Multiple sequence alignment - TraesCS6A01G175500

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 TraesCS6A01G175500 chr6A 100.000 5238 0 0 1 5238 190742039 190736802 0.000000e+00 9673.0
1 TraesCS6A01G175500 chr6A 99.255 2550 18 1 2584 5132 190661533 190658984 0.000000e+00 4602.0
2 TraesCS6A01G175500 chr6A 99.098 2551 20 3 2584 5132 190688799 190686250 0.000000e+00 4580.0
3 TraesCS6A01G175500 chr6A 99.203 2134 12 4 1 2130 190690942 190688810 0.000000e+00 3842.0
4 TraesCS6A01G175500 chr6A 99.298 1853 12 1 1 1852 190663705 190661853 0.000000e+00 3349.0
5 TraesCS6A01G175500 chr6A 99.115 113 1 0 5126 5238 190658554 190658442 2.470000e-48 204.0
6 TraesCS6A01G175500 chr6A 98.230 113 2 0 5126 5238 190685832 190685720 1.150000e-46 198.0
7 TraesCS6A01G175500 chr6A 92.308 130 6 3 757 886 130415770 130415895 1.160000e-41 182.0
8 TraesCS6A01G175500 chr6A 97.753 89 2 0 3679 3767 258133155 258133067 2.530000e-33 154.0
9 TraesCS6A01G175500 chr6A 88.506 87 6 1 3727 3813 62810626 62810544 9.280000e-18 102.0
10 TraesCS6A01G175500 chr6A 97.917 48 1 0 3773 3820 190660390 190660343 3.360000e-12 84.2
11 TraesCS6A01G175500 chr6D 96.288 1751 36 8 1954 3687 152257373 152259111 0.000000e+00 2846.0
12 TraesCS6A01G175500 chr6D 96.200 1079 24 7 880 1957 152256280 152257342 0.000000e+00 1749.0
13 TraesCS6A01G175500 chr6D 97.279 588 13 2 181 766 152255641 152256227 0.000000e+00 994.0
14 TraesCS6A01G175500 chr6D 98.283 466 8 0 3810 4275 152259104 152259569 0.000000e+00 817.0
15 TraesCS6A01G175500 chr6D 100.000 59 0 0 5126 5184 152259842 152259900 5.550000e-20 110.0
16 TraesCS6A01G175500 chr6D 86.170 94 8 3 11 100 418629722 418629814 4.320000e-16 97.1
17 TraesCS6A01G175500 chr6D 100.000 28 0 0 179 206 454741305 454741278 9.000000e-03 52.8
18 TraesCS6A01G175500 chrUn 99.604 1009 2 1 2132 3140 451646885 451645879 0.000000e+00 1840.0
19 TraesCS6A01G175500 chrUn 98.237 397 6 1 4700 5095 479104263 479104659 0.000000e+00 693.0
20 TraesCS6A01G175500 chrUn 90.000 50 3 2 3764 3813 26701869 26701916 4.380000e-06 63.9
21 TraesCS6A01G175500 chr6B 96.875 1088 32 2 870 1957 276732222 276733307 0.000000e+00 1820.0
22 TraesCS6A01G175500 chr6B 95.666 923 14 4 2778 3684 276734766 276735678 0.000000e+00 1459.0
23 TraesCS6A01G175500 chr6B 90.000 880 48 15 4274 5132 532140266 532139406 0.000000e+00 1101.0
24 TraesCS6A01G175500 chr6B 95.784 593 15 3 181 766 276731634 276732223 0.000000e+00 948.0
25 TraesCS6A01G175500 chr6B 98.507 469 4 1 3810 4275 276735678 276736146 0.000000e+00 824.0
26 TraesCS6A01G175500 chr6B 96.791 187 5 1 1963 2148 276733600 276733786 1.420000e-80 311.0
27 TraesCS6A01G175500 chr6B 98.305 59 1 0 5126 5184 276736246 276736304 2.580000e-18 104.0
28 TraesCS6A01G175500 chr6B 92.308 52 4 0 5173 5224 143964652 143964703 2.020000e-09 75.0
29 TraesCS6A01G175500 chr3A 93.750 880 24 6 4274 5132 251369407 251368538 0.000000e+00 1291.0
30 TraesCS6A01G175500 chr3A 90.116 172 16 1 2369 2539 600921021 600920850 6.830000e-54 222.0
