Multiple sequence alignment - TraesCS5B01G123700

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 TraesCS5B01G123700 chr5B 100.000 2174 0 0 1 2174 222755962 222753789 0.000000e+00 4015
1 TraesCS5B01G123700 chr7D 86.140 2179 278 21 7 2174 556869602 556867437 0.000000e+00 2329
2 TraesCS5B01G123700 chr1D 86.029 2176 270 19 13 2174 193688298 193686143 0.000000e+00 2303
3 TraesCS5B01G123700 chr2D 85.858 2185 285 21 1 2174 620261176 620263347 0.000000e+00 2302
4 TraesCS5B01G123700 chr2D 83.815 2181 321 28 7 2174 131527751 131525590 0.000000e+00 2043
5 TraesCS5B01G123700 chr5D 85.584 2185 287 25 7 2174 282194304 282192131 0.000000e+00 2265
6 TraesCS5B01G123700 chr5A 85.485 2177 303 13 7 2174 689877559 689875387 0.000000e+00 2257
7 TraesCS5B01G123700 chr2A 85.250 2183 306 14 1 2174 691688125 691690300 0.000000e+00 2233
8 TraesCS5B01G123700 chr2A 85.750 1979 265 16 205 2174 100229322 100231292 0.000000e+00 2076
9 TraesCS5B01G123700 chr2A 77.835 194 40 3 1 193 100229145 100229336 1.360000e-22 117
10 TraesCS5B01G123700 chr7A 84.022 2178 329 19 7 2174 540051790 540053958 0.000000e+00 2076


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 TraesCS5B01G123700 chr5B 222753789 222755962 2173 True 4015.0 4015 100.0000 1 2174 1 chr5B.!!$R1 2173
1 TraesCS5B01G123700 chr7D 556867437 556869602 2165 True 2329.0 2329 86.1400 7 2174 1 chr7D.!!$R1 2167
2 TraesCS5B01G123700 chr1D 193686143 193688298 2155 True 2303.0 2303 86.0290 13 2174 1 chr1D.!!$R1 2161
3 TraesCS5B01G123700 chr2D 620261176 620263347 2171 False 2302.0 2302 85.8580 1 2174 1 chr2D.!!$F1 2173
4 TraesCS5B01G123700 chr2D 131525590 131527751 2161 True 2043.0 2043 83.8150 7 2174 1 chr2D.!!$R1 2167
5 TraesCS5B01G123700 chr5D 282192131 282194304 2173 True 2265.0 2265 85.5840 7 2174 1 chr5D.!!$R1 2167
6 TraesCS5B01G123700 chr5A 689875387 689877559 2172 True 2257.0 2257 85.4850 7 2174 1 chr5A.!!$R1 2167
7 TraesCS5B01G123700 chr2A 691688125 691690300 2175 False 2233.0 2233 85.2500 1 2174 1 chr2A.!!$F1 2173
8 TraesCS5B01G123700 chr2A 100229145 100231292 2147 False 1096.5 2076 81.7925 1 2174 2 chr2A.!!$F2 2173
9 TraesCS5B01G123700 chr7A 540051790 540053958 2168 False 2076.0 2076 84.0220 7 2174 1 chr7A.!!$F1 2167

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
