Multiple sequence alignment - TraesCS3B01G569500

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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 TraesCS3B01G569500 chr3B 100.000 2726 0 0 1 2726 801157434 801160159 0.000000e+00 5035.0
1 TraesCS3B01G569500 chr3B 90.616 2760 124 52 1 2724 803012296 803014956 0.000000e+00 3537.0
2 TraesCS3B01G569500 chr3D 90.230 1740 114 16 6 1733 596881751 596880056 0.000000e+00 2220.0
3 TraesCS3B01G569500 chr3D 76.598 923 177 30 506 1403 596160841 596161749 3.180000e-129 472.0
4 TraesCS3B01G569500 chr7B 78.846 572 93 19 2058 2602 629014201 629013631 7.180000e-96 361.0
5 TraesCS3B01G569500 chr7D 91.489 47 4 0 1797 1843 559212936 559212890 6.300000e-07 65.8


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 TraesCS3B01G569500 chr3B 801157434 801160159 2725 False 5035 5035 100.000 1 2726 1 chr3B.!!$F1 2725
1 TraesCS3B01G569500 chr3B 803012296 803014956 2660 False 3537 3537 90.616 1 2724 1 chr3B.!!$F2 2723
2 TraesCS3B01G569500 chr3D 596880056 596881751 1695 True 2220 2220 90.230 6 1733 1 chr3D.!!$R1 1727
3 TraesCS3B01G569500 chr3D 596160841 596161749 908 False 472 472 76.598 506 1403 1 chr3D.!!$F1 897
4 TraesCS3B01G569500 chr7B 629013631 629014201 570 True 361 361 78.846 2058 2602 1 chr7B.!!$R1 544

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
357 360 0.386113 GAGTAAGGCTAGCCGGTGAG 59.614 60.0 27.83 1.17 41.95 3.51 F
1087 1124 0.447801 CCCATGTCAAGCTACGCAAC 59.552 55.0 0.00 0.00 0.00 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1519 1564 0.104120 AGCTTGTATGCGCCGTGATA 59.896 50.0 4.18 0.0 38.13 2.15 R
1931 1987 0.319211 CGCCTAGAACACACAACGGA 60.319 55.0 0.00 0.0 0.00 4.69 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
58 59 9.797473 GTTATTTTTGAAAGCATTTTAGAGTGC 57.203 29.630 0.00 0.00 39.27 4.40
105 106 9.350357 CAACTTCCATGAATGTCATTTTAAGAG 57.650 33.333 0.00 0.00 34.28 2.85
139 142 9.952188 TGTGATCACGTAAAACATTTTTCAATA 57.048 25.926 20.54 0.00 0.00 1.90
357 360 0.386113 GAGTAAGGCTAGCCGGTGAG 59.614 60.000 27.83 1.17 41.95 3.51
504 508 8.528643 TGGAGTATATTTACATACCGAATCCAG 58.471 37.037 0.00 0.00 31.84 3.86
869 892 5.485353 TGAGATCCACCTACATTCTCAAACT 59.515 40.000 0.00 0.00 39.72 2.66
870 893 6.667848 TGAGATCCACCTACATTCTCAAACTA 59.332 38.462 0.00 0.00 39.72 2.24
