Multiple sequence alignment - TraesCS2A01G549700

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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 TraesCS2A01G549700 chr2A 100.000 2759 0 0 1 2759 757367149 757364391 0.000000e+00 5096.0
1 TraesCS2A01G549700 chr2A 99.094 2759 24 1 1 2759 757332476 757335233 0.000000e+00 4955.0
2 TraesCS2A01G549700 chr2A 84.330 1755 257 8 29 1771 756370379 756368631 0.000000e+00 1701.0
3 TraesCS2A01G549700 chr2A 84.129 1739 252 23 29 1758 756029335 756031058 0.000000e+00 1661.0
4 TraesCS2A01G549700 chr2A 84.129 1739 252 23 29 1758 757001783 757000060 0.000000e+00 1661.0
5 TraesCS2A01G549700 chr2A 87.429 525 51 4 2007 2529 764329465 764328954 8.510000e-165 590.0
6 TraesCS2A01G549700 chr2A 90.055 181 12 2 2581 2757 764328955 764328777 2.140000e-56 230.0
7 TraesCS2A01G549700 chr2D 97.501 2001 49 1 1 2000 626587678 626589678 0.000000e+00 3417.0
8 TraesCS2A01G549700 chr2D 84.874 1752 243 21 29 1772 626386238 626387975 0.000000e+00 1748.0
9 TraesCS2A01G549700 chr2D 84.289 1814 256 20 1 1797 626171239 626173040 0.000000e+00 1744.0
10 TraesCS2A01G549700 chr2D 90.395 760 52 7 2007 2759 638817247 638816502 0.000000e+00 979.0
11 TraesCS2A01G549700 chr2D 91.129 248 20 1 2126 2373 144288532 144288287 4.400000e-88 335.0
12 TraesCS2A01G549700 chr2D 91.270 126 9 2 2006 2129 144297127 144297002 1.310000e-38 171.0
13 TraesCS2A01G549700 chr2B 93.347 2014 114 8 1 2004 768053127 768055130 0.000000e+00 2959.0
14 TraesCS2A01G549700 chr2B 83.610 1806 268 18 1 1790 767774283 767776076 0.000000e+00 1670.0
15 TraesCS2A01G549700 chr2B 83.862 1766 260 20 29 1787 768026362 768024615 0.000000e+00 1659.0
16 TraesCS2A01G549700 chr2B 85.060 1004 130 12 776 1772 768006165 768005175 0.000000e+00 1005.0
17 TraesCS2A01G549700 chr2B 87.649 753 60 9 2007 2757 798141870 798141149 0.000000e+00 845.0
18 TraesCS2A01G549700 chrUn 84.129 1739 252 23 29 1758 180890499 180892222 0.000000e+00 1661.0
19 TraesCS2A01G549700 chr6B 91.219 763 61 2 2001 2759 75280224 75279464 0.000000e+00 1033.0
20 TraesCS2A01G549700 chr7A 91.270 756 59 6 2007 2759 518810173 518810924 0.000000e+00 1024.0
21 TraesCS2A01G549700 chr7A 79.085 1334 247 23 288 1614 660544242 660545550 0.000000e+00 889.0
22 TraesCS2A01G549700 chr7B 78.951 1335 247 24 288 1614 627952297 627953605 0.000000e+00 878.0
23 TraesCS2A01G549700 chr3D 82.627 708 115 6 2056 2759 38373461 38372758 1.090000e-173 619.0
24 TraesCS2A01G549700 chr6A 93.353 346 21 1 2414 2759 420408354 420408011 6.820000e-141 510.0
25 TraesCS2A01G549700 chr3A 88.571 70 8 0 2064 2133 49603239 49603170 4.900000e-13 86.1


