Multiple sequence alignment - TraesCS7D01G319600

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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 TraesCS7D01G319600 chr7D 100.000 2954 0 0 1 2954 409162015 409164968 0.000000e+00 5456
1 TraesCS7D01G319600 chr7B 94.805 3003 80 23 3 2954 423548404 423551381 0.000000e+00 4612
2 TraesCS7D01G319600 chr7A 94.113 2735 51 24 294 2954 469356415 469359113 0.000000e+00 4058
3 TraesCS7D01G319600 chr7A 89.597 298 28 2 1 297 469353932 469354227 2.780000e-100 375


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 TraesCS7D01G319600 chr7D 409162015 409164968 2953 False 5456.0 5456 100.000 1 2954 1 chr7D.!!$F1 2953
1 TraesCS7D01G319600 chr7B 423548404 423551381 2977 False 4612.0 4612 94.805 3 2954 1 chr7B.!!$F1 2951
2 TraesCS7D01G319600 chr7A 469353932 469359113 5181 False 2216.5 4058 91.855 1 2954 2 chr7A.!!$F1 2953

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
281 284 0.249868 CGTGAGTTTGAGGTCCTGCA 60.25 55.0 0.0 0.0 0.0 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2107 4341 0.039764 TCGCAAGGAGAGGAGGAAGA 59.96 55.0 0.0 0.0 38.47 2.87 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
72 73 0.468585 ACTCCATGTATACCGGCCGA 60.469 55.000 30.73 8.21 0.00 5.54
74 75 2.097036 CTCCATGTATACCGGCCGATA 58.903 52.381 30.73 16.86 0.00 2.92
125 126 1.441729 CATGACTATGGCGACGGGT 59.558 57.895 0.00 0.00 0.00 5.28
228 231 2.354729 CCGGACAATGCCCCTTGA 59.645 61.111 0.00 0.00 0.00 3.02
233 236 1.477558 GGACAATGCCCCTTGATCGAT 60.478 52.381 0.00 0.00 0.00 3.59
259 262 3.284793 TGGACGAAAAGGGAAAAGACA 57.715 42.857 0.00 0.00 0.00 3.41
260 263 3.622630 TGGACGAAAAGGGAAAAGACAA 58.377 40.909 0.00 0.00 0.00 3.18
265 268 3.789224 CGAAAAGGGAAAAGACAAACGTG 59.211 43.478 0.00 0.00 0.00 4.49
281 284 0.249868 CGTGAGTTTGAGGTCCTGCA 60.250 55.000 0.00 0.00 0.00 4.41
297 300 1.474077 CTGCATTGGAGTTGGCCTAAC 59.526 52.381 3.32 7.14 39.65 2.34
299 302 1.892474 GCATTGGAGTTGGCCTAACAA 59.108 47.619 16.93 10.51 41.88 2.83
300 303 2.094545 GCATTGGAGTTGGCCTAACAAG 60.095 50.000 16.93 6.68 41.88 3.16
341 2535 2.769095 CCAAGAAGGGAAGGTAGAGGAG 59.231 54.545 0.00 0.00 0.00 3.69
342 2536 3.566775 CCAAGAAGGGAAGGTAGAGGAGA 60.567 52.174 0.00 0.00 0.00 3.71
353 2547 3.581332 AGGTAGAGGAGAGAGAGGATACG 59.419 52.174 0.00 0.00 46.39 3.06
470 2665 5.407502 GTTCTACTGCTCCTCTTTCTTCTC 58.592 45.833 0.00 0.00 0.00 2.87
1068 3283 1.050988 ACATGAGCCTCGGTAGCCAT 61.051 55.000 0.00 0.00 0.00 4.40
1134 3358 2.111043 CCGCCACCGCCATTATCT 59.889 61.111 0.00 0.00 0.00 1.98
1179 3403 0.609131 CACCCCCTCATCAACACCAC 60.609 60.000 0.00 0.00 0.00 4.16
