Multiple sequence alignment - TraesCS4A01G104900

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 TraesCS4A01G104900 chr4A 100.000 3245 0 0 1 3245 118959665 118956421 0 5993
1 TraesCS4A01G104900 chr4B 94.553 2717 97 13 556 3245 427742220 427744912 0 4150
2 TraesCS4A01G104900 chr4D 94.440 2716 97 12 556 3245 346748210 346750897 0 4130
3 TraesCS4A01G104900 chr4D 94.224 554 29 3 1 554 483168493 483169043 0 843
4 TraesCS4A01G104900 chr4D 93.885 556 33 1 1 556 55272598 55272044 0 837
5 TraesCS4A01G104900 chr5B 94.614 557 29 1 1 556 711254013 711254569 0 861
6 TraesCS4A01G104900 chr2A 94.775 555 25 2 1 555 469224861 469225411 0 861
7 TraesCS4A01G104900 chr3B 94.054 555 32 1 1 555 312167941 312168494 0 841
8 TraesCS4A01G104900 chr3D 93.874 555 33 1 1 555 165731852 165731299 0 835
9 TraesCS4A01G104900 chr1D 93.705 556 34 1 1 556 269355610 269356164 0 832
10 TraesCS4A01G104900 chr7D 93.369 558 36 1 1 557 533431413 533430856 0 824
11 TraesCS4A01G104900 chr2B 93.502 554 35 1 3 556 728231002 728230450 0 822


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 TraesCS4A01G104900 chr4A 118956421 118959665 3244 True 5993 5993 100.000 1 3245 1 chr4A.!!$R1 3244
1 TraesCS4A01G104900 chr4B 427742220 427744912 2692 False 4150 4150 94.553 556 3245 1 chr4B.!!$F1 2689
2 TraesCS4A01G104900 chr4D 346748210 346750897 2687 False 4130 4130 94.440 556 3245 1 chr4D.!!$F1 2689
3 TraesCS4A01G104900 chr4D 483168493 483169043 550 False 843 843 94.224 1 554 1 chr4D.!!$F2 553
4 TraesCS4A01G104900 chr4D 55272044 55272598 554 True 837 837 93.885 1 556 1 chr4D.!!$R1 555
5 TraesCS4A01G104900 chr5B 711254013 711254569 556 False 861 861 94.614 1 556 1 chr5B.!!$F1 555
6 TraesCS4A01G104900 chr2A 469224861 469225411 550 False 861 861 94.775 1 555 1 chr2A.!!$F1 554
7 TraesCS4A01G104900 chr3B 312167941 312168494 553 False 841 841 94.054 1 555 1 chr3B.!!$F1 554
8 TraesCS4A01G104900 chr3D 165731299 165731852 553 True 835 835 93.874 1 555 1 chr3D.!!$R1 554
9 TraesCS4A01G104900 chr1D 269355610 269356164 554 False 832 832 93.705 1 556 1 chr1D.!!$F1 555
10 TraesCS4A01G104900 chr7D 533430856 533431413 557 True 824 824 93.369 1 557 1 chr7D.!!$R1 556
11 TraesCS4A01G104900 chr2B 728230450 728231002 552 True 822 822 93.502 3 556 1 chr2B.!!$R1 553

