Multiple sequence alignment - TraesCS7A01G294700

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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 TraesCS7A01G294700 chr7A 100.000 3428 0 0 1 3428 380517837 380514410 0.000000e+00 6331
1 TraesCS7A01G294700 chr7A 98.140 860 13 1 1 860 638146162 638147018 0.000000e+00 1496
2 TraesCS7A01G294700 chr7D 96.760 2006 45 8 861 2846 362376662 362374657 0.000000e+00 3326
3 TraesCS7A01G294700 chr7D 95.563 586 24 2 2845 3428 21712351 21711766 0.000000e+00 937
4 TraesCS7A01G294700 chr7D 94.558 588 30 2 2842 3428 16200288 16200874 0.000000e+00 907
5 TraesCS7A01G294700 chr7B 95.950 2000 53 10 874 2846 324388151 324390149 0.000000e+00 3219
6 TraesCS7A01G294700 chr7B 97.919 865 17 1 1 864 739460340 739459476 0.000000e+00 1496
7 TraesCS7A01G294700 chr3A 98.374 861 14 0 1 861 610374113 610374973 0.000000e+00 1513
8 TraesCS7A01G294700 chr3A 97.919 865 15 1 1 862 645103872 645104736 0.000000e+00 1495
9 TraesCS7A01G294700 chrUn 98.142 861 16 0 1 861 321167584 321168444 0.000000e+00 1502
10 TraesCS7A01G294700 chrUn 94.017 585 33 2 2845 3428 290539032 290538449 0.000000e+00 885
11 TraesCS7A01G294700 chr2A 98.142 861 16 0 1 861 684396585 684395725 0.000000e+00 1502
12 TraesCS7A01G294700 chr1B 98.142 861 13 1 1 861 481286896 481286039 0.000000e+00 1498
13 TraesCS7A01G294700 chr1A 98.032 864 14 1 1 861 590339367 590340230 0.000000e+00 1498
14 TraesCS7A01G294700 chr6A 98.026 861 17 0 1 861 315476045 315475185 0.000000e+00 1496
15 TraesCS7A01G294700 chr3D 95.517 580 24 2 2851 3428 584688146 584687567 0.000000e+00 926
16 TraesCS7A01G294700 chr5D 95.043 585 28 1 2845 3428 310557473 310556889 0.000000e+00 918
17 TraesCS7A01G294700 chr6D 94.746 590 29 2 2840 3428 455129554 455128966 0.000000e+00 917
18 TraesCS7A01G294700 chr6B 94.158 582 33 1 2848 3428 705855235 705855816 0.000000e+00 885
19 TraesCS7A01G294700 chr5B 93.686 586 35 2 2845 3428 669688576 669689161 0.000000e+00 876
20 TraesCS7A01G294700 chr4D 93.434 594 32 5 2841 3428 297381693 297381101 0.000000e+00 874
21 TraesCS7A01G294700 chr5A 89.431 123 10 2 1671 1790 570777589 570777711 5.930000e-33 152


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 TraesCS7A01G294700 chr7A 380514410 380517837 3427 True 6331 6331 100.000 1 3428 1 chr7A.!!$R1 3427
1 TraesCS7A01G294700 chr7A 638146162 638147018 856 False 1496 1496 98.140 1 860 1 chr7A.!!$F1 859
2 TraesCS7A01G294700 chr7D 362374657 362376662 2005 True 3326 3326 96.760 861 2846 1 chr7D.!!$R2 1985
3 TraesCS7A01G294700 chr7D 21711766 21712351 585 True 937 937 95.563 2845 3428 1 chr7D.!!$R1 583
4 TraesCS7A01G294700 chr7D 16200288 16200874 586 False 907 907 94.558 2842 3428 1 chr7D.!!$F1 586
5 TraesCS7A01G294700 chr7B 324388151 324390149 1998 False 3219 3219 95.950 874 2846 1 chr7B.!!$F1 1972
6 TraesCS7A01G294700 chr7B 739459476 739460340 864 True 1496 1496 97.919 1 864 1 chr7B.!!$R1 863
