Multiple sequence alignment - TraesCS6B01G332600

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 TraesCS6B01G332600 chr6B 100.000 2447 0 0 1 2447 583723914 583726360 0.000000e+00 4519.0
1 TraesCS6B01G332600 chr6B 90.028 351 28 4 2080 2430 38763130 38762787 4.800000e-122 448.0
2 TraesCS6B01G332600 chr6D 94.189 1893 72 12 1 1866 390781022 390779141 0.000000e+00 2852.0
3 TraesCS6B01G332600 chr6D 92.487 1930 116 11 1 1913 390486223 390484306 0.000000e+00 2734.0
4 TraesCS6B01G332600 chr6D 94.219 1505 74 4 1 1493 390729344 390727841 0.000000e+00 2285.0
5 TraesCS6B01G332600 chr6D 93.739 591 11 3 1514 2078 390727545 390726955 0.000000e+00 863.0
6 TraesCS6B01G332600 chr6D 96.196 368 13 1 2080 2447 390725636 390725270 3.480000e-168 601.0
7 TraesCS6B01G332600 chr6D 94.253 261 15 0 2080 2340 14898107 14898367 1.360000e-107 399.0
8 TraesCS6B01G332600 chr6D 91.935 186 15 0 2080 2265 14900033 14899848 6.710000e-66 261.0
9 TraesCS6B01G332600 chr6D 95.890 73 3 0 2006 2078 390484266 390484194 4.270000e-23 119.0
10 TraesCS6B01G332600 chr6D 94.030 67 4 0 2012 2078 390778980 390778914 4.300000e-18 102.0
11 TraesCS6B01G332600 chr6D 86.792 53 5 1 1863 1913 390779078 390779026 9.450000e-05 58.4
12 TraesCS6B01G332600 chr6A 93.460 1942 93 16 1 1913 537020566 537018630 0.000000e+00 2852.0
13 TraesCS6B01G332600 chr6A 96.206 369 12 2 2080 2447 537004229 537003862 9.680000e-169 603.0
14 TraesCS6B01G332600 chr6A 88.710 186 21 0 2080 2265 537002621 537002806 6.810000e-56 228.0
15 TraesCS6B01G332600 chr6A 95.495 111 5 0 1968 2078 537018649 537018539 6.950000e-41 178.0
16 TraesCS6B01G332600 chr6A 93.548 62 3 1 1909 1969 596292798 596292859 9.320000e-15 91.6
17 TraesCS6B01G332600 chr5B 91.967 361 27 2 2080 2439 207580596 207580955 2.810000e-139 505.0
18 TraesCS6B01G332600 chr5B 89.785 186 16 3 2080 2264 207582451 207582268 4.070000e-58 235.0
19 TraesCS6B01G332600 chr4D 88.556 367 31 5 2081 2445 112197748 112198105 3.740000e-118 435.0
20 TraesCS6B01G332600 chr2A 85.088 114 16 1 2332 2445 710461439 710461551 5.530000e-22 115.0
21 TraesCS6B01G332600 chr2A 96.552 58 1 1 1901 1957 65244348 65244291 7.200000e-16 95.3
22 TraesCS6B01G332600 chr1D 98.214 56 0 1 1902 1957 285451240 285451294 2.000000e-16 97.1
23 TraesCS6B01G332600 chr5D 98.148 54 1 0 1904 1957 220689913 220689860 7.200000e-16 95.3
24 TraesCS6B01G332600 chr7B 98.113 53 1 0 1905 1957 446143074 446143022 2.590000e-15 93.5
25 TraesCS6B01G332600 chr2B 98.113 53 1 0 1905 1957 225578224 225578276 2.590000e-15 93.5
26 TraesCS6B01G332600 chr2B 96.429 56 1 1 1903 1957 53783653 53783708 9.320000e-15 91.6
27 TraesCS6B01G332600 chrUn 96.429 56 1 1 1903 1957 478658069 478658124 9.320000e-15 91.6


