Multiple sequence alignment - TraesCS4A01G152600

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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 TraesCS4A01G152600 chr4A 100.000 2174 0 0 1 2174 309446413 309448586 0 4015
1 TraesCS4A01G152600 chr5D 95.883 2186 75 6 1 2174 6253281 6255463 0 3524
2 TraesCS4A01G152600 chr5D 95.221 2197 78 7 1 2174 503339435 503337243 0 3450
3 TraesCS4A01G152600 chr5D 94.766 2197 85 7 1 2174 503313497 503311308 0 3393
4 TraesCS4A01G152600 chr5D 95.336 1072 31 1 1122 2174 481593895 481594966 0 1685
5 TraesCS4A01G152600 chr5D 94.670 863 27 2 1331 2174 503334791 503333929 0 1321
6 TraesCS4A01G152600 chr1D 95.728 2177 78 8 1 2174 254459403 254457239 0 3491
7 TraesCS4A01G152600 chr1D 94.713 2194 90 7 1 2174 51831965 51834152 0 3386
8 TraesCS4A01G152600 chr1D 95.330 1135 34 1 1059 2174 254455573 254454439 0 1784
9 TraesCS4A01G152600 chr3A 95.407 2199 74 5 1 2174 105556962 105559158 0 3476
10 TraesCS4A01G152600 chr1B 95.436 2191 80 5 1 2174 633716966 633714779 0 3474
11 TraesCS4A01G152600 chr3B 95.613 2120 70 5 1 2099 101924871 101922754 0 3378
12 TraesCS4A01G152600 chr7B 95.332 2035 77 3 1 2019 662755040 662757072 0 3216
13 TraesCS4A01G152600 chr4D 93.612 1174 57 2 1018 2174 19889440 19888268 0 1736


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 TraesCS4A01G152600 chr4A 309446413 309448586 2173 False 4015.0 4015 100.0000 1 2174 1 chr4A.!!$F1 2173
1 TraesCS4A01G152600 chr5D 6253281 6255463 2182 False 3524.0 3524 95.8830 1 2174 1 chr5D.!!$F1 2173
2 TraesCS4A01G152600 chr5D 503311308 503313497 2189 True 3393.0 3393 94.7660 1 2174 1 chr5D.!!$R1 2173
3 TraesCS4A01G152600 chr5D 503333929 503339435 5506 True 2385.5 3450 94.9455 1 2174 2 chr5D.!!$R2 2173
4 TraesCS4A01G152600 chr5D 481593895 481594966 1071 False 1685.0 1685 95.3360 1122 2174 1 chr5D.!!$F2 1052
5 TraesCS4A01G152600 chr1D 51831965 51834152 2187 False 3386.0 3386 94.7130 1 2174 1 chr1D.!!$F1 2173
6 TraesCS4A01G152600 chr1D 254454439 254459403 4964 True 2637.5 3491 95.5290 1 2174 2 chr1D.!!$R1 2173
7 TraesCS4A01G152600 chr3A 105556962 105559158 2196 False 3476.0 3476 95.4070 1 2174 1 chr3A.!!$F1 2173
8 TraesCS4A01G152600 chr1B 633714779 633716966 2187 True 3474.0 3474 95.4360 1 2174 1 chr1B.!!$R1 2173
9 TraesCS4A01G152600 chr3B 101922754 101924871 2117 True 3378.0 3378 95.6130 1 2099 1 chr3B.!!$R1 2098
10 TraesCS4A01G152600 chr7B 662755040 662757072 2032 False 3216.0 3216 95.3320 1 2019 1 chr7B.!!$F1 2018
11 TraesCS4A01G152600 chr4D 19888268 19889440 1172 True 1736.0 1736 93.6120 1018 2174 1 chr4D.!!$R1 1156

