Multiple sequence alignment - TraesCS3A01G458800

Loading Multiple Alignment...

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 TraesCS3A01G458800 chr3A 100.000 2300 0 0 1 2300 695640583 695642882 0.000000e+00 4248.0
1 TraesCS3A01G458800 chr3A 98.219 2302 39 2 1 2300 66004937 66002636 0.000000e+00 4023.0
2 TraesCS3A01G458800 chr6D 98.089 2302 42 2 1 2300 389245626 389243325 0.000000e+00 4006.0
3 TraesCS3A01G458800 chr5D 98.045 2302 43 2 1 2300 503264580 503262279 0.000000e+00 4000.0
4 TraesCS3A01G458800 chr5D 97.958 2302 45 2 1 2300 503245468 503247769 0.000000e+00 3989.0
5 TraesCS3A01G458800 chr2D 98.002 2302 44 2 1 2300 591984805 591987106 0.000000e+00 3995.0
6 TraesCS3A01G458800 chr2A 98.002 2302 44 2 1 2300 726906259 726903958 0.000000e+00 3995.0
7 TraesCS3A01G458800 chr2A 97.088 2301 64 3 1 2300 335847510 335849808 0.000000e+00 3875.0
8 TraesCS3A01G458800 chr2A 96.536 1357 46 1 945 2300 335821662 335820306 0.000000e+00 2244.0
9 TraesCS3A01G458800 chr2A 95.726 117 4 1 495 611 656137322 656137207 1.080000e-43 187.0
10 TraesCS3A01G458800 chr2A 96.875 96 3 0 430 525 158052844 158052939 6.580000e-36 161.0
11 TraesCS3A01G458800 chr2A 97.500 40 1 0 336 375 608906659 608906620 4.100000e-08 69.4
12 TraesCS3A01G458800 chr3D 97.958 2302 44 3 1 2300 589263330 589261030 0.000000e+00 3988.0


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 TraesCS3A01G458800 chr3A 695640583 695642882 2299 False 4248 4248 100.000 1 2300 1 chr3A.!!$F1 2299
1 TraesCS3A01G458800 chr3A 66002636 66004937 2301 True 4023 4023 98.219 1 2300 1 chr3A.!!$R1 2299
2 TraesCS3A01G458800 chr6D 389243325 389245626 2301 True 4006 4006 98.089 1 2300 1 chr6D.!!$R1 2299
3 TraesCS3A01G458800 chr5D 503262279 503264580 2301 True 4000 4000 98.045 1 2300 1 chr5D.!!$R1 2299
4 TraesCS3A01G458800 chr5D 503245468 503247769 2301 False 3989 3989 97.958 1 2300 1 chr5D.!!$F1 2299
5 TraesCS3A01G458800 chr2D 591984805 591987106 2301 False 3995 3995 98.002 1 2300 1 chr2D.!!$F1 2299
6 TraesCS3A01G458800 chr2A 726903958 726906259 2301 True 3995 3995 98.002 1 2300 1 chr2A.!!$R4 2299
7 TraesCS3A01G458800 chr2A 335847510 335849808 2298 False 3875 3875 97.088 1 2300 1 chr2A.!!$F2 2299
8 TraesCS3A01G458800 chr2A 335820306 335821662 1356 True 2244 2244 96.536 945 2300 1 chr2A.!!$R1 1355
9 TraesCS3A01G458800 chr3D 589261030 589263330 2300 True 3988 3988 97.958 1 2300 1 chr3D.!!$R1 2299

