Multiple sequence alignment - TraesCS5D01G348200

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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 TraesCS5D01G348200 chr5D 100.000 3707 0 0 1 3707 433675819 433679525 0.000000e+00 6846.0
1 TraesCS5D01G348200 chr5D 96.799 3780 34 18 1 3707 431790131 431786366 0.000000e+00 6229.0
2 TraesCS5D01G348200 chr5D 96.766 3772 42 23 1 3707 513317615 513313859 0.000000e+00 6216.0
3 TraesCS5D01G348200 chr5D 81.838 914 110 26 896 1785 124541912 124541031 0.000000e+00 717.0
4 TraesCS5D01G348200 chr5D 84.412 680 106 0 1774 2453 124506235 124505556 0.000000e+00 669.0
5 TraesCS5D01G348200 chr5D 89.251 307 22 7 1 296 526445662 526445356 1.260000e-99 374.0
6 TraesCS5D01G348200 chr5D 88.667 150 6 3 1 139 559837806 559837657 4.920000e-39 172.0
7 TraesCS5D01G348200 chr5A 93.085 2415 108 27 505 2872 546761895 546764297 0.000000e+00 3480.0
8 TraesCS5D01G348200 chr5A 91.509 742 39 11 2169 2891 546845987 546845251 0.000000e+00 1000.0
9 TraesCS5D01G348200 chr5A 95.599 568 19 2 1604 2171 546864565 546864004 0.000000e+00 905.0
10 TraesCS5D01G348200 chr5A 95.087 346 14 2 834 1176 546864909 546864564 3.260000e-150 542.0
11 TraesCS5D01G348200 chr5A 86.577 298 19 6 505 794 546879708 546879424 3.600000e-80 309.0
12 TraesCS5D01G348200 chr5B 96.396 1998 35 10 1732 3705 522854706 522856690 0.000000e+00 3256.0
13 TraesCS5D01G348200 chr5B 96.093 1331 46 6 839 2168 522489300 522487975 0.000000e+00 2165.0
14 TraesCS5D01G348200 chr5B 99.218 895 7 0 833 1727 522849384 522850278 0.000000e+00 1615.0
15 TraesCS5D01G348200 chr5B 80.496 1492 256 16 928 2406 137325670 137324201 0.000000e+00 1110.0
16 TraesCS5D01G348200 chr5B 92.091 746 22 15 2165 2891 522483033 522482306 0.000000e+00 1016.0
17 TraesCS5D01G348200 chr5B 94.737 437 19 1 362 794 522846992 522847428 0.000000e+00 676.0
18 TraesCS5D01G348200 chr5B 93.939 330 18 1 1 328 522846598 522846927 7.150000e-137 497.0
19 TraesCS5D01G348200 chr5B 88.525 305 23 5 1 293 421463399 421463095 3.520000e-95 359.0
20 TraesCS5D01G348200 chr5B 88.202 178 14 3 505 682 522489720 522489550 4.850000e-49 206.0
21 TraesCS5D01G348200 chr5B 93.651 126 4 1 673 794 522489516 522489391 6.320000e-43 185.0
22 TraesCS5D01G348200 chr3B 75.490 1326 270 47 1227 2530 663421408 663422700 6.850000e-167 597.0
23 TraesCS5D01G348200 chr3B 90.789 304 16 8 1 293 232009582 232009884 2.680000e-106 396.0
24 TraesCS5D01G348200 chr3B 89.251 307 20 9 1 296 488547772 488547468 4.520000e-99 372.0
25 TraesCS5D01G348200 chr3B 95.146 103 5 0 505 607 368322927 368323029 2.960000e-36 163.0
26 TraesCS5D01G348200 chr1D 83.702 497 58 13 3198 3686 485621493 485621974 7.300000e-122 448.0
