Multiple sequence alignment - TraesCS7B01G091400

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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 TraesCS7B01G091400 chr7B 100.000 2192 0 0 1 2192 105239270 105237079 0 4048
1 TraesCS7B01G091400 chr7B 96.586 2197 70 5 1 2192 622432609 622430413 0 3637
2 TraesCS7B01G091400 chr7B 96.533 2192 71 5 1 2188 662732274 662734464 0 3622
3 TraesCS7B01G091400 chr2A 96.574 2189 70 5 9 2192 543187028 543189216 0 3622
4 TraesCS7B01G091400 chr3B 96.359 2197 74 6 1 2192 201548661 201550856 0 3609
5 TraesCS7B01G091400 chr3B 96.264 2168 76 5 30 2192 201565993 201563826 0 3550
6 TraesCS7B01G091400 chr1B 96.040 2197 81 6 1 2192 633734111 633731916 0 3570
7 TraesCS7B01G091400 chr3A 95.996 2198 79 9 1 2192 672883669 672881475 0 3563
8 TraesCS7B01G091400 chr3A 95.630 2197 90 6 1 2192 695635760 695637955 0 3520
9 TraesCS7B01G091400 chr5D 95.949 2197 83 6 1 2192 503259416 503257221 0 3559


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 TraesCS7B01G091400 chr7B 105237079 105239270 2191 True 4048 4048 100.000 1 2192 1 chr7B.!!$R1 2191
1 TraesCS7B01G091400 chr7B 622430413 622432609 2196 True 3637 3637 96.586 1 2192 1 chr7B.!!$R2 2191
2 TraesCS7B01G091400 chr7B 662732274 662734464 2190 False 3622 3622 96.533 1 2188 1 chr7B.!!$F1 2187
3 TraesCS7B01G091400 chr2A 543187028 543189216 2188 False 3622 3622 96.574 9 2192 1 chr2A.!!$F1 2183
4 TraesCS7B01G091400 chr3B 201548661 201550856 2195 False 3609 3609 96.359 1 2192 1 chr3B.!!$F1 2191
5 TraesCS7B01G091400 chr3B 201563826 201565993 2167 True 3550 3550 96.264 30 2192 1 chr3B.!!$R1 2162
6 TraesCS7B01G091400 chr1B 633731916 633734111 2195 True 3570 3570 96.040 1 2192 1 chr1B.!!$R1 2191
7 TraesCS7B01G091400 chr3A 672881475 672883669 2194 True 3563 3563 95.996 1 2192 1 chr3A.!!$R1 2191
8 TraesCS7B01G091400 chr3A 695635760 695637955 2195 False 3520 3520 95.630 1 2192 1 chr3A.!!$F1 2191
9 TraesCS7B01G091400 chr5D 503257221 503259416 2195 True 3559 3559 95.949 1 2192 1 chr5D.!!$R1 2191

