Multiple sequence alignment - TraesCS2A01G241100

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 TraesCS2A01G241100 chr2A 100.000 2114 0 0 1 2114 335825693 335827806 0.000000e+00 3904
1 TraesCS2A01G241100 chr2A 96.086 1022 25 4 1 1009 276441671 276440652 0.000000e+00 1652
2 TraesCS2A01G241100 chr2A 98.889 270 2 1 1845 2114 588083887 588084155 4.080000e-132 481
3 TraesCS2A01G241100 chr2A 97.255 255 6 1 214 468 490417821 490417568 4.170000e-117 431
4 TraesCS2A01G241100 chr2A 100.000 74 0 0 80 153 715783628 715783701 1.020000e-28 137
5 TraesCS2A01G241100 chr1D 97.108 2144 31 8 1 2114 394178317 394180459 0.000000e+00 3587
6 TraesCS2A01G241100 chr1D 93.806 1776 78 12 359 2114 244443826 244445589 0.000000e+00 2641
7 TraesCS2A01G241100 chr1D 97.206 1181 11 4 952 2114 483922592 483921416 0.000000e+00 1978
8 TraesCS2A01G241100 chr3D 96.987 2124 43 8 1 2114 21896969 21899081 0.000000e+00 3548
9 TraesCS2A01G241100 chrUn 96.780 2143 36 8 1 2114 317473782 317471644 0.000000e+00 3544
10 TraesCS2A01G241100 chrUn 98.128 1389 19 5 91 1474 404957738 404959124 0.000000e+00 2414
11 TraesCS2A01G241100 chrUn 97.647 765 11 3 328 1091 53261896 53261138 0.000000e+00 1306
12 TraesCS2A01G241100 chr6D 96.821 2139 35 7 1 2114 431399438 431401568 0.000000e+00 3542
13 TraesCS2A01G241100 chr6D 97.287 1032 9 3 1102 2114 431403702 431402671 0.000000e+00 1733
14 TraesCS2A01G241100 chr6D 96.570 758 7 8 1375 2114 431403693 431404449 0.000000e+00 1238
15 TraesCS2A01G241100 chr3B 96.412 2146 40 7 1 2114 201505980 201508120 0.000000e+00 3502
16 TraesCS2A01G241100 chr2D 95.897 2145 43 11 1 2114 334225328 334227458 0.000000e+00 3432
17 TraesCS2A01G241100 chr5D 97.372 1332 12 5 764 2072 554200515 554201846 0.000000e+00 2244
18 TraesCS2A01G241100 chr5D 97.097 930 8 3 1203 2114 554197429 554198357 0.000000e+00 1550
19 TraesCS2A01G241100 chr1A 97.848 1069 17 3 1 1068 256026752 256025689 0.000000e+00 1842
20 TraesCS2A01G241100 chr7D 94.348 1150 40 6 1 1133 88604987 88606128 0.000000e+00 1740
21 TraesCS2A01G241100 chr5A 97.725 967 19 3 1 966 684325003 684325967 0.000000e+00 1661


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 TraesCS2A01G241100 chr2A 335825693 335827806 2113 False 3904 3904 100.0000 1 2114 1 chr2A.!!$F1 2113
1 TraesCS2A01G241100 chr2A 276440652 276441671 1019 True 1652 1652 96.0860 1 1009 1 chr2A.!!$R1 1008
2 TraesCS2A01G241100 chr1D 394178317 394180459 2142 False 3587 3587 97.1080 1 2114 1 chr1D.!!$F2 2113
3 TraesCS2A01G241100 chr1D 244443826 244445589 1763 False 2641 2641 93.8060 359 2114 1 chr1D.!!$F1 1755
4 TraesCS2A01G241100 chr1D 483921416 483922592 1176 True 1978 1978 97.2060 952 2114 1 chr1D.!!$R1 1162
5 TraesCS2A01G241100 chr3D 21896969 21899081 2112 False 3548 3548 96.9870 1 2114 1 chr3D.!!$F1 2113
6 TraesCS2A01G241100 chrUn 317471644 317473782 2138 True 3544 3544 96.7800 1 2114 1 chrUn.!!$R2 2113
7 TraesCS2A01G241100 chrUn 404957738 404959124 1386 False 2414 2414 98.1280 91 1474 1 chrUn.!!$F1 1383
8 TraesCS2A01G241100 chrUn 53261138 53261896 758 True 1306 1306 97.6470 328 1091 1 chrUn.!!$R1 763
9 TraesCS2A01G241100 chr6D 431399438 431404449 5011 False 2390 3542 96.6955 1 2114 2 chr6D.!!$F1 2113
10 TraesCS2A01G241100 chr6D 431402671 431403702 1031 True 1733 1733 97.2870 1102 2114 1 chr6D.!!$R1 1012
11 TraesCS2A01G241100 chr3B 201505980 201508120 2140 False 3502 3502 96.4120 1 2114 1 chr3B.!!$F1 2113
12 TraesCS2A01G241100 chr2D 334225328 334227458 2130 False 3432 3432 95.8970 1 2114 1 chr2D.!!$F1 2113
13 TraesCS2A01G241100 chr5D 554197429 554201846 4417 False 1897 2244 97.2345 764 2114 2 chr5D.!!$F1 1350
14 TraesCS2A01G241100 chr1A 256025689 256026752 1063 True 1842 1842 97.8480 1 1068 1 chr1A.!!$R1 1067
15 TraesCS2A01G241100 chr7D 88604987 88606128 1141 False 1740 1740 94.3480 1 1133 1 chr7D.!!$F1 1132
16 TraesCS2A01G241100 chr5A 684325003 684325967 964 False 1661 1661 97.7250 1 966 1 chr5A.!!$F1 965

