Multiple sequence alignment - TraesCS4A01G152400

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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 TraesCS4A01G152400 chr4A 100.000 2246 0 0 1 2246 309447750 309445505 0 4148
1 TraesCS4A01G152400 chr3A 96.099 2256 74 8 1 2244 105558303 105556050 0 3666
2 TraesCS4A01G152400 chr7B 96.004 2252 80 7 1 2244 662756375 662754126 0 3651
3 TraesCS4A01G152400 chr1B 96.002 2251 80 8 1 2244 633715631 633717878 0 3650
4 TraesCS4A01G152400 chr5B 95.745 2256 82 9 1 2244 57516469 57514216 0 3622
5 TraesCS4A01G152400 chr5D 95.656 2256 80 12 1 2244 503338097 503340346 0 3607
6 TraesCS4A01G152400 chr5D 95.447 2262 81 10 1 2244 6254626 6252369 0 3587
7 TraesCS4A01G152400 chr5D 95.342 2254 86 11 1 2244 503312162 503314406 0 3563
8 TraesCS4A01G152400 chr1D 95.346 2256 80 14 1 2244 254458075 254460317 0 3561
9 TraesCS4A01G152400 chr1D 94.896 2253 96 12 1 2244 51833301 51831059 0 3506


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 TraesCS4A01G152400 chr4A 309445505 309447750 2245 True 4148 4148 100.000 1 2246 1 chr4A.!!$R1 2245
1 TraesCS4A01G152400 chr3A 105556050 105558303 2253 True 3666 3666 96.099 1 2244 1 chr3A.!!$R1 2243
2 TraesCS4A01G152400 chr7B 662754126 662756375 2249 True 3651 3651 96.004 1 2244 1 chr7B.!!$R1 2243
3 TraesCS4A01G152400 chr1B 633715631 633717878 2247 False 3650 3650 96.002 1 2244 1 chr1B.!!$F1 2243
4 TraesCS4A01G152400 chr5B 57514216 57516469 2253 True 3622 3622 95.745 1 2244 1 chr5B.!!$R1 2243
5 TraesCS4A01G152400 chr5D 503338097 503340346 2249 False 3607 3607 95.656 1 2244 1 chr5D.!!$F2 2243
6 TraesCS4A01G152400 chr5D 6252369 6254626 2257 True 3587 3587 95.447 1 2244 1 chr5D.!!$R1 2243
7 TraesCS4A01G152400 chr5D 503312162 503314406 2244 False 3563 3563 95.342 1 2244 1 chr5D.!!$F1 2243
8 TraesCS4A01G152400 chr1D 254458075 254460317 2242 False 3561 3561 95.346 1 2244 1 chr1D.!!$F1 2243
9 TraesCS4A01G152400 chr1D 51831059 51833301 2242 True 3506 3506 94.896 1 2244 1 chr1D.!!$R1 2243

