Multiple sequence alignment - TraesCS5B01G005900

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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 TraesCS5B01G005900 chr5B 100.000 2651 0 0 1 2651 7150225 7147575 0.000000e+00 4896
1 TraesCS5B01G005900 chr5B 97.151 2668 42 7 2 2651 7185963 7183312 0.000000e+00 4475
2 TraesCS5B01G005900 chr5B 92.535 2706 138 14 4 2646 7384289 7381585 0.000000e+00 3819
3 TraesCS5B01G005900 chr5B 91.630 2700 150 20 1 2644 7305704 7303025 0.000000e+00 3664
4 TraesCS5B01G005900 chr5B 96.992 2128 41 3 545 2651 7163305 7161180 0.000000e+00 3554
5 TraesCS5B01G005900 chr5B 94.615 780 26 1 999 1762 7355437 7354658 0.000000e+00 1194
6 TraesCS5B01G005900 chr5B 98.812 505 5 1 1 504 7163802 7163298 0.000000e+00 898
7 TraesCS5B01G005900 chr5B 89.058 722 63 8 1 710 7448909 7448192 0.000000e+00 881
8 TraesCS5B01G005900 chr5D 86.616 2645 269 32 3 2568 7121025 7118387 0.000000e+00 2844
9 TraesCS5B01G005900 chr5D 86.353 2638 273 36 3 2562 3868802 3871430 0.000000e+00 2796
10 TraesCS5B01G005900 chr5D 86.594 2566 256 37 85 2568 7126237 7123678 0.000000e+00 2752
11 TraesCS5B01G005900 chr5D 84.275 2620 281 61 121 2646 3889440 3892022 0.000000e+00 2435
12 TraesCS5B01G005900 chr5D 86.892 1831 175 20 3 1780 7131601 7129783 0.000000e+00 1991
13 TraesCS5B01G005900 chr5D 85.895 1184 128 13 1 1150 3879710 3880888 0.000000e+00 1225
14 TraesCS5B01G005900 chr4A 85.973 2481 257 36 1 2408 18738392 18735930 0.000000e+00 2569
15 TraesCS5B01G005900 chr4A 83.688 2728 314 60 5 2646 18732042 18729360 0.000000e+00 2451
16 TraesCS5B01G005900 chr4A 82.326 215 21 9 2432 2646 18735786 18735589 1.260000e-38 171
17 TraesCS5B01G005900 chr5A 85.703 2483 267 38 1 2408 4791891 4789422 0.000000e+00 2538
18 TraesCS5B01G005900 chr5A 83.974 2652 299 54 88 2646 4785419 4782801 0.000000e+00 2427
19 TraesCS5B01G005900 chr5A 87.337 1769 143 36 1 1708 4864735 4866483 0.000000e+00 1951
20 TraesCS5B01G005900 chr5A 88.880 1295 98 13 524 1780 4796993 4795707 0.000000e+00 1552
21 TraesCS5B01G005900 chr5A 90.061 815 53 7 990 1780 4875805 4876615 0.000000e+00 1031
22 TraesCS5B01G005900 chr5A 86.759 793 99 5 1782 2570 4866810 4867600 0.000000e+00 878
23 TraesCS5B01G005900 chr5A 81.614 223 30 8 2432 2646 4789278 4789059 9.750000e-40 174


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 TraesCS5B01G005900 chr5B 7147575 7150225 2650 True 4896.000000 4896 100.000000 1 2651 1 chr5B.!!$R1 2650
1 TraesCS5B01G005900 chr5B 7183312 7185963 2651 True 4475.000000 4475 97.151000 2 2651 1 chr5B.!!$R2 2649
2 TraesCS5B01G005900 chr5B 7381585 7384289 2704 True 3819.000000 3819 92.535000 4 2646 1 chr5B.!!$R5 2642
3 TraesCS5B01G005900 chr5B 7303025 7305704 2679 True 3664.000000 3664 91.630000 1 2644 1 chr5B.!!$R3 2643
4 TraesCS5B01G005900 chr5B 7161180 7163802 2622 True 2226.000000 3554 97.902000 1 2651 2 chr5B.!!$R7 2650
5 TraesCS5B01G005900 chr5B 7354658 7355437 779 True 1194.000000 1194 94.615000 999 1762 1 chr5B.!!$R4 763
6 TraesCS5B01G005900 chr5B 7448192 7448909 717 True 881.000000 881 89.058000 1 710 1 chr5B.!!$R6 709
7 TraesCS5B01G005900 chr5D 3868802 3871430 2628 False 2796.000000 2796 86.353000 3 2562 1 chr5D.!!$F1 2559
8 TraesCS5B01G005900 chr5D 7118387 7131601 13214 True 2529.000000 2844 86.700667 3 2568 3 chr5D.!!$R1 2565
9 TraesCS5B01G005900 chr5D 3889440 3892022 2582 False 2435.000000 2435 84.275000 121 2646 1 chr5D.!!$F3 2525
10 TraesCS5B01G005900 chr5D 3879710 3880888 1178 False 1225.000000 1225 85.895000 1 1150 1 chr5D.!!$F2 1149
11 TraesCS5B01G005900 chr4A 18729360 18738392 9032 True 1730.333333 2569 83.995667 1 2646 3 chr4A.!!$R1 2645
12 TraesCS5B01G005900 chr5A 4782801 4796993 14192 True 1672.750000 2538 85.042750 1 2646 4 chr5A.!!$R1 2645
13 TraesCS5B01G005900 chr5A 4864735 4867600 2865 False 1414.500000 1951 87.048000 1 2570 2 chr5A.!!$F2 2569
14 TraesCS5B01G005900 chr5A 4875805 4876615 810 False 1031.000000 1031 90.061000 990 1780 1 chr5A.!!$F1 790