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
303 307 1.077787 CCTACGGCCAATCCAGCAA 60.078 57.895 2.24 0.0 34.01 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1206 6805 0.099968 TACTCACGTCAGCGGCATAC 59.9 55.0 1.45 0.0 43.45 2.39 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
120 124 4.329462 AAAGGGTTCGCAAATAAAAGCA 57.671 36.364 0.00 0.00 0.00 3.91
122 126 2.029380 AGGGTTCGCAAATAAAAGCACC 60.029 45.455 0.00 0.00 0.00 5.01
203 207 9.605275 AATAAAGTACCTCGTATTTTACCTTCC 57.395 33.333 2.74 0.00 34.66 3.46
234 238 4.744570 CTGTCTCGCAATACCTTCTACAA 58.255 43.478 0.00 0.00 0.00 2.41
243 247 6.403878 GCAATACCTTCTACAACTTGTCCTA 58.596 40.000 0.00 0.00 0.00 2.94
265 269 2.037772 CAGCAGTACCTTGACCAACTCT 59.962 50.000 0.00 0.00 0.00 3.24
303 307 1.077787 CCTACGGCCAATCCAGCAA 60.078 57.895 2.24 0.00 34.01 3.91
310 314 2.101249 CGGCCAATCCAGCAACAATAAT 59.899 45.455 2.24 0.00 34.01 1.28
318 322 7.259882 CAATCCAGCAACAATAATAGAAGCAA 58.740 34.615 0.00 0.00 0.00 3.91
321 325 6.208402 TCCAGCAACAATAATAGAAGCAACAA 59.792 34.615 0.00 0.00 0.00 2.83
339 343 6.015180 AGCAACAACAATTAGTGGATTCATGT 60.015 34.615 0.00 0.00 0.00 3.21
344 348 6.199937 ACAATTAGTGGATTCATGTTGAGC 57.800 37.500 0.00 0.00 0.00 4.26
435 439 6.325286 AGCTCTATTGGGGAGAAGTAAAGTAG 59.675 42.308 0.00 0.00 33.03 2.57
436 440 6.098552 GCTCTATTGGGGAGAAGTAAAGTAGT 59.901 42.308 0.00 0.00 33.03 2.73
494 498 5.801350 ATGTGAATTGTCCGAACTACATG 57.199 39.130 0.00 0.00 0.00 3.21
520 524 7.845537 AAGGGAATTCCATATCCATATACCA 57.154 36.000 25.67 0.00 37.46 3.25
642 656 6.738114 TGAATCGGATTCTAAAATCATTGCC 58.262 36.000 26.15 1.74 42.66 4.52
647 661 8.287439 TCGGATTCTAAAATCATTGCCTAAAA 57.713 30.769 1.05 0.00 42.66 1.52
657 671 5.659440 TCATTGCCTAAAATGGAAACCTC 57.341 39.130 0.00 0.00 37.98 3.85
658 672 5.083122 TCATTGCCTAAAATGGAAACCTCA 58.917 37.500 0.00 0.00 37.98 3.86
744 758 7.770897 CCACCCTCCTTAATGCATATATACTTC 59.229 40.741 0.00 0.00 0.00 3.01
811 825 7.932335 ACTCTAGGCTATATATTCATACGCAC 58.068 38.462 0.00 0.00 0.00 5.34
874 888 4.202121 CCATGCATGAATTGAGCTAAGCTT 60.202 41.667 28.31 3.48 39.88 3.74
938 957 5.173246 ACCCTCCATGGATTCACCTATATT 58.827 41.667 16.63 0.00 39.86 1.28
941 960 5.014544 CCTCCATGGATTCACCTATATTGGT 59.985 44.000 16.63 2.68 38.41 3.67
970 989 6.254373 GGCTAATGTTGCAAAAATAAGAGCTC 59.746 38.462 5.27 5.27 29.43 4.09
1041 1060 5.877491 ACTAAGGGGACTAAAGAAACAAGG 58.123 41.667 0.00 0.00 42.68 3.61
1068 3868 2.277084 ACGACTAATTCATCCGCCAAC 58.723 47.619 0.00 0.00 0.00 3.77
1102 3902 7.766219 AAAAGTCGAAAGCTAAGCGATAATA 57.234 32.000 8.42 0.00 36.37 0.98
1326 6925 1.995376 AAAGAGCACCCGACCAAATT 58.005 45.000 0.00 0.00 0.00 1.82
1420 7019 6.260050 AGTTTTGCTCAAGTCTCGAATAAACA 59.740 34.615 0.00 0.00 0.00 2.83
1434 7033 7.494625 TCTCGAATAAACACAAGGACATATTCC 59.505 37.037 0.00 0.00 46.33 3.01
1452 7051 8.859090 ACATATTCCAAAAATTTCTGACTGTCA 58.141 29.630 10.50 10.50 0.00 3.58
1556 7155 3.390639 ACTTGGGCATGAATTTGGAAACA 59.609 39.130 0.00 0.00 39.83 2.83
1596 7195 2.302157 GTGTTGGCCTACTTCTACACCT 59.698 50.000 18.31 0.00 34.98 4.00
1614 7213 8.330993 TCTACACCTGATATATCGTATAACCCA 58.669 37.037 8.19 0.00 0.00 4.51
