Multiple sequence alignment - TraesCS1B01G276600

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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 TraesCS1B01G276600 chr1B 100.000 3079 0 0 968 4046 484354272 484357350 0 5686
1 TraesCS1B01G276600 chr1B 100.000 787 0 0 1 787 484353305 484354091 0 1454
2 TraesCS1B01G276600 chr1B 94.790 787 40 1 1 787 418404986 418405771 0 1225
3 TraesCS1B01G276600 chr1A 98.701 3079 40 0 968 4046 71702592 71705670 0 5465
4 TraesCS1B01G276600 chr1A 97.662 3079 72 0 968 4046 48215085 48212007 0 5288
5 TraesCS1B01G276600 chr1A 98.475 787 11 1 1 787 71701889 71702674 0 1386
6 TraesCS1B01G276600 chr1A 96.696 787 26 0 1 787 48215789 48215003 0 1310
7 TraesCS1B01G276600 chr3A 98.409 3080 47 2 968 4046 351150479 351147401 0 5415
8 TraesCS1B01G276600 chr3A 97.713 787 17 1 1 787 351151182 351150397 0 1352
9 TraesCS1B01G276600 chr4A 97.986 3079 62 0 968 4046 488746886 488743808 0 5343
10 TraesCS1B01G276600 chr4A 96.696 787 23 1 1 787 488747587 488746804 0 1306
11 TraesCS1B01G276600 chr3B 96.623 3080 101 3 968 4046 752649589 752652666 0 5108
12 TraesCS1B01G276600 chr3B 95.910 3081 123 3 968 4046 70001186 69998107 0 4988
13 TraesCS1B01G276600 chr3B 95.044 787 38 1 1 787 752648886 752649671 0 1236
14 TraesCS1B01G276600 chr3B 94.663 787 42 0 1 787 70001890 70001104 0 1221
15 TraesCS1B01G276600 chr6A 96.005 3079 123 0 968 4046 497012190 497015268 0 5005
16 TraesCS1B01G276600 chr2B 95.973 3079 116 3 968 4046 673600035 673603105 0 4992
17 TraesCS1B01G276600 chr2B 94.790 787 41 0 1 787 673599331 673600117 0 1227
18 TraesCS1B01G276600 chr7A 95.810 3079 126 1 968 4046 473657845 473654770 0 4968
19 TraesCS1B01G276600 chr5A 97.205 787 22 0 1 787 555163657 555164443 0 1332


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 TraesCS1B01G276600 chr1B 484353305 484357350 4045 False 3570.0 5686 100.0000 1 4046 2 chr1B.!!$F2 4045
1 TraesCS1B01G276600 chr1B 418404986 418405771 785 False 1225.0 1225 94.7900 1 787 1 chr1B.!!$F1 786
2 TraesCS1B01G276600 chr1A 71701889 71705670 3781 False 3425.5 5465 98.5880 1 4046 2 chr1A.!!$F1 4045
3 TraesCS1B01G276600 chr1A 48212007 48215789 3782 True 3299.0 5288 97.1790 1 4046 2 chr1A.!!$R1 4045
4 TraesCS1B01G276600 chr3A 351147401 351151182 3781 True 3383.5 5415 98.0610 1 4046 2 chr3A.!!$R1 4045
5 TraesCS1B01G276600 chr4A 488743808 488747587 3779 True 3324.5 5343 97.3410 1 4046 2 chr4A.!!$R1 4045
6 TraesCS1B01G276600 chr3B 752648886 752652666 3780 False 3172.0 5108 95.8335 1 4046 2 chr3B.!!$F1 4045
7 TraesCS1B01G276600 chr3B 69998107 70001890 3783 True 3104.5 4988 95.2865 1 4046 2 chr3B.!!$R1 4045
8 TraesCS1B01G276600 chr6A 497012190 497015268 3078 False 5005.0 5005 96.0050 968 4046 1 chr6A.!!$F1 3078
9 TraesCS1B01G276600 chr2B 673599331 673603105 3774 False 3109.5 4992 95.3815 1 4046 2 chr2B.!!$F1 4045
10 TraesCS1B01G276600 chr7A 473654770 473657845 3075 True 4968.0 4968 95.8100 968 4046 1 chr7A.!!$R1 3078
11 TraesCS1B01G276600 chr5A 555163657 555164443 786 False 1332.0 1332 97.2050 1 787 1 chr5A.!!$F1 786

