Multiple sequence alignment - TraesCS6A01G357000

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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 TraesCS6A01G357000 chr6A 100.000 3085 0 0 1 3085 587750848 587753932 0.000000e+00 5698.0
1 TraesCS6A01G357000 chr1B 96.019 3090 68 12 14 3085 145358053 145355001 0.000000e+00 4974.0
2 TraesCS6A01G357000 chr1B 97.607 2591 44 1 513 3085 660901991 660904581 0.000000e+00 4425.0
3 TraesCS6A01G357000 chr1B 88.723 470 20 18 17 486 660901574 660902010 7.520000e-151 544.0
4 TraesCS6A01G357000 chr4A 97.761 2591 40 1 513 3085 734095349 734097939 0.000000e+00 4447.0
5 TraesCS6A01G357000 chr4A 97.639 2414 37 3 15 2410 636019182 636021593 0.000000e+00 4124.0
6 TraesCS6A01G357000 chr4A 88.559 472 21 18 15 486 734094930 734095368 2.710000e-150 542.0
7 TraesCS6A01G357000 chr3A 97.723 2591 41 1 513 3085 17164188 17166778 0.000000e+00 4442.0
8 TraesCS6A01G357000 chr3A 97.619 42 1 0 445 486 17164166 17164207 4.270000e-09 73.1
9 TraesCS6A01G357000 chr4B 97.137 2585 55 2 519 3085 630676813 630674230 0.000000e+00 4346.0
10 TraesCS6A01G357000 chr4B 87.871 1921 193 19 1175 3083 345280038 345278146 0.000000e+00 2220.0
11 TraesCS6A01G357000 chr4B 95.070 284 13 1 15 298 630677090 630676808 2.180000e-121 446.0
12 TraesCS6A01G357000 chr7A 96.944 2585 48 4 519 3085 82999793 82997222 0.000000e+00 4307.0
13 TraesCS6A01G357000 chr7A 87.315 473 27 17 14 486 83000219 82999780 7.630000e-141 510.0
14 TraesCS6A01G357000 chrUn 97.339 2405 46 4 699 3085 334760395 334757991 0.000000e+00 4071.0
15 TraesCS6A01G357000 chrUn 97.048 1626 30 1 699 2306 383795608 383793983 0.000000e+00 2721.0
16 TraesCS6A01G357000 chrUn 94.718 284 14 1 15 298 337907003 337906721 1.020000e-119 440.0
17 TraesCS6A01G357000 chrUn 94.718 284 14 1 15 298 471254074 471253792 1.020000e-119 440.0
18 TraesCS6A01G357000 chr7D 91.582 2471 173 8 642 3085 591556136 591558598 0.000000e+00 3378.0
19 TraesCS6A01G357000 chr7D 87.385 872 83 14 1211 2071 85225848 85224993 0.000000e+00 976.0
20 TraesCS6A01G357000 chr1A 93.734 1564 52 6 581 2126 230145445 230146980 0.000000e+00 2303.0
21 TraesCS6A01G357000 chr1A 93.808 323 20 0 15 337 230144777 230145099 1.290000e-133 486.0
22 TraesCS6A01G357000 chr1A 93.333 330 8 9 312 641 230145130 230145445 2.780000e-130 475.0
23 TraesCS6A01G357000 chr2A 83.704 2068 310 17 1027 3083 729815470 729813419 0.000000e+00 1927.0
24 TraesCS6A01G357000 chr2D 83.325 2057 312 16 1037 3083 596140962 596138927 0.000000e+00 1869.0
25 TraesCS6A01G357000 chr1D 91.695 1168 93 2 1918 3085 225418136 225416973 0.000000e+00 1616.0
26 TraesCS6A01G357000 chr7B 85.666 1179 121 25 915 2074 34831713 34830564 0.000000e+00 1197.0