985 1011 0.031515 TCGAGGGGCCTAGGAATTCA 60.032 55.0 14.75 0.0 0.0 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2079 2112 0.98655 AAGCCGTATTAGCACCCCCT 60.987 55.0 0.0 0.0 0.0 4.79 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
20 21 2.990479 CTCCTACTGGTGGTGGGC 59.010 66.667 0.00 0.00 44.91 5.36
71 72 2.584391 GCGTCAGGGAGTGGGTCTT 61.584 63.158 0.00 0.00 0.00 3.01
77 78 0.104409 AGGGAGTGGGTCTTTGGTCT 60.104 55.000 0.00 0.00 0.00 3.85
83 84 1.133915 GTGGGTCTTTGGTCTTGGACA 60.134 52.381 0.14 0.00 33.68 4.02
90 91 0.401395 TTGGTCTTGGACACCCCTCT 60.401 55.000 0.14 0.00 33.68 3.69
91 92 0.401395 TGGTCTTGGACACCCCTCTT 60.401 55.000 0.14 0.00 33.68 2.85
92 93 0.771755 GGTCTTGGACACCCCTCTTT 59.228 55.000 0.14 0.00 33.68 2.52
100 101 1.122019 ACACCCCTCTTTCTGTCGCT 61.122 55.000 0.00 0.00 0.00 4.93
101 102 0.390472 CACCCCTCTTTCTGTCGCTC 60.390 60.000 0.00 0.00 0.00 5.03
104 105 1.261238 CCCTCTTTCTGTCGCTCCCT 61.261 60.000 0.00 0.00 0.00 4.20
136 137 0.644380 TGGAGACCATGGAGGAGGAT 59.356 55.000 21.47 0.00 41.22 3.24
169 170 4.115199 ATGGAGGTGCGCCCTTCC 62.115 66.667 14.18 14.18 46.51 3.46
262 269 3.358076 CTCGGACGTGGAGCCTTCC 62.358 68.421 0.00 0.00 44.31 3.46
270 278 3.087906 GGAGCCTTCCCCGCCTTA 61.088 66.667 0.00 0.00 37.53 2.69
378 386 2.608988 AGCCAGTCCCAGGTCCTG 60.609 66.667 12.40 12.40 0.00 3.86
415 423 1.135094 GATGATCCAGGAGAAGGCCA 58.865 55.000 5.01 0.00 0.00 5.36
454 464 2.249139 GTGACTTGTCCTCAGGTACCT 58.751 52.381 9.21 9.21 34.06 3.08
459 469 1.382833 GTCCTCAGGTACCTCCCCC 60.383 68.421 12.84 0.00 36.75 5.40
464 475 3.374742 AGGTACCTCCCCCTCCCC 61.375 72.222 9.21 0.00 36.75 4.81
496 508 4.334481 TCTTGTTCTGGTTCTCGTTTTTCC 59.666 41.667 0.00 0.00 0.00 3.13
518 530 1.937546 GCTTGGTTCCGCTCCATTGG 61.938 60.000 0.00 0.00 34.75 3.16
519 531 1.304052 TTGGTTCCGCTCCATTGGG 60.304 57.895 2.09 0.00 34.75 4.12
552 564 3.107601 AGGTAGCTTCAGATAGTGGCAA 58.892 45.455 0.00 0.00 0.00 4.52
562 574 3.012518 AGATAGTGGCAATGTGTTCTGC 58.987 45.455 0.00 0.00 37.86 4.26
565 578 1.528076 TGGCAATGTGTTCTGCGGT 60.528 52.632 0.00 0.00 39.55 5.68
740 753 2.358737 CCCAGTTGGAGACCGTGC 60.359 66.667 0.00 0.00 37.39 5.34
744 757 3.050275 GTTGGAGACCGTGCTGGC 61.050 66.667 0.00 0.00 43.94 4.85
827 848 1.933021 TCCCACTGAACACCGACTAT 58.067 50.000 0.00 0.00 0.00 2.12