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
727 732 0.458543 CTTCGTGCTCATACGCCACT 60.459 55.0 0.0 0.0 43.4 4.00 F
728 733 0.735978 TTCGTGCTCATACGCCACTG 60.736 55.0 0.0 0.0 43.4 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2167 2172 0.684535 TTGTCAAGGTCAGATGGCGA 59.315 50.000 0.0 0.0 0.00 5.54 R
3235 3250 3.969117 GCATTAGATGATGCGGTTTCA 57.031 42.857 0.0 0.0 42.51 2.69 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
721 726 4.857251 CCCCCTTCGTGCTCATAC 57.143 61.111 0.00 0.00 0.00 2.39
722 727 1.227263 CCCCCTTCGTGCTCATACG 60.227 63.158 0.00 0.00 44.98 3.06
723 728 1.883084 CCCCTTCGTGCTCATACGC 60.883 63.158 0.00 0.00 43.40 4.42
724 729 1.883084 CCCTTCGTGCTCATACGCC 60.883 63.158 0.00 0.00 43.40 5.68
725 730 1.153647 CCTTCGTGCTCATACGCCA 60.154 57.895 0.00 0.00 43.40 5.69
726 731 1.421410 CCTTCGTGCTCATACGCCAC 61.421 60.000 0.00 0.00 43.40 5.01
727 732 0.458543 CTTCGTGCTCATACGCCACT 60.459 55.000 0.00 0.00 43.40 4.00
728 733 0.735978 TTCGTGCTCATACGCCACTG 60.736 55.000 0.00 0.00 43.40 3.66
729 734 2.802667 CGTGCTCATACGCCACTGC 61.803 63.158 0.00 0.00 37.24 4.40
759 764 3.998672 GTCCCGCCGGAGTGACAA 61.999 66.667 15.45 0.00 39.51 3.18
760 765 3.691342 TCCCGCCGGAGTGACAAG 61.691 66.667 5.05 0.00 32.86 3.16
765 770 4.410400 CCGGAGTGACAAGCCCCC 62.410 72.222 0.00 0.00 0.00 5.40
779 784 2.687200 CCCCCATGTCTCCACCGA 60.687 66.667 0.00 0.00 0.00 4.69
780 785 2.072487 CCCCCATGTCTCCACCGAT 61.072 63.158 0.00 0.00 0.00 4.18
781 786 1.447643 CCCCATGTCTCCACCGATC 59.552 63.158 0.00 0.00 0.00 3.69
782 787 1.447643 CCCATGTCTCCACCGATCC 59.552 63.158 0.00 0.00 0.00 3.36
783 788 1.447643 CCATGTCTCCACCGATCCC 59.552 63.158 0.00 0.00 0.00 3.85
784 789 1.068083 CATGTCTCCACCGATCCCG 59.932 63.158 0.00 0.00 0.00 5.14
1643 1648 1.906824 TTCGTGCCCCTCTCGTCTT 60.907 57.895 0.00 0.00 33.77 3.01
1777 1782 1.212229 GACCAGTTCTCGGTCGTCC 59.788 63.158 0.00 0.00 43.36 4.79
1961 1966 2.359169 ACGTGGATCGCCTCATGGT 61.359 57.895 0.00 0.00 44.19 3.55
2131 2136 3.907260 CTTGAGGCAGAAGCGGGCA 62.907 63.158 0.00 0.00 43.41 5.36
2344 2355 2.266055 CTCAGGAACGGGAGGTGC 59.734 66.667 0.00 0.00 38.67 5.01
2915 2929 1.546460 AAGGTAACCCCATGCCCCT 60.546 57.895 0.00 0.00 34.66 4.79
3040 3055 2.672874 CTCATTCGTGCGAAGGAAATCA 59.327 45.455 19.44 1.25 42.97 2.57
3043 3058 2.150424 CGTGCGAAGGAAATCACGT 58.850 52.632 5.58 0.00 44.84 4.49