957 985 1.133294 TCGTACTATCTGGATGCCCCA 60.133 52.381 0.00 0.00 44.25 4.96
971 999 0.881600 GCCCCAAGCAACAAAGCAAG 60.882 55.000 0.00 0.00 42.97 4.01
1087 1124 0.447801 CCCATGTCAAGCTACGCAAC 59.552 55.000 0.00 0.00 0.00 4.17
1124 1161 5.345472 CGATCTATGACACAGAAGATCATGC 59.655 44.000 18.17 0.00 42.89 4.06
1519 1564 1.068474 CATTTTTCGCGTCGAGAGGT 58.932 50.000 5.77 0.00 37.14 3.85
1578 1634 1.730547 GTGCAAACATGAGCCGTGC 60.731 57.895 0.00 1.84 35.75 5.34
1579 1635 2.502510 GCAAACATGAGCCGTGCG 60.503 61.111 0.00 0.00 0.00 5.34
1580 1636 2.176546 CAAACATGAGCCGTGCGG 59.823 61.111 6.22 6.22 38.57 5.69
1581 1637 2.281484 AAACATGAGCCGTGCGGT 60.281 55.556 12.46 0.00 37.65 5.68
1582 1638 1.896660 AAACATGAGCCGTGCGGTT 60.897 52.632 12.46 6.04 37.65 4.44
1583 1639 2.128853 AAACATGAGCCGTGCGGTTG 62.129 55.000 12.46 7.72 37.65 3.77
1584 1640 4.465512 CATGAGCCGTGCGGTTGC 62.466 66.667 12.46 2.98 43.20 4.17
1629 1685 1.567357 ACAAAAAGTGGTGGCTGGTT 58.433 45.000 0.00 0.00 0.00 3.67
1688 1744 5.008217 TGGTTGTGTTCGAAAAATGTCCTAG 59.992 40.000 0.00 0.00 0.00 3.02
1734 1790 4.014406 TGCCTCACGAGTAATCTTGTAGA 58.986 43.478 0.00 0.00 36.62 2.59
1777 1833 5.914033 AGCTTGCTAGTTAACCGATCATTA 58.086 37.500 0.88 0.00 0.00 1.90
1871 1927 4.571580 ACCGTTCGATTTGTGTTGTCTTTA 59.428 37.500 0.00 0.00 0.00 1.85
1878 1934 9.574458 TTCGATTTGTGTTGTCTTTAATTTTCA 57.426 25.926 0.00 0.00 0.00 2.69
1882 1938 6.746104 TGTGTTGTCTTTAATTTTCATGCG 57.254 33.333 0.00 0.00 0.00 4.73
1904 1960 2.611751 CGGATGATTTGGCGTTGTCATA 59.388 45.455 0.00 0.00 31.86 2.15
1910 1966 1.141645 TTGGCGTTGTCATACGTGTC 58.858 50.000 0.00 0.00 43.22 3.67
1920 1976 5.456548 TGTCATACGTGTCAGACCTTTTA 57.543 39.130 0.00 0.00 0.00 1.52
1923 1979 7.255569 TGTCATACGTGTCAGACCTTTTATAG 58.744 38.462 0.00 0.00 0.00 1.31
1924 1980 7.094075 TGTCATACGTGTCAGACCTTTTATAGT 60.094 37.037 0.00 0.00 0.00 2.12
1925 1981 7.758528 GTCATACGTGTCAGACCTTTTATAGTT 59.241 37.037 0.00 0.00 0.00 2.24
1926 1982 8.308931 TCATACGTGTCAGACCTTTTATAGTTT 58.691 33.333 0.00 0.00 0.00 2.66
1927 1983 6.780706 ACGTGTCAGACCTTTTATAGTTTG 57.219 37.500 0.00 0.00 0.00 2.93
1928 1984 5.178809 ACGTGTCAGACCTTTTATAGTTTGC 59.821 40.000 0.00 0.00 0.00 3.68
1929 1985 5.618561 GTGTCAGACCTTTTATAGTTTGCG 58.381 41.667 0.00 0.00 0.00 4.85
1930 1986 4.693566 TGTCAGACCTTTTATAGTTTGCGG 59.306 41.667 0.00 0.00 0.00 5.69
