Multiple sequence alignment - TraesCS6B01G255600

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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 TraesCS6B01G255600 chr6B 100.000 2447 0 0 1 2447 459603564 459601118 0.000000e+00 4519
1 TraesCS6B01G255600 chr6A 92.500 1720 86 17 3 1706 425656591 425658283 0.000000e+00 2422
2 TraesCS6B01G255600 chr6A 93.836 292 12 3 1925 2210 425658422 425658713 3.740000e-118 435
3 TraesCS6B01G255600 chr6A 94.821 251 8 1 2202 2447 425658886 425659136 1.060000e-103 387
4 TraesCS6B01G255600 chr6A 96.667 60 2 0 1765 1824 425658284 425658343 1.550000e-17 100
5 TraesCS6B01G255600 chr6D 95.895 1291 41 6 536 1822 295355464 295354182 0.000000e+00 2080
6 TraesCS6B01G255600 chr6D 92.505 547 31 6 2 543 295356146 295355605 0.000000e+00 774
7 TraesCS6B01G255600 chr6D 95.122 287 10 3 2162 2447 295306697 295306414 1.330000e-122 449
8 TraesCS6B01G255600 chr6D 92.969 256 12 3 1923 2172 295354174 295353919 3.840000e-98 368
9 TraesCS6B01G255600 chr6D 98.901 91 1 0 1839 1929 461690208 461690118 1.950000e-36 163
10 TraesCS6B01G255600 chr2B 97.895 95 1 1 1833 1927 772448240 772448333 1.950000e-36 163
11 TraesCS6B01G255600 chr1A 97.872 94 2 0 1836 1929 373317577 373317670 1.950000e-36 163
12 TraesCS6B01G255600 chr7D 97.849 93 2 0 1835 1927 45835321 45835413 7.000000e-36 161
13 TraesCS6B01G255600 chr4B 97.849 93 2 0 1836 1928 600126328 600126420 7.000000e-36 161
14 TraesCS6B01G255600 chr3D 95.960 99 4 0 1832 1930 194928308 194928210 7.000000e-36 161
15 TraesCS6B01G255600 chr5D 92.593 108 4 3 1822 1926 52603868 52603974 4.210000e-33 152
16 TraesCS6B01G255600 chr5D 94.059 101 4 2 1827 1927 343797553 343797651 4.210000e-33 152
17 TraesCS6B01G255600 chr5B 95.455 88 4 0 1841 1928 63462136 63462049 9.120000e-30 141


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 TraesCS6B01G255600 chr6B 459601118 459603564 2446 True 4519 4519 100.000000 1 2447 1 chr6B.!!$R1 2446
1 TraesCS6B01G255600 chr6A 425656591 425659136 2545 False 836 2422 94.456000 3 2447 4 chr6A.!!$F1 2444
2 TraesCS6B01G255600 chr6D 295353919 295356146 2227 True 1074 2080 93.789667 2 2172 3 chr6D.!!$R3 2170

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
97 98 0.036164 CGTGAGTGGTCCCCAATGAA 59.964 55.0 0.0 0.0 34.18 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1915 2148 0.105039 GGAGCAATGTACTCCCTCCG 59.895 60.0 0.0 0.0 46.81 4.63 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
23 24 0.628522 TGGGCAAGGGCATTTAGCTA 59.371 50.000 0.00 0.00 44.79 3.32
85 86 2.651361 ACGAGGGAAGCGTGAGTG 59.349 61.111 0.00 0.00 40.94 3.51
86 87 2.125912 CGAGGGAAGCGTGAGTGG 60.126 66.667 0.00 0.00 0.00 4.00
