Multiple sequence alignment - TraesCS5D01G451500

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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 TraesCS5D01G451500 chr5D 100.000 3161 0 0 1 3161 499733914 499730754 0.000000e+00 5838
1 TraesCS5D01G451500 chr5D 95.020 2008 47 23 246 2223 213948614 213950598 0.000000e+00 3105
2 TraesCS5D01G451500 chr5D 85.535 477 32 23 22 487 213948347 213948797 6.180000e-127 464
3 TraesCS5D01G451500 chr3D 94.891 3171 112 39 21 3161 171137817 171134667 0.000000e+00 4913
4 TraesCS5D01G451500 chr3D 97.833 2677 58 0 485 3161 123683298 123680622 0.000000e+00 4623
5 TraesCS5D01G451500 chr3D 95.131 2670 102 7 511 3161 232468841 232466181 0.000000e+00 4185
6 TraesCS5D01G451500 chr3D 90.074 272 20 7 21 290 266411871 266411605 2.330000e-91 346
7 TraesCS5D01G451500 chr3D 88.603 272 22 8 21 290 303391463 303391727 3.930000e-84 322
8 TraesCS5D01G451500 chr3D 88.000 275 23 9 22 290 232469376 232469106 1.830000e-82 316
9 TraesCS5D01G451500 chr6D 97.539 2804 46 16 360 3161 409840840 409838058 0.000000e+00 4774
10 TraesCS5D01G451500 chr6D 97.910 2680 53 2 484 3161 273916537 273919215 0.000000e+00 4636
11 TraesCS5D01G451500 chr6D 97.796 2677 52 5 485 3161 428158131 428155462 0.000000e+00 4610
12 TraesCS5D01G451500 chr6D 86.667 420 39 14 21 433 428158664 428158255 1.730000e-122 449
13 TraesCS5D01G451500 chr6D 85.714 343 21 18 21 354 86936997 86937320 1.400000e-88 337
14 TraesCS5D01G451500 chr4D 97.500 2680 62 3 485 3161 323569687 323572364 0.000000e+00 4573
15 TraesCS5D01G451500 chr4D 94.419 215 8 3 21 233 83868780 83868992 8.450000e-86 327
16 TraesCS5D01G451500 chr7D 98.090 2618 47 3 544 3161 536805026 536807640 0.000000e+00 4554
17 TraesCS5D01G451500 chr7D 98.089 2616 40 7 546 3161 681119 683724 0.000000e+00 4545
18 TraesCS5D01G451500 chr7D 98.157 2604 41 3 558 3161 334847718 334845122 0.000000e+00 4536
19 TraesCS5D01G451500 chr7D 86.620 426 28 20 16 429 536804386 536804794 8.050000e-121 444
20 TraesCS5D01G451500 chr7D 95.023 221 9 2 21 239 285244385 285244605 2.330000e-91 346
21 TraesCS5D01G451500 chr1D 96.413 223 5 2 19 240 137637769 137637989 6.440000e-97 364


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 TraesCS5D01G451500 chr5D 499730754 499733914 3160 True 5838.0 5838 100.0000 1 3161 1 chr5D.!!$R1 3160
1 TraesCS5D01G451500 chr5D 213948347 213950598 2251 False 1784.5 3105 90.2775 22 2223 2 chr5D.!!$F1 2201
2 TraesCS5D01G451500 chr3D 171134667 171137817 3150 True 4913.0 4913 94.8910 21 3161 1 chr3D.!!$R2 3140
3 TraesCS5D01G451500 chr3D 123680622 123683298 2676 True 4623.0 4623 97.8330 485 3161 1 chr3D.!!$R1 2676
4 TraesCS5D01G451500 chr3D 232466181 232469376 3195 True 2250.5 4185 91.5655 22 3161 2 chr3D.!!$R4 3139
5 TraesCS5D01G451500 chr6D 409838058 409840840 2782 True 4774.0 4774 97.5390 360 3161 1 chr6D.!!$R1 2801
6 TraesCS5D01G451500 chr6D 273916537 273919215 2678 False 4636.0 4636 97.9100 484 3161 1 chr6D.!!$F2 2677
7 TraesCS5D01G451500 chr6D 428155462 428158664 3202 True 2529.5 4610 92.2315 21 3161 2 chr6D.!!$R2 3140
8 TraesCS5D01G451500 chr4D 323569687 323572364 2677 False 4573.0 4573 97.5000 485 3161 1 chr4D.!!$F2 2676
9 TraesCS5D01G451500 chr7D 681119 683724 2605 False 4545.0 4545 98.0890 546 3161 1 chr7D.!!$F1 2615
10 TraesCS5D01G451500 chr7D 334845122 334847718 2596 True 4536.0 4536 98.1570 558 3161 1 chr7D.!!$R1 2603
11 TraesCS5D01G451500 chr7D 536804386 536807640 3254 False 2499.0 4554 92.3550 16 3161 2 chr7D.!!$F3 3145

