Multiple sequence alignment - TraesCS6D01G110700

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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 TraesCS6D01G110700 chr6D 100.000 3239 0 0 1 3239 77171547 77174785 0.000000e+00 5982.0
1 TraesCS6D01G110700 chr6D 90.141 71 7 0 1003 1073 37659998 37659928 3.440000e-15 93.5
2 TraesCS6D01G110700 chr6A 95.435 3242 125 11 1 3239 92574981 92578202 0.000000e+00 5145.0
3 TraesCS6D01G110700 chr6B 94.198 2792 147 11 450 3239 149876141 149878919 0.000000e+00 4244.0
4 TraesCS6D01G110700 chr6B 92.908 423 18 6 1 421 149875732 149876144 3.570000e-169 604.0
5 TraesCS6D01G110700 chr6B 72.301 982 206 42 1003 1955 87999649 87998705 2.500000e-61 246.0
6 TraesCS6D01G110700 chr7D 82.203 118 9 8 256 366 550462230 550462342 1.240000e-14 91.6
7 TraesCS6D01G110700 chr7D 82.203 118 9 8 256 366 550642496 550642608 1.240000e-14 91.6
8 TraesCS6D01G110700 chr7A 97.059 34 1 0 264 297 635859452 635859485 1.260000e-04 58.4


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 TraesCS6D01G110700 chr6D 77171547 77174785 3238 False 5982 5982 100.000 1 3239 1 chr6D.!!$F1 3238
1 TraesCS6D01G110700 chr6A 92574981 92578202 3221 False 5145 5145 95.435 1 3239 1 chr6A.!!$F1 3238
2 TraesCS6D01G110700 chr6B 149875732 149878919 3187 False 2424 4244 93.553 1 3239 2 chr6B.!!$F1 3238
3 TraesCS6D01G110700 chr6B 87998705 87999649 944 True 246 246 72.301 1003 1955 1 chr6B.!!$R1 952

