Multiple sequence alignment - TraesCS1A01G179600

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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 TraesCS1A01G179600 chr1A 100.000 2435 0 0 1 2435 324501943 324499509 0 4497
1 TraesCS1A01G179600 chr1D 95.186 2472 72 19 1 2435 252924632 252922171 0 3862
2 TraesCS1A01G179600 chr1B 94.919 2460 82 17 1 2435 359894074 359896515 0 3810


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 TraesCS1A01G179600 chr1A 324499509 324501943 2434 True 4497 4497 100.000 1 2435 1 chr1A.!!$R1 2434
1 TraesCS1A01G179600 chr1D 252922171 252924632 2461 True 3862 3862 95.186 1 2435 1 chr1D.!!$R1 2434
2 TraesCS1A01G179600 chr1B 359894074 359896515 2441 False 3810 3810 94.919 1 2435 1 chr1B.!!$F1 2434

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
542 563 0.949397 GGGACTTTGTGGGTTCGTTC 59.051 55.0 0.0 0.0 0.0 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1713 1749 0.947244 AGTTGGAGCAAACAAGAGCG 59.053 50.0 0.0 0.0 35.48 5.03 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
73 92 1.827789 CTGGCGGAGAGAGAGAGGG 60.828 68.421 0.00 0.0 0.00 4.30
87 106 3.039526 AGGGAGGGAGGGAGAGGG 61.040 72.222 0.00 0.0 0.00 4.30
183 202 2.546162 GCCTCTGCCCTCTATTACGTTC 60.546 54.545 0.00 0.0 0.00 3.95
184 203 2.959707 CCTCTGCCCTCTATTACGTTCT 59.040 50.000 0.00 0.0 0.00 3.01
187 206 5.416271 TCTGCCCTCTATTACGTTCTTTT 57.584 39.130 0.00 0.0 0.00 2.27
190 209 5.175859 TGCCCTCTATTACGTTCTTTTCTG 58.824 41.667 0.00 0.0 0.00 3.02
303 322 1.140252 CGGTCCGAATCCCTAATTGGT 59.860 52.381 4.91 0.0 0.00 3.67
308 327 3.389983 TCCGAATCCCTAATTGGTGTAGG 59.610 47.826 0.00 0.0 38.32 3.18
415 436 2.230266 CTGGTAAATTTGTGAACCGGGG 59.770 50.000 6.32 0.0 35.17 5.73
421 442 1.354168 TTTGTGAACCGGGGAAGGGA 61.354 55.000 6.32 0.0 35.02 4.20
443 464 3.137728 ACAGCTAGGTGTTTGGTTTACCT 59.862 43.478 21.62 0.0 46.13 3.08
542 563 0.949397 GGGACTTTGTGGGTTCGTTC 59.051 55.000 0.00 0.0 0.00 3.95
617 638 3.227614 GGTGTTGTGGGATTTTACTGGT 58.772 45.455 0.00 0.0 0.00 4.00
622 643 5.422331 TGTTGTGGGATTTTACTGGTTTTGA 59.578 36.000 0.00 0.0 0.00 2.69
633 654 2.629617 ACTGGTTTTGATCTGCCAAAGG 59.370 45.455 0.00 0.0 37.34 3.11
663 684 6.480320 ACGGATTTATAGTGAATCTTGTCAGC 59.520 38.462 0.00 0.0 34.65 4.26
721 742 8.883731 AGATTTATCTGTAGAAAATTGTGGTCG 58.116 33.333 0.00 0.0 35.42 4.79
877 913 1.013596 CAACAAGAACTGTCACCGCA 58.986 50.000 0.00 0.0 37.23 5.69
989 1025 2.368875 GGGTCTGTGAAGAGGTTTCTCA 59.631 50.000 0.00 0.0 42.34 3.27
1150 1186 2.094752 GGAAACATGTACCGCTGCAAAT 60.095 45.455 0.00 0.0 0.00 2.32
1246 1282 0.532862 AGTGAGTGGGCAGTTGTTCG 60.533 55.000 0.00 0.0 0.00 3.95
1374 1410 2.025887 GCATCCTTCCCCTTTTGAGAGA 60.026 50.000 0.00 0.0 0.00 3.10
1528 1564 7.733773 TTGACAGGATGGAAACTATAAGAGA 57.266 36.000 0.00 0.0 43.62 3.10
1713 1749 4.425520 AGATTATTTCTCTATAGCGCGGC 58.574 43.478 8.83 0.0 0.00 6.53
2041 2077 4.904241 ACATCTATATTGCTTCCTCCTGC 58.096 43.478 0.00 0.0 0.00 4.85
2219 2260 2.034053 GGTGAATTGGTGTTCTTTCGCA 59.966 45.455 0.00 0.0 31.80 5.10
2278 2319 3.701205 TTGAGATCCTTTGCAGCAGTA 57.299 42.857 0.00 0.0 0.00 2.74
2286 2327 2.286294 CCTTTGCAGCAGTAGAATAGCG 59.714 50.000 7.92 0.0 0.00 4.26
2364 2405 7.301054 CGCTTGTCAGTTTATTTTGAAGAGAT 58.699 34.615 0.00 0.0 0.00 2.75