31 TraesCS6A01G175500 chr3A 86.364 176 22 2 870 1044 9129664 9129490 1.930000e-44 191.0
32 TraesCS6A01G175500 chr3A 90.647 139 5 6 735 871 713911018 713911150 1.500000e-40 178.0
33 TraesCS6A01G175500 chr3A 100.000 40 0 0 5185 5224 453737875 453737914 2.020000e-09 75.0
34 TraesCS6A01G175500 chr7A 92.614 880 33 18 4275 5132 534408804 534407935 0.000000e+00 1236.0
35 TraesCS6A01G175500 chr7A 91.473 129 9 1 634 760 671938885 671938757 5.390000e-40 176.0
36 TraesCS6A01G175500 chr7A 90.840 131 10 1 3683 3813 7041022 7041150 1.940000e-39 174.0
37 TraesCS6A01G175500 chr7A 94.444 54 0 3 3768 3820 42986167 42986116 4.350000e-11 80.5
38 TraesCS6A01G175500 chr1A 91.183 862 56 8 4273 5132 231644203 231643360 0.000000e+00 1153.0
39 TraesCS6A01G175500 chr1A 88.333 180 18 2 2373 2552 84012547 84012371 4.110000e-51 213.0
40 TraesCS6A01G175500 chr1A 91.228 57 3 2 5183 5238 432933001 432932946 5.620000e-10 76.8
41 TraesCS6A01G175500 chr7B 90.169 885 45 18 4269 5132 509508330 509509193 0.000000e+00 1114.0
42 TraesCS6A01G175500 chr7B 91.603 131 9 1 632 760 678657221 678657091 4.170000e-41 180.0
43 TraesCS6A01G175500 chr7B 83.495 103 12 3 2 100 504808301 504808402 2.010000e-14 91.6
44 TraesCS6A01G175500 chr4B 93.440 564 33 2 4570 5132 340551380 340550820 0.000000e+00 833.0
45 TraesCS6A01G175500 chr4B 86.525 141 15 4 3696 3832 136675230 136675370 9.090000e-33 152.0
46 TraesCS6A01G175500 chr4B 91.176 68 6 0 37 104 515827265 515827198 5.590000e-15 93.5
47 TraesCS6A01G175500 chr4B 82.692 104 13 3 1 100 604620659 604620761 2.600000e-13 87.9
48 TraesCS6A01G175500 chr4B 97.959 49 1 0 3773 3821 474386378 474386330 9.350000e-13 86.1
49 TraesCS6A01G175500 chr4D 81.064 808 92 29 4280 5051 495110694 495109912 5.840000e-164 588.0
50 TraesCS6A01G175500 chr4D 92.169 166 12 1 2373 2538 21147893 21147729 3.150000e-57 233.0
51 TraesCS6A01G175500 chr4D 91.411 163 14 0 2372 2534 75266910 75266748 1.900000e-54 224.0
52 TraesCS6A01G175500 chr4D 89.855 138 12 2 735 872 481177579 481177444 5.390000e-40 176.0
53 TraesCS6A01G175500 chr4D 88.750 80 9 0 5053 5132 495109873 495109794 1.200000e-16 99.0
54 TraesCS6A01G175500 chr1D 78.486 925 123 43 4273 5132 186715317 186716230 2.150000e-148 536.0
55 TraesCS6A01G175500 chr1D 94.681 94 4 1 3674 3767 318382786 318382878 1.520000e-30 145.0
56 TraesCS6A01G175500 chr7D 91.667 168 13 1 2371 2537 416234068 416234235 1.130000e-56 231.0
57 TraesCS6A01G175500 chr3D 89.535 172 18 0 2373 2544 187836308 187836479 8.830000e-53 219.0
58 TraesCS6A01G175500 chr5D 88.764 178 19 1 2360 2536 330893597 330893420 3.180000e-52 217.0
59 TraesCS6A01G175500 chr5D 92.000 125 8 1 632 754 13239763 13239887 1.940000e-39 174.0
60 TraesCS6A01G175500 chr5D 98.864 88 1 0 3680 3767 446918258 446918171 1.950000e-34 158.0
61 TraesCS6A01G175500 chr5B 97.436 117 3 0 755 871 278886870 278886986 3.200000e-47 200.0
62 TraesCS6A01G175500 chr5B 86.207 174 22 2 871 1043 28234959 28234787 2.490000e-43 187.0
