Multiple sequence alignment - TraesCS6D01G338600

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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 TraesCS6D01G338600 chr6D 100.000 2231 0 0 1 2231 438804104 438806334 0.000000e+00 4120
1 TraesCS6D01G338600 chr6D 91.304 621 34 8 1043 1653 438460898 438461508 0.000000e+00 830
2 TraesCS6D01G338600 chr6A 92.123 1333 61 21 927 2231 587563827 587565143 0.000000e+00 1840
3 TraesCS6D01G338600 chr6A 94.629 931 44 5 1 928 19886746 19885819 0.000000e+00 1437
4 TraesCS6D01G338600 chr6A 87.609 460 28 7 1043 1502 586877750 586878180 7.110000e-140 507
5 TraesCS6D01G338600 chr6A 88.578 429 32 10 1518 1934 587762629 587762206 2.560000e-139 505
6 TraesCS6D01G338600 chr6A 90.288 278 15 8 1474 1747 586878190 586878459 9.800000e-94 353
7 TraesCS6D01G338600 chr6A 78.298 235 28 13 2010 2230 587762158 587761933 1.800000e-26 130
8 TraesCS6D01G338600 chr6A 89.773 88 5 4 1690 1774 587700606 587700520 2.340000e-20 110
9 TraesCS6D01G338600 chr2D 96.228 928 33 2 1 927 587201929 587201003 0.000000e+00 1519
10 TraesCS6D01G338600 chr2D 95.187 935 36 4 1 929 10308616 10309547 0.000000e+00 1469
11 TraesCS6D01G338600 chr4B 95.577 927 39 2 1 927 339483789 339482865 0.000000e+00 1483
12 TraesCS6D01G338600 chr7A 95.274 931 39 4 1 928 408592853 408591925 0.000000e+00 1471
13 TraesCS6D01G338600 chr5D 95.187 935 36 5 1 928 537168585 537169517 0.000000e+00 1469
14 TraesCS6D01G338600 chr4A 94.839 930 42 5 1 927 90431716 90432642 0.000000e+00 1447
15 TraesCS6D01G338600 chr7B 94.737 931 41 7 1 929 2135361 2134437 0.000000e+00 1441
16 TraesCS6D01G338600 chr7B 94.720 928 47 2 1 928 66815942 66815017 0.000000e+00 1441
17 TraesCS6D01G338600 chr6B 90.909 1100 54 16 1156 2231 663840261 663841338 0.000000e+00 1435
18 TraesCS6D01G338600 chr6B 88.743 533 47 8 1043 1573 663800502 663801023 6.720000e-180 640
19 TraesCS6D01G338600 chr6B 88.591 149 16 1 927 1074 663800346 663800494 1.760000e-41 180


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 TraesCS6D01G338600 chr6D 438804104 438806334 2230 False 4120.0 4120 100.0000 1 2231 1 chr6D.!!$F2 2230
1 TraesCS6D01G338600 chr6D 438460898 438461508 610 False 830.0 830 91.3040 1043 1653 1 chr6D.!!$F1 610
2 TraesCS6D01G338600 chr6A 587563827 587565143 1316 False 1840.0 1840 92.1230 927 2231 1 chr6A.!!$F1 1304
3 TraesCS6D01G338600 chr6A 19885819 19886746 927 True 1437.0 1437 94.6290 1 928 1 chr6A.!!$R1 927
4 TraesCS6D01G338600 chr6A 586877750 586878459 709 False 430.0 507 88.9485 1043 1747 2 chr6A.!!$F2 704
5 TraesCS6D01G338600 chr6A 587761933 587762629 696 True 317.5 505 83.4380 1518 2230 2 chr6A.!!$R3 712
6 TraesCS6D01G338600 chr2D 587201003 587201929 926 True 1519.0 1519 96.2280 1 927 1 chr2D.!!$R1 926
7 TraesCS6D01G338600 chr2D 10308616 10309547 931 False 1469.0 1469 95.1870 1 929 1 chr2D.!!$F1 928
8 TraesCS6D01G338600 chr4B 339482865 339483789 924 True 1483.0 1483 95.5770 1 927 1 chr4B.!!$R1 926
9 TraesCS6D01G338600 chr7A 408591925 408592853 928 True 1471.0 1471 95.2740 1 928 1 chr7A.!!$R1 927
10 TraesCS6D01G338600 chr5D 537168585 537169517 932 False 1469.0 1469 95.1870 1 928 1 chr5D.!!$F1 927
11 TraesCS6D01G338600 chr4A 90431716 90432642 926 False 1447.0 1447 94.8390 1 927 1 chr4A.!!$F1 926
12 TraesCS6D01G338600 chr7B 2134437 2135361 924 True 1441.0 1441 94.7370 1 929 1 chr7B.!!$R1 928
13 TraesCS6D01G338600 chr7B 66815017 66815942 925 True 1441.0 1441 94.7200 1 928 1 chr7B.!!$R2 927
14 TraesCS6D01G338600 chr6B 663840261 663841338 1077 False 1435.0 1435 90.9090 1156 2231 1 chr6B.!!$F1 1075
15 TraesCS6D01G338600 chr6B 663800346 663801023 677 False 410.0 640 88.6670 927 1573 2 chr6B.!!$F2 646