97 98 0.036164 CGTGAGTGGTCCCCAATGAA 59.964 55.000 0.00 0.00 34.18 2.57
99 100 1.144691 TGAGTGGTCCCCAATGAACA 58.855 50.000 0.00 0.00 34.18 3.18
130 131 1.542187 GGCACCTCCTCGTTGTAGGT 61.542 60.000 0.00 0.00 44.54 3.08
171 173 0.247736 CCACATAGCTATCGCCTCCC 59.752 60.000 2.34 0.00 36.60 4.30
193 195 4.302455 CCATGTTCTCTCTTAGTATGCGG 58.698 47.826 0.00 0.00 0.00 5.69
210 212 2.039746 TGCGGATGAAGGAGAAAAAGGA 59.960 45.455 0.00 0.00 0.00 3.36
227 229 0.316204 GGAAGGAGACGACGTGGAAA 59.684 55.000 4.58 0.00 0.00 3.13
246 248 0.667993 ACAAACTTCGCACATGTGGG 59.332 50.000 31.17 31.17 43.85 4.61
257 263 3.324993 GCACATGTGGGTGTAAAATTGG 58.675 45.455 26.55 0.00 40.89 3.16
282 291 0.971959 AAGGCACGTCATACCGGGTA 60.972 55.000 9.76 9.76 32.65 3.69
296 305 6.869913 TCATACCGGGTAAACATCGATTATTC 59.130 38.462 11.57 0.00 0.00 1.75
338 347 3.614616 GTGTGTCGCATGGAAAAACAAAA 59.385 39.130 0.00 0.00 0.00 2.44
345 354 2.880963 TGGAAAAACAAAAGAGCGGG 57.119 45.000 0.00 0.00 0.00 6.13
348 357 0.249280 AAAAACAAAAGAGCGGGCGG 60.249 50.000 0.00 0.00 0.00 6.13
448 457 6.706295 CCTGAGAGGTAATGAGAGAACTTTT 58.294 40.000 0.00 0.00 0.00 2.27
559 717 1.487482 CATGCCCACACGACGTATAG 58.513 55.000 0.00 0.00 0.00 1.31
570 728 5.003496 CACACGACGTATAGAATGACAACTG 59.997 44.000 0.00 0.00 0.00 3.16
798 956 1.459592 CAAAATCTCCGCTTCGTTCGT 59.540 47.619 0.00 0.00 0.00 3.85
815 973 2.708051 TCGTCGCCTTCTCTCTTTCTA 58.292 47.619 0.00 0.00 0.00 2.10
924 1082 5.261216 TCCTTTTTCCTCCGCATATTTTCT 58.739 37.500 0.00 0.00 0.00 2.52
1012 1170 1.735973 CTCGGGATGTCGATCTGCA 59.264 57.895 0.00 0.00 38.55 4.41
1457 1621 0.904865 AAGGAGTGATGGAGGCACGA 60.905 55.000 0.00 0.00 41.04 4.35
1709 1878 8.458212 AGTAGTACTACTTTTTAACATGCGTC 57.542 34.615 26.61 0.00 43.35 5.19
1820 1989 6.449635 AATCCTTCGCTTGCATATGTTTAA 57.550 33.333 4.29 0.00 0.00 1.52
1827 2060 6.714492 TCGCTTGCATATGTTTAATACAGTG 58.286 36.000 4.29 0.00 40.83 3.66
1848 2081 9.097946 ACAGTGTAATTTTAACTAGTACTCCCT 57.902 33.333 0.00 0.00 0.00 4.20
1849 2082 9.583765 CAGTGTAATTTTAACTAGTACTCCCTC 57.416 37.037 0.00 0.00 0.00 4.30
1850 2083 9.544579 AGTGTAATTTTAACTAGTACTCCCTCT 57.455 33.333 0.00 0.00 0.00 3.69
1851 2084 9.583765 GTGTAATTTTAACTAGTACTCCCTCTG 57.416 37.037 0.00 0.00 0.00 3.35
1852 2085 9.317827 TGTAATTTTAACTAGTACTCCCTCTGT 57.682 33.333 0.00 0.00 0.00 3.41
1857 2090 8.946797 TTTAACTAGTACTCCCTCTGTAAACT 57.053 34.615 0.00 0.00 0.00 2.66
1868 2101 9.939424 ACTCCCTCTGTAAACTAATATAAGAGT 57.061 33.333 0.00 0.00 0.00 3.24
1870 2103 9.710818 TCCCTCTGTAAACTAATATAAGAGTGT 57.289 33.333 0.00 0.00 0.00 3.55
1917 2150 9.669353 TCTAAACGCTCTTATATTAGTTTACGG 57.331 33.333 0.00 0.00 34.29 4.02
