Multiple sequence alignment - TraesCS3A01G105200

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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 TraesCS3A01G105200 chr3A 100.000 2507 0 0 1 2507 69054191 69056697 0.000000e+00 4630.0
1 TraesCS3A01G105200 chr3A 97.802 1683 31 3 1 1683 36135276 36133600 0.000000e+00 2898.0
2 TraesCS3A01G105200 chr3A 86.667 210 20 5 687 894 723146023 723146226 2.510000e-55 226.0
3 TraesCS3A01G105200 chr3A 92.188 128 9 1 488 614 723145456 723145583 1.980000e-41 180.0
4 TraesCS3A01G105200 chr3A 92.958 71 4 1 617 686 723145612 723145682 4.410000e-18 102.0
5 TraesCS3A01G105200 chr6A 96.211 1135 22 3 1 1120 77502211 77503339 0.000000e+00 1838.0
6 TraesCS3A01G105200 chr6A 94.076 422 21 3 1112 1532 77503771 77504189 2.720000e-179 638.0
7 TraesCS3A01G105200 chr6A 96.226 159 6 0 1526 1684 77509650 77509808 6.880000e-66 261.0
8 TraesCS3A01G105200 chr3D 91.478 575 19 12 1957 2507 60011318 60010750 0.000000e+00 763.0
9 TraesCS3A01G105200 chr3D 96.951 164 3 1 1689 1852 60011886 60011725 8.830000e-70 274.0
10 TraesCS3A01G105200 chr3D 82.727 110 9 5 1852 1961 60011445 60011346 3.430000e-14 89.8
11 TraesCS3A01G105200 chr3B 86.932 704 34 10 1852 2503 96062296 96062993 0.000000e+00 737.0
12 TraesCS3A01G105200 chr3B 89.733 487 37 6 1 479 460342784 460342303 5.930000e-171 610.0
13 TraesCS3A01G105200 chr3B 89.178 499 39 7 1 489 460324102 460323609 2.130000e-170 608.0
14 TraesCS3A01G105200 chr3B 89.200 500 36 14 1 490 550727275 550726784 2.130000e-170 608.0
15 TraesCS3A01G105200 chr3B 89.485 485 38 6 1 477 460336798 460336319 3.570000e-168 601.0
16 TraesCS3A01G105200 chr3B 88.330 497 44 7 1 489 460329901 460329411 3.590000e-163 584.0
17 TraesCS3A01G105200 chr3B 95.513 156 5 1 1695 1850 96061860 96062013 5.350000e-62 248.0
18 TraesCS3A01G105200 chr3B 85.377 212 23 7 687 894 460328797 460328590 1.950000e-51 213.0
19 TraesCS3A01G105200 chr3B 85.377 212 22 8 687 894 460341493 460341287 7.030000e-51 211.0
20 TraesCS3A01G105200 chr3B 84.906 212 23 8 687 894 460335511 460335305 3.270000e-49 206.0
21 TraesCS3A01G105200 chr3B 84.762 210 24 5 687 894 550726172 550725969 1.180000e-48 204.0
22 TraesCS3A01G105200 chr3B 90.625 128 11 1 488 614 460329362 460329235 4.290000e-38 169.0
23 TraesCS3A01G105200 chr3B 90.625 128 11 1 488 614 460336260 460336133 4.290000e-38 169.0
24 TraesCS3A01G105200 chr3B 90.625 128 11 1 488 614 460342242 460342115 4.290000e-38 169.0
25 TraesCS3A01G105200 chr3B 89.844 128 12 1 488 614 460323560 460323433 2.000000e-36 163.0
26 TraesCS3A01G105200 chr3B 84.167 120 18 1 1571 1690 658391227 658391345 5.670000e-22 115.0
27 TraesCS3A01G105200 chr3B 92.958 71 4 1 617 686 550726583 550726513 4.410000e-18 102.0
28 TraesCS3A01G105200 chr3B 85.393 89 13 0 1596 1684 129384429 129384517 2.660000e-15 93.5
29 TraesCS3A01G105200 chr3B 92.424 66 4 1 617 681 460323404 460323339 2.660000e-15 93.5
30 TraesCS3A01G105200 chrUn 90.323 496 34 8 1 487 96417679 96418169 2.720000e-179 638.0
