Multiple sequence alignment - TraesCS4A01G151400

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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 TraesCS4A01G151400 chr4A 100.000 2495 0 0 1 2495 303107187 303109681 0.000000e+00 4608
1 TraesCS4A01G151400 chr4A 97.357 2497 63 3 1 2495 311576287 311573792 0.000000e+00 4242
2 TraesCS4A01G151400 chr4A 97.158 2498 68 2 1 2495 303046157 303048654 0.000000e+00 4217
3 TraesCS4A01G151400 chr4A 92.009 463 36 1 519 980 309751031 309750569 0.000000e+00 649
4 TraesCS4A01G151400 chr2D 91.896 617 47 3 988 1602 87728639 87729254 0.000000e+00 859
5 TraesCS4A01G151400 chr2D 88.889 477 51 2 1642 2117 87729248 87729723 9.940000e-164 586
6 TraesCS4A01G151400 chr2D 91.272 401 34 1 1 400 87728194 87728594 1.690000e-151 545
7 TraesCS4A01G151400 chr2D 89.894 188 18 1 1354 1541 497899972 497899786 8.920000e-60 241
8 TraesCS4A01G151400 chr7B 84.497 845 105 12 1660 2493 257649021 257649850 0.000000e+00 811
9 TraesCS4A01G151400 chr1D 92.275 466 33 3 513 977 405679977 405680440 0.000000e+00 658
10 TraesCS4A01G151400 chr1D 91.828 465 36 2 514 977 142118986 142119449 0.000000e+00 647
11 TraesCS4A01G151400 chr1D 91.258 469 39 2 513 980 188561391 188560924 2.710000e-179 638
12 TraesCS4A01G151400 chr1D 79.482 502 96 6 1027 1526 206801794 206801298 1.420000e-92 350
13 TraesCS4A01G151400 chr3D 89.689 514 52 1 1 513 553472388 553471875 0.000000e+00 654
14 TraesCS4A01G151400 chr3D 91.416 466 37 3 513 977 183559823 183560286 9.730000e-179 636
15 TraesCS4A01G151400 chr3D 86.972 545 54 8 1475 2013 553469655 553469122 4.590000e-167 597
16 TraesCS4A01G151400 chr3D 91.014 434 37 1 988 1419 553471880 553471447 3.580000e-163 584
17 TraesCS4A01G151400 chr3D 87.295 488 49 5 2012 2495 553456079 553455601 1.690000e-151 545
18 TraesCS4A01G151400 chr3D 78.764 518 105 4 1028 1544 597168684 597168171 2.380000e-90 342
19 TraesCS4A01G151400 chr7D 91.416 466 38 2 513 977 262741719 262742183 2.710000e-179 638
20 TraesCS4A01G151400 chr5D 91.258 469 39 2 513 980 132665731 132665264 2.710000e-179 638
21 TraesCS4A01G151400 chr3B 87.873 536 63 2 988 1523 13609284 13609817 1.630000e-176 628
22 TraesCS4A01G151400 chr3B 84.466 515 70 7 7 513 13608777 13609289 1.330000e-137 499
23 TraesCS4A01G151400 chr2B 88.202 534 49 8 988 1520 153854049 153854569 2.110000e-175 625
24 TraesCS4A01G151400 chr2B 87.961 515 54 5 7 513 153853540 153854054 3.550000e-168 601
25 TraesCS4A01G151400 chr6B 89.429 350 36 1 1186 1535 11247939 11247591 8.190000e-120 440
26 TraesCS4A01G151400 chr7A 88.652 141 14 2 2357 2495 310225975 310225835 1.190000e-38 171
27 TraesCS4A01G151400 chr6D 81.215 181 19 4 2320 2495 469347872 469347702 5.600000e-27 132


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 TraesCS4A01G151400 chr4A 303107187 303109681 2494 False 4608.000000 4608 100.000000 1 2495 1 chr4A.!!$F2 2494
1 TraesCS4A01G151400 chr4A 311573792 311576287 2495 True 4242.000000 4242 97.357000 1 2495 1 chr4A.!!$R2 2494
2 TraesCS4A01G151400 chr4A 303046157 303048654 2497 False 4217.000000 4217 97.158000 1 2495 1 chr4A.!!$F1 2494
3 TraesCS4A01G151400 chr2D 87728194 87729723 1529 False 663.333333 859 90.685667 1 2117 3 chr2D.!!$F1 2116
4 TraesCS4A01G151400 chr7B 257649021 257649850 829 False 811.000000 811 84.497000 1660 2493 1 chr7B.!!$F1 833
5 TraesCS4A01G151400 chr3D 553469122 553472388 3266 True 611.666667 654 89.225000 1 2013 3 chr3D.!!$R3 2012
6 TraesCS4A01G151400 chr3D 597168171 597168684 513 True 342.000000 342 78.764000 1028 1544 1 chr3D.!!$R2 516
7 TraesCS4A01G151400 chr3B 13608777 13609817 1040 False 563.500000 628 86.169500 7 1523 2 chr3B.!!$F1 1516
8 TraesCS4A01G151400 chr2B 153853540 153854569 1029 False 613.000000 625 88.081500 7 1520 2 chr2B.!!$F1 1513

