Multiple sequence alignment - TraesCS6D01G267000

Loading Multiple Alignment...

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 TraesCS6D01G267000 chr6D 100.000 2264 0 0 1 2264 377212207 377214470 0.000000e+00 4181
1 TraesCS6D01G267000 chr4D 97.124 1947 55 1 1 1946 470196636 470194690 0.000000e+00 3284
2 TraesCS6D01G267000 chr4D 84.262 305 39 7 1967 2264 470194623 470194321 2.850000e-74 289
3 TraesCS6D01G267000 chr4D 83.456 272 39 3 1979 2244 495818712 495818441 4.830000e-62 248
4 TraesCS6D01G267000 chr4D 81.379 290 43 7 1981 2262 495818441 495818727 2.260000e-55 226
5 TraesCS6D01G267000 chr7D 96.662 1947 63 2 1 1946 528561189 528563134 0.000000e+00 3234
6 TraesCS6D01G267000 chr7D 96.511 1949 66 2 1 1949 131689396 131691342 0.000000e+00 3221
7 TraesCS6D01G267000 chr7D 83.232 328 47 8 1940 2264 131691379 131691701 6.120000e-76 294
8 TraesCS6D01G267000 chr7D 82.051 273 46 3 1979 2250 131691684 131691414 1.750000e-56 230
9 TraesCS6D01G267000 chr2D 96.608 1946 65 1 1 1946 619853633 619855577 0.000000e+00 3227
10 TraesCS6D01G267000 chr3D 96.562 1949 58 3 1 1949 446922426 446924365 0.000000e+00 3219
11 TraesCS6D01G267000 chrUn 96.254 1949 70 3 1 1949 10399175 10401120 0.000000e+00 3192
12 TraesCS6D01G267000 chrUn 84.074 270 40 3 1982 2250 86409189 86408922 8.020000e-65 257
13 TraesCS6D01G267000 chr1D 95.023 1949 80 9 1 1948 446419310 446421242 0.000000e+00 3046
14 TraesCS6D01G267000 chr1B 94.513 1950 103 4 1 1949 571422402 571420456 0.000000e+00 3005
15 TraesCS6D01G267000 chr2B 94.513 1950 102 5 1 1949 454449227 454451172 0.000000e+00 3003
16 TraesCS6D01G267000 chr2A 86.646 322 39 4 1943 2263 770003186 770002868 9.950000e-94 353
17 TraesCS6D01G267000 chr6A 91.626 203 15 2 1940 2142 7031708 7031908 1.710000e-71 279
18 TraesCS6D01G267000 chr3B 83.333 270 36 7 1994 2261 420919097 420918835 8.080000e-60 241


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 TraesCS6D01G267000 chr6D 377212207 377214470 2263 False 4181.0 4181 100.0000 1 2264 1 chr6D.!!$F1 2263
1 TraesCS6D01G267000 chr4D 470194321 470196636 2315 True 1786.5 3284 90.6930 1 2264 2 chr4D.!!$R2 2263
2 TraesCS6D01G267000 chr7D 528561189 528563134 1945 False 3234.0 3234 96.6620 1 1946 1 chr7D.!!$F1 1945
3 TraesCS6D01G267000 chr7D 131689396 131691701 2305 False 1757.5 3221 89.8715 1 2264 2 chr7D.!!$F2 2263
4 TraesCS6D01G267000 chr2D 619853633 619855577 1944 False 3227.0 3227 96.6080 1 1946 1 chr2D.!!$F1 1945
5 TraesCS6D01G267000 chr3D 446922426 446924365 1939 False 3219.0 3219 96.5620 1 1949 1 chr3D.!!$F1 1948
6 TraesCS6D01G267000 chrUn 10399175 10401120 1945 False 3192.0 3192 96.2540 1 1949 1 chrUn.!!$F1 1948
7 TraesCS6D01G267000 chr1D 446419310 446421242 1932 False 3046.0 3046 95.0230 1 1948 1 chr1D.!!$F1 1947
8 TraesCS6D01G267000 chr1B 571420456 571422402 1946 True 3005.0 3005 94.5130 1 1949 1 chr1B.!!$R1 1948
9 TraesCS6D01G267000 chr2B 454449227 454451172 1945 False 3003.0 3003 94.5130 1 1949 1 chr2B.!!$F1 1948