31 TraesCS3A01G105200 chrUn 88.571 210 16 5 687 894 96427362 96427565 5.350000e-62 248.0
32 TraesCS3A01G105200 chrUn 91.057 123 10 1 493 614 96418225 96418347 5.550000e-37 165.0
33 TraesCS3A01G105200 chrUn 94.366 71 3 1 617 686 96418375 96418445 9.480000e-20 108.0
34 TraesCS3A01G105200 chr2D 89.485 485 38 9 1 477 295578207 295578686 3.570000e-168 601.0
35 TraesCS3A01G105200 chr2D 86.190 210 21 7 687 894 295579303 295579506 1.170000e-53 220.0
36 TraesCS3A01G105200 chr2D 90.625 128 11 1 488 614 295578742 295578869 4.290000e-38 169.0
37 TraesCS3A01G105200 chr2D 92.958 71 4 1 617 686 295578898 295578968 4.410000e-18 102.0
38 TraesCS3A01G105200 chr6D 78.673 633 96 24 1091 1686 227790297 227789667 3.910000e-103 385.0
39 TraesCS3A01G105200 chr2A 80.374 214 28 12 1487 1691 609731760 609731968 1.550000e-32 150.0
40 TraesCS3A01G105200 chr1B 83.784 111 17 1 1576 1685 303070458 303070348 1.230000e-18 104.0
41 TraesCS3A01G105200 chr5B 85.556 90 12 1 1598 1686 379853686 379853775 2.660000e-15 93.5
42 TraesCS3A01G105200 chr4B 84.211 95 12 3 1577 1670 175763554 175763462 3.430000e-14 89.8
43 TraesCS3A01G105200 chr4B 84.211 95 12 3 1577 1670 175900279 175900187 3.430000e-14 89.8
44 TraesCS3A01G105200 chr7B 82.474 97 17 0 1589 1685 179912261 179912165 4.440000e-13 86.1


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 TraesCS3A01G105200 chr3A 69054191 69056697 2506 False 4630.000000 4630 100.000000 1 2507 1 chr3A.!!$F1 2506
1 TraesCS3A01G105200 chr3A 36133600 36135276 1676 True 2898.000000 2898 97.802000 1 1683 1 chr3A.!!$R1 1682
2 TraesCS3A01G105200 chr6A 77502211 77504189 1978 False 1238.000000 1838 95.143500 1 1532 2 chr6A.!!$F2 1531
3 TraesCS3A01G105200 chr3D 60010750 60011886 1136 True 375.600000 763 90.385333 1689 2507 3 chr3D.!!$R1 818
4 TraesCS3A01G105200 chr3B 96061860 96062993 1133 False 492.500000 737 91.222500 1695 2503 2 chr3B.!!$F3 808
5 TraesCS3A01G105200 chr3B 460341287 460342784 1497 True 330.000000 610 88.578333 1 894 3 chr3B.!!$R4 893
6 TraesCS3A01G105200 chr3B 460335305 460336798 1493 True 325.333333 601 88.338667 1 894 3 chr3B.!!$R3 893
7 TraesCS3A01G105200 chr3B 460328590 460329901 1311 True 322.000000 584 88.110667 1 894 3 chr3B.!!$R2 893
8 TraesCS3A01G105200 chr3B 550725969 550727275 1306 True 304.666667 608 88.973333 1 894 3 chr3B.!!$R5 893
9 TraesCS3A01G105200 chr3B 460323339 460324102 763 True 288.166667 608 90.482000 1 681 3 chr3B.!!$R1 680
10 TraesCS3A01G105200 chrUn 96417679 96418445 766 False 303.666667 638 91.915333 1 686 3 chrUn.!!$F2 685
11 TraesCS3A01G105200 chr2D 295578207 295579506 1299 False 273.000000 601 89.814500 1 894 4 chr2D.!!$F1 893
12 TraesCS3A01G105200 chr6D 227789667 227790297 630 True 385.000000 385 78.673000 1091 1686 1 chr6D.!!$R1 595

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
601 679 5.161943 ACGAATTAAGTACTGAGCCCTTT 57.838 39.13 0.0 0.0 0.0 3.11 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1995 3432 0.383949 GAAAAGCAAGCCGGTGTTCA 59.616 50.0 1.9 0.0 38.91 3.18 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
