Multiple sequence alignment - TraesCS3A01G265300

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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 TraesCS3A01G265300 chr3A 100.000 2786 0 0 1 2786 489640583 489643368 0 5145
1 TraesCS3A01G265300 chr7A 96.413 2788 98 2 1 2786 300976630 300979417 0 4593
2 TraesCS3A01G265300 chr7A 96.266 2785 103 1 3 2786 78788797 78791581 0 4566
3 TraesCS3A01G265300 chr7A 96.234 2788 103 2 1 2786 305127574 305124787 0 4566
4 TraesCS3A01G265300 chr7A 96.198 2788 104 2 1 2786 300948381 300951168 0 4560
5 TraesCS3A01G265300 chr6A 96.409 2785 98 2 3 2786 467288497 467285714 0 4588
6 TraesCS3A01G265300 chr2B 96.373 2785 99 2 3 2786 45492833 45490050 0 4582
7 TraesCS3A01G265300 chr2A 96.270 2788 101 3 1 2786 261645822 261648608 0 4569
8 TraesCS3A01G265300 chr2A 96.263 2783 102 2 3 2783 531964758 531967540 0 4562
9 TraesCS3A01G265300 chr1A 96.230 2785 103 2 3 2786 165561705 165564488 0 4560


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 TraesCS3A01G265300 chr3A 489640583 489643368 2785 False 5145 5145 100.000 1 2786 1 chr3A.!!$F1 2785
1 TraesCS3A01G265300 chr7A 300976630 300979417 2787 False 4593 4593 96.413 1 2786 1 chr7A.!!$F3 2785
2 TraesCS3A01G265300 chr7A 78788797 78791581 2784 False 4566 4566 96.266 3 2786 1 chr7A.!!$F1 2783
3 TraesCS3A01G265300 chr7A 305124787 305127574 2787 True 4566 4566 96.234 1 2786 1 chr7A.!!$R1 2785
4 TraesCS3A01G265300 chr7A 300948381 300951168 2787 False 4560 4560 96.198 1 2786 1 chr7A.!!$F2 2785
5 TraesCS3A01G265300 chr6A 467285714 467288497 2783 True 4588 4588 96.409 3 2786 1 chr6A.!!$R1 2783
6 TraesCS3A01G265300 chr2B 45490050 45492833 2783 True 4582 4582 96.373 3 2786 1 chr2B.!!$R1 2783
7 TraesCS3A01G265300 chr2A 261645822 261648608 2786 False 4569 4569 96.270 1 2786 1 chr2A.!!$F1 2785
8 TraesCS3A01G265300 chr2A 531964758 531967540 2782 False 4562 4562 96.263 3 2783 1 chr2A.!!$F2 2780
9 TraesCS3A01G265300 chr1A 165561705 165564488 2783 False 4560 4560 96.230 3 2786 1 chr1A.!!$F1 2783

