Multiple sequence alignment - TraesCS5B01G451700

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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 TraesCS5B01G451700 chr5B 100.000 7856 0 0 1 7856 623166065 623173920 0.000000e+00 14508.0
1 TraesCS5B01G451700 chr5B 99.440 7856 34 3 1 7856 626837041 626844886 0.000000e+00 14255.0
2 TraesCS5B01G451700 chr5B 96.072 2342 70 4 218 2559 628693680 628695999 0.000000e+00 3795.0
3 TraesCS5B01G451700 chr5B 95.524 2346 79 8 218 2559 625114127 625116450 0.000000e+00 3727.0
4 TraesCS5B01G451700 chr5B 92.669 2578 126 22 1 2559 629894681 629897214 0.000000e+00 3655.0
5 TraesCS5B01G451700 chr5B 96.368 1955 55 6 5199 7138 629897205 629899158 0.000000e+00 3203.0
6 TraesCS5B01G451700 chr5B 96.435 1683 58 2 5418 7099 625117263 625118944 0.000000e+00 2774.0
7 TraesCS5B01G451700 chr5B 96.376 1683 59 2 5418 7099 628696812 628698493 0.000000e+00 2769.0
8 TraesCS5B01G451700 chr5B 94.428 1723 90 4 5418 7138 633176722 633175004 0.000000e+00 2645.0
9 TraesCS5B01G451700 chr5B 91.304 1472 56 21 893 2336 633179460 633178033 0.000000e+00 1943.0
10 TraesCS5B01G451700 chr5B 93.169 732 44 3 7130 7856 482315249 482314519 0.000000e+00 1070.0
11 TraesCS5B01G451700 chr5B 91.597 714 55 4 7143 7856 19644852 19645560 0.000000e+00 981.0
12 TraesCS5B01G451700 chr5B 78.398 1236 185 38 3999 5199 562302860 562301672 0.000000e+00 728.0
13 TraesCS5B01G451700 chr5B 90.638 235 2 2 5199 5413 625116441 625116675 2.140000e-75 294.0
14 TraesCS5B01G451700 chr5B 90.638 235 2 2 5199 5413 628695990 628696224 2.140000e-75 294.0
15 TraesCS5B01G451700 chr5B 82.927 164 27 1 4013 4176 317270014 317269852 6.350000e-31 147.0
16 TraesCS5B01G451700 chr5B 95.122 41 2 0 7098 7138 625119059 625119099 1.830000e-06 65.8
17 TraesCS5B01G451700 chr5B 95.122 41 2 0 7098 7138 628698608 628698648 1.830000e-06 65.8
18 TraesCS5B01G451700 chr7B 99.131 2646 12 6 2556 5200 438012074 438009439 0.000000e+00 4748.0
19 TraesCS5B01G451700 chr7B 92.788 721 48 3 7138 7856 678967963 678968681 0.000000e+00 1040.0
20 TraesCS5B01G451700 chr7B 78.827 307 52 10 3998 4302 444440164 444439869 2.240000e-45 195.0
21 TraesCS5B01G451700 chr7B 79.623 265 45 7 3998 4261 474277661 474277917 1.740000e-41 182.0
22 TraesCS5B01G451700 chrUn 100.000 2193 0 0 3690 5882 349939685 349941877 0.000000e+00 4050.0
23 TraesCS5B01G451700 chrUn 99.863 2193 3 0 3690 5882 349937392 349939584 0.000000e+00 4034.0
24 TraesCS5B01G451700 chrUn 81.818 143 18 3 452 594 104050860 104050726 6.440000e-21 113.0
25 TraesCS5B01G451700 chr5A 95.370 1620 73 2 5519 7138 625733836 625732219 0.000000e+00 2575.0
26 TraesCS5B01G451700 chr5A 93.665 1610 68 12 893 2486 625738874 625737283 0.000000e+00 2377.0
27 TraesCS5B01G451700 chr5A 80.460 435 54 18 48 454 681936465 681936034 3.560000e-78 303.0
28 TraesCS5B01G451700 chr5A 85.306 245 4 9 5199 5413 625737176 625736934 2.850000e-54 224.0
29 TraesCS5B01G451700 chr5A 97.959 98 2 0 5418 5515 625734890 625734793 3.770000e-38 171.0
30 TraesCS5B01G451700 chr1B 86.485 1539 160 29 3157 4686 136962277 136960778 0.000000e+00 1646.0
