Multiple sequence alignment - TraesCS3D01G270600

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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 TraesCS3D01G270600 chr3D 100.000 2352 0 0 1 2352 375204576 375202225 0.000000e+00 4344.0
1 TraesCS3D01G270600 chr3B 91.289 861 35 16 25 871 489359498 489358664 0.000000e+00 1138.0
2 TraesCS3D01G270600 chr3B 90.291 618 22 10 915 1501 489358663 489358053 0.000000e+00 774.0
3 TraesCS3D01G270600 chr3A 89.987 769 25 15 766 1499 498237288 498236537 0.000000e+00 946.0
4 TraesCS3D01G270600 chr3A 86.446 332 13 12 127 436 498243634 498243313 3.750000e-88 335.0
5 TraesCS3D01G270600 chr3A 86.728 324 9 9 448 771 498243328 498243039 1.740000e-86 329.0
6 TraesCS3D01G270600 chr2B 89.084 742 74 5 1526 2263 382246217 382245479 0.000000e+00 915.0
7 TraesCS3D01G270600 chr5D 94.398 482 17 1 1500 1971 367989653 367989172 0.000000e+00 732.0
8 TraesCS3D01G270600 chr5D 93.279 491 23 1 1500 1980 106690090 106689600 0.000000e+00 715.0
9 TraesCS3D01G270600 chr5D 94.474 380 18 1 1973 2352 106689653 106689277 1.210000e-162 582.0
10 TraesCS3D01G270600 chr5D 95.783 332 14 0 1974 2305 367989215 367988884 9.570000e-149 536.0
11 TraesCS3D01G270600 chr2D 95.833 408 17 0 1898 2305 14399581 14399988 0.000000e+00 660.0
12 TraesCS3D01G270600 chr2D 93.466 352 13 1 1494 1835 14399232 14399583 4.480000e-142 514.0
13 TraesCS3D01G270600 chr2D 83.705 448 62 10 1498 1940 328337258 328336817 1.680000e-111 412.0
14 TraesCS3D01G270600 chr2D 92.000 250 20 0 1921 2170 328336725 328336476 3.720000e-93 351.0
15 TraesCS3D01G270600 chr2D 100.000 36 0 0 2315 2350 14399979 14400014 1.510000e-07 67.6
16 TraesCS3D01G270600 chr7D 89.106 358 24 5 1921 2263 5476317 5476674 4.640000e-117 431.0
17 TraesCS3D01G270600 chr7A 82.493 377 44 10 1500 1859 25704751 25704380 6.310000e-81 311.0
18 TraesCS3D01G270600 chr7A 81.481 378 48 15 1499 1859 545710281 545710653 8.220000e-75 291.0
19 TraesCS3D01G270600 chr7A 79.404 369 61 13 1500 1859 608533310 608533672 1.810000e-61 246.0
20 TraesCS3D01G270600 chr2A 81.890 381 49 12 1495 1859 41626831 41627207 1.060000e-78 303.0
21 TraesCS3D01G270600 chr2A 80.339 295 45 8 1499 1781 706901684 706901391 6.590000e-51 211.0
22 TraesCS3D01G270600 chrUn 80.272 294 46 7 1500 1781 68808824 68808531 6.590000e-51 211.0
23 TraesCS3D01G270600 chr1B 79.932 294 48 6 1500 1782 181309897 181309604 3.060000e-49 206.0
24 TraesCS3D01G270600 chr5B 93.671 79 5 0 2185 2263 686751754 686751676 4.110000e-23 119.0
25 TraesCS3D01G270600 chr5B 91.525 59 5 0 119 177 660665138 660665080 5.390000e-12 82.4
26 TraesCS3D01G270600 chr6B 88.312 77 7 1 123 199 86399913 86399839 8.950000e-15 91.6
27 TraesCS3D01G270600 chr5A 89.394 66 6 1 119 183 652993986 652993921 5.390000e-12 82.4
