Multiple sequence alignment - TraesCS1A01G428800

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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 TraesCS1A01G428800 chr1A 100.000 2366 0 0 1 2366 582510765 582508400 0.000000e+00 4370
1 TraesCS1A01G428800 chr1A 96.117 1133 32 3 772 1900 582560789 582559665 0.000000e+00 1838
2 TraesCS1A01G428800 chr1A 90.461 608 35 5 125 731 582561369 582560784 0.000000e+00 780
3 TraesCS1A01G428800 chr1A 84.248 565 44 19 1511 2069 582638475 582637950 2.100000e-140 508
4 TraesCS1A01G428800 chr1D 96.088 1636 55 6 735 2366 485326573 485324943 0.000000e+00 2658
5 TraesCS1A01G428800 chr1D 95.846 337 14 0 411 747 485326925 485326589 1.600000e-151 545
6 TraesCS1A01G428800 chr1B 96.480 767 18 3 735 1500 675655867 675655109 0.000000e+00 1258
7 TraesCS1A01G428800 chr1B 94.667 750 36 3 1 747 675656631 675655883 0.000000e+00 1160
8 TraesCS1A01G428800 chr1B 86.916 535 36 9 1536 2040 675653352 675652822 9.490000e-159 569
9 TraesCS1A01G428800 chr1B 78.161 261 53 4 426 684 567956261 567956003 1.880000e-36 163
10 TraesCS1A01G428800 chr7D 83.979 387 60 2 314 700 252550936 252550552 1.030000e-98 370
11 TraesCS1A01G428800 chr5A 79.903 413 72 10 309 717 564550948 564550543 2.300000e-75 292
12 TraesCS1A01G428800 chr6B 78.753 433 83 8 266 695 590664722 590665148 4.980000e-72 281
13 TraesCS1A01G428800 chr2D 78.000 450 91 8 266 714 557269859 557270301 2.320000e-70 276
14 TraesCS1A01G428800 chr6A 78.241 432 87 7 269 698 48053053 48052627 1.080000e-68 270
15 TraesCS1A01G428800 chr4A 78.353 425 87 5 274 697 709742750 709743170 1.080000e-68 270
16 TraesCS1A01G428800 chr2A 73.821 424 86 20 295 708 719380385 719380793 6.820000e-31 145


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 TraesCS1A01G428800 chr1A 582508400 582510765 2365 True 4370.000000 4370 100.000000 1 2366 1 chr1A.!!$R1 2365
1 TraesCS1A01G428800 chr1A 582559665 582561369 1704 True 1309.000000 1838 93.289000 125 1900 2 chr1A.!!$R3 1775
2 TraesCS1A01G428800 chr1A 582637950 582638475 525 True 508.000000 508 84.248000 1511 2069 1 chr1A.!!$R2 558
3 TraesCS1A01G428800 chr1D 485324943 485326925 1982 True 1601.500000 2658 95.967000 411 2366 2 chr1D.!!$R1 1955
4 TraesCS1A01G428800 chr1B 675652822 675656631 3809 True 995.666667 1258 92.687667 1 2040 3 chr1B.!!$R2 2039

