Multiple sequence alignment - TraesCS4A01G323900

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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 TraesCS4A01G323900 chr4A 100.000 2786 0 0 1 2786 611655148 611657933 0 5145
1 TraesCS4A01G323900 chr4A 98.744 2787 34 1 1 2786 739023759 739020973 0 4951
2 TraesCS4A01G323900 chr4A 99.468 940 5 0 1 940 611663428 611664367 0 1709
3 TraesCS4A01G323900 chr4A 98.935 939 10 0 1 939 739015479 739014541 0 1679
4 TraesCS4A01G323900 chr1B 98.852 2787 31 1 1 2786 610379322 610382108 0 4968
5 TraesCS4A01G323900 chr6A 98.816 2787 31 2 1 2786 570352997 570355782 0 4963
6 TraesCS4A01G323900 chr6A 97.260 2810 47 4 1 2786 584410214 584413017 0 4735
7 TraesCS4A01G323900 chr6A 98.722 939 12 0 1 939 584418508 584419446 0 1668
8 TraesCS4A01G323900 chr7B 97.757 2809 39 2 1 2786 535642002 535644809 0 4817
9 TraesCS4A01G323900 chr2B 98.694 2297 29 1 491 2786 626032645 626034941 0 4074
10 TraesCS4A01G323900 chr2B 99.043 940 8 1 1 940 626040435 626041373 0 1685
11 TraesCS4A01G323900 chr6B 91.791 2826 146 29 1 2786 47737738 47734959 0 3855
12 TraesCS4A01G323900 chr6B 91.720 2826 148 28 1 2786 47698648 47695869 0 3843
13 TraesCS4A01G323900 chr6B 91.578 2826 150 29 1 2786 47658685 47655908 0 3819


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 TraesCS4A01G323900 chr4A 611655148 611657933 2785 False 5145 5145 100.000 1 2786 1 chr4A.!!$F1 2785
1 TraesCS4A01G323900 chr4A 739020973 739023759 2786 True 4951 4951 98.744 1 2786 1 chr4A.!!$R2 2785
2 TraesCS4A01G323900 chr4A 611663428 611664367 939 False 1709 1709 99.468 1 940 1 chr4A.!!$F2 939
3 TraesCS4A01G323900 chr4A 739014541 739015479 938 True 1679 1679 98.935 1 939 1 chr4A.!!$R1 938
4 TraesCS4A01G323900 chr1B 610379322 610382108 2786 False 4968 4968 98.852 1 2786 1 chr1B.!!$F1 2785
5 TraesCS4A01G323900 chr6A 570352997 570355782 2785 False 4963 4963 98.816 1 2786 1 chr6A.!!$F1 2785
6 TraesCS4A01G323900 chr6A 584410214 584413017 2803 False 4735 4735 97.260 1 2786 1 chr6A.!!$F2 2785
7 TraesCS4A01G323900 chr6A 584418508 584419446 938 False 1668 1668 98.722 1 939 1 chr6A.!!$F3 938
8 TraesCS4A01G323900 chr7B 535642002 535644809 2807 False 4817 4817 97.757 1 2786 1 chr7B.!!$F1 2785
9 TraesCS4A01G323900 chr2B 626032645 626034941 2296 False 4074 4074 98.694 491 2786 1 chr2B.!!$F1 2295
10 TraesCS4A01G323900 chr2B 626040435 626041373 938 False 1685 1685 99.043 1 940 1 chr2B.!!$F2 939
11 TraesCS4A01G323900 chr6B 47734959 47737738 2779 True 3855 3855 91.791 1 2786 1 chr6B.!!$R3 2785
12 TraesCS4A01G323900 chr6B 47695869 47698648 2779 True 3843 3843 91.720 1 2786 1 chr6B.!!$R2 2785
13 TraesCS4A01G323900 chr6B 47655908 47658685 2777 True 3819 3819 91.578 1 2786 1 chr6B.!!$R1 2785