138 143 9.816354 GGGAATGCTATAAGCTGAAAAATAAAA 57.184 29.630 0.03 0.00 42.97 1.52
601 679 5.161943 ACGAATTAAGTACTGAGCCCTTT 57.838 39.130 0.00 0.00 0.00 3.11
673 779 7.448748 ACATCCAACACAATTAGGAGTTAAC 57.551 36.000 0.00 0.00 32.91 2.01
1004 1648 4.163078 CAGTGGATACTTGAAGGAGATGGT 59.837 45.833 0.00 0.00 34.07 3.55
1174 2258 0.174389 GAAGCATGAGAGTCCTCGCA 59.826 55.000 0.00 3.20 43.19 5.10
1498 2611 4.508124 CGCTAGTTCGCTTCCATATTTCTT 59.492 41.667 0.00 0.00 0.00 2.52
1558 2677 2.103941 GAGGGATCTGGACCATGAGAAC 59.896 54.545 0.00 0.00 0.00 3.01
1769 2889 2.287915 GACAGCGTGTTCACACTTGAAT 59.712 45.455 14.67 0.00 43.72 2.57
1854 3258 3.627395 TGGTGACGAAAGATAGGCAAT 57.373 42.857 0.00 0.00 0.00 3.56
1866 3270 1.544724 TAGGCAATGTCACCCAAAGC 58.455 50.000 0.00 0.00 0.00 3.51
1872 3276 3.857010 GCAATGTCACCCAAAGCTAACAC 60.857 47.826 0.00 0.00 0.00 3.32
1902 3306 2.476185 GGAACGCACACACAAGATATGC 60.476 50.000 0.00 0.00 0.00 3.14
1911 3315 3.689161 CACACAAGATATGCCTCCGAAAA 59.311 43.478 0.00 0.00 0.00 2.29
1912 3316 3.689649 ACACAAGATATGCCTCCGAAAAC 59.310 43.478 0.00 0.00 0.00 2.43
1913 3317 3.941483 CACAAGATATGCCTCCGAAAACT 59.059 43.478 0.00 0.00 0.00 2.66
1914 3318 3.941483 ACAAGATATGCCTCCGAAAACTG 59.059 43.478 0.00 0.00 0.00 3.16
1915 3319 2.565841 AGATATGCCTCCGAAAACTGC 58.434 47.619 0.00 0.00 0.00 4.40
1916 3320 2.092968 AGATATGCCTCCGAAAACTGCA 60.093 45.455 0.00 0.00 36.23 4.41
1917 3321 2.418368 TATGCCTCCGAAAACTGCAT 57.582 45.000 0.00 0.00 44.28 3.96
1918 3322 2.418368 ATGCCTCCGAAAACTGCATA 57.582 45.000 0.00 0.00 40.62 3.14
1919 3323 1.737838 TGCCTCCGAAAACTGCATAG 58.262 50.000 0.00 0.00 0.00 2.23
1920 3324 1.277842 TGCCTCCGAAAACTGCATAGA 59.722 47.619 0.00 0.00 0.00 1.98
1921 3325 2.092968 TGCCTCCGAAAACTGCATAGAT 60.093 45.455 0.00 0.00 0.00 1.98
1922 3326 3.133901 TGCCTCCGAAAACTGCATAGATA 59.866 43.478 0.00 0.00 0.00 1.98
1958 3362 6.783708 ACCTAGCCTGATTATATACAGAGC 57.216 41.667 0.00 0.00 36.38 4.09
2001 3438 2.546321 CGCTGTCGCAGTGAACAC 59.454 61.111 13.02 0.00 43.78 3.32
2008 3445 2.639286 GCAGTGAACACCGGCTTG 59.361 61.111 0.00 0.00 31.79 4.01
2082 3519 1.297158 GAGTCATGCATGCGTTCGC 60.297 57.895 22.25 10.34 0.00 4.70
2090 3527 1.011904 CATGCGTTCGCTTCCATCG 60.012 57.895 17.63 0.00 0.00 3.84
2109 3546 1.142748 GGAGGTGGCAGTCATCGAG 59.857 63.158 0.00 0.00 0.00 4.04
2131 3568 1.544759 GGTAGTGGGGGTGACACAAAG 60.545 57.143 8.08 0.00 41.21 2.77
2302 3763 2.773661 TCCCCGGGATAAGAAAACTACC 59.226 50.000 26.32 0.00 0.00 3.18
2323 3784 0.750546 CCACTAGACATCGTCGGGGA 60.751 60.000 0.00 0.00 37.67 4.81
2324 3785 0.663688 CACTAGACATCGTCGGGGAG 59.336 60.000 0.00 0.00 37.67 4.30
2325 3786 0.465824 ACTAGACATCGTCGGGGAGG 60.466 60.000 0.00 0.00 37.67 4.30
2326 3787 0.179026 CTAGACATCGTCGGGGAGGA 60.179 60.000 0.00 0.00 37.67 3.71
2401 3875 0.878523 TTGCCGTGTCCTCAACTTCG 60.879 55.000 0.00 0.00 0.00 3.79
2425 3899 2.872370 GCTGTCAAGCCAACATGAATC 58.128 47.619 0.00 0.00 44.22 2.52
2429 3903 3.236816 GTCAAGCCAACATGAATCGTTG 58.763 45.455 0.00 0.00 42.73 4.10