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
41 42 0.539986 GGACCGCATCTTAGGTGGAA 59.460 55.000 0.00 0.00 41.51 3.53 F
509 510 1.836802 TAAAGTGGCTGCATGCATCA 58.163 45.000 22.97 19.21 45.15 3.07 F
1701 1719 1.336887 GCTGCTCAGGTAGAAACGTCA 60.337 52.381 0.00 0.00 0.00 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1701 1719 0.856641 CGTTGATCACCGTGTCGTTT 59.143 50.000 4.24 0.0 0.0 3.60 R
1765 1783 2.047465 CGTCTCTGCCTGCTGCTT 60.047 61.111 0.00 0.0 42.0 3.91 R
2685 2723 2.431997 TGCTATGAGGGGGAATGGATT 58.568 47.619 0.00 0.0 0.0 3.01 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
41 42 0.539986 GGACCGCATCTTAGGTGGAA 59.460 55.000 0.00 0.00 41.51 3.53
66 67 5.368145 GGTGCTTCATCCTACACATTGATA 58.632 41.667 0.00 0.00 34.69 2.15
107 108 3.869272 GCAGTGCAGATTCGGCGG 61.869 66.667 11.09 0.00 0.00 6.13
228 229 2.356535 GCTCTGAAGATGGATTGGTGGT 60.357 50.000 0.00 0.00 0.00 4.16
453 454 4.951715 TGGACGATGGCTTTAGTCTTACTA 59.048 41.667 0.00 0.00 34.34 1.82
509 510 1.836802 TAAAGTGGCTGCATGCATCA 58.163 45.000 22.97 19.21 45.15 3.07
550 551 4.527944 GGGTCCTCCTCCATTTCTAAAAG 58.472 47.826 0.00 0.00 0.00 2.27
611 612 3.469008 AGGGTCGAATTATGATCGCAA 57.531 42.857 0.00 0.00 40.04 4.85
791 800 5.030874 AGCACTAAACACACGCTTAATTC 57.969 39.130 0.00 0.00 0.00 2.17
1024 1042 4.760047 CCTCACCGCCAAGGACCG 62.760 72.222 0.00 0.00 45.00 4.79
1629 1647 4.457496 CCAGTGTGCCGAGCCGAT 62.457 66.667 0.00 0.00 0.00 4.18
1701 1719 1.336887 GCTGCTCAGGTAGAAACGTCA 60.337 52.381 0.00 0.00 0.00 4.35
1754 1772 2.507484 TCCAGCACCAGTTGAAGATTG 58.493 47.619 0.00 0.00 0.00 2.67
1765 1783 2.577449 TGAAGATTGCGCGTCTGATA 57.423 45.000 14.80 3.50 0.00 2.15
1848 1866 0.183971 TGAGGAGGGAGATCGAGGAC 59.816 60.000 0.00 0.00 0.00 3.85
2271 2293 8.253113 AGCCAAGGAAATACATTTAGTTGATTG 58.747 33.333 8.85 0.00 30.12 2.67
2307 2329 4.225942 AGCATTGAAAGTAGTGGAGATCCA 59.774 41.667 0.00 0.00 45.30 3.41
2332 2354 4.013050 TGTTGTTCTGTTGAATGTGACCA 58.987 39.130 0.00 0.00 34.40 4.02
2448 2474 2.768253 ATTGTGAATCAGTCTCGCCA 57.232 45.000 0.00 0.00 0.00 5.69
2470 2496 2.064762 CCTAGCTACTTCATGCATCGC 58.935 52.381 0.00 0.00 0.00 4.58
2471 2497 1.718178 CTAGCTACTTCATGCATCGCG 59.282 52.381 0.00 0.00 0.00 5.87
2572 2598 2.749076 TCCATCTTGGAAATCAGCAACG 59.251 45.455 0.00 0.00 45.00 4.10
2627 2653 1.954382 CCACAAGCCATGAGATGATGG 59.046 52.381 0.00 0.00 45.20 3.51
2685 2723 6.544928 TGACTTGCTCTAGTCCATGAATAA 57.455 37.500 8.54 0.00 43.11 1.40
2799 2838 2.878406 ACGGTGGAGACAGAAAACAATG 59.122 45.455 0.00 0.00 44.46 2.82
2851 2890 6.882072 GTGACTCTGAAATAACTTGTCACAG 58.118 40.000 15.51 0.00 46.68 3.66
3038 3077 6.127758 GCGGAACCATAAATATCATATGCCAA 60.128 38.462 0.00 0.00 30.91 4.52
3055 3094 3.565482 TGCCAACTTCACAGAAGATCAAC 59.435 43.478 13.23 0.66 0.00 3.18
3091 3130 8.587952 AATGGTTTTAATTGAAGTAACAGCAC 57.412 30.769 5.72 0.00 0.00 4.40
3130 3169 6.431234 GGTTATGACCTCAACATCTTGACTTT 59.569 38.462 0.00 0.00 42.99 2.66