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
379 397 0.179059 TCTTGACCAAACTGCGAGCA 60.179 50.0 0.0 0.0 0.0 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1584 6813 4.754618 TGAATGAAAGCGCTCTTAGTTCAA 59.245 37.5 21.52 6.56 30.85 2.69 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
169 186 7.871463 GGTTCTACTTACTTTTCAGTAGCTTCA 59.129 37.037 0.00 0.0 41.59 3.02
171 188 7.091443 TCTACTTACTTTTCAGTAGCTTCAGC 58.909 38.462 0.00 0.0 41.59 4.26
379 397 0.179059 TCTTGACCAAACTGCGAGCA 60.179 50.000 0.00 0.0 0.00 4.26
862 3186 7.327214 GGAATTAGGGACTCATGTATCATCTC 58.673 42.308 0.00 0.0 41.75 2.75
1073 3416 4.018779 ACTGGCTGCTTTAACTATAACCCA 60.019 41.667 0.00 0.0 0.00 4.51
1584 6813 1.140375 GACCCGCGTTCTACCGAAT 59.860 57.895 4.92 0.0 0.00 3.34
1704 6933 7.664318 ACCCACTTTACTTTAATTGATCTCGTT 59.336 33.333 0.00 0.0 0.00 3.85
1921 7184 8.905660 TCTATCTATATATAGAACCCTCGTGC 57.094 38.462 23.08 0.0 42.20 5.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
161 178 8.855279 CGAATTACTCTATTATGCTGAAGCTAC 58.145 37.037 3.61 0.00 42.66 3.58
163 180 6.870965 CCGAATTACTCTATTATGCTGAAGCT 59.129 38.462 3.61 0.00 42.66 3.74
169 186 8.531982 TGCTATTCCGAATTACTCTATTATGCT 58.468 33.333 0.00 0.00 0.00 3.79
171 188 8.812329 GCTGCTATTCCGAATTACTCTATTATG 58.188 37.037 0.00 0.00 0.00 1.90
379 397 7.042335 CCCTATTTCATCTCGTAAAGTTCTGT 58.958 38.462 0.00 0.00 0.00 3.41
762 799 6.487299 AAGAACTAGATCATCTAACCCCAC 57.513 41.667 0.00 0.00 0.00 4.61
862 3186 8.571336 AGAAGTGTAAAAGAAAGTGGATTCATG 58.429 33.333 0.00 0.00 0.00 3.07
1073 3416 7.394359 TCTTGTTCAAGCCAATAAATAGAGCTT 59.606 33.333 7.58 0.00 44.27 3.74
1166 3509 4.220821 TCTGGAAAAGAGTCGTAGAATGCT 59.779 41.667 0.00 0.00 39.69 3.79
1533 6762 5.509163 CCGATGTCGTAGGTTCAAATCCTAT 60.509 44.000 1.44 0.00 39.36 2.57
1584 6813 4.754618 TGAATGAAAGCGCTCTTAGTTCAA 59.245 37.500 21.52 6.56 30.85 2.69
1704 6933 7.182817 TCTTTCTTCTTTATAGGCAGTAGCA 57.817 36.000 0.00 0.00 44.61 3.49


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

AutoCloner maintained by Alex Coulton.