31 TraesCS5B01G451700 chr1B 88.813 438 38 8 2591 3019 136962727 136962292 1.940000e-145 527.0
32 TraesCS5B01G451700 chr1B 83.784 518 73 4 4684 5198 136933338 136932829 1.530000e-131 481.0
33 TraesCS5B01G451700 chr1B 76.372 419 64 28 452 857 677389251 677389647 8.040000e-45 193.0
34 TraesCS5B01G451700 chr1B 76.019 417 69 23 452 857 677393739 677394135 3.740000e-43 187.0
35 TraesCS5B01G451700 chr1B 75.143 350 64 13 452 788 14651883 14652222 8.220000e-30 143.0
36 TraesCS5B01G451700 chr1B 83.333 132 20 2 3996 4126 31159688 31159818 3.850000e-23 121.0
37 TraesCS5B01G451700 chr1D 86.308 1541 161 30 3155 4686 83939147 83937648 0.000000e+00 1631.0
38 TraesCS5B01G451700 chr1D 89.751 722 64 8 7134 7854 302826026 302826738 0.000000e+00 915.0
39 TraesCS5B01G451700 chr1D 84.534 472 41 12 2566 3029 83939597 83939150 9.360000e-119 438.0
40 TraesCS5B01G451700 chr1D 77.723 202 37 6 659 856 18267070 18266873 4.980000e-22 117.0
41 TraesCS5B01G451700 chr6A 83.821 1026 158 7 5813 6833 32898759 32897737 0.000000e+00 968.0
42 TraesCS5B01G451700 chr6A 89.736 721 64 6 7138 7856 607695867 607695155 0.000000e+00 913.0
43 TraesCS5B01G451700 chr6A 80.352 967 181 8 5864 6825 614162790 614161828 0.000000e+00 725.0
44 TraesCS5B01G451700 chr6A 76.201 1374 225 61 1000 2315 32900824 32899495 4.000000e-177 632.0
45 TraesCS5B01G451700 chr6A 86.328 256 34 1 198 452 463161973 463162228 2.160000e-70 278.0
46 TraesCS5B01G451700 chr6A 75.245 408 67 26 470 857 2055295 2055688 6.310000e-36 163.0
47 TraesCS5B01G451700 chr7D 90.483 725 61 4 7134 7856 595981040 595981758 0.000000e+00 950.0
48 TraesCS5B01G451700 chr7D 89.612 722 63 9 7137 7856 264984447 264983736 0.000000e+00 907.0
49 TraesCS5B01G451700 chr7D 77.465 426 69 14 452 858 566575003 566574586 6.130000e-56 230.0
50 TraesCS5B01G451700 chr5D 89.765 723 65 4 7138 7856 420995203 420994486 0.000000e+00 917.0
51 TraesCS5B01G451700 chr5D 87.027 370 38 4 6776 7136 297092971 297092603 7.340000e-110 409.0
52 TraesCS5B01G451700 chr5D 81.436 404 50 9 470 857 499443816 499444210 2.750000e-79 307.0
53 TraesCS5B01G451700 chr5D 77.778 396 64 16 473 858 505933936 505933555 1.030000e-53 222.0
54 TraesCS5B01G451700 chr6D 80.435 966 182 6 5864 6825 468096600 468095638 0.000000e+00 730.0
55 TraesCS5B01G451700 chr6D 77.405 1372 197 62 1000 2315 29768994 29770308 0.000000e+00 712.0
56 TraesCS5B01G451700 chr6D 77.000 300 51 16 4010 4302 444669537 444669825 1.060000e-33 156.0
57 TraesCS5B01G451700 chr2B 77.045 880 132 35 4357 5198 672321997 672321150 7.230000e-120 442.0
58 TraesCS5B01G451700 chr2B 79.052 654 88 24 4357 4993 658483761 658484382 3.410000e-108 403.0
59 TraesCS5B01G451700 chr2B 81.818 407 44 18 48 452 415034274 415033896 1.650000e-81 315.0
60 TraesCS5B01G451700 chr2B 97.500 40 1 0 4412 4451 384318982 384318943 1.410000e-07 69.4
61 TraesCS5B01G451700 chr3B 91.270 252 21 1 203 454 741337483 741337733 7.550000e-90 342.0
62 TraesCS5B01G451700 chr3B 77.368 380 64 13 485 855 816093917 816093551 1.030000e-48 206.0