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 TraesCS6A01G357000 chr6A 587750848 587753932 3084 False 5698.00 5698 100.0000 1 3085 1 chr6A.!!$F1 3084
1 TraesCS6A01G357000 chr1B 145355001 145358053 3052 True 4974.00 4974 96.0190 14 3085 1 chr1B.!!$R1 3071
2 TraesCS6A01G357000 chr1B 660901574 660904581 3007 False 2484.50 4425 93.1650 17 3085 2 chr1B.!!$F1 3068
3 TraesCS6A01G357000 chr4A 636019182 636021593 2411 False 4124.00 4124 97.6390 15 2410 1 chr4A.!!$F1 2395
4 TraesCS6A01G357000 chr4A 734094930 734097939 3009 False 2494.50 4447 93.1600 15 3085 2 chr4A.!!$F2 3070
5 TraesCS6A01G357000 chr3A 17164166 17166778 2612 False 2257.55 4442 97.6710 445 3085 2 chr3A.!!$F1 2640
6 TraesCS6A01G357000 chr4B 630674230 630677090 2860 True 2396.00 4346 96.1035 15 3085 2 chr4B.!!$R2 3070
7 TraesCS6A01G357000 chr4B 345278146 345280038 1892 True 2220.00 2220 87.8710 1175 3083 1 chr4B.!!$R1 1908
8 TraesCS6A01G357000 chr7A 82997222 83000219 2997 True 2408.50 4307 92.1295 14 3085 2 chr7A.!!$R1 3071
9 TraesCS6A01G357000 chrUn 334757991 334760395 2404 True 4071.00 4071 97.3390 699 3085 1 chrUn.!!$R1 2386
10 TraesCS6A01G357000 chrUn 383793983 383795608 1625 True 2721.00 2721 97.0480 699 2306 1 chrUn.!!$R3 1607
11 TraesCS6A01G357000 chr7D 591556136 591558598 2462 False 3378.00 3378 91.5820 642 3085 1 chr7D.!!$F1 2443
12 TraesCS6A01G357000 chr7D 85224993 85225848 855 True 976.00 976 87.3850 1211 2071 1 chr7D.!!$R1 860
13 TraesCS6A01G357000 chr1A 230144777 230146980 2203 False 1088.00 2303 93.6250 15 2126 3 chr1A.!!$F1 2111
14 TraesCS6A01G357000 chr2A 729813419 729815470 2051 True 1927.00 1927 83.7040 1027 3083 1 chr2A.!!$R1 2056
15 TraesCS6A01G357000 chr2D 596138927 596140962 2035 True 1869.00 1869 83.3250 1037 3083 1 chr2D.!!$R1 2046
16 TraesCS6A01G357000 chr1D 225416973 225418136 1163 True 1616.00 1616 91.6950 1918 3085 1 chr1D.!!$R1 1167
17 TraesCS6A01G357000 chr7B 34830564 34831713 1149 True 1197.00 1197 85.6660 915 2074 1 chr7B.!!$R1 1159

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
36 37 2.040606 ACCGGTATGAGGGCCTGT 59.959 61.111 12.95 1.03 0.0 4.00 F
194 195 3.243134 GCCTCTCTCGTTCTACATGGTAC 60.243 52.174 0.00 0.00 0.0 3.34 F
977 1132 3.692257 ATGGAAGAAGTGGAGTGTCAG 57.308 47.619 0.00 0.00 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1673 1921 1.227793 GCATAGCTGGGAGCAGTCC 60.228 63.158 0.00 0.0 45.56 3.85 R
1733 1981 8.988934 CAGAGTTTATTTTATAGGCTGCGATTA 58.011 33.333 0.00 0.0 0.00 1.75 R
2754 3021 1.745087 GATGGTGTGCGGTTGATCAAT 59.255 47.619 12.12 0.0 0.00 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
36 37 2.040606 ACCGGTATGAGGGCCTGT 59.959 61.111 12.95 1.03 0.00 4.00
