Multiple sequence alignment - TraesCS2D01G349000

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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 TraesCS2D01G349000 chr2D 100.000 3060 0 0 1 3060 446728916 446725857 0.000000e+00 5651
1 TraesCS2D01G349000 chr2D 98.008 3062 41 10 1 3060 446698249 446695206 0.000000e+00 5299
2 TraesCS2D01G349000 chr2D 81.850 1135 143 28 874 1960 446653392 446652273 0.000000e+00 896
3 TraesCS2D01G349000 chr2D 83.019 1007 104 38 1253 2216 446932198 446933180 0.000000e+00 850
4 TraesCS2D01G349000 chr2D 83.871 806 118 12 1 804 8475615 8476410 0.000000e+00 758
5 TraesCS2D01G349000 chr2D 85.668 307 26 6 838 1128 446931892 446932196 1.070000e-79 307
6 TraesCS2D01G349000 chr2A 93.279 1979 76 20 846 2787 590966481 590964523 0.000000e+00 2865
7 TraesCS2D01G349000 chr2A 81.245 1141 145 32 874 1957 590817997 590816869 0.000000e+00 857
8 TraesCS2D01G349000 chr2A 82.196 1011 106 40 1255 2216 590974796 590973811 0.000000e+00 802
9 TraesCS2D01G349000 chr2A 87.829 304 20 4 842 1128 590975103 590974800 1.050000e-89 340
10 TraesCS2D01G349000 chr2B 91.762 1396 71 17 842 2196 526734616 526733224 0.000000e+00 1901
11 TraesCS2D01G349000 chr2B 81.338 1136 153 27 874 1960 526671141 526670016 0.000000e+00 869
12 TraesCS2D01G349000 chr2B 83.045 808 119 17 1 804 11219913 11220706 0.000000e+00 717
13 TraesCS2D01G349000 chr4A 84.920 809 109 8 4 802 548303295 548302490 0.000000e+00 806
14 TraesCS2D01G349000 chr4A 80.649 801 141 11 7 804 24498886 24498097 2.610000e-170 608
15 TraesCS2D01G349000 chr3D 84.218 754 104 7 1 751 155554678 155553937 0.000000e+00 719
16 TraesCS2D01G349000 chr3D 82.861 811 122 10 1 804 495217424 495218224 0.000000e+00 712
17 TraesCS2D01G349000 chr1B 81.727 799 135 8 2 796 499657584 499656793 0.000000e+00 656
18 TraesCS2D01G349000 chr3B 81.615 805 129 11 4 804 675412844 675412055 0.000000e+00 649
19 TraesCS2D01G349000 chr7D 82.579 729 103 12 53 772 634886221 634886934 3.350000e-174 621
20 TraesCS2D01G349000 chr4D 74.074 405 67 19 2594 2987 381145655 381146032 6.880000e-27 132


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 TraesCS2D01G349000 chr2D 446725857 446728916 3059 True 5651.0 5651 100.0000 1 3060 1 chr2D.!!$R3 3059
1 TraesCS2D01G349000 chr2D 446695206 446698249 3043 True 5299.0 5299 98.0080 1 3060 1 chr2D.!!$R2 3059
2 TraesCS2D01G349000 chr2D 446652273 446653392 1119 True 896.0 896 81.8500 874 1960 1 chr2D.!!$R1 1086
3 TraesCS2D01G349000 chr2D 8475615 8476410 795 False 758.0 758 83.8710 1 804 1 chr2D.!!$F1 803
