Multiple sequence alignment - TraesCS4A01G227400

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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 TraesCS4A01G227400 chr4A 100.000 2558 0 0 1 2558 535818032 535820589 0.000000e+00 4724.0
1 TraesCS4A01G227400 chr4B 91.825 2581 143 24 3 2558 89928102 89930639 0.000000e+00 3535.0
2 TraesCS4A01G227400 chr4D 91.751 2570 138 18 3 2558 62302784 62305293 0.000000e+00 3504.0
3 TraesCS4A01G227400 chr2A 80.083 241 32 15 3 240 490612023 490611796 5.660000e-37 165.0
4 TraesCS4A01G227400 chr1B 85.093 161 16 7 138 295 598846294 598846449 9.470000e-35 158.0
5 TraesCS4A01G227400 chr1B 79.670 182 30 5 117 292 660533828 660533648 9.610000e-25 124.0
6 TraesCS4A01G227400 chr3D 84.768 151 22 1 138 288 369560528 369560379 1.590000e-32 150.0
7 TraesCS4A01G227400 chr5D 81.522 184 28 6 116 295 446496013 446495832 2.050000e-31 147.0
8 TraesCS4A01G227400 chr6B 80.663 181 27 7 116 294 643531423 643531597 1.600000e-27 134.0
9 TraesCS4A01G227400 chr7D 82.099 162 21 6 117 274 506676720 506676563 5.740000e-27 132.0
10 TraesCS4A01G227400 chr7D 76.889 225 42 7 70 292 159412168 159411952 4.470000e-23 119.0
11 TraesCS4A01G227400 chr7B 74.074 270 56 10 31 295 696350465 696350205 5.820000e-17 99.0
12 TraesCS4A01G227400 chr5A 83.516 91 14 1 1912 2001 106732629 106732539 1.630000e-12 84.2


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 TraesCS4A01G227400 chr4A 535818032 535820589 2557 False 4724 4724 100.000 1 2558 1 chr4A.!!$F1 2557
1 TraesCS4A01G227400 chr4B 89928102 89930639 2537 False 3535 3535 91.825 3 2558 1 chr4B.!!$F1 2555
2 TraesCS4A01G227400 chr4D 62302784 62305293 2509 False 3504 3504 91.751 3 2558 1 chr4D.!!$F1 2555

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
282 283 0.320596 AATTTACGGGTCGGCGTTGA 60.321 50.0 6.85 0.0 0.0 3.18 F
706 707 1.381928 GGGAGGCGACACGTATCAGA 61.382 60.0 0.00 0.0 0.0 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1500 1512 0.736325 GGGACCACTCGTCATTGTCG 60.736 60.0 0.0 0.0 43.95 4.35 R
1568 1580 1.171308 TCCGACCTCTACGAACCAAG 58.829 55.0 0.0 0.0 0.00 3.61 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
60 61 6.883756 AGCGTAGACTAGTTTTACCTTAGTCT 59.116 38.462 15.28 15.28 46.24 3.24
127 128 4.217550 CGTCTGGTTTGGGTTTGTATGAAT 59.782 41.667 0.00 0.00 0.00 2.57
136 137 6.381498 TGGGTTTGTATGAATTCCTCTGTA 57.619 37.500 2.27 0.00 0.00 2.74
140 141 8.406297 GGGTTTGTATGAATTCCTCTGTATTTC 58.594 37.037 2.27 0.00 0.00 2.17
172 173 6.998968 TTGTCCGGTTAGTTCAAAAAGTTA 57.001 33.333 0.00 0.00 0.00 2.24
187 188 9.469807 TTCAAAAAGTTATTGAAATGTATGCGT 57.530 25.926 0.00 0.00 42.19 5.24
268 269 1.210967 ACGGATGCGGGAGGAAATTTA 59.789 47.619 12.44 0.00 0.00 1.40
