Multiple sequence alignment - TraesCS4A01G275800

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 TraesCS4A01G275800 chr4A 100.000 2840 0 0 1 2840 584678839 584681678 0.000000e+00 5245.0
1 TraesCS4A01G275800 chr4A 99.683 2840 9 0 1 2840 584736088 584733249 0.000000e+00 5195.0
2 TraesCS4A01G275800 chr4A 83.867 781 114 12 1067 1841 632944749 632943975 0.000000e+00 734.0
3 TraesCS4A01G275800 chr4A 93.023 86 6 0 716 801 17388752 17388837 2.970000e-25 126.0
4 TraesCS4A01G275800 chr4A 91.954 87 7 0 715 801 445063173 445063087 3.840000e-24 122.0
5 TraesCS4A01G275800 chr4A 87.097 93 10 2 710 801 715367471 715367562 1.390000e-18 104.0
6 TraesCS4A01G275800 chr4A 97.727 44 1 0 1 44 600468647 600468690 3.030000e-10 76.8
7 TraesCS4A01G275800 chr4D 93.698 1079 38 5 832 1881 15913248 15912171 0.000000e+00 1589.0
8 TraesCS4A01G275800 chr4D 91.770 486 27 8 188 664 15915475 15914994 0.000000e+00 664.0
9 TraesCS4A01G275800 chr4D 95.763 118 4 1 2379 2495 87364128 87364011 3.740000e-44 189.0
10 TraesCS4A01G275800 chr4D 89.655 116 12 0 832 947 15872669 15872554 6.340000e-32 148.0
11 TraesCS4A01G275800 chr4D 88.976 127 4 5 2598 2714 123334577 123334451 6.340000e-32 148.0
12 TraesCS4A01G275800 chr4D 83.146 89 4 2 2265 2342 123705852 123705764 1.410000e-08 71.3
13 TraesCS4A01G275800 chr4B 95.116 778 38 0 1067 1844 27251751 27252528 0.000000e+00 1227.0
14 TraesCS4A01G275800 chr4B 94.473 778 43 0 1067 1844 27519745 27518968 0.000000e+00 1199.0
15 TraesCS4A01G275800 chr4B 87.534 369 37 6 300 666 525517907 525517546 4.380000e-113 418.0
16 TraesCS4A01G275800 chr4B 86.000 300 9 4 799 1069 27520261 27519966 9.950000e-75 291.0
17 TraesCS4A01G275800 chr4B 90.000 220 21 1 2379 2597 564091757 564091976 1.670000e-72 283.0
18 TraesCS4A01G275800 chr4B 87.037 270 6 8 829 1069 27251388 27251657 7.750000e-71 278.0
19 TraesCS4A01G275800 chr4B 89.655 116 12 0 832 947 27396733 27396618 6.340000e-32 148.0
20 TraesCS4A01G275800 chr4B 89.412 85 9 0 717 801 25794977 25794893 1.080000e-19 108.0
21 TraesCS4A01G275800 chr4B 82.022 89 5 2 2265 2342 209304665 209304753 6.570000e-07 65.8
22 TraesCS4A01G275800 chr5B 85.861 778 104 6 1067 1841 560442213 560441439 0.000000e+00 822.0
23 TraesCS4A01G275800 chr5B 98.077 52 1 0 2207 2258 128681751 128681802 1.080000e-14 91.6
24 TraesCS4A01G275800 chr5B 98.077 52 1 0 2207 2258 128702315 128702366 1.080000e-14 91.6
25 TraesCS4A01G275800 chr5D 85.714 777 107 4 1067 1841 458095563 458094789 0.000000e+00 817.0
26 TraesCS4A01G275800 chr5D 83.505 776 124 4 1067 1840 458180827 458180054 0.000000e+00 721.0
27 TraesCS4A01G275800 chr5D 94.915 118 5 1 2379 2495 80064853 80064970 1.740000e-42 183.0
28 TraesCS4A01G275800 chr5A 85.586 777 108 4 1067 1841 575706812 575706038 0.000000e+00 811.0
29 TraesCS4A01G275800 chr5A 86.737 377 39 8 292 666 547492940 547492573 2.630000e-110 409.0
