACGTGGCTTGCG 60.930 55.000 0.00 0.00 0.00 4.85
1890 2461 0.316689 CGTGCCGGAACAGAAACAAC 60.317 55.000 14.51 0.00 0.00 3.32
2022 2593 2.679716 GCATCCCAGTGAGGCCTT 59.320 61.111 6.77 0.00 44.88 4.35
2057 2629 1.383248 AGCGAGGCCAAGATAGGGT 60.383 57.895 5.01 0.00 0.00 4.34
2062 2634 0.250209 CATAGCAGCGAGGCCAAGAT 60.250 55.000 5.01 0.00 0.00 2.40
2096 2668 2.301346 CAACAAGGCTGAGACAAGGTT 58.699 47.619 0.00 0.00 0.00 3.50
2138 2710 8.591312 GTTTTGTCGAAGTCATTTTTCATGAAA 58.409 29.630 16.91 16.91 0.00 2.69
2189 2776 2.140717 CACTTCGAGTTGGGGTGTTAC 58.859 52.381 0.00 0.00 0.00 2.50
2237 2825 6.597832 TCAAATAAAACGATTTGGACCCAT 57.402 33.333 0.28 0.00 43.87 4.00


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

AutoCloner maintained by Alex Coulton.