3721 3736 0.599204 GGAGCGGACAAGAACAACGA 60.599 55.000 0.00 0.00 0.00 3.85
3830 3845 0.954452 CCTGGACCAACAAACAGCTC 59.046 55.000 0.00 0.00 0.00 4.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
331 332 0.258774 AGTCACTTTGGCCCAACACT 59.741 50.000 0.00 0.00 0.00 3.55
704 709 1.227263 CGTATGAGCACGAAGGGGG 60.227 63.158 0.00 0.00 44.69 5.40
705 710 1.883084 GCGTATGAGCACGAAGGGG 60.883 63.158 0.00 0.00 44.69 4.79
706 711 1.883084 GGCGTATGAGCACGAAGGG 60.883 63.158 0.00 0.00 44.69 3.95
707 712 1.153647 TGGCGTATGAGCACGAAGG 60.154 57.895 0.00 0.00 44.69 3.46
708 713 0.458543 AGTGGCGTATGAGCACGAAG 60.459 55.000 0.00 0.00 44.69 3.79
709 714 0.735978 CAGTGGCGTATGAGCACGAA 60.736 55.000 0.00 0.00 44.69 3.85
710 715 1.153842 CAGTGGCGTATGAGCACGA 60.154 57.895 0.00 0.00 44.69 4.35
711 716 2.802667 GCAGTGGCGTATGAGCACG 61.803 63.158 0.00 0.00 44.71 5.34
712 717 3.093278 GCAGTGGCGTATGAGCAC 58.907 61.111 0.00 0.00 39.27 4.40
742 747 3.934391 CTTGTCACTCCGGCGGGAC 62.934 68.421 27.98 20.08 37.43 4.46
743 748 3.691342 CTTGTCACTCCGGCGGGA 61.691 66.667 27.98 13.13 41.08 5.14
748 753 4.410400 GGGGGCTTGTCACTCCGG 62.410 72.222 0.00 0.00 0.00 5.14
762 767 2.044806 GATCGGTGGAGACATGGGGG 62.045 65.000 0.00 0.00 46.14 5.40
763 768 1.447643 GATCGGTGGAGACATGGGG 59.552 63.158 0.00 0.00 46.14 4.96
764 769 1.447643 GGATCGGTGGAGACATGGG 59.552 63.158 0.00 0.00 46.14 4.00
765 770 1.447643 GGGATCGGTGGAGACATGG 59.552 63.158 0.00 0.00 46.14 3.66
766 771 1.068083 CGGGATCGGTGGAGACATG 59.932 63.158 0.00 0.00 46.14 3.21
767 772 3.538614 CGGGATCGGTGGAGACAT 58.461 61.111 0.00 0.00 46.14 3.06
1643 1648 1.778334 CGAAATGATCGCCGTATCCA 58.222 50.000 0.00 0.00 45.89 3.41
1777 1782 1.751927 GCATGGCCTTGTCTGGGAG 60.752 63.158 19.05 0.00 0.00 4.30
1961 1966 2.418609 CGTCCAATCATCACAGTGGCTA 60.419 50.000 0.00 0.00 0.00 3.93
2131 2136 2.919856 AGCCGTGTCCTGCTGAGT 60.920 61.111 0.00 0.00 36.23 3.41
2167 2172 0.684535 TTGTCAAGGTCAGATGGCGA 59.315 50.000 0.00 0.00 0.00 5.54
3235 3250 3.969117 GCATTAGATGATGCGGTTTCA 57.031 42.857 0.00 0.00 42.51 2.69
3721 3736 6.068670 GCCACCCTTGACCAGTTAATAATAT 58.931 40.000 0.00 0.00 0.00 1.28
3893 3908 0.523519 CTGCGTGTAGAGAGCACAGA 59.476 55.000 0.00 0.00 36.71 3.41


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

AutoCloner maintained by Alex Coulton.