3219 3258 7.769220 TCTTATAACTACACAAGCACCTAGTC 58.231 38.462 0.00 0.00 0.00 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 1.066143 CACCTAAGATGCGGTCCACTT 60.066 52.381 0.00 0.00 0.00 3.16
41 42 0.973632 TGTGTAGGATGAAGCACCGT 59.026 50.000 0.00 0.00 0.00 4.83
66 67 3.574445 CCGTCGAGATCCGTCGCT 61.574 66.667 14.16 0.00 45.60 4.93
107 108 2.969238 CCATCCTCGCACATCGGC 60.969 66.667 0.00 0.00 39.05 5.54
243 244 3.480133 GCCTGCCGGGTATGAGGT 61.480 66.667 2.18 0.00 37.43 3.85
431 432 4.388378 AGTAAGACTAAAGCCATCGTCC 57.612 45.455 0.00 0.00 0.00 4.79
436 437 9.765795 GTCATACAATAGTAAGACTAAAGCCAT 57.234 33.333 4.35 0.00 42.62 4.40
487 488 2.658373 TGCATGCAGCCACTTTATTG 57.342 45.000 18.46 0.00 44.83 1.90
509 510 2.815945 CCGGCCTCTGCATCTGGAT 61.816 63.158 0.00 0.00 40.13 3.41
550 551 4.827284 TCTGACCATGGAGAAAGGTTTTTC 59.173 41.667 21.47 0.70 42.44 2.29
611 612 4.017591 TGTGGGGTTTATGGATCATCACTT 60.018 41.667 0.00 0.00 0.00 3.16
773 782 4.435121 GGACCGAATTAAGCGTGTGTTTAG 60.435 45.833 0.00 0.00 0.00 1.85
791 800 4.006989 TGACATTGTTAATTCAGGGACCG 58.993 43.478 0.00 0.00 0.00 4.79
1020 1038 2.404789 CGGTGAATGCATGCGGTC 59.595 61.111 14.09 13.06 0.00 4.79
1024 1042 2.202650 GTGGCGGTGAATGCATGC 60.203 61.111 11.82 11.82 0.00 4.06
1518 1536 2.282958 AGCTTCTCCCCGTCGTCA 60.283 61.111 0.00 0.00 0.00 4.35
1701 1719 0.856641 CGTTGATCACCGTGTCGTTT 59.143 50.000 4.24 0.00 0.00 3.60
1754 1772 2.087095 CTGCTGCTTATCAGACGCGC 62.087 60.000 5.73 0.00 45.72 6.86
1765 1783 2.047465 CGTCTCTGCCTGCTGCTT 60.047 61.111 0.00 0.00 42.00 3.91
2044 2062 4.683334 GGCGGCGTGAGTTTGCAC 62.683 66.667 9.37 0.00 35.46 4.57
2241 2263 7.961326 ACTAAATGTATTTCCTTGGCTTCAT 57.039 32.000 0.00 0.00 0.00 2.57
2271 2293 6.729187 ACTTTCAATGCTACAGAAAGACAAC 58.271 36.000 17.85 0.00 46.88 3.32
2307 2329 5.393027 GGTCACATTCAACAGAACAACACTT 60.393 40.000 0.00 0.00 0.00 3.16
2377 2399 7.225011 ACTTATGTACAGAGAGTCGGATATCA 58.775 38.462 14.09 0.00 0.00 2.15
2378 2400 7.675962 ACTTATGTACAGAGAGTCGGATATC 57.324 40.000 14.09 0.00 0.00 1.63
2448 2474 3.616076 GCGATGCATGAAGTAGCTAGGAT 60.616 47.826 2.46 0.00 0.00 3.24
2470 2496 3.489785 GGTAATCGTTAGCTTGGTGATCG 59.510 47.826 0.00 0.00 0.00 3.69
2471 2497 4.508124 CAGGTAATCGTTAGCTTGGTGATC 59.492 45.833 0.00 0.00 41.68 2.92
2570 2596 2.534019 CGCTGAATATTGGCGCCGT 61.534 57.895 23.90 15.96 42.28 5.68
2627 2653 3.791245 TCCAAAAACAACACTTCCATGC 58.209 40.909 0.00 0.00 0.00 4.06
2685 2723 2.431997 TGCTATGAGGGGGAATGGATT 58.568 47.619 0.00 0.00 0.00 3.01
2851 2890 2.605366 GCTTCGTTGACTAAGATCTGCC 59.395 50.000 0.00 0.00 0.00 4.85
2989 3028 8.671921 CGCAGCTATTAGATTCATTTATCCAAT 58.328 33.333 0.00 0.00 0.00 3.16
3074 3113 9.724839 GTTAAAACTGTGCTGTTACTTCAATTA 57.275 29.630 0.00 0.00 0.00 1.40
3088 3127 7.095816 GGTCATAACCAATTGTTAAAACTGTGC 60.096 37.037 4.43 0.00 45.68 4.57
3159 3198 4.070716 CAGTGCATTTTGGTCTTCTCTCT 58.929 43.478 0.00 0.00 0.00 3.10


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

AutoCloner maintained by Alex Coulton.