Multiple sequence alignment - TraesCS5D01G471800

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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 TraesCS5D01G471800 chr5D 100.000 2878 0 0 1 2878 512430433 512433310 0.000000e+00 5315
1 TraesCS5D01G471800 chr6D 96.407 1141 32 3 778 1910 380486806 380487945 0.000000e+00 1871
2 TraesCS5D01G471800 chr6D 97.125 974 22 4 1910 2878 469521546 469520574 0.000000e+00 1639
3 TraesCS5D01G471800 chr6D 94.246 782 28 3 1 780 379324355 379323589 0.000000e+00 1179
4 TraesCS5D01G471800 chr7A 93.236 1168 70 6 3 1161 83235733 83234566 0.000000e+00 1711
5 TraesCS5D01G471800 chr7A 92.277 764 47 3 1157 1909 83232924 83232162 0.000000e+00 1074
6 TraesCS5D01G471800 chr4D 97.425 971 15 8 1914 2878 30029403 30028437 0.000000e+00 1646
7 TraesCS5D01G471800 chr4D 97.035 978 22 5 1906 2878 138267397 138266422 0.000000e+00 1639
8 TraesCS5D01G471800 chr4D 97.116 971 24 2 1911 2878 134681219 134682188 0.000000e+00 1635
9 TraesCS5D01G471800 chrUn 97.225 973 22 3 1910 2878 29547676 29548647 0.000000e+00 1642
10 TraesCS5D01G471800 chr7D 97.222 972 22 3 1911 2878 160695865 160696835 0.000000e+00 1640
11 TraesCS5D01G471800 chr7D 97.026 975 23 4 1908 2878 491852780 491853752 0.000000e+00 1635
12 TraesCS5D01G471800 chr1D 97.214 969 21 4 1914 2878 224905516 224904550 0.000000e+00 1635
13 TraesCS5D01G471800 chr1D 96.173 993 33 3 1890 2878 445596911 445597902 0.000000e+00 1618
14 TraesCS5D01G471800 chr3B 80.273 659 107 19 4 653 65311699 65312343 2.590000e-130 475
15 TraesCS5D01G471800 chr3B 77.451 714 125 26 988 1681 65312634 65313331 7.470000e-106 394


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 TraesCS5D01G471800 chr5D 512430433 512433310 2877 False 5315.0 5315 100.0000 1 2878 1 chr5D.!!$F1 2877
1 TraesCS5D01G471800 chr6D 380486806 380487945 1139 False 1871.0 1871 96.4070 778 1910 1 chr6D.!!$F1 1132
2 TraesCS5D01G471800 chr6D 469520574 469521546 972 True 1639.0 1639 97.1250 1910 2878 1 chr6D.!!$R2 968
3 TraesCS5D01G471800 chr6D 379323589 379324355 766 True 1179.0 1179 94.2460 1 780 1 chr6D.!!$R1 779
4 TraesCS5D01G471800 chr7A 83232162 83235733 3571 True 1392.5 1711 92.7565 3 1909 2 chr7A.!!$R1 1906
5 TraesCS5D01G471800 chr4D 30028437 30029403 966 True 1646.0 1646 97.4250 1914 2878 1 chr4D.!!$R1 964
6 TraesCS5D01G471800 chr4D 138266422 138267397 975 True 1639.0 1639 97.0350 1906 2878 1 chr4D.!!$R2 972
7 TraesCS5D01G471800 chr4D 134681219 134682188 969 False 1635.0 1635 97.1160 1911 2878 1 chr4D.!!$F1 967
8 TraesCS5D01G471800 chrUn 29547676 29548647 971 False 1642.0 1642 97.2250 1910 2878 1 chrUn.!!$F1 968
9 TraesCS5D01G471800 chr7D 160695865 160696835 970 False 1640.0 1640 97.2220 1911 2878 1 chr7D.!!$F1 967
10 TraesCS5D01G471800 chr7D 491852780 491853752 972 False 1635.0 1635 97.0260 1908 2878 1 chr7D.!!$F2 970
11 TraesCS5D01G471800 chr1D 224904550 224905516 966 True 1635.0 1635 97.2140 1914 2878 1 chr1D.!!$R1 964
12 TraesCS5D01G471800 chr1D 445596911 445597902 991 False 1618.0 1618 96.1730 1890 2878 1 chr1D.!!$F1 988
13 TraesCS5D01G471800 chr3B 65311699 65313331 1632 False 434.5 475 78.8620 4 1681 2 chr3B.!!$F1 1677