4 TraesCS2D01G349000 chr2D 446931892 446933180 1288 False 578.5 850 84.3435 838 2216 2 chr2D.!!$F2 1378
5 TraesCS2D01G349000 chr2A 590964523 590966481 1958 True 2865.0 2865 93.2790 846 2787 1 chr2A.!!$R2 1941
6 TraesCS2D01G349000 chr2A 590816869 590817997 1128 True 857.0 857 81.2450 874 1957 1 chr2A.!!$R1 1083
7 TraesCS2D01G349000 chr2A 590973811 590975103 1292 True 571.0 802 85.0125 842 2216 2 chr2A.!!$R3 1374
8 TraesCS2D01G349000 chr2B 526733224 526734616 1392 True 1901.0 1901 91.7620 842 2196 1 chr2B.!!$R2 1354
9 TraesCS2D01G349000 chr2B 526670016 526671141 1125 True 869.0 869 81.3380 874 1960 1 chr2B.!!$R1 1086
10 TraesCS2D01G349000 chr2B 11219913 11220706 793 False 717.0 717 83.0450 1 804 1 chr2B.!!$F1 803
11 TraesCS2D01G349000 chr4A 548302490 548303295 805 True 806.0 806 84.9200 4 802 1 chr4A.!!$R2 798
12 TraesCS2D01G349000 chr4A 24498097 24498886 789 True 608.0 608 80.6490 7 804 1 chr4A.!!$R1 797
13 TraesCS2D01G349000 chr3D 155553937 155554678 741 True 719.0 719 84.2180 1 751 1 chr3D.!!$R1 750
14 TraesCS2D01G349000 chr3D 495217424 495218224 800 False 712.0 712 82.8610 1 804 1 chr3D.!!$F1 803
15 TraesCS2D01G349000 chr1B 499656793 499657584 791 True 656.0 656 81.7270 2 796 1 chr1B.!!$R1 794
16 TraesCS2D01G349000 chr3B 675412055 675412844 789 True 649.0 649 81.6150 4 804 1 chr3B.!!$R1 800
17 TraesCS2D01G349000 chr7D 634886221 634886934 713 False 621.0 621 82.5790 53 772 1 chr7D.!!$F1 719

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
168 174 0.104855 GCCATGACTCCATAGCGTCA 59.895 55.0 0.00 0.00 43.51 4.35 F
839 878 0.110644 GTTTGCGCGGCTATAGATGC 60.111 55.0 8.83 5.26 0.00 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1983 2233 1.821332 GGAGCATCGCCAGAAAGGG 60.821 63.158 0.0 0.0 38.09 3.95 R
2784 3062 2.422479 GCCCGAGTGAAGTTTATTTCCC 59.578 50.000 0.0 0.0 0.00 3.97 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
168 174 0.104855 GCCATGACTCCATAGCGTCA 59.895 55.000 0.00 0.00 43.51 4.35
246 253 1.214305 CCCTCCCCTTTCCCATCACA 61.214 60.000 0.00 0.00 0.00 3.58
524 563 2.992114 ACTGCGAGGACGGCTTCT 60.992 61.111 0.00 0.00 40.15 2.85
545 584 1.153549 GACGAGCAGAATCCGGCTT 60.154 57.895 0.00 0.00 43.75 4.35
636 675 3.065786 CAGACGTGAATGAATTCCCCATG 59.934 47.826 2.27 6.29 35.97 3.66
672 711 6.924612 TCAAATTTTGATAATCCGATGGCATG 59.075 34.615 3.81 0.00 34.08 4.06
701 740 6.551601 AGTTAGAAGTGATGGAGTAATCGGAT 59.448 38.462 0.00 0.00 0.00 4.18
801 840 0.988832 TTATTTGAGGGGTGCTCGGT 59.011 50.000 0.00 0.00 0.00 4.69