63 TraesCS6A01G175500 chr5B 77.848 158 21 6 457 604 53220679 53220832 9.350000e-13 86.1
64 TraesCS6A01G175500 chr5B 95.833 48 2 0 5184 5231 661220028 661220075 1.560000e-10 78.7
65 TraesCS6A01G175500 chr2B 90.196 153 12 3 883 1033 236703604 236703453 4.140000e-46 196.0
66 TraesCS6A01G175500 chr2B 90.541 148 13 1 870 1017 384329260 384329406 1.490000e-45 195.0
67 TraesCS6A01G175500 chr2B 86.047 172 20 3 876 1046 636136726 636136894 1.160000e-41 182.0
68 TraesCS6A01G175500 chr2B 92.800 125 7 1 632 754 164025001 164025125 4.170000e-41 180.0
69 TraesCS6A01G175500 chr2B 100.000 45 0 0 5186 5230 369588894 369588938 3.360000e-12 84.2
70 TraesCS6A01G175500 chr4A 97.368 114 3 0 758 871 381221440 381221327 1.490000e-45 195.0
71 TraesCS6A01G175500 chr4A 91.603 131 9 1 632 760 166836881 166836751 4.170000e-41 180.0
72 TraesCS6A01G175500 chr1B 95.082 122 5 1 755 876 687253933 687254053 1.930000e-44 191.0
73 TraesCS6A01G175500 chr5A 91.111 135 9 3 765 896 6567664 6567798 4.170000e-41 180.0
74 TraesCS6A01G175500 chr5A 93.846 65 3 1 5175 5238 78918292 78918356 4.320000e-16 97.1
75 TraesCS6A01G175500 chr5A 82.692 104 8 8 2 98 48180956 48181056 3.360000e-12 84.2
76 TraesCS6A01G175500 chr2D 96.809 94 2 1 3674 3767 150380745 150380653 7.020000e-34 156.0
77 TraesCS6A01G175500 chr2D 92.453 106 6 2 3678 3782 100900316 100900212 3.270000e-32 150.0
78 TraesCS6A01G175500 chr2D 93.846 65 3 1 37 101 417546566 417546503 4.320000e-16 97.1
79 TraesCS6A01G175500 chr2D 82.857 105 15 3 1 103 568780597 568780494 2.010000e-14 91.6
80 TraesCS6A01G175500 chr2A 94.545 55 2 1 5185 5238 705050565 705050511 3.360000e-12 84.2
81 TraesCS6A01G175500 chr2A 84.416 77 7 5 3773 3845 607600077 607600002 2.620000e-08 71.3
82 TraesCS6A01G175500 chr2A 91.304 46 2 2 3764 3808 751214240 751214196 1.570000e-05 62.1


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 TraesCS6A01G175500 chr6A 190736802 190742039 5237 True 9673.000000 9673 100.000000 1 5238 1 chr6A.!!$R2 5237
1 TraesCS6A01G175500 chr6A 190685720 190690942 5222 True 2873.333333 4580 98.843667 1 5238 3 chr6A.!!$R5 5237
2 TraesCS6A01G175500 chr6A 190658442 190663705 5263 True 2059.800000 4602 98.896250 1 5238 4 chr6A.!!$R4 5237
3 TraesCS6A01G175500 chr6D 152255641 152259900 4259 False 1303.200000 2846 97.610000 181 5184 5 chr6D.!!$F2 5003
4 TraesCS6A01G175500 chrUn 451645879 451646885 1006 True 1840.000000 1840 99.604000 2132 3140 1 chrUn.!!$R1 1008
5 TraesCS6A01G175500 chr6B 532139406 532140266 860 True 1101.000000 1101 90.000000 4274 5132 1 chr6B.!!$R1 858
6 TraesCS6A01G175500 chr6B 276731634 276736304 4670 False 911.000000 1820 96.988000 181 5184 6 chr6B.!!$F2 5003
7 TraesCS6A01G175500 chr3A 251368538 251369407 869 True 1291.000000 1291 93.750000 4274 5132 1 chr3A.!!$R2 858
8 TraesCS6A01G175500 chr7A 534407935 534408804 869 True 1236.000000 1236 92.614000 4275 5132 1 chr7A.!!$R2 857
