Multiple sequence alignment - TraesCS2A01G154700

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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 TraesCS2A01G154700 chr2A 100.000 2507 0 0 1 2507 102021909 102019403 0.000000e+00 4630.0
1 TraesCS2A01G154700 chr2A 96.952 525 16 0 1983 2507 79710945 79710421 0.000000e+00 881.0
2 TraesCS2A01G154700 chr2A 96.952 525 16 0 1983 2507 647640747 647641271 0.000000e+00 881.0
3 TraesCS2A01G154700 chr2A 97.959 147 2 1 1837 1983 102024272 102024417 1.150000e-63 254.0
4 TraesCS2A01G154700 chr1A 96.454 2002 37 8 1 1982 299542013 299544000 0.000000e+00 3273.0
5 TraesCS2A01G154700 chr1A 96.324 1741 41 6 262 1982 97423109 97421372 0.000000e+00 2839.0
6 TraesCS2A01G154700 chr1A 97.143 525 14 1 1983 2507 333695958 333696481 0.000000e+00 885.0
7 TraesCS2A01G154700 chr1A 98.658 149 2 0 1835 1983 97423909 97424057 5.320000e-67 265.0
8 TraesCS2A01G154700 chr1A 96.732 153 4 1 1835 1987 299539639 299539488 1.150000e-63 254.0
9 TraesCS2A01G154700 chr1D 96.623 1925 43 6 80 1983 50969151 50971074 0.000000e+00 3175.0
10 TraesCS2A01G154700 chr1D 96.575 146 4 1 1837 1982 50967022 50966878 8.960000e-60 241.0
11 TraesCS2A01G154700 chr1D 95.890 146 6 0 1837 1982 51000141 50999996 1.160000e-58 237.0
12 TraesCS2A01G154700 chr7A 91.124 890 45 9 1099 1967 533036607 533037483 0.000000e+00 1175.0
13 TraesCS2A01G154700 chr7A 97.338 526 13 1 1983 2507 649174183 649174708 0.000000e+00 893.0
14 TraesCS2A01G154700 chr3A 97.143 525 15 0 1983 2507 124586222 124586746 0.000000e+00 887.0
15 TraesCS2A01G154700 chr3A 97.143 525 14 1 1983 2507 391153352 391153875 0.000000e+00 885.0
16 TraesCS2A01G154700 chr4A 97.143 525 14 1 1983 2507 578410848 578411371 0.000000e+00 885.0
17 TraesCS2A01G154700 chr6A 96.952 525 15 1 1983 2507 570284558 570285081 0.000000e+00 880.0
18 TraesCS2A01G154700 chr6A 96.762 525 17 0 1983 2507 493057751 493057227 0.000000e+00 876.0
19 TraesCS2A01G154700 chr3B 90.646 449 17 7 1558 1983 448752602 448753048 7.780000e-160 573.0
20 TraesCS2A01G154700 chr4D 85.072 489 30 10 1518 1982 76028347 76028816 2.270000e-125 459.0
21 TraesCS2A01G154700 chr2B 91.489 47 4 0 123 169 697521724 697521770 5.790000e-07 65.8
22 TraesCS2A01G154700 chr7D 89.362 47 5 0 123 169 552506640 552506686 2.690000e-05 60.2


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 TraesCS2A01G154700 chr2A 102019403 102021909 2506 True 4630 4630 100.000 1 2507 1 chr2A.!!$R2 2506
1 TraesCS2A01G154700 chr2A 79710421 79710945 524 True 881 881 96.952 1983 2507 1 chr2A.!!$R1 524
2 TraesCS2A01G154700 chr2A 647640747 647641271 524 False 881 881 96.952 1983 2507 1 chr2A.!!$F2 524
3 TraesCS2A01G154700 chr1A 299542013 299544000 1987 False 3273 3273 96.454 1 1982 1 chr1A.!!$F2 1981
4 TraesCS2A01G154700 chr1A 97421372 97423109 1737 True 2839 2839 96.324 262 1982 1 chr1A.!!$R1 1720
5 TraesCS2A01G154700 chr1A 333695958 333696481 523 False 885 885 97.143 1983 2507 1 chr1A.!!$F3 524
6 TraesCS2A01G154700 chr1D 50969151 50971074 1923 False 3175 3175 96.623 80 1983 1 chr1D.!!$F1 1903
7 TraesCS2A01G154700 chr7A 533036607 533037483 876 False 1175 1175 91.124 1099 1967 1 chr7A.!!$F1 868
8 TraesCS2A01G154700 chr7A 649174183 649174708 525 False 893 893 97.338 1983 2507 1 chr7A.!!$F2 524
9 TraesCS2A01G154700 chr3A 124586222 124586746 524 False 887 887 97.143 1983 2507 1 chr3A.!!$F1 524
10 TraesCS2A01G154700 chr3A 391153352 391153875 523 False 885 885 97.143 1983 2507 1 chr3A.!!$F2 524
11 TraesCS2A01G154700 chr4A 578410848 578411371 523 False 885 885 97.143 1983 2507 1 chr4A.!!$F1 524
12 TraesCS2A01G154700 chr6A 570284558 570285081 523 False 880 880 96.952 1983 2507 1 chr6A.!!$F1 524
13 TraesCS2A01G154700 chr6A 493057227 493057751 524 True 876 876 96.762 1983 2507 1 chr6A.!!$R1 524