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
426 442 0.034896 GAGAACTTCAACGGGGCTCA 59.965 55.0 0.0 0.0 0.00 4.26 F
485 502 0.683412 AAGCTAACGACGGTTTCCCT 59.317 50.0 0.0 0.0 37.58 4.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1435 3123 0.320771 GCAGCGTTCCTCCTCTCAAA 60.321 55.0 0.0 0.0 0.0 2.69 R
2309 4008 0.328258 GGCACCCCATAGACACAACT 59.672 55.0 0.0 0.0 0.0 3.16 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
98 99 3.804518 TGTACGTGTTTGACATGCATC 57.195 42.857 0.00 0.0 38.65 3.91
239 255 4.202253 TGTTAGACGATGGATGGAAGATGG 60.202 45.833 0.00 0.0 0.00 3.51
240 256 2.682594 AGACGATGGATGGAAGATGGA 58.317 47.619 0.00 0.0 0.00 3.41
241 257 2.366916 AGACGATGGATGGAAGATGGAC 59.633 50.000 0.00 0.0 0.00 4.02
242 258 2.103094 GACGATGGATGGAAGATGGACA 59.897 50.000 0.00 0.0 0.00 4.02
243 259 2.707791 ACGATGGATGGAAGATGGACAT 59.292 45.455 0.00 0.0 0.00 3.06
244 260 3.903714 ACGATGGATGGAAGATGGACATA 59.096 43.478 0.00 0.0 0.00 2.29
245 261 4.533707 ACGATGGATGGAAGATGGACATAT 59.466 41.667 0.00 0.0 0.00 1.78
246 262 5.114780 CGATGGATGGAAGATGGACATATC 58.885 45.833 0.00 0.0 0.00 1.63
247 263 5.337813 CGATGGATGGAAGATGGACATATCA 60.338 44.000 0.00 0.0 0.00 2.15
248 264 5.233083 TGGATGGAAGATGGACATATCAC 57.767 43.478 0.00 0.0 0.00 3.06
249 265 4.659835 TGGATGGAAGATGGACATATCACA 59.340 41.667 0.00 0.0 0.00 3.58
250 266 5.221783 TGGATGGAAGATGGACATATCACAG 60.222 44.000 0.00 0.0 0.00 3.66
251 267 5.012458 GGATGGAAGATGGACATATCACAGA 59.988 44.000 0.00 0.0 0.00 3.41
252 268 5.541953 TGGAAGATGGACATATCACAGAG 57.458 43.478 0.00 0.0 0.00 3.35
253 269 4.346127 TGGAAGATGGACATATCACAGAGG 59.654 45.833 0.00 0.0 0.00 3.69
422 438 1.202651 ACACAGAGAACTTCAACGGGG 60.203 52.381 0.00 0.0 0.00 5.73
426 442 0.034896 GAGAACTTCAACGGGGCTCA 59.965 55.000 0.00 0.0 0.00 4.26
457 474 2.353889 GACGTACCGCATGTAAGAGAGA 59.646 50.000 0.00 0.0 33.68 3.10
485 502 0.683412 AAGCTAACGACGGTTTCCCT 59.317 50.000 0.00 0.0 37.58 4.20
748 766 1.298859 GGTGACGTGGACAATGCTCC 61.299 60.000 0.00 0.0 0.00 4.70
851 871 2.732844 TAATGCAGTGCCATCCATCA 57.267 45.000 13.72 0.0 0.00 3.07
883 903 1.918262 TGATGGCTCCTTCTGTCCAAT 59.082 47.619 3.87 0.0 31.66 3.16
888 908 2.290577 GGCTCCTTCTGTCCAATGTCTT 60.291 50.000 0.00 0.0 0.00 3.01
1084 1126 4.963373 TCGTAGATGTTTTTCTGGACCAA 58.037 39.130 0.00 0.0 0.00 3.67
1244 2932 1.352156 CGCTCGAGGGTAAGTGCAAC 61.352 60.000 20.59 0.0 0.00 4.17
1329 3017 2.094286 ACTCTGCCTCTGTGATCTTTCG 60.094 50.000 0.00 0.0 0.00 3.46
1506 3194 2.100749 TGAAGCGGCAAATCTATCTCGA 59.899 45.455 1.45 0.0 0.00 4.04
1573 3261 3.196207 ATGGTGGCTCGTGTGGCTT 62.196 57.895 0.00 0.0 0.00 4.35
1782 3470 3.319137 TGCATCTGTAGGAGTTGTGTC 57.681 47.619 0.00 0.0 0.00 3.67
1912 3610 2.437716 GCGGCGGGAAAGGATTGA 60.438 61.111 9.78 0.0 0.00 2.57
1937 3635 7.527568 TGGGGAACGTAGTAATTTCAAAAAT 57.472 32.000 0.00 0.0 45.00 1.82
1940 3638 8.918658 GGGGAACGTAGTAATTTCAAAAATTTC 58.081 33.333 3.24 0.0 45.00 2.17
