Multiple sequence alignment - TraesCS5B01G330000

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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 TraesCS5B01G330000 chr5B 100.000 2679 0 0 1 2679 514056285 514053607 0.000000e+00 4948
1 TraesCS5B01G330000 chr5B 96.065 1423 56 0 1 1423 34300561 34299139 0.000000e+00 2318
2 TraesCS5B01G330000 chr5B 97.059 1258 37 0 1422 2679 123791115 123789858 0.000000e+00 2119
3 TraesCS5B01G330000 chr5B 94.290 1261 47 6 1424 2679 18188162 18186922 0.000000e+00 1906
4 TraesCS5B01G330000 chr5B 94.290 1261 47 6 1424 2679 353926685 353927925 0.000000e+00 1906
5 TraesCS5B01G330000 chr5B 95.076 1178 35 10 1422 2576 34297419 34296242 0.000000e+00 1832
6 TraesCS5B01G330000 chr5B 91.517 389 18 8 1454 1830 677837563 677837178 3.060000e-144 521
7 TraesCS5B01G330000 chr4B 97.261 1424 33 3 4 1423 522411061 522409640 0.000000e+00 2409
8 TraesCS5B01G330000 chr4B 92.762 525 15 8 1422 1923 522407919 522407395 0.000000e+00 737
9 TraesCS5B01G330000 chr7B 96.908 1423 44 0 1 1423 379918739 379917317 0.000000e+00 2385
10 TraesCS5B01G330000 chr7B 96.702 1425 45 1 1 1423 664945079 664946503 0.000000e+00 2370
11 TraesCS5B01G330000 chr7B 96.275 1423 53 0 1 1423 666623280 666621858 0.000000e+00 2335
12 TraesCS5B01G330000 chr7B 93.980 1279 32 5 1424 2679 664948227 664949483 0.000000e+00 1893
13 TraesCS5B01G330000 chr7B 93.667 1279 38 2 1424 2679 666620135 666618877 0.000000e+00 1873
14 TraesCS5B01G330000 chr7B 90.077 1431 125 17 1 1421 692404192 692402769 0.000000e+00 1840
15 TraesCS5B01G330000 chr2D 92.712 1427 98 5 1 1423 126682366 126683790 0.000000e+00 2054
16 TraesCS5B01G330000 chr2D 92.877 365 17 5 1473 1830 126685610 126685972 3.060000e-144 521
17 TraesCS5B01G330000 chr4A 90.922 1432 113 14 1 1423 716489734 716488311 0.000000e+00 1908
18 TraesCS5B01G330000 chr4A 89.944 1432 127 14 1 1423 692369621 692371044 0.000000e+00 1831
19 TraesCS5B01G330000 chr4A 95.342 644 30 0 2036 2679 692373579 692374222 0.000000e+00 1024
20 TraesCS5B01G330000 chr4A 92.714 398 20 6 1485 1875 692372901 692373296 1.390000e-157 566
21 TraesCS5B01G330000 chr4A 92.208 154 11 1 1872 2024 692373333 692373486 1.620000e-52 217
22 TraesCS5B01G330000 chr3B 93.589 1279 39 4 1424 2679 734223016 734224274 0.000000e+00 1868
23 TraesCS5B01G330000 chr6B 93.916 641 39 0 2036 2676 77324753 77325393 0.000000e+00 968
24 TraesCS5B01G330000 chr6B 88.806 536 42 14 1499 2023 77324131 77324659 2.250000e-180 641
25 TraesCS5B01G330000 chr6B 87.065 402 32 13 1446 1830 715467715 715468113 1.140000e-118 436
26 TraesCS5B01G330000 chr3D 93.810 420 14 8 1422 1830 581476716 581476298 2.930000e-174 621


