Multiple sequence alignment - TraesCS7A01G543600

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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 TraesCS7A01G543600 chr7A 100.000 2852 0 0 1 2852 720405272 720402421 0.000000e+00 5267.0
1 TraesCS7A01G543600 chr7A 95.129 2710 76 18 106 2788 720449907 720447227 0.000000e+00 4222.0
2 TraesCS7A01G543600 chr7A 94.908 2710 82 18 106 2788 720389259 720386579 0.000000e+00 4189.0
3 TraesCS7A01G543600 chr7A 99.068 1932 14 2 924 2852 720475116 720473186 0.000000e+00 3465.0
4 TraesCS7A01G543600 chr7A 99.195 1491 9 1 1365 2852 720464047 720462557 0.000000e+00 2684.0
5 TraesCS7A01G543600 chr7A 98.132 1499 23 3 1357 2852 720489158 720487662 0.000000e+00 2608.0
6 TraesCS7A01G543600 chr7A 98.237 1361 23 1 1 1360 720490842 720489482 0.000000e+00 2379.0
7 TraesCS7A01G543600 chr7A 98.771 1302 7 4 78 1370 720465283 720463982 0.000000e+00 2307.0
8 TraesCS7A01G543600 chr7A 98.661 896 7 4 1 891 720475988 720475093 0.000000e+00 1583.0
9 TraesCS7A01G543600 chr7A 96.436 477 13 3 1 473 730800609 730800133 0.000000e+00 784.0
10 TraesCS7A01G543600 chr7A 96.067 178 7 0 2611 2788 586335456 586335633 1.000000e-74 291.0
11 TraesCS7A01G543600 chr7A 98.529 68 1 0 2785 2852 720207614 720207547 1.390000e-23 121.0
12 TraesCS7A01G543600 chr7A 98.529 68 1 0 2785 2852 720216171 720216104 1.390000e-23 121.0
13 TraesCS7A01G543600 chr7A 97.059 68 2 0 2785 2852 720291070 720291003 6.460000e-22 115.0
14 TraesCS7A01G543600 chr1A 94.845 2328 90 9 482 2785 42559060 42561381 0.000000e+00 3607.0
15 TraesCS7A01G543600 chr3A 93.934 2242 80 19 484 2698 36273604 36271392 0.000000e+00 3336.0
16 TraesCS7A01G543600 chr3A 87.500 56 4 2 1323 1378 36272705 36272653 8.530000e-06 62.1
17 TraesCS7A01G543600 chr2A 84.230 2137 204 49 658 2726 58178367 58180438 0.000000e+00 1956.0
18 TraesCS7A01G543600 chr5A 93.602 1266 52 12 1354 2619 626172966 626171730 0.000000e+00 1862.0
19 TraesCS7A01G543600 chr5A 92.622 881 30 6 487 1341 626174084 626173213 0.000000e+00 1234.0
20 TraesCS7A01G543600 chr5B 82.592 2114 253 80 589 2659 452661573 452663614 0.000000e+00 1759.0
21 TraesCS7A01G543600 chr4B 84.388 1659 145 56 622 2252 616612041 616613613 0.000000e+00 1524.0
22 TraesCS7A01G543600 chr3B 86.576 1326 132 22 1365 2658 135747425 135746114 0.000000e+00 1421.0
23 TraesCS7A01G543600 chr3B 89.957 468 43 4 7 473 502245859 502246323 4.070000e-168 601.0
24 TraesCS7A01G543600 chr3B 89.316 468 47 3 7 473 513252986 513253451 4.090000e-163 584.0
25 TraesCS7A01G543600 chrUn 99.828 582 1 0 1 582 445961958 445961377 0.000000e+00 1070.0
26 TraesCS7A01G543600 chr2D 84.263 896 118 17 486 1362 409597118 409596227 0.000000e+00 852.0
27 TraesCS7A01G543600 chr7D 91.729 133 10 1 8 139 548021800 548021932 1.750000e-42 183.0


