Multiple sequence alignment - TraesCS4D01G044300

Loading Multiple Alignment...

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 TraesCS4D01G044300 chr4D 100.000 2211 0 0 1 2211 19933451 19931241 0 4084
1 TraesCS4D01G044300 chr3B 97.614 2221 42 4 1 2211 101916062 101913843 0 3797
2 TraesCS4D01G044300 chr5D 97.564 2217 48 3 1 2211 503223102 503220886 0 3790
3 TraesCS4D01G044300 chr5D 97.112 2216 58 4 1 2211 6193822 6191608 0 3733
4 TraesCS4D01G044300 chrUn 97.562 2215 48 3 1 2211 216513723 216515935 0 3786
5 TraesCS4D01G044300 chrUn 97.562 2215 48 3 1 2211 286269660 286267448 0 3786
6 TraesCS4D01G044300 chr3D 97.517 2215 50 3 1 2211 589272074 589274287 0 3781
7 TraesCS4D01G044300 chr1D 97.201 2215 58 2 1 2211 254393230 254395444 0 3744
8 TraesCS4D01G044300 chr3A 97.154 2214 59 3 1 2211 672905130 672907342 0 3736
9 TraesCS4D01G044300 chr3A 97.019 2214 62 3 1 2211 594894745 594896957 0 3720


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 TraesCS4D01G044300 chr4D 19931241 19933451 2210 True 4084 4084 100.000 1 2211 1 chr4D.!!$R1 2210
1 TraesCS4D01G044300 chr3B 101913843 101916062 2219 True 3797 3797 97.614 1 2211 1 chr3B.!!$R1 2210
2 TraesCS4D01G044300 chr5D 503220886 503223102 2216 True 3790 3790 97.564 1 2211 1 chr5D.!!$R2 2210
3 TraesCS4D01G044300 chr5D 6191608 6193822 2214 True 3733 3733 97.112 1 2211 1 chr5D.!!$R1 2210
4 TraesCS4D01G044300 chrUn 216513723 216515935 2212 False 3786 3786 97.562 1 2211 1 chrUn.!!$F1 2210
5 TraesCS4D01G044300 chrUn 286267448 286269660 2212 True 3786 3786 97.562 1 2211 1 chrUn.!!$R1 2210
6 TraesCS4D01G044300 chr3D 589272074 589274287 2213 False 3781 3781 97.517 1 2211 1 chr3D.!!$F1 2210
7 TraesCS4D01G044300 chr1D 254393230 254395444 2214 False 3744 3744 97.201 1 2211 1 chr1D.!!$F1 2210
8 TraesCS4D01G044300 chr3A 672905130 672907342 2212 False 3736 3736 97.154 1 2211 1 chr3A.!!$F2 2210
9 TraesCS4D01G044300 chr3A 594894745 594896957 2212 False 3720 3720 97.019 1 2211 1 chr3A.!!$F1 2210