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
131 132 0.099968 TACTCACGTCAGCGGCATAC 59.9 55.0 1.45 0.0 43.45 2.39 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1827 1862 0.249868 CTCGCACACACTCCCTTTCA 60.25 55.0 0.0 0.0 0.0 2.69 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
131 132 0.099968 TACTCACGTCAGCGGCATAC 59.900 55.000 1.45 0.00 43.45 2.39
139 140 2.607635 CGTCAGCGGCATACTTTTATGT 59.392 45.455 1.45 0.00 37.92 2.29
235 236 8.697507 AACATCCTAGAAGATTTCACAAAACT 57.302 30.769 0.00 0.00 0.00 2.66
269 270 4.332819 AGCTTTCGACTTTTCGGGAATATG 59.667 41.667 0.00 0.00 45.90 1.78
296 297 4.724036 GCGGATGAATTAGTCGTTGTTGTC 60.724 45.833 0.00 0.00 0.00 3.18
367 368 8.826710 TCTTGGATTATTTACAAGCAGTATTCG 58.173 33.333 0.00 0.00 40.93 3.34
396 397 2.515926 TTTTGCAACATTAGCCGCAA 57.484 40.000 0.00 0.00 42.29 4.85
399 400 1.175347 TGCAACATTAGCCGCAACCA 61.175 50.000 0.00 0.00 0.00 3.67
679 690 9.268282 TGTCTATAAGTGGAGTCCTCTTTTATT 57.732 33.333 26.93 14.45 38.19 1.40
680 691 9.535878 GTCTATAAGTGGAGTCCTCTTTTATTG 57.464 37.037 26.93 17.30 38.19 1.90
695 706 9.860898 CCTCTTTTATTGAGGTTTCCATTTTAG 57.139 33.333 0.00 0.00 44.42 1.85
929 952 3.922171 ACTTCTCCCCAATAGAGCTTG 57.078 47.619 0.00 0.00 0.00 4.01
998 1021 0.750249 TGACACGAGGAACTGCTCAA 59.250 50.000 0.00 0.00 41.55 3.02
1016 1039 5.711506 TGCTCAACATGAATCCACTAATTGT 59.288 36.000 0.00 0.00 0.00 2.71
1019 1042 7.523293 TCAACATGAATCCACTAATTGTTGT 57.477 32.000 0.00 0.00 41.76 3.32
1027 1050 7.446931 TGAATCCACTAATTGTTGTTGCTTCTA 59.553 33.333 0.00 0.00 0.00 2.10
1072 1095 2.172717 GGGCTTGCTTCTATTGGACCTA 59.827 50.000 0.00 0.00 0.00 3.08
1094 1117 1.768870 AGTTGGTCAAGGTACTGCTGT 59.231 47.619 0.66 0.66 40.86 4.40
1103 1126 2.890814 AGGTACTGCTGTAGGACAAGT 58.109 47.619 10.37 0.00 42.48 3.16
1215 1238 2.479566 ATGGACTAGTTGTGGCACTG 57.520 50.000 19.83 6.42 0.00 3.66
1217 1240 0.396811 GGACTAGTTGTGGCACTGGT 59.603 55.000 19.83 6.63 40.92 4.00
1409 1436 7.079700 TCAGGACAGATAATACCCCATTCTAA 58.920 38.462 0.00 0.00 0.00 2.10
1438 1465 9.125026 AGGGCTGAGTTGAGTATTATTAATTTG 57.875 33.333 0.00 0.00 0.00 2.32
1490 1517 6.484308 CGTCCTTAGTTTAGGAAAGTGGAAAA 59.516 38.462 0.00 0.00 45.62 2.29
1553 1581 3.553828 ACAAAGGAAGTCTTTCACCGA 57.446 42.857 0.00 0.00 43.32 4.69
1565 1593 4.272504 GTCTTTCACCGATCAAACAAGACA 59.727 41.667 13.16 0.00 38.89 3.41
1822 1856 6.603997 ACTGTAGTGGTTGGTGTTTTGATTTA 59.396 34.615 0.00 0.00 0.00 1.40
1827 1862 8.800370 AGTGGTTGGTGTTTTGATTTATTTTT 57.200 26.923 0.00 0.00 0.00 1.94
1851 1886 0.032952 GGGAGTGTGTGCGAGTTGTA 59.967 55.000 0.00 0.00 0.00 2.41
1940 1975 2.568623 AGAAAAGGGTGCACGATCTT 57.431 45.000 11.45 11.38 0.00 2.40
1943 1978 2.496899 AAAGGGTGCACGATCTTGAT 57.503 45.000 11.45 0.00 0.00 2.57
2083 2118 3.820557 AGCTAAACTGCTTGAAGTCCAA 58.179 40.909 0.00 0.00 40.93 3.53
2084 2119 4.207165 AGCTAAACTGCTTGAAGTCCAAA 58.793 39.130 0.00 0.00 40.93 3.28
2098 2133 5.358725 TGAAGTCCAAACAAAAAGAGGTACC 59.641 40.000 2.73 2.73 0.00 3.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 1.995376 AAAGAGCACCCGACCAAATT 58.005 45.000 0.00 0.00 0.00 1.82
13 14 2.223745 GTAAAAGAGCACCCGACCAAA 58.776 47.619 0.00 0.00 0.00 3.28
235 236 7.766219 AAAAGTCGAAAGCTAAGCGATAATA 57.234 32.000 8.42 0.00 36.37 0.98