1931 1987 4.694037 GTCAGACCTTTTATAGTTTGCGGT 59.306 41.667 0.00 0.00 0.00 5.68
1932 1988 4.933400 TCAGACCTTTTATAGTTTGCGGTC 59.067 41.667 0.00 0.00 39.68 4.79
1933 1989 4.094442 CAGACCTTTTATAGTTTGCGGTCC 59.906 45.833 0.00 0.00 40.11 4.46
1934 1990 3.004862 ACCTTTTATAGTTTGCGGTCCG 58.995 45.455 6.99 6.99 0.00 4.79
1935 1991 3.004862 CCTTTTATAGTTTGCGGTCCGT 58.995 45.455 13.94 0.00 0.00 4.69
1936 1992 3.437741 CCTTTTATAGTTTGCGGTCCGTT 59.562 43.478 13.94 0.00 0.00 4.44
1937 1993 4.399978 CTTTTATAGTTTGCGGTCCGTTG 58.600 43.478 13.94 0.00 0.00 4.10
1938 1994 2.747396 TATAGTTTGCGGTCCGTTGT 57.253 45.000 13.94 0.00 0.00 3.32
1939 1995 1.153353 ATAGTTTGCGGTCCGTTGTG 58.847 50.000 13.94 0.00 0.00 3.33
1940 1996 0.179078 TAGTTTGCGGTCCGTTGTGT 60.179 50.000 13.94 0.00 0.00 3.72
1941 1997 1.298041 GTTTGCGGTCCGTTGTGTG 60.298 57.895 13.94 0.00 0.00 3.82
1942 1998 1.745864 TTTGCGGTCCGTTGTGTGT 60.746 52.632 13.94 0.00 0.00 3.72
1943 1999 1.306642 TTTGCGGTCCGTTGTGTGTT 61.307 50.000 13.94 0.00 0.00 3.32
1944 2000 1.707239 TTGCGGTCCGTTGTGTGTTC 61.707 55.000 13.94 0.00 0.00 3.18
1945 2001 1.885850 GCGGTCCGTTGTGTGTTCT 60.886 57.895 13.94 0.00 0.00 3.01
1946 2002 0.598158 GCGGTCCGTTGTGTGTTCTA 60.598 55.000 13.94 0.00 0.00 2.10
1947 2003 1.415374 CGGTCCGTTGTGTGTTCTAG 58.585 55.000 2.08 0.00 0.00 2.43
1948 2004 1.792006 GGTCCGTTGTGTGTTCTAGG 58.208 55.000 0.00 0.00 0.00 3.02
1949 2005 1.145803 GTCCGTTGTGTGTTCTAGGC 58.854 55.000 0.00 0.00 0.00 3.93
1977 2033 3.142838 ATGCAACTGCGGCCCATC 61.143 61.111 0.00 0.00 45.83 3.51
2009 2065 0.390603 TGGGCCACGAAATAGTGTCG 60.391 55.000 0.00 0.00 44.10 4.35
2120 2176 0.533491 AAATACCACGAGCGGCAGTA 59.467 50.000 1.45 0.00 0.00 2.74
2126 2182 0.249073 CACGAGCGGCAGTATAGCTT 60.249 55.000 1.45 0.00 41.84 3.74
2133 2189 3.561725 AGCGGCAGTATAGCTTCATTTTC 59.438 43.478 1.45 0.00 38.13 2.29
2147 2203 7.765307 AGCTTCATTTTCCATATACAACAGTG 58.235 34.615 0.00 0.00 0.00 3.66
2151 2207 8.208718 TCATTTTCCATATACAACAGTGTAGC 57.791 34.615 0.00 0.00 43.42 3.58
2257 2313 6.051646 GTGAAAAGCACGACCTAGTTTTTA 57.948 37.500 0.00 0.00 37.83 1.52
2514 2608 2.993220 TCATGACCGTTTGATCTGTTCG 59.007 45.455 0.00 0.00 0.00 3.95
2567 2661 3.827551 TTTTCTCGCACGCGTCCGA 62.828 57.895 25.33 25.33 40.74 4.55
2717 2811 2.154798 TTGAGTTCGTCCCTGCCTCG 62.155 60.000 0.00 0.00 0.00 4.63