1918 2151 9.669353 CTAAACGCTCTTATATTAGTTTACGGA 57.331 33.333 0.00 0.00 34.29 4.69
1919 2152 8.571461 AAACGCTCTTATATTAGTTTACGGAG 57.429 34.615 0.00 0.00 31.14 4.63
1920 2153 6.675987 ACGCTCTTATATTAGTTTACGGAGG 58.324 40.000 0.00 0.00 0.00 4.30
1921 2154 6.091437 CGCTCTTATATTAGTTTACGGAGGG 58.909 44.000 0.00 0.00 0.00 4.30
1922 2155 6.072286 CGCTCTTATATTAGTTTACGGAGGGA 60.072 42.308 0.00 0.00 34.63 4.20
1923 2156 7.314393 GCTCTTATATTAGTTTACGGAGGGAG 58.686 42.308 0.00 0.00 0.00 4.30
1924 2157 7.039853 GCTCTTATATTAGTTTACGGAGGGAGT 60.040 40.741 0.00 0.00 0.00 3.85
1925 2158 9.512588 CTCTTATATTAGTTTACGGAGGGAGTA 57.487 37.037 0.00 0.00 0.00 2.59
1926 2159 9.289782 TCTTATATTAGTTTACGGAGGGAGTAC 57.710 37.037 0.00 0.00 0.00 2.73
1927 2160 8.995027 TTATATTAGTTTACGGAGGGAGTACA 57.005 34.615 0.00 0.00 0.00 2.90
1928 2161 9.592196 TTATATTAGTTTACGGAGGGAGTACAT 57.408 33.333 0.00 0.00 0.00 2.29
1929 2162 6.803366 ATTAGTTTACGGAGGGAGTACATT 57.197 37.500 0.00 0.00 0.00 2.71
1930 2163 4.467198 AGTTTACGGAGGGAGTACATTG 57.533 45.455 0.00 0.00 0.00 2.82
2065 2304 8.564574 GTTATTAATTACCAGGCGATTTGATCA 58.435 33.333 0.00 0.00 0.00 2.92
2069 2308 6.560253 ATTACCAGGCGATTTGATCAATAC 57.440 37.500 9.40 5.71 0.00 1.89
2102 2341 2.350895 CACCGATGCCTCCCACAA 59.649 61.111 0.00 0.00 0.00 3.33
2160 2399 6.519679 AGAATCTGTTGCATTTGCTATCAA 57.480 33.333 3.94 0.00 42.66 2.57
2169 2408 3.624900 CATTTGCTATCAAGGCGATGTG 58.375 45.455 0.00 0.00 35.39 3.21
2174 2413 0.815213 TATCAAGGCGATGTGCTGGC 60.815 55.000 0.00 0.00 45.43 4.85
2183 2422 1.068402 CGATGTGCTGGCATGTTTTCA 60.068 47.619 0.00 0.00 0.00 2.69
2219 2639 9.642327 TTTTGACATTTTATTCATGATGAGGTG 57.358 29.630 0.00 0.00 0.00 4.00
2328 2753 7.461182 TTTCTCAAGGAAACAAAAGAGTGAA 57.539 32.000 0.00 0.00 38.81 3.18
2331 2756 5.636837 TCAAGGAAACAAAAGAGTGAAACG 58.363 37.500 0.00 0.00 45.86 3.60
2388 2813 3.006247 GGCTGAGAAGTCATTGTTCTCC 58.994 50.000 12.13 1.77 46.42 3.71
2407 2832 7.013274 TGTTCTCCATTTCTCGTTCAATTTTCT 59.987 33.333 0.00 0.00 0.00 2.52
2426 2851 4.430137 TCTGTCAATTCTTCTTGCATGC 57.570 40.909 11.82 11.82 0.00 4.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.684983 CTAAATGCCCTTGCCCATGAG 59.315 52.381 0.00 0.00 36.33 2.90
15 16 6.936900 CACAACTATGTATGCCCTAGCTAAAT 59.063 38.462 0.00 0.00 37.82 1.40
23 24 1.494721 CCCCACAACTATGTATGCCCT 59.505 52.381 0.00 0.00 37.82 5.19
86 87 1.066929 GCCAACATGTTCATTGGGGAC 60.067 52.381 8.48 0.00 44.76 4.46
97 98 4.634703 TGCCGACCGCCAACATGT 62.635 61.111 0.00 0.00 36.24 3.21
130 131 2.032634 GGAGCACCGAATTGCACGA 61.033 57.895 6.43 0.00 45.62 4.35
171 173 4.038042 TCCGCATACTAAGAGAGAACATGG 59.962 45.833 0.00 0.00 0.00 3.66
