Multiple sequence alignment - TraesCS1D01G151200

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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 TraesCS1D01G151200 chr1D 100.000 2945 0 0 1 2945 209506646 209503702 0.000000e+00 5439.0
1 TraesCS1D01G151200 chr1D 94.649 1383 49 10 656 2035 219722088 219720728 0.000000e+00 2121.0
2 TraesCS1D01G151200 chr1D 86.616 792 53 19 3 744 219722825 219722037 0.000000e+00 826.0
3 TraesCS1D01G151200 chr1D 95.652 46 2 0 2370 2415 209504191 209504146 1.130000e-09 75.0
4 TraesCS1D01G151200 chr5B 95.768 2954 68 11 25 2945 203516670 203519599 0.000000e+00 4710.0
5 TraesCS1D01G151200 chr5B 94.833 1200 55 4 835 2032 668661299 668660105 0.000000e+00 1866.0
6 TraesCS1D01G151200 chr5B 92.969 256 14 4 2692 2945 247244333 247244586 1.290000e-98 370.0
7 TraesCS1D01G151200 chr2B 93.015 2663 106 23 13 2631 545000151 545002777 0.000000e+00 3814.0
8 TraesCS1D01G151200 chr2B 85.106 188 18 5 2413 2593 43626722 43626538 1.800000e-42 183.0
9 TraesCS1D01G151200 chr2A 93.110 2061 91 10 78 2107 610125789 610127829 0.000000e+00 2972.0
10 TraesCS1D01G151200 chr2A 92.300 2117 100 24 1 2107 524837264 524835201 0.000000e+00 2948.0
11 TraesCS1D01G151200 chr2A 90.000 550 42 8 6 543 73281992 73281444 0.000000e+00 699.0
12 TraesCS1D01G151200 chr2A 88.579 359 21 4 2136 2490 610160104 610160446 4.540000e-113 418.0
13 TraesCS1D01G151200 chr2A 93.061 245 11 1 2701 2945 524832706 524832468 1.300000e-93 353.0
14 TraesCS1D01G151200 chr2A 94.175 103 6 0 2257 2359 524835195 524835093 1.090000e-34 158.0
15 TraesCS1D01G151200 chr2A 92.381 105 8 0 2497 2601 610160420 610160524 1.830000e-32 150.0
16 TraesCS1D01G151200 chr2A 100.000 44 0 0 2097 2140 610127836 610127879 6.760000e-12 82.4
17 TraesCS1D01G151200 chr1B 93.302 1717 80 12 608 2303 59638315 59640017 0.000000e+00 2501.0
18 TraesCS1D01G151200 chr1B 88.228 773 58 14 1 744 342029298 342030066 0.000000e+00 893.0
19 TraesCS1D01G151200 chr1B 84.375 192 21 5 2407 2594 342031907 342032093 2.330000e-41 180.0
20 TraesCS1D01G151200 chr1B 89.231 130 11 1 2465 2594 428058303 428058177 3.040000e-35 159.0
21 TraesCS1D01G151200 chr1B 93.846 65 3 1 2300 2363 428058688 428058624 2.420000e-16 97.1
22 TraesCS1D01G151200 chr3B 88.943 2071 145 40 13 2035 456106882 456104848 0.000000e+00 2479.0
23 TraesCS1D01G151200 chr3B 92.847 1356 70 11 681 2032 650014599 650015931 0.000000e+00 1941.0
24 TraesCS1D01G151200 chr3B 92.537 67 4 1 2297 2362 650016084 650016150 8.690000e-16 95.3
25 TraesCS1D01G151200 chr4A 95.069 1379 59 4 656 2032 130453366 130454737 0.000000e+00 2161.0
26 TraesCS1D01G151200 chr4A 85.478 785 69 21 1 744 130452637 130453417 0.000000e+00 776.0
27 TraesCS1D01G151200 chr4A 90.351 114 8 1 2409 2519 130456568 130456455 2.370000e-31 147.0
28 TraesCS1D01G151200 chr7B 91.719 1594 59 12 608 2181 417608459 417606919 0.000000e+00 2145.0
29 TraesCS1D01G151200 chr7B 95.277 1355 57 6 681 2032 709841172 709842522 0.000000e+00 2141.0