7 TraesCS7A01G294700 chr3A 610374113 610374973 860 False 1513 1513 98.374 1 861 1 chr3A.!!$F1 860
8 TraesCS7A01G294700 chr3A 645103872 645104736 864 False 1495 1495 97.919 1 862 1 chr3A.!!$F2 861
9 TraesCS7A01G294700 chrUn 321167584 321168444 860 False 1502 1502 98.142 1 861 1 chrUn.!!$F1 860
10 TraesCS7A01G294700 chrUn 290538449 290539032 583 True 885 885 94.017 2845 3428 1 chrUn.!!$R1 583
11 TraesCS7A01G294700 chr2A 684395725 684396585 860 True 1502 1502 98.142 1 861 1 chr2A.!!$R1 860
12 TraesCS7A01G294700 chr1B 481286039 481286896 857 True 1498 1498 98.142 1 861 1 chr1B.!!$R1 860
13 TraesCS7A01G294700 chr1A 590339367 590340230 863 False 1498 1498 98.032 1 861 1 chr1A.!!$F1 860
14 TraesCS7A01G294700 chr6A 315475185 315476045 860 True 1496 1496 98.026 1 861 1 chr6A.!!$R1 860
15 TraesCS7A01G294700 chr3D 584687567 584688146 579 True 926 926 95.517 2851 3428 1 chr3D.!!$R1 577
16 TraesCS7A01G294700 chr5D 310556889 310557473 584 True 918 918 95.043 2845 3428 1 chr5D.!!$R1 583
17 TraesCS7A01G294700 chr6D 455128966 455129554 588 True 917 917 94.746 2840 3428 1 chr6D.!!$R1 588
18 TraesCS7A01G294700 chr6B 705855235 705855816 581 False 885 885 94.158 2848 3428 1 chr6B.!!$F1 580
19 TraesCS7A01G294700 chr5B 669688576 669689161 585 False 876 876 93.686 2845 3428 1 chr5B.!!$F1 583
20 TraesCS7A01G294700 chr4D 297381101 297381693 592 True 874 874 93.434 2841 3428 1 chr4D.!!$R1 587

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
964 972 1.737838 TTTCGCGCATCATCTTCCTT 58.262 45.0 8.75 0.0 0.0 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2901 2942 0.032952 GCCGGGTGTCGCTCATTATA 59.967 55.0 2.18 0.0 37.59 0.98 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
870 877 3.657634 ACAGTCTAACACATGCTCACTG 58.342 45.455 0.00 0.00 36.63 3.66
946 954 3.028850 CCACAGCATCTCCATCCAAATT 58.971 45.455 0.00 0.00 0.00 1.82
947 955 3.449737 CCACAGCATCTCCATCCAAATTT 59.550 43.478 0.00 0.00 0.00 1.82
964 972 1.737838 TTTCGCGCATCATCTTCCTT 58.262 45.000 8.75 0.00 0.00 3.36
973 981 3.871463 GCATCATCTTCCTTCACACCACT 60.871 47.826 0.00 0.00 0.00 4.00
996 1004 2.367377 CCATCCTCCCAGCCCAGA 60.367 66.667 0.00 0.00 0.00 3.86
1026 1034 3.432588 ACGCTCTCCTCCGTGTCG 61.433 66.667 0.00 0.00 36.18 4.35
1226 1238 0.843309 TTTCCTTGGTGGACAGCAGA 59.157 50.000 4.30 0.00 46.14 4.26
1440 1452 5.012148 TCTCTTCCAGAAAATATCGGATCCC 59.988 44.000 6.06 0.00 33.02 3.85
1454 1478 3.135712 TCGGATCCCAATTTAGCTGCTTA 59.864 43.478 7.79 0.00 0.00 3.09
1669 1695 2.749441 GCAGGGCTCAAGTCAGGC 60.749 66.667 0.00 0.00 38.25 4.85
1835 1861 1.336755 GCCTCCGAAGCTTTTGTTCAA 59.663 47.619 0.00 0.00 0.00 2.69
1909 1938 2.097036 CTCATTTTGCTCCATGGCAGA 58.903 47.619 6.96 0.00 43.39 4.26
2681 2716 1.067635 GTTGTGGGCATTCATGTGGTC 60.068 52.381 0.00 0.00 0.00 4.02
2757 2798 2.229784 CCCCTTTGATGAGTTGTTGCTC 59.770 50.000 0.00 0.00 36.12 4.26