63 TraesCS5B01G451700 chr3B 83.333 222 17 6 48 269 596435323 596435122 3.740000e-43 187.0
64 TraesCS5B01G451700 chr3A 81.081 407 53 6 48 452 19187722 19187338 3.560000e-78 303.0
65 TraesCS5B01G451700 chr3A 83.422 187 27 3 671 855 661470272 661470456 3.770000e-38 171.0
66 TraesCS5B01G451700 chr3A 91.837 49 4 0 3 51 624927864 624927816 1.410000e-07 69.4
67 TraesCS5B01G451700 chr2D 80.788 406 54 9 470 861 601984952 601984557 5.960000e-76 296.0
68 TraesCS5B01G451700 chr4D 75.126 398 73 17 472 858 400168500 400168882 6.310000e-36 163.0
69 TraesCS5B01G451700 chr6B 84.713 157 24 0 1093 1249 714336607 714336451 2.930000e-34 158.0
70 TraesCS5B01G451700 chr3D 77.985 268 40 14 4013 4277 268047035 268046784 4.910000e-32 150.0
71 TraesCS5B01G451700 chr4B 78.534 191 31 7 654 838 135000003 135000189 4.980000e-22 117.0


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 TraesCS5B01G451700 chr5B 623166065 623173920 7855 False 14508.00 14508 100.00000 1 7856 1 chr5B.!!$F2 7855
1 TraesCS5B01G451700 chr5B 626837041 626844886 7845 False 14255.00 14255 99.44000 1 7856 1 chr5B.!!$F3 7855
2 TraesCS5B01G451700 chr5B 629894681 629899158 4477 False 3429.00 3655 94.51850 1 7138 2 chr5B.!!$F6 7137
3 TraesCS5B01G451700 chr5B 633175004 633179460 4456 True 2294.00 2645 92.86600 893 7138 2 chr5B.!!$R4 6245
4 TraesCS5B01G451700 chr5B 628693680 628698648 4968 False 1730.95 3795 94.55200 218 7138 4 chr5B.!!$F5 6920
5 TraesCS5B01G451700 chr5B 625114127 625119099 4972 False 1715.20 3727 94.42975 218 7138 4 chr5B.!!$F4 6920
6 TraesCS5B01G451700 chr5B 482314519 482315249 730 True 1070.00 1070 93.16900 7130 7856 1 chr5B.!!$R2 726
7 TraesCS5B01G451700 chr5B 19644852 19645560 708 False 981.00 981 91.59700 7143 7856 1 chr5B.!!$F1 713
8 TraesCS5B01G451700 chr5B 562301672 562302860 1188 True 728.00 728 78.39800 3999 5199 1 chr5B.!!$R3 1200
9 TraesCS5B01G451700 chr7B 438009439 438012074 2635 True 4748.00 4748 99.13100 2556 5200 1 chr7B.!!$R1 2644
10 TraesCS5B01G451700 chr7B 678967963 678968681 718 False 1040.00 1040 92.78800 7138 7856 1 chr7B.!!$F2 718
11 TraesCS5B01G451700 chrUn 349937392 349941877 4485 False 4042.00 4050 99.93150 3690 5882 2 chrUn.!!$F1 2192
12 TraesCS5B01G451700 chr5A 625732219 625738874 6655 True 1336.75 2575 93.07500 893 7138 4 chr5A.!!$R2 6245
13 TraesCS5B01G451700 chr1B 136960778 136962727 1949 True 1086.50 1646 87.64900 2591 4686 2 chr1B.!!$R2 2095
14 TraesCS5B01G451700 chr1B 136932829 136933338 509 True 481.00 481 83.78400 4684 5198 1 chr1B.!!$R1 514
15 TraesCS5B01G451700 chr1D 83937648 83939597 1949 True 1034.50 1631 85.42100 2566 4686 2 chr1D.!!$R2 2120
16 TraesCS5B01G451700 chr1D 302826026 302826738 712 False 915.00 915 89.75100 7134 7854 1 chr1D.!!$F1 720
17 TraesCS5B01G451700 chr6A 607695155 607695867 712 True 913.00 913 89.73600 7138 7856 1 chr6A.!!$R1 718
18 TraesCS5B01G451700 chr6A 32897737 32900824 3087 True 800.00 968 80.01100 1000 6833 2 chr6A.!!$R3 5833
19 TraesCS5B01G451700 chr6A 614161828 614162790 962 True 725.00 725 80.35200 5864 6825 1 chr6A.!!$R2 961