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 TraesCS5B01G330000 chr5B 514053607 514056285 2678 True 4948.0 4948 100.0000 1 2679 1 chr5B.!!$R3 2678
1 TraesCS5B01G330000 chr5B 123789858 123791115 1257 True 2119.0 2119 97.0590 1422 2679 1 chr5B.!!$R2 1257
2 TraesCS5B01G330000 chr5B 34296242 34300561 4319 True 2075.0 2318 95.5705 1 2576 2 chr5B.!!$R5 2575
3 TraesCS5B01G330000 chr5B 18186922 18188162 1240 True 1906.0 1906 94.2900 1424 2679 1 chr5B.!!$R1 1255
4 TraesCS5B01G330000 chr5B 353926685 353927925 1240 False 1906.0 1906 94.2900 1424 2679 1 chr5B.!!$F1 1255
5 TraesCS5B01G330000 chr4B 522407395 522411061 3666 True 1573.0 2409 95.0115 4 1923 2 chr4B.!!$R1 1919
6 TraesCS5B01G330000 chr7B 379917317 379918739 1422 True 2385.0 2385 96.9080 1 1423 1 chr7B.!!$R1 1422
7 TraesCS5B01G330000 chr7B 664945079 664949483 4404 False 2131.5 2370 95.3410 1 2679 2 chr7B.!!$F1 2678
8 TraesCS5B01G330000 chr7B 666618877 666623280 4403 True 2104.0 2335 94.9710 1 2679 2 chr7B.!!$R3 2678
9 TraesCS5B01G330000 chr7B 692402769 692404192 1423 True 1840.0 1840 90.0770 1 1421 1 chr7B.!!$R2 1420
10 TraesCS5B01G330000 chr2D 126682366 126685972 3606 False 1287.5 2054 92.7945 1 1830 2 chr2D.!!$F1 1829
11 TraesCS5B01G330000 chr4A 716488311 716489734 1423 True 1908.0 1908 90.9220 1 1423 1 chr4A.!!$R1 1422
12 TraesCS5B01G330000 chr4A 692369621 692374222 4601 False 909.5 1831 92.5520 1 2679 4 chr4A.!!$F1 2678
13 TraesCS5B01G330000 chr3B 734223016 734224274 1258 False 1868.0 1868 93.5890 1424 2679 1 chr3B.!!$F1 1255
14 TraesCS5B01G330000 chr6B 77324131 77325393 1262 False 804.5 968 91.3610 1499 2676 2 chr6B.!!$F2 1177

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
405 416 1.684049 CTGAGCCTCCCCGTCTTCT 60.684 63.158 0.0 0.0 0.0 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2318 4437 1.207089 CAAGTTCCTCGGTGCCAGATA 59.793 52.381 0.0 0.0 0.0 1.98 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
55 56 2.556622 ACGATTTGACCCGCTTTTGAAT 59.443 40.909 0.00 0.0 0.00 2.57
193 194 4.636435 CCCGACGTGGCAAAGGGT 62.636 66.667 0.00 0.0 37.36 4.34
244 245 2.282180 GAGCAGAAAACCGGCCCA 60.282 61.111 0.00 0.0 36.60 5.36
273 275 2.283101 GTGCAGCCCAACCCATCA 60.283 61.111 0.00 0.0 0.00 3.07
360 365 1.899142 CCCAAATCAACCCCAAATCGT 59.101 47.619 0.00 0.0 0.00 3.73
399 410 2.444706 TGGATCTGAGCCTCCCCG 60.445 66.667 13.80 0.0 0.00 5.73
405 416 1.684049 CTGAGCCTCCCCGTCTTCT 60.684 63.158 0.00 0.0 0.00 2.85
431 442 3.208692 AGGTATTCTCCACCAGATCCTCT 59.791 47.826 0.00 0.0 38.62 3.69
634 646 2.435372 TGTGATAGGGTTGGGCATTC 57.565 50.000 0.00 0.0 0.00 2.67
1077 1105 1.873591 GCGCGGGACATTGAGAATAAT 59.126 47.619 8.83 0.0 0.00 1.28