1323 3550 2.365941 TCACCATGACTACCAACGTGAA 59.634 45.455 0.00 0.00 35.35 3.18
1837 4064 2.284625 TGATCGACTGGGCAGGGT 60.285 61.111 0.00 0.00 0.00 4.34
2085 4319 4.177783 CTCCTAACGCTTCTTCTTCTTCC 58.822 47.826 0.00 0.00 0.00 3.46
2088 4322 2.753055 ACGCTTCTTCTTCTTCCTCC 57.247 50.000 0.00 0.00 0.00 4.30
2100 4334 4.775253 TCTTCTTCCTCCTCTTCTTCTTCC 59.225 45.833 0.00 0.00 0.00 3.46
2104 4338 4.412060 TCCTCCTCTTCTTCTTCCTCTT 57.588 45.455 0.00 0.00 0.00 2.85
2105 4339 4.349365 TCCTCCTCTTCTTCTTCCTCTTC 58.651 47.826 0.00 0.00 0.00 2.87
2106 4340 4.045334 TCCTCCTCTTCTTCTTCCTCTTCT 59.955 45.833 0.00 0.00 0.00 2.85
2107 4341 4.777366 CCTCCTCTTCTTCTTCCTCTTCTT 59.223 45.833 0.00 0.00 0.00 2.52
2108 4342 5.105351 CCTCCTCTTCTTCTTCCTCTTCTTC 60.105 48.000 0.00 0.00 0.00 2.87
2109 4343 5.650283 TCCTCTTCTTCTTCCTCTTCTTCT 58.350 41.667 0.00 0.00 0.00 2.85
2110 4344 6.081356 TCCTCTTCTTCTTCCTCTTCTTCTT 58.919 40.000 0.00 0.00 0.00 2.52
2111 4345 6.210584 TCCTCTTCTTCTTCCTCTTCTTCTTC 59.789 42.308 0.00 0.00 0.00 2.87
2112 4346 6.353404 TCTTCTTCTTCCTCTTCTTCTTCC 57.647 41.667 0.00 0.00 0.00 3.46
2113 4347 6.081356 TCTTCTTCTTCCTCTTCTTCTTCCT 58.919 40.000 0.00 0.00 0.00 3.36
2114 4348 5.993748 TCTTCTTCCTCTTCTTCTTCCTC 57.006 43.478 0.00 0.00 0.00 3.71
2115 4349 4.775253 TCTTCTTCCTCTTCTTCTTCCTCC 59.225 45.833 0.00 0.00 0.00 4.30
2357 4591 6.093771 ACTGCTACACATACACAGTACTAGTC 59.906 42.308 0.00 0.00 39.69 2.59
2593 4851 3.383825 GCCCTCTCTCTGTCCGTTATTTA 59.616 47.826 0.00 0.00 0.00 1.40
2865 5147 1.505425 TCTTTCTCTGACGACGACGA 58.495 50.000 15.32 0.00 42.66 4.20
2949 5234 8.354426 GTCCTCTCCAGTATACTCATTCTTTAC 58.646 40.741 1.26 0.00 0.00 2.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 1.002069 TTGGGGAAGGACATGCAGAT 58.998 50.000 0.00 0.00 0.00 2.90
46 47 5.061179 GCCGGTATACATGGAGTTAATTGT 58.939 41.667 15.50 0.00 0.00 2.71
72 73 2.446848 ATGCCGGCCAGAGTGCTAT 61.447 57.895 26.77 3.74 0.00 2.97
74 75 4.790962 CATGCCGGCCAGAGTGCT 62.791 66.667 26.77 0.00 0.00 4.40
233 236 2.961531 TCCCTTTTCGTCCATTTGGA 57.038 45.000 0.00 0.00 43.08 3.53
259 262 2.561569 CAGGACCTCAAACTCACGTTT 58.438 47.619 0.00 0.00 43.85 3.60
260 263 1.810412 GCAGGACCTCAAACTCACGTT 60.810 52.381 0.00 0.00 34.03 3.99
265 268 1.815003 CCAATGCAGGACCTCAAACTC 59.185 52.381 0.00 0.00 0.00 3.01
277 280 1.474077 GTTAGGCCAACTCCAATGCAG 59.526 52.381 5.01 0.00 34.06 4.41
281 284 2.557452 CCCTTGTTAGGCCAACTCCAAT 60.557 50.000 5.01 0.00 40.50 3.16
297 300 1.952621 TCAACTCTCCCCTACCCTTG 58.047 55.000 0.00 0.00 0.00 3.61
299 302 1.651770 TCATCAACTCTCCCCTACCCT 59.348 52.381 0.00 0.00 0.00 4.34
300 303 1.763545 GTCATCAACTCTCCCCTACCC 59.236 57.143 0.00 0.00 0.00 3.69