20 TraesCS5B01G451700 chr7D 595981040 595981758 718 False 950.00 950 90.48300 7134 7856 1 chr7D.!!$F1 722
21 TraesCS5B01G451700 chr7D 264983736 264984447 711 True 907.00 907 89.61200 7137 7856 1 chr7D.!!$R1 719
22 TraesCS5B01G451700 chr5D 420994486 420995203 717 True 917.00 917 89.76500 7138 7856 1 chr5D.!!$R2 718
23 TraesCS5B01G451700 chr6D 468095638 468096600 962 True 730.00 730 80.43500 5864 6825 1 chr6D.!!$R1 961
24 TraesCS5B01G451700 chr6D 29768994 29770308 1314 False 712.00 712 77.40500 1000 2315 1 chr6D.!!$F1 1315
25 TraesCS5B01G451700 chr2B 672321150 672321997 847 True 442.00 442 77.04500 4357 5198 1 chr2B.!!$R3 841
26 TraesCS5B01G451700 chr2B 658483761 658484382 621 False 403.00 403 79.05200 4357 4993 1 chr2B.!!$F1 636

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
790 793 1.919240 TGTAGAGGACGGATGTGTGT 58.081 50.000 0.0 0.0 0.0 3.72 F
792 795 2.631062 TGTAGAGGACGGATGTGTGTTT 59.369 45.455 0.0 0.0 0.0 2.83 F
4816 5457 3.039988 CGTCGGTAGATGGCGGAT 58.960 61.111 0.0 0.0 0.0 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
4816 5457 1.544825 GCCACACACTCCTGCCTAGA 61.545 60.000 0.00 0.0 0.0 2.43 R
6353 12531 7.751768 AGGATTTTGGTGTTTGTTTTTGAAA 57.248 28.000 0.00 0.0 0.0 2.69 R
7360 13659 1.220749 GCAGTTATGAGGCGTCCCA 59.779 57.895 3.56 0.0 0.0 4.37 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
790 793 1.919240 TGTAGAGGACGGATGTGTGT 58.081 50.000 0.00 0.00 0.00 3.72
792 795 2.631062 TGTAGAGGACGGATGTGTGTTT 59.369 45.455 0.00 0.00 0.00 2.83
4816 5457 3.039988 CGTCGGTAGATGGCGGAT 58.960 61.111 0.00 0.00 0.00 4.18
6353 12531 3.276857 CAGATGGTCTTGCTTACATGCT 58.723 45.455 0.00 0.00 0.00 3.79
7125 13424 1.276421 TGAAGCTAGTTCTGGCTGACC 59.724 52.381 11.14 5.34 38.91 4.02
7146 13445 2.542595 CGTGACTGTTAAGGGTGTGTTC 59.457 50.000 0.00 0.00 0.00 3.18
7360 13659 4.521062 GCAGCGCGGGAGACAGAT 62.521 66.667 8.83 0.00 0.00 2.90
7378 13681 0.179045 ATGGGACGCCTCATAACTGC 60.179 55.000 0.00 0.00 0.00 4.40
7379 13682 1.523938 GGGACGCCTCATAACTGCC 60.524 63.158 0.00 0.00 0.00 4.85
7616 13923 2.435693 GCCGTCCCCTATCTGCTGT 61.436 63.158 0.00 0.00 0.00 4.40
7624 13934 1.007964 CTATCTGCTGTCGGCCTCG 60.008 63.158 0.00 0.00 40.92 4.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
112 113 1.000955 GTGACAACGATGACCCTGAGT 59.999 52.381 0.00 0.00 0.00 3.41
1484 1550 2.255554 GTCTGCGAGACTGCGACA 59.744 61.111 8.50 0.00 41.88 4.35
1485 1551 2.872001 CGTCTGCGAGACTGCGAC 60.872 66.667 12.45 5.61 42.92 5.19
1486 1552 4.760840 GCGTCTGCGAGACTGCGA 62.761 66.667 12.45 0.00 42.92 5.10
4816 5457 1.544825 GCCACACACTCCTGCCTAGA 61.545 60.000 0.00 0.00 0.00 2.43
6353 12531 7.751768 AGGATTTTGGTGTTTGTTTTTGAAA 57.248 28.000 0.00 0.00 0.00 2.69
7125 13424 2.234300 ACACACCCTTAACAGTCACG 57.766 50.000 0.00 0.00 0.00 4.35
7357 13656 1.414181 CAGTTATGAGGCGTCCCATCT 59.586 52.381 3.56 0.00 0.00 2.90
7360 13659 1.220749 GCAGTTATGAGGCGTCCCA 59.779 57.895 3.56 0.00 0.00 4.37


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

AutoCloner maintained by Alex Coulton.