Multiple sequence alignment - TraesCS6D01G202400

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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 TraesCS6D01G202400 chr6D 100.000 2257 0 0 1 2257 285868336 285870592 0.000000e+00 4169
1 TraesCS6D01G202400 chr6B 95.648 2275 74 11 1 2257 446834879 446837146 0.000000e+00 3629
2 TraesCS6D01G202400 chr6A 94.221 2284 89 17 1 2257 407084208 407086475 0.000000e+00 3446
3 TraesCS6D01G202400 chr2B 81.732 843 154 0 1399 2241 531466730 531467572 0.000000e+00 704
4 TraesCS6D01G202400 chr2B 82.192 146 19 4 994 1138 531466328 531466467 3.940000e-23 119
5 TraesCS6D01G202400 chr2D 81.279 860 157 4 1399 2256 451287829 451288686 0.000000e+00 693
6 TraesCS6D01G202400 chr2D 82.192 146 19 4 994 1138 451287397 451287536 3.940000e-23 119


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 TraesCS6D01G202400 chr6D 285868336 285870592 2256 False 4169.0 4169 100.0000 1 2257 1 chr6D.!!$F1 2256
1 TraesCS6D01G202400 chr6B 446834879 446837146 2267 False 3629.0 3629 95.6480 1 2257 1 chr6B.!!$F1 2256
2 TraesCS6D01G202400 chr6A 407084208 407086475 2267 False 3446.0 3446 94.2210 1 2257 1 chr6A.!!$F1 2256
3 TraesCS6D01G202400 chr2B 531466328 531467572 1244 False 411.5 704 81.9620 994 2241 2 chr2B.!!$F1 1247
4 TraesCS6D01G202400 chr2D 451287397 451288686 1289 False 406.0 693 81.7355 994 2256 2 chr2D.!!$F1 1262

