Multiple sequence alignment - TraesCS1A01G028100

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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 TraesCS1A01G028100 chr1A 100.000 2236 0 0 1 2236 13279353 13277118 0.000000e+00 4130.0
1 TraesCS1A01G028100 chr1A 87.684 1356 91 37 856 2199 12684690 12685981 0.000000e+00 1509.0
2 TraesCS1A01G028100 chr1A 97.150 421 11 1 173 592 12684071 12684491 0.000000e+00 710.0
3 TraesCS1A01G028100 chr1A 96.429 112 4 0 632 743 12684580 12684691 3.790000e-43 185.0
4 TraesCS1A01G028100 chr1A 83.333 72 7 5 1636 1704 60289567 60289636 6.670000e-06 62.1
5 TraesCS1A01G028100 chrUn 97.506 2245 30 4 1 2236 261626621 261628848 0.000000e+00 3812.0
6 TraesCS1A01G028100 chr7B 87.684 1356 91 37 856 2199 192784211 192785502 0.000000e+00 1509.0
7 TraesCS1A01G028100 chr7B 97.150 421 11 1 173 592 192783592 192784012 0.000000e+00 710.0
8 TraesCS1A01G028100 chr7B 96.429 112 4 0 632 743 192784101 192784212 3.790000e-43 185.0
9 TraesCS1A01G028100 chr7B 89.600 125 11 2 737 860 642777101 642776978 8.270000e-35 158.0
10 TraesCS1A01G028100 chr7B 85.600 125 14 4 735 857 167627859 167627737 6.480000e-26 128.0
11 TraesCS1A01G028100 chr7B 84.800 125 13 6 738 859 166661422 166661543 1.080000e-23 121.0
12 TraesCS1A01G028100 chr2B 87.731 1353 90 37 859 2199 47186070 47184782 0.000000e+00 1509.0
13 TraesCS1A01G028100 chr2B 96.934 424 12 1 173 595 47186692 47186269 0.000000e+00 710.0
14 TraesCS1A01G028100 chr2B 92.913 254 18 0 1 254 723425957 723426210 9.750000e-99 370.0
15 TraesCS1A01G028100 chr2B 92.430 251 19 0 1 251 263653177 263653427 2.110000e-95 359.0
16 TraesCS1A01G028100 chr2B 92.126 254 19 1 1 254 452910430 452910178 7.590000e-95 357.0
17 TraesCS1A01G028100 chr2B 96.429 112 4 0 632 743 47186183 47186072 3.790000e-43 185.0
18 TraesCS1A01G028100 chr2B 85.039 127 16 3 741 865 587232332 587232207 2.330000e-25 126.0
19 TraesCS1A01G028100 chr1D 90.101 495 30 4 252 742 11200773 11200294 1.890000e-175 625.0
20 TraesCS1A01G028100 chr1D 82.008 528 59 18 859 1384 11200291 11199798 1.240000e-112 416.0
21 TraesCS1A01G028100 chr1D 88.462 52 6 0 1672 1723 398867427 398867376 1.850000e-06 63.9
22 TraesCS1A01G028100 chr4B 92.126 254 20 0 1 254 665294072 665293819 2.110000e-95 359.0
23 TraesCS1A01G028100 chr3B 92.126 254 20 0 1 254 752076378 752076631 2.110000e-95 359.0
24 TraesCS1A01G028100 chr3B 87.200 125 14 2 742 864 770690491 770690367 8.330000e-30 141.0
25 TraesCS1A01G028100 chr2D 91.829 257 21 0 1 257 590028733 590028477 2.110000e-95 359.0
26 TraesCS1A01G028100 chr4D 91.506 259 20 2 1 258 37603893 37604150 2.730000e-94 355.0
27 TraesCS1A01G028100 chr3D 91.765 255 21 0 1 255 341473667 341473413 2.730000e-94 355.0
28 TraesCS1A01G028100 chr6D 85.470 117 15 2 742 857 470660635 470660520 1.080000e-23 121.0
29 TraesCS1A01G028100 chr5B 85.593 118 14 3 742 857 472739665 472739549 1.080000e-23 121.0
30 TraesCS1A01G028100 chr1B 84.800 125 13 6 738 859 146924151 146924272 1.080000e-23 121.0
31 TraesCS1A01G028100 chr1B 91.304 46 4 0 1672 1717 673866412 673866367 1.850000e-06 63.9
32 TraesCS1A01G028100 chr5D 87.143 70 6 3 1653 1719 50827506 50827437 2.380000e-10 76.8


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 TraesCS1A01G028100 chr1A 13277118 13279353 2235 True 4130.000000 4130 100.000000 1 2236 1 chr1A.!!$R1 2235
1 TraesCS1A01G028100 chr1A 12684071 12685981 1910 False 801.333333 1509 93.754333 173 2199 3 chr1A.!!$F2 2026
2 TraesCS1A01G028100 chrUn 261626621 261628848 2227 False 3812.000000 3812 97.506000 1 2236 1 chrUn.!!$F1 2235
3 TraesCS1A01G028100 chr7B 192783592 192785502 1910 False 801.333333 1509 93.754333 173 2199 3 chr7B.!!$F2 2026
4 TraesCS1A01G028100 chr2B 47184782 47186692 1910 True 801.333333 1509 93.698000 173 2199 3 chr2B.!!$R3 2026
5 TraesCS1A01G028100 chr1D 11199798 11200773 975 True 520.500000 625 86.054500 252 1384 2 chr1D.!!$R2 1132