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
587 1186 0.958876 TTGTCTGCTGCATCAGGCTG 60.959 55.000 21.6 8.58 45.15 4.85 F
845 1444 1.133482 TCGTGCCTATGATGAGAGGGA 60.133 52.381 0.0 0.00 30.39 4.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2158 2763 1.831106 ACCAAGTCGATGATGCCACTA 59.169 47.619 0.00 0.0 0.00 2.74 R
2639 3245 2.699809 GATGCTTGCGCTCAGACG 59.300 61.111 9.73 0.0 36.97 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
17 18 4.316823 TCTCTGGGCCCACTCGGT 62.317 66.667 24.45 0.00 0.00 4.69
179 180 7.302948 TCCTAACATGGTATTAGAGCCTTAGA 58.697 38.462 0.00 0.00 32.31 2.10
225 229 1.440938 CTCCGATCTTCTCTCGCCGT 61.441 60.000 0.00 0.00 34.84 5.68
243 247 2.126463 CGCCGCGTCTTCTTCTCA 60.126 61.111 4.92 0.00 0.00 3.27
309 401 4.383861 CAGTGCTGCTCGCCAGGA 62.384 66.667 0.00 0.00 42.03 3.86
372 464 3.771160 GACACATCTCCCGCCCGT 61.771 66.667 0.00 0.00 0.00 5.28
560 1147 4.098416 GCTATTTTCGGATCTTTGCACAC 58.902 43.478 0.00 0.00 0.00 3.82
587 1186 0.958876 TTGTCTGCTGCATCAGGCTG 60.959 55.000 21.60 8.58 45.15 4.85
609 1208 3.695606 GCTGTCCCTCGCTGTCCA 61.696 66.667 0.00 0.00 0.00 4.02
845 1444 1.133482 TCGTGCCTATGATGAGAGGGA 60.133 52.381 0.00 0.00 30.39 4.20
991 1590 5.006896 TGAGTTTCTGGGTCTTCCTACTA 57.993 43.478 0.00 0.00 36.20 1.82
1679 2284 2.202623 CTCGACGGGTACTGCTGC 60.203 66.667 0.00 0.00 39.14 5.25
2158 2763 5.367945 TTCTGTTACTGGTTCCTTCAAGT 57.632 39.130 0.00 0.00 0.00 3.16
2499 3105 1.501169 GTTTTGCTGCCATGGTTCAC 58.499 50.000 14.67 1.32 0.00 3.18
2639 3245 0.381089 GCTCATGCTCAGAATGGTGC 59.619 55.000 0.00 0.00 36.16 5.01
2868 3474 4.580167 TGTGTTTGCTATGTTCTTCTTGCT 59.420 37.500 0.00 0.00 0.00 3.91
3101 3707 1.455217 CCCCTATCACTCCCGTCGT 60.455 63.158 0.00 0.00 0.00 4.34
3102 3708 0.179009 CCCCTATCACTCCCGTCGTA 60.179 60.000 0.00 0.00 0.00 3.43
3106 3712 2.224378 CCTATCACTCCCGTCGTACCTA 60.224 54.545 0.00 0.00 0.00 3.08
3116 3722 2.555325 CCGTCGTACCTATGCCTATTCA 59.445 50.000 0.00 0.00 0.00 2.57
3119 3725 4.156190 CGTCGTACCTATGCCTATTCATCT 59.844 45.833 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.856039 CTACCGAGTGGGCCCAGAGA 62.856 65.000 29.55 0.00 40.62 3.10
3 4 2.683933 ACTACCGAGTGGGCCCAG 60.684 66.667 29.55 17.01 40.62 4.45
225 229 1.934220 ATGAGAAGAAGACGCGGCGA 61.934 55.000 30.94 1.91 0.00 5.54
349 441 2.509336 GGGAGATGTGTCGTGGCG 60.509 66.667 0.00 0.00 0.00 5.69
354 446 4.873129 CGGGCGGGAGATGTGTCG 62.873 72.222 0.00 0.00 0.00 4.35
356 448 3.771160 GACGGGCGGGAGATGTGT 61.771 66.667 0.00 0.00 0.00 3.72
463 630 3.423154 CTGGGCAGGAACGAACGC 61.423 66.667 0.00 0.00 0.00 4.84
609 1208 3.769844 AGTTGGTACCATCGAAGATCACT 59.230 43.478 17.17 9.86 45.12 3.41
845 1444 2.782341 AGAGCCTCCTCATAAGCCAAAT 59.218 45.455 0.00 0.00 40.68 2.32
1679 2284 2.354259 GGGAAGCATCAGTCACAGAAG 58.646 52.381 0.00 0.00 0.00 2.85
2158 2763 1.831106 ACCAAGTCGATGATGCCACTA 59.169 47.619 0.00 0.00 0.00 2.74
2499 3105 3.692257 ATGGGTGAAGAGAACTGAGTG 57.308 47.619 0.00 0.00 0.00 3.51
2639 3245 2.699809 GATGCTTGCGCTCAGACG 59.300 61.111 9.73 0.00 36.97 4.18
2868 3474 3.793775 TTTGGTGCGTTCGCGAGGA 62.794 57.895 9.59 0.00 44.71 3.71
3101 3707 5.717178 GGAGTGAGATGAATAGGCATAGGTA 59.283 44.000 0.00 0.00 0.00 3.08
3102 3708 4.530161 GGAGTGAGATGAATAGGCATAGGT 59.470 45.833 0.00 0.00 0.00 3.08
3106 3712 3.582208 GAGGGAGTGAGATGAATAGGCAT 59.418 47.826 0.00 0.00 0.00 4.40
3116 3722 2.387757 GAGAAGCAGAGGGAGTGAGAT 58.612 52.381 0.00 0.00 0.00 2.75
3119 3725 0.115152 TGGAGAAGCAGAGGGAGTGA 59.885 55.000 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.