2267 3965 7.362315 CGGTATTATCGAGGTGTAATATGGTGA 60.362 40.741 0.00 0.0 0.00 4.02
2559 4262 4.993705 TTTGAGGCCTTTCTCTCCTTTA 57.006 40.909 6.77 0.0 34.98 1.85
2560 4263 5.520748 TTTGAGGCCTTTCTCTCCTTTAT 57.479 39.130 6.77 0.0 34.98 1.40
2561 4264 6.636454 TTTGAGGCCTTTCTCTCCTTTATA 57.364 37.500 6.77 0.0 34.98 0.98
2562 4265 5.615925 TGAGGCCTTTCTCTCCTTTATAC 57.384 43.478 6.77 0.0 34.98 1.47
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
98 99 2.726760 CGAGGACGTTCAGTTTCTTCAG 59.273 50.000 0.00 0.0 34.56 3.02
247 263 0.111832 TGTACCTCACGGTCCTCTGT 59.888 55.000 0.00 0.0 44.21 3.41
248 264 1.067776 GTTGTACCTCACGGTCCTCTG 60.068 57.143 0.00 0.0 44.21 3.35
249 265 1.254954 GTTGTACCTCACGGTCCTCT 58.745 55.000 0.00 0.0 44.21 3.69
250 266 0.963962 TGTTGTACCTCACGGTCCTC 59.036 55.000 0.00 0.0 44.21 3.71
251 267 1.275291 CATGTTGTACCTCACGGTCCT 59.725 52.381 0.00 0.0 44.21 3.85
252 268 1.274167 TCATGTTGTACCTCACGGTCC 59.726 52.381 0.00 0.0 44.21 4.46
253 269 2.735134 GTTCATGTTGTACCTCACGGTC 59.265 50.000 0.00 0.0 44.21 4.79
404 420 0.250338 GCCCCGTTGAAGTTCTCTGT 60.250 55.000 4.17 0.0 0.00 3.41
457 474 7.436376 GGAAACCGTCGTTAGCTTAAATAGTAT 59.564 37.037 0.00 0.0 0.00 2.12
553 570 6.350277 CGTACAACATCCTCTTCCTTCTAACT 60.350 42.308 0.00 0.0 0.00 2.24
748 766 2.094545 GCCCTAACCAAAAGACATGCAG 60.095 50.000 0.00 0.0 0.00 4.41
851 871 2.283298 GAGCCATCACATCGAACACAT 58.717 47.619 0.00 0.0 0.00 3.21
883 903 7.721286 TTCAAGTTCAAAAAGCAAAAAGACA 57.279 28.000 0.00 0.0 0.00 3.41
888 908 8.499967 GGTTACTTTCAAGTTCAAAAAGCAAAA 58.500 29.630 0.00 0.0 40.37 2.44
980 1000 1.075600 CCAACACCACCCACCCTTT 60.076 57.895 0.00 0.0 0.00 3.11
1149 1191 0.239347 CTGCTTTTGGCTTCTCACGG 59.761 55.000 0.00 0.0 42.39 4.94
1244 2932 6.373774 AGGAAGCAAGAACATCATACTTCAAG 59.626 38.462 0.00 0.0 35.01 3.02
1329 3017 0.992695 AACCTCCCCTCTAACCAAGC 59.007 55.000 0.00 0.0 0.00 4.01
1435 3123 0.320771 GCAGCGTTCCTCCTCTCAAA 60.321 55.000 0.00 0.0 0.00 2.69
1506 3194 5.234466 ACTCCATAGCTTCTGAAAGTTGT 57.766 39.130 0.00 0.0 34.79 3.32
1564 3252 1.165907 ACATCACCACAAGCCACACG 61.166 55.000 0.00 0.0 0.00 4.49
1573 3261 2.368548 ACTGTCTAGCAACATCACCACA 59.631 45.455 0.00 0.0 0.00 4.17
1729 3417 8.641155 CACAAACTAACAATAACTCATGCATTG 58.359 33.333 0.00 0.0 36.07 2.82
1782 3470 8.612619 GTGGTGACTAATACAATTTGATACAGG 58.387 37.037 2.79 0.0 0.00 4.00
1835 3533 8.158132 ACTATCTTTCATGATCTGAAGCATCAT 58.842 33.333 0.00 0.0 44.48 2.45
1878 3576 3.608241 CGCCGCAACACTTTTCAAATCTA 60.608 43.478 0.00 0.0 0.00 1.98
1912 3610 7.527568 TTTTTGAAATTACTACGTTCCCCAT 57.472 32.000 0.00 0.0 0.00 4.00
2107 3805 2.495409 TCGAGCTGAACGTGTGTAAA 57.505 45.000 0.00 0.0 0.00 2.01
2108 3806 2.030628 TCATCGAGCTGAACGTGTGTAA 60.031 45.455 0.00 0.0 0.00 2.41
2309 4008 0.328258 GGCACCCCATAGACACAACT 59.672 55.000 0.00 0.0 0.00 3.16


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

AutoCloner maintained by Alex Coulton.