1104 1132 9.190317 GGGGTAAGACTCAATCTATTTGAATTT 57.810 33.333 0.00 0.0 43.64 1.82
1229 1261 2.713770 GCGACGAGCGGTATGAGA 59.286 61.111 0.00 0.0 41.29 3.27
1306 1338 1.077787 GTCGATCAACCATGGGGCA 60.078 57.895 18.09 0.0 37.90 5.36
1702 3594 1.235724 GGCGTGAACTTTGCTACCTT 58.764 50.000 0.00 0.0 0.00 3.50
1872 3910 3.011818 TGCTGTCATCCTTGCTGTTATG 58.988 45.455 0.00 0.0 0.00 1.90
1873 3911 2.223433 GCTGTCATCCTTGCTGTTATGC 60.223 50.000 0.00 0.0 0.00 3.14
1874 3912 3.276857 CTGTCATCCTTGCTGTTATGCT 58.723 45.455 0.00 0.0 0.00 3.79
1875 3913 3.011818 TGTCATCCTTGCTGTTATGCTG 58.988 45.455 0.00 0.0 0.00 4.41
1876 3914 3.012518 GTCATCCTTGCTGTTATGCTGT 58.987 45.455 0.00 0.0 0.00 4.40
1877 3915 3.064545 GTCATCCTTGCTGTTATGCTGTC 59.935 47.826 0.00 0.0 0.00 3.51
1878 3916 2.857186 TCCTTGCTGTTATGCTGTCA 57.143 45.000 0.00 0.0 0.00 3.58
1879 3917 3.354948 TCCTTGCTGTTATGCTGTCAT 57.645 42.857 0.00 0.0 36.73 3.06
1880 3918 3.273434 TCCTTGCTGTTATGCTGTCATC 58.727 45.455 0.00 0.0 34.22 2.92
1881 3919 2.357009 CCTTGCTGTTATGCTGTCATCC 59.643 50.000 0.00 0.0 34.22 3.51
1882 3920 3.276857 CTTGCTGTTATGCTGTCATCCT 58.723 45.455 0.00 0.0 34.22 3.24
1883 3921 3.354948 TGCTGTTATGCTGTCATCCTT 57.645 42.857 0.00 0.0 34.22 3.36
1884 3922 4.486125 TGCTGTTATGCTGTCATCCTTA 57.514 40.909 0.00 0.0 34.22 2.69
1885 3923 4.191544 TGCTGTTATGCTGTCATCCTTAC 58.808 43.478 0.00 0.0 34.22 2.34
1886 3924 3.561725 GCTGTTATGCTGTCATCCTTACC 59.438 47.826 0.00 0.0 34.22 2.85
1887 3925 4.684485 GCTGTTATGCTGTCATCCTTACCT 60.684 45.833 0.00 0.0 34.22 3.08
1888 3926 5.431765 CTGTTATGCTGTCATCCTTACCTT 58.568 41.667 0.00 0.0 34.22 3.50
1889 3927 5.815581 TGTTATGCTGTCATCCTTACCTTT 58.184 37.500 0.00 0.0 34.22 3.11
1890 3928 6.245408 TGTTATGCTGTCATCCTTACCTTTT 58.755 36.000 0.00 0.0 34.22 2.27
1958 3996 4.966787 TTTGCCCCTGGACGCCAC 62.967 66.667 0.00 0.0 0.00 5.01
1962 4000 2.035626 CCCCTGGACGCCACAAAT 59.964 61.111 0.00 0.0 0.00 2.32
2049 4168 4.399303 AGATCCACGACAAATCCCAAATTC 59.601 41.667 0.00 0.0 0.00 2.17
2054 4173 3.818773 ACGACAAATCCCAAATTCGAACT 59.181 39.130 0.00 0.0 0.00 3.01
2317 4436 0.606604 CTTCTTGCTTGCATTGGCCT 59.393 50.000 3.32 0.0 40.13 5.19
2318 4437 1.001633 CTTCTTGCTTGCATTGGCCTT 59.998 47.619 3.32 0.0 40.13 4.35
2487 4606 4.402474 GGTATTTCAAGAACCCAATCCCAG 59.598 45.833 0.00 0.0 0.00 4.45
2641 4761 4.999950 CACTTCTACAATCAAGTTCAGCCT 59.000 41.667 0.00 0.0 30.06 4.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
176 177 2.734948 TAACCCTTTGCCACGTCGGG 62.735 60.000 0.00 0.0 40.79 5.14
193 194 1.254284 CCAAGGGCCATGGCGTTTAA 61.254 55.000 29.90 0.0 43.06 1.52
360 365 8.690203 TCCACACTTTTGATGAAGAGAATAAA 57.310 30.769 0.00 0.0 0.00 1.40