28 TraesCS3D01G270600 chr6A 83.721 86 10 2 121 206 48627136 48627055 6.970000e-11 78.7


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 TraesCS3D01G270600 chr3D 375202225 375204576 2351 True 4344.000000 4344 100.0000 1 2352 1 chr3D.!!$R1 2351
1 TraesCS3D01G270600 chr3B 489358053 489359498 1445 True 956.000000 1138 90.7900 25 1501 2 chr3B.!!$R1 1476
2 TraesCS3D01G270600 chr3A 498236537 498237288 751 True 946.000000 946 89.9870 766 1499 1 chr3A.!!$R1 733
3 TraesCS3D01G270600 chr3A 498243039 498243634 595 True 332.000000 335 86.5870 127 771 2 chr3A.!!$R2 644
4 TraesCS3D01G270600 chr2B 382245479 382246217 738 True 915.000000 915 89.0840 1526 2263 1 chr2B.!!$R1 737
5 TraesCS3D01G270600 chr5D 106689277 106690090 813 True 648.500000 715 93.8765 1500 2352 2 chr5D.!!$R1 852
6 TraesCS3D01G270600 chr5D 367988884 367989653 769 True 634.000000 732 95.0905 1500 2305 2 chr5D.!!$R2 805
7 TraesCS3D01G270600 chr2D 14399232 14400014 782 False 413.866667 660 96.4330 1494 2350 3 chr2D.!!$F1 856
8 TraesCS3D01G270600 chr2D 328336476 328337258 782 True 381.500000 412 87.8525 1498 2170 2 chr2D.!!$R1 672

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
908 948 0.247736 GTCAGGCACGTCTCTTCCAT 59.752 55.0 0.0 0.0 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1824 1918 1.645402 AATACCCTTGGCGGCCATCT 61.645 55.0 24.49 7.95 31.53 2.9 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
56 57 4.208686 CTACTGCCTCCCGCCGAC 62.209 72.222 0.00 0.0 36.24 4.79
63 64 4.712425 CTCCCGCCGACGTTCGTT 62.712 66.667 0.00 0.0 38.40 3.85
79 80 2.503331 TCGTTGTTGGTCTACCTCGTA 58.497 47.619 0.02 0.0 36.82 3.43
82 83 3.128242 CGTTGTTGGTCTACCTCGTATCT 59.872 47.826 0.02 0.0 36.82 1.98
113 114 4.386951 CCATGACGGTGCGGTGGA 62.387 66.667 0.00 0.0 32.64 4.02
118 119 2.125147 ACGGTGCGGTGGATCATG 60.125 61.111 0.00 0.0 0.00 3.07
125 126 0.464036 GCGGTGGATCATGGAGTACA 59.536 55.000 0.00 0.0 0.00 2.90
131 132 6.333416 CGGTGGATCATGGAGTACATATTAG 58.667 44.000 0.00 0.0 37.84 1.73
172 173 3.069158 GCCGGCTATTAGGTTGACTCTAA 59.931 47.826 22.15 0.0 0.00 2.10
179 180 9.998106 GGCTATTAGGTTGACTCTAAATGAATA 57.002 33.333 0.00 0.0 31.49 1.75
273 278 1.129811 CGGGTTAAACAATGGACGAGC 59.870 52.381 0.00 0.0 0.00 5.03
274 279 1.471287 GGGTTAAACAATGGACGAGCC 59.529 52.381 0.00 0.0 37.10 4.70
442 476 5.712917 ACAATTAACCCGGCTGATTCTAAAA 59.287 36.000 0.00 0.0 0.00 1.52
590 624 1.691434 GAGAGAATCAGGCCGGAGATT 59.309 52.381 12.27 15.3 37.82 2.40
742 782 1.267121 GGACTCTTGACCCAGTAGCA 58.733 55.000 0.00 0.0 0.00 3.49
743 783 1.205893 GGACTCTTGACCCAGTAGCAG 59.794 57.143 0.00 0.0 0.00 4.24
744 784 0.610687 ACTCTTGACCCAGTAGCAGC 59.389 55.000 0.00 0.0 0.00 5.25
745 785 0.610174 CTCTTGACCCAGTAGCAGCA 59.390 55.000 0.00 0.0 0.00 4.41
