Multiple sequence alignment - TraesCS6D01G236800

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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 TraesCS6D01G236800 chr6D 100.000 2282 0 0 1 2282 334342193 334339912 0.000000e+00 4215
1 TraesCS6D01G236800 chr6A 94.963 814 23 13 1475 2282 473737935 473737134 0.000000e+00 1260
2 TraesCS6D01G236800 chr6A 92.634 801 23 12 532 1322 473739315 473738541 0.000000e+00 1120
3 TraesCS6D01G236800 chr6A 87.090 457 22 18 129 553 473742413 473741962 1.230000e-132 483
4 TraesCS6D01G236800 chr6A 94.656 131 6 1 1326 1456 473738506 473738377 3.840000e-48 202
5 TraesCS6D01G236800 chr6A 92.308 130 9 1 1 130 473742581 473742453 1.390000e-42 183
6 TraesCS6D01G236800 chr6B 87.552 715 42 14 129 818 485874515 485875207 0.000000e+00 784
7 TraesCS6D01G236800 chr6B 93.690 523 27 3 1475 1991 485876442 485876964 0.000000e+00 778
8 TraesCS6D01G236800 chr6B 87.812 681 29 23 817 1453 485875322 485875992 0.000000e+00 749
9 TraesCS6D01G236800 chr6B 84.062 320 28 10 1982 2282 485878103 485878418 1.030000e-73 287
10 TraesCS6D01G236800 chr6B 93.382 136 6 2 1 136 485874348 485874480 4.970000e-47 198


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 TraesCS6D01G236800 chr6D 334339912 334342193 2281 True 4215.0 4215 100.0000 1 2282 1 chr6D.!!$R1 2281
1 TraesCS6D01G236800 chr6A 473737134 473742581 5447 True 649.6 1260 92.3302 1 2282 5 chr6A.!!$R1 2281
2 TraesCS6D01G236800 chr6B 485874348 485878418 4070 False 559.2 784 89.2996 1 2282 5 chr6B.!!$F1 2281