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
937 992 1.44425 GGTGAGTCACAACACCGGA 59.556 57.895 24.2 0.0 45.16 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1802 1885 4.270008 ACAAGCAAAACTAGTTCACACCT 58.73 39.13 8.95 0.0 0.0 4.0 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
189 190 1.686355 TCAGTTTTGCCATGTCGGTT 58.314 45.000 0.00 0.00 36.97 4.44
250 252 9.941325 AATGAGAAACATATTACCATGCAAAAA 57.059 25.926 0.00 0.00 38.38 1.94
754 809 3.379372 TCAAATTACTACTCCTCCGTCCG 59.621 47.826 0.00 0.00 0.00 4.79
786 841 9.743057 ACTTGTCGTAAAAATTGATGAAAATGA 57.257 25.926 0.00 0.00 0.00 2.57
844 899 2.827322 TCTTCCCGACAAGTATTTCCGA 59.173 45.455 0.00 0.00 0.00 4.55
848 903 1.657094 CCGACAAGTATTTCCGAACGG 59.343 52.381 6.94 6.94 0.00 4.44
850 905 2.597305 CGACAAGTATTTCCGAACGGAG 59.403 50.000 15.34 5.60 46.06 4.63
851 906 3.671433 CGACAAGTATTTCCGAACGGAGA 60.671 47.826 15.34 12.07 46.06 3.71
937 992 1.444250 GGTGAGTCACAACACCGGA 59.556 57.895 24.20 0.00 45.16 5.14
1027 1099 4.459331 CCGACAACATTGCCGGCG 62.459 66.667 23.90 10.49 46.60 6.46
1028 1100 3.418913 CGACAACATTGCCGGCGA 61.419 61.111 21.20 21.20 30.17 5.54
1029 1101 2.175811 GACAACATTGCCGGCGAC 59.824 61.111 21.40 0.22 0.00 5.19
1041 1113 2.100603 GGCGACGAGAAGACGAGG 59.899 66.667 0.00 0.00 40.26 4.63
1367 1439 2.413634 GCGTGTTTTCAATTCCCCTACG 60.414 50.000 0.00 0.00 0.00 3.51
1494 1569 8.374743 AGTATATTTTGCCCTTGTTGAAATGTT 58.625 29.630 0.00 0.00 0.00 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 2.581354 CTCTGCGGACCTCCAAGG 59.419 66.667 0.00 0.00 42.49 3.61
189 190 6.108015 AGGTCAAAGTACAAGTCACGTAAAA 58.892 36.000 0.00 0.00 0.00 1.52
754 809 9.834628 TCATCAATTTTTACGACAAGTATTTCC 57.165 29.630 0.00 0.00 34.88 3.13
813 868 5.745227 ACTTGTCGGGAAGATGAATGTATT 58.255 37.500 1.87 0.00 0.00 1.89
844 899 6.388435 ACGCTATTTAATACTCTCTCCGTT 57.612 37.500 0.00 0.00 0.00 4.44
848 903 6.578172 GGAACGACGCTATTTAATACTCTCTC 59.422 42.308 0.00 0.00 0.00 3.20
850 905 6.204359 TGGAACGACGCTATTTAATACTCTC 58.796 40.000 0.00 0.00 0.00 3.20
851 906 6.140303 TGGAACGACGCTATTTAATACTCT 57.860 37.500 0.00 0.00 0.00 3.24
937 992 7.477945 AGATTTCTCAAGAAAATTGAGGCAT 57.522 32.000 15.52 9.09 45.81 4.40
1025 1097 1.512310 CACCTCGTCTTCTCGTCGC 60.512 63.158 0.00 0.00 0.00 5.19
1026 1098 1.134901 CCACCTCGTCTTCTCGTCG 59.865 63.158 0.00 0.00 0.00 5.12
1027 1099 1.153997 GCCACCTCGTCTTCTCGTC 60.154 63.158 0.00 0.00 0.00 4.20
1028 1100 2.637383 GGCCACCTCGTCTTCTCGT 61.637 63.158 0.00 0.00 0.00 4.18
1029 1101 2.182030 GGCCACCTCGTCTTCTCG 59.818 66.667 0.00 0.00 0.00 4.04
1030 1102 2.182030 CGGCCACCTCGTCTTCTC 59.818 66.667 2.24 0.00 0.00 2.87
1031 1103 3.382832 CCGGCCACCTCGTCTTCT 61.383 66.667 2.24 0.00 0.00 2.85
1032 1104 3.358076 CTCCGGCCACCTCGTCTTC 62.358 68.421 2.24 0.00 0.00 2.87
1033 1105 3.382832 CTCCGGCCACCTCGTCTT 61.383 66.667 2.24 0.00 0.00 3.01
1037 1109 4.760047 CAACCTCCGGCCACCTCG 62.760 72.222 2.24 0.00 0.00 4.63
1038 1110 3.607370 GACAACCTCCGGCCACCTC 62.607 68.421 2.24 0.00 0.00 3.85
1039 1111 3.637273 GACAACCTCCGGCCACCT 61.637 66.667 2.24 0.00 0.00 4.00
1294 1366 1.283029 ACATGCTAATGCTCCACCAGT 59.717 47.619 0.00 0.00 40.48 4.00
1802 1885 4.270008 ACAAGCAAAACTAGTTCACACCT 58.730 39.130 8.95 0.00 0.00 4.00
2116 2205 9.890352 GCAAGTCTCATGGATAATCTTTATTTC 57.110 33.333 0.00 0.00 0.00 2.17


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

AutoCloner maintained by Alex Coulton.