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
369 373 0.173708 GGACCTCGTCGAGAAGCATT 59.826 55.0 23.74 0.39 32.65 3.56 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2304 4097 0.322816 ACGGACGGGTAGAAGCACTA 60.323 55.0 0.0 0.0 0.0 2.74 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
289 293 1.195115 CTAGTAAGCAGAGGCCACCA 58.805 55.000 5.01 0.00 42.56 4.17
369 373 0.173708 GGACCTCGTCGAGAAGCATT 59.826 55.000 23.74 0.39 32.65 3.56
451 455 3.093717 TGAGGATCGAAGCGTTATTCC 57.906 47.619 0.00 0.00 38.61 3.01
850 882 7.551035 TGCATTTAATGTGATTAATTTGGCC 57.449 32.000 6.81 0.00 34.92 5.36
904 936 5.833131 ACATATTGGATTGGTATCAACCCAC 59.167 40.000 0.00 0.00 45.87 4.61
935 967 6.939132 AGGCTTGACATTTCATATCTTCTG 57.061 37.500 0.00 0.00 0.00 3.02
1011 1043 2.403252 AAGCCAAGATGAGGGTAACG 57.597 50.000 0.00 0.00 35.44 3.18
1116 1148 8.550710 TTTCTCCATCAAATTTTGCCAATAAG 57.449 30.769 4.19 0.00 0.00 1.73
1406 1441 3.689161 TGTATGCTGAAATGGTTTCCTCG 59.311 43.478 0.47 0.00 38.90 4.63
1564 3320 0.468226 TTGCCTTCCAGACGTGTCTT 59.532 50.000 0.00 0.00 37.98 3.01
2044 3831 2.393271 AGCTACCTGCATCTTGTGAC 57.607 50.000 0.00 0.00 45.94 3.67
2083 3875 1.664333 GTGCGGCCACAATGGTTTG 60.664 57.895 2.24 0.00 40.46 2.93
2090 3882 0.604578 CCACAATGGTTTGCAGAGGG 59.395 55.000 0.00 0.00 36.22 4.30
2108 3900 0.535797 GGTCCCCTAACCGTCTGAAG 59.464 60.000 0.00 0.00 0.00 3.02
2109 3901 0.535797 GTCCCCTAACCGTCTGAAGG 59.464 60.000 8.14 8.14 0.00 3.46
2165 3957 9.736023 GAATTACTGTTTTCACTGTTTCTGAAT 57.264 29.630 0.00 0.00 36.53 2.57
2207 3999 0.253044 TGGCAAGCATGGACTCTACC 59.747 55.000 0.00 0.00 0.00 3.18
2219 4011 1.396301 GACTCTACCGTCTACACCACG 59.604 57.143 0.00 0.00 36.99 4.94
2256 4049 2.554032 CGCTCTCCCTTTGTTCACATTT 59.446 45.455 0.00 0.00 0.00 2.32
2264 4057 2.166821 TTGTTCACATTTGGGCATGC 57.833 45.000 9.90 9.90 0.00 4.06
2280 4073 4.170292 GCATGCCTTGGCTTAATCTATG 57.830 45.455 6.36 7.25 0.00 2.23
2288 4081 6.744339 GCCTTGGCTTAATCTATGCCTACTAA 60.744 42.308 4.11 0.00 46.12 2.24
2331 4124 2.445427 TCTACCCGTCCGTCACATAAA 58.555 47.619 0.00 0.00 0.00 1.40
2334 4127 2.624636 ACCCGTCCGTCACATAAATTC 58.375 47.619 0.00 0.00 0.00 2.17
2357 4150 4.030216 AGAGAAAACCCCTTGCTTTTTCA 58.970 39.130 8.33 0.00 40.29 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
289 293 3.064324 GCTTTCTGGCCACCGCAT 61.064 61.111 0.00 0.00 36.38 4.73
391 395 5.065218 CCACTGTTGTTTCCATCTAGCATAC 59.935 44.000 0.00 0.00 0.00 2.39
439 443 1.300481 GCCCTCAGGAATAACGCTTC 58.700 55.000 0.00 0.00 33.47 3.86
850 882 6.438186 AGGAATGCCATTAAAAATATGGGG 57.562 37.500 0.00 0.00 42.32 4.96
935 967 1.541233 CCCGGTTGTAGGATGAGATGC 60.541 57.143 0.00 0.00 0.00 3.91
1011 1043 2.036604 GAGGGTCAGGAGTAGCATAAGC 59.963 54.545 0.00 0.00 42.56 3.09
1128 1160 0.905357 ACCAATCGACAGGAAGAGGG 59.095 55.000 11.63 0.00 0.00 4.30
1139 1174 6.758254 TCAGCATCTGAAATATACCAATCGA 58.242 36.000 0.00 0.00 37.57 3.59
1474 1509 4.935205 TGTAGTCTACGCATGCAAGAATTT 59.065 37.500 20.71 12.52 0.00 1.82
1848 3613 4.649692 CAGCATCATACTTTCTGGGCTAT 58.350 43.478 0.00 0.00 0.00 2.97
2044 3831 2.361119 CCACCAGATGCAAGGAATCATG 59.639 50.000 9.85 0.00 0.00 3.07
2090 3882 0.535797 CCTTCAGACGGTTAGGGGAC 59.464 60.000 0.00 0.00 0.00 4.46
2144 3936 8.711457 CAAAAATTCAGAAACAGTGAAAACAGT 58.289 29.630 0.00 0.00 37.46 3.55
2145 3937 8.711457 ACAAAAATTCAGAAACAGTGAAAACAG 58.289 29.630 0.00 0.00 37.46 3.16
2146 3938 8.600449 ACAAAAATTCAGAAACAGTGAAAACA 57.400 26.923 0.00 0.00 37.46 2.83
2156 3948 8.764287 CCAGGTTGAATACAAAAATTCAGAAAC 58.236 33.333 0.18 0.00 44.43 2.78
2165 3957 4.892934 ACTCTGCCAGGTTGAATACAAAAA 59.107 37.500 0.00 0.00 37.77 1.94
2207 3999 2.341318 TCAATCACGTGGTGTAGACG 57.659 50.000 17.00 0.00 42.62 4.18
2219 4011 4.290155 GAGAGCGAGAGAGAATCAATCAC 58.710 47.826 0.00 0.00 37.82 3.06
2256 4049 0.325484 ATTAAGCCAAGGCATGCCCA 60.325 50.000 33.14 7.47 44.88 5.36
2304 4097 0.322816 ACGGACGGGTAGAAGCACTA 60.323 55.000 0.00 0.00 0.00 2.74
2312 4105 2.945447 TTTATGTGACGGACGGGTAG 57.055 50.000 0.00 0.00 0.00 3.18
2331 4124 3.532641 AGCAAGGGGTTTTCTCTGAAT 57.467 42.857 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.