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
215 216 1.133025 CCGTTCCATGCCTCATTTCAC 59.867 52.381 0.0 0.0 0.0 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1811 1817 3.482156 TTGCCAAATAAGCCAGCAAAA 57.518 38.095 0.0 0.0 40.26 2.44 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
59 60 5.818678 ACCTATGACCAGTCAGTTAACAA 57.181 39.130 8.61 0.0 43.61 2.83
75 76 1.255667 ACAACCGACCGCTCTACCAT 61.256 55.000 0.00 0.0 0.00 3.55
91 92 5.023452 TCTACCATTGAGCTACTGAGGAAA 58.977 41.667 0.00 0.0 0.00 3.13
92 93 4.213564 ACCATTGAGCTACTGAGGAAAG 57.786 45.455 0.00 0.0 0.00 2.62
98 99 1.362932 AGCTACTGAGGAAAGAGGGGA 59.637 52.381 0.00 0.0 0.00 4.81
185 186 8.857694 TCTTTCGTAACTCCCATAATTTCTTT 57.142 30.769 0.00 0.0 0.00 2.52
215 216 1.133025 CCGTTCCATGCCTCATTTCAC 59.867 52.381 0.00 0.0 0.00 3.18
498 500 1.956297 AATTTGGTCGTTGTGGTCGA 58.044 45.000 0.00 0.0 34.91 4.20
600 602 1.954382 AGATATTCGCGACTACTGGCA 59.046 47.619 9.15 0.0 0.00 4.92
614 616 5.765510 ACTACTGGCAATTTCATTATGGGA 58.234 37.500 0.00 0.0 0.00 4.37
634 636 5.072736 TGGGACAGCTCATGATCTTCATATT 59.927 40.000 0.00 0.0 34.28 1.28
652 654 8.496534 TTCATATTGATCTATTCTCCACCTCA 57.503 34.615 0.00 0.0 0.00 3.86
686 688 9.449719 TTCTTTCTTAGCTAAATAGGTGAAAGG 57.550 33.333 26.80 16.7 40.46 3.11
729 731 4.795970 ATATCATGGACTCGAAAAACGC 57.204 40.909 0.00 0.0 42.26 4.84
734 736 3.306917 TGGACTCGAAAAACGCATCTA 57.693 42.857 0.00 0.0 42.26 1.98
811 813 3.372822 GGTGGAATAGCGATTTTCGAACA 59.627 43.478 0.00 0.0 43.74 3.18
940 942 6.404184 CGCGGAATGATAGTGAATAGAGAGAT 60.404 42.308 0.00 0.0 0.00 2.75
1022 1024 6.687604 TCATGTCTTTCAATTCTCGTACTCA 58.312 36.000 0.00 0.0 0.00 3.41
1077 1079 8.763356 TCATTTTGCAATGAAAACAACAGATAC 58.237 29.630 0.00 0.0 44.89 2.24
1164 1166 5.103728 TGGCCCACCATTGATTAGAAGATTA 60.104 40.000 0.00 0.0 42.67 1.75
1166 1168 6.323739 GGCCCACCATTGATTAGAAGATTAAA 59.676 38.462 0.00 0.0 35.26 1.52
1701 1707 6.840780 AATAGGGGTTCTGTTGAATTTCAG 57.159 37.500 0.00 0.0 34.40 3.02
1728 1734 9.309516 GTATTCAGTTTCACCAATAAGATACGA 57.690 33.333 0.00 0.0 0.00 3.43
1811 1817 2.610833 GACTTTTGGGAAAACGTCGACT 59.389 45.455 14.70 0.0 0.00 4.18
1882 1888 3.880047 TCGGTCAGTTGAATATTCGGT 57.120 42.857 10.80 0.0 0.00 4.69
1883 1889 4.196626 TCGGTCAGTTGAATATTCGGTT 57.803 40.909 10.80 0.0 0.00 4.44
1894 1900 8.303876 AGTTGAATATTCGGTTGCAGTAATTTT 58.696 29.630 10.80 0.0 0.00 1.82
1974 1981 7.235935 AGATTTTTCATTTTGATGAGCCTCA 57.764 32.000 0.00 0.0 31.46 3.86
2107 2114 1.477553 ACACCCATCAATGCATGGTC 58.522 50.000 0.00 0.0 41.84 4.02
2153 2160 8.493607 TCTTGATGGTGAGGATGTTATTGATTA 58.506 33.333 0.00 0.0 0.00 1.75