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
953 3832 2.108514 TACGTCGACCGCTACCCTG 61.109 63.158 10.58 0.0 41.42 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1960 5323 1.369091 CCCGCAGTGAGGAAAATCGG 61.369 60.0 15.36 4.51 35.6 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
76 77 2.158234 TGGCCAACCCCAAACTTTAGAT 60.158 45.455 0.61 0.00 33.59 1.98
202 243 3.090952 TGTGGGCGAAACTTTGAATTG 57.909 42.857 0.00 0.00 0.00 2.32
205 246 2.287308 TGGGCGAAACTTTGAATTGTCG 60.287 45.455 0.00 0.00 0.00 4.35
275 316 3.181495 TGCCTTCACAAAACACCTTTACG 60.181 43.478 0.00 0.00 0.00 3.18
332 374 3.004419 CGACGTCTTATTCCTCCTGCATA 59.996 47.826 14.70 0.00 0.00 3.14
334 376 3.243434 ACGTCTTATTCCTCCTGCATACG 60.243 47.826 0.00 0.00 0.00 3.06
367 409 4.802039 GTCAGTTTTTGCAGCATATGGATG 59.198 41.667 4.56 0.00 35.52 3.51
371 413 6.019075 CAGTTTTTGCAGCATATGGATGATTG 60.019 38.462 4.56 0.00 33.82 2.67
668 3417 3.435186 GCCTCAAGCCCTCAACGC 61.435 66.667 0.00 0.00 34.35 4.84
669 3418 2.747855 CCTCAAGCCCTCAACGCC 60.748 66.667 0.00 0.00 0.00 5.68
748 3498 4.886579 TGCTGATATGATACGCTTGACAT 58.113 39.130 0.00 0.00 0.00 3.06
793 3543 6.194142 CGAATACGTACTGCTAGTAACAAGTG 59.806 42.308 0.00 0.00 31.62 3.16
828 3694 7.167136 GCTGGTATAAGTTTGTGACGAGTATAC 59.833 40.741 0.00 0.00 32.70 1.47
953 3832 2.108514 TACGTCGACCGCTACCCTG 61.109 63.158 10.58 0.00 41.42 4.45
954 3833 2.520465 TACGTCGACCGCTACCCTGA 62.520 60.000 10.58 0.00 41.42 3.86
955 3834 2.488820 GTCGACCGCTACCCTGAC 59.511 66.667 3.51 0.00 0.00 3.51
956 3835 2.753043 TCGACCGCTACCCTGACC 60.753 66.667 0.00 0.00 0.00 4.02
957 3836 2.754658 CGACCGCTACCCTGACCT 60.755 66.667 0.00 0.00 0.00 3.85
958 3837 2.772691 CGACCGCTACCCTGACCTC 61.773 68.421 0.00 0.00 0.00 3.85
959 3838 2.754658 ACCGCTACCCTGACCTCG 60.755 66.667 0.00 0.00 0.00 4.63
960 3839 3.528370 CCGCTACCCTGACCTCGG 61.528 72.222 0.00 0.00 0.00 4.63
962 3841 3.851128 GCTACCCTGACCTCGGGC 61.851 72.222 0.00 0.00 46.04 6.13
963 3842 3.155167 CTACCCTGACCTCGGGCC 61.155 72.222 0.00 0.00 46.04 5.80
1215 4111 4.888325 CTGGATCGCCCCCTCCCT 62.888 72.222 0.00 0.00 0.00 4.20
1285 4181 3.788766 GCGACGCCAAATGACGCT 61.789 61.111 9.14 0.00 44.67 5.07
1322 4218 5.607939 TGGCTACGATCATTCTTTCCTTA 57.392 39.130 0.00 0.00 0.00 2.69
1425 4352 1.950472 CGCATGACTTGTTCCGTTTC 58.050 50.000 0.00 0.00 0.00 2.78
1433 4360 3.628008 ACTTGTTCCGTTTCCCTTTTCT 58.372 40.909 0.00 0.00 0.00 2.52
1437 4364 2.816087 GTTCCGTTTCCCTTTTCTACCC 59.184 50.000 0.00 0.00 0.00 3.69
1438 4365 2.056359 TCCGTTTCCCTTTTCTACCCA 58.944 47.619 0.00 0.00 0.00 4.51
1439 4366 2.645797 TCCGTTTCCCTTTTCTACCCAT 59.354 45.455 0.00 0.00 0.00 4.00
1453 4406 6.852420 TTCTACCCATAGTATAGTCATGGC 57.148 41.667 0.00 0.00 38.32 4.40
1472 4425 4.993028 TGGCCTAAACTTCACAAATAGGT 58.007 39.130 3.32 0.00 36.37 3.08
1854 5217 3.526385 ACGCGCTGCAATATATTTCAG 57.474 42.857 17.66 17.66 34.77 3.02
2018 6529 1.846439 AGCATAGCTCCTTTTGCCCTA 59.154 47.619 0.00 0.00 30.62 3.53
2025 6538 3.117851 AGCTCCTTTTGCCCTACCTATTC 60.118 47.826 0.00 0.00 0.00 1.75