2724 2818 1.079750 GTCCCTGCCTCGTCAGTTC 60.080 63.158 0.00 0.00 32.32 3.01
2725 2819 2.266055 CCCTGCCTCGTCAGTTCC 59.734 66.667 0.00 0.00 32.32 3.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 8.699749 GTTTTGGAGCATAATTACTGTGTTTTC 58.300 33.333 0.00 0.00 0.00 2.29
74 75 7.523293 AATGACATTCATGGAAGTTGTTGTA 57.477 32.000 0.00 0.00 37.15 2.41
75 76 6.409524 AATGACATTCATGGAAGTTGTTGT 57.590 33.333 0.00 0.00 37.15 3.32
77 78 9.480053 CTTAAAATGACATTCATGGAAGTTGTT 57.520 29.630 0.05 0.00 37.15 2.83
80 81 8.526147 CCTCTTAAAATGACATTCATGGAAGTT 58.474 33.333 0.05 0.00 37.15 2.66
93 94 9.346725 GATCACAAAATGTCCTCTTAAAATGAC 57.653 33.333 0.00 0.00 0.00 3.06
105 106 6.202937 TGTTTTACGTGATCACAAAATGTCC 58.797 36.000 24.93 12.60 0.00 4.02
199 202 1.507562 TTTGAGCTCGCGATGAACAA 58.492 45.000 10.36 11.34 0.00 2.83
229 232 3.887716 ACTGCAAAAGTCATCTTCTGCTT 59.112 39.130 7.58 0.00 44.93 3.91
504 508 6.803807 GGCTTCATTAGTGTCACAGATTTTTC 59.196 38.462 5.62 0.00 0.00 2.29
580 589 8.958060 AGTATTCTGAGATTATAGGTGGCTTA 57.042 34.615 0.00 0.00 0.00 3.09
721 741 2.486982 GGCAGGCAGATATACAATGCTG 59.513 50.000 5.83 0.00 39.88 4.41
782 805 9.582431 TTTTTCGTAGATAAGTCTCATTAGTGG 57.418 33.333 0.00 0.00 35.04 4.00
894 917 9.013490 GTGAGCAACATTAATTTACTAGCATTG 57.987 33.333 0.00 0.00 0.00 2.82
903 926 5.536538 TGGTGTGGTGAGCAACATTAATTTA 59.463 36.000 0.00 0.00 30.15 1.40
957 985 1.136891 GGTGTCCTTGCTTTGTTGCTT 59.863 47.619 0.00 0.00 0.00 3.91
971 999 2.282701 TGTATTAACTCGCGGTGTCC 57.717 50.000 6.13 0.00 0.00 4.02
1087 1124 0.824109 TAGATCGGTTGTGGCTGAGG 59.176 55.000 0.00 0.00 0.00 3.86
1124 1161 2.755650 AGAAGTTGTCACCTGTTAGCG 58.244 47.619 0.00 0.00 0.00 4.26
1395 1436 4.508128 CCTGCGCCGACGTACCAT 62.508 66.667 4.18 0.00 42.83 3.55
1488 1533 4.041723 CGCGAAAAATGAACTTTTGGTCT 58.958 39.130 0.00 0.00 37.14 3.85
1519 1564 0.104120 AGCTTGTATGCGCCGTGATA 59.896 50.000 4.18 0.00 38.13 2.15
1579 1635 0.889186 AACACCAGATCACGGCAACC 60.889 55.000 0.00 0.00 0.00 3.77
1580 1636 0.238289 CAACACCAGATCACGGCAAC 59.762 55.000 0.00 0.00 0.00 4.17
1581 1637 0.179032 ACAACACCAGATCACGGCAA 60.179 50.000 0.00 0.00 0.00 4.52
1582 1638 0.682292 TACAACACCAGATCACGGCA 59.318 50.000 0.00 0.00 0.00 5.69
1583 1639 1.076332 GTACAACACCAGATCACGGC 58.924 55.000 0.00 0.00 0.00 5.68
1584 1640 2.448926 TGTACAACACCAGATCACGG 57.551 50.000 0.00 0.00 0.00 4.94
