Multiple sequence alignment - TraesCS7D01G489700

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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 TraesCS7D01G489700 chr7D 100.000 1689 0 0 1 1689 599255778 599254090 0.000000e+00 3120
1 TraesCS7D01G489700 chr7D 100.000 433 0 0 1922 2354 599253857 599253425 0.000000e+00 800
2 TraesCS7D01G489700 chr7D 97.448 431 11 0 1924 2354 563360721 563360291 0.000000e+00 736
3 TraesCS7D01G489700 chr7D 98.842 259 2 1 1 259 48002572 48002315 5.930000e-126 460
4 TraesCS7D01G489700 chr7D 98.837 258 3 0 1 258 610168241 610167984 5.930000e-126 460
5 TraesCS7D01G489700 chr7D 98.101 158 3 0 1532 1689 599249080 599248923 2.300000e-70 276
6 TraesCS7D01G489700 chr7B 96.512 946 31 1 590 1533 678663469 678662524 0.000000e+00 1563
7 TraesCS7D01G489700 chr7A 96.226 530 18 1 1006 1533 691472873 691472344 0.000000e+00 867
8 TraesCS7D01G489700 chr7A 89.853 611 38 9 2 589 691011458 691010849 0.000000e+00 763
9 TraesCS7D01G489700 chr7A 79.200 875 152 22 599 1463 691522037 691521183 4.360000e-162 580
10 TraesCS7D01G489700 chr7A 93.407 273 12 1 590 856 691473549 691473277 1.310000e-107 399
11 TraesCS7D01G489700 chr5D 90.924 595 42 11 2 589 410339423 410340012 0.000000e+00 789
12 TraesCS7D01G489700 chr5D 96.970 429 13 0 1926 2354 318491093 318490665 0.000000e+00 721
13 TraesCS7D01G489700 chr5D 96.752 431 14 0 1924 2354 414777521 414777091 0.000000e+00 719
14 TraesCS7D01G489700 chr5D 97.406 347 9 0 248 594 356787769 356788115 2.010000e-165 592
15 TraesCS7D01G489700 chr5D 99.605 253 0 1 1 253 53631368 53631619 5.930000e-126 460
16 TraesCS7D01G489700 chr5A 90.492 610 31 12 2 589 645081987 645081383 0.000000e+00 780
17 TraesCS7D01G489700 chr5A 89.508 610 39 9 2 589 503207242 503207848 0.000000e+00 749
18 TraesCS7D01G489700 chr5A 97.452 157 4 0 1533 1689 578848837 578848681 3.860000e-68 268
19 TraesCS7D01G489700 chr5A 96.835 158 5 0 1532 1689 564947988 564947831 4.990000e-67 265
20 TraesCS7D01G489700 chr1A 90.164 610 37 7 2 589 273325813 273325205 0.000000e+00 773
21 TraesCS7D01G489700 chr1A 85.900 617 53 18 2 589 551685487 551684876 5.520000e-176 627
22 TraesCS7D01G489700 chr1A 97.452 157 4 0 1533 1689 45820033 45819877 3.860000e-68 268
23 TraesCS7D01G489700 chr3D 97.448 431 11 0 1924 2354 113579925 113580355 0.000000e+00 736
24 TraesCS7D01G489700 chr3D 96.984 431 13 0 1924 2354 19830705 19831135 0.000000e+00 725
25 TraesCS7D01G489700 chr3D 96.984 431 13 0 1924 2354 597463955 597463525 0.000000e+00 725
26 TraesCS7D01G489700 chr3D 96.977 430 13 0 1925 2354 522306562 522306133 0.000000e+00 723
27 TraesCS7D01G489700 chr3D 97.668 343 8 0 248 590 58333795 58333453 7.250000e-165 590
28 TraesCS7D01G489700 chr6D 96.752 431 14 0 1924 2354 80593418 80593848 0.000000e+00 719
29 TraesCS7D01G489700 chr6D 95.625 160 7 0 1530 1689 80593230 80593389 8.350000e-65 257
30 TraesCS7D01G489700 chr1D 96.752 431 14 0 1924 2354 11339749 11340179 0.000000e+00 719
31 TraesCS7D01G489700 chr1D 97.953 342 7 0 248 589 325898338 325898679 5.600000e-166 593
32 TraesCS7D01G489700 chr1D 96.078 357 13 1 248 604 450935637 450935282 4.360000e-162 580
33 TraesCS7D01G489700 chr1D 98.734 158 2 0 1532 1689 339329474 339329317 4.950000e-72 281
34 TraesCS7D01G489700 chr1D 97.452 157 4 0 1533 1689 339342517 339342361 3.860000e-68 268
35 TraesCS7D01G489700 chr2D 98.246 342 6 0 248 589 16638931 16638590 1.200000e-167 599
36 TraesCS7D01G489700 chr2D 97.953 342 7 0 248 589 510276609 510276950 5.600000e-166 593
37 TraesCS7D01G489700 chr2D 97.668 343 8 0 248 590 282870364 282870022 7.250000e-165 590
38 TraesCS7D01G489700 chr4D 97.668 343 8 0 248 590 83327609 83327951 7.250000e-165 590
39 TraesCS7D01G489700 chr6A 97.452 157 4 0 1533 1689 586372447 586372603 3.860000e-68 268
40 TraesCS7D01G489700 chr3A 97.419 155 4 0 1533 1687 721220920 721220766 4.990000e-67 265