2032 6545 8.065007 TCCTTTTGCCCTACCTATTCATATTTT 58.935 33.333 0.00 0.00 0.00 1.82
2049 6563 8.495160 TCATATTTTCCGGGGTATTTCTAGTA 57.505 34.615 0.00 0.00 0.00 1.82
2060 6574 9.049523 CGGGGTATTTCTAGTAATTTTTACCTC 57.950 37.037 10.06 6.63 0.00 3.85
2189 6716 9.377312 AGTTTTCAAGCTGTTTTTGCTATTTTA 57.623 25.926 0.00 0.00 40.22 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
76 77 9.838339 GGATGAGGAGTTTGAGAGAATAATTAA 57.162 33.333 0.00 0.00 0.00 1.40
164 205 5.241285 GCCCACATTTTGACCAAATTTTGAT 59.759 36.000 10.72 0.00 32.24 2.57
202 243 7.089249 ACTTTTCGCAAATATTTTGAACGAC 57.911 32.000 10.64 0.00 0.00 4.34
205 246 9.695884 TTTGAACTTTTCGCAAATATTTTGAAC 57.304 25.926 10.64 3.01 0.00 3.18
275 316 7.554476 AGAGACTAGGATGCATTTTTAGTTTCC 59.446 37.037 20.64 9.79 30.18 3.13
332 374 0.672342 AAACTGACCGACTACTGCGT 59.328 50.000 0.00 0.00 0.00 5.24
334 376 2.349532 GCAAAAACTGACCGACTACTGC 60.350 50.000 0.00 0.00 0.00 4.40
336 378 3.131396 CTGCAAAAACTGACCGACTACT 58.869 45.455 0.00 0.00 0.00 2.57
367 409 6.966534 AATAATTGTCACCTCATCCCAATC 57.033 37.500 0.00 0.00 0.00 2.67
371 413 4.452455 CGCTAATAATTGTCACCTCATCCC 59.548 45.833 0.00 0.00 0.00 3.85
748 3498 4.278310 TCGCTAGCTATATCTAATGGCCA 58.722 43.478 8.56 8.56 0.00 5.36
793 3543 4.423625 AACTTATACCAGCACTGATCCC 57.576 45.455 0.00 0.00 0.00 3.85
941 3820 2.772691 CGAGGTCAGGGTAGCGGTC 61.773 68.421 0.00 0.00 0.00 4.79
942 3821 2.754658 CGAGGTCAGGGTAGCGGT 60.755 66.667 0.00 0.00 0.00 5.68
1215 4111 4.357947 GACTCCACGGCGCTGTCA 62.358 66.667 21.45 8.23 0.00 3.58
1285 4181 1.496060 AGCCATAGATCGACCAACCA 58.504 50.000 0.00 0.00 0.00 3.67
1322 4218 3.938963 AGACGTGTTGATGTTCTTTGTGT 59.061 39.130 0.00 0.00 0.00 3.72
1407 4334 1.068541 GGGAAACGGAACAAGTCATGC 60.069 52.381 0.00 0.00 0.00 4.06
1425 4352 7.850935 TGACTATACTATGGGTAGAAAAGGG 57.149 40.000 0.00 0.00 33.51 3.95
1433 4360 5.285317 AGGCCATGACTATACTATGGGTA 57.715 43.478 5.01 0.00 41.28 3.69
1437 4364 8.367911 TGAAGTTTAGGCCATGACTATACTATG 58.632 37.037 5.01 0.00 35.07 2.23
1438 4365 8.368668 GTGAAGTTTAGGCCATGACTATACTAT 58.631 37.037 5.01 9.47 35.07 2.12
1439 4366 7.343574 TGTGAAGTTTAGGCCATGACTATACTA 59.656 37.037 5.01 4.75 35.07 1.82
1472 4425 6.855914 GCAAAAACGAAAATAGAGATGTCACA 59.144 34.615 0.00 0.00 0.00 3.58
1784 5147 5.551760 AGTTTATGGAAAAGATCTGCACG 57.448 39.130 0.00 0.00 0.00 5.34
1960 5323 1.369091 CCCGCAGTGAGGAAAATCGG 61.369 60.000 15.36 4.51 35.60 4.18
2018 6529 6.713731 ATACCCCGGAAAATATGAATAGGT 57.286 37.500 0.73 0.00 0.00 3.08
2025 6538 9.734984 ATTACTAGAAATACCCCGGAAAATATG 57.265 33.333 0.73 0.00 0.00 1.78
2032 6545 7.992608 GGTAAAAATTACTAGAAATACCCCGGA 59.007 37.037 0.73 0.00 0.00 5.14
2095 6610 9.154847 GGAAAACCTTGAGAATAATGGAAAATG 57.845 33.333 0.00 0.00 0.00 2.32
2104 6619 7.998964 ACTGAGAAAGGAAAACCTTGAGAATAA 59.001 33.333 2.18 0.00 0.00 1.40
2109 6624 7.751768 AATACTGAGAAAGGAAAACCTTGAG 57.248 36.000 2.18 0.67 0.00 3.02


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

AutoCloner maintained by Alex Coulton.