1887 8020 0.314935 ACGCAGTTGCCCAAGAATTG 59.685 50.000 0.00 0.00 43.33 2.32
1930 8063 9.958234 CAATGATTTCTTATCTAGAGAGAACGA 57.042 33.333 16.71 7.71 34.61 3.85
1939 8072 1.540267 AGAGAGAACGACCCTCACAG 58.460 55.000 0.00 0.00 33.25 3.66
1958 8091 9.793252 CCTCACAGATTGAAAATACTAATTTGG 57.207 33.333 0.00 0.00 35.46 3.28
1993 8126 8.667076 ATCGAATTGAAATCATAGTGTCATCA 57.333 30.769 0.00 0.00 0.00 3.07
2031 8164 3.518998 CGCGAGATCCGGGTCACT 61.519 66.667 19.03 0.00 44.85 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
120 124 0.396811 GGACTAGTTGTGGCACTGGT 59.603 55.000 19.83 6.63 40.92 4.00
122 126 2.479566 ATGGACTAGTTGTGGCACTG 57.520 50.000 19.83 6.42 0.00 3.66
234 238 2.890814 AGGTACTGCTGTAGGACAAGT 58.109 47.619 10.37 0.00 42.48 3.16
243 247 1.768870 AGTTGGTCAAGGTACTGCTGT 59.231 47.619 0.66 0.66 40.86 4.40
265 269 2.172717 GGGCTTGCTTCTATTGGACCTA 59.827 50.000 0.00 0.00 0.00 3.08
310 314 7.446931 TGAATCCACTAATTGTTGTTGCTTCTA 59.553 33.333 0.00 0.00 0.00 2.10
318 322 7.523293 TCAACATGAATCCACTAATTGTTGT 57.477 32.000 0.00 0.00 41.76 3.32
321 325 5.711506 TGCTCAACATGAATCCACTAATTGT 59.288 36.000 0.00 0.00 0.00 2.71
339 343 0.750249 TGACACGAGGAACTGCTCAA 59.250 50.000 0.00 0.00 41.55 3.02
408 412 3.922171 ACTTCTCCCCAATAGAGCTTG 57.078 47.619 0.00 0.00 0.00 4.01
642 656 9.860898 CCTCTTTTATTGAGGTTTCCATTTTAG 57.139 33.333 0.00 0.00 44.42 1.85
657 671 9.535878 GTCTATAAGTGGAGTCCTCTTTTATTG 57.464 37.037 26.93 17.30 38.19 1.90
658 672 9.268282 TGTCTATAAGTGGAGTCCTCTTTTATT 57.732 33.333 26.93 14.45 38.19 1.40
938 957 1.175347 TGCAACATTAGCCGCAACCA 61.175 50.000 0.00 0.00 0.00 3.67
941 960 2.515926 TTTTGCAACATTAGCCGCAA 57.484 40.000 0.00 0.00 42.29 4.85
970 989 8.826710 TCTTGGATTATTTACAAGCAGTATTCG 58.173 33.333 0.00 0.00 40.93 3.34
1041 1060 4.724036 GCGGATGAATTAGTCGTTGTTGTC 60.724 45.833 0.00 0.00 0.00 3.18
1068 3868 4.332819 AGCTTTCGACTTTTCGGGAATATG 59.667 41.667 0.00 0.00 45.90 1.78
1102 3902 8.697507 AACATCCTAGAAGATTTCACAAAACT 57.302 30.769 0.00 0.00 0.00 2.66
1206 6805 0.099968 TACTCACGTCAGCGGCATAC 59.900 55.000 1.45 0.00 43.45 2.39
1373 6972 6.590068 ACTCAGATTGGAGAAGAATATGGTG 58.410 40.000 0.00 0.00 38.30 4.17
1448 7047 2.487086 CCACAAACCATCCTGACTGACA 60.487 50.000 0.00 0.00 0.00 3.58
1452 7051 3.562176 GGAATCCACAAACCATCCTGACT 60.562 47.826 0.00 0.00 0.00 3.41
1456 7055 1.633432 TCGGAATCCACAAACCATCCT 59.367 47.619 0.00 0.00 0.00 3.24
1556 7155 6.322201 CCAACACTTCTATTGGCAAATAGGAT 59.678 38.462 18.86 4.27 43.75 3.24
1596 7195 9.031537 ACACTCAATGGGTTATACGATATATCA 57.968 33.333 13.11 0.00 0.00 2.15
1614 7213 7.360113 ACCTTGTTCCATTAAAACACTCAAT 57.640 32.000 0.00 0.00 36.41 2.57
1867 8000 0.314935 AATTCTTGGGCAACTGCGTG 59.685 50.000 0.00 0.00 43.26 5.34
1918 8051 2.680841 CTGTGAGGGTCGTTCTCTCTAG 59.319 54.545 10.43 6.37 43.66 2.43
1930 8063 9.533831 AAATTAGTATTTTCAATCTGTGAGGGT 57.466 29.630 0.00 0.00 37.61 4.34
1979 8112 4.103627 TCCAGCCAATGATGACACTATGAT 59.896 41.667 0.00 0.00 0.00 2.45
2113 8246 1.511850 TGCCAGACTTTGTGATCGTG 58.488 50.000 0.00 0.00 0.00 4.35
2124 8257 5.991933 ATATATGACGAGATTGCCAGACT 57.008 39.130 0.00 0.00 0.00 3.24


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

AutoCloner maintained by Alex Coulton.