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 TraesCS7A01G543600 chr7A 720402421 720405272 2851 True 5267.00 5267 100.0000 1 2852 1 chr7A.!!$R5 2851
1 TraesCS7A01G543600 chr7A 720447227 720449907 2680 True 4222.00 4222 95.1290 106 2788 1 chr7A.!!$R6 2682
2 TraesCS7A01G543600 chr7A 720386579 720389259 2680 True 4189.00 4189 94.9080 106 2788 1 chr7A.!!$R4 2682
3 TraesCS7A01G543600 chr7A 720473186 720475988 2802 True 2524.00 3465 98.8645 1 2852 2 chr7A.!!$R9 2851
4 TraesCS7A01G543600 chr7A 720462557 720465283 2726 True 2495.50 2684 98.9830 78 2852 2 chr7A.!!$R8 2774
5 TraesCS7A01G543600 chr7A 720487662 720490842 3180 True 2493.50 2608 98.1845 1 2852 2 chr7A.!!$R10 2851
6 TraesCS7A01G543600 chr1A 42559060 42561381 2321 False 3607.00 3607 94.8450 482 2785 1 chr1A.!!$F1 2303
7 TraesCS7A01G543600 chr3A 36271392 36273604 2212 True 1699.05 3336 90.7170 484 2698 2 chr3A.!!$R1 2214
8 TraesCS7A01G543600 chr2A 58178367 58180438 2071 False 1956.00 1956 84.2300 658 2726 1 chr2A.!!$F1 2068
9 TraesCS7A01G543600 chr5A 626171730 626174084 2354 True 1548.00 1862 93.1120 487 2619 2 chr5A.!!$R1 2132
10 TraesCS7A01G543600 chr5B 452661573 452663614 2041 False 1759.00 1759 82.5920 589 2659 1 chr5B.!!$F1 2070
11 TraesCS7A01G543600 chr4B 616612041 616613613 1572 False 1524.00 1524 84.3880 622 2252 1 chr4B.!!$F1 1630
12 TraesCS7A01G543600 chr3B 135746114 135747425 1311 True 1421.00 1421 86.5760 1365 2658 1 chr3B.!!$R1 1293
13 TraesCS7A01G543600 chrUn 445961377 445961958 581 True 1070.00 1070 99.8280 1 582 1 chrUn.!!$R1 581
14 TraesCS7A01G543600 chr2D 409596227 409597118 891 True 852.00 852 84.2630 486 1362 1 chr2D.!!$R1 876