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
638 642 0.037605 AGTCAACCAACCGGATCGAC 60.038 55.0 9.46 5.77 35.59 4.2 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2414 2444 0.250295 CCCTCTGTCCTTCGTGCAAA 60.25 55.0 0.0 0.0 0.0 3.68 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
40 41 5.179368 CCCGCAATTTAAGACGATGATGTAT 59.821 40.000 0.00 0.00 0.00 2.29
170 171 0.610174 TGCCGAGGATGGATATCTGC 59.390 55.000 2.05 0.00 33.68 4.26
184 185 2.593346 ATCTGCTCTCACCGAATCAC 57.407 50.000 0.00 0.00 0.00 3.06
340 343 3.869272 CGTGCGCTGATTCTGGGC 61.869 66.667 20.84 20.84 40.48 5.36
416 420 5.362430 CCTTTGCCAAGTCTAGTCTAGAGAT 59.638 44.000 9.97 0.00 35.04 2.75
417 421 6.127196 CCTTTGCCAAGTCTAGTCTAGAGATT 60.127 42.308 9.97 5.75 35.04 2.40
418 422 7.068839 CCTTTGCCAAGTCTAGTCTAGAGATTA 59.931 40.741 9.97 0.00 35.04 1.75
419 423 7.956328 TTGCCAAGTCTAGTCTAGAGATTAA 57.044 36.000 9.97 0.00 35.04 1.40
420 424 8.540507 TTGCCAAGTCTAGTCTAGAGATTAAT 57.459 34.615 9.97 0.00 35.04 1.40
421 425 9.642343 TTGCCAAGTCTAGTCTAGAGATTAATA 57.358 33.333 9.97 0.00 35.04 0.98
422 426 9.815306 TGCCAAGTCTAGTCTAGAGATTAATAT 57.185 33.333 9.97 0.00 35.04 1.28
501 505 1.250328 TCATGCAGGTTGAAGCAAGG 58.750 50.000 0.00 0.00 44.88 3.61
551 555 4.738740 GCGCCAGAACATATATATACGGAC 59.261 45.833 0.00 0.00 0.00 4.79
599 603 2.595750 ATCTCGGCATCTAGCTAGGT 57.404 50.000 20.58 11.30 44.79 3.08
638 642 0.037605 AGTCAACCAACCGGATCGAC 60.038 55.000 9.46 5.77 35.59 4.20
742 746 7.448748 TCTTGGTTTCTACTCCAAATTTAGC 57.551 36.000 0.00 0.00 42.14 3.09
978 982 1.105167 CATGGCCATGGACGAGCAAT 61.105 55.000 34.31 0.00 35.24 3.56
1007 1011 1.000163 CAGATGATACTCGGAACCGGG 60.000 57.143 11.78 11.78 46.76 5.73
1397 1417 0.514255 CGTAATGGATGATGCAGGCG 59.486 55.000 0.00 0.00 0.00 5.52
1769 1789 2.365768 GGGGAGGAGGTGGAGACC 60.366 72.222 0.00 0.00 43.52 3.85
2013 2042 2.573869 CCAGGCATCAGACGACGT 59.426 61.111 0.00 0.00 0.00 4.34
2045 2074 0.454285 AAACGCCGAACATTCATGCG 60.454 50.000 18.50 18.50 46.76 4.73
2198 2227 2.997485 TCGATATGAGCGGATGAGTG 57.003 50.000 0.00 0.00 0.00 3.51
2367 2397 7.608761 AGTGTATACGGTTGTGTGGAAATATTT 59.391 33.333 0.00 0.00 0.00 1.40
2398 2428 8.699130 TGAGAAAGATGACATGTATGACTATGT 58.301 33.333 0.00 0.00 40.04 2.29
2414 2444 6.588204 TGACTATGTTGGTACAGAAAAGTGT 58.412 36.000 0.00 0.00 42.39 3.55
2548 2578 1.892209 ACGGTCCACAAAGATTGGTC 58.108 50.000 0.00 0.00 35.42 4.02
2846 2878 8.797438 CAAGATACAAGGATATGCTAGAGTACA 58.203 37.037 0.00 0.00 0.00 2.90
2853 2885 0.663688 ATGCTAGAGTACACGCCTCG 59.336 55.000 0.00 0.00 34.08 4.63
2881 2913 1.302033 CCTTGCTCACGAGTGCCTT 60.302 57.895 4.49 0.00 33.44 4.35
2973 3005 1.300963 CTAGAAGGCCTGGCTGCAA 59.699 57.895 19.68 0.00 0.00 4.08
2993 3025 0.179020 CCTTGCCTTGGCGATCCATA 60.179 55.000 7.18 0.00 43.05 2.74
3060 3092 2.227757 TTCCCCTGGCAATGTCGGA 61.228 57.895 0.00 0.00 0.00 4.55