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 TraesCS2A01G549700 chr2A 757364391 757367149 2758 True 5096 5096 100.000 1 2759 1 chr2A.!!$R3 2758
1 TraesCS2A01G549700 chr2A 757332476 757335233 2757 False 4955 4955 99.094 1 2759 1 chr2A.!!$F2 2758
2 TraesCS2A01G549700 chr2A 756368631 756370379 1748 True 1701 1701 84.330 29 1771 1 chr2A.!!$R1 1742
3 TraesCS2A01G549700 chr2A 756029335 756031058 1723 False 1661 1661 84.129 29 1758 1 chr2A.!!$F1 1729
4 TraesCS2A01G549700 chr2A 757000060 757001783 1723 True 1661 1661 84.129 29 1758 1 chr2A.!!$R2 1729
5 TraesCS2A01G549700 chr2A 764328777 764329465 688 True 410 590 88.742 2007 2757 2 chr2A.!!$R4 750
6 TraesCS2A01G549700 chr2D 626587678 626589678 2000 False 3417 3417 97.501 1 2000 1 chr2D.!!$F3 1999
7 TraesCS2A01G549700 chr2D 626386238 626387975 1737 False 1748 1748 84.874 29 1772 1 chr2D.!!$F2 1743
8 TraesCS2A01G549700 chr2D 626171239 626173040 1801 False 1744 1744 84.289 1 1797 1 chr2D.!!$F1 1796
9 TraesCS2A01G549700 chr2D 638816502 638817247 745 True 979 979 90.395 2007 2759 1 chr2D.!!$R3 752
10 TraesCS2A01G549700 chr2B 768053127 768055130 2003 False 2959 2959 93.347 1 2004 1 chr2B.!!$F2 2003
11 TraesCS2A01G549700 chr2B 767774283 767776076 1793 False 1670 1670 83.610 1 1790 1 chr2B.!!$F1 1789
12 TraesCS2A01G549700 chr2B 768024615 768026362 1747 True 1659 1659 83.862 29 1787 1 chr2B.!!$R2 1758
13 TraesCS2A01G549700 chr2B 768005175 768006165 990 True 1005 1005 85.060 776 1772 1 chr2B.!!$R1 996
14 TraesCS2A01G549700 chr2B 798141149 798141870 721 True 845 845 87.649 2007 2757 1 chr2B.!!$R3 750
15 TraesCS2A01G549700 chrUn 180890499 180892222 1723 False 1661 1661 84.129 29 1758 1 chrUn.!!$F1 1729
16 TraesCS2A01G549700 chr6B 75279464 75280224 760 True 1033 1033 91.219 2001 2759 1 chr6B.!!$R1 758
17 TraesCS2A01G549700 chr7A 518810173 518810924 751 False 1024 1024 91.270 2007 2759 1 chr7A.!!$F1 752
18 TraesCS2A01G549700 chr7A 660544242 660545550 1308 False 889 889 79.085 288 1614 1 chr7A.!!$F2 1326
19 TraesCS2A01G549700 chr7B 627952297 627953605 1308 False 878 878 78.951 288 1614 1 chr7B.!!$F1 1326
20 TraesCS2A01G549700 chr3D 38372758 38373461 703 True 619 619 82.627 2056 2759 1 chr3D.!!$R1 703

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
406 419 1.964608 CTGGGCGCAGAAGATCTCCA 61.965 60.0 25.55 2.46 0.0 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2268 2296 6.072064 CCACTCTTGCTGATTTCTTCAATCTT 60.072 38.462 0.0 0.0 41.91 2.4 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
406 419 1.964608 CTGGGCGCAGAAGATCTCCA 61.965 60.000 25.55 2.46 0.00 3.86
1350 1363 4.457496 CCGGCGCTGACCATGTCT 62.457 66.667 20.25 0.00 33.15 3.41
2268 2296 4.265893 TGTAACAAGCAAGACCAGAAACA 58.734 39.130 0.00 0.00 0.00 2.83
2353 2385 2.328099 GCTTTCACCGCCTCCACTG 61.328 63.158 0.00 0.00 0.00 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
406 419 2.267961 GATGGTCCGCCGGAACTT 59.732 61.111 23.57 16.81 40.68 2.66
931 944 1.745653 CCACACATAGAGCTCTCGTCA 59.254 52.381 22.17 2.19 34.09 4.35
2268 2296 6.072064 CCACTCTTGCTGATTTCTTCAATCTT 60.072 38.462 0.00 0.00 41.91 2.40


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

AutoCloner maintained by Alex Coulton.