193 195 5.645929 GTCTCCTTCCTTTTTCTCCTTCATC 59.354 44.000 0.00 0.00 0.00 2.92
210 212 0.748450 TGTTTCCACGTCGTCTCCTT 59.252 50.000 0.00 0.00 0.00 3.36
227 229 0.667993 CCCACATGTGCGAAGTTTGT 59.332 50.000 20.81 0.00 0.00 2.83
246 248 5.627780 CGTGCCTTCTTTACCAATTTTACAC 59.372 40.000 0.00 0.00 0.00 2.90
257 263 2.601763 CGGTATGACGTGCCTTCTTTAC 59.398 50.000 0.00 0.00 0.00 2.01
296 305 1.860950 CGCTTATGACCACTTGATCCG 59.139 52.381 0.00 0.00 0.00 4.18
362 371 1.143684 GGTGATGGGATAGTGTGGCAT 59.856 52.381 0.00 0.00 0.00 4.40
476 486 6.968904 AGTAATTAGCTCATTCAATTGCGTTG 59.031 34.615 0.00 0.00 39.25 4.10
559 717 3.003480 GCTGAGGGTACAGTTGTCATTC 58.997 50.000 0.00 0.00 39.73 2.67
570 728 1.276622 TCTGGAAAGGCTGAGGGTAC 58.723 55.000 0.00 0.00 0.00 3.34
624 782 3.698029 ATAACAAGAATGCCATCGTGC 57.302 42.857 2.49 0.00 32.88 5.34
767 925 2.749621 CGGAGATTTTGGTGGAAAGAGG 59.250 50.000 0.00 0.00 0.00 3.69
798 956 2.100989 GGGTAGAAAGAGAGAAGGCGA 58.899 52.381 0.00 0.00 0.00 5.54
815 973 2.056223 CCGTACGATCACAGGGGGT 61.056 63.158 18.76 0.00 0.00 4.95
924 1082 1.692749 ATAGCGGCAGGGGAAGGAA 60.693 57.895 1.45 0.00 0.00 3.36
1709 1878 2.772568 CTCACATAGCAGAGACGGAG 57.227 55.000 0.00 0.00 33.74 4.63
1775 1944 7.223387 GGATTTCCATGCACTTCAATTATCAAC 59.777 37.037 0.00 0.00 35.64 3.18
1844 2077 9.710818 ACACTCTTATATTAGTTTACAGAGGGA 57.289 33.333 2.59 0.00 34.50 4.20
1891 2124 9.669353 CCGTAAACTAATATAAGAGCGTTTAGA 57.331 33.333 0.00 0.00 30.36 2.10
1892 2125 9.669353 TCCGTAAACTAATATAAGAGCGTTTAG 57.331 33.333 0.00 0.00 30.36 1.85
1893 2126 9.669353 CTCCGTAAACTAATATAAGAGCGTTTA 57.331 33.333 0.00 0.00 0.00 2.01
1894 2127 7.650903 CCTCCGTAAACTAATATAAGAGCGTTT 59.349 37.037 0.00 0.00 0.00 3.60
1895 2128 7.144000 CCTCCGTAAACTAATATAAGAGCGTT 58.856 38.462 0.00 0.00 0.00 4.84
1896 2129 6.294397 CCCTCCGTAAACTAATATAAGAGCGT 60.294 42.308 0.00 0.00 0.00 5.07
1897 2130 6.072286 TCCCTCCGTAAACTAATATAAGAGCG 60.072 42.308 0.00 0.00 0.00 5.03
1898 2131 7.039853 ACTCCCTCCGTAAACTAATATAAGAGC 60.040 40.741 0.00 0.00 0.00 4.09
1899 2132 8.406730 ACTCCCTCCGTAAACTAATATAAGAG 57.593 38.462 0.00 0.00 0.00 2.85
1900 2133 9.289782 GTACTCCCTCCGTAAACTAATATAAGA 57.710 37.037 0.00 0.00 0.00 2.10
1901 2134 9.071276 TGTACTCCCTCCGTAAACTAATATAAG 57.929 37.037 0.00 0.00 0.00 1.73
1902 2135 8.995027 TGTACTCCCTCCGTAAACTAATATAA 57.005 34.615 0.00 0.00 0.00 0.98
1903 2136 9.592196 AATGTACTCCCTCCGTAAACTAATATA 57.408 33.333 0.00 0.00 0.00 0.86
1904 2137 8.365647 CAATGTACTCCCTCCGTAAACTAATAT 58.634 37.037 0.00 0.00 0.00 1.28
1905 2138 7.685155 GCAATGTACTCCCTCCGTAAACTAATA 60.685 40.741 0.00 0.00 0.00 0.98
1906 2139 6.579865 CAATGTACTCCCTCCGTAAACTAAT 58.420 40.000 0.00 0.00 0.00 1.73