30 TraesCS4A01G275800 chr5A 94.915 118 5 1 2379 2495 157795229 157795346 1.740000e-42 183.0
31 TraesCS4A01G275800 chr5A 96.703 91 3 0 1884 1974 3326916 3327006 4.900000e-33 152.0
32 TraesCS4A01G275800 chr5A 96.739 92 1 2 1884 1974 569989625 569989715 4.900000e-33 152.0
33 TraesCS4A01G275800 chr5A 95.699 93 2 2 1884 1974 473306003 473306095 6.340000e-32 148.0
34 TraesCS4A01G275800 chr5A 86.087 115 16 0 833 947 576086004 576085890 1.070000e-24 124.0
35 TraesCS4A01G275800 chr5A 86.087 115 16 0 833 947 576271427 576271541 1.070000e-24 124.0
36 TraesCS4A01G275800 chr5A 90.476 84 8 0 718 801 177604934 177604851 8.320000e-21 111.0
37 TraesCS4A01G275800 chr5A 97.727 44 1 0 1 44 696989193 696989150 3.030000e-10 76.8
38 TraesCS4A01G275800 chr7A 89.559 431 36 6 238 666 698493900 698494323 3.220000e-149 538.0
39 TraesCS4A01G275800 chr7A 87.298 433 45 7 236 666 645528113 645528537 1.180000e-133 486.0
40 TraesCS4A01G275800 chr7A 95.699 93 2 2 1884 1974 690534414 690534322 6.340000e-32 148.0
41 TraesCS4A01G275800 chr7A 92.941 85 6 0 717 801 264847822 264847906 1.070000e-24 124.0
42 TraesCS4A01G275800 chr2A 88.222 433 42 6 236 666 675367911 675367486 2.520000e-140 508.0
43 TraesCS4A01G275800 chr2A 87.805 369 36 6 300 666 704436987 704436626 9.410000e-115 424.0
44 TraesCS4A01G275800 chr2A 91.954 87 7 0 715 801 394582836 394582922 3.840000e-24 122.0
45 TraesCS4A01G275800 chr2A 90.476 84 8 0 716 799 760634580 760634497 8.320000e-21 111.0
46 TraesCS4A01G275800 chr1A 87.558 434 43 8 236 666 425581129 425581554 2.540000e-135 492.0
47 TraesCS4A01G275800 chr1A 100.000 41 0 0 3 43 31314949 31314989 3.030000e-10 76.8
48 TraesCS4A01G275800 chr1A 100.000 41 0 0 3 43 553052367 553052407 3.030000e-10 76.8
49 TraesCS4A01G275800 chr1A 83.146 89 4 2 2265 2342 498686225 498686137 1.410000e-08 71.3
50 TraesCS4A01G275800 chr1A 82.955 88 4 2 2265 2341 22564449 22564536 5.080000e-08 69.4
51 TraesCS4A01G275800 chr6D 96.610 118 3 1 2379 2495 458950981 458951098 8.030000e-46 195.0
52 TraesCS4A01G275800 chr6D 90.551 127 2 5 2598 2714 124516630 124516504 2.930000e-35 159.0
53 TraesCS4A01G275800 chr6D 88.976 127 4 5 2598 2714 458897294 458897168 6.340000e-32 148.0
54 TraesCS4A01G275800 chr6D 93.939 66 2 2 2768 2832 108498347 108498283 6.480000e-17 99.0
55 TraesCS4A01G275800 chr6D 93.878 49 3 0 3 51 10798632 10798584 1.090000e-09 75.0
56 TraesCS4A01G275800 chrUn 96.460 113 3 1 2379 2490 217898055 217897943 4.830000e-43 185.0
57 TraesCS4A01G275800 chrUn 96.460 113 3 1 2379 2490 335930415 335930303 4.830000e-43 185.0
58 TraesCS4A01G275800 chrUn 90.551 127 2 5 2598 2714 326125499 326125373 2.930000e-35 159.0
59 TraesCS4A01G275800 chrUn 90.551 127 2 5 2598 2714 335371436 335371562 2.930000e-35 159.0
60 TraesCS4A01G275800 chrUn 90.551 127 2 5 2598 2714 413951680 413951554 2.930000e-35 159.0