282 283 0.320596 AATTTACGGGTCGGCGTTGA 60.321 50.000 6.85 0.00 0.00 3.18
307 308 6.215495 GATGCCCTTAGCTTCTACCTATAG 57.785 45.833 0.00 0.00 44.23 1.31
343 344 7.934665 TCATAAAAGTTGACACTAGCCACTTTA 59.065 33.333 2.06 0.00 30.68 1.85
368 369 5.765510 AGTGCCATATATCCTTTTCCACAA 58.234 37.500 0.00 0.00 0.00 3.33
526 527 5.678132 GCATAGTGCATCACATCATAACA 57.322 39.130 0.00 0.00 44.26 2.41
613 614 2.024918 CTGCCGGTGGATAATGCAC 58.975 57.895 1.90 0.00 38.03 4.57
635 636 3.560503 CATCGCGGTATCTCTCTCTTTC 58.439 50.000 6.13 0.00 0.00 2.62
706 707 1.381928 GGGAGGCGACACGTATCAGA 61.382 60.000 0.00 0.00 0.00 3.27
865 877 3.571590 AGTCGATCTCTGCCCTTTCTAT 58.428 45.455 0.00 0.00 0.00 1.98
866 878 3.572255 AGTCGATCTCTGCCCTTTCTATC 59.428 47.826 0.00 0.00 0.00 2.08
867 879 2.894126 TCGATCTCTGCCCTTTCTATCC 59.106 50.000 0.00 0.00 0.00 2.59
868 880 2.028567 CGATCTCTGCCCTTTCTATCCC 60.029 54.545 0.00 0.00 0.00 3.85
869 881 2.877154 TCTCTGCCCTTTCTATCCCT 57.123 50.000 0.00 0.00 0.00 4.20
924 936 2.440539 ACACCAACTTAGAGCTCACG 57.559 50.000 17.77 5.93 0.00 4.35
946 958 1.571460 CGACACTCCTGCAGCAAAC 59.429 57.895 8.66 0.00 0.00 2.93
957 969 2.855963 CTGCAGCAAACAACTTCTTGTG 59.144 45.455 0.00 0.00 39.88 3.33
1260 1272 4.767255 CCTGACACTGCCGAGCCC 62.767 72.222 0.00 0.00 0.00 5.19
1568 1580 2.189342 GAGCTACTGATCGCACAACTC 58.811 52.381 0.00 0.00 0.00 3.01
1586 1598 1.132643 CTCTTGGTTCGTAGAGGTCGG 59.867 57.143 0.00 0.00 38.43 4.79
1599 1611 7.098477 TCGTAGAGGTCGGAATTAATCAAAAA 58.902 34.615 0.00 0.00 0.00 1.94
1691 1704 7.976734 CGGTAGCTTAAGGGATTCTTATGATAG 59.023 40.741 4.29 0.00 35.83 2.08
1731 1744 5.825679 AGTGTGGCATTTCTTTGTACTACAA 59.174 36.000 0.00 0.00 36.11 2.41
1821 1834 9.891828 CTAATTACTGGCGCAATCAAATAAATA 57.108 29.630 10.83 0.00 0.00 1.40
1828 1841 8.074474 TGGCGCAATCAAATAAATATGAATTG 57.926 30.769 10.83 0.00 0.00 2.32
1851 1864 4.389374 CAATATACATCTGGCGTTCCCTT 58.611 43.478 0.00 0.00 0.00 3.95
1854 1867 1.299648 CATCTGGCGTTCCCTTGGA 59.700 57.895 0.00 0.00 0.00 3.53
1885 1898 4.197750 CTGAGAGAACAATCATTCCCCAG 58.802 47.826 0.00 0.00 0.00 4.45
1887 1900 4.195416 GAGAGAACAATCATTCCCCAGAC 58.805 47.826 0.00 0.00 0.00 3.51
1891 1904 4.043310 AGAACAATCATTCCCCAGACAGAA 59.957 41.667 0.00 0.00 0.00 3.02
1898 1911 2.342406 TCCCCAGACAGAAAGGATCA 57.658 50.000 0.00 0.00 0.00 2.92
1906 1919 4.511454 CAGACAGAAAGGATCAAACGAACA 59.489 41.667 0.00 0.00 0.00 3.18
1907 1920 5.180117 CAGACAGAAAGGATCAAACGAACAT 59.820 40.000 0.00 0.00 0.00 2.71
1910 1923 6.805713 ACAGAAAGGATCAAACGAACATTTT 58.194 32.000 0.00 0.00 0.00 1.82
1911 1924 6.918022 ACAGAAAGGATCAAACGAACATTTTC 59.082 34.615 0.00 0.00 0.00 2.29
1932 1945 3.734231 TCGTTCGCTAAAGAAACTCACTG 59.266 43.478 0.00 0.00 0.00 3.66