27 TraesCS5D01G348200 chr4D 82.887 485 53 15 3188 3658 38285338 38285806 3.450000e-110 409.0
28 TraesCS5D01G348200 chr4D 88.535 314 13 14 1 293 414041687 414041998 3.520000e-95 359.0
29 TraesCS5D01G348200 chr4D 79.412 102 18 2 3195 3296 391052087 391052185 6.640000e-08 69.4
30 TraesCS5D01G348200 chr1A 81.590 478 68 15 3190 3647 583181407 583181884 9.720000e-101 377.0
31 TraesCS5D01G348200 chr1A 89.865 148 4 3 1 137 427702084 427702231 2.940000e-41 180.0
32 TraesCS5D01G348200 chr1A 91.892 111 9 0 507 617 89573131 89573241 4.960000e-34 156.0
33 TraesCS5D01G348200 chr1A 86.486 148 9 5 1 137 585364832 585364685 6.410000e-33 152.0
34 TraesCS5D01G348200 chr1A 96.970 66 2 0 3104 3169 583181276 583181341 1.090000e-20 111.0
35 TraesCS5D01G348200 chr7B 89.474 304 21 8 1 293 462736563 462736260 1.260000e-99 374.0
36 TraesCS5D01G348200 chr7B 88.350 309 19 12 2 293 572960851 572961159 4.550000e-94 355.0
37 TraesCS5D01G348200 chr7B 90.370 135 12 1 382 515 63543540 63543406 3.800000e-40 176.0
38 TraesCS5D01G348200 chr7B 95.146 103 5 0 505 607 737071244 737071142 2.960000e-36 163.0
39 TraesCS5D01G348200 chr1B 89.456 294 28 3 1 293 643929682 643929973 5.850000e-98 368.0
40 TraesCS5D01G348200 chr1B 75.281 445 78 13 3195 3631 445881092 445880672 2.270000e-42 183.0
41 TraesCS5D01G348200 chr4A 78.914 479 62 16 3188 3659 562636387 562635941 4.680000e-74 289.0
42 TraesCS5D01G348200 chr4A 94.845 97 5 0 3073 3169 562636546 562636450 6.410000e-33 152.0
43 TraesCS5D01G348200 chr4A 85.345 116 16 1 167 282 1152982 1153096 6.500000e-23 119.0
44 TraesCS5D01G348200 chr4A 80.851 94 17 1 3074 3167 4197213 4197121 5.140000e-09 73.1
45 TraesCS5D01G348200 chr6B 94.309 123 7 0 386 508 457263617 457263495 4.890000e-44 189.0
46 TraesCS5D01G348200 chr6B 92.969 128 9 0 382 509 136008076 136007949 1.760000e-43 187.0
47 TraesCS5D01G348200 chr6B 86.813 91 9 3 3074 3163 227714186 227714274 8.470000e-17 99.0
48 TraesCS5D01G348200 chr6A 94.958 119 6 0 386 504 36496007 36496125 1.760000e-43 187.0
49 TraesCS5D01G348200 chr2A 90.000 150 4 3 1 139 657125395 657125544 2.270000e-42 183.0
50 TraesCS5D01G348200 chr2A 84.667 150 12 3 1 139 471178917 471179066 4.990000e-29 139.0
51 TraesCS5D01G348200 chr2A 100.000 42 0 0 1 42 763681548 763681507 1.100000e-10 78.7
52 TraesCS5D01G348200 chr7D 92.188 128 10 0 386 513 49806776 49806903 8.180000e-42 182.0
53 TraesCS5D01G348200 chr7D 89.209 139 14 1 386 524 89896330 89896193 4.920000e-39 172.0
54 TraesCS5D01G348200 chr7D 85.567 97 13 1 3073 3169 544629101 544629006 2.360000e-17 100.0
55 TraesCS5D01G348200 chr4B 88.991 109 12 0 3188 3296 55637178 55637286 6.460000e-28 135.0
56 TraesCS5D01G348200 chr7A 88.660 97 10 1 3073 3169 626329297 626329202 2.340000e-22 117.0