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 TraesCS6B01G332600 chr6B 583723914 583726360 2446 False 4519.000000 4519 100.000000 1 2447 1 chr6B.!!$F1 2446
1 TraesCS6B01G332600 chr6D 390484194 390486223 2029 True 1426.500000 2734 94.188500 1 2078 2 chr6D.!!$R2 2077
2 TraesCS6B01G332600 chr6D 390725270 390729344 4074 True 1249.666667 2285 94.718000 1 2447 3 chr6D.!!$R3 2446
3 TraesCS6B01G332600 chr6D 390778914 390781022 2108 True 1004.133333 2852 91.670333 1 2078 3 chr6D.!!$R4 2077
4 TraesCS6B01G332600 chr6A 537018539 537020566 2027 True 1515.000000 2852 94.477500 1 2078 2 chr6A.!!$R2 2077

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 1.235281 GCCCTCGGTTGGTTTGTCTC 61.235 60.0 0.00 0.00 0.0 3.36 F
222 234 1.589716 GCCGCCCATGGAGAATATGC 61.590 60.0 15.22 4.93 0.0 3.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1246 1270 3.114809 CACAGTTTGCTTTCAATTGCGA 58.885 40.909 0.00 0.0 31.33 5.10 R
2131 3878 1.819928 ATACGCATGCACTGGAACAA 58.180 45.000 19.57 0.0 38.70 2.83 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 1.235281 GCCCTCGGTTGGTTTGTCTC 61.235 60.000 0.00 0.00 0.00 3.36
56 59 5.182380 GTCTCTCTTGCCTATAAGTATCGCT 59.818 44.000 0.00 0.00 0.00 4.93
101 113 2.793232 CGTAATAAGGAGCTTACGGCAC 59.207 50.000 5.65 0.00 43.87 5.01
222 234 1.589716 GCCGCCCATGGAGAATATGC 61.590 60.000 15.22 4.93 0.00 3.14
548 572 4.608269 TGATCACTTCTGATGAGAGGTCT 58.392 43.478 0.00 0.00 36.42 3.85
604 628 4.042062 ACAGATTGTTCTCCCATCAGTGAA 59.958 41.667 0.00 0.00 0.00 3.18
608 632 7.012138 CAGATTGTTCTCCCATCAGTGAATTAG 59.988 40.741 0.00 0.00 0.00 1.73
988 1012 2.557056 CCTACTGTCACAAGGAAGACGA 59.443 50.000 0.00 0.00 37.58 4.20
1015 1039 8.908786 TCTGGGTGACATGAAGAATTATATTC 57.091 34.615 0.00 0.00 0.00 1.75
1246 1270 4.780021 AGTGTCTCAGTGTGGGAGAATATT 59.220 41.667 0.00 0.00 42.63 1.28
1870 2253 4.818546 AGGACATCCTTATCTTTGAATGCG 59.181 41.667 0.00 0.00 46.09 4.73
1957 2340 2.304761 TCTAGCCTACCCCAACTTGTTG 59.695 50.000 6.52 6.52 0.00 3.33
1958 2341 0.539669 AGCCTACCCCAACTTGTTGC 60.540 55.000 7.89 0.00 0.00 4.17
1959 2342 0.539669 GCCTACCCCAACTTGTTGCT 60.540 55.000 7.89 0.00 0.00 3.91
2010 2440 8.398665 GGTTTCCATATCAGTTGAGTTATTGTC 58.601 37.037 0.00 0.00 0.00 3.18
2040 2470 3.212685 GAGATGGAAGATCAAAGGCCTG 58.787 50.000 5.69 0.00 0.00 4.85
2052 2482 1.708341 AAGGCCTGCAGATGTTTGTT 58.292 45.000 17.39 0.00 0.00 2.83
2131 3878 7.068103 TGTCATTTGGTTCAAATACAGTCACTT 59.932 33.333 5.68 0.00 41.40 3.16
2140 3887 6.119536 TCAAATACAGTCACTTTGTTCCAGT 58.880 36.000 0.00 0.00 32.89 4.00
