Multiple sequence alignment - TraesCS5D01G472700

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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 TraesCS5D01G472700 chr5D 100.000 3803 0 0 1 3803 513317633 513313831 0.000000e+00 7023.0
1 TraesCS5D01G472700 chr5D 98.453 3815 43 10 1 3803 431790149 431786339 0.000000e+00 6704.0
2 TraesCS5D01G472700 chr5D 96.752 3818 44 23 1 3803 433675801 433679553 0.000000e+00 6290.0
3 TraesCS5D01G472700 chr5D 82.057 914 108 23 941 1830 124541912 124541031 0.000000e+00 728.0
4 TraesCS5D01G472700 chr5D 83.824 680 110 0 1819 2498 124506235 124505556 0.000000e+00 647.0
5 TraesCS5D01G472700 chr5D 96.296 162 6 0 172 333 423830430 423830269 2.250000e-67 267.0
6 TraesCS5D01G472700 chr5D 96.296 162 6 0 172 333 539448356 539448517 2.250000e-67 267.0
7 TraesCS5D01G472700 chr5A 93.931 2422 117 16 526 2936 546761895 546764297 0.000000e+00 3631.0
8 TraesCS5D01G472700 chr5A 92.349 745 46 5 2214 2955 546845987 546845251 0.000000e+00 1050.0
9 TraesCS5D01G472700 chr5A 95.070 568 22 2 1649 2216 546864565 546864004 0.000000e+00 889.0
10 TraesCS5D01G472700 chr5A 95.376 346 13 2 879 1221 546864909 546864564 7.180000e-152 547.0
11 TraesCS5D01G472700 chr5A 86.333 300 21 5 526 818 546879708 546879422 3.690000e-80 309.0
12 TraesCS5D01G472700 chr5A 96.000 75 3 0 331 405 546761591 546761665 5.160000e-24 122.0
13 TraesCS5D01G472700 chr5A 94.872 78 4 0 331 408 546880013 546879936 5.160000e-24 122.0
14 TraesCS5D01G472700 chr5B 96.994 2029 45 6 1777 3803 522854706 522856720 0.000000e+00 3395.0
15 TraesCS5D01G472700 chr5B 93.730 1547 65 21 694 2213 522489516 522487975 0.000000e+00 2290.0
16 TraesCS5D01G472700 chr5B 99.330 895 6 0 878 1772 522849384 522850278 0.000000e+00 1620.0
17 TraesCS5D01G472700 chr5B 80.496 1492 256 16 973 2451 137325670 137324201 0.000000e+00 1110.0
18 TraesCS5D01G472700 chr5B 89.521 897 59 9 1 863 522846580 522847475 0.000000e+00 1103.0
19 TraesCS5D01G472700 chr5B 92.800 750 28 10 2210 2955 522483033 522482306 0.000000e+00 1062.0
20 TraesCS5D01G472700 chr5B 93.590 78 5 0 331 408 522490018 522489941 2.400000e-22 117.0
21 TraesCS5D01G472700 chr3B 75.283 1327 271 48 1272 2575 663421408 663422700 7.080000e-162 580.0
22 TraesCS5D01G472700 chr3B 91.291 333 16 4 2 333 400653945 400654265 3.490000e-120 442.0
23 TraesCS5D01G472700 chr3B 90.683 161 11 2 1 157 47677354 47677514 1.070000e-50 211.0
24 TraesCS5D01G472700 chr3B 90.683 161 11 2 1 157 48020371 48020531 1.070000e-50 211.0
25 TraesCS5D01G472700 chr3B 94.175 103 6 0 526 628 368322927 368323029 1.410000e-34 158.0
26 TraesCS5D01G472700 chr1D 83.968 499 58 11 3261 3754 485621493 485621974 3.460000e-125 459.0
27 TraesCS5D01G472700 chr1D 93.204 103 7 0 526 628 105944271 105944169 6.580000e-33 152.0
28 TraesCS5D01G472700 chr6B 90.663 332 28 3 4 333 710771656 710771326 4.510000e-119 438.0
29 TraesCS5D01G472700 chr6B 94.531 128 7 0 403 530 136008076 136007949 8.330000e-47 198.0
30 TraesCS5D01G472700 chr6B 94.309 123 7 0 407 529 457263617 457263495 5.020000e-44 189.0
31 TraesCS5D01G472700 chr6B 86.813 91 9 3 3136 3225 227714186 227714274 8.690000e-17 99.0
32 TraesCS5D01G472700 chr4D 82.716 486 56 12 3251 3725 38285338 38285806 1.270000e-109 407.0