1585 1641 6.662414 ATATTTGTACAACACCAGATCACG 57.338 37.500 8.07 0.00 0.00 4.35
1586 1642 8.941977 TGTTATATTTGTACAACACCAGATCAC 58.058 33.333 8.07 0.00 0.00 3.06
1587 1643 9.508642 TTGTTATATTTGTACAACACCAGATCA 57.491 29.630 8.07 0.00 31.00 2.92
1629 1685 2.962421 CTGCCACCCTTTTTCCTTAACA 59.038 45.455 0.00 0.00 0.00 2.41
1688 1744 0.744771 CTTAGGAGGAAAGCACGGCC 60.745 60.000 0.00 0.00 0.00 6.13
1792 1848 7.828717 TCATCTAGATGTGAATTAGCAAAACCA 59.171 33.333 27.80 4.02 39.72 3.67
1871 1927 3.441496 AATCATCCGCGCATGAAAATT 57.559 38.095 17.99 4.02 36.36 1.82
1878 1934 2.723746 GCCAAATCATCCGCGCAT 59.276 55.556 8.75 0.00 0.00 4.73
1882 1938 0.523335 GACAACGCCAAATCATCCGC 60.523 55.000 0.00 0.00 0.00 5.54
1904 1960 5.178809 GCAAACTATAAAAGGTCTGACACGT 59.821 40.000 10.38 0.00 0.00 4.49
1910 1966 4.094442 GGACCGCAAACTATAAAAGGTCTG 59.906 45.833 10.90 0.00 44.26 3.51
1920 1976 1.153353 CACAACGGACCGCAAACTAT 58.847 50.000 15.39 0.00 0.00 2.12
1923 1979 1.298041 CACACAACGGACCGCAAAC 60.298 57.895 15.39 0.00 0.00 2.93
1924 1980 1.306642 AACACACAACGGACCGCAAA 61.307 50.000 15.39 0.00 0.00 3.68
1925 1981 1.707239 GAACACACAACGGACCGCAA 61.707 55.000 15.39 0.00 0.00 4.85
1926 1982 2.125065 AACACACAACGGACCGCA 60.125 55.556 15.39 0.00 0.00 5.69
1927 1983 0.598158 TAGAACACACAACGGACCGC 60.598 55.000 15.39 0.00 0.00 5.68
1928 1984 1.415374 CTAGAACACACAACGGACCG 58.585 55.000 13.61 13.61 0.00 4.79
1929 1985 1.792006 CCTAGAACACACAACGGACC 58.208 55.000 0.00 0.00 0.00 4.46
1930 1986 1.145803 GCCTAGAACACACAACGGAC 58.854 55.000 0.00 0.00 0.00 4.79
1931 1987 0.319211 CGCCTAGAACACACAACGGA 60.319 55.000 0.00 0.00 0.00 4.69
1932 1988 0.599204 ACGCCTAGAACACACAACGG 60.599 55.000 0.00 0.00 0.00 4.44
1933 1989 1.070843 CAACGCCTAGAACACACAACG 60.071 52.381 0.00 0.00 0.00 4.10
1934 1990 1.937899 ACAACGCCTAGAACACACAAC 59.062 47.619 0.00 0.00 0.00 3.32
1935 1991 1.937223 CACAACGCCTAGAACACACAA 59.063 47.619 0.00 0.00 0.00 3.33
1936 1992 1.134640 ACACAACGCCTAGAACACACA 60.135 47.619 0.00 0.00 0.00 3.72
1937 1993 1.578583 ACACAACGCCTAGAACACAC 58.421 50.000 0.00 0.00 0.00 3.82
1938 1994 2.319136 AACACAACGCCTAGAACACA 57.681 45.000 0.00 0.00 0.00 3.72
1939 1995 3.125316 TGTAACACAACGCCTAGAACAC 58.875 45.455 0.00 0.00 0.00 3.32
1940 1996 3.455990 TGTAACACAACGCCTAGAACA 57.544 42.857 0.00 0.00 0.00 3.18