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
919 920 3.370978 CGGCGACTGTCACATTTATTTCT 59.629 43.478 0.0 0.0 0.0 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1836 1864 1.66783 CGACACCTCACGCCATGTT 60.668 57.895 0.0 0.0 0.0 2.71 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
340 341 4.485834 CGGCGTCGTGATTCCCGA 62.486 66.667 0.00 0.0 41.34 5.14
919 920 3.370978 CGGCGACTGTCACATTTATTTCT 59.629 43.478 0.00 0.0 0.00 2.52
970 994 4.159120 GCATCAGAGCCTCGTTTAAAAAC 58.841 43.478 0.00 0.0 35.59 2.43
1063 1089 3.406498 AGGAGATAACCCTGGCCTAGTAT 59.594 47.826 3.32 0.0 31.66 2.12
1099 1125 3.497942 GGTTGGTTTGAGTATGGTGAGGT 60.498 47.826 0.00 0.0 0.00 3.85
1525 1553 2.323599 CAGCATCAGGTGGAGGATCTA 58.676 52.381 0.00 0.0 39.53 1.98
1623 1651 2.492449 TTTCTGGAGCGCCTCACTCG 62.492 60.000 8.34 0.0 34.87 4.18
1836 1864 1.899142 GGTTTTGGGGCTGCAAGATAA 59.101 47.619 0.50 0.0 34.07 1.75
1853 1881 1.803334 TAAACATGGCGTGAGGTGTC 58.197 50.000 14.82 0.0 0.00 3.67
1910 1943 5.070580 GGAGCCTCTAGTTATGGTGTTATGT 59.929 44.000 0.00 0.0 0.00 2.29
1911 1944 6.408206 GGAGCCTCTAGTTATGGTGTTATGTT 60.408 42.308 0.00 0.0 0.00 2.71
1912 1945 6.349300 AGCCTCTAGTTATGGTGTTATGTTG 58.651 40.000 0.00 0.0 0.00 3.33
1913 1946 6.070194 AGCCTCTAGTTATGGTGTTATGTTGT 60.070 38.462 0.00 0.0 0.00 3.32
1914 1947 6.037172 GCCTCTAGTTATGGTGTTATGTTGTG 59.963 42.308 0.00 0.0 0.00 3.33
1959 1997 3.515502 CTCTGTGTTGGGATGGTCTAAGA 59.484 47.826 0.00 0.0 0.00 2.10
1989 2027 0.721718 GTTGCCGTGTAGCTCATGTC 59.278 55.000 0.00 0.0 0.00 3.06
2686 2745 4.129380 CGTCAAATGGATATTCTGGAGCA 58.871 43.478 0.00 0.0 0.00 4.26
2743 2802 4.408596 TGGGGAATTTCAAAAACTCAAGCT 59.591 37.500 0.00 0.0 0.00 3.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1063 1089 2.616524 ACCAACCAGCACTACTTCCTA 58.383 47.619 0.00 0.0 0.00 2.94
1099 1125 9.559732 TTACTATGCAACCTATTCTAGTACGTA 57.440 33.333 0.00 0.0 0.00 3.57
1623 1651 1.523095 GAATGCGACGATAGAACCTGC 59.477 52.381 0.00 0.0 41.38 4.85
1836 1864 1.667830 CGACACCTCACGCCATGTT 60.668 57.895 0.00 0.0 0.00 2.71
1910 1943 5.616270 TCAGTCCTTACATTACAAGCACAA 58.384 37.500 0.00 0.0 0.00 3.33
1911 1944 5.221641 ACTCAGTCCTTACATTACAAGCACA 60.222 40.000 0.00 0.0 0.00 4.57
1912 1945 5.238583 ACTCAGTCCTTACATTACAAGCAC 58.761 41.667 0.00 0.0 0.00 4.40
1913 1946 5.483685 ACTCAGTCCTTACATTACAAGCA 57.516 39.130 0.00 0.0 0.00 3.91
1914 1947 6.166982 AGAACTCAGTCCTTACATTACAAGC 58.833 40.000 0.00 0.0 0.00 4.01
2686 2745 4.634443 GGTGGCTATCATTCTTTACAACGT 59.366 41.667 0.00 0.0 0.00 3.99
2743 2802 2.040442 TCCCGGAGAATGAGGGCA 59.960 61.111 0.73 0.0 44.70 5.36


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

AutoCloner maintained by Alex Coulton.