Multiple sequence alignment - TraesCS2A01G156600

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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 TraesCS2A01G156600 chr2A 100.000 2531 0 0 1 2531 103224493 103227023 0.000000e+00 4674.0
1 TraesCS2A01G156600 chr2B 92.193 1806 73 22 291 2034 157242593 157244392 0.000000e+00 2492.0
2 TraesCS2A01G156600 chr2B 93.413 501 30 3 2032 2529 157244674 157245174 0.000000e+00 739.0
3 TraesCS2A01G156600 chr2B 93.141 277 12 4 1 275 157242110 157242381 1.410000e-107 399.0
4 TraesCS2A01G156600 chr2B 93.333 60 3 1 2019 2077 157244109 157244168 1.250000e-13 87.9
5 TraesCS2A01G156600 chr2D 91.383 1822 107 20 310 2095 106950829 106952636 0.000000e+00 2449.0
6 TraesCS2A01G156600 chr2D 94.422 251 9 4 1 249 106950573 106950820 5.110000e-102 381.0


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 TraesCS2A01G156600 chr2A 103224493 103227023 2530 False 4674.000 4674 100.0000 1 2531 1 chr2A.!!$F1 2530
1 TraesCS2A01G156600 chr2B 157242110 157245174 3064 False 929.475 2492 93.0200 1 2529 4 chr2B.!!$F1 2528
2 TraesCS2A01G156600 chr2D 106950573 106952636 2063 False 1415.000 2449 92.9025 1 2095 2 chr2D.!!$F1 2094

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
314 514 0.109873 GCTGCTCATGTGACAACTGC 60.11 55.0 0.0 0.0 0.0 4.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2313 2859 0.557238 ATATCATGGTGGGCAGGCAA 59.443 50.0 0.0 0.0 0.0 4.52 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
47 48 9.383519 CAGAATAAGTTTAGCCTTGAACTATCA 57.616 33.333 0.00 0.00 35.17 2.15
94 96 3.152341 CCATGGTCTTGAAGCAGACTTT 58.848 45.455 2.57 0.00 42.63 2.66
197 201 0.322322 CAACACAGGCATGCCCAAAT 59.678 50.000 33.14 12.24 36.58 2.32
206 210 2.289569 GGCATGCCCAAATGAGAAAACA 60.290 45.455 27.24 0.00 0.00 2.83
237 241 5.966742 AGAAAAAGAATACAAGGCTCCAC 57.033 39.130 0.00 0.00 0.00 4.02
275 279 2.003301 GCGAAGAGGCTAAGAAAGTGG 58.997 52.381 0.00 0.00 0.00 4.00
276 280 2.003301 CGAAGAGGCTAAGAAAGTGGC 58.997 52.381 0.00 0.00 0.00 5.01
277 281 2.003301 GAAGAGGCTAAGAAAGTGGCG 58.997 52.381 0.00 0.00 0.00 5.69
278 282 0.391793 AGAGGCTAAGAAAGTGGCGC 60.392 55.000 0.00 0.00 0.00 6.53
279 283 1.696832 GAGGCTAAGAAAGTGGCGCG 61.697 60.000 0.00 0.00 0.00 6.86
280 284 2.098489 GCTAAGAAAGTGGCGCGC 59.902 61.111 25.94 25.94 0.00 6.86
281 285 2.391389 GCTAAGAAAGTGGCGCGCT 61.391 57.895 32.29 10.98 0.00 5.92