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
242 10629 1.078918 CATGCGCTGTCTGAAGGGA 60.079 57.895 9.73 0.0 32.03 4.2 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1822 17848 0.875059 GGTGCTTCACAGCCTGTTAC 59.125 55.0 0.0 0.0 46.74 2.5 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
242 10629 1.078918 CATGCGCTGTCTGAAGGGA 60.079 57.895 9.73 0.0 32.03 4.20
285 10672 5.441709 GAACTTATAGGGAGTTCCGAGAG 57.558 47.826 5.86 0.0 44.50 3.20
342 10731 1.268999 GGCAAGTGCGACATTTTCACA 60.269 47.619 0.00 0.0 43.26 3.58
1055 11495 7.097192 GTCATACACTCATCAACTCCACTTAA 58.903 38.462 0.00 0.0 0.00 1.85
1711 12183 4.399483 TTGTCTCCTCCTAGGTGTACTT 57.601 45.455 9.08 0.0 36.53 2.24
1822 17848 5.574891 TGGATGGGTGAACAATAATTTCG 57.425 39.130 0.00 0.0 0.00 3.46
1978 18005 5.885912 AGAGTGTGGTGTTCTGTTTTAACAT 59.114 36.000 0.00 0.0 38.95 2.71
2154 18182 5.510520 CCATCTAGGACTGCTGGTCTATTTC 60.511 48.000 9.50 0.0 43.97 2.17
2222 18252 3.498774 AATCACATGGGCTACAGATCC 57.501 47.619 0.00 0.0 0.00 3.36
2417 18453 3.053455 GTTATGGACATAGACAGCGAGC 58.947 50.000 0.00 0.0 0.00 5.03
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
242 10629 1.303317 CCTTGCCGCTACCAACCTT 60.303 57.895 0.00 0.00 0.00 3.50
497 10909 7.910584 AGATTAATTATGGGATGGCCATTTTC 58.089 34.615 21.84 8.16 35.15 2.29
869 11308 7.979786 AAGATTCATGGTTCCTTCTAGAGTA 57.020 36.000 0.00 0.00 0.00 2.59
1055 11495 5.432060 AGGCTATTAATGGGTGGTACTCTTT 59.568 40.000 0.00 0.00 0.00 2.52
1632 12104 8.707796 TGTAAATGGTAGGTAACAAATCCAAA 57.292 30.769 0.00 0.00 41.41 3.28
1711 12183 3.367321 TGTCCACCATAGTTCCACGATA 58.633 45.455 0.00 0.00 0.00 2.92
1769 12478 2.319136 AGTACGTGCGAGAGAGAGAT 57.681 50.000 0.00 0.00 0.00 2.75
1822 17848 0.875059 GGTGCTTCACAGCCTGTTAC 59.125 55.000 0.00 0.00 46.74 2.50
1978 18005 8.740123 TTAAGGTTTATGTGTGAAAGAAGTCA 57.260 30.769 0.00 0.00 0.00 3.41
2154 18182 7.764443 TCAACTCTGGTTCGAATCCTAATAAAG 59.236 37.037 5.84 0.00 32.73 1.85
2222 18252 1.537814 TTGCAGGCAAGCCAAGATGG 61.538 55.000 14.40 0.00 41.55 3.51
2360 18396 0.249911 ACGGCAGAAGTGAAGGTGTC 60.250 55.000 0.00 0.00 0.00 3.67


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

AutoCloner maintained by Alex Coulton.