3061 3093 1.570857 TTCCCCTGGCAATGTCGGAT 61.571 55.000 0.00 0.00 0.00 4.18
3144 3176 2.621407 GGGCCTCTGTTCCATGATTCAA 60.621 50.000 0.84 0.00 0.00 2.69
3205 3237 2.022129 CACGAGGCGTTCTCACCAC 61.022 63.158 0.00 0.00 42.55 4.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 2.029380 CGAAGTGTGTGTGTATCCCTCA 60.029 50.000 0.00 0.00 0.00 3.86
170 171 3.129462 TGAGCTAAGTGATTCGGTGAGAG 59.871 47.826 0.00 0.00 0.00 3.20
461 465 0.546507 TCCTGGGGTGTGCTGTATCA 60.547 55.000 0.00 0.00 0.00 2.15
462 466 0.839946 ATCCTGGGGTGTGCTGTATC 59.160 55.000 0.00 0.00 0.00 2.24
501 505 1.583967 CGTGCATCGTCGAGGAGTC 60.584 63.158 11.71 8.00 34.52 3.36
599 603 1.584724 TGCAAAACCCCAGGGAAAAA 58.415 45.000 7.25 0.00 38.96 1.94
643 647 2.720758 CTGGCTTCTGTTCGCGTCG 61.721 63.158 5.77 0.00 0.00 5.12
865 869 4.599434 TGGCAAACGACGCGCAAC 62.599 61.111 5.73 0.00 0.00 4.17
974 978 6.237781 CGAGTATCATCTGCTATAAGCATTGC 60.238 42.308 0.00 0.00 43.03 3.56
978 982 5.010282 TCCGAGTATCATCTGCTATAAGCA 58.990 41.667 1.09 1.09 42.15 3.91
1397 1417 7.231925 TCCTCCAAAGTATTACAAAACCTTTCC 59.768 37.037 0.00 0.00 0.00 3.13
1684 1704 1.277557 CCTCCTCACCTTCACCTTCAG 59.722 57.143 0.00 0.00 0.00 3.02
1769 1789 3.155167 GGAGGCTCCACTACCGGG 61.155 72.222 28.55 0.00 36.28 5.73
1921 1950 1.226686 GATGTAGATGCTGCCCTGCG 61.227 60.000 0.00 0.00 35.36 5.18
2013 2042 1.692148 GGCGTTTCATCGACGATGCA 61.692 55.000 28.87 18.63 42.82 3.96
2045 2074 8.529911 CGACTCTAAAACTACGGAAATAATGAC 58.470 37.037 0.00 0.00 0.00 3.06
2178 2207 2.416566 GCACTCATCCGCTCATATCGAT 60.417 50.000 2.16 2.16 0.00 3.59
2198 2227 0.826256 AACCGAACAAAAGAGGGGGC 60.826 55.000 0.00 0.00 0.00 5.80
2367 2397 7.924947 GTCATACATGTCATCTTTCTCATCTCA 59.075 37.037 0.00 0.00 0.00 3.27
2386 2416 8.372459 ACTTTTCTGTACCAACATAGTCATACA 58.628 33.333 0.00 0.00 34.37 2.29
2398 2428 4.673061 CGTGCAAACACTTTTCTGTACCAA 60.673 41.667 0.00 0.00 45.10 3.67
2414 2444 0.250295 CCCTCTGTCCTTCGTGCAAA 60.250 55.000 0.00 0.00 0.00 3.68
2786 2818 8.675705 TTGAATGTAGAATCTCAGTGTTTTGA 57.324 30.769 0.00 0.00 0.00 2.69
2796 2828 8.044060 TGTTGATGGTTTGAATGTAGAATCTC 57.956 34.615 0.00 0.00 0.00 2.75
2862 2894 2.738213 AAGGCACTCGTGAGCAAGGG 62.738 60.000 9.05 0.00 38.49 3.95
2881 2913 2.554142 GTGCGGATCAGATCATGTGAA 58.446 47.619 12.66 0.00 0.00 3.18
2973 3005 2.044946 GGATCGCCAAGGCAAGGT 60.045 61.111 12.19 0.00 42.06 3.50
2993 3025 3.895704 TTCTTAGAAGTTGGGCCCTTT 57.104 42.857 25.70 14.92 0.00 3.11
3060 3092 6.239186 AGCTAAGCTTTTATAGGGGCCCTAT 61.239 44.000 39.69 39.69 42.11 2.57
3061 3093 3.329814 GCTAAGCTTTTATAGGGGCCCTA 59.670 47.826 33.72 33.72 40.71 3.53
3144 3176 8.265055 TGAAGATGATAAAAATCTACCGAGGTT 58.735 33.333 0.00 0.00 33.17 3.50
3205 3237 7.553044 CCCTACTCCTACTTTGTTTTGGATTAG 59.447 40.741 0.00 0.00 32.97 1.73


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

AutoCloner maintained by Alex Coulton.