Multiple sequence alignment - TraesCS5A01G179100

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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 TraesCS5A01G179100 chr5A 100.000 2120 0 0 1 2120 377125242 377123123 0.000000e+00 3916.0
1 TraesCS5A01G179100 chr5B 94.653 2132 92 12 1 2120 322864524 322862403 0.000000e+00 3286.0
2 TraesCS5A01G179100 chr5D 94.920 1634 73 10 488 2120 285252583 285250959 0.000000e+00 2549.0
3 TraesCS5A01G179100 chr5D 95.434 438 11 3 1 429 285253308 285252871 0.000000e+00 689.0
4 TraesCS5A01G179100 chr1D 96.078 51 2 0 1054 1104 453288109 453288159 1.350000e-12 84.2
5 TraesCS5A01G179100 chr1D 86.765 68 9 0 1054 1121 452898583 452898650 2.260000e-10 76.8
6 TraesCS5A01G179100 chr1A 96.078 51 2 0 1054 1104 547959127 547959177 1.350000e-12 84.2
7 TraesCS5A01G179100 chr1A 96.078 51 2 0 1054 1104 547978064 547978114 1.350000e-12 84.2
8 TraesCS5A01G179100 chr1A 85.294 68 10 0 1054 1121 547687372 547687305 1.050000e-08 71.3
9 TraesCS5A01G179100 chr3A 88.406 69 7 1 1053 1120 34580240 34580172 4.850000e-12 82.4
10 TraesCS5A01G179100 chr1B 86.567 67 9 0 1054 1120 623194814 623194748 8.110000e-10 75.0


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 TraesCS5A01G179100 chr5A 377123123 377125242 2119 True 3916 3916 100.000 1 2120 1 chr5A.!!$R1 2119
1 TraesCS5A01G179100 chr5B 322862403 322864524 2121 True 3286 3286 94.653 1 2120 1 chr5B.!!$R1 2119
2 TraesCS5A01G179100 chr5D 285250959 285253308 2349 True 1619 2549 95.177 1 2120 2 chr5D.!!$R1 2119