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
694 695 1.408405 CCTTGCTCTCATGCCATCAGT 60.408 52.381 0.0 0.0 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2465 2489 1.187087 CGTAGAACTCCAGAAGCCCT 58.813 55.0 0.0 0.0 0.0 5.19 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
58 59 2.134789 AAGTTGGAGATGGTGATGGC 57.865 50.000 0.00 0.00 0.00 4.40
72 73 4.892934 TGGTGATGGCTGGGTTATAATTTC 59.107 41.667 0.00 0.00 0.00 2.17
140 141 3.370840 TGGCAGAGCATAGGAATTGTT 57.629 42.857 0.00 0.00 0.00 2.83
414 415 9.950306 ATGGATAGTTGAGGCTAGATTATATCT 57.050 33.333 0.00 0.00 43.33 1.98
694 695 1.408405 CCTTGCTCTCATGCCATCAGT 60.408 52.381 0.00 0.00 0.00 3.41
891 892 9.106070 GTAGGAAAAAGAAGTGTAGAACAAGAA 57.894 33.333 0.00 0.00 0.00 2.52
1029 1030 3.491342 CCTAGTGCTAGTGCTCCATCTA 58.509 50.000 5.62 0.00 40.48 1.98
1048 1049 5.390087 TCTACTTCTGCTCCTAGTGGTAT 57.610 43.478 0.00 0.00 34.23 2.73
1097 1098 2.005960 CTAGGGGAAGTGCTCGTCCG 62.006 65.000 13.43 0.00 41.88 4.79
1495 1496 0.951558 GTTTCGAAGCTTGCTGGGAA 59.048 50.000 2.10 0.48 0.00 3.97
1537 1538 1.213182 TGTGCTTGTGAGGTTTGGGTA 59.787 47.619 0.00 0.00 0.00 3.69
1830 1833 0.678684 CATGGCATGCTGACTGGACA 60.679 55.000 18.92 4.44 0.00 4.02
1839 1861 2.698274 TGCTGACTGGACAAGTTGACTA 59.302 45.455 10.54 0.00 40.07 2.59
2154 2178 2.943978 CGCACCTTCTCCCTTCCGT 61.944 63.158 0.00 0.00 0.00 4.69
2156 2180 2.058675 CACCTTCTCCCTTCCGTGT 58.941 57.895 0.00 0.00 0.00 4.49
2223 2247 3.780173 GCCGCAGCTCCTCCTCTT 61.780 66.667 0.00 0.00 35.50 2.85
2465 2489 2.235155 TCCAATTCATCCGTTTCTCCGA 59.765 45.455 0.00 0.00 0.00 4.55
2483 2507 1.135333 CGAGGGCTTCTGGAGTTCTAC 59.865 57.143 0.00 0.00 0.00 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
58 59 7.572523 TTGCTGATCAGAAATTATAACCCAG 57.427 36.000 27.04 0.00 0.00 4.45
72 73 9.031360 CATTCAATATTCCTTTTTGCTGATCAG 57.969 33.333 18.84 18.84 0.00 2.90
140 141 6.016555 TCCAGTTAGCATATATGTGCCTAGA 58.983 40.000 19.57 6.96 46.19 2.43
807 808 0.612229 CTCTGAGACACAGGCCATGT 59.388 55.000 12.20 12.20 45.76 3.21
891 892 8.138074 GCTAGTCTTTGGTTTTTCTTCATCTTT 58.862 33.333 0.00 0.00 0.00 2.52
896 897 6.767524 TTGCTAGTCTTTGGTTTTTCTTCA 57.232 33.333 0.00 0.00 0.00 3.02
1029 1030 3.118592 GCAATACCACTAGGAGCAGAAGT 60.119 47.826 0.00 0.00 38.69 3.01
1048 1049 2.413837 GCGTAGAAGAAAGTGGAGCAA 58.586 47.619 0.00 0.00 0.00 3.91
1097 1098 0.312102 GAACAGGTGCTTCACTTGGC 59.688 55.000 12.53 2.40 44.08 4.52
1163 1164 6.455647 TGTACTACATTATATCAGCAGTGGC 58.544 40.000 0.00 0.00 41.61 5.01
1495 1496 8.981647 GCACACAAATAACTCTCAATTTTCAAT 58.018 29.630 0.00 0.00 0.00 2.57
1537 1538 6.597672 GTCTCACATAGATAGGTCTGATCGAT 59.402 42.308 0.00 0.00 36.36 3.59
1830 1833 4.461198 CCTGGTTTTGGTCTAGTCAACTT 58.539 43.478 0.00 0.00 0.00 2.66
2137 2161 1.376037 CACGGAAGGGAGAAGGTGC 60.376 63.158 0.00 0.00 35.60 5.01
2154 2178 4.871513 GGATACGCTCTGATGAATACACA 58.128 43.478 0.00 0.00 0.00 3.72
2223 2247 3.333219 CTGAGGGCTGGAAGGGCA 61.333 66.667 0.00 0.00 0.00 5.36
2465 2489 1.187087 CGTAGAACTCCAGAAGCCCT 58.813 55.000 0.00 0.00 0.00 5.19


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

AutoCloner maintained by Alex Coulton.