57 TraesCS5D01G348200 chrUn 87.755 98 11 1 3073 3169 31746799 31746702 3.030000e-21 113.0
58 TraesCS5D01G348200 chrUn 81.395 129 21 2 3195 3320 82617896 82618024 6.550000e-18 102.0
59 TraesCS5D01G348200 chrUn 81.395 129 21 2 3195 3320 353626149 353626277 6.550000e-18 102.0
60 TraesCS5D01G348200 chrUn 94.340 53 3 0 3117 3169 134454288 134454340 8.530000e-12 82.4
61 TraesCS5D01G348200 chr3D 96.875 32 1 0 3230 3261 61050173 61050142 2.000000e-03 54.7


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 TraesCS5D01G348200 chr5D 433675819 433679525 3706 False 6846.000000 6846 100.000000 1 3707 1 chr5D.!!$F1 3706
1 TraesCS5D01G348200 chr5D 431786366 431790131 3765 True 6229.000000 6229 96.799000 1 3707 1 chr5D.!!$R3 3706
2 TraesCS5D01G348200 chr5D 513313859 513317615 3756 True 6216.000000 6216 96.766000 1 3707 1 chr5D.!!$R4 3706
3 TraesCS5D01G348200 chr5D 124541031 124541912 881 True 717.000000 717 81.838000 896 1785 1 chr5D.!!$R2 889
4 TraesCS5D01G348200 chr5D 124505556 124506235 679 True 669.000000 669 84.412000 1774 2453 1 chr5D.!!$R1 679
5 TraesCS5D01G348200 chr5A 546761895 546764297 2402 False 3480.000000 3480 93.085000 505 2872 1 chr5A.!!$F1 2367
6 TraesCS5D01G348200 chr5A 546845251 546845987 736 True 1000.000000 1000 91.509000 2169 2891 1 chr5A.!!$R1 722
7 TraesCS5D01G348200 chr5A 546864004 546864909 905 True 723.500000 905 95.343000 834 2171 2 chr5A.!!$R3 1337
8 TraesCS5D01G348200 chr5B 522854706 522856690 1984 False 3256.000000 3256 96.396000 1732 3705 1 chr5B.!!$F1 1973
9 TraesCS5D01G348200 chr5B 137324201 137325670 1469 True 1110.000000 1110 80.496000 928 2406 1 chr5B.!!$R1 1478
10 TraesCS5D01G348200 chr5B 522482306 522483033 727 True 1016.000000 1016 92.091000 2165 2891 1 chr5B.!!$R3 726
11 TraesCS5D01G348200 chr5B 522846598 522850278 3680 False 929.333333 1615 95.964667 1 1727 3 chr5B.!!$F2 1726
12 TraesCS5D01G348200 chr5B 522487975 522489720 1745 True 852.000000 2165 92.648667 505 2168 3 chr5B.!!$R4 1663
13 TraesCS5D01G348200 chr3B 663421408 663422700 1292 False 597.000000 597 75.490000 1227 2530 1 chr3B.!!$F3 1303
14 TraesCS5D01G348200 chr1A 583181276 583181884 608 False 244.000000 377 89.280000 3104 3647 2 chr1A.!!$F3 543
15 TraesCS5D01G348200 chr4A 562635941 562636546 605 True 220.500000 289 86.879500 3073 3659 2 chr4A.!!$R2 586

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
150 151 1.002134 CCCAAGGCATCTCCAACGT 60.002 57.895 0.0 0.0 37.29 3.99 F
153 154 1.238439 CAAGGCATCTCCAACGTGTT 58.762 50.000 0.0 0.0 37.29 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1466 3547 2.561885 CGTCGCACGAGAAGGACT 59.438 61.111 3.04 0.0 46.05 3.85 R