853 874 1.149288 TGTGGGTCTAGTTCCAGGTCT 59.851 52.381 6.98 0.00 33.13 3.85
856 877 0.537653 GGTCTAGTTCCAGGTCTGCC 59.462 60.000 0.00 0.00 0.00 4.85
865 886 3.999285 AGGTCTGCCTCCCTCGGT 61.999 66.667 0.00 0.00 42.67 4.69
985 1011 0.031515 TCGAGGGGCCTAGGAATTCA 60.032 55.000 14.75 0.00 0.00 2.57
986 1012 1.059913 CGAGGGGCCTAGGAATTCAT 58.940 55.000 14.75 2.14 0.00 2.57
988 1014 1.002544 GAGGGGCCTAGGAATTCATCG 59.997 57.143 14.75 0.00 0.00 3.84
995 1021 3.433740 GCCTAGGAATTCATCGGAGGTTT 60.434 47.826 14.75 0.00 34.54 3.27
1092 1118 2.609244 GCGGCAAGAGGAGATAGACATC 60.609 54.545 0.00 0.00 0.00 3.06
1095 1121 3.305064 GGCAAGAGGAGATAGACATCGTC 60.305 52.174 0.00 0.00 36.20 4.20
1112 1138 0.448593 GTCGGACTTCAGGAGACGAG 59.551 60.000 0.00 0.00 38.32 4.18
1133 1159 0.176680 CGCCAGGACTTCAGTATGCT 59.823 55.000 0.00 0.00 34.76 3.79
1135 1161 2.284190 GCCAGGACTTCAGTATGCTTC 58.716 52.381 0.00 0.00 34.76 3.86
1229 1256 2.435693 CGGGGTCAGGGAGGATGTC 61.436 68.421 0.00 0.00 0.00 3.06
1250 1277 4.282195 GTCTTCTCGGTTGAGGATATGGAT 59.718 45.833 0.00 0.00 42.79 3.41
1362 1389 2.360475 GCTCTGCCGCCTTCCTTT 60.360 61.111 0.00 0.00 0.00 3.11
1373 1400 2.675348 CGCCTTCCTTTCTGAGCTTAAG 59.325 50.000 0.00 0.00 0.00 1.85
1374 1401 2.421775 GCCTTCCTTTCTGAGCTTAAGC 59.578 50.000 20.09 20.09 42.49 3.09
1493 1520 2.475111 CCGCATGCGTCTATTTAACGAT 59.525 45.455 35.55 0.00 42.62 3.73
1508 1535 1.063006 CGATTGCATTGCGGACCTG 59.937 57.895 3.84 0.00 0.00 4.00
1743 1772 1.668919 CGCTTTGAGACGTTCTGGCTA 60.669 52.381 0.00 0.00 0.00 3.93
1751 1780 0.969894 ACGTTCTGGCTAGAGCAACT 59.030 50.000 14.06 0.00 44.36 3.16
1759 1788 1.079503 GCTAGAGCAACTGGGTTTCG 58.920 55.000 0.00 0.00 41.59 3.46
1775 1804 1.011968 TTCGTTGAGATGGTTCGCGG 61.012 55.000 6.13 0.00 0.00 6.46
1800 1829 4.592936 CTAGAGGCGGTCGCGACG 62.593 72.222 30.99 25.57 43.06 5.12
1821 1850 1.668151 GCCTCGGGTGTTCTGTGTC 60.668 63.158 0.00 0.00 0.00 3.67
1827 1856 0.878961 GGGTGTTCTGTGTCGTGGAC 60.879 60.000 0.00 0.00 0.00 4.02
1830 1859 0.173935 TGTTCTGTGTCGTGGACGTT 59.826 50.000 0.00 0.00 40.80 3.99
1857 1886 2.584791 CACTGTGCTAAATTGTTCCGC 58.415 47.619 0.00 0.00 0.00 5.54
1860 1889 1.957177 TGTGCTAAATTGTTCCGCCAA 59.043 42.857 0.00 0.00 0.00 4.52
1911 1943 2.439701 TGACCTCCGAGCCCGTAG 60.440 66.667 0.00 0.00 0.00 3.51