1946 1959 4.320844 ACTGCCAGTGAACCCTCT 57.679 55.556 0.00 0.00 0.00 3.69
1955 1968 4.508662 CCAGTGAACCCTCTAGAATTGTC 58.491 47.826 0.00 0.00 0.00 3.18
1960 1973 4.019411 TGAACCCTCTAGAATTGTCATGCA 60.019 41.667 0.00 0.00 0.00 3.96
2036 2061 4.751098 TGCCAAAGATTGTCAGAAAATTGC 59.249 37.500 0.00 0.00 0.00 3.56
2046 2071 4.082625 TGTCAGAAAATTGCCATGCTACAG 60.083 41.667 0.00 0.00 0.00 2.74
2071 2096 2.178984 AGTTCTTCCATGGGTTTTGGGA 59.821 45.455 13.02 0.00 34.85 4.37
2075 2100 4.238669 TCTTCCATGGGTTTTGGGAAAAT 58.761 39.130 13.02 0.00 38.83 1.82
2089 2114 5.973899 TGGGAAAATCGTCATGATTGAAA 57.026 34.783 0.00 0.00 46.65 2.69
2105 2130 3.940209 TGAAACATGGAGATTTGCCAC 57.060 42.857 0.00 0.00 38.44 5.01
2106 2131 3.499338 TGAAACATGGAGATTTGCCACT 58.501 40.909 0.00 0.00 38.44 4.00
2107 2132 3.896888 TGAAACATGGAGATTTGCCACTT 59.103 39.130 0.00 0.00 38.44 3.16
2108 2133 5.076182 TGAAACATGGAGATTTGCCACTTA 58.924 37.500 0.00 0.00 38.44 2.24
2171 2196 2.348125 CGTCTTGCGACATCAACGAAAA 60.348 45.455 0.00 0.00 44.77 2.29
2172 2197 3.613563 GTCTTGCGACATCAACGAAAAA 58.386 40.909 0.00 0.00 39.98 1.94
2192 2217 2.406596 AAATGTGGGAATTGCCATGC 57.593 45.000 22.56 10.71 38.95 4.06
2201 2226 3.253230 GGAATTGCCATGCTGTACAAAC 58.747 45.455 0.00 0.00 36.34 2.93
2207 2232 5.459536 TGCCATGCTGTACAAACATAAAA 57.540 34.783 9.96 0.00 34.37 1.52
2211 2236 6.034898 GCCATGCTGTACAAACATAAAATGAC 59.965 38.462 9.96 0.00 34.37 3.06
2244 2269 3.248602 GTGTTCGCTCATATTGTCATCCC 59.751 47.826 0.00 0.00 0.00 3.85
2245 2270 3.118445 TGTTCGCTCATATTGTCATCCCA 60.118 43.478 0.00 0.00 0.00 4.37
2251 2277 4.098349 GCTCATATTGTCATCCCAAGCAAA 59.902 41.667 0.00 0.00 0.00 3.68
2263 2289 6.211184 TCATCCCAAGCAAATCAAATACTGTT 59.789 34.615 0.00 0.00 0.00 3.16
2324 2350 1.226746 GTGCATAGGGTATTCGTGCC 58.773 55.000 0.00 0.00 35.03 5.01
2348 2374 7.229530 CCGAAAACCTATAAAACTAACGTCAC 58.770 38.462 0.00 0.00 0.00 3.67
2354 2380 9.933723 AACCTATAAAACTAACGTCACTTGTAT 57.066 29.630 0.00 0.00 0.00 2.29
2379 2405 9.880157 ATTAGCATTTGAGATAAATTTTGCTGT 57.120 25.926 16.27 5.87 0.00 4.40
2466 2493 3.659183 AAGACAGGATTCCATGGAAGG 57.341 47.619 29.98 20.84 37.56 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.762418 TCCATTCTCACAACACGGGT 59.238 50.000 0.00 0.00 0.00 5.28
1 2 2.113860 ATCCATTCTCACAACACGGG 57.886 50.000 0.00 0.00 0.00 5.28
4 5 4.201950 GGCACATATCCATTCTCACAACAC 60.202 45.833 0.00 0.00 0.00 3.32
8 9 2.485302 CCGGCACATATCCATTCTCACA 60.485 50.000 0.00 0.00 0.00 3.58
38 39 8.347004 ACCAGACTAAGGTAAAACTAGTCTAC 57.653 38.462 9.92 1.11 43.75 2.59
127 128 8.421249 ACAAAATTCATGGAAATACAGAGGAA 57.579 30.769 0.00 0.00 0.00 3.36
136 137 5.482163 AACCGGACAAAATTCATGGAAAT 57.518 34.783 9.46 0.00 0.00 2.17
140 141 5.048364 TGAACTAACCGGACAAAATTCATGG 60.048 40.000 9.46 0.00 0.00 3.66