746 786 0.610174 TCTTGACCCAGTAGCAGCAG 59.390 55.000 0.00 0.0 0.00 4.24
747 787 1.003355 TTGACCCAGTAGCAGCAGC 60.003 57.895 0.00 0.0 42.56 5.25
896 936 4.704833 GCTTCCAGCGGTCAGGCA 62.705 66.667 0.00 0.0 34.64 4.75
903 943 4.057428 GCGGTCAGGCACGTCTCT 62.057 66.667 0.00 0.0 0.00 3.10
904 944 2.651361 CGGTCAGGCACGTCTCTT 59.349 61.111 0.00 0.0 0.00 2.85
905 945 1.444553 CGGTCAGGCACGTCTCTTC 60.445 63.158 0.00 0.0 0.00 2.87
906 946 1.079750 GGTCAGGCACGTCTCTTCC 60.080 63.158 0.00 0.0 0.00 3.46
907 947 1.666011 GTCAGGCACGTCTCTTCCA 59.334 57.895 0.00 0.0 0.00 3.53
908 948 0.247736 GTCAGGCACGTCTCTTCCAT 59.752 55.000 0.00 0.0 0.00 3.41
1009 1053 1.078848 GCTATAGCCATGCTCGGGG 60.079 63.158 14.13 0.0 40.44 5.73
1027 1071 1.304134 GGGAGAAACAATGGGCCGT 60.304 57.895 0.00 0.0 0.00 5.68
1652 1746 9.836864 ACTGCTACAATGAATAGTGATGAATAA 57.163 29.630 0.00 0.0 0.00 1.40
1824 1918 0.397187 TGCCACCGCCTGTAAAACTA 59.603 50.000 0.00 0.0 0.00 2.24
2004 2209 4.779733 GCCCTCTCCCCGACCTCA 62.780 72.222 0.00 0.0 0.00 3.86
2223 2428 2.563620 GACCTCTCTCCTCGTTTTCCTT 59.436 50.000 0.00 0.0 0.00 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 3.701604 CTCGGTGCAGGGTACGAGC 62.702 68.421 10.37 0.00 44.90 5.03
8 9 2.490217 CTCGGTGCAGGGTACGAG 59.510 66.667 9.31 9.31 45.34 4.18
9 10 3.755628 GCTCGGTGCAGGGTACGA 61.756 66.667 0.00 0.00 42.31 3.43
18 19 0.955919 AACCTTAGCTTGCTCGGTGC 60.956 55.000 14.38 0.00 43.25 5.01
19 20 1.464997 GAAACCTTAGCTTGCTCGGTG 59.535 52.381 14.38 0.28 0.00 4.94
20 21 1.348036 AGAAACCTTAGCTTGCTCGGT 59.652 47.619 9.69 9.69 0.00 4.69
21 22 2.100605 AGAAACCTTAGCTTGCTCGG 57.899 50.000 0.00 3.97 0.00 4.63
22 23 3.614616 CAGTAGAAACCTTAGCTTGCTCG 59.385 47.826 0.00 0.00 0.00 5.03
23 24 3.372514 GCAGTAGAAACCTTAGCTTGCTC 59.627 47.826 0.00 0.00 0.00 4.26
33 34 1.900545 GCGGGAGGCAGTAGAAACCT 61.901 60.000 0.00 0.00 42.87 3.50
56 57 2.056577 GAGGTAGACCAACAACGAACG 58.943 52.381 0.66 0.00 38.89 3.95
57 58 2.056577 CGAGGTAGACCAACAACGAAC 58.943 52.381 0.66 0.00 38.89 3.95
58 59 1.682854 ACGAGGTAGACCAACAACGAA 59.317 47.619 0.66 0.00 38.89 3.85
59 60 1.321474 ACGAGGTAGACCAACAACGA 58.679 50.000 0.66 0.00 38.89 3.85
60 61 2.995466 TACGAGGTAGACCAACAACG 57.005 50.000 0.66 0.00 38.89 4.10
61 62 4.715527 AGATACGAGGTAGACCAACAAC 57.284 45.455 0.66 0.00 38.89 3.32
62 63 4.525487 ACAAGATACGAGGTAGACCAACAA 59.475 41.667 0.66 0.00 38.89 2.83
63 64 4.082408 CACAAGATACGAGGTAGACCAACA 60.082 45.833 0.66 0.00 38.89 3.33
64 65 4.421948 CACAAGATACGAGGTAGACCAAC 58.578 47.826 0.66 0.00 38.89 3.77
65 66 3.446161 CCACAAGATACGAGGTAGACCAA 59.554 47.826 0.66 0.00 38.89 3.67
97 98 2.125147 ATCCACCGCACCGTCATG 60.125 61.111 0.00 0.00 0.00 3.07
98 99 1.971505 ATGATCCACCGCACCGTCAT 61.972 55.000 0.00 0.00 0.00 3.06
101 102 2.125147 CATGATCCACCGCACCGT 60.125 61.111 0.00 0.00 0.00 4.83