2435 3909 3.181397 CCAACATGAATCGTTGCCAATC 58.819 45.455 0.00 0.00 41.94 2.67
2442 3916 3.435327 TGAATCGTTGCCAATCAGTACAC 59.565 43.478 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
673 779 2.679355 CACGTAATTGTGTGTGTGGG 57.321 50.000 0.00 0.0 35.12 4.61
1174 2258 2.282958 TGTCCGCCCTTCGAGTCT 60.283 61.111 0.00 0.0 41.67 3.24
1365 2460 1.152008 CCTCCCTACCCCATCTCCC 60.152 68.421 0.00 0.0 0.00 4.30
1498 2611 5.008316 CCAATGAAGCAATCGATCATTCTGA 59.992 40.000 7.97 0.0 40.75 3.27
1687 2807 9.994432 CCAAGAATTTCAGAAACATACTGTATC 57.006 33.333 0.00 0.0 36.81 2.24
1789 2909 5.045869 TCACCTCGTCATCCTCCTTTTAATT 60.046 40.000 0.00 0.0 0.00 1.40
1790 2910 4.469945 TCACCTCGTCATCCTCCTTTTAAT 59.530 41.667 0.00 0.0 0.00 1.40
1854 3258 2.092646 ACTGTGTTAGCTTTGGGTGACA 60.093 45.455 0.00 0.0 37.16 3.58
1900 3304 1.277842 TCTATGCAGTTTTCGGAGGCA 59.722 47.619 0.00 0.0 39.03 4.75
1902 3306 6.677781 TTTTATCTATGCAGTTTTCGGAGG 57.322 37.500 0.00 0.0 0.00 4.30
1911 3315 8.903820 GGTTAAGGTGATTTTTATCTATGCAGT 58.096 33.333 0.00 0.0 0.00 4.40
1912 3316 9.125026 AGGTTAAGGTGATTTTTATCTATGCAG 57.875 33.333 0.00 0.0 0.00 4.41
1916 3320 9.794719 GGCTAGGTTAAGGTGATTTTTATCTAT 57.205 33.333 0.00 0.0 0.00 1.98
1917 3321 8.999895 AGGCTAGGTTAAGGTGATTTTTATCTA 58.000 33.333 0.00 0.0 0.00 1.98
1918 3322 7.775561 CAGGCTAGGTTAAGGTGATTTTTATCT 59.224 37.037 0.00 0.0 0.00 1.98
1919 3323 7.773690 TCAGGCTAGGTTAAGGTGATTTTTATC 59.226 37.037 0.00 0.0 0.00 1.75
1920 3324 7.639378 TCAGGCTAGGTTAAGGTGATTTTTAT 58.361 34.615 0.00 0.0 0.00 1.40
1921 3325 7.023171 TCAGGCTAGGTTAAGGTGATTTTTA 57.977 36.000 0.00 0.0 0.00 1.52
1922 3326 5.887754 TCAGGCTAGGTTAAGGTGATTTTT 58.112 37.500 0.00 0.0 0.00 1.94
1958 3362 1.942586 GCCAAGGAATTTTGCTGGCTG 60.943 52.381 13.78 0.0 38.63 4.85
1995 3432 0.383949 GAAAAGCAAGCCGGTGTTCA 59.616 50.000 1.90 0.0 38.91 3.18
2001 3438 1.286880 CCAGTGAAAAGCAAGCCGG 59.713 57.895 0.00 0.0 0.00 6.13
2082 3519 2.190578 GCCACCTCCCGATGGAAG 59.809 66.667 0.00 0.0 41.17 3.46
2090 3527 2.187946 CGATGACTGCCACCTCCC 59.812 66.667 0.00 0.0 0.00 4.30
2109 3546 3.315949 TGTCACCCCCACTACCGC 61.316 66.667 0.00 0.0 0.00 5.68
2131 3568 2.665603 GCTCACCTCACCTCACCC 59.334 66.667 0.00 0.0 0.00 4.61
2302 3763 1.298413 CCGACGATGTCTAGTGGCG 60.298 63.158 0.00 0.0 0.00 5.69
2323 3784 1.761198 GTTACGTATGGCCTCCTTCCT 59.239 52.381 3.32 0.0 0.00 3.36
2324 3785 1.202615 GGTTACGTATGGCCTCCTTCC 60.203 57.143 3.32 0.0 0.00 3.46
2325 3786 1.483415 TGGTTACGTATGGCCTCCTTC 59.517 52.381 3.32 0.0 0.00 3.46
2326 3787 1.575419 TGGTTACGTATGGCCTCCTT 58.425 50.000 3.32 0.0 0.00 3.36
2401 3875 1.470098 CATGTTGGCTTGACAGCTACC 59.530 52.381 0.00 0.0 46.44 3.18
2425 3899 0.442310 CCGTGTACTGATTGGCAACG 59.558 55.000 0.00 0.0 42.51 4.10
2429 3903 0.391130 TGCTCCGTGTACTGATTGGC 60.391 55.000 0.00 0.0 0.00 4.52
2435 3909 1.630148 GTTAGCTGCTCCGTGTACTG 58.370 55.000 4.91 0.0 0.00 2.74
2442 3916 1.197721 CAGTTTTGGTTAGCTGCTCCG 59.802 52.381 4.91 0.0 0.00 4.63


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

AutoCloner maintained by Alex Coulton.