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 TraesCS7D01G489700 chr7D 599253425 599255778 2353 True 1960 3120 100.0000 1 2354 2 chr7D.!!$R5 2353
1 TraesCS7D01G489700 chr7B 678662524 678663469 945 True 1563 1563 96.5120 590 1533 1 chr7B.!!$R1 943
2 TraesCS7D01G489700 chr7A 691010849 691011458 609 True 763 763 89.8530 2 589 1 chr7A.!!$R1 587
3 TraesCS7D01G489700 chr7A 691472344 691473549 1205 True 633 867 94.8165 590 1533 2 chr7A.!!$R3 943
4 TraesCS7D01G489700 chr7A 691521183 691522037 854 True 580 580 79.2000 599 1463 1 chr7A.!!$R2 864
5 TraesCS7D01G489700 chr5D 410339423 410340012 589 False 789 789 90.9240 2 589 1 chr5D.!!$F3 587
6 TraesCS7D01G489700 chr5A 645081383 645081987 604 True 780 780 90.4920 2 589 1 chr5A.!!$R3 587
7 TraesCS7D01G489700 chr5A 503207242 503207848 606 False 749 749 89.5080 2 589 1 chr5A.!!$F1 587
8 TraesCS7D01G489700 chr1A 273325205 273325813 608 True 773 773 90.1640 2 589 1 chr1A.!!$R2 587
9 TraesCS7D01G489700 chr1A 551684876 551685487 611 True 627 627 85.9000 2 589 1 chr1A.!!$R3 587
10 TraesCS7D01G489700 chr6D 80593230 80593848 618 False 488 719 96.1885 1530 2354 2 chr6D.!!$F1 824