802 841 0.539986 TATTTGAGGGGTGCTCGGTC 59.460 55.000 0.00 0.00 0.00 4.79
839 878 0.110644 GTTTGCGCGGCTATAGATGC 60.111 55.000 8.83 5.26 0.00 3.91
1298 1399 1.227031 ACCGACGCGTTCTTTGACA 60.227 52.632 15.53 0.00 0.00 3.58
1935 2080 3.782443 GGCGTCGACCCAGGGAAT 61.782 66.667 14.54 0.00 0.00 3.01
1983 2233 1.573156 GAATTGATCGACGCGCAAAAC 59.427 47.619 5.73 0.00 0.00 2.43
2571 2847 5.598416 TTGGAGGTGTGTATGATGTAGAG 57.402 43.478 0.00 0.00 0.00 2.43
2664 2940 0.543277 CATAGAGGCCCAAGCTCACA 59.457 55.000 0.00 0.00 39.73 3.58
2690 2966 5.122707 TGTATGGCCCAAGATAATGTCAA 57.877 39.130 0.00 0.00 0.00 3.18
2770 3048 0.468226 ACAAAGCAACCCTCACTCGA 59.532 50.000 0.00 0.00 0.00 4.04
2771 3049 1.134220 ACAAAGCAACCCTCACTCGAA 60.134 47.619 0.00 0.00 0.00 3.71
2772 3050 2.154462 CAAAGCAACCCTCACTCGAAT 58.846 47.619 0.00 0.00 0.00 3.34
2773 3051 3.244422 ACAAAGCAACCCTCACTCGAATA 60.244 43.478 0.00 0.00 0.00 1.75
2774 3052 3.695830 AAGCAACCCTCACTCGAATAA 57.304 42.857 0.00 0.00 0.00 1.40
2775 3053 3.695830 AGCAACCCTCACTCGAATAAA 57.304 42.857 0.00 0.00 0.00 1.40
2776 3054 3.335579 AGCAACCCTCACTCGAATAAAC 58.664 45.455 0.00 0.00 0.00 2.01
2777 3055 3.008049 AGCAACCCTCACTCGAATAAACT 59.992 43.478 0.00 0.00 0.00 2.66
2778 3056 3.751698 GCAACCCTCACTCGAATAAACTT 59.248 43.478 0.00 0.00 0.00 2.66
2779 3057 4.142881 GCAACCCTCACTCGAATAAACTTC 60.143 45.833 0.00 0.00 0.00 3.01
2780 3058 4.884668 ACCCTCACTCGAATAAACTTCA 57.115 40.909 0.00 0.00 0.00 3.02
2781 3059 4.566987 ACCCTCACTCGAATAAACTTCAC 58.433 43.478 0.00 0.00 0.00 3.18
2782 3060 4.283722 ACCCTCACTCGAATAAACTTCACT 59.716 41.667 0.00 0.00 0.00 3.41
2783 3061 4.865365 CCCTCACTCGAATAAACTTCACTC 59.135 45.833 0.00 0.00 0.00 3.51
2784 3062 4.559251 CCTCACTCGAATAAACTTCACTCG 59.441 45.833 0.00 0.00 0.00 4.18
2785 3063 4.482386 TCACTCGAATAAACTTCACTCGG 58.518 43.478 0.00 0.00 0.00 4.63
2786 3064 3.612860 CACTCGAATAAACTTCACTCGGG 59.387 47.826 0.00 0.00 36.10 5.14
2787 3065 3.508793 ACTCGAATAAACTTCACTCGGGA 59.491 43.478 0.00 0.00 34.16 5.14
2935 3213 4.141287 GGGCAGGCATTATTACACACATA 58.859 43.478 0.00 0.00 0.00 2.29
2997 3275 0.117541 TAAGGCTACCCCTGGTGACA 59.882 55.000 0.00 0.00 45.62 3.58
3003 3281 1.207329 CTACCCCTGGTGACAAGCTAC 59.793 57.143 0.00 0.00 42.06 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
246 253 2.203640 TCACAGTCTGCCCGACCT 60.204 61.111 0.00 0.00 43.91 3.85
287 294 2.840640 TATCCTCTCTTTCCCACGGA 57.159 50.000 0.00 0.00 0.00 4.69
545 584 1.068402 TCGAAAACGCAGTACGGATCA 60.068 47.619 0.00 0.00 45.00 2.92