102 103 2.896854 CCATGATCCACCGCACCG 60.897 66.667 0.00 0.00 0.00 4.94
105 106 0.464036 GTACTCCATGATCCACCGCA 59.536 55.000 0.00 0.00 0.00 5.69
108 109 7.482169 TCTAATATGTACTCCATGATCCACC 57.518 40.000 0.00 0.00 34.86 4.61
131 132 5.503520 GCCGGCATGTACAGTAGTAAATTTC 60.504 44.000 24.80 0.00 30.67 2.17
243 247 5.861787 CCATTGTTTAACCCGAGTGAATTTC 59.138 40.000 0.00 0.00 0.00 2.17
248 252 3.404899 GTCCATTGTTTAACCCGAGTGA 58.595 45.455 0.00 0.00 0.00 3.41
446 480 4.277476 TGATTGATCAGCCGGGTTAATTT 58.723 39.130 1.64 0.00 32.11 1.82
460 494 4.333649 TCCGTTTCTGCAATCTGATTGATC 59.666 41.667 29.34 15.54 42.83 2.92
590 624 1.828595 ACATAGTGTGTACCCGCATCA 59.171 47.619 0.00 0.00 39.91 3.07
738 778 0.946528 CAAATATGCCGCTGCTGCTA 59.053 50.000 16.81 7.47 38.71 3.49
742 782 0.394216 TGGTCAAATATGCCGCTGCT 60.394 50.000 0.70 0.00 38.71 4.24
743 783 0.029834 CTGGTCAAATATGCCGCTGC 59.970 55.000 0.00 0.00 38.26 5.25
744 784 0.664761 CCTGGTCAAATATGCCGCTG 59.335 55.000 0.00 0.00 0.00 5.18
745 785 0.546122 TCCTGGTCAAATATGCCGCT 59.454 50.000 0.00 0.00 0.00 5.52
746 786 1.065551 GTTCCTGGTCAAATATGCCGC 59.934 52.381 0.00 0.00 0.00 6.53
747 787 1.330521 CGTTCCTGGTCAAATATGCCG 59.669 52.381 0.00 0.00 0.00 5.69
748 788 2.614057 CTCGTTCCTGGTCAAATATGCC 59.386 50.000 0.00 0.00 0.00 4.40
749 789 2.614057 CCTCGTTCCTGGTCAAATATGC 59.386 50.000 0.00 0.00 0.00 3.14
750 790 4.137116 TCCTCGTTCCTGGTCAAATATG 57.863 45.455 0.00 0.00 0.00 1.78
888 928 1.079750 GGAAGAGACGTGCCTGACC 60.080 63.158 0.00 0.00 0.00 4.02
896 936 2.105821 TGGTTGGAAATGGAAGAGACGT 59.894 45.455 0.00 0.00 0.00 4.34
903 943 3.304911 TGTGACTGGTTGGAAATGGAA 57.695 42.857 0.00 0.00 0.00 3.53
904 944 2.955660 GTTGTGACTGGTTGGAAATGGA 59.044 45.455 0.00 0.00 0.00 3.41
905 945 2.958355 AGTTGTGACTGGTTGGAAATGG 59.042 45.455 0.00 0.00 33.99 3.16
906 946 3.303990 CGAGTTGTGACTGGTTGGAAATG 60.304 47.826 0.00 0.00 35.88 2.32
907 947 2.878406 CGAGTTGTGACTGGTTGGAAAT 59.122 45.455 0.00 0.00 35.88 2.17
908 948 2.285083 CGAGTTGTGACTGGTTGGAAA 58.715 47.619 0.00 0.00 35.88 3.13
990 1034 1.446792 CCCGAGCATGGCTATAGCG 60.447 63.158 18.30 6.21 39.88 4.26
1009 1053 1.304134 ACGGCCCATTGTTTCTCCC 60.304 57.895 0.00 0.00 0.00 4.30
1113 1157 3.671411 ACGACGAACTGCGAGGCT 61.671 61.111 0.00 0.00 44.57 4.58
1116 1160 2.710971 CTGCACGACGAACTGCGAG 61.711 63.158 0.00 0.00 44.57 5.03
1148 1192 2.432444 AGATCGATCGAGGAGGTGATC 58.568 52.381 23.84 12.93 38.08 2.92
1152 1196 3.210232 TGTTAGATCGATCGAGGAGGT 57.790 47.619 23.84 5.85 0.00 3.85
1652 1746 7.227512 CAGTAAGAAAAATCGAATGGAGGCTAT 59.772 37.037 0.00 0.00 0.00 2.97
1824 1918 1.645402 AATACCCTTGGCGGCCATCT 61.645 55.000 24.49 7.95 31.53 2.90


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

AutoCloner maintained by Alex Coulton.