9 TraesCS6A01G175500 chr1A 231643360 231644203 843 True 1153.000000 1153 91.183000 4273 5132 1 chr1A.!!$R2 859
10 TraesCS6A01G175500 chr7B 509508330 509509193 863 False 1114.000000 1114 90.169000 4269 5132 1 chr7B.!!$F2 863
11 TraesCS6A01G175500 chr4B 340550820 340551380 560 True 833.000000 833 93.440000 4570 5132 1 chr4B.!!$R1 562
12 TraesCS6A01G175500 chr4D 495109794 495110694 900 True 343.500000 588 84.907000 4280 5132 2 chr4D.!!$R4 852
13 TraesCS6A01G175500 chr1D 186715317 186716230 913 False 536.000000 536 78.486000 4273 5132 1 chr1D.!!$F1 859

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
177 179 0.601558 TCTAAACGGTTCAGCGAGCT 59.398 50.000 5.23 0.0 0.00 4.09 F
745 755 7.278646 GCCAGAAACAGTCTTTTTGAATTTCTT 59.721 33.333 0.00 0.0 34.30 2.52 F
1269 1279 0.963355 TGCCAGGCGGTGAATAAACC 60.963 55.000 7.03 0.0 36.82 3.27 F
3085 3976 4.002982 GCACAGTATGAACTTGGATGTCA 58.997 43.478 0.00 0.0 39.69 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1269 1279 2.486982 CCATCTCTGCAACCACAAAGAG 59.513 50.000 0.0 0.0 37.99 2.85 R
3085 3976 5.071115 AGAGTGAAAACCTCAACTCTTAGCT 59.929 40.000 0.0 0.0 38.40 3.32 R
3230 4122 5.178797 ACTGAGGTGAAGAAATATTCCACG 58.821 41.667 0.0 0.0 0.00 4.94 R
4427 5338 2.915869 TGGTGGGACTTACCAGAATCT 58.084 47.619 0.0 0.0 43.00 2.40 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
177 179 0.601558 TCTAAACGGTTCAGCGAGCT 59.398 50.000 5.23 0.0 0.00 4.09
745 755 7.278646 GCCAGAAACAGTCTTTTTGAATTTCTT 59.721 33.333 0.00 0.0 34.30 2.52
1269 1279 0.963355 TGCCAGGCGGTGAATAAACC 60.963 55.000 7.03 0.0 36.82 3.27
2581 3471 4.588951 GGGTCAAAACCTCTTCAAAATCCT 59.411 41.667 0.00 0.0 45.66 3.24
2582 3472 5.070446 GGGTCAAAACCTCTTCAAAATCCTT 59.930 40.000 0.00 0.0 45.66 3.36
3085 3976 4.002982 GCACAGTATGAACTTGGATGTCA 58.997 43.478 0.00 0.0 39.69 3.58
3230 4122 8.753497 ATAGTTTCATTCCTTAGACCATTTCC 57.247 34.615 0.00 0.0 0.00 3.13
4187 5097 2.224354 GGTTTACGGTGGTTGAAGAGGA 60.224 50.000 0.00 0.0 0.00 3.71
4427 5338 8.421249 AAACATAGATTTTCACAGAATCCCAA 57.579 30.769 0.00 0.0 34.74 4.12
5029 6018 5.069781 TGCTACTTGGTGCTTGGTAATTTTT 59.930 36.000 0.00 0.0 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
204 206 2.606213 TCGATGTGGACTGGGCCA 60.606 61.111 5.85 5.85 35.02 5.36
745 755 8.446394 AGGAAGTAGTAGATAGTGCATACCTTA 58.554 37.037 0.00 0.00 0.00 2.69
1038 1048 2.914289 CAGAGGGGATGACAGGGC 59.086 66.667 0.00 0.00 0.00 5.19
1269 1279 2.486982 CCATCTCTGCAACCACAAAGAG 59.513 50.000 0.00 0.00 37.99 2.85
3085 3976 5.071115 AGAGTGAAAACCTCAACTCTTAGCT 59.929 40.000 0.00 0.00 38.40 3.32
3230 4122 5.178797 ACTGAGGTGAAGAAATATTCCACG 58.821 41.667 0.00 0.00 0.00 4.94
4187 5097 4.157840 GGGCTGTTTTTCGTAATCTCCAAT 59.842 41.667 0.00 0.00 0.00 3.16
4427 5338 2.915869 TGGTGGGACTTACCAGAATCT 58.084 47.619 0.00 0.00 43.00 2.40
5029 6018 4.687483 CGCATCTATTCATCAGCACATACA 59.313 41.667 0.00 0.00 0.00 2.29


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

AutoCloner maintained by Alex Coulton.