610 649 1.401905 GAATTCATTCACGTCTGCCCC 59.598 52.381 0.00 0.00 36.80 5.80
660 699 5.290493 TCTAACTAAACATGCCATCGGAT 57.710 39.130 0.00 0.00 0.00 4.18
672 711 9.021863 CGATTACTCCATCACTTCTAACTAAAC 57.978 37.037 0.00 0.00 0.00 2.01
701 740 4.311606 ACTACGTTAATGCACACACATCA 58.688 39.130 0.00 0.00 0.00 3.07
772 811 7.712537 AGCACCCCTCAAATAATATAATCCAT 58.287 34.615 0.00 0.00 0.00 3.41
801 840 1.827315 CGTCCGCAAACGCTCTTTGA 61.827 55.000 7.68 0.00 38.22 2.69
802 841 1.438710 CGTCCGCAAACGCTCTTTG 60.439 57.895 0.00 0.48 38.22 2.77
839 878 4.156739 GGGGTCATGTTTCAAAGCTTAGAG 59.843 45.833 0.00 0.00 0.00 2.43
1935 2080 2.257207 AGCACCTAGCAAGTGAGGTTA 58.743 47.619 5.11 0.00 43.87 2.85
1983 2233 1.821332 GGAGCATCGCCAGAAAGGG 60.821 63.158 0.00 0.00 38.09 3.95
2571 2847 2.901249 TCCACAACCTTCGCTATAAGC 58.099 47.619 0.00 0.00 38.02 3.09
2664 2940 4.354987 ACATTATCTTGGGCCATACAGGAT 59.645 41.667 7.26 7.71 41.22 3.24
2770 3048 8.631480 AGTTTATTTCCCGAGTGAAGTTTATT 57.369 30.769 0.00 0.00 0.00 1.40
2771 3049 8.631480 AAGTTTATTTCCCGAGTGAAGTTTAT 57.369 30.769 0.00 0.00 0.00 1.40
2772 3050 7.716123 TGAAGTTTATTTCCCGAGTGAAGTTTA 59.284 33.333 0.00 0.00 0.00 2.01
2773 3051 6.544564 TGAAGTTTATTTCCCGAGTGAAGTTT 59.455 34.615 0.00 0.00 0.00 2.66
2774 3052 6.017357 GTGAAGTTTATTTCCCGAGTGAAGTT 60.017 38.462 0.00 0.00 0.00 2.66
2775 3053 5.469084 GTGAAGTTTATTTCCCGAGTGAAGT 59.531 40.000 0.00 0.00 0.00 3.01
2776 3054 5.701290 AGTGAAGTTTATTTCCCGAGTGAAG 59.299 40.000 0.00 0.00 0.00 3.02
2777 3055 5.617252 AGTGAAGTTTATTTCCCGAGTGAA 58.383 37.500 0.00 0.00 0.00 3.18
2778 3056 5.223449 AGTGAAGTTTATTTCCCGAGTGA 57.777 39.130 0.00 0.00 0.00 3.41
2779 3057 4.091509 CGAGTGAAGTTTATTTCCCGAGTG 59.908 45.833 0.00 0.00 0.00 3.51
2780 3058 4.243270 CGAGTGAAGTTTATTTCCCGAGT 58.757 43.478 0.00 0.00 0.00 4.18
2781 3059 3.617263 CCGAGTGAAGTTTATTTCCCGAG 59.383 47.826 0.00 0.00 0.00 4.63
2782 3060 3.592059 CCGAGTGAAGTTTATTTCCCGA 58.408 45.455 0.00 0.00 0.00 5.14
2783 3061 2.676342 CCCGAGTGAAGTTTATTTCCCG 59.324 50.000 0.00 0.00 0.00 5.14
2784 3062 2.422479 GCCCGAGTGAAGTTTATTTCCC 59.578 50.000 0.00 0.00 0.00 3.97
2785 3063 2.422479 GGCCCGAGTGAAGTTTATTTCC 59.578 50.000 0.00 0.00 0.00 3.13
2786 3064 3.078837 TGGCCCGAGTGAAGTTTATTTC 58.921 45.455 0.00 0.00 0.00 2.17
2787 3065 3.149005 TGGCCCGAGTGAAGTTTATTT 57.851 42.857 0.00 0.00 0.00 1.40
2935 3213 5.885912 CCTGGGTTGTTGTTAGCTACATTAT 59.114 40.000 0.00 0.00 36.44 1.28


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

AutoCloner maintained by Alex Coulton.