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
900 1020 0.320946 CCACCGACGCCTTCCTTTAA 60.321 55.0 0.0 0.0 0.0 1.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2322 3172 7.201367 CGAAAATGTTTGTACCGAACACTTTTT 60.201 33.333 15.25 15.55 37.32 1.94 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
758 822 2.620112 GGGGACGAGACGACACGAA 61.620 63.158 11.70 0.00 34.51 3.85
897 1017 4.016706 CCCACCGACGCCTTCCTT 62.017 66.667 0.00 0.00 0.00 3.36
898 1018 2.032071 CCACCGACGCCTTCCTTT 59.968 61.111 0.00 0.00 0.00 3.11
899 1019 1.294138 CCACCGACGCCTTCCTTTA 59.706 57.895 0.00 0.00 0.00 1.85
900 1020 0.320946 CCACCGACGCCTTCCTTTAA 60.321 55.000 0.00 0.00 0.00 1.52
901 1021 1.515081 CACCGACGCCTTCCTTTAAA 58.485 50.000 0.00 0.00 0.00 1.52
902 1022 1.874872 CACCGACGCCTTCCTTTAAAA 59.125 47.619 0.00 0.00 0.00 1.52
903 1023 1.875514 ACCGACGCCTTCCTTTAAAAC 59.124 47.619 0.00 0.00 0.00 2.43
904 1024 1.136169 CCGACGCCTTCCTTTAAAACG 60.136 52.381 0.00 0.00 0.00 3.60
905 1025 1.723701 CGACGCCTTCCTTTAAAACGC 60.724 52.381 0.00 0.00 0.00 4.84
906 1026 0.594602 ACGCCTTCCTTTAAAACGCC 59.405 50.000 0.00 0.00 0.00 5.68
907 1027 0.453782 CGCCTTCCTTTAAAACGCCG 60.454 55.000 0.00 0.00 0.00 6.46
908 1028 0.731514 GCCTTCCTTTAAAACGCCGC 60.732 55.000 0.00 0.00 0.00 6.53
909 1029 0.879090 CCTTCCTTTAAAACGCCGCT 59.121 50.000 0.00 0.00 0.00 5.52
910 1030 1.135774 CCTTCCTTTAAAACGCCGCTC 60.136 52.381 0.00 0.00 0.00 5.03
911 1031 0.513820 TTCCTTTAAAACGCCGCTCG 59.486 50.000 0.00 0.00 45.38 5.03
2322 3172 6.096987 TGGGCATGTTTGTAAGTTACAGAAAA 59.903 34.615 15.06 5.33 40.24 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
638 665 1.188573 CTTTGGTCGTCGTTGTACGTG 59.811 52.381 0.00 0.00 43.14 4.49
880 1000 2.175035 TAAAGGAAGGCGTCGGTGGG 62.175 60.000 0.00 0.00 0.00 4.61
881 1001 0.320946 TTAAAGGAAGGCGTCGGTGG 60.321 55.000 0.00 0.00 0.00 4.61
882 1002 1.515081 TTTAAAGGAAGGCGTCGGTG 58.485 50.000 0.00 0.00 0.00 4.94
883 1003 1.875514 GTTTTAAAGGAAGGCGTCGGT 59.124 47.619 0.00 0.00 0.00 4.69
884 1004 1.136169 CGTTTTAAAGGAAGGCGTCGG 60.136 52.381 0.00 0.00 0.00 4.79
885 1005 1.723701 GCGTTTTAAAGGAAGGCGTCG 60.724 52.381 1.30 0.00 0.00 5.12
886 1006 1.400629 GGCGTTTTAAAGGAAGGCGTC 60.401 52.381 1.30 0.00 38.42 5.19
887 1007 0.594602 GGCGTTTTAAAGGAAGGCGT 59.405 50.000 1.30 0.00 38.42 5.68
888 1008 0.453782 CGGCGTTTTAAAGGAAGGCG 60.454 55.000 0.00 7.22 38.42 5.52
889 1009 0.731514 GCGGCGTTTTAAAGGAAGGC 60.732 55.000 9.37 0.00 37.21 4.35
890 1010 0.879090 AGCGGCGTTTTAAAGGAAGG 59.121 50.000 9.37 0.00 0.00 3.46
891 1011 1.463528 CGAGCGGCGTTTTAAAGGAAG 60.464 52.381 9.37 0.00 34.64 3.46
892 1012 0.513820 CGAGCGGCGTTTTAAAGGAA 59.486 50.000 9.37 0.00 34.64 3.36
893 1013 2.155665 CGAGCGGCGTTTTAAAGGA 58.844 52.632 9.37 0.00 34.64 3.36
894 1014 4.737601 CGAGCGGCGTTTTAAAGG 57.262 55.556 9.37 0.00 34.64 3.11
917 1037 3.465403 CTGGAGGGAGGCAGACGG 61.465 72.222 0.00 0.00 0.00 4.79
918 1038 2.681778 ACTGGAGGGAGGCAGACG 60.682 66.667 0.00 0.00 0.00 4.18
919 1039 2.363172 GGACTGGAGGGAGGCAGAC 61.363 68.421 0.00 0.00 0.00 3.51
920 1040 2.039624 GGACTGGAGGGAGGCAGA 59.960 66.667 0.00 0.00 0.00 4.26
921 1041 2.284921 TGGACTGGAGGGAGGCAG 60.285 66.667 0.00 0.00 0.00 4.85
922 1042 2.607750 GTGGACTGGAGGGAGGCA 60.608 66.667 0.00 0.00 0.00 4.75
923 1043 2.284995 AGTGGACTGGAGGGAGGC 60.285 66.667 0.00 0.00 0.00 4.70
924 1044 2.055042 CGAGTGGACTGGAGGGAGG 61.055 68.421 0.00 0.00 0.00 4.30
925 1045 1.000771 TCGAGTGGACTGGAGGGAG 60.001 63.158 0.00 0.00 0.00 4.30
926 1046 1.304217 GTCGAGTGGACTGGAGGGA 60.304 63.158 0.00 0.00 42.62 4.20
927 1047 2.701780 CGTCGAGTGGACTGGAGGG 61.702 68.421 3.67 0.00 43.79 4.30
928 1048 2.878429 CGTCGAGTGGACTGGAGG 59.122 66.667 3.67 0.00 43.79 4.30
929 1049 2.179517 GCGTCGAGTGGACTGGAG 59.820 66.667 3.67 0.00 43.79 3.86
957 1077 4.567597 TCGGTGGGTGGGGTGAGT 62.568 66.667 0.00 0.00 0.00 3.41
2322 3172 7.201367 CGAAAATGTTTGTACCGAACACTTTTT 60.201 33.333 15.25 15.55 37.32 1.94


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

AutoCloner maintained by Alex Coulton.