2393 2434 6.624423 CAAAACTGTTTGCTGCTATCCTTAT 58.376 36.000 6.53 0.0 37.89 1.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 48 3.316573 CTCTCCGCCAGGGAACACC 62.317 68.421 0.00 0.0 46.61 4.16
48 49 2.232298 CTCTCTCCGCCAGGGAACAC 62.232 65.000 0.00 0.0 46.61 3.32
73 92 2.015726 TCCTCCCTCTCCCTCCCTC 61.016 68.421 0.00 0.0 0.00 4.30
87 106 2.776913 CGGCCTTCGGTCTCTCCTC 61.777 68.421 0.00 0.0 34.75 3.71
108 127 3.644738 AGGAGGAGACGAGGTAAAAACAA 59.355 43.478 0.00 0.0 0.00 2.83
303 322 1.169661 CCACAGCGCCAAAACCTACA 61.170 55.000 2.29 0.0 0.00 2.74
308 327 2.658268 GCACCACAGCGCCAAAAC 60.658 61.111 2.29 0.0 0.00 2.43
415 436 2.427506 CAAACACCTAGCTGTCCCTTC 58.572 52.381 0.00 0.0 0.00 3.46
421 442 3.137728 AGGTAAACCAAACACCTAGCTGT 59.862 43.478 0.00 0.0 40.93 4.40
443 464 2.923629 ACCTACCCCTTTTAATCCTGCA 59.076 45.455 0.00 0.0 0.00 4.41
519 540 1.770294 GAACCCACAAAGTCCCACAA 58.230 50.000 0.00 0.0 0.00 3.33
520 541 0.464735 CGAACCCACAAAGTCCCACA 60.465 55.000 0.00 0.0 0.00 4.17
521 542 0.464916 ACGAACCCACAAAGTCCCAC 60.465 55.000 0.00 0.0 0.00 4.61
522 543 0.256464 AACGAACCCACAAAGTCCCA 59.744 50.000 0.00 0.0 0.00 4.37
523 544 0.949397 GAACGAACCCACAAAGTCCC 59.051 55.000 0.00 0.0 0.00 4.46
524 545 0.584876 CGAACGAACCCACAAAGTCC 59.415 55.000 0.00 0.0 0.00 3.85
525 546 1.292992 ACGAACGAACCCACAAAGTC 58.707 50.000 0.14 0.0 0.00 3.01
526 547 2.159057 ACTACGAACGAACCCACAAAGT 60.159 45.455 0.14 0.0 0.00 2.66
531 552 2.472816 TCAAACTACGAACGAACCCAC 58.527 47.619 0.14 0.0 0.00 4.61
535 556 2.477375 TGGCATCAAACTACGAACGAAC 59.523 45.455 0.14 0.0 0.00 3.95
542 563 1.086696 CCACCTGGCATCAAACTACG 58.913 55.000 0.00 0.0 0.00 3.51
589 610 0.555769 ATCCCACAACACCACAACCT 59.444 50.000 0.00 0.0 0.00 3.50
633 654 5.063880 AGATTCACTATAAATCCGTTGGCC 58.936 41.667 0.00 0.0 34.34 5.36
795 831 2.069273 AGAGGACTTTTGCATCGAACG 58.931 47.619 0.00 0.0 0.00 3.95
845 881 6.992715 ACAGTTCTTGTTGCTATTACTGAACT 59.007 34.615 0.00 0.0 36.31 3.01
877 913 2.742428 AGCACTTGCATATGACCCAT 57.258 45.000 6.97 0.0 45.16 4.00
989 1025 0.981183 TACCTCCATTGTTCTGCCGT 59.019 50.000 0.00 0.0 0.00 5.68
1103 1139 2.068915 TGCTCATTCTGGCACCTCA 58.931 52.632 0.00 0.0 33.23 3.86
1150 1186 4.644234 ACAAATGTGTGTCATTCCAGTCAA 59.356 37.500 0.00 0.0 44.85 3.18
1246 1282 2.125753 CTCCAGTGGTGAGAGCGC 60.126 66.667 9.54 0.0 31.26 5.92
1310 1346 2.679716 AGGAGCACCCTTCATGGC 59.320 61.111 0.00 0.0 44.85 4.40
1374 1410 1.076923 AGACACGGCGGAGTAGGAT 60.077 57.895 13.24 0.0 0.00 3.24
1609 1645 4.829872 ACGATTACAACAAGGTCCCATA 57.170 40.909 0.00 0.0 0.00 2.74
1713 1749 0.947244 AGTTGGAGCAAACAAGAGCG 59.053 50.000 0.00 0.0 35.48 5.03
2041 2077 6.101997 AGGAAAGAAGCAAGTCAAAACAAAG 58.898 36.000 0.00 0.0 0.00 2.77
2133 2170 8.141268 TGAAATCAACTTAACAAAGGGAACATC 58.859 33.333 0.00 0.0 0.00 3.06
2167 2204 7.510549 AGCATACAAAACAAGTGAACACTAT 57.489 32.000 7.90 0.0 41.58 2.12
2168 2205 6.935741 AGCATACAAAACAAGTGAACACTA 57.064 33.333 7.90 0.0 41.58 2.74
2219 2260 0.995024 CCTCCCATGGACCAAGAAGT 59.005 55.000 15.22 0.0 0.00 3.01
2278 2319 4.406003 ACTTTGATGGTACCTCGCTATTCT 59.594 41.667 14.36 0.0 0.00 2.40
2286 2327 3.522553 CCGAAGACTTTGATGGTACCTC 58.477 50.000 14.36 8.8 0.00 3.85
2393 2434 7.446931 TCACAATGCACTGGAAAAGACTAATTA 59.553 33.333 0.00 0.0 0.00 1.40


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

AutoCloner maintained by Alex Coulton.