1987 2020 0.389166 GTCTCCTGACGACTGGCTTG 60.389 60.000 5.95 0.26 35.51 4.01
2001 2034 1.362224 GGCTTGGGAGATATGCCCTA 58.638 55.000 10.73 3.70 46.19 3.53
2027 2060 3.242543 GCTTCGCTCATGGACATTTACAG 60.243 47.826 0.00 0.00 0.00 2.74
2031 2064 3.679917 CGCTCATGGACATTTACAGGAGT 60.680 47.826 7.53 0.00 44.69 3.85
2060 2093 2.326773 TTTTGGCAACGTCGAGGGGA 62.327 55.000 10.27 0.00 42.51 4.81
2088 2122 1.691823 GCTCCTTAAAGGGGGTGCT 59.308 57.895 0.00 0.00 35.97 4.40
2091 2125 2.091830 GCTCCTTAAAGGGGGTGCTAAT 60.092 50.000 0.00 0.00 35.97 1.73
2094 2128 3.135167 TCCTTAAAGGGGGTGCTAATACG 59.865 47.826 0.00 0.00 35.59 3.06
2097 2131 0.986550 AAGGGGGTGCTAATACGGCT 60.987 55.000 0.00 0.00 0.00 5.52
2107 2141 5.107133 GTGCTAATACGGCTTACTTTCAGA 58.893 41.667 0.00 0.00 0.00 3.27
2109 2143 5.107133 GCTAATACGGCTTACTTTCAGACA 58.893 41.667 0.00 0.00 0.00 3.41
2118 2152 6.086871 GGCTTACTTTCAGACAATTGCTAAC 58.913 40.000 5.05 0.00 0.00 2.34
2170 2204 0.409484 CTGGGATGGGGGTGTTCTTT 59.591 55.000 0.00 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 2.670148 GGCCCACCACCAGTAGGAG 61.670 68.421 0.00 0.00 38.69 3.69
5 6 3.728373 GGGCCCACCACCAGTAGG 61.728 72.222 19.95 0.00 39.85 3.18
62 63 1.143073 GTCCAAGACCAAAGACCCACT 59.857 52.381 0.00 0.00 0.00 4.00
71 72 0.401395 AGAGGGGTGTCCAAGACCAA 60.401 55.000 0.00 0.00 38.24 3.67
77 78 1.420138 GACAGAAAGAGGGGTGTCCAA 59.580 52.381 0.00 0.00 38.24 3.53
83 84 1.545706 GGAGCGACAGAAAGAGGGGT 61.546 60.000 0.00 0.00 0.00 4.95
90 91 1.906824 ACCGAGGGAGCGACAGAAA 60.907 57.895 0.00 0.00 0.00 2.52
91 92 2.282958 ACCGAGGGAGCGACAGAA 60.283 61.111 0.00 0.00 0.00 3.02
92 93 3.062466 CACCGAGGGAGCGACAGA 61.062 66.667 0.00 0.00 0.00 3.41
112 113 0.176680 CCTCCATGGTCTCCAAGTCG 59.823 60.000 12.58 0.00 36.95 4.18
116 117 0.417437 TCCTCCTCCATGGTCTCCAA 59.583 55.000 12.58 0.00 36.95 3.53
122 123 0.253347 ACCACATCCTCCTCCATGGT 60.253 55.000 12.58 0.00 35.60 3.55
136 137 1.760527 CATCCCCACACTCACCACA 59.239 57.895 0.00 0.00 0.00 4.17
259 266 1.993391 CCAGGTCTAAGGCGGGGAA 60.993 63.158 0.00 0.00 0.00 3.97
270 278 3.626924 GTCACCACGGCCAGGTCT 61.627 66.667 13.74 0.00 37.23 3.85
378 386 2.737376 GGAACACGGTCGTCCAGC 60.737 66.667 0.00 0.00 0.00 4.85
384 392 0.870307 GGATCATCGGAACACGGTCG 60.870 60.000 0.00 0.00 44.45 4.79