33 TraesCS5D01G472700 chr4D 86.376 367 17 16 1 335 414041669 414042034 1.670000e-98 370.0
34 TraesCS5D01G472700 chr4D 80.392 102 17 2 3258 3359 391052087 391052185 1.470000e-09 75.0
35 TraesCS5D01G472700 chr1A 81.165 515 74 16 3254 3752 583181408 583181915 3.560000e-105 392.0
36 TraesCS5D01G472700 chr1A 90.991 111 10 0 528 638 89573131 89573241 2.370000e-32 150.0
37 TraesCS5D01G472700 chr1A 96.970 66 2 0 3166 3231 583181276 583181341 1.120000e-20 111.0
38 TraesCS5D01G472700 chr1B 87.500 344 31 5 2 333 643929665 643930008 1.660000e-103 387.0
39 TraesCS5D01G472700 chr1B 94.737 171 7 2 172 341 45357616 45357785 8.100000e-67 265.0
40 TraesCS5D01G472700 chr4A 78.661 478 63 16 3254 3726 562636384 562635941 8.040000e-72 281.0
41 TraesCS5D01G472700 chr4A 94.845 97 5 0 3135 3231 562636546 562636450 6.580000e-33 152.0
42 TraesCS5D01G472700 chr4A 80.851 94 17 1 3136 3229 4197213 4197121 5.270000e-09 73.1
43 TraesCS5D01G472700 chr7D 96.988 166 5 0 169 334 500520978 500520813 2.890000e-71 279.0
44 TraesCS5D01G472700 chr7D 94.767 172 6 2 172 341 77497538 77497708 8.100000e-67 265.0
45 TraesCS5D01G472700 chr7D 92.188 128 10 0 407 534 49806776 49806903 8.390000e-42 182.0
46 TraesCS5D01G472700 chr7D 85.567 97 13 1 3135 3231 544629101 544629006 2.420000e-17 100.0
47 TraesCS5D01G472700 chr3D 97.546 163 4 0 171 333 417080291 417080453 2.890000e-71 279.0
48 TraesCS5D01G472700 chr3A 96.341 164 5 1 172 335 738820288 738820126 6.260000e-68 268.0
49 TraesCS5D01G472700 chr3A 90.506 158 14 1 1 157 79332276 79332433 1.380000e-49 207.0
50 TraesCS5D01G472700 chr7B 95.041 121 6 0 407 527 478730425 478730545 1.390000e-44 191.0
51 TraesCS5D01G472700 chr7B 91.852 135 10 1 403 536 63543540 63543406 1.800000e-43 187.0
52 TraesCS5D01G472700 chr7B 94.175 103 6 0 526 628 737071244 737071142 1.410000e-34 158.0
53 TraesCS5D01G472700 chr6A 94.958 119 6 0 407 525 36496007 36496125 1.800000e-43 187.0
54 TraesCS5D01G472700 chr6A 88.710 62 7 0 3264 3325 67040528 67040589 4.070000e-10 76.8
55 TraesCS5D01G472700 chr4B 88.991 109 12 0 3251 3359 55637178 55637286 6.630000e-28 135.0
56 TraesCS5D01G472700 chr7A 88.660 97 10 1 3135 3231 626329297 626329202 2.400000e-22 117.0
57 TraesCS5D01G472700 chrUn 87.755 98 11 1 3135 3231 31746799 31746702 3.100000e-21 113.0
58 TraesCS5D01G472700 chrUn 82.171 129 20 2 3258 3383 82617896 82618024 1.440000e-19 108.0
59 TraesCS5D01G472700 chrUn 82.171 129 20 2 3258 3383 353626149 353626277 1.440000e-19 108.0
60 TraesCS5D01G472700 chrUn 94.340 53 3 0 3179 3231 134454288 134454340 8.760000e-12 82.4


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 TraesCS5D01G472700 chr5D 513313831 513317633 3802 True 7023.0 7023 100.0000 1 3803 1 chr5D.!!$R5 3802
1 TraesCS5D01G472700 chr5D 431786339 431790149 3810 True 6704.0 6704 98.4530 1 3803 1 chr5D.!!$R4 3802
2 TraesCS5D01G472700 chr5D 433675801 433679553 3752 False 6290.0 6290 96.7520 1 3803 1 chr5D.!!$F1 3802
3 TraesCS5D01G472700 chr5D 124541031 124541912 881 True 728.0 728 82.0570 941 1830 1 chr5D.!!$R2 889
4 TraesCS5D01G472700 chr5D 124505556 124506235 679 True 647.0 647 83.8240 1819 2498 1 chr5D.!!$R1 679