282 286 1.912371 GCTAAGAAAGTGGCGCGCTT 61.912 55.000 32.29 17.77 35.58 4.68
283 287 0.179215 CTAAGAAAGTGGCGCGCTTG 60.179 55.000 32.29 5.34 34.24 4.01
284 288 2.182614 TAAGAAAGTGGCGCGCTTGC 62.183 55.000 32.29 16.51 34.24 4.01
285 289 4.030452 GAAAGTGGCGCGCTTGCT 62.030 61.111 32.29 22.16 34.24 3.91
286 290 3.542629 GAAAGTGGCGCGCTTGCTT 62.543 57.895 32.29 26.17 34.24 3.91
287 291 3.542629 AAAGTGGCGCGCTTGCTTC 62.543 57.895 32.29 13.79 34.24 3.86
314 514 0.109873 GCTGCTCATGTGACAACTGC 60.110 55.000 0.00 0.00 0.00 4.40
328 528 4.202040 TGACAACTGCAATATGCCTAATGC 60.202 41.667 2.40 2.40 44.23 3.56
331 531 4.579454 ACTGCAATATGCCTAATGCTTG 57.421 40.909 9.95 6.04 44.23 4.01
452 653 5.070446 TGCTACCTATTCCATTGACCTACTG 59.930 44.000 0.00 0.00 0.00 2.74
471 680 8.100791 ACCTACTGCACAAATGAAGATTAACTA 58.899 33.333 0.00 0.00 34.64 2.24
659 868 6.463995 TGGATAAGAACAATGGCCATAAAC 57.536 37.500 21.15 11.05 0.00 2.01
681 890 4.178540 CAATGGAAAGCATGACATGAACC 58.821 43.478 19.76 14.50 0.00 3.62
693 902 4.744570 TGACATGAACCTAGATCACGAAC 58.255 43.478 0.00 0.00 0.00 3.95
765 974 5.349817 CCATACAGAGATGATTACGATTGGC 59.650 44.000 0.00 0.00 0.00 4.52
789 998 8.133627 GGCGACTAGTTATGTGACTAATCTAAA 58.866 37.037 0.00 0.00 32.10 1.85
858 1067 7.950496 GGAATATATTTTACTTCTAGCGTTGCG 59.050 37.037 0.00 0.00 0.00 4.85
871 1080 2.481568 AGCGTTGCGTATATACTAGCGA 59.518 45.455 19.62 11.15 0.00 4.93
880 1089 5.338365 CGTATATACTAGCGACCAATTCCC 58.662 45.833 11.05 0.00 0.00 3.97
881 1090 5.125097 CGTATATACTAGCGACCAATTCCCT 59.875 44.000 11.05 0.00 0.00 4.20
895 1104 1.426251 TTCCCTGCTCAGCCTCCAAA 61.426 55.000 0.00 0.00 0.00 3.28
951 1163 3.004944 GCAGACGAGCTAAGCTACCTTAT 59.995 47.826 0.00 0.00 39.88 1.73
952 1164 4.215827 GCAGACGAGCTAAGCTACCTTATA 59.784 45.833 0.00 0.00 39.88 0.98
953 1165 5.618195 GCAGACGAGCTAAGCTACCTTATAG 60.618 48.000 0.00 0.00 39.88 1.31
1014 1226 0.891373 CGGCCATGTCGATATCCTCT 59.109 55.000 2.24 0.00 29.41 3.69
1134 1346 0.111530 GCGTCTTCATAATCGCGCTG 60.112 55.000 5.56 0.00 41.37 5.18
1285 1497 1.000955 CGTTCTTGTACCACAGAGGCT 59.999 52.381 0.00 0.00 43.14 4.58
1532 1744 2.468015 AGGTGCCTCCTGTGTGATT 58.532 52.632 0.00 0.00 46.19 2.57
1534 1746 1.279271 AGGTGCCTCCTGTGTGATTAC 59.721 52.381 0.00 0.00 46.19 1.89
1546 1758 3.125146 TGTGTGATTACTGCGAGATTTGC 59.875 43.478 0.00 0.00 0.00 3.68
1547 1759 3.125146 GTGTGATTACTGCGAGATTTGCA 59.875 43.478 0.00 0.00 40.70 4.08