2188 2195 5.957771 AGGCTATTTACACAGAGGAATGA 57.042 39.130 0.00 0.0 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
59 60 0.968901 TCAATGGTAGAGCGGTCGGT 60.969 55.000 9.28 0.00 0.00 4.69
75 76 2.834549 CCCTCTTTCCTCAGTAGCTCAA 59.165 50.000 0.00 0.00 0.00 3.02
91 92 0.105913 GGAGGTCGAATCTCCCCTCT 60.106 60.000 19.83 0.00 43.71 3.69
92 93 2.432119 GGAGGTCGAATCTCCCCTC 58.568 63.158 19.83 14.66 43.71 4.30
98 99 5.246429 AGTTGAACTTTAGGAGGTCGAATCT 59.754 40.000 0.00 0.00 45.55 2.40
113 114 1.048601 TGAGAGCGGGAGTTGAACTT 58.951 50.000 0.00 0.00 0.00 2.66
185 186 0.249120 CATGGAACGGAGCCACTACA 59.751 55.000 0.00 0.00 38.44 2.74
215 216 4.102113 CCACTTTGGGCTTCCCTG 57.898 61.111 3.27 0.00 45.70 4.45
419 421 8.857694 AGAAAAGATTTGAAAATCATGGCATT 57.142 26.923 16.06 0.64 45.59 3.56
448 450 7.932335 TCCTCATCGAGAAAAATAGACTACTC 58.068 38.462 0.00 0.00 0.00 2.59
600 602 6.131264 TCATGAGCTGTCCCATAATGAAATT 58.869 36.000 0.00 0.00 41.28 1.82
614 616 7.681679 AGATCAATATGAAGATCATGAGCTGT 58.318 34.615 15.42 6.63 42.36 4.40
634 636 6.857848 AGATACTGAGGTGGAGAATAGATCA 58.142 40.000 0.00 0.00 0.00 2.92
643 645 7.595819 AGAAAGAATAGATACTGAGGTGGAG 57.404 40.000 0.00 0.00 0.00 3.86
676 678 6.011981 ACCAAATTGGATAGACCTTTCACCTA 60.012 38.462 20.25 0.00 40.96 3.08
729 731 7.022979 TCGTGCATTTCAGTCAAATTTAGATG 58.977 34.615 0.00 0.00 31.79 2.90
734 736 6.017400 AGATCGTGCATTTCAGTCAAATTT 57.983 33.333 0.00 0.00 31.79 1.82
811 813 9.942526 ATGGAAACCATTCTCTTATAGGAAATT 57.057 29.630 0.00 0.00 42.23 1.82
894 896 5.051173 CGCGTCTTCGACTTCTATTAGTCTA 60.051 44.000 0.00 0.00 41.89 2.59
896 898 3.961240 CGCGTCTTCGACTTCTATTAGTC 59.039 47.826 0.00 0.00 40.90 2.59
978 980 8.777865 ACATGAAAATTCTCAATTCTCTACGA 57.222 30.769 0.00 0.00 0.00 3.43
1022 1024 6.887002 GTCTCCTTCCAGAACTTTCCAATTAT 59.113 38.462 0.00 0.00 0.00 1.28
1073 1075 6.721571 TTCGAAATTGTCCAGAGTTGTATC 57.278 37.500 0.00 0.00 0.00 2.24
1077 1079 6.000891 TGATTTCGAAATTGTCCAGAGTTG 57.999 37.500 23.49 0.00 0.00 3.16
1164 1166 7.391148 AACCAATAGCGATTCATACAAGTTT 57.609 32.000 0.00 0.00 0.00 2.66
1166 1168 6.597672 TCAAACCAATAGCGATTCATACAAGT 59.402 34.615 0.00 0.00 0.00 3.16
1680 1686 4.105697 ACCTGAAATTCAACAGAACCCCTA 59.894 41.667 0.00 0.00 36.38 3.53
1701 1707 8.548721 CGTATCTTATTGGTGAAACTGAATACC 58.451 37.037 0.00 0.00 36.74 2.73
1728 1734 5.796424 ATTCCAAATGTGAAGCAAGTCTT 57.204 34.783 0.00 0.00 37.83 3.01
1811 1817 3.482156 TTGCCAAATAAGCCAGCAAAA 57.518 38.095 0.00 0.00 40.26 2.44
1974 1981 8.242729 GGATTATTCCATGAATTCCTCAAAGT 57.757 34.615 2.27 0.00 42.12 2.66
2153 2160 8.444783 TGTGTAAATAGCCTAATATGGGTTCAT 58.555 33.333 0.00 0.00 38.86 2.57


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

AutoCloner maintained by Alex Coulton.