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
825 867 0.390866 CGAGGCACATGAAGAGCACT 60.391 55.0 0.0 0.0 35.32 4.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1943 2241 0.456312 CCGTCTTCGAGGAGTTTCGG 60.456 60.0 9.38 9.38 40.83 4.3 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
43 44 8.230486 GTGATCTCGTTAATCAAATGACAACTT 58.770 33.333 0.00 0.0 35.04 2.66
301 314 3.520721 TCCATCATCGATCCAATGCCTAT 59.479 43.478 0.00 0.0 0.00 2.57
438 471 6.757897 TTGCTACTAAATACTTTGCTGCAT 57.242 33.333 1.84 0.0 0.00 3.96
634 667 4.093952 GCGCGCACATCAGCAAGT 62.094 61.111 29.10 0.0 0.00 3.16
689 722 1.551019 GCCCTGGGAAAGACGTACCT 61.551 60.000 19.27 0.0 0.00 3.08
825 867 0.390866 CGAGGCACATGAAGAGCACT 60.391 55.000 0.00 0.0 35.32 4.40
892 934 0.957395 CATCAGCTTTGGCAGGACGT 60.957 55.000 0.00 0.0 41.70 4.34
973 1015 1.451207 AGTGGTTGCGTGCTTGACA 60.451 52.632 0.00 0.0 0.00 3.58
1010 1306 1.134521 GGGTACGTTCATGATCAGGCA 60.135 52.381 1.57 0.0 0.00 4.75
1111 1407 3.898627 CTCTGCTTCCGCGTGACGT 62.899 63.158 6.91 0.0 41.42 4.34
1185 1481 2.250939 CCTTGTGCTCACGCCGAAA 61.251 57.895 0.00 0.0 34.43 3.46
1372 1668 6.263392 CGTCTAGGATTGATCTTCTGTTCCTA 59.737 42.308 0.00 0.0 35.33 2.94
1541 1839 4.735662 TCGTTTTCAAAATGTAGACGGG 57.264 40.909 1.98 0.0 0.00 5.28
1563 1861 6.196353 CGGGAAAGTTTGCAATACAATAATCG 59.804 38.462 9.48 0.0 38.31 3.34
1609 1907 9.084164 GTGCACGTATATATAATACAAGGGAAG 57.916 37.037 0.00 0.0 0.00 3.46
1661 1959 1.357420 TGGGCCACAACTCCAATACAT 59.643 47.619 0.00 0.0 0.00 2.29
1662 1960 1.750778 GGGCCACAACTCCAATACATG 59.249 52.381 4.39 0.0 0.00 3.21
1943 2241 0.523966 CGGAGACACAGAGACTGGAC 59.476 60.000 0.00 0.0 35.51 4.02
1982 2280 3.755112 GGAGTAGGCAATCCCTTAGTC 57.245 52.381 0.00 0.0 43.06 2.59
2160 2458 1.625818 AGTAGACAAGAGTGGCCTTGG 59.374 52.381 3.32 0.0 45.76 3.61
2217 2515 4.379243 AAGAGCACTCGGCCACGG 62.379 66.667 2.24 0.0 46.50 4.94
2248 2546 2.835705 CGCGATACTCTGCCTCGGT 61.836 63.158 0.00 0.0 33.17 4.69
2256 2554 3.699894 CTGCCTCGGTGCTGGAGT 61.700 66.667 0.00 0.0 0.00 3.85
2301 2599 3.181496 CGATGACCAAGAGATCAACGAGA 60.181 47.826 0.00 0.0 41.92 4.04
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 6.662414 TGTCATTTGATTAACGAGATCACC 57.338 37.500 0.00 0.00 33.51 4.02
43 44 7.291416 TGGTTATGTTTCCTAGCCATAGACATA 59.709 37.037 0.00 0.00 30.64 2.29
301 314 6.602179 CGAAGAACAATATGTGAAAAGCTCA 58.398 36.000 0.00 0.00 0.00 4.26
438 471 8.994500 TCAACCACACCTGGATAACTTAATATA 58.006 33.333 0.00 0.00 40.55 0.86
634 667 0.468226 ACTCCGTGGCTTCTGAAACA 59.532 50.000 0.00 0.00 0.00 2.83
689 722 2.628178 CCCAGTAACCAGATGAGCGATA 59.372 50.000 0.00 0.00 0.00 2.92
727 763 2.107366 GAAGAGGCAGTAGGAGAAGCT 58.893 52.381 0.00 0.00 0.00 3.74
789 831 2.967397 GTGTCGACCGGGATGTCA 59.033 61.111 14.12 0.00 34.88 3.58
825 867 1.152735 CTCGGGGTAGAGCAGCCTA 60.153 63.158 0.00 0.00 44.81 3.93
910 952 2.047560 GCGCCTTAACACCTCCGT 60.048 61.111 0.00 0.00 0.00 4.69
973 1015 3.015145 CCCCCAGAACATCCCGGT 61.015 66.667 0.00 0.00 0.00 5.28
1010 1306 0.385751 CTCCAGGATGTCGTACGCAT 59.614 55.000 20.10 20.10 0.00 4.73
1111 1407 2.359850 GTGCGACAAGATGGCCCA 60.360 61.111 0.00 0.00 0.00 5.36
1113 1409 2.401766 CCAGTGCGACAAGATGGCC 61.402 63.158 0.00 0.00 0.00 5.36
1185 1481 1.035139 CCTGCAGGACAAACAGCTTT 58.965 50.000 29.88 0.00 37.39 3.51
1372 1668 1.208535 TCGAATTGGGTTGACCGCTAT 59.791 47.619 0.00 0.00 44.64 2.97
1513 1811 4.783764 ACATTTTGAAAACGATCTCCCC 57.216 40.909 0.00 0.00 0.00 4.81
1519 1817 4.998672 TCCCGTCTACATTTTGAAAACGAT 59.001 37.500 0.00 0.00 0.00 3.73
1541 1839 8.911662 ACAACGATTATTGTATTGCAAACTTTC 58.088 29.630 1.71 0.00 41.04 2.62
1563 1861 1.750778 CCAGCACCCCATCAATACAAC 59.249 52.381 0.00 0.00 0.00 3.32
1609 1907 4.894114 TCTTGTATAGTTGAGGTAGAGGCC 59.106 45.833 0.00 0.00 0.00 5.19
1661 1959 6.625873 TGAGTATGTGTTTTGTATTGCACA 57.374 33.333 0.00 0.00 44.43 4.57
1662 1960 6.915300 TGTTGAGTATGTGTTTTGTATTGCAC 59.085 34.615 0.00 0.00 0.00 4.57
1921 2219 0.808125 CAGTCTCTGTGTCTCCGGAG 59.192 60.000 26.32 26.32 0.00 4.63
1922 2220 0.609406 CCAGTCTCTGTGTCTCCGGA 60.609 60.000 2.93 2.93 0.00 5.14
1943 2241 0.456312 CCGTCTTCGAGGAGTTTCGG 60.456 60.000 9.38 9.38 40.83 4.30
2017 2315 1.593209 GGCCGTGTTCGTGTTCTCA 60.593 57.895 0.00 0.00 35.01 3.27
2018 2316 1.155424 TTGGCCGTGTTCGTGTTCTC 61.155 55.000 0.00 0.00 35.01 2.87
2160 2458 2.887152 AGGAGTTGCTTTGTGATGTTCC 59.113 45.455 0.00 0.00 0.00 3.62
2229 2527 2.727647 CGAGGCAGAGTATCGCGC 60.728 66.667 0.00 0.00 42.67 6.86
2231 2529 1.299468 CACCGAGGCAGAGTATCGC 60.299 63.158 0.00 0.00 42.67 4.58
2248 2546 2.997315 CGGTCTCCCACTCCAGCA 60.997 66.667 0.00 0.00 0.00 4.41
2301 2599 0.613853 TACTGCGTCTACCTTGGGCT 60.614 55.000 0.00 0.00 0.00 5.19


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

AutoCloner maintained by Alex Coulton.