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
466 468 0.179142 GGACTCCTTACGAGCGTTCC 60.179 60.0 0.0 0.0 43.01 3.62 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1343 1345 1.338973 CGGGGAATGCTCATTGAATGG 59.661 52.381 5.2 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
36 37 7.776500 TCTCATCAAATGAATGGCATCTTCTTA 59.224 33.333 0.00 0.00 39.11 2.10
85 86 4.396357 TTTTGGGGAATCTCCTTGCTAA 57.604 40.909 0.00 0.00 36.57 3.09
421 423 0.478072 TTCTGGTGTGGATGGCAAGT 59.522 50.000 0.00 0.00 0.00 3.16
466 468 0.179142 GGACTCCTTACGAGCGTTCC 60.179 60.000 0.00 0.00 43.01 3.62
537 539 7.404481 ACGAAACCAAGAAATAACCCCTTATA 58.596 34.615 0.00 0.00 0.00 0.98
715 717 9.543231 TCTTAGTTCAAGATCCCTCTTACTAAA 57.457 33.333 9.97 3.12 39.62 1.85
757 759 7.860691 TAGATCTGTTCTGCCCAAAATGGGG 62.861 48.000 16.88 4.03 45.84 4.96
816 818 8.903570 AATCGACTCGATCATCAGATTATAAC 57.096 34.615 14.25 0.00 46.30 1.89
836 838 4.295141 ACTTCATTCCATACCGAACCAA 57.705 40.909 0.00 0.00 0.00 3.67
961 963 7.598759 TTAGGAATAGGTGTAATCAGACCTC 57.401 40.000 0.00 0.00 45.10 3.85
1015 1017 1.922447 ACCATATGCACCTCTTTGGGA 59.078 47.619 0.00 0.00 41.11 4.37
1095 1097 9.996554 ATCGATTTTGATACATATAAGGTGTCA 57.003 29.630 0.00 4.07 35.06 3.58
1151 1153 2.229302 GACTCAGGCCTATATGACCGAC 59.771 54.545 3.98 0.00 0.00 4.79
1368 1370 2.103094 TCAATGAGCATTCCCCGTAGAG 59.897 50.000 0.00 0.00 0.00 2.43
1388 1390 2.852449 AGGTATTCCTGAAATCTGGGCA 59.148 45.455 6.51 0.00 43.33 5.36
1614 1616 1.482593 CCCAACCTCTATTGCTCTCGT 59.517 52.381 0.00 0.00 0.00 4.18
1832 1844 6.772605 TGAAGAGATGAGAACCATGAAAAGA 58.227 36.000 0.00 0.00 35.17 2.52
1841 1853 5.644188 AGAACCATGAAAAGAAAGATCCCA 58.356 37.500 0.00 0.00 0.00 4.37
1932 1944 6.545666 TGTCATTCTTTGCTCCTTTTTCACTA 59.454 34.615 0.00 0.00 0.00 2.74
1954 1966 5.404466 AAATGATTCCTTCGAATTTGCCA 57.596 34.783 0.00 0.00 38.88 4.92
2057 2072 2.128771 AAGGGATTGGATTGGTGACG 57.871 50.000 0.00 0.00 0.00 4.35
2108 2123 4.244862 GTTCCAAAAACGGGTACTATCGA 58.755 43.478 9.86 0.00 0.00 3.59
2111 2126 5.490159 TCCAAAAACGGGTACTATCGAATT 58.510 37.500 9.86 0.00 0.00 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 6.266103 GGATTTCCATAAGAAGATGCCATTCA 59.734 38.462 0.00 0.00 35.40 2.57
85 86 5.689383 ACGTTTCATGCTTGTTTGAGTAT 57.311 34.783 0.00 0.00 0.00 2.12
235 236 8.564509 ACCAAATAATACAATGCAAGCAAAAT 57.435 26.923 0.00 0.00 0.00 1.82
395 397 4.411869 TGCCATCCACACCAGAATAGATAA 59.588 41.667 0.00 0.00 0.00 1.75
421 423 9.793259 CTATTGAAACCAAGAAATATAGGCCTA 57.207 33.333 16.60 16.60 0.00 3.93
537 539 6.380079 AGGGGATCTTCTATAATTTCGCAT 57.620 37.500 0.00 0.00 0.00 4.73
729 731 5.344743 TTTGGGCAGAACAGATCTACTAG 57.655 43.478 0.00 0.00 36.32 2.57
757 759 0.685097 TCATAACCCTAGCGCCCATC 59.315 55.000 2.29 0.00 0.00 3.51
816 818 4.142469 GGTTTGGTTCGGTATGGAATGAAG 60.142 45.833 0.00 0.00 0.00 3.02
836 838 6.112734 TCTCATAATAAGAATGTGCACGGTT 58.887 36.000 13.13 9.73 0.00 4.44
1095 1097 8.743085 ATAGCTTCGATTTGCATTATCCATAT 57.257 30.769 0.00 0.00 0.00 1.78
1098 1100 6.882610 AATAGCTTCGATTTGCATTATCCA 57.117 33.333 0.00 0.00 0.00 3.41
1151 1153 4.291783 GAGTCTTGGAGTATTTCGATCGG 58.708 47.826 16.41 0.00 0.00 4.18
1218 1220 7.307493 TGAAAGTGAATCGTATTCCATGAAG 57.693 36.000 0.00 0.00 0.00 3.02
1343 1345 1.338973 CGGGGAATGCTCATTGAATGG 59.661 52.381 5.20 0.00 0.00 3.16
1368 1370 3.297134 TGCCCAGATTTCAGGAATACC 57.703 47.619 0.00 0.00 0.00 2.73
1376 1378 2.417257 GCGCCATGCCCAGATTTCA 61.417 57.895 0.00 0.00 37.76 2.69
1388 1390 1.892474 GAAGATAGAGGAGAGCGCCAT 59.108 52.381 2.29 0.00 0.00 4.40
1631 1637 7.174946 GGAATTCATAGTCACTTTTTCCTGTCA 59.825 37.037 7.93 0.00 0.00 3.58
1810 1822 7.941238 TCTTTCTTTTCATGGTTCTCATCTCTT 59.059 33.333 0.00 0.00 32.92 2.85
1859 1871 3.045634 TCTTGTGGTTTCCTCTTCCTCA 58.954 45.455 0.00 0.00 0.00 3.86
1903 1915 7.769970 TGAAAAAGGAGCAAAGAATGACAAAAT 59.230 29.630 0.00 0.00 0.00 1.82
1932 1944 5.404466 TGGCAAATTCGAAGGAATCATTT 57.596 34.783 3.35 0.00 41.99 2.32
2057 2072 2.488153 GCCAAAGTCACTGAATGGGTAC 59.512 50.000 6.66 0.00 0.00 3.34
2108 2123 8.772250 TCTGTCTATTCTCTAATTCACCCAATT 58.228 33.333 0.00 0.00 38.35 2.32
2111 2126 6.325028 CCTCTGTCTATTCTCTAATTCACCCA 59.675 42.308 0.00 0.00 0.00 4.51


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

AutoCloner maintained by Alex Coulton.