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
150 151 0.983467 TGCATACTCCACTTGGCTCA 59.017 50.0 0.0 0.0 34.44 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1440 1444 0.186386 TCCCACAACCCCGTTTTCAT 59.814 50.0 0.0 0.0 0.0 2.57 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
57 58 1.597663 CGATGATTTACTTCACGGGCC 59.402 52.381 0.00 0.00 0.00 5.80
150 151 0.983467 TGCATACTCCACTTGGCTCA 59.017 50.000 0.00 0.00 34.44 4.26
312 313 2.906389 AGAGGACTGAAACATGCCACTA 59.094 45.455 0.00 0.00 0.00 2.74
341 342 5.308237 ACTCTACTGAGACAAAAAGATGGGT 59.692 40.000 0.00 0.00 42.73 4.51
480 481 2.562296 AGAGGATCAAGTTGGCCCTTA 58.438 47.619 15.10 0.00 37.82 2.69
726 727 4.215613 GGGCAATCACTCGTTCTTAAAACT 59.784 41.667 0.00 0.00 0.00 2.66
917 918 5.065988 ACGATGAAAGTTGTAAGCTGTGTTT 59.934 36.000 0.00 0.00 0.00 2.83
1030 1032 1.676529 CTCGAGTCCGCTTATCTCCAA 59.323 52.381 3.62 0.00 35.37 3.53
1032 1034 1.405821 CGAGTCCGCTTATCTCCAACT 59.594 52.381 0.00 0.00 0.00 3.16
1169 1171 1.072331 AGGATGGCATAGCCTTAACGG 59.928 52.381 9.71 0.00 44.62 4.44
1226 1228 2.493687 GGATACCTAGGCACCCAGAGAT 60.494 54.545 9.30 0.00 0.00 2.75
1377 1381 5.812642 CGAACTGAAACATCTTAGTAGCCAT 59.187 40.000 0.00 0.00 0.00 4.40
1431 1435 0.749454 GGTGAGCGAAATGGGAGCAT 60.749 55.000 0.00 0.00 0.00 3.79
1631 1635 4.517285 CTTGCAAGGCTAAATACTCCTGA 58.483 43.478 19.14 0.00 0.00 3.86
1725 1729 2.345244 CGTGCTGAGCTCCCAAGT 59.655 61.111 12.15 0.00 0.00 3.16
1831 1835 0.907704 AACCCACCGGAGTCATAGCA 60.908 55.000 9.46 0.00 0.00 3.49
2024 2028 0.322546 GCTGGTTCTCCCCGAAATGT 60.323 55.000 0.00 0.00 32.41 2.71
2084 2088 4.555709 TGTTTCGGTGCGGGCTGT 62.556 61.111 0.00 0.00 0.00 4.40
2170 2174 1.977009 TCGGCCAGTGAGACGATGT 60.977 57.895 2.24 0.00 0.00 3.06
2186 2190 3.070018 CGATGTGGGATAAGCTTCATCC 58.930 50.000 19.02 19.02 41.17 3.51
2280 2284 2.310538 CAAAGACAGCCAGGAGGTTTT 58.689 47.619 0.00 0.00 37.19 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
57 58 1.694150 TGGACTTGAACCAGAGACCTG 59.306 52.381 0.00 0.00 40.09 4.00
312 313 9.050601 CATCTTTTTGTCTCAGTAGAGTCTTTT 57.949 33.333 0.00 0.00 42.66 2.27
341 342 5.012768 CCTACCTCCTCTACCTTTTTGACAA 59.987 44.000 0.00 0.00 0.00 3.18
480 481 5.986135 GGAGATAGTGCATCAAGTTATTCGT 59.014 40.000 0.00 0.00 35.96 3.85
726 727 6.980978 CCGACTCTTTGATCTTAAGAATGCTA 59.019 38.462 9.71 0.00 31.67 3.49
892 893 4.024893 ACACAGCTTACAACTTTCATCGTG 60.025 41.667 0.00 0.00 0.00 4.35
924 926 3.805207 AGGCCAACGATAGACAATAACC 58.195 45.455 5.01 0.00 41.38 2.85
1010 1012 1.309950 TGGAGATAAGCGGACTCGAG 58.690 55.000 11.84 11.84 39.00 4.04
1030 1032 2.223203 CGTATCCGCTAAGTTCACGAGT 60.223 50.000 0.00 0.00 0.00 4.18
1032 1034 2.009051 TCGTATCCGCTAAGTTCACGA 58.991 47.619 0.00 0.00 34.87 4.35
1051 1053 5.869753 AATTTGGTGCTATCGCTATCATC 57.130 39.130 0.00 0.00 36.97 2.92
1169 1171 3.127030 CCTCTTTTGAACCTCGCCATTAC 59.873 47.826 0.00 0.00 0.00 1.89
1226 1228 1.596934 CTTGCTACGCCCTTCCTCA 59.403 57.895 0.00 0.00 0.00 3.86
1248 1250 0.811281 CAACTCCCCGAAGCATTTCC 59.189 55.000 0.00 0.00 0.00 3.13
1377 1381 5.705609 ATCGCTTTTGCTTTCTTTTCCTA 57.294 34.783 0.00 0.00 44.80 2.94
1414 1418 0.464373 GGATGCTCCCATTTCGCTCA 60.464 55.000 0.00 0.00 0.00 4.26
1431 1435 4.914177 ACCCCGTTTTCATAGTTTAGGA 57.086 40.909 0.00 0.00 0.00 2.94
1439 1443 1.424302 TCCCACAACCCCGTTTTCATA 59.576 47.619 0.00 0.00 0.00 2.15
1440 1444 0.186386 TCCCACAACCCCGTTTTCAT 59.814 50.000 0.00 0.00 0.00 2.57
1487 1491 2.664851 CGGCACTCAACCGCTTCA 60.665 61.111 0.00 0.00 44.90 3.02
1631 1635 2.641305 ACTACTTCGCTATCGGTCACT 58.359 47.619 0.00 0.00 36.13 3.41
1725 1729 2.045885 AGATCACTTTCCCCTCCCACTA 59.954 50.000 0.00 0.00 0.00 2.74
1824 1828 6.701841 CCTATTAAGACTCGCTTTTGCTATGA 59.298 38.462 0.00 0.00 44.80 2.15
1826 1830 5.992217 CCCTATTAAGACTCGCTTTTGCTAT 59.008 40.000 0.00 0.00 44.80 2.97
1831 1835 3.118884 TCGCCCTATTAAGACTCGCTTTT 60.119 43.478 0.00 0.00 38.05 2.27
2024 2028 2.203195 AACTGCTGCGCCTCAACA 60.203 55.556 4.18 0.00 0.00 3.33
2084 2088 1.807981 CGATTTGGTACCGCTCGCA 60.808 57.895 14.94 0.00 0.00 5.10
2170 2174 2.630098 CTCGAGGATGAAGCTTATCCCA 59.370 50.000 21.59 9.02 44.19 4.37
2186 2190 1.219393 GGGCTGTTTCCCTCTCGAG 59.781 63.158 5.93 5.93 43.13 4.04
2280 2284 0.547712 AAGGGTGGCTGCTTCTAGGA 60.548 55.000 0.00 0.00 0.00 2.94


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

AutoCloner maintained by Alex Coulton.