30 TraesCS1D01G151200 chr6D 94.130 971 40 7 545 1508 55697528 55698488 0.000000e+00 1461.0
31 TraesCS1D01G151200 chr6D 92.683 451 13 5 1872 2303 55727435 55727884 1.490000e-177 632.0
32 TraesCS1D01G151200 chr6D 93.145 248 14 2 2701 2945 381184071 381183824 7.760000e-96 361.0
33 TraesCS1D01G151200 chr6D 82.305 243 8 11 2382 2590 381184491 381184250 8.390000e-41 178.0
34 TraesCS1D01G151200 chr4B 92.929 891 37 9 1733 2601 577159925 577159039 0.000000e+00 1273.0
35 TraesCS1D01G151200 chr5D 88.966 725 46 13 1 691 453975206 453975930 0.000000e+00 865.0
36 TraesCS1D01G151200 chr5D 85.912 795 58 21 1 744 540989423 540988632 0.000000e+00 798.0
37 TraesCS1D01G151200 chr5D 82.617 512 50 30 2465 2945 453979029 453978526 1.630000e-112 416.0
38 TraesCS1D01G151200 chr5D 84.127 189 18 5 2409 2593 540869526 540869706 3.900000e-39 172.0
39 TraesCS1D01G151200 chr5D 92.453 53 3 1 2360 2412 453979095 453979044 1.130000e-09 75.0
40 TraesCS1D01G151200 chr4D 92.460 557 33 5 1 550 9729052 9729606 0.000000e+00 787.0
41 TraesCS1D01G151200 chr4D 95.968 248 10 0 2698 2945 370058467 370058714 1.270000e-108 403.0
42 TraesCS1D01G151200 chr4D 91.892 74 3 3 2296 2366 370059838 370059765 1.870000e-17 100.0
43 TraesCS1D01G151200 chr4D 87.692 65 7 1 545 609 462680065 462680128 1.130000e-09 75.0
44 TraesCS1D01G151200 chr6A 86.649 734 54 16 1 691 352671725 352672457 0.000000e+00 773.0
45 TraesCS1D01G151200 chr6A 81.053 570 58 36 2407 2945 352806887 352806337 2.730000e-110 409.0
46 TraesCS1D01G151200 chr5A 86.620 710 59 15 1 677 544032182 544031476 0.000000e+00 752.0
47 TraesCS1D01G151200 chr7D 86.111 720 67 20 1 691 137856174 137856889 0.000000e+00 745.0
48 TraesCS1D01G151200 chr1A 89.748 556 44 8 1 543 374536053 374536608 0.000000e+00 699.0
49 TraesCS1D01G151200 chr1A 90.182 275 19 5 2676 2945 11914194 11914465 4.670000e-93 351.0
50 TraesCS1D01G151200 chr2D 92.040 402 25 2 545 940 460552749 460552349 2.560000e-155 558.0
51 TraesCS1D01G151200 chr3D 95.510 245 11 0 2701 2945 53984009 53983765 2.750000e-105 392.0
52 TraesCS1D01G151200 chr3D 81.690 213 23 7 545 744 143619823 143619614 2.350000e-36 163.0
53 TraesCS1D01G151200 chr6B 91.333 150 10 2 2445 2594 126610938 126610792 4.980000e-48 202.0
54 TraesCS1D01G151200 chr6B 88.235 136 5 6 2496 2625 633630528 633630658 5.080000e-33 152.0
55 TraesCS1D01G151200 chr6B 95.455 66 2 1 2302 2366 126611282 126611217 1.440000e-18 104.0
56 TraesCS1D01G151200 chr6B 100.000 28 0 0 2651 2678 633630653 633630680 5.000000e-03 52.8


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 TraesCS1D01G151200 chr1D 209503702 209506646 2944 True 2757.00 5439 97.826000 1 2945 2 chr1D.!!$R1 2944
1 TraesCS1D01G151200 chr1D 219720728 219722825 2097 True 1473.50 2121 90.632500 3 2035 2 chr1D.!!$R2 2032
2 TraesCS1D01G151200 chr5B 203516670 203519599 2929 False 4710.00 4710 95.768000 25 2945 1 chr5B.!!$F1 2920
3 TraesCS1D01G151200 chr5B 668660105 668661299 1194 True 1866.00 1866 94.833000 835 2032 1 chr5B.!!$R1 1197