5 TraesCS5D01G472700 chr5A 546761591 546764297 2706 False 1876.5 3631 94.9655 331 2936 2 chr5A.!!$F1 2605
6 TraesCS5D01G472700 chr5A 546845251 546845987 736 True 1050.0 1050 92.3490 2214 2955 1 chr5A.!!$R1 741
7 TraesCS5D01G472700 chr5A 546864004 546864909 905 True 718.0 889 95.2230 879 2216 2 chr5A.!!$R2 1337
8 TraesCS5D01G472700 chr5A 546879422 546880013 591 True 215.5 309 90.6025 331 818 2 chr5A.!!$R3 487
9 TraesCS5D01G472700 chr5B 522854706 522856720 2014 False 3395.0 3395 96.9940 1777 3803 1 chr5B.!!$F1 2026
10 TraesCS5D01G472700 chr5B 522846580 522850278 3698 False 1361.5 1620 94.4255 1 1772 2 chr5B.!!$F2 1771
11 TraesCS5D01G472700 chr5B 522487975 522490018 2043 True 1203.5 2290 93.6600 331 2213 2 chr5B.!!$R3 1882
12 TraesCS5D01G472700 chr5B 137324201 137325670 1469 True 1110.0 1110 80.4960 973 2451 1 chr5B.!!$R1 1478
13 TraesCS5D01G472700 chr5B 522482306 522483033 727 True 1062.0 1062 92.8000 2210 2955 1 chr5B.!!$R2 745
14 TraesCS5D01G472700 chr3B 663421408 663422700 1292 False 580.0 580 75.2830 1272 2575 1 chr3B.!!$F5 1303
15 TraesCS5D01G472700 chr1A 583181276 583181915 639 False 251.5 392 89.0675 3166 3752 2 chr1A.!!$F2 586
16 TraesCS5D01G472700 chr4A 562635941 562636546 605 True 216.5 281 86.7530 3135 3726 2 chr4A.!!$R2 591

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
297 311 4.360951 TTTACATCTCCGGTTTTGGACT 57.639 40.909 0.0 0.0 33.48 3.85 F
1118 3347 2.665000 CTGCGTCCACCACCAGAT 59.335 61.111 0.0 0.0 0.00 2.90 F
1974 4213 4.856607 GGGCTTCTCTCGGTCGCG 62.857 72.222 0.0 0.0 0.00 5.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2023 4262 0.460284 CCCGACTTGATGGACCGAAG 60.460 60.000 0.00 0.0 0.00 3.79 R
2633 4876 1.213013 CGAGTCTTCACCGACAGGG 59.787 63.158 0.00 0.0 43.47 4.45 R
3099 5359 1.228552 GGGTGGAGCTGCAAAAGGA 60.229 57.895 10.44 0.0 0.00 3.36 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
203 217 5.819991 TCTATTGGAGTTGCTCTTTTGGAT 58.180 37.500 0.00 0.00 0.00 3.41
297 311 4.360951 TTTACATCTCCGGTTTTGGACT 57.639 40.909 0.00 0.00 33.48 3.85
585 815 8.557029 GGCAGAAATGTTGGTGTACTATTATAC 58.443 37.037 0.00 0.00 0.00 1.47
1118 3347 2.665000 CTGCGTCCACCACCAGAT 59.335 61.111 0.00 0.00 0.00 2.90
1974 4213 4.856607 GGGCTTCTCTCGGTCGCG 62.857 72.222 0.00 0.00 0.00 5.87
2633 4876 2.024918 CCATGCGTAAGATGGTGGC 58.975 57.895 0.00 0.00 39.01 5.01
3099 5359 1.692173 GGAATGGCCCTTGCATGCAT 61.692 55.000 23.37 2.99 40.13 3.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 2.893404 GCGGGCGGCGAAGAATAA 60.893 61.111 12.98 0.00 0.00 1.40
203 217 4.463539 CCAACAGATGGTCCAAATTCATGA 59.536 41.667 0.00 0.00 44.85 3.07
297 311 6.934056 CCAATAGATGGTCCAAATTTTGACA 58.066 36.000 20.41 9.76 44.85 3.58
409 454 1.819208 CAGGATTTCCGGCGATGCA 60.819 57.895 9.30 0.00 42.08 3.96
585 815 9.458374 AAAGTCTTTTATGTTTGACCGTATTTG 57.542 29.630 0.00 0.00 0.00 2.32
765 1056 3.708890 CAAACCGGTTTTGGAAGGTTAC 58.291 45.455 29.74 0.00 45.25 2.50
2023 4262 0.460284 CCCGACTTGATGGACCGAAG 60.460 60.000 0.00 0.00 0.00 3.79
2633 4876 1.213013 CGAGTCTTCACCGACAGGG 59.787 63.158 0.00 0.00 43.47 4.45
3099 5359 1.228552 GGGTGGAGCTGCAAAAGGA 60.229 57.895 10.44 0.00 0.00 3.36
3556 5877 4.674281 AGAGAACTTTCGAACAAGACCT 57.326 40.909 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.