1608 1828 6.128090 ACACATCAGATGTAGAAATTGCTGTG 60.128 38.462 15.98 3.28 42.70 3.66
1611 1831 4.393990 TCAGATGTAGAAATTGCTGTGCTG 59.606 41.667 0.00 0.00 0.00 4.41
1667 1889 7.304497 AGTTTCACCTGTTATGTTCTCTACT 57.696 36.000 0.00 0.00 0.00 2.57
1668 1890 7.736893 AGTTTCACCTGTTATGTTCTCTACTT 58.263 34.615 0.00 0.00 0.00 2.24
1686 1908 6.157211 TCTACTTTTTCTCTGGATGTCGTTC 58.843 40.000 0.00 0.00 0.00 3.95
1701 1926 4.314961 TGTCGTTCATGCTTGAATGTAGT 58.685 39.130 25.43 0.00 45.31 2.73
1726 1973 3.373001 GGGGATGAAATGGTTGATCCAGA 60.373 47.826 7.16 0.00 46.33 3.86
1735 1982 2.019984 GGTTGATCCAGACTGATTGGC 58.980 52.381 3.32 0.00 35.62 4.52
1767 2022 8.802267 CATAAAAGTCCCTTATTGGTTCTTGAA 58.198 33.333 0.00 0.00 31.06 2.69
1857 2114 3.609853 CAAGAAATCCCGATTGAGGACA 58.390 45.455 0.00 0.00 35.85 4.02
1870 2127 4.974645 TTGAGGACAACACTATTGGTCT 57.025 40.909 0.00 0.00 0.00 3.85
1930 2187 0.535102 ACCCGTGGCAGCATATAAGC 60.535 55.000 0.00 0.00 0.00 3.09
1987 2244 1.335597 GGCTTAGTTGGCGGTGTTTTC 60.336 52.381 0.00 0.00 0.00 2.29
2017 2279 7.240674 TGCGAAGATACATAAACACATTTGAC 58.759 34.615 0.00 0.00 0.00 3.18
2184 2730 4.575885 CCTCGTCTTGTAGGAATTTGGAA 58.424 43.478 0.00 0.00 34.58 3.53
2188 2734 7.309194 CCTCGTCTTGTAGGAATTTGGAATTTT 60.309 37.037 0.00 0.00 34.58 1.82
2189 2735 7.367285 TCGTCTTGTAGGAATTTGGAATTTTG 58.633 34.615 0.00 0.00 0.00 2.44
2237 2783 7.148120 CGAAGACTTAGTAGAACTCACCCAATA 60.148 40.741 0.00 0.00 0.00 1.90
2264 2810 3.794536 GTGTGCACACAACTACATTACG 58.205 45.455 38.42 0.00 45.75 3.18
2269 2815 4.862574 TGCACACAACTACATTACGAGATC 59.137 41.667 0.00 0.00 0.00 2.75
2271 2817 5.577164 GCACACAACTACATTACGAGATCTT 59.423 40.000 0.00 0.00 0.00 2.40
2348 2897 6.084277 CCATGATATTGCACATGATTCTTCG 58.916 40.000 14.72 0.00 44.28 3.79
2371 2920 5.116983 CGTGCAAATTTCAGAACACATAACC 59.883 40.000 0.00 0.00 0.00 2.85
2411 2960 2.202892 GGGGCTTCCACGATCGAC 60.203 66.667 24.34 3.43 35.00 4.20
2481 3030 3.373565 GCCAAAAGCACCCTCCCG 61.374 66.667 0.00 0.00 42.97 5.14
2511 3060 3.803162 GAGAGGGAGCCTTGGCCC 61.803 72.222 8.17 9.06 45.04 5.80
2523 3072 2.750814 CCTTGGCCCAGTCCAAAATAT 58.249 47.619 0.00 0.00 44.73 1.28
2529 3078 2.427095 GCCCAGTCCAAAATATCCACAC 59.573 50.000 0.00 0.00 0.00 3.82
2530 3079 3.023832 CCCAGTCCAAAATATCCACACC 58.976 50.000 0.00 0.00 0.00 4.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 5.365314 AGGCTAAACTTATTCTGCTAGCTCT 59.635 40.000 17.23 0.29 33.78 4.09