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
462 471 0.163788 GACGACGATGGTGCTTGTTG 59.836 55.0 0.0 0.0 0.0 3.33 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1769 1884 0.811281 GCCCAAATCCTGAAGGTTCG 59.189 55.0 0.0 0.0 36.34 3.95 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
144 145 1.674057 CTTCTTGGAGGCACCGTCT 59.326 57.895 0.00 0.00 42.61 4.18
245 252 2.283676 TGGAGGGTCCCTGACGAC 60.284 66.667 17.72 0.00 35.03 4.34
373 382 2.101582 CAGCGCTACCCTTTGATCTACT 59.898 50.000 10.99 0.00 0.00 2.57
462 471 0.163788 GACGACGATGGTGCTTGTTG 59.836 55.000 0.00 0.00 0.00 3.33
681 690 4.430423 CACGAAGCTTGCGCGGTC 62.430 66.667 8.83 0.00 42.32 4.79
876 885 2.120312 TGTAATCCTGGCCGGTTGATA 58.880 47.619 11.58 0.00 0.00 2.15
877 886 2.708861 TGTAATCCTGGCCGGTTGATAT 59.291 45.455 11.58 1.65 0.00 1.63
942 951 1.318576 AAAAACGGAGGCTGAAGTGG 58.681 50.000 0.00 0.00 0.00 4.00
1057 1106 1.866601 CTGTGTGCTCGATTGTGAACA 59.133 47.619 0.00 0.00 0.00 3.18
1058 1107 1.866601 TGTGTGCTCGATTGTGAACAG 59.133 47.619 0.00 0.00 27.93 3.16
1059 1108 1.867233 GTGTGCTCGATTGTGAACAGT 59.133 47.619 0.00 0.00 27.93 3.55
1089 1138 0.318441 CTCCTGCCACTGACTCGAAA 59.682 55.000 0.00 0.00 0.00 3.46
1405 1464 6.620877 ACTGATGACTGACTTTATGGGTTA 57.379 37.500 0.00 0.00 0.00 2.85
1406 1465 6.407202 ACTGATGACTGACTTTATGGGTTAC 58.593 40.000 0.00 0.00 0.00 2.50
1407 1466 5.741011 TGATGACTGACTTTATGGGTTACC 58.259 41.667 0.00 0.00 37.24 2.85
1485 1554 6.461927 GGCATGGAAGATGCAATATTCTTGAA 60.462 38.462 5.04 0.00 43.75 2.69
1489 1558 8.296211 TGGAAGATGCAATATTCTTGAAATGA 57.704 30.769 5.04 0.00 43.75 2.57
1769 1884 3.446570 GCAGTCCATGGCAGGCAC 61.447 66.667 6.96 0.00 0.00 5.01
1851 1992 0.482446 TCCTTGGCTGGAACAATGGT 59.518 50.000 0.00 0.00 38.70 3.55
1890 2031 0.249699 TCACCGACGCAAATGTCAGT 60.250 50.000 0.00 0.00 38.84 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
359 368 5.360591 CAGCGATAAAGTAGATCAAAGGGT 58.639 41.667 0.00 0.00 0.00 4.34
360 369 4.212214 GCAGCGATAAAGTAGATCAAAGGG 59.788 45.833 0.00 0.00 0.00 3.95
373 382 1.094785 GCAAGGGAAGCAGCGATAAA 58.905 50.000 0.00 0.00 0.00 1.40
681 690 1.026718 GGTCTTGGGAGGAATGCACG 61.027 60.000 0.00 0.00 0.00 5.34
933 942 5.465051 GGAAAAGAGAAAATCCACTTCAGC 58.535 41.667 0.00 0.00 32.08 4.26
942 951 1.476891 GGGCGGGGAAAAGAGAAAATC 59.523 52.381 0.00 0.00 0.00 2.17
1089 1138 3.462021 GCAGCATATCTTCTTCTTCGGT 58.538 45.455 0.00 0.00 0.00 4.69
1405 1464 7.781324 ACACCAAGAAAATTTCTCATATGGT 57.219 32.000 18.89 18.89 44.12 3.55
1406 1465 8.306038 TGAACACCAAGAAAATTTCTCATATGG 58.694 33.333 17.86 17.86 39.61 2.74
1407 1466 9.865321 ATGAACACCAAGAAAATTTCTCATATG 57.135 29.630 8.86 7.91 39.61 1.78
1438 1497 1.999648 ACAAAGCAGAGATGGGCAAA 58.000 45.000 0.00 0.00 0.00 3.68
1769 1884 0.811281 GCCCAAATCCTGAAGGTTCG 59.189 55.000 0.00 0.00 36.34 3.95
1851 1992 4.175337 GGCGCAGGGCATGAGGTA 62.175 66.667 10.83 0.00 46.16 3.08
1890 2031 2.832129 GTGGTCTGAGGTGTATGAAGGA 59.168 50.000 0.00 0.00 0.00 3.36
1937 2078 1.746220 ACAACAAAGCGGCACTGTAAA 59.254 42.857 1.45 0.00 0.00 2.01
1977 2128 3.392285 AGGTACTCATGATGCCATTGCTA 59.608 43.478 0.00 0.00 38.71 3.49


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

AutoCloner maintained by Alex Coulton.