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
541 564 1.003851 TTCGATCCGCGGTGAAATTC 58.996 50.0 27.15 12.15 41.33 2.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1781 1883 0.035056 ATTCAGGAAGGCAACCTCGG 60.035 55.0 0.0 0.0 35.35 4.63 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
252 258 1.815003 GGTGACTTTCCCATCTTGCAG 59.185 52.381 0.00 0.00 0.00 4.41
316 328 2.584608 CCCACCACCATCTCGTCC 59.415 66.667 0.00 0.00 0.00 4.79
367 379 1.397692 TCGTCCGTTTGCTTTCGTTTT 59.602 42.857 0.00 0.00 0.00 2.43
415 428 3.371097 GATCCGTCGCTTGCTCCCA 62.371 63.158 0.00 0.00 0.00 4.37
436 458 1.337817 CTCGAGGTTTGTGACGAGCG 61.338 60.000 3.91 0.00 43.71 5.03
541 564 1.003851 TTCGATCCGCGGTGAAATTC 58.996 50.000 27.15 12.15 41.33 2.17
551 574 2.481185 GCGGTGAAATTCGTTTCCTGTA 59.519 45.455 0.00 0.00 0.00 2.74
677 704 6.683974 ATATGCAACACAGTCAGGAATTAC 57.316 37.500 0.00 0.00 0.00 1.89
822 855 6.060788 GCCTGGAATAGTCATCTTCAAATCT 58.939 40.000 0.00 0.00 0.00 2.40
897 931 7.360607 CCTTTACTTTATGTACCTGGTGAAACG 60.361 40.741 10.23 0.00 38.12 3.60
905 939 1.024579 CCTGGTGAAACGGGGAATCG 61.025 60.000 0.00 0.00 38.12 3.34
924 958 6.809196 GGAATCGCAGAAGGATATTAGTACTG 59.191 42.308 5.39 0.00 43.58 2.74
955 989 4.508124 CCTCGCAATATGTTCTGTACTTCC 59.492 45.833 0.00 0.00 0.00 3.46
971 1005 4.360951 ACTTCCATCGTTTCTAACCCAA 57.639 40.909 0.00 0.00 0.00 4.12
983 1017 4.028993 TCTAACCCAAATCAACCCACTC 57.971 45.455 0.00 0.00 0.00 3.51
1176 1238 2.350868 GCTCCTCCTTTCTTTTCGTTGC 60.351 50.000 0.00 0.00 0.00 4.17
1269 1331 3.169099 CCATCCTGATAATCCCTCTCGT 58.831 50.000 0.00 0.00 0.00 4.18
1322 1393 7.421684 TCCCCTTTCAATTCATCTTCCTAAAT 58.578 34.615 0.00 0.00 0.00 1.40
1428 1530 3.380393 TGGGTTCGAGGGATATGAGAAA 58.620 45.455 0.00 0.00 0.00 2.52
1781 1883 2.805099 CTCCACACAAGAACTTCTCTGC 59.195 50.000 0.00 0.00 33.37 4.26
1805 1907 1.260544 GTTGCCTTCCTGAATGGCTT 58.739 50.000 16.13 0.00 46.23 4.35
1982 2084 6.127479 GCTTCTATCTTCTTCAAGACCTCTGA 60.127 42.308 0.00 0.00 41.64 3.27
2250 2352 1.203001 TCCTTTGGCCCGTCTGAATTT 60.203 47.619 0.00 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
252 258 5.034797 GCTAAATAAACAAATGAGGCGACC 58.965 41.667 0.00 0.00 0.00 4.79
316 328 5.932303 TCTCACTCCGAATTTCTAGGTTTTG 59.068 40.000 0.00 0.00 0.00 2.44
367 379 1.195115 CCTCCTCACGGATCTCCAAA 58.805 55.000 0.00 0.00 39.01 3.28
370 382 1.834822 CCCCTCCTCACGGATCTCC 60.835 68.421 0.00 0.00 39.01 3.71
415 428 0.039074 CTCGTCACAAACCTCGAGCT 60.039 55.000 6.99 0.00 41.98 4.09
474 496 6.550938 TGAGCTGATGGAGAGAAATCTTAA 57.449 37.500 0.00 0.00 0.00 1.85
541 564 3.028850 TGATCCCTAGGTACAGGAAACG 58.971 50.000 8.29 0.00 38.00 3.60
551 574 4.589374 CGAAAAGGAGTATGATCCCTAGGT 59.411 45.833 8.29 0.00 40.53 3.08
677 704 3.488310 GCATATTCGTACAGTAACACGGG 59.512 47.826 0.00 0.00 38.66 5.28
863 896 8.683615 CAGGTACATAAAGTAAAGGGATTTTCC 58.316 37.037 0.00 0.00 33.72 3.13
867 901 7.037153 TCACCAGGTACATAAAGTAAAGGGATT 60.037 37.037 0.00 0.00 33.72 3.01
870 904 6.057321 TCACCAGGTACATAAAGTAAAGGG 57.943 41.667 0.00 0.00 33.72 3.95
874 908 5.933463 CCGTTTCACCAGGTACATAAAGTAA 59.067 40.000 0.00 0.00 33.72 2.24
897 931 3.425162 AATATCCTTCTGCGATTCCCC 57.575 47.619 0.00 0.00 0.00 4.81
905 939 7.793927 AAAAGCAGTACTAATATCCTTCTGC 57.206 36.000 0.00 0.00 44.44 4.26
924 958 5.739161 CAGAACATATTGCGAGGTAAAAAGC 59.261 40.000 0.00 0.00 0.00 3.51
955 989 5.399013 GGTTGATTTGGGTTAGAAACGATG 58.601 41.667 0.00 0.00 0.00 3.84
971 1005 4.739793 TCAAATTCTGGAGTGGGTTGATT 58.260 39.130 0.00 0.00 0.00 2.57
983 1017 5.840243 TTCCATAGCACATCAAATTCTGG 57.160 39.130 0.00 0.00 0.00 3.86
1176 1238 9.216117 TGAGCATCTAATCATCAACAAGATATG 57.784 33.333 0.00 0.00 32.67 1.78
1269 1331 2.782925 TCTAAGCAATTAGGATGGGGCA 59.217 45.455 0.00 0.00 0.00 5.36
1428 1530 1.205893 GAGAAAGTGATCTCCAGGCGT 59.794 52.381 0.00 0.00 39.98 5.68
1781 1883 0.035056 ATTCAGGAAGGCAACCTCGG 60.035 55.000 0.00 0.00 35.35 4.63
1805 1907 2.104792 CCAGACTTGAGTCCACCAAAGA 59.895 50.000 7.50 0.00 45.85 2.52
1963 2065 6.408320 CCATCATCAGAGGTCTTGAAGAAGAT 60.408 42.308 0.00 0.00 40.40 2.40
1982 2084 2.519771 ACAAGATGTGTGGCCATCAT 57.480 45.000 21.06 21.06 43.00 2.45


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

AutoCloner maintained by Alex Coulton.