172 173 6.314018 CAACACTGTACGCATACATTTCAAT 58.686 36.000 0.00 0.00 40.57 2.57
187 188 1.376683 GCCGCCATCCAACACTGTA 60.377 57.895 0.00 0.00 0.00 2.74
211 212 0.037882 CAGTCCGCAGACACTCATGT 60.038 55.000 2.32 0.00 46.15 3.21
268 269 2.939261 ATCTTCAACGCCGACCCGT 61.939 57.895 0.00 0.00 44.41 5.28
282 283 3.388913 AGGTAGAAGCTAAGGGCATCTT 58.611 45.455 0.93 0.00 45.24 2.40
307 308 9.463443 AGTGTCAACTTTTATGAAAGCAAATAC 57.537 29.630 9.73 4.95 44.92 1.89
343 344 7.090319 TGTGGAAAAGGATATATGGCACTAT 57.910 36.000 0.00 0.00 0.00 2.12
382 383 5.216566 ACCACGAATTTTGTCATATGTCG 57.783 39.130 1.90 5.42 0.00 4.35
390 391 3.626028 AGCTCAACCACGAATTTTGTC 57.374 42.857 0.00 0.00 0.00 3.18
391 392 5.240623 TCAATAGCTCAACCACGAATTTTGT 59.759 36.000 0.00 0.00 0.00 2.83
451 452 9.325198 CTTGGCCTTGTAACTTCTTTTATTTTT 57.675 29.630 3.32 0.00 0.00 1.94
526 527 3.197549 ACAGTGCAATGGTTTTGGAGTTT 59.802 39.130 19.57 0.00 0.00 2.66
613 614 1.529226 AGAGAGAGATACCGCGATGG 58.471 55.000 8.23 0.00 46.41 3.51
623 624 7.786943 TGTGTTGGGATATAGAAAGAGAGAGAT 59.213 37.037 0.00 0.00 0.00 2.75
635 636 5.500234 CCATATGGGTGTGTTGGGATATAG 58.500 45.833 14.52 0.00 0.00 1.31
691 692 0.248539 GGAGTCTGATACGTGTCGCC 60.249 60.000 7.84 0.77 0.00 5.54
865 877 5.596763 GTGTGGGTATATATAGGGAAGGGA 58.403 45.833 0.00 0.00 0.00 4.20
866 878 4.404715 CGTGTGGGTATATATAGGGAAGGG 59.595 50.000 0.00 0.00 0.00 3.95
867 879 4.142004 GCGTGTGGGTATATATAGGGAAGG 60.142 50.000 0.00 0.00 0.00 3.46
868 880 4.464951 TGCGTGTGGGTATATATAGGGAAG 59.535 45.833 0.00 0.00 0.00 3.46
869 881 4.221262 GTGCGTGTGGGTATATATAGGGAA 59.779 45.833 0.00 0.00 0.00 3.97
924 936 3.117171 CTGCAGGAGTGTCGCAGC 61.117 66.667 5.57 0.00 45.85 5.25
957 969 1.298157 TGTGATGCGCCTGTGTAAGC 61.298 55.000 4.18 0.00 0.00 3.09
1368 1380 3.060000 ACGTCATCGAGCCGGTCA 61.060 61.111 1.90 0.00 40.62 4.02
1500 1512 0.736325 GGGACCACTCGTCATTGTCG 60.736 60.000 0.00 0.00 43.95 4.35
1568 1580 1.171308 TCCGACCTCTACGAACCAAG 58.829 55.000 0.00 0.00 0.00 3.61
1599 1611 9.463443 CTAAATTTTCTGTTGTCTTTCGGAAAT 57.537 29.630 3.24 0.00 38.28 2.17
1691 1704 4.554723 GCCACACTCACAATACTGACAAAC 60.555 45.833 0.00 0.00 0.00 2.93
1821 1834 5.474532 ACGCCAGATGTATATTGCAATTCAT 59.525 36.000 18.75 18.17 0.00 2.57
1828 1841 2.484264 GGGAACGCCAGATGTATATTGC 59.516 50.000 0.00 0.00 35.15 3.56
1851 1864 3.971305 TGTTCTCTCAGGTTACCTTTCCA 59.029 43.478 0.00 0.00 0.00 3.53
1854 1867 6.187727 TGATTGTTCTCTCAGGTTACCTTT 57.812 37.500 0.00 0.00 0.00 3.11
1885 1898 5.613358 ATGTTCGTTTGATCCTTTCTGTC 57.387 39.130 0.00 0.00 0.00 3.51
1887 1900 7.325599 GAAAATGTTCGTTTGATCCTTTCTG 57.674 36.000 0.00 0.00 0.00 3.02
1906 1919 6.018180 AGTGAGTTTCTTTAGCGAACGAAAAT 60.018 34.615 11.74 11.04 0.00 1.82