1907 2140 5.625197 GCAATGTACTCCCTCCGTAAACTAA 60.625 44.000 0.00 0.00 0.00 2.24
1908 2141 4.142093 GCAATGTACTCCCTCCGTAAACTA 60.142 45.833 0.00 0.00 0.00 2.24
1909 2142 3.369157 GCAATGTACTCCCTCCGTAAACT 60.369 47.826 0.00 0.00 0.00 2.66
1910 2143 2.934553 GCAATGTACTCCCTCCGTAAAC 59.065 50.000 0.00 0.00 0.00 2.01
1911 2144 2.835764 AGCAATGTACTCCCTCCGTAAA 59.164 45.455 0.00 0.00 0.00 2.01
1912 2145 2.429610 GAGCAATGTACTCCCTCCGTAA 59.570 50.000 0.00 0.00 0.00 3.18
1913 2146 2.029623 GAGCAATGTACTCCCTCCGTA 58.970 52.381 0.00 0.00 0.00 4.02
1914 2147 0.824759 GAGCAATGTACTCCCTCCGT 59.175 55.000 0.00 0.00 0.00 4.69
1915 2148 0.105039 GGAGCAATGTACTCCCTCCG 59.895 60.000 0.00 0.00 46.81 4.63
1921 2154 7.224753 TCAATTTAATCTCGGAGCAATGTACTC 59.775 37.037 0.00 0.00 0.00 2.59
1922 2155 7.047891 TCAATTTAATCTCGGAGCAATGTACT 58.952 34.615 0.00 0.00 0.00 2.73
1923 2156 7.246674 TCAATTTAATCTCGGAGCAATGTAC 57.753 36.000 0.00 0.00 0.00 2.90
1924 2157 6.017934 GCTCAATTTAATCTCGGAGCAATGTA 60.018 38.462 0.00 0.00 45.23 2.29
1925 2158 5.220931 GCTCAATTTAATCTCGGAGCAATGT 60.221 40.000 0.00 0.00 45.23 2.71
1926 2159 5.210715 GCTCAATTTAATCTCGGAGCAATG 58.789 41.667 0.00 0.00 45.23 2.82
1927 2160 5.429957 GCTCAATTTAATCTCGGAGCAAT 57.570 39.130 0.00 0.00 45.23 3.56
1928 2161 4.882671 GCTCAATTTAATCTCGGAGCAA 57.117 40.909 0.00 0.00 45.23 3.91
1930 2163 4.592179 GTTGCTCAATTTAATCTCGGAGC 58.408 43.478 0.00 0.00 45.89 4.70
2051 2287 3.213506 TGGGTATTGATCAAATCGCCTG 58.786 45.455 13.09 0.00 0.00 4.85
2065 2304 4.220602 GGTGCAAAATCAGAGTTGGGTATT 59.779 41.667 0.00 0.00 0.00 1.89
2069 2308 1.068333 CGGTGCAAAATCAGAGTTGGG 60.068 52.381 0.00 0.00 0.00 4.12
2102 2341 3.119101 GGGACAATCGAGACACAGTACAT 60.119 47.826 0.00 0.00 0.00 2.29
2160 2399 2.827190 CATGCCAGCACATCGCCT 60.827 61.111 0.00 0.00 44.04 5.52
2169 2408 2.229543 TCAGTCATGAAAACATGCCAGC 59.770 45.455 0.00 0.00 30.61 4.85
2198 2437 7.924412 GCAATCACCTCATCATGAATAAAATGT 59.076 33.333 0.00 0.00 0.00 2.71
2219 2639 9.630098 TTCTTTTTCTGATAAGAACATGCAATC 57.370 29.630 9.91 0.00 35.93 2.67
2274 2694 3.249189 TGCCCAGGTGACCAGGTC 61.249 66.667 13.35 13.35 0.00 3.85
2328 2753 4.638304 ACAAAGACTAATACTGCCACGTT 58.362 39.130 0.00 0.00 0.00 3.99
2331 2756 5.932303 TGAGAACAAAGACTAATACTGCCAC 59.068 40.000 0.00 0.00 0.00 5.01
2388 2813 7.912949 TTGACAGAAAATTGAACGAGAAATG 57.087 32.000 0.00 0.00 0.00 2.32
2407 2832 4.490743 CATGCATGCAAGAAGAATTGACA 58.509 39.130 26.68 0.00 31.55 3.58
2426 2851 0.604511 TGCTGTGACACCTCTGCATG 60.605 55.000 2.45 0.00 36.36 4.06


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

AutoCloner maintained by Alex Coulton.