341 2535 3.818773 CTCTTTCCCTCGTATCCTCTCTC 59.181 52.174 0.00 0.00 0.00 3.20
342 2536 3.460340 TCTCTTTCCCTCGTATCCTCTCT 59.540 47.826 0.00 0.00 0.00 3.10
353 2547 0.544223 GGCCTCCTTCTCTTTCCCTC 59.456 60.000 0.00 0.00 0.00 4.30
419 2614 5.295950 GCATATGCAAGAGTGATGTAGAGT 58.704 41.667 22.84 0.00 41.59 3.24
1068 3283 1.536073 CGAAGAGCAGAGGGTGGTGA 61.536 60.000 0.00 0.00 36.87 4.02
1134 3358 0.840722 GAGGAGGGTGGAGGTGGAAA 60.841 60.000 0.00 0.00 0.00 3.13
1179 3403 4.960866 TGCTGCTGGTGGTGCTGG 62.961 66.667 0.00 0.00 0.00 4.85
1323 3550 2.680352 ATCTCGTCCGGGTGCTGT 60.680 61.111 0.00 0.00 0.00 4.40
1710 3937 1.003355 ATAGTGCTGCTGTTGCGGT 60.003 52.632 0.00 0.00 46.77 5.68
1807 4034 4.688966 GATCAGGGATCCGGCGCC 62.689 72.222 19.07 19.07 33.37 6.53
1833 4060 2.526873 ACCTGCCTCGTCAACCCT 60.527 61.111 0.00 0.00 0.00 4.34
1837 4064 1.412710 GATATCCACCTGCCTCGTCAA 59.587 52.381 0.00 0.00 0.00 3.18
2027 4261 9.261035 TCAAAATTACCTCTCTCTAGTCATCTT 57.739 33.333 0.00 0.00 0.00 2.40
2085 4319 5.716703 AGAAGAAGAGGAAGAAGAAGAGGAG 59.283 44.000 0.00 0.00 0.00 3.69
2088 4322 6.211384 AGGAAGAAGAAGAGGAAGAAGAAGAG 59.789 42.308 0.00 0.00 0.00 2.85
2100 4334 3.981212 AGGAGAGGAGGAAGAAGAAGAG 58.019 50.000 0.00 0.00 0.00 2.85
2104 4338 2.183679 GCAAGGAGAGGAGGAAGAAGA 58.816 52.381 0.00 0.00 0.00 2.87
2105 4339 1.134848 CGCAAGGAGAGGAGGAAGAAG 60.135 57.143 0.00 0.00 0.00 2.85
2106 4340 0.898320 CGCAAGGAGAGGAGGAAGAA 59.102 55.000 0.00 0.00 0.00 2.52
2107 4341 0.039764 TCGCAAGGAGAGGAGGAAGA 59.960 55.000 0.00 0.00 38.47 2.87
2108 4342 0.459489 CTCGCAAGGAGAGGAGGAAG 59.541 60.000 0.00 0.00 46.23 3.46
2109 4343 0.251832 ACTCGCAAGGAGAGGAGGAA 60.252 55.000 2.22 0.00 46.23 3.36
2110 4344 0.251832 AACTCGCAAGGAGAGGAGGA 60.252 55.000 2.22 0.00 46.23 3.71
2111 4345 0.610687 AAACTCGCAAGGAGAGGAGG 59.389 55.000 2.22 0.00 46.23 4.30
2112 4346 1.001406 ACAAACTCGCAAGGAGAGGAG 59.999 52.381 2.22 0.00 46.23 3.69
2113 4347 1.048601 ACAAACTCGCAAGGAGAGGA 58.951 50.000 2.22 0.00 46.23 3.71
2114 4348 1.151668 CACAAACTCGCAAGGAGAGG 58.848 55.000 2.22 0.00 46.23 3.69
2115 4349 1.871080 ACACAAACTCGCAAGGAGAG 58.129 50.000 0.00 0.00 46.23 3.20
2180 4414 6.602009 GCTAATTGGAGAAAACCCTAGCTAAA 59.398 38.462 0.00 0.00 33.15 1.85
2194 4428 2.224992 TGGCAAACCAGCTAATTGGAGA 60.225 45.455 0.00 0.00 42.67 3.71
2407 4641 4.233408 GCAAGCTTTGCTTCCACG 57.767 55.556 0.00 0.00 46.77 4.94
2593 4851 8.543774 TCTCTTTTATTCACTCCTTGAGCTTAT 58.456 33.333 0.00 0.00 34.94 1.73
2865 5147 4.043561 AGGTAGATGGATAGAGGTGATCGT 59.956 45.833 0.00 0.00 0.00 3.73


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

AutoCloner maintained by Alex Coulton.