1907 1920 5.292589 AGTGAGTTTCTTTAGCGAACGAAAA 59.707 36.000 11.74 0.00 0.00 2.29
1910 1923 3.734231 CAGTGAGTTTCTTTAGCGAACGA 59.266 43.478 0.00 0.00 0.00 3.85
1911 1924 3.661936 GCAGTGAGTTTCTTTAGCGAACG 60.662 47.826 0.00 0.00 0.00 3.95
1912 1925 3.364068 GGCAGTGAGTTTCTTTAGCGAAC 60.364 47.826 0.00 0.00 0.00 3.95
1913 1926 2.806244 GGCAGTGAGTTTCTTTAGCGAA 59.194 45.455 0.00 0.00 0.00 4.70
1914 1927 2.224185 TGGCAGTGAGTTTCTTTAGCGA 60.224 45.455 0.00 0.00 0.00 4.93
1915 1928 2.143122 TGGCAGTGAGTTTCTTTAGCG 58.857 47.619 0.00 0.00 0.00 4.26
1916 1929 3.142174 ACTGGCAGTGAGTTTCTTTAGC 58.858 45.455 21.37 0.00 0.00 3.09
1932 1945 3.274288 CAATTCTAGAGGGTTCACTGGC 58.726 50.000 0.00 0.00 0.00 4.85
1976 1989 5.006261 GGCAAATCCTTTACAACAACACAAC 59.994 40.000 0.00 0.00 0.00 3.32
2015 2029 5.299148 TGGCAATTTTCTGACAATCTTTGG 58.701 37.500 0.00 0.00 28.87 3.28
2046 2071 2.206576 AACCCATGGAAGAACTCTGC 57.793 50.000 15.22 0.00 0.00 4.26
2052 2077 3.336509 TTCCCAAAACCCATGGAAGAA 57.663 42.857 15.22 2.32 40.56 2.52
2054 2079 4.578871 GATTTTCCCAAAACCCATGGAAG 58.421 43.478 15.22 0.00 40.56 3.46
2071 2096 6.923012 TCCATGTTTCAATCATGACGATTTT 58.077 32.000 9.66 0.00 41.83 1.82
2075 2100 4.831107 TCTCCATGTTTCAATCATGACGA 58.169 39.130 9.66 0.00 43.47 4.20
2089 2114 6.418057 TTTTTAAGTGGCAAATCTCCATGT 57.582 33.333 0.00 0.00 35.81 3.21
2124 2149 3.220507 TCTTGAGCATGGCAATTTTCG 57.779 42.857 0.00 0.00 0.00 3.46
2171 2196 3.083293 GCATGGCAATTCCCACATTTTT 58.917 40.909 0.00 0.00 37.79 1.94
2172 2197 2.306512 AGCATGGCAATTCCCACATTTT 59.693 40.909 0.00 0.00 37.79 1.82
2180 2205 3.253230 GTTTGTACAGCATGGCAATTCC 58.747 45.455 0.00 0.00 43.62 3.01
2192 2217 7.484641 CGGGAATGTCATTTTATGTTTGTACAG 59.515 37.037 0.00 0.00 37.77 2.74
2235 2260 4.952071 TTTGATTTGCTTGGGATGACAA 57.048 36.364 0.00 0.00 0.00 3.18
2236 2261 5.716228 AGTATTTGATTTGCTTGGGATGACA 59.284 36.000 0.00 0.00 0.00 3.58
2244 2269 9.409312 TGATAACAACAGTATTTGATTTGCTTG 57.591 29.630 0.00 0.00 0.00 4.01
2263 2289 5.580691 CCTCTAAGCGAACAACATGATAACA 59.419 40.000 0.00 0.00 0.00 2.41
2271 2297 1.876416 GCACCCTCTAAGCGAACAACA 60.876 52.381 0.00 0.00 0.00 3.33
2306 2332 3.698250 GGCACGAATACCCTATGCA 57.302 52.632 0.00 0.00 38.05 3.96
2324 2350 8.011067 AGTGACGTTAGTTTTATAGGTTTTCG 57.989 34.615 0.00 0.00 0.00 3.46
2354 2380 9.357652 GACAGCAAAATTTATCTCAAATGCTAA 57.642 29.630 8.88 0.00 40.62 3.09
2379 2405 9.958180 TTCAGTTAATCCTACAAATTCTCATGA 57.042 29.630 0.00 0.00 0.00 3.07
2450 2476 2.756760 CACAACCTTCCATGGAATCCTG 59.243 50.000 27.20 23.01 33.28 3.86
2466 2493 1.897398 ATTTCCTCGCGCGTCACAAC 61.897 55.000 30.98 0.00 0.00 3.32


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

AutoCloner maintained by Alex Coulton.