4 TraesCS1D01G151200 chr2B 545000151 545002777 2626 False 3814.00 3814 93.015000 13 2631 1 chr2B.!!$F1 2618
5 TraesCS1D01G151200 chr2A 610125789 610127879 2090 False 1527.20 2972 96.555000 78 2140 2 chr2A.!!$F1 2062
6 TraesCS1D01G151200 chr2A 524832468 524837264 4796 True 1153.00 2948 93.178667 1 2945 3 chr2A.!!$R2 2944
7 TraesCS1D01G151200 chr2A 73281444 73281992 548 True 699.00 699 90.000000 6 543 1 chr2A.!!$R1 537
8 TraesCS1D01G151200 chr1B 59638315 59640017 1702 False 2501.00 2501 93.302000 608 2303 1 chr1B.!!$F1 1695
9 TraesCS1D01G151200 chr1B 342029298 342032093 2795 False 536.50 893 86.301500 1 2594 2 chr1B.!!$F2 2593
10 TraesCS1D01G151200 chr3B 456104848 456106882 2034 True 2479.00 2479 88.943000 13 2035 1 chr3B.!!$R1 2022
11 TraesCS1D01G151200 chr3B 650014599 650016150 1551 False 1018.15 1941 92.692000 681 2362 2 chr3B.!!$F1 1681
12 TraesCS1D01G151200 chr4A 130452637 130454737 2100 False 1468.50 2161 90.273500 1 2032 2 chr4A.!!$F1 2031
13 TraesCS1D01G151200 chr7B 417606919 417608459 1540 True 2145.00 2145 91.719000 608 2181 1 chr7B.!!$R1 1573
14 TraesCS1D01G151200 chr7B 709841172 709842522 1350 False 2141.00 2141 95.277000 681 2032 1 chr7B.!!$F1 1351
15 TraesCS1D01G151200 chr6D 55697528 55698488 960 False 1461.00 1461 94.130000 545 1508 1 chr6D.!!$F1 963
16 TraesCS1D01G151200 chr6D 381183824 381184491 667 True 269.50 361 87.725000 2382 2945 2 chr6D.!!$R1 563
17 TraesCS1D01G151200 chr4B 577159039 577159925 886 True 1273.00 1273 92.929000 1733 2601 1 chr4B.!!$R1 868
18 TraesCS1D01G151200 chr5D 453975206 453975930 724 False 865.00 865 88.966000 1 691 1 chr5D.!!$F1 690
19 TraesCS1D01G151200 chr5D 540988632 540989423 791 True 798.00 798 85.912000 1 744 1 chr5D.!!$R1 743
20 TraesCS1D01G151200 chr5D 453978526 453979095 569 True 245.50 416 87.535000 2360 2945 2 chr5D.!!$R2 585
21 TraesCS1D01G151200 chr4D 9729052 9729606 554 False 787.00 787 92.460000 1 550 1 chr4D.!!$F1 549
22 TraesCS1D01G151200 chr6A 352671725 352672457 732 False 773.00 773 86.649000 1 691 1 chr6A.!!$F1 690
23 TraesCS1D01G151200 chr6A 352806337 352806887 550 True 409.00 409 81.053000 2407 2945 1 chr6A.!!$R1 538
24 TraesCS1D01G151200 chr5A 544031476 544032182 706 True 752.00 752 86.620000 1 677 1 chr5A.!!$R1 676
25 TraesCS1D01G151200 chr7D 137856174 137856889 715 False 745.00 745 86.111000 1 691 1 chr7D.!!$F1 690
26 TraesCS1D01G151200 chr1A 374536053 374536608 555 False 699.00 699 89.748000 1 543 1 chr1A.!!$F2 542

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
837 1049 1.065600 CCACCCAACAACTTGCACG 59.934 57.895 0.0 0.0 0.0 5.34 F
1659 1897 1.209019 GAGAAGGAGCAGGCAATGAGA 59.791 52.381 0.0 0.0 0.0 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1879 2124 0.467290 TTGGTGGCCTCTTTGTGGTC 60.467 55.000 3.32 0.0 0.0 4.02 R
2825 5446 3.181513 CCAACATGAAGAAGATGCAGTCG 60.182 47.826 0.00 0.0 0.0 4.18 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
230 292 7.661847 GGCACTATAGGCAGAACTAATTATGTT 59.338 37.037 4.43 1.47 29.32 2.71