14 15 5.606505 AGGCTAAACTTATTCTGCTAGCTC 58.393 41.667 17.23 0.00 33.78 4.09
47 48 6.183360 CCGTAGCATGAATTCTCACAAAAGAT 60.183 38.462 7.05 0.00 33.30 2.40
94 96 2.658373 TTATGTACAAAGCGAGGCGA 57.342 45.000 0.00 0.00 0.00 5.54
123 125 6.263617 CACATGAACATGATGTTGGGATATGA 59.736 38.462 16.52 0.00 41.28 2.15
160 162 3.181434 TGTTGTTGCCCCTGTAGATCTTT 60.181 43.478 0.00 0.00 0.00 2.52
161 163 2.375174 TGTTGTTGCCCCTGTAGATCTT 59.625 45.455 0.00 0.00 0.00 2.40
212 216 7.210174 GTGGAGCCTTGTATTCTTTTTCTTTT 58.790 34.615 0.00 0.00 0.00 2.27
221 225 2.678190 GCTTCGTGGAGCCTTGTATTCT 60.678 50.000 0.00 0.00 36.66 2.40
237 241 2.648102 CGCGAGTAGTCGGCTTCG 60.648 66.667 20.94 11.97 46.91 3.79
280 284 4.394712 AGCGGGACCGGAAGCAAG 62.395 66.667 9.46 0.00 40.19 4.01
281 285 4.697756 CAGCGGGACCGGAAGCAA 62.698 66.667 9.46 0.00 40.19 3.91
284 288 4.821589 GAGCAGCGGGACCGGAAG 62.822 72.222 9.46 0.00 40.19 3.46
288 292 4.457496 ACATGAGCAGCGGGACCG 62.457 66.667 6.35 6.35 43.09 4.79
289 293 2.821366 CACATGAGCAGCGGGACC 60.821 66.667 0.00 0.00 0.00 4.46
294 494 0.165295 CAGTTGTCACATGAGCAGCG 59.835 55.000 0.00 0.00 0.00 5.18
300 500 4.359971 GCATATTGCAGTTGTCACATGA 57.640 40.909 0.00 0.00 44.26 3.07
328 528 5.240403 GCAGGAAAATAGAGGGCTTATCAAG 59.760 44.000 0.00 0.00 0.00 3.02
331 531 4.718961 TGCAGGAAAATAGAGGGCTTATC 58.281 43.478 0.00 0.00 0.00 1.75
471 680 4.649218 ACATTTGGCAACTCTGGTTAGTTT 59.351 37.500 0.00 0.00 37.61 2.66
659 868 4.081862 AGGTTCATGTCATGCTTTCCATTG 60.082 41.667 8.03 0.00 29.71 2.82
871 1080 1.000396 GGCTGAGCAGGGAATTGGT 60.000 57.895 6.82 0.00 0.00 3.67
880 1089 5.824624 TCTTATATTTTTGGAGGCTGAGCAG 59.175 40.000 6.82 0.00 0.00 4.24
881 1090 5.754782 TCTTATATTTTTGGAGGCTGAGCA 58.245 37.500 6.82 0.00 0.00 4.26
951 1163 3.354948 TTCTAGCCGTGTCACCTACTA 57.645 47.619 0.00 0.00 0.00 1.82
952 1164 2.211250 TTCTAGCCGTGTCACCTACT 57.789 50.000 0.00 0.00 0.00 2.57
953 1165 2.230750 AGTTTCTAGCCGTGTCACCTAC 59.769 50.000 0.00 0.00 0.00 3.18
1014 1226 0.670546 GCAGCGTCTTGTTGGAGCTA 60.671 55.000 0.00 0.00 36.28 3.32
1134 1346 1.154150 GCAGCACAGGCAATCGAAC 60.154 57.895 0.00 0.00 44.61 3.95
1256 1468 1.373748 TACAAGAACGACGGCAGCC 60.374 57.895 0.00 0.00 0.00 4.85
1304 1516 3.245315 CACGACCGTCCGAATCGC 61.245 66.667 0.00 0.00 39.47 4.58
1307 1519 4.789075 CGCCACGACCGTCCGAAT 62.789 66.667 6.35 0.00 0.00 3.34