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
149 150 0.460109 CACGATGGCGATCCTGTCAA 60.460 55.0 2.84 0.0 41.64 3.18 F
314 315 0.905357 ATCTTGTCGGGTCCAGAAGG 59.095 55.0 0.00 0.0 0.00 3.46 F
1348 1352 0.527565 GACCATGGCAGTTTTCGCAT 59.472 50.0 13.04 0.0 0.00 4.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1102 1106 0.031716 TACTCCCTCAGCTCCTGCAT 60.032 55.0 0.00 0.0 42.74 3.96 R
1672 1676 0.035820 CCTACAGTAAGCCCGGCAAA 60.036 55.0 13.15 0.0 0.00 3.68 R
2732 2737 1.607801 CTCCTGCTGACACGATGGGA 61.608 60.0 0.00 0.0 0.00 4.37 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
71 72 2.750814 CAGGGGACAAGGGCATTAAAT 58.249 47.619 0.00 0.00 0.00 1.40
149 150 0.460109 CACGATGGCGATCCTGTCAA 60.460 55.000 2.84 0.00 41.64 3.18
309 310 1.066430 GCTGTTATCTTGTCGGGTCCA 60.066 52.381 0.00 0.00 0.00 4.02
314 315 0.905357 ATCTTGTCGGGTCCAGAAGG 59.095 55.000 0.00 0.00 0.00 3.46
340 341 2.838225 CACCGGGCCTCGAGGTAT 60.838 66.667 31.43 10.88 42.43 2.73
343 344 2.565645 CCGGGCCTCGAGGTATCTG 61.566 68.421 31.43 23.40 42.43 2.90
346 347 2.737830 GCCTCGAGGTATCTGGGC 59.262 66.667 31.43 12.80 37.57 5.36
354 355 1.840635 GAGGTATCTGGGCTGGTCTTT 59.159 52.381 0.00 0.00 0.00 2.52
482 483 2.674220 GGGGCCTTGTCTCCTGAGG 61.674 68.421 0.84 0.00 0.00 3.86
514 515 2.108075 TGTTCTTGAATGGCTCCAAGGA 59.892 45.455 11.84 3.58 39.98 3.36
889 891 1.952367 GCTGGTTGCTGCTACTCCATT 60.952 52.381 13.54 0.00 38.95 3.16
906 908 2.295909 CCATTTTCAAGAACCTTCGCCA 59.704 45.455 0.00 0.00 0.00 5.69
974 978 2.359107 CACCAGCATCACCACGCT 60.359 61.111 0.00 0.00 39.66 5.07
1027 1031 1.605753 GAAAGCCGACAAGGGAAAGT 58.394 50.000 0.00 0.00 41.48 2.66
1095 1099 1.338136 GGGCGATCTTCTCCCCTCAA 61.338 60.000 0.00 0.00 35.37 3.02
1102 1106 1.535444 TTCTCCCCTCAACTCGGCA 60.535 57.895 0.00 0.00 0.00 5.69
1143 1147 1.344065 TCTACCTCTTTTGGGCGACA 58.656 50.000 0.00 0.00 0.00 4.35
1146 1150 0.693049 ACCTCTTTTGGGCGACAGAT 59.307 50.000 0.00 0.00 0.00 2.90
1245 1249 2.483889 GCTATTCTTCTACTGCGGGCTT 60.484 50.000 0.00 0.00 0.00 4.35
1348 1352 0.527565 GACCATGGCAGTTTTCGCAT 59.472 50.000 13.04 0.00 0.00 4.73
1439 1443 1.304879 AGAGAGGAGAGCCGCTTGT 60.305 57.895 0.00 0.00 45.01 3.16
1672 1676 0.261991 TAGGATCCTTCGCCTCAGGT 59.738 55.000 22.03 0.00 35.73 4.00
1683 1687 2.282462 CTCAGGTTTGCCGGGCTT 60.282 61.111 21.46 0.00 40.50 4.35
1700 1704 1.404391 GCTTACTGTAGGCGCTGTAGA 59.596 52.381 7.64 0.00 0.00 2.59
1788 1793 2.021068 CTCGGCGGACATCATGAGGT 62.021 60.000 13.77 13.77 0.00 3.85
1951 1956 1.501741 GCGCCATGATGTCGTTGTT 59.498 52.632 0.00 0.00 0.00 2.83
2079 2084 2.764547 TCACCCGTGACACCACCA 60.765 61.111 0.00 0.00 40.12 4.17
2213 2218 3.918220 GAGCGCGCGGAGTTCATG 61.918 66.667 33.06 0.00 0.00 3.07
2647 2652 9.890629 TGTTTATATCTTGTATCTGACTTGCTT 57.109 29.630 0.00 0.00 0.00 3.91