239 301 6.292381 GCAGAACTAATTATGTTAGCTCCACG 60.292 42.308 0.00 0.00 29.32 4.94
299 361 5.782047 CTGTTAGGATTAGGCAGAGAGATG 58.218 45.833 0.00 0.00 0.00 2.90
417 479 7.183460 AGTAGGTGTAGGTGTTCTAAGAGATT 58.817 38.462 0.00 0.00 0.00 2.40
773 985 1.271597 CCAGGTCCCCTTTCTCAACAG 60.272 57.143 0.00 0.00 0.00 3.16
837 1049 1.065600 CCACCCAACAACTTGCACG 59.934 57.895 0.00 0.00 0.00 5.34
959 1191 4.033709 CCCTTCTCTCCTCTGTCCAATAA 58.966 47.826 0.00 0.00 0.00 1.40
974 1206 2.025416 CCAATAACACCACCAGATCCCA 60.025 50.000 0.00 0.00 0.00 4.37
1220 1452 5.645056 TTAGATGTGGGCATGGATCTTTA 57.355 39.130 0.00 0.00 35.07 1.85
1540 1775 6.959639 AAAAACAAAGGCTCAGACAGAATA 57.040 33.333 0.00 0.00 0.00 1.75
1659 1897 1.209019 GAGAAGGAGCAGGCAATGAGA 59.791 52.381 0.00 0.00 0.00 3.27
1879 2124 5.601662 AGTACATGATTGGTGACCTATTCG 58.398 41.667 2.11 0.00 0.00 3.34
1952 2197 7.329962 GCTGAATGAATTTGATTGAATGTGTCA 59.670 33.333 0.00 0.00 0.00 3.58
1958 2205 9.978044 TGAATTTGATTGAATGTGTCATTGTAA 57.022 25.926 0.00 0.00 35.70 2.41
2255 2529 3.679389 ACTATAGTTGCTGCTGCTGTTT 58.321 40.909 17.00 2.88 40.48 2.83
2625 5015 8.579006 ACAACATCAATAAGACAACATCAACAT 58.421 29.630 0.00 0.00 0.00 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 5.121925 CCAGAAATCACAAGTGACATGAGAG 59.878 44.000 4.84 0.00 43.11 3.20
17 19 1.872952 CGCCAGAAATCACAAGTGACA 59.127 47.619 4.84 0.00 43.11 3.58
230 292 4.022242 GCATACTTATTCTCCGTGGAGCTA 60.022 45.833 11.17 2.30 41.71 3.32
444 507 1.069049 GAGCAAACAACCACAATGGCT 59.931 47.619 0.00 0.00 42.67 4.75
773 985 4.032703 TGCTTGCTTTTGAGTTCAGTTC 57.967 40.909 0.00 0.00 0.00 3.01
837 1049 3.198872 GTGGACCAAAGCTACATCTAGC 58.801 50.000 0.00 0.00 45.30 3.42
855 1067 2.124693 GTGGTGGTTGTGGTGGTGG 61.125 63.158 0.00 0.00 0.00 4.61
856 1068 2.124693 GGTGGTGGTTGTGGTGGTG 61.125 63.158 0.00 0.00 0.00 4.17
857 1069 2.277404 GGTGGTGGTTGTGGTGGT 59.723 61.111 0.00 0.00 0.00 4.16
865 1083 2.277404 GTGGTGGTGGTGGTGGTT 59.723 61.111 0.00 0.00 0.00 3.67
959 1191 1.561542 GAGAATGGGATCTGGTGGTGT 59.438 52.381 0.00 0.00 0.00 4.16
974 1206 4.774660 ACTGCTGGATGAAGATGAGAAT 57.225 40.909 0.00 0.00 0.00 2.40
1220 1452 2.139323 ATGCCACATGCTTCTCACAT 57.861 45.000 0.00 0.00 42.00 3.21
1540 1775 5.357878 TCAAGTTTTCTTCAGCACTCACAAT 59.642 36.000 0.00 0.00 38.17 2.71
1659 1897 2.586425 AGTTGTGTGCTGCCTAATTGT 58.414 42.857 0.00 0.00 0.00 2.71
1879 2124 0.467290 TTGGTGGCCTCTTTGTGGTC 60.467 55.000 3.32 0.00 0.00 4.02
2255 2529 8.474025 ACTTCAATTTGAGTTAACAACAATGGA 58.526 29.630 8.61 2.95 0.00 3.41
2303 2625 5.177881 CAGTTTGCAGCAAATTCAGCAATAA 59.822 36.000 23.26 0.00 45.23 1.40
2442 4727 9.778741 TTGTCAGATAACTAAATTCAGTCAACT 57.221 29.630 0.00 0.00 0.00 3.16
2625 5015 6.653020 ACTAAGTAAGTGGCAATGATGATGA 58.347 36.000 0.00 0.00 36.93 2.92
2825 5446 3.181513 CCAACATGAAGAAGATGCAGTCG 60.182 47.826 0.00 0.00 0.00 4.18
2826 5447 3.427233 GCCAACATGAAGAAGATGCAGTC 60.427 47.826 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.