1941 1997 3.424433 GCATGTAACACAACGCCTAGAAC 60.424 47.826 0.00 0.00 0.00 3.01
1942 1998 2.739913 GCATGTAACACAACGCCTAGAA 59.260 45.455 0.00 0.00 0.00 2.10
1943 1999 2.289133 TGCATGTAACACAACGCCTAGA 60.289 45.455 0.00 0.00 31.82 2.43
1944 2000 2.073056 TGCATGTAACACAACGCCTAG 58.927 47.619 0.00 0.00 31.82 3.02
1945 2001 2.171341 TGCATGTAACACAACGCCTA 57.829 45.000 0.00 0.00 31.82 3.93
1946 2002 1.001815 GTTGCATGTAACACAACGCCT 60.002 47.619 20.20 0.00 34.89 5.52
1947 2003 1.001815 AGTTGCATGTAACACAACGCC 60.002 47.619 25.60 0.00 46.41 5.68
1948 2004 2.043411 CAGTTGCATGTAACACAACGC 58.957 47.619 25.60 0.08 46.41 4.84
1949 2005 2.043411 GCAGTTGCATGTAACACAACG 58.957 47.619 25.60 12.59 46.41 4.10
1977 2033 2.050442 GCCCACGCCTTCAAAACG 60.050 61.111 0.00 0.00 0.00 3.60
1999 2055 1.202154 CGCGTCTCTCCGACACTATTT 60.202 52.381 0.00 0.00 42.98 1.40
2002 2058 2.747822 GCGCGTCTCTCCGACACTA 61.748 63.158 8.43 0.00 42.98 2.74
2009 2065 4.427661 AGTGCAGCGCGTCTCTCC 62.428 66.667 8.43 0.00 0.00 3.71
2024 2080 3.284617 ACGGGAAAAGTAAACAAGCAGT 58.715 40.909 0.00 0.00 0.00 4.40
2120 2176 9.632638 ACTGTTGTATATGGAAAATGAAGCTAT 57.367 29.630 0.00 0.00 0.00 2.97
2126 2182 8.046708 AGCTACACTGTTGTATATGGAAAATGA 58.953 33.333 0.00 0.00 37.58 2.57
2133 2189 8.718102 AACTAAAGCTACACTGTTGTATATGG 57.282 34.615 0.00 0.00 37.58 2.74
2142 2198 5.671493 ACTGACAAACTAAAGCTACACTGT 58.329 37.500 0.00 0.00 0.00 3.55
2257 2313 4.487714 ACACGGATGAATTGGTGACTAT 57.512 40.909 0.00 0.00 34.59 2.12
2431 2520 8.424133 AGAATGAGCAAACCTGTTTAAAAAGAT 58.576 29.630 6.98 0.00 0.00 2.40
2432 2521 7.781056 AGAATGAGCAAACCTGTTTAAAAAGA 58.219 30.769 6.98 0.00 0.00 2.52
2433 2522 7.706179 TGAGAATGAGCAAACCTGTTTAAAAAG 59.294 33.333 0.00 0.00 0.00 2.27
2438 2532 9.679661 TTATATGAGAATGAGCAAACCTGTTTA 57.320 29.630 0.00 0.00 0.00 2.01
2443 2537 8.985315 TCATTTATATGAGAATGAGCAAACCT 57.015 30.769 6.80 0.00 37.35 3.50
2636 2730 7.917720 AACAAAACAAAATATGACACCGTAC 57.082 32.000 0.00 0.00 0.00 3.67
2640 2734 9.705290 AGGATAAACAAAACAAAATATGACACC 57.295 29.630 0.00 0.00 0.00 4.16
2699 2793 2.636412 CGAGGCAGGGACGAACTCA 61.636 63.158 0.00 0.00 0.00 3.41
2705 2799 2.820767 GAACTGACGAGGCAGGGACG 62.821 65.000 11.04 0.00 40.20 4.79


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

AutoCloner maintained by Alex Coulton.