Multiple sequence alignment - TraesCS5D01G356700

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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 TraesCS5D01G356700 chr5D 100.000 2972 0 0 1 2972 437806616 437803645 0.000000e+00 5489
1 TraesCS5D01G356700 chr5B 96.667 3000 51 19 1 2972 531645340 531648318 0.000000e+00 4940
2 TraesCS5D01G356700 chr5A 93.502 1816 90 12 1175 2972 552745933 552744128 0.000000e+00 2675
3 TraesCS5D01G356700 chr5A 82.812 768 49 31 1 745 552747694 552746987 7.040000e-171 610
4 TraesCS5D01G356700 chr5A 92.658 395 24 4 788 1178 552746619 552746226 5.560000e-157 564


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 TraesCS5D01G356700 chr5D 437803645 437806616 2971 True 5489 5489 100.000000 1 2972 1 chr5D.!!$R1 2971
1 TraesCS5D01G356700 chr5B 531645340 531648318 2978 False 4940 4940 96.667000 1 2972 1 chr5B.!!$F1 2971
2 TraesCS5D01G356700 chr5A 552744128 552747694 3566 True 1283 2675 89.657333 1 2972 3 chr5A.!!$R1 2971

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
366 373 0.256752 TGTTCCATGAGGCATGAGGG 59.743 55.000 8.87 0.0 43.81 4.30 F
679 703 0.511221 CCCAAACTGACGTTGCGTAG 59.489 55.000 0.00 0.0 41.37 3.51 F
1169 1522 1.541147 TCAAGCTGCACCTTATGTTGC 59.459 47.619 1.02 0.0 0.00 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1315 1964 0.178961 GGAAGTTGCCCCACCTTCTT 60.179 55.0 3.18 0.0 35.90 2.52 R
1858 2508 0.625316 TGCTGGGCATTACCATCAGT 59.375 50.0 0.00 0.0 40.36 3.41 R
1976 2643 5.010282 AGAATTACCCAAAAAGCATCGAGT 58.990 37.5 0.00 0.0 0.00 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
216 223 4.191544 TCACACTATGTTGCTAGGATTGC 58.808 43.478 0.00 0.00 0.00 3.56
275 282 2.583024 TGGATGTGTTCTGGCAATCA 57.417 45.000 0.00 0.00 0.00 2.57
276 283 3.090210 TGGATGTGTTCTGGCAATCAT 57.910 42.857 0.00 0.00 0.00 2.45
277 284 3.018856 TGGATGTGTTCTGGCAATCATC 58.981 45.455 0.00 0.00 0.00 2.92
342 349 2.021723 GCCTGTCAACTGTTTGGTGGA 61.022 52.381 0.00 0.00 33.29 4.02
359 366 2.360165 GTGGATGAATGTTCCATGAGGC 59.640 50.000 0.00 0.00 44.75 4.70
362 369 3.005472 GGATGAATGTTCCATGAGGCATG 59.995 47.826 0.00 0.00 41.10 4.06
363 370 3.369242 TGAATGTTCCATGAGGCATGA 57.631 42.857 8.87 0.00 43.81 3.07
364 371 3.284617 TGAATGTTCCATGAGGCATGAG 58.715 45.455 8.87 0.31 43.81 2.90
365 372 2.359981 ATGTTCCATGAGGCATGAGG 57.640 50.000 8.87 0.00 43.81 3.86
366 373 0.256752 TGTTCCATGAGGCATGAGGG 59.743 55.000 8.87 0.00 43.81 4.30
367 374 0.548031 GTTCCATGAGGCATGAGGGA 59.452 55.000 8.87 0.00 43.81 4.20
368 375 1.144503 GTTCCATGAGGCATGAGGGAT 59.855 52.381 8.87 0.00 43.81 3.85
439 446 6.985188 TGTAGGCTGTTTAAATAGCTGAAG 57.015 37.500 28.82 0.43 42.09 3.02
452 459 1.853319 CTGAAGTTGCGACCGTGTC 59.147 57.895 0.00 0.00 0.00 3.67
458 465 1.590525 TTGCGACCGTGTCACTGTC 60.591 57.895 15.43 15.43 32.09 3.51
679 703 0.511221 CCCAAACTGACGTTGCGTAG 59.489 55.000 0.00 0.00 41.37 3.51
811 1160 9.094578 CATATCTTCTCCCTCTTTTACTATCCA 57.905 37.037 0.00 0.00 0.00 3.41
952 1301 4.065088 TGTTCTGCAGAATTTTAGACGCT 58.935 39.130 30.65 0.00 36.33 5.07
990 1339 5.121768 CGGTTTGATTACAGGTCTTGGTTAG 59.878 44.000 0.00 0.00 0.00 2.34
1169 1522 1.541147 TCAAGCTGCACCTTATGTTGC 59.459 47.619 1.02 0.00 0.00 4.17