2908 5029 5.476091 TTTTGAACCAAACTGTGAAACCT 57.524 34.783 0.00 0.0 32.79 3.50 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
125 126 2.244651 GCGCACAAGGTGTTCGACT 61.245 57.895 0.30 0.0 39.26 4.18
150 151 1.002134 CCCAAGGCATCTCCAACGT 60.002 57.895 0.00 0.0 37.29 3.99
153 154 1.238439 CAAGGCATCTCCAACGTGTT 58.762 50.000 0.00 0.0 37.29 3.32
154 155 1.608590 CAAGGCATCTCCAACGTGTTT 59.391 47.619 0.00 0.0 37.29 2.83
155 156 1.981256 AGGCATCTCCAACGTGTTTT 58.019 45.000 0.00 0.0 37.29 2.43
156 157 1.608590 AGGCATCTCCAACGTGTTTTG 59.391 47.619 0.00 0.0 37.29 2.44
157 158 1.335872 GGCATCTCCAACGTGTTTTGG 60.336 52.381 0.00 0.0 46.64 3.28
165 166 3.428746 CAACGTGTTTTGGACCATGAA 57.571 42.857 0.00 0.0 0.00 2.57
339 368 4.397417 GCCATCTATATGCCCAAATCTGAC 59.603 45.833 0.00 0.0 0.00 3.51
491 551 3.713764 AGTCCCTCTAACCATCCAATCAG 59.286 47.826 0.00 0.0 0.00 2.90
794 907 2.945008 CGAAGCCAAGGATGCTATTGAA 59.055 45.455 0.00 0.0 38.34 2.69
991 3057 4.717629 CGAGGTGCGCCGTCTGAA 62.718 66.667 11.42 0.0 40.50 3.02
3009 5131 4.038763 CCCGAGGTTGTGCATAGATTAGTA 59.961 45.833 0.00 0.0 0.00 1.82
3250 5418 3.823873 TGTGCGGAATCCAACAACTTTAT 59.176 39.130 0.00 0.0 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
67 68 1.213537 CGGTTGGATTGGCTGCTTG 59.786 57.895 0.00 0.00 0.00 4.01
68 69 1.978617 CCGGTTGGATTGGCTGCTT 60.979 57.895 0.00 0.00 37.49 3.91
125 126 1.063717 GGAGATGCCTTGGGGAATTCA 60.064 52.381 7.93 0.00 28.94 2.57
150 151 4.202305 GGTCCAAATTCATGGTCCAAAACA 60.202 41.667 0.00 0.00 44.93 2.83
156 157 3.635591 AGATGGTCCAAATTCATGGTCC 58.364 45.455 0.00 5.71 45.54 4.46
157 158 6.239120 CCAATAGATGGTCCAAATTCATGGTC 60.239 42.308 0.00 0.00 44.85 4.02
158 159 5.599656 CCAATAGATGGTCCAAATTCATGGT 59.400 40.000 0.00 0.00 44.85 3.55
159 160 6.092955 CCAATAGATGGTCCAAATTCATGG 57.907 41.667 0.00 0.00 44.85 3.66
236 250 1.118356 AAATGCGTTTTGGGGCTCCA 61.118 50.000 0.00 0.00 42.25 3.86
491 551 8.087982 TCATGATAAAATAGCGAATCAACCTC 57.912 34.615 0.00 0.00 32.47 3.85
794 907 1.383456 TTTGTGCGTGCTTCTTGGCT 61.383 50.000 0.00 0.00 0.00 4.75
796 909 0.381801 ACTTTGTGCGTGCTTCTTGG 59.618 50.000 0.00 0.00 0.00 3.61
797 910 2.193306 AACTTTGTGCGTGCTTCTTG 57.807 45.000 0.00 0.00 0.00 3.02
798 911 2.290641 CCTAACTTTGTGCGTGCTTCTT 59.709 45.455 0.00 0.00 0.00 2.52
799 912 1.873591 CCTAACTTTGTGCGTGCTTCT 59.126 47.619 0.00 0.00 0.00 2.85
1466 3547 2.561885 CGTCGCACGAGAAGGACT 59.438 61.111 3.04 0.00 46.05 3.85
2908 5029 5.476091 TTTTGAACCAAACTGTGAAACCT 57.524 34.783 0.00 0.00 32.79 3.50
3009 5131 0.190815 AGGGGCCATTCCAAAGTTGT 59.809 50.000 4.39 0.00 36.21 3.32
3250 5418 3.950397 ACCCAATTTAGCTCACGATTCA 58.050 40.909 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.