2773 2814 2.610433 TGCTCATGAAGTGATGTCGTC 58.390 47.619 0.00 0.00 35.97 4.20
2834 2875 4.747108 TGAGATCGATTAGCTAAGCTTTGC 59.253 41.667 22.97 22.97 40.44 3.68
2858 2899 3.585732 ACACCCTCTTTTCCGATAAAGGA 59.414 43.478 8.66 3.17 36.12 3.36
2931 2972 0.759436 ACACCCGGCCTCTGTATAGG 60.759 60.000 0.00 0.00 39.87 2.57
3055 3103 0.621862 GGAGGAGGTGGACCAATCCT 60.622 60.000 23.60 23.60 46.43 3.24
3119 3167 0.107214 CCCGCTCCAACCACATACAT 60.107 55.000 0.00 0.00 0.00 2.29
3152 3200 1.404391 AGCGATTGATACTCCGTTCGT 59.596 47.619 0.00 0.00 0.00 3.85
3228 3276 7.680588 GCATAGAAGAAGAGGTTTTGCCATTAG 60.681 40.741 0.00 0.00 40.61 1.73
3309 3357 9.677567 CCCGTATTAGCGTACTAAAAGTATTTA 57.322 33.333 0.00 0.00 41.62 1.40
3338 3387 6.701340 TCCATCAAGCAGTGACCATATATAC 58.299 40.000 0.00 0.00 39.72 1.47
3389 3438 3.430929 GGACGCTATTTGGATGACTGACT 60.431 47.826 0.00 0.00 0.00 3.41
3404 3453 2.095869 ACTGACTATATAGAACGCGCGG 60.096 50.000 35.22 16.31 0.00 6.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
346 347 2.107750 CATCGCGCCCTCTGTCAT 59.892 61.111 0.00 0.00 0.00 3.06
694 698 2.107901 TCCGCCTAAAAACCCTAAACCA 59.892 45.455 0.00 0.00 0.00 3.67
885 893 0.813821 GTGGCCTCAAAATCAGGAGC 59.186 55.000 3.32 0.00 31.91 4.70
946 954 1.290203 GAAGGAAGATGATGCGCGAA 58.710 50.000 12.10 0.00 0.00 4.70
947 955 0.175531 TGAAGGAAGATGATGCGCGA 59.824 50.000 12.10 0.00 0.00 5.87
964 972 0.613260 GATGGCTGGTAGTGGTGTGA 59.387 55.000 0.00 0.00 0.00 3.58
973 981 2.072487 GCTGGGAGGATGGCTGGTA 61.072 63.158 0.00 0.00 0.00 3.25
1026 1034 2.413142 GCAGTGCTTGGATGAGGCC 61.413 63.158 8.18 0.00 0.00 5.19
1032 1040 1.078848 GACGGAGCAGTGCTTGGAT 60.079 57.895 20.80 5.42 39.88 3.41
1909 1938 3.523157 TCACATCAATATCACCACCACCT 59.477 43.478 0.00 0.00 0.00 4.00
1998 2027 2.872858 GCGACCAGGGACTATTTTGATC 59.127 50.000 0.00 0.00 36.02 2.92
2681 2716 3.074412 AGGCACGTCTTTCAATACCAAG 58.926 45.455 0.00 0.00 0.00 3.61
2757 2798 6.372981 TCAAATTTGACGACATCACTTCATG 58.627 36.000 16.91 0.00 36.92 3.07
2773 2814 9.807386 GCTTCATTCAGAATTTCTTCAAATTTG 57.193 29.630 12.15 12.15 41.47 2.32
2834 2875 3.343941 TTATCGGAAAAGAGGGTGTGG 57.656 47.619 0.00 0.00 0.00 4.17
2858 2899 9.104965 TGCTACATTATGAGTTAATAAAAGCGT 57.895 29.630 0.00 0.00 34.42 5.07
2901 2942 0.032952 GCCGGGTGTCGCTCATTATA 59.967 55.000 2.18 0.00 37.59 0.98
2931 2972 6.677781 TTGTTAAGGCTATGTGCATCTTAC 57.322 37.500 0.00 0.00 45.15 2.34
3055 3103 5.178096 ACATGGGTGACAACATAATCTCA 57.822 39.130 0.00 0.00 0.00 3.27
3112 3160 3.531538 CTGTTCAAGGCGGTATGTATGT 58.468 45.455 0.00 0.00 0.00 2.29
3152 3200 3.009026 TCGTATGTGGTCTACGCTACAA 58.991 45.455 0.00 0.00 41.24 2.41
3309 3357 3.264193 TGGTCACTGCTTGATGGAATACT 59.736 43.478 0.00 0.00 36.32 2.12
3389 3438 2.919387 GCAAGTCCGCGCGTTCTATATA 60.919 50.000 29.95 0.03 0.00 0.86
3404 3453 3.249559 CACCTCTTCTTTCAGTGCAAGTC 59.750 47.826 2.38 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.