386 394 0.175760 CTGGATCATCGGAACACGGT 59.824 55.000 0.00 0.00 44.45 4.83
454 464 3.791076 GGATCAGGGGGAGGGGGA 61.791 72.222 0.00 0.00 0.00 4.81
459 469 0.978146 ACAAGACGGATCAGGGGGAG 60.978 60.000 0.00 0.00 0.00 4.30
464 475 1.276421 ACCAGAACAAGACGGATCAGG 59.724 52.381 0.00 0.00 0.00 3.86
472 483 4.877323 AAAACGAGAACCAGAACAAGAC 57.123 40.909 0.00 0.00 0.00 3.01
496 508 3.423154 GGAGCGGAACCAAGCACG 61.423 66.667 0.00 0.00 35.48 5.34
529 541 2.287909 GCCACTATCTGAAGCTACCTCG 60.288 54.545 0.00 0.00 0.00 4.63
535 547 3.276857 CACATTGCCACTATCTGAAGCT 58.723 45.455 0.00 0.00 0.00 3.74
552 564 1.609061 CCTTCTCACCGCAGAACACAT 60.609 52.381 0.00 0.00 0.00 3.21
562 574 3.406595 GATGGGCCCCTTCTCACCG 62.407 68.421 22.27 0.00 0.00 4.94
565 578 1.230281 AAGGATGGGCCCCTTCTCA 60.230 57.895 22.27 0.00 39.72 3.27
726 739 2.743718 CCAGCACGGTCTCCAACT 59.256 61.111 0.00 0.00 0.00 3.16
727 740 3.050275 GCCAGCACGGTCTCCAAC 61.050 66.667 0.00 0.00 36.97 3.77
801 822 2.549992 CGGTGTTCAGTGGGATTGAGAA 60.550 50.000 0.00 0.00 0.00 2.87
808 829 1.933021 ATAGTCGGTGTTCAGTGGGA 58.067 50.000 0.00 0.00 0.00 4.37
827 848 2.158279 TGGAACTAGACCCACACACCTA 60.158 50.000 0.00 0.00 0.00 3.08
967 993 1.002544 GATGAATTCCTAGGCCCCTCG 59.997 57.143 2.96 0.00 0.00 4.63
985 1011 5.125578 GGAGCTTCATTTAAAAACCTCCGAT 59.874 40.000 0.00 0.00 0.00 4.18
986 1012 4.457949 GGAGCTTCATTTAAAAACCTCCGA 59.542 41.667 0.00 0.00 0.00 4.55
988 1014 5.984695 AGGAGCTTCATTTAAAAACCTCC 57.015 39.130 0.00 12.24 38.27 4.30
995 1021 7.450014 TGTTCCAACATAGGAGCTTCATTTAAA 59.550 33.333 0.00 0.00 39.39 1.52
1063 1089 2.027192 TCTCCTCTTGCCGCAAATACTT 60.027 45.455 7.33 0.00 0.00 2.24
1092 1118 1.134901 CGTCTCCTGAAGTCCGACG 59.865 63.158 0.00 0.00 40.92 5.12
1095 1121 0.448593 GACTCGTCTCCTGAAGTCCG 59.551 60.000 0.00 0.00 0.00 4.79
1112 1138 1.927895 CATACTGAAGTCCTGGCGAC 58.072 55.000 0.00 0.00 42.32 5.19
1125 1151 1.474677 CCCTGGAGCTGAAGCATACTG 60.475 57.143 4.90 0.00 45.16 2.74
1133 1159 1.992277 GAGAGCCCCTGGAGCTGAA 60.992 63.158 7.70 0.00 41.75 3.02
1135 1161 2.365370 AGAGAGCCCCTGGAGCTG 60.365 66.667 7.70 0.00 41.75 4.24
1229 1256 4.617067 CGATCCATATCCTCAACCGAGAAG 60.617 50.000 0.00 0.00 42.34 2.85
1271 1298 3.252979 TCGGTCGGTGACAGACATA 57.747 52.632 17.11 2.10 40.20 2.29