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
608 609 0.163788 GTGGAGAATGCAACGACACG 59.836 55.0 0.0 0.0 39.09 4.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1963 2014 0.808755 GTTTGGTCCTACCGCCAATG 59.191 55.0 0.0 0.0 42.58 2.82 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
27 28 6.770746 ACGAGTACTTCCTAAAGCATTCTA 57.229 37.500 0.00 0.00 35.81 2.10
96 97 4.081752 GGGTTCATGATTGGTTGTTGCATA 60.082 41.667 0.00 0.00 0.00 3.14
383 384 1.327303 GAACAAGGTTGACATGGGCA 58.673 50.000 0.00 0.00 0.00 5.36
608 609 0.163788 GTGGAGAATGCAACGACACG 59.836 55.000 0.00 0.00 39.09 4.49
660 661 0.534203 AACCAACACGGGCACTAGTG 60.534 55.000 18.93 18.93 41.09 2.74
767 768 0.910088 GGACTAGCCTTGGAGGTGGT 60.910 60.000 0.00 0.00 37.80 4.16
1483 1486 2.757868 CGTCAGAAAGAGAGGATGGAGT 59.242 50.000 0.00 0.00 0.00 3.85
1624 1627 1.409661 GGAAATGGCCCCGTATGACTT 60.410 52.381 0.00 0.00 0.00 3.01
1682 1686 2.800629 CGGATGAAGCCATGCCAAATTC 60.801 50.000 0.00 0.00 37.79 2.17
1777 1781 7.592938 TGTATTGAATTTGGTGTGAAGATGTC 58.407 34.615 0.00 0.00 0.00 3.06
1789 1793 2.104622 TGAAGATGTCTGCAAGGTGTCA 59.895 45.455 0.00 0.00 0.00 3.58
1867 1873 1.425066 TGGTTGTGCTGGGAAGAGAAT 59.575 47.619 0.00 0.00 0.00 2.40
1961 2012 2.096819 TGCTGTGACGAAGAAACCAAAC 59.903 45.455 0.00 0.00 0.00 2.93
1963 2014 2.018515 TGTGACGAAGAAACCAAACCC 58.981 47.619 0.00 0.00 0.00 4.11
1965 2016 2.621526 GTGACGAAGAAACCAAACCCAT 59.378 45.455 0.00 0.00 0.00 4.00
1996 2048 1.674322 CAAACCCTACCGCCACAGG 60.674 63.158 0.00 0.00 37.30 4.00
2031 2083 2.682494 TGGACCCTACCGCCAGTC 60.682 66.667 0.00 0.00 0.00 3.51
2050 2102 3.087253 CCATGGCGGTAGGGGTGA 61.087 66.667 0.00 0.00 0.00 4.02
2067 2120 2.546789 GGTGACAAACCTTCTGTAACGG 59.453 50.000 0.00 0.00 46.55 4.44
2068 2121 3.200483 GTGACAAACCTTCTGTAACGGT 58.800 45.455 0.00 0.00 0.00 4.83
2073 2126 5.184711 ACAAACCTTCTGTAACGGTAAACA 58.815 37.500 0.00 0.00 0.00 2.83
2163 2219 2.334838 GGTGCTCGTGTTTCTCGTTAT 58.665 47.619 0.00 0.00 0.00 1.89
2203 2261 1.301623 CCATGGTTCCTGGCGGTAA 59.698 57.895 2.57 0.00 0.00 2.85
2224 2282 4.408821 CCAGCAGCCTACCGCCAA 62.409 66.667 0.00 0.00 38.78 4.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 0.827507 ATCCACTTGGCCGTGCTTTT 60.828 50.000 5.31 0.00 33.60 2.27
73 74 2.036992 TGCAACAACCAATCATGAACCC 59.963 45.455 0.00 0.00 0.00 4.11
144 145 7.276438 CGGCTCATCGATTTGATAGATCATTTA 59.724 37.037 0.00 0.00 36.56 1.40
383 384 0.253327 GGAAAGGATTGAGCCGAGGT 59.747 55.000 0.00 0.00 0.00 3.85
390 391 3.629087 AGGCATCAAGGAAAGGATTGAG 58.371 45.455 0.00 0.00 38.72 3.02
608 609 2.423538 GCATGTCCTAATGTTGTGTCCC 59.576 50.000 0.00 0.00 0.00 4.46
660 661 0.942884 GTCCTCCGTCCACGTGTTTC 60.943 60.000 15.65 3.40 37.74 2.78
767 768 2.669133 CCTTCCTCCATGGCCACGA 61.669 63.158 8.16 5.76 35.26 4.35
997 999 0.749454 GAACCGGATGAAGCCATGCT 60.749 55.000 9.46 0.00 42.56 3.79
1038 1041 0.883833 GTGGCATGTCTTCTTGGTGG 59.116 55.000 0.00 0.00 0.00 4.61
1483 1486 2.048222 CTCCTCGCGTTGCTTCCA 60.048 61.111 5.77 0.00 0.00 3.53
1682 1686 8.360390 TGCCTTAGTACTACATAGTTCATGATG 58.640 37.037 0.91 0.00 38.10 3.07
1777 1781 4.713824 ATTCATTCATGACACCTTGCAG 57.286 40.909 0.00 0.00 36.36 4.41
1789 1793 6.335471 TGCTGACAAACTGAATTCATTCAT 57.665 33.333 8.96 0.00 44.92 2.57
1847 1852 0.843309 TTCTCTTCCCAGCACAACCA 59.157 50.000 0.00 0.00 0.00 3.67
1867 1873 6.136857 AGCACTATGTTCTGTTCTATCCCTA 58.863 40.000 0.00 0.00 0.00 3.53
1961 2012 2.192175 GGTCCTACCGCCAATGGG 59.808 66.667 0.00 0.00 37.18 4.00
1963 2014 0.808755 GTTTGGTCCTACCGCCAATG 59.191 55.000 0.00 0.00 42.58 2.82
1965 2016 1.073548 GGTTTGGTCCTACCGCCAA 59.926 57.895 0.00 0.00 42.58 4.52
2048 2100 3.547054 ACCGTTACAGAAGGTTTGTCA 57.453 42.857 0.00 0.00 33.96 3.58
2050 2102 5.065090 GTGTTTACCGTTACAGAAGGTTTGT 59.935 40.000 0.00 0.00 39.31 2.83
2067 2120 2.332654 CCAGGGCGCTGGTGTTTAC 61.333 63.158 35.34 0.00 39.56 2.01
2068 2121 2.033448 CCAGGGCGCTGGTGTTTA 59.967 61.111 35.34 0.00 39.56 2.01
2192 2250 1.987855 CTGGACCTTACCGCCAGGA 60.988 63.158 0.00 0.00 44.24 3.86
2203 2261 3.077556 CGGTAGGCTGCTGGACCT 61.078 66.667 3.14 0.00 40.24 3.85
2230 2288 1.301954 GACCAAACCCTACCGCCAT 59.698 57.895 0.00 0.00 0.00 4.40


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

AutoCloner maintained by Alex Coulton.