1313 1962 4.338964 TCAGAAGAAAGCTGCAATTGTTCA 59.661 37.500 21.34 0.00 32.83 3.18
1314 1963 4.680110 CAGAAGAAAGCTGCAATTGTTCAG 59.320 41.667 21.34 14.15 32.83 3.02
1315 1964 4.581824 AGAAGAAAGCTGCAATTGTTCAGA 59.418 37.500 21.34 0.00 32.83 3.27
1501 2150 7.704472 TCAATGGACATGTTGTGTAAGTTTTTC 59.296 33.333 0.00 0.00 42.36 2.29
1707 2357 3.238108 ACTGGTAGCAGAACATCTTCG 57.762 47.619 27.87 0.00 0.00 3.79
1858 2508 3.054728 TGGGAGACAAACAAGTGAAGTGA 60.055 43.478 0.00 0.00 0.00 3.41
1952 2619 3.558033 AGTTCTCTAAGTCGGAGATCCC 58.442 50.000 0.00 0.00 40.67 3.85
1976 2643 5.010112 CGAGGAAGCCTAATATCTGAAGACA 59.990 44.000 0.00 0.00 31.76 3.41
2393 3062 7.973048 TGATACTAACAGGGACTACTTGATT 57.027 36.000 0.00 0.00 36.02 2.57
2631 3301 5.983333 ATTTGATGTTACTCCCTGGATCT 57.017 39.130 0.00 0.00 0.00 2.75
2632 3302 5.779241 TTTGATGTTACTCCCTGGATCTT 57.221 39.130 0.00 0.00 0.00 2.40
2633 3303 5.779241 TTGATGTTACTCCCTGGATCTTT 57.221 39.130 0.00 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
216 223 3.107601 TGGAGAAGACATTAGGACCAGG 58.892 50.000 0.00 0.00 0.00 4.45
359 366 3.834489 AACAGCAGTCTATCCCTCATG 57.166 47.619 0.00 0.00 0.00 3.07
362 369 3.449018 TCTGAAACAGCAGTCTATCCCTC 59.551 47.826 0.00 0.00 37.20 4.30
363 370 3.445008 TCTGAAACAGCAGTCTATCCCT 58.555 45.455 0.00 0.00 37.20 4.20
364 371 3.895232 TCTGAAACAGCAGTCTATCCC 57.105 47.619 0.00 0.00 37.20 3.85
365 372 5.988561 CCTAATCTGAAACAGCAGTCTATCC 59.011 44.000 0.00 0.00 37.20 2.59
366 373 6.810911 TCCTAATCTGAAACAGCAGTCTATC 58.189 40.000 0.00 0.00 37.20 2.08
367 374 6.798427 TCCTAATCTGAAACAGCAGTCTAT 57.202 37.500 0.00 0.00 37.20 1.98
368 375 6.605471 TTCCTAATCTGAAACAGCAGTCTA 57.395 37.500 0.00 0.00 37.20 2.59
439 446 1.818221 GACAGTGACACGGTCGCAAC 61.818 60.000 20.56 1.47 44.42 4.17
452 459 5.974158 CCAACTGATAGACTTATCGACAGTG 59.026 44.000 3.82 0.00 38.83 3.66
458 465 7.327275 GCAGATTACCAACTGATAGACTTATCG 59.673 40.741 0.00 0.00 38.83 2.92
786 1128 9.095700 GTGGATAGTAAAAGAGGGAGAAGATAT 57.904 37.037 0.00 0.00 0.00 1.63
811 1160 2.907042 ACTAGCTAAAACAGAGCAGGGT 59.093 45.455 0.00 0.00 42.69 4.34
990 1339 0.532862 CGGGATCCATGGTACTGTGC 60.533 60.000 15.23 0.00 0.00 4.57
1110 1463 6.701400 CCAGTACATCTTTTTCAAAAACCTGG 59.299 38.462 0.00 0.00 0.00 4.45
1169 1522 0.598065 GGGCCGCATATTAAGCCTTG 59.402 55.000 0.00 0.00 45.07 3.61
1313 1962 0.853530 AAGTTGCCCCACCTTCTTCT 59.146 50.000 0.00 0.00 0.00 2.85
1314 1963 1.248486 GAAGTTGCCCCACCTTCTTC 58.752 55.000 0.00 0.00 33.45 2.87
1315 1964 0.178961 GGAAGTTGCCCCACCTTCTT 60.179 55.000 3.18 0.00 35.90 2.52
1707 2357 0.886563 AGCAGCACCAGCAATCTTTC 59.113 50.000 0.00 0.00 45.49 2.62
1858 2508 0.625316 TGCTGGGCATTACCATCAGT 59.375 50.000 0.00 0.00 40.36 3.41
1952 2619 5.010112 TGTCTTCAGATATTAGGCTTCCTCG 59.990 44.000 0.00 0.00 34.61 4.63
1976 2643 5.010282 AGAATTACCCAAAAAGCATCGAGT 58.990 37.500 0.00 0.00 0.00 4.18
2118 2787 8.548880 TGTTCTTTCCATAGCTACTTAGGTAT 57.451 34.615 0.00 2.70 45.06 2.73
2302 2971 6.828273 CAGAAATCACCATGGTCCTTTATGTA 59.172 38.462 23.22 4.13 0.00 2.29


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

AutoCloner maintained by Alex Coulton.