2141 3888 6.038161 TCAAATACAGTCACTTTGTTCCAGTG 59.962 38.462 0.00 0.00 42.74 3.66
2207 3954 3.567478 TTCATGCCGACACGCTCGT 62.567 57.895 2.76 0.00 41.18 4.18
2260 4007 2.582202 CTATTTGTGGCTGCCGCGTG 62.582 60.000 25.57 10.73 36.72 5.34
2297 4044 1.612146 TCCTGACCATTCCGAGGCA 60.612 57.895 0.00 0.00 0.00 4.75
2373 4120 2.202570 CCCACGTCGTCGACATCC 60.203 66.667 24.13 1.06 40.62 3.51
2374 4121 2.564458 CCACGTCGTCGACATCCA 59.436 61.111 24.13 0.00 40.62 3.41
2385 4132 1.344438 TCGACATCCAAGTGAAGCAGT 59.656 47.619 0.00 0.00 0.00 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 4.218635 TCCAGCGATACTTATAGGCAAGAG 59.781 45.833 0.00 0.00 0.00 2.85
101 113 2.846652 CGTCGGGTGCCTAGCTAGG 61.847 68.421 32.12 32.12 46.42 3.02
490 514 4.551671 AGAGCCAATCAGATACCTACTGT 58.448 43.478 0.00 0.00 36.81 3.55
548 572 2.224744 TGGATTTACAAGGTGCAGCTCA 60.225 45.455 20.46 7.24 0.00 4.26
596 620 6.471146 ACTTGCTCAAGACTAATTCACTGAT 58.529 36.000 15.74 0.00 40.79 2.90
988 1012 9.872684 AATATAATTCTTCATGTCACCCAGAAT 57.127 29.630 0.00 0.00 36.04 2.40
1015 1039 5.277011 CCTGAACAATGTATATGTGCTCACG 60.277 44.000 0.00 0.00 0.00 4.35
1238 1262 7.274250 AGTTTGCTTTCAATTGCGAATATTCTC 59.726 33.333 13.45 6.20 35.38 2.87
1246 1270 3.114809 CACAGTTTGCTTTCAATTGCGA 58.885 40.909 0.00 0.00 31.33 5.10
1794 2111 7.011389 TGTGTGTCTAATGCTCATAATTACAGC 59.989 37.037 10.21 10.21 0.00 4.40
1795 2112 8.424274 TGTGTGTCTAATGCTCATAATTACAG 57.576 34.615 0.00 0.00 0.00 2.74
1883 2266 8.434733 AATAAAATCCTAAAAGGTAGACGAGC 57.565 34.615 0.00 0.00 36.53 5.03
1889 2272 7.913821 GCGACCAAATAAAATCCTAAAAGGTAG 59.086 37.037 0.00 0.00 36.53 3.18
2010 2440 7.400599 TTTGATCTTCCATCTCCAAAGAATG 57.599 36.000 0.00 0.00 34.49 2.67
2040 2470 4.319177 AGAGTACCTCAACAAACATCTGC 58.681 43.478 0.00 0.00 32.06 4.26
2052 2482 8.307582 CTAATTTTAGGAAGGAGAGTACCTCA 57.692 38.462 11.82 0.00 43.76 3.86
2131 3878 1.819928 ATACGCATGCACTGGAACAA 58.180 45.000 19.57 0.00 38.70 2.83
2260 4007 2.223852 GGAGATGAAGCGGTTAGGAGAC 60.224 54.545 0.00 0.00 0.00 3.36
2340 4087 2.491022 GGGTCGTCCATCTCCTCCG 61.491 68.421 0.04 0.00 35.00 4.63
2359 4106 0.386858 CACTTGGATGTCGACGACGT 60.387 55.000 22.13 22.13 40.69 4.34
2370 4117 0.957395 CGGCACTGCTTCACTTGGAT 60.957 55.000 0.00 0.00 0.00 3.41
2373 4120 1.159713 TGACGGCACTGCTTCACTTG 61.160 55.000 0.00 0.00 0.00 3.16
2374 4121 0.250467 ATGACGGCACTGCTTCACTT 60.250 50.000 0.00 0.00 0.00 3.16
2385 4132 3.296854 AGAGACTAACCATATGACGGCA 58.703 45.455 3.65 0.00 0.00 5.69


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

AutoCloner maintained by Alex Coulton.