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
540 552 0.993509 CCTGGATTAAGGGGCCCTCA 60.994 60.0 28.97 18.26 33.28 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2076 3837 0.394762 GCAAGGCATCTCCATGGTCA 60.395 55.0 12.58 0.0 34.23 4.02 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
269 273 4.460731 GCTCTTGGATTAGCAAAGGAAGTT 59.539 41.667 0.00 0.00 38.63 2.66
301 305 1.599047 CAGTGGACCGAGCTGGATT 59.401 57.895 8.91 0.00 42.00 3.01
339 343 3.118482 CCTGCTATGTGACCAATCTGTCT 60.118 47.826 0.00 0.00 36.21 3.41
370 374 8.879759 ACTATATTTGGACATTGTTGAAGTACG 58.120 33.333 0.00 0.00 0.00 3.67
540 552 0.993509 CCTGGATTAAGGGGCCCTCA 60.994 60.000 28.97 18.26 33.28 3.86
566 578 4.598807 TGTTCAGGCTGTATGATATGGGAT 59.401 41.667 15.27 0.00 0.00 3.85
937 949 5.455872 TCCTGTTACCTTCGATCCTAAGAT 58.544 41.667 4.42 0.00 34.57 2.40
980 992 1.276989 TGAGATCGGCCGGTTTTTACT 59.723 47.619 27.83 11.41 0.00 2.24
982 994 1.553704 AGATCGGCCGGTTTTTACTCT 59.446 47.619 27.83 6.49 0.00 3.24
1712 3470 6.347888 CGTTTAAGAAAAATGGGTCTTCGCTA 60.348 38.462 0.00 0.00 35.69 4.26
1938 3696 1.517242 CTCAAGAACCTGGAGTGTGC 58.483 55.000 0.00 0.00 27.51 4.57
2028 3789 2.967397 CGGTGCCGGAGTACTTCA 59.033 61.111 5.05 0.00 35.56 3.02
2076 3837 3.069729 GGTAGAGTATTTGCAGGACCGAT 59.930 47.826 0.00 0.00 0.00 4.18
2278 4042 0.763035 ACGAACAAGCCCTGGTTAGT 59.237 50.000 0.00 0.00 0.00 2.24
2305 4069 3.195396 GCTTGGAGGTTTCATTAATGGCA 59.805 43.478 15.36 0.00 0.00 4.92
2313 4077 4.382901 GGTTTCATTAATGGCAGCCAATCA 60.383 41.667 20.84 0.85 36.95 2.57
2338 4102 0.770557 AAGTAGGAAGTGGCCACCCA 60.771 55.000 32.29 14.35 39.32 4.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
269 273 3.709633 ACTGGCGAGGCATCAGCA 61.710 61.111 14.93 3.51 44.61 4.41
301 305 1.820519 GCAGGAAATCAATCACAGCCA 59.179 47.619 0.00 0.00 0.00 4.75
339 343 7.269316 TCAACAATGTCCAAATATAGTCGCTA 58.731 34.615 0.00 0.00 0.00 4.26
370 374 3.375299 ACATGCCGCTGAAAATAGTTCTC 59.625 43.478 0.00 0.00 0.00 2.87
540 552 4.202398 CCATATCATACAGCCTGAACACCT 60.202 45.833 0.00 0.00 0.00 4.00
566 578 2.184020 CTTCACGGCCCATCAGTCCA 62.184 60.000 0.00 0.00 0.00 4.02
879 891 3.517901 ACGATGTTTTACCCAGGATCAGA 59.482 43.478 0.00 0.00 0.00 3.27
881 893 3.008594 ACACGATGTTTTACCCAGGATCA 59.991 43.478 0.00 0.00 0.00 2.92
937 949 3.948719 GGGGTCCCGAACTGTGCA 61.949 66.667 0.48 0.00 0.00 4.57
980 992 1.300620 CGTGGAACTTGGCGACAGA 60.301 57.895 0.00 0.00 44.54 3.41
982 994 2.970324 GCGTGGAACTTGGCGACA 60.970 61.111 0.00 0.00 39.83 4.35
1093 1106 1.607148 TCCTCGATTGTCGCGTATCAT 59.393 47.619 5.77 0.00 40.21 2.45
1184 1197 3.092301 GCTAATTGAAGCCCTTCCAACT 58.908 45.455 5.64 0.00 38.77 3.16
1527 3278 8.453238 ACAAAGTTTTGGTTTTAGTTTTTGGT 57.547 26.923 9.22 0.00 42.34 3.67
2028 3789 0.894141 TGTTGCAGTTTGTTGCCACT 59.106 45.000 4.27 0.00 43.43 4.00
2076 3837 0.394762 GCAAGGCATCTCCATGGTCA 60.395 55.000 12.58 0.00 34.23 4.02
2203 3964 1.380785 ATCCCGTCCGTAGAAGGCA 60.381 57.895 0.00 0.00 40.08 4.75
2251 4015 2.629763 GCTTGTTCGTCGCGGTTT 59.370 55.556 6.13 0.00 0.00 3.27
2278 4042 6.295236 CCATTAATGAAACCTCCAAGCTTCAA 60.295 38.462 17.23 0.00 31.94 2.69
2305 4069 3.445008 TCCTACTTCTGTCTGATTGGCT 58.555 45.455 0.00 0.00 0.00 4.75
2313 4077 1.903183 GGCCACTTCCTACTTCTGTCT 59.097 52.381 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.