1334 1361 2.887568 GCAGAGCGTCCATGGTCG 60.888 66.667 24.49 24.49 41.16 4.79
1362 1389 3.774766 TCCACCTTATGCTTAAGCTCAGA 59.225 43.478 26.90 8.34 42.66 3.27
1373 1400 0.253044 TGCACCTCTCCACCTTATGC 59.747 55.000 0.00 0.00 0.00 3.14
1374 1401 1.407437 GGTGCACCTCTCCACCTTATG 60.407 57.143 29.12 0.00 46.23 1.90
1493 1520 3.372730 GCCAGGTCCGCAATGCAA 61.373 61.111 5.91 0.00 0.00 4.08
1508 1535 2.355244 GCTATCTCACGGAGCGCC 60.355 66.667 2.29 0.00 0.00 6.53
1712 1740 0.391130 CTCAAAGCGGAATGACGGGA 60.391 55.000 0.00 0.00 0.00 5.14
1743 1772 1.134220 TCAACGAAACCCAGTTGCTCT 60.134 47.619 3.71 0.00 45.15 4.09
1751 1780 2.500229 GAACCATCTCAACGAAACCCA 58.500 47.619 0.00 0.00 0.00 4.51
1759 1788 2.750888 GGCCGCGAACCATCTCAAC 61.751 63.158 8.23 0.00 0.00 3.18
1809 1838 1.213094 CGTCCACGACACAGAACACC 61.213 60.000 0.00 0.00 43.02 4.16
1821 1850 2.897846 TGGTGCCAAACGTCCACG 60.898 61.111 0.00 0.00 46.33 4.94
1853 1882 2.045045 CCTTCATGGCTTGGCGGA 60.045 61.111 0.09 0.00 0.00 5.54
1877 1906 4.660938 AGCACCAAGGTTCGCCCC 62.661 66.667 0.00 0.00 38.27 5.80
1878 1907 3.365265 CAGCACCAAGGTTCGCCC 61.365 66.667 0.00 0.00 38.27 6.13
1911 1943 2.276309 CTGATCCAACAGGGCCCCTC 62.276 65.000 21.43 4.75 36.21 4.30
1922 1954 3.523157 TCCAGCACCTTAATCTGATCCAA 59.477 43.478 0.00 0.00 0.00 3.53
2007 2040 3.055458 TCCTGTAAATGTCCATGAGCGAA 60.055 43.478 0.00 0.00 0.00 4.70
2027 2060 1.528129 CCAAAACAGCTCCTCACTCC 58.472 55.000 0.00 0.00 0.00 3.85
2031 2064 1.032014 GTTGCCAAAACAGCTCCTCA 58.968 50.000 0.00 0.00 0.00 3.86
2060 2093 2.040412 CCTTTAAGGAGCCAGTTCTGGT 59.960 50.000 18.42 7.08 37.67 4.00
2079 2112 0.986550 AAGCCGTATTAGCACCCCCT 60.987 55.000 0.00 0.00 0.00 4.79
2088 2122 7.413657 GCAATTGTCTGAAAGTAAGCCGTATTA 60.414 37.037 7.40 0.00 33.76 0.98
2091 2125 4.153475 GCAATTGTCTGAAAGTAAGCCGTA 59.847 41.667 7.40 0.00 33.76 4.02
2094 2128 4.773323 AGCAATTGTCTGAAAGTAAGCC 57.227 40.909 7.40 0.00 33.76 4.35
2097 2131 5.334569 GCCGTTAGCAATTGTCTGAAAGTAA 60.335 40.000 7.40 0.00 42.97 2.24
2107 2141 1.922135 CTGCGGCCGTTAGCAATTGT 61.922 55.000 28.70 0.00 46.50 2.71
2109 2143 2.406616 CCTGCGGCCGTTAGCAATT 61.407 57.895 28.70 0.00 46.50 2.32
2118 2152 2.040544 ACATTTTCTCCTGCGGCCG 61.041 57.895 24.05 24.05 0.00 6.13


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

AutoCloner maintained by Alex Coulton.