61 TraesCS4A01G275800 chrUn 89.844 128 2 6 2598 2714 186209319 186209446 1.360000e-33 154.0
62 TraesCS4A01G275800 chrUn 95.161 62 2 1 2768 2828 86517622 86517683 2.330000e-16 97.1
63 TraesCS4A01G275800 chrUn 95.161 62 2 1 2768 2828 206785139 206785200 2.330000e-16 97.1
64 TraesCS4A01G275800 chrUn 95.161 62 2 1 2768 2828 301688359 301688420 2.330000e-16 97.1
65 TraesCS4A01G275800 chrUn 95.161 62 2 1 2768 2828 312173146 312173207 2.330000e-16 97.1
66 TraesCS4A01G275800 chrUn 95.161 62 2 1 2768 2828 345388161 345388100 2.330000e-16 97.1
67 TraesCS4A01G275800 chrUn 95.161 62 2 1 2768 2828 389106939 389106878 2.330000e-16 97.1
68 TraesCS4A01G275800 chrUn 83.146 89 4 2 2265 2342 186203418 186203330 1.410000e-08 71.3
69 TraesCS4A01G275800 chr6B 94.915 118 5 1 2379 2495 633605509 633605392 1.740000e-42 183.0
70 TraesCS4A01G275800 chr3B 91.339 127 1 5 2598 2714 797593827 797593953 6.290000e-37 165.0
71 TraesCS4A01G275800 chr1D 90.551 127 2 5 2598 2714 269405909 269405783 2.930000e-35 159.0
72 TraesCS4A01G275800 chr1D 89.764 127 2 6 2598 2714 43237891 43238016 4.900000e-33 152.0
73 TraesCS4A01G275800 chr1D 100.000 41 0 0 1 41 47645485 47645525 3.030000e-10 76.8
74 TraesCS4A01G275800 chr1D 95.652 46 1 1 3 48 408749045 408749001 3.920000e-09 73.1
75 TraesCS4A01G275800 chr3A 96.703 91 2 1 1884 1974 719340358 719340447 1.760000e-32 150.0
76 TraesCS4A01G275800 chr3A 96.703 91 2 1 1884 1974 719375311 719375400 1.760000e-32 150.0
77 TraesCS4A01G275800 chr3A 96.703 91 2 1 1885 1974 736938385 736938295 1.760000e-32 150.0
78 TraesCS4A01G275800 chr3A 91.954 87 7 0 715 801 16682902 16682816 3.840000e-24 122.0
79 TraesCS4A01G275800 chr3A 89.011 91 10 0 711 801 82242711 82242621 2.310000e-21 113.0
80 TraesCS4A01G275800 chr3A 88.043 92 9 2 710 801 653330505 653330594 1.080000e-19 108.0
81 TraesCS4A01G275800 chr3A 86.957 92 10 2 711 801 654059921 654060011 5.010000e-18 102.0
82 TraesCS4A01G275800 chr6A 95.652 92 3 1 1884 1974 234189647 234189738 2.280000e-31 147.0
83 TraesCS4A01G275800 chr6A 92.941 85 6 0 717 801 65065794 65065710 1.070000e-24 124.0
84 TraesCS4A01G275800 chr6A 90.588 85 8 0 717 801 332188132 332188048 2.310000e-21 113.0
85 TraesCS4A01G275800 chr6A 96.774 62 1 1 2768 2828 338459170 338459231 5.010000e-18 102.0
86 TraesCS4A01G275800 chr7B 88.800 125 4 3 2598 2712 47250809 47250685 8.200000e-31 145.0
87 TraesCS4A01G275800 chr7B 91.860 86 7 0 716 801 23007684 23007599 1.380000e-23 121.0
88 TraesCS4A01G275800 chr2B 92.857 84 6 0 718 801 779041410 779041493 3.840000e-24 122.0
89 TraesCS4A01G275800 chr1B 95.833 48 1 1 1 48 613025648 613025602 3.030000e-10 76.8
90 TraesCS4A01G275800 chr1B 100.000 29 0 0 2265 2293 667884620 667884648 1.000000e-03 54.7
91 TraesCS4A01G275800 chr7D 83.146 89 4 2 2265 2342 208640452 208640540 1.410000e-08 71.3