1532 1744 2.029020 ACTCTGTGCAAATCTCGCAGTA 60.029 45.455 0.00 0.00 40.78 2.74
1534 1746 1.436600 ACTCTGTGCAAATCTCGCAG 58.563 50.000 0.00 0.00 40.78 5.18
1586 1806 5.066117 AGCACAGCAATTTCTACATCTGATG 59.934 40.000 15.83 15.83 0.00 3.07
1608 1828 2.730672 CTTGGTACGCACTCGCAGC 61.731 63.158 0.00 0.00 39.84 5.25
1611 1831 1.060698 GAATTCTTGGTACGCACTCGC 59.939 52.381 0.00 0.00 39.84 5.03
1667 1889 4.083324 GCATGAACGACATCCAGAGAAAAA 60.083 41.667 0.00 0.00 37.07 1.94
1668 1890 3.436704 GCATGAACGACATCCAGAGAAAA 59.563 43.478 0.00 0.00 37.07 2.29
1686 1908 3.763360 TCCCCAAACTACATTCAAGCATG 59.237 43.478 0.00 0.00 0.00 4.06
1701 1926 3.774216 GGATCAACCATTTCATCCCCAAA 59.226 43.478 0.00 0.00 38.79 3.28
1726 1973 3.737559 TTTATGTCAGGGCCAATCAGT 57.262 42.857 6.18 0.00 0.00 3.41
1846 2103 4.253685 ACCAATAGTGTTGTCCTCAATCG 58.746 43.478 0.00 0.00 35.92 3.34
1857 2114 4.099573 CCGGTGAGATAGACCAATAGTGTT 59.900 45.833 0.00 0.00 32.45 3.32
1870 2127 4.901511 ACCAACCCCGGTGAGATA 57.098 55.556 0.00 0.00 38.07 1.98
1930 2187 1.375523 GCCTATGGGTTATCCGCCG 60.376 63.158 0.00 0.00 38.76 6.46
1982 2239 9.989394 GTTTATGTATCTTCGCAAAAAGAAAAC 57.011 29.630 0.00 1.52 38.69 2.43
1987 2244 8.673626 ATGTGTTTATGTATCTTCGCAAAAAG 57.326 30.769 0.00 0.00 0.00 2.27
2017 2279 7.678947 ATTACAAGTCAATCTCAAGAACCAG 57.321 36.000 0.00 0.00 0.00 4.00
2050 2596 5.349817 AGAAAGCACATTGACTATGAAGACG 59.650 40.000 3.80 0.00 37.69 4.18
2065 2611 4.442375 TCGAAAAACCAAAGAAAGCACA 57.558 36.364 0.00 0.00 0.00 4.57
2127 2673 4.864334 GGATCAGTGCCAGCCCCG 62.864 72.222 0.00 0.00 0.00 5.73
2158 2704 1.601419 TTCCTACAAGACGAGGCCCG 61.601 60.000 11.48 11.48 45.44 6.13
2212 2758 5.979288 TGGGTGAGTTCTACTAAGTCTTC 57.021 43.478 0.00 0.00 0.00 2.87
2304 2850 1.374947 GGGCAGGCAACAGACACTA 59.625 57.895 0.00 0.00 41.41 2.74
2313 2859 0.557238 ATATCATGGTGGGCAGGCAA 59.443 50.000 0.00 0.00 0.00 4.52
2315 2861 0.963962 CAATATCATGGTGGGCAGGC 59.036 55.000 0.00 0.00 0.00 4.85
2348 2897 5.982516 TGGTTATGTGTTCTGAAATTTGCAC 59.017 36.000 0.00 0.00 0.00 4.57
2371 2920 1.945394 GTCATCATGCTACAAGGGCTG 59.055 52.381 0.00 0.00 0.00 4.85
2411 2960 0.523072 CATGCCTCCTTTGGTCAACG 59.477 55.000 0.00 0.00 0.00 4.10
2487 3036 1.885887 CAAGGCTCCCTCTCGAGATAG 59.114 57.143 17.03 14.40 30.89 2.08


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

AutoCloner maintained by Alex Coulton.