194 195 3.243134 GCCTCTCTCGTTCTACATGGTAC 60.243 52.174 0.00 0.00 0.00 3.34
977 1132 3.692257 ATGGAAGAAGTGGAGTGTCAG 57.308 47.619 0.00 0.00 0.00 3.51
1733 1981 6.343716 TGAAGGTAATGTTGAACATGCATT 57.656 33.333 12.09 11.43 37.97 3.56
1744 1992 1.683943 ACATGCATTAATCGCAGCCT 58.316 45.000 14.81 0.85 43.88 4.58
2104 2361 0.675522 GGGGTTGTGGTACATGGACG 60.676 60.000 0.92 0.00 44.52 4.79
2393 2659 3.895041 TGTCCAGTGTTATCTGTCAGTGA 59.105 43.478 0.00 0.00 37.22 3.41
2501 2767 6.198966 CAGTGTTTCAAAGTCTTTTATGCACC 59.801 38.462 0.00 0.00 0.00 5.01
2593 2859 2.562298 GCCATTGGTTCCTTCATGTCAA 59.438 45.455 4.26 0.00 0.00 3.18
2754 3021 1.408683 GCTGTCATGATGGCCACCTTA 60.409 52.381 8.16 0.00 0.00 2.69
2824 3091 6.098679 TGTGAGTTGGTTTTCACAGAAAATG 58.901 36.000 8.02 0.00 46.27 2.32
2825 3092 5.005682 GTGAGTTGGTTTTCACAGAAAATGC 59.994 40.000 8.02 0.00 42.47 3.56
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.036388 TCAACAATCCCTCTCGGTGC 60.036 55.000 0.00 0.00 0.00 5.01
1 2 1.676014 GGTCAACAATCCCTCTCGGTG 60.676 57.143 0.00 0.00 0.00 4.94
2 3 0.613777 GGTCAACAATCCCTCTCGGT 59.386 55.000 0.00 0.00 0.00 4.69
4 5 0.460284 CCGGTCAACAATCCCTCTCG 60.460 60.000 0.00 0.00 0.00 4.04
5 6 0.613777 ACCGGTCAACAATCCCTCTC 59.386 55.000 0.00 0.00 0.00 3.20
6 7 1.946984 TACCGGTCAACAATCCCTCT 58.053 50.000 12.40 0.00 0.00 3.69
7 8 2.169769 TCATACCGGTCAACAATCCCTC 59.830 50.000 12.40 0.00 0.00 4.30
8 9 2.170607 CTCATACCGGTCAACAATCCCT 59.829 50.000 12.40 0.00 0.00 4.20
9 10 2.561569 CTCATACCGGTCAACAATCCC 58.438 52.381 12.40 0.00 0.00 3.85
10 11 2.561569 CCTCATACCGGTCAACAATCC 58.438 52.381 12.40 0.00 0.00 3.01
11 12 2.561569 CCCTCATACCGGTCAACAATC 58.438 52.381 12.40 0.00 0.00 2.67
12 13 1.408266 GCCCTCATACCGGTCAACAAT 60.408 52.381 12.40 0.00 0.00 2.71
36 37 4.408921 CCTATACCAACAGTGAAGATGGGA 59.591 45.833 0.00 0.00 37.26 4.37
125 126 0.676184 TCTGGCGGCTGACATCTATC 59.324 55.000 14.64 0.00 27.97 2.08
126 127 0.390860 GTCTGGCGGCTGACATCTAT 59.609 55.000 33.97 0.00 33.75 1.98
977 1132 0.729690 GGCCAAAATCAGAGAGTCGC 59.270 55.000 0.00 0.00 0.00 5.19
1065 1220 2.361757 CCTTGTGAACAACATGCTCCAA 59.638 45.455 0.00 0.00 38.99 3.53
1673 1921 1.227793 GCATAGCTGGGAGCAGTCC 60.228 63.158 0.00 0.00 45.56 3.85
1733 1981 8.988934 CAGAGTTTATTTTATAGGCTGCGATTA 58.011 33.333 0.00 0.00 0.00 1.75
1744 1992 9.474313 AAGCACCCATTCAGAGTTTATTTTATA 57.526 29.630 0.00 0.00 0.00 0.98
2501 2767 9.734620 TTTTCACATTAAATTGAGTCTGAACAG 57.265 29.630 0.00 0.00 0.00 3.16
2681 2947 2.283472 GAACATCAATGCACGGGCCC 62.283 60.000 13.57 13.57 40.13 5.80
2754 3021 1.745087 GATGGTGTGCGGTTGATCAAT 59.255 47.619 12.12 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.