92 TraesCS4A01G275800 chr2D 83.146 89 4 2 2265 2342 115462207 115462295 1.410000e-08 71.3


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 TraesCS4A01G275800 chr4A 584678839 584681678 2839 False 5245.0 5245 100.0000 1 2840 1 chr4A.!!$F2 2839
1 TraesCS4A01G275800 chr4A 584733249 584736088 2839 True 5195.0 5195 99.6830 1 2840 1 chr4A.!!$R2 2839
2 TraesCS4A01G275800 chr4A 632943975 632944749 774 True 734.0 734 83.8670 1067 1841 1 chr4A.!!$R3 774
3 TraesCS4A01G275800 chr4D 15912171 15915475 3304 True 1126.5 1589 92.7340 188 1881 2 chr4D.!!$R5 1693
4 TraesCS4A01G275800 chr4B 27251388 27252528 1140 False 752.5 1227 91.0765 829 1844 2 chr4B.!!$F3 1015
5 TraesCS4A01G275800 chr4B 27518968 27520261 1293 True 745.0 1199 90.2365 799 1844 2 chr4B.!!$R4 1045
6 TraesCS4A01G275800 chr5B 560441439 560442213 774 True 822.0 822 85.8610 1067 1841 1 chr5B.!!$R1 774
7 TraesCS4A01G275800 chr5D 458094789 458095563 774 True 817.0 817 85.7140 1067 1841 1 chr5D.!!$R1 774
8 TraesCS4A01G275800 chr5D 458180054 458180827 773 True 721.0 721 83.5050 1067 1840 1 chr5D.!!$R2 773
9 TraesCS4A01G275800 chr5A 575706038 575706812 774 True 811.0 811 85.5860 1067 1841 1 chr5A.!!$R3 774

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
732 742 0.669077 CGAGTACTCCCTCCATTCGG 59.331 60.0 17.23 0.0 0.0 4.3 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2492 4339 2.379005 GTCTTGGGTGGAATGGAATCC 58.621 52.381 0.0 0.0 40.1 3.01 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
732 742 0.669077 CGAGTACTCCCTCCATTCGG 59.331 60.000 17.23 0.00 0.00 4.30
2014 3861 2.139382 AGAAAATCCCCCTGATCCCTC 58.861 52.381 0.00 0.00 31.61 4.30
2237 4084 1.125711 ACCCAACTCCAAGCCGTAGT 61.126 55.000 0.00 0.00 0.00 2.73
2469 4316 1.797025 AGTTCACCAGAAACGCTAGC 58.203 50.000 4.06 4.06 35.08 3.42
2492 4339 4.706842 ATATGCTTAACACAGGGTAGGG 57.293 45.455 0.00 0.00 0.00 3.53
2695 4542 8.767478 TTTCGTTACCGAGATATCTTTTCTTT 57.233 30.769 6.70 0.00 45.24 2.52
2769 4616 0.818296 ACTGGAATCCGAGGAGAACG 59.182 55.000 0.00 0.00 0.00 3.95
2772 4619 1.897133 TGGAATCCGAGGAGAACGAAA 59.103 47.619 0.00 0.00 0.00 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
732 742 6.074676 ACGTATATTTCCGCGACAAGTAATTC 60.075 38.462 8.23 0.00 0.00 2.17
2014 3861 4.908736 AGGAACGATTAATTGCAATCACG 58.091 39.130 13.38 16.74 35.09 4.35
2237 4084 5.255397 AGTAATCTGGTTGGGATTGAACA 57.745 39.130 0.00 0.00 35.40 3.18
2469 4316 5.280011 CCCCTACCCTGTGTTAAGCATATAG 60.280 48.000 0.00 0.00 0.00 1.31
2492 4339 2.379005 GTCTTGGGTGGAATGGAATCC 58.621 52.381 0.00 0.00 40.10 3.01
2769 4616 4.767409 ACCAACTGAGCTATTTCCCTTTTC 59.233 41.667 0.00 0.00 0.00 2.29
2772 4619 4.388577 AACCAACTGAGCTATTTCCCTT 57.611 40.909 0.00 0.00 0.00 3.95


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

AutoCloner maintained by Alex Coulton.