2718 2723 3.061848 CCAAGGCCGCGGTGATTT 61.062 61.111 28.70 13.04 0.00 2.17
2760 2765 2.930019 CAGCAGGAGGTGGGTCCA 60.930 66.667 0.00 0.00 39.34 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 2.830321 AGGTAGGGTACACTGTACAAGC 59.170 50.000 18.91 13.13 0.00 4.01
30 31 1.063717 CCGTCAGGGTTAGGTAGGGTA 60.064 57.143 0.00 0.00 0.00 3.69
143 144 0.110056 GTGGCATGCGAAGTTGACAG 60.110 55.000 12.44 0.00 31.88 3.51
220 221 2.903547 GCGCATCCACCAACGTGTT 61.904 57.895 0.30 0.00 38.41 3.32
309 310 1.006102 CGGTGAGCGACAACCTTCT 60.006 57.895 0.00 0.00 31.55 2.85
340 341 2.592993 CCGGAAAGACCAGCCCAGA 61.593 63.158 0.00 0.00 38.90 3.86
343 344 3.860930 TTGCCGGAAAGACCAGCCC 62.861 63.158 5.05 0.00 41.07 5.19
346 347 1.301677 GAGCTTGCCGGAAAGACCAG 61.302 60.000 27.40 0.00 38.90 4.00
354 355 2.665000 CAAGAGGAGCTTGCCGGA 59.335 61.111 5.05 0.00 46.67 5.14
462 463 1.463214 TCAGGAGACAAGGCCCCAA 60.463 57.895 0.00 0.00 0.00 4.12
463 464 1.920325 CTCAGGAGACAAGGCCCCA 60.920 63.158 0.00 0.00 0.00 4.96
482 483 9.129209 GAGCCATTCAAGAACAAAGTATTTAAC 57.871 33.333 0.00 0.00 35.03 2.01
514 515 1.614317 CGCCAAGATCCTCCAAGGTTT 60.614 52.381 0.00 0.00 36.53 3.27
673 674 3.636231 CCCGTGCCCTGTCTTGGA 61.636 66.667 0.00 0.00 0.00 3.53
713 715 1.068741 GGTGGATACGGAGCGAGATTT 59.931 52.381 0.00 0.00 42.51 2.17
889 891 2.218603 GAGTGGCGAAGGTTCTTGAAA 58.781 47.619 0.00 0.00 0.00 2.69
906 908 2.606751 TTCGAGAAGAAGAGGGGAGT 57.393 50.000 0.00 0.00 34.26 3.85
974 978 1.906824 GTGGTGAGGGAGGTCGACA 60.907 63.158 18.91 0.00 0.00 4.35
1027 1031 4.717629 CTCGGCCGACTTCACGCA 62.718 66.667 27.28 0.00 0.00 5.24
1095 1099 3.397439 AGCTCCTGCATGCCGAGT 61.397 61.111 24.75 13.82 42.74 4.18
1102 1106 0.031716 TACTCCCTCAGCTCCTGCAT 60.032 55.000 0.00 0.00 42.74 3.96
1348 1352 4.035324 TCCGACAAAGTTTTCGCACAAATA 59.965 37.500 12.02 0.00 33.78 1.40
1439 1443 3.452621 ATCCAGGCGATCCCTCCGA 62.453 63.158 0.13 0.86 44.09 4.55
1469 1473 1.002087 CCAAGTACGCCTCCTTCTTGT 59.998 52.381 0.00 0.00 35.26 3.16
1573 1577 1.745087 CACTATTGGAGTTTGGCGCAT 59.255 47.619 10.83 0.00 35.64 4.73
1672 1676 0.035820 CCTACAGTAAGCCCGGCAAA 60.036 55.000 13.15 0.00 0.00 3.68
1683 1687 1.012086 CGTCTACAGCGCCTACAGTA 58.988 55.000 2.29 0.00 0.00 2.74
1835 1840 2.479566 TGAACAACTCCAGGAGCATC 57.520 50.000 17.31 9.97 32.04 3.91
2057 2062 2.426023 GTGTCACGGGTGAGGCTT 59.574 61.111 0.94 0.00 40.75 4.35
2138 2143 1.101049 CAGTGAACCCAAACACGCCT 61.101 55.000 0.00 0.00 41.22 5.52
2535 2540 3.715854 CGGAAAGATCGAAGTCCGT 57.284 52.632 16.73 0.00 46.26 4.69
2647 2652 5.940617 TGAAAAGAAAGGAGTCCAGATTGA 58.059 37.500 12.86 0.00 0.00 2.57
2732 2737 1.607801 CTCCTGCTGACACGATGGGA 61.608 60.000 0.00 0.00 0.00 4.37
2760 2765 1.752833 GGTCCGTCAAGGTGGTCTT 59.247 57.895 0.00 0.00 41.99 3.01


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

AutoCloner maintained by Alex Coulton.