269 270 2.277084 ACGACTAATTCATCCGCCAAC 58.723 47.619 0.00 0.00 0.00 3.77
296 297 5.877491 ACTAAGGGGACTAAAGAAACAAGG 58.123 41.667 0.00 0.00 42.68 3.61
367 368 6.254373 GGCTAATGTTGCAAAAATAAGAGCTC 59.746 38.462 5.27 5.27 29.43 4.09
396 397 5.014544 CCTCCATGGATTCACCTATATTGGT 59.985 44.000 16.63 2.68 38.41 3.67
399 400 5.173246 ACCCTCCATGGATTCACCTATATT 58.827 41.667 16.63 0.00 39.86 1.28
463 472 4.202121 CCATGCATGAATTGAGCTAAGCTT 60.202 41.667 28.31 3.48 39.88 3.74
526 535 7.932335 ACTCTAGGCTATATATTCATACGCAC 58.068 38.462 0.00 0.00 0.00 5.34
593 604 7.770897 CCACCCTCCTTAATGCATATATACTTC 59.229 40.741 0.00 0.00 0.00 3.01
679 690 5.083122 TCATTGCCTAAAATGGAAACCTCA 58.917 37.500 0.00 0.00 37.98 3.86
680 691 5.659440 TCATTGCCTAAAATGGAAACCTC 57.341 39.130 0.00 0.00 37.98 3.85
690 701 8.287439 TCGGATTCTAAAATCATTGCCTAAAA 57.713 30.769 1.05 0.00 42.66 1.52
695 706 6.738114 TGAATCGGATTCTAAAATCATTGCC 58.262 36.000 26.15 1.74 42.66 4.52
817 840 7.845537 AAGGGAATTCCATATCCATATACCA 57.154 36.000 25.67 0.00 37.46 3.25
843 866 5.801350 ATGTGAATTGTCCGAACTACATG 57.199 39.130 0.00 0.00 0.00 3.21
901 924 6.098552 GCTCTATTGGGGAGAAGTAAAGTAGT 59.901 42.308 0.00 0.00 33.03 2.73
902 925 6.325286 AGCTCTATTGGGGAGAAGTAAAGTAG 59.675 42.308 0.00 0.00 33.03 2.57
979 1002 0.750249 TTGAGCAGTTCCTCGTGTCA 59.250 50.000 0.00 0.00 34.56 3.58
993 1016 6.199937 ACAATTAGTGGATTCATGTTGAGC 57.800 37.500 0.00 0.00 0.00 4.26
998 1021 6.015180 AGCAACAACAATTAGTGGATTCATGT 60.015 34.615 0.00 0.00 0.00 3.21
1016 1039 6.208402 TCCAGCAACAATAATAGAAGCAACAA 59.792 34.615 0.00 0.00 0.00 2.83
1019 1042 7.259882 CAATCCAGCAACAATAATAGAAGCAA 58.740 34.615 0.00 0.00 0.00 3.91
1027 1050 2.101249 CGGCCAATCCAGCAACAATAAT 59.899 45.455 2.24 0.00 34.01 1.28
1034 1057 1.077787 CCTACGGCCAATCCAGCAA 60.078 57.895 2.24 0.00 34.01 3.91
1072 1095 2.037772 CAGCAGTACCTTGACCAACTCT 59.962 50.000 0.00 0.00 0.00 3.24
1094 1117 6.403878 GCAATACCTTCTACAACTTGTCCTA 58.596 40.000 0.00 0.00 0.00 2.94
1103 1126 4.744570 CTGTCTCGCAATACCTTCTACAA 58.255 43.478 0.00 0.00 0.00 2.41
1134 1157 9.605275 AATAAAGTACCTCGTATTTTACCTTCC 57.395 33.333 2.74 0.00 34.66 3.46
1215 1238 2.029380 AGGGTTCGCAAATAAAAGCACC 60.029 45.455 0.00 0.00 0.00 5.01
1217 1240 4.329462 AAAGGGTTCGCAAATAAAAGCA 57.671 36.364 0.00 0.00 0.00 3.91
1386 1413 7.313731 TCTTAGAATGGGGTATTATCTGTCCT 58.686 38.462 0.00 0.00 0.00 3.85
1409 1436 6.567602 AATAATACTCAACTCAGCCCTTCT 57.432 37.500 0.00 0.00 0.00 2.85
1438 1465 7.174080 GGAAATAAGAAGGTGAGCATATCTTCC 59.826 40.741 8.97 0.00 37.05 3.46
1509 1536 7.821359 TGTTGAAATGTTCTGTTCCAAAATTCA 59.179 29.630 0.00 0.00 0.00 2.57
1742 1774 2.404566 TAAGCCCGAAACTGCCAGCA 62.405 55.000 0.00 0.00 0.00 4.41
1822 1856 3.490761 CGCACACACTCCCTTTCAAAAAT 60.491 43.478 0.00 0.00 0.00 1.82
1827 1862 0.249868 CTCGCACACACTCCCTTTCA 60.250 55.000 0.00 0.00 0.00 2.69
1912 1947 6.177610 TCGTGCACCCTTTTCTTATTTATCT 58.822 36.000 12.15 0.00 0.00 1.98
1995 2030 6.485313 TCAAAGTTGATTTACCAATGAGTCGT 59.515 34.615 0.00 0.00 31.01 4.34
2044 2079 7.661027 AGTTTAGCTTTAACCGTGTTAATGGTA 59.339 33.333 18.87 18.87 45.51 3.25


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

AutoCloner maintained by Alex Coulton.