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
891 1136 0.473755 TCAACTGACACAGCCCACAT 59.526 50.0 0.0 0.0 34.37 3.21 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1889 2135 1.594331 ACGAGGAAGGCACTGTTTTC 58.406 50.0 0.0 0.0 40.86 2.29 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
118 125 5.048013 GGGAAAGGAAAACACTGATCGATTT 60.048 40.000 0.00 0.00 0.00 2.17
153 160 2.162338 TAACTGACGGGCAGGTTCGG 62.162 60.000 16.62 0.00 43.69 4.30
164 171 1.657094 GCAGGTTCGGTGTACATAACG 59.343 52.381 0.00 5.01 0.00 3.18
168 175 2.159057 GGTTCGGTGTACATAACGGGAT 60.159 50.000 14.64 0.00 0.00 3.85
276 292 7.842982 TGCATAACAAGTGGTAGTTGACTATA 58.157 34.615 3.59 0.00 32.96 1.31
377 393 2.308866 ACATTGGCTTAGTTAGGTGCCT 59.691 45.455 0.00 0.00 45.11 4.75
474 490 4.577693 CAGATACATGCTGTGCTTACCATT 59.422 41.667 0.00 0.00 0.00 3.16
559 804 5.314923 TGAGCTGTTTAATCCTTGAATGC 57.685 39.130 0.00 0.00 0.00 3.56
789 1034 5.606348 ACTCCAGGATCACATAAGACTTC 57.394 43.478 0.00 0.00 0.00 3.01
875 1120 3.194116 GGCATTGAAAGAAGCCTCATCAA 59.806 43.478 6.16 6.16 43.70 2.57
891 1136 0.473755 TCAACTGACACAGCCCACAT 59.526 50.000 0.00 0.00 34.37 3.21
897 1142 1.278985 TGACACAGCCCACATAGAAGG 59.721 52.381 0.00 0.00 0.00 3.46
911 1156 6.398918 CACATAGAAGGCGCCTATATAAACT 58.601 40.000 33.07 20.39 0.00 2.66
976 1222 2.692041 GGATTCCAAATCCAAGAGGCAG 59.308 50.000 12.74 0.00 38.09 4.85
988 1234 3.285484 CAAGAGGCAGCCACATTTCTAT 58.715 45.455 15.80 0.00 0.00 1.98
1251 1497 7.868415 GCTGTATATAACCTGTCAAAGTAGGAG 59.132 40.741 0.00 0.00 37.52 3.69
1265 1511 6.012508 TCAAAGTAGGAGGACTGGAAATGAAT 60.013 38.462 0.00 0.00 0.00 2.57
1377 1623 5.947503 TTTTGATGCGTGTTTGAGAAAAG 57.052 34.783 0.00 0.00 0.00 2.27
1387 1633 6.453791 GCGTGTTTGAGAAAAGAAAAGGAAAC 60.454 38.462 0.00 0.00 0.00 2.78
1392 1638 8.946085 GTTTGAGAAAAGAAAAGGAAACCAAAT 58.054 29.630 0.00 0.00 0.00 2.32
1396 1642 9.773328 GAGAAAAGAAAAGGAAACCAAATTTTG 57.227 29.630 1.99 1.99 0.00 2.44
1403 1649 2.948315 GGAAACCAAATTTTGCTTGGCA 59.052 40.909 3.50 0.00 46.20 4.92
1404 1650 3.569277 GGAAACCAAATTTTGCTTGGCAT 59.431 39.130 3.50 0.00 46.20 4.40
1405 1651 4.538917 GAAACCAAATTTTGCTTGGCATG 58.461 39.130 3.50 0.00 46.20 4.06
1406 1652 1.881324 ACCAAATTTTGCTTGGCATGC 59.119 42.857 17.62 17.62 46.20 4.06
1411 1657 0.321021 TTTTGCTTGGCATGCGGAAT 59.679 45.000 18.90 0.00 38.76 3.01
1413 1659 1.401761 TTGCTTGGCATGCGGAATAT 58.598 45.000 18.90 0.00 38.76 1.28
1414 1660 0.953727 TGCTTGGCATGCGGAATATC 59.046 50.000 18.90 0.00 31.71 1.63
1415 1661 0.953727 GCTTGGCATGCGGAATATCA 59.046 50.000 12.44 0.00 0.00 2.15
1416 1662 1.542915 GCTTGGCATGCGGAATATCAT 59.457 47.619 12.44 0.00 0.00 2.45
1417 1663 2.415090 GCTTGGCATGCGGAATATCATC 60.415 50.000 12.44 0.00 0.00 2.92
1420 1666 3.599343 TGGCATGCGGAATATCATCTAC 58.401 45.455 12.44 0.00 0.00 2.59
1422 1668 3.620374 GGCATGCGGAATATCATCTACTG 59.380 47.826 12.44 0.00 0.00 2.74
1428 1674 4.859798 GCGGAATATCATCTACTGTAGCAC 59.140 45.833 9.98 0.00 0.00 4.40
1429 1675 5.336055 GCGGAATATCATCTACTGTAGCACT 60.336 44.000 9.98 0.00 0.00 4.40
1486 1732 9.079833 CAACAGATTTGATATGGAATTTGTCAC 57.920 33.333 0.00 0.00 31.71 3.67
1490 1736 3.909732 TGATATGGAATTTGTCACCCCC 58.090 45.455 0.00 0.00 0.00 5.40
1518 1764 4.724279 AGTTGGTACCATTTCCAAGTCT 57.276 40.909 17.17 1.01 41.72 3.24
1545 1791 4.755411 CTGATGGCTTTTGATGCTTGATT 58.245 39.130 0.00 0.00 0.00 2.57
1571 1817 1.739466 TGCACCGATTTCTCTGAATGC 59.261 47.619 0.00 0.00 0.00 3.56
1576 1822 3.264947 CCGATTTCTCTGAATGCTCACA 58.735 45.455 0.00 0.00 0.00 3.58
1691 1937 1.020333 TTATGGGGTTTTCGACGCGG 61.020 55.000 12.47 0.00 41.82 6.46
1734 1980 3.199946 CAGTCTAATTGGCTTCCTACCCA 59.800 47.826 0.00 0.00 0.00 4.51
1777 2023 2.812609 CGAGCAGCAGACGCACAT 60.813 61.111 0.00 0.00 42.27 3.21
1811 2057 9.646427 GCTTGAGTACTCCAATAATATCCTAAG 57.354 37.037 20.11 12.20 0.00 2.18
2074 2321 5.757850 TGTTTGTGTTGGTTTTGCTTTTT 57.242 30.435 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
118 125 0.597568 GTTACATGTTGGCTGCTGCA 59.402 50.000 17.89 0.88 41.91 4.41
153 160 2.102588 AGCTCCATCCCGTTATGTACAC 59.897 50.000 0.00 0.00 0.00 2.90
164 171 2.158696 AGATGCAAGTAAGCTCCATCCC 60.159 50.000 0.00 0.00 34.35 3.85
168 175 3.423539 AACAGATGCAAGTAAGCTCCA 57.576 42.857 0.00 0.00 34.99 3.86
276 292 5.700402 ACAGGGCTATCACAATAACTTCT 57.300 39.130 0.00 0.00 0.00 2.85
292 308 2.163613 GCACCAATTACTTGTACAGGGC 59.836 50.000 10.04 0.00 0.00 5.19
377 393 5.813672 GGGATAACGTAAACAGAGCATGTAA 59.186 40.000 0.00 0.00 43.00 2.41
474 490 4.787551 AGGGTTGACATGAGTAACACAAA 58.212 39.130 0.00 0.00 30.30 2.83
789 1034 5.644644 GTCCATGTCTGCATAAAGAAAAGG 58.355 41.667 0.00 0.00 33.30 3.11
875 1120 1.644509 TCTATGTGGGCTGTGTCAGT 58.355 50.000 0.00 0.00 33.43 3.41
891 1136 6.718454 AGTACAGTTTATATAGGCGCCTTCTA 59.282 38.462 37.74 25.88 0.00 2.10
897 1142 7.810658 TGTAGTAGTACAGTTTATATAGGCGC 58.189 38.462 6.31 0.00 34.02 6.53
911 1156 6.767423 GGGTTTTTGGAGTTTGTAGTAGTACA 59.233 38.462 6.31 6.31 37.38 2.90
976 1222 8.789825 ATCTTCTGATGATATAGAAATGTGGC 57.210 34.615 4.39 0.00 32.96 5.01
1008 1254 0.532417 GCTTCAGATCATGAGCGCCT 60.532 55.000 2.29 0.00 39.68 5.52
1251 1497 2.827921 AGTTGCCATTCATTTCCAGTCC 59.172 45.455 0.00 0.00 0.00 3.85
1265 1511 3.318839 CCACATCAAGAAAGAAGTTGCCA 59.681 43.478 0.00 0.00 0.00 4.92
1363 1609 6.034577 GGTTTCCTTTTCTTTTCTCAAACACG 59.965 38.462 0.00 0.00 0.00 4.49
1369 1615 9.513906 AAAATTTGGTTTCCTTTTCTTTTCTCA 57.486 25.926 0.00 0.00 0.00 3.27
1387 1633 1.135916 CGCATGCCAAGCAAAATTTGG 60.136 47.619 13.15 0.00 43.62 3.28
1392 1638 0.321021 ATTCCGCATGCCAAGCAAAA 59.679 45.000 13.15 0.00 43.62 2.44
1396 1642 0.953727 TGATATTCCGCATGCCAAGC 59.046 50.000 13.15 0.00 0.00 4.01
1403 1649 5.185828 TGCTACAGTAGATGATATTCCGCAT 59.814 40.000 12.15 0.00 0.00 4.73
1404 1650 4.522789 TGCTACAGTAGATGATATTCCGCA 59.477 41.667 12.15 0.00 0.00 5.69
1405 1651 4.859798 GTGCTACAGTAGATGATATTCCGC 59.140 45.833 12.15 0.00 0.00 5.54
1406 1652 6.260870 AGTGCTACAGTAGATGATATTCCG 57.739 41.667 12.15 0.00 0.00 4.30
1411 1657 6.831868 TGTGGTAAGTGCTACAGTAGATGATA 59.168 38.462 12.15 0.00 31.45 2.15
1413 1659 5.014202 TGTGGTAAGTGCTACAGTAGATGA 58.986 41.667 12.15 0.00 31.45 2.92
1414 1660 5.324784 TGTGGTAAGTGCTACAGTAGATG 57.675 43.478 12.15 0.00 31.45 2.90
1415 1661 4.402793 CCTGTGGTAAGTGCTACAGTAGAT 59.597 45.833 12.15 0.00 43.55 1.98
1416 1662 3.762288 CCTGTGGTAAGTGCTACAGTAGA 59.238 47.826 12.15 0.00 43.55 2.59
1417 1663 3.510360 ACCTGTGGTAAGTGCTACAGTAG 59.490 47.826 10.96 2.85 43.55 2.57
1420 1666 2.688507 CACCTGTGGTAAGTGCTACAG 58.311 52.381 6.02 6.02 44.31 2.74
1428 1674 0.534877 TGCACTGCACCTGTGGTAAG 60.535 55.000 0.00 0.00 32.11 2.34
1429 1675 0.534877 CTGCACTGCACCTGTGGTAA 60.535 55.000 0.00 0.00 32.11 2.85
1486 1732 2.512056 TGGTACCAACTAATGATGGGGG 59.488 50.000 13.60 0.00 40.04 5.40
1490 1736 7.122650 ACTTGGAAATGGTACCAACTAATGATG 59.877 37.037 20.76 7.31 40.59 3.07
1518 1764 2.097036 CATCAAAAGCCATCAGCCTCA 58.903 47.619 0.00 0.00 45.47 3.86
1545 1791 3.055891 TCAGAGAAATCGGTGCATTGAGA 60.056 43.478 0.00 0.00 0.00 3.27
1571 1817 4.946772 TGATAAGAGGAGAGTGAGTGTGAG 59.053 45.833 0.00 0.00 0.00 3.51
1576 1822 5.186797 CAGGTTTGATAAGAGGAGAGTGAGT 59.813 44.000 0.00 0.00 0.00 3.41
1722 1968 5.731957 TTGTAATTTTTGGGTAGGAAGCC 57.268 39.130 0.00 0.00 44.02 4.35
1734 1980 6.031471 ACGCGTCTCTTGTTTTGTAATTTTT 58.969 32.000 5.58 0.00 0.00 1.94
1772 2018 5.523369 AGTACTCAAGCAAAGAAAATGTGC 58.477 37.500 0.00 0.00 38.59 4.57
1777 2023 6.959639 ATTGGAGTACTCAAGCAAAGAAAA 57.040 33.333 23.91 0.00 0.00 2.29
1811 2057 6.803807 ACTTTTGAGATCTTTTCTAATTGCGC 59.196 34.615 0.00 0.00 33.74 6.09
1889 2135 1.594331 ACGAGGAAGGCACTGTTTTC 58.406 50.000 0.00 0.00 40.86 2.29


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

AutoCloner maintained by Alex Coulton.