399 410 5.179533 GGTGGAGAATACCTCAAAGAAGAC 58.820 45.833 0.00 0.0 43.76 3.01
405 416 4.164221 GGATCTGGTGGAGAATACCTCAAA 59.836 45.833 0.00 0.0 43.76 2.69
807 835 8.298854 TCAATGTTGAGATAACAAGACCAATTG 58.701 33.333 0.00 0.0 33.42 2.32
1077 1105 6.884472 TCAAATAGATTGAGTCTTACCCCA 57.116 37.500 0.00 0.0 43.08 4.96
1104 1132 7.777095 AGCAAAACTGACAAGTAATAACCAAA 58.223 30.769 0.00 0.0 34.77 3.28
1229 1261 2.103263 GGCCCAATCTCTCGAAGTATGT 59.897 50.000 0.00 0.0 0.00 2.29
1306 1338 2.006888 CGGTCAATAAGTGCGGTCATT 58.993 47.619 0.00 0.0 0.00 2.57
1702 3594 7.651304 CCATAAGTGCAAATTAAACACAAGTCA 59.349 33.333 0.00 0.0 36.76 3.41
1872 3910 3.084786 AGCAAAAGGTAAGGATGACAGC 58.915 45.455 0.00 0.0 0.00 4.40
1873 3911 4.074970 ACAGCAAAAGGTAAGGATGACAG 58.925 43.478 0.00 0.0 0.00 3.51
1874 3912 4.098914 ACAGCAAAAGGTAAGGATGACA 57.901 40.909 0.00 0.0 0.00 3.58
1875 3913 6.555315 CATAACAGCAAAAGGTAAGGATGAC 58.445 40.000 0.00 0.0 0.00 3.06
1876 3914 5.125417 GCATAACAGCAAAAGGTAAGGATGA 59.875 40.000 0.00 0.0 0.00 2.92
1877 3915 5.126061 AGCATAACAGCAAAAGGTAAGGATG 59.874 40.000 0.00 0.0 36.85 3.51
1878 3916 5.126061 CAGCATAACAGCAAAAGGTAAGGAT 59.874 40.000 0.00 0.0 36.85 3.24
1879 3917 4.458989 CAGCATAACAGCAAAAGGTAAGGA 59.541 41.667 0.00 0.0 36.85 3.36
1880 3918 4.458989 TCAGCATAACAGCAAAAGGTAAGG 59.541 41.667 0.00 0.0 36.85 2.69
1881 3919 5.627499 TCAGCATAACAGCAAAAGGTAAG 57.373 39.130 0.00 0.0 36.85 2.34
1882 3920 5.534654 ACTTCAGCATAACAGCAAAAGGTAA 59.465 36.000 0.00 0.0 34.54 2.85
1883 3921 5.070001 ACTTCAGCATAACAGCAAAAGGTA 58.930 37.500 0.00 0.0 34.54 3.08
1884 3922 3.891366 ACTTCAGCATAACAGCAAAAGGT 59.109 39.130 0.00 0.0 34.54 3.50
1885 3923 4.510038 ACTTCAGCATAACAGCAAAAGG 57.490 40.909 0.00 0.0 34.54 3.11
1886 3924 6.143438 CAGAAACTTCAGCATAACAGCAAAAG 59.857 38.462 0.00 0.0 36.85 2.27
1887 3925 5.978919 CAGAAACTTCAGCATAACAGCAAAA 59.021 36.000 0.00 0.0 36.85 2.44
1888 3926 5.067674 ACAGAAACTTCAGCATAACAGCAAA 59.932 36.000 0.00 0.0 36.85 3.68
1889 3927 4.580167 ACAGAAACTTCAGCATAACAGCAA 59.420 37.500 0.00 0.0 36.85 3.91
1890 3928 4.136796 ACAGAAACTTCAGCATAACAGCA 58.863 39.130 0.00 0.0 36.85 4.41
1958 3996 2.107950 TACCAGGACGCCAAGATTTG 57.892 50.000 0.00 0.0 0.00 2.32
1962 4000 1.220749 GCATACCAGGACGCCAAGA 59.779 57.895 0.00 0.0 0.00 3.02
2049 4168 9.724839 TTTATGAGTTTCCAAAAAGTTAGTTCG 57.275 29.630 0.00 0.0 0.00 3.95
2117 4236 6.045955 TGAACTATGTAATGCTTATGTCGCA 58.954 36.000 0.00 0.0 42.25 5.10
2118 4237 6.525121 TGAACTATGTAATGCTTATGTCGC 57.475 37.500 0.00 0.0 0.00 5.19
2279 4398 9.420551 GCAAGAAGAAGAAAAAGAATGATTCAT 57.579 29.630 8.03 0.0 0.00 2.57
2317 4436 1.568504 AGTTCCTCGGTGCCAGATAA 58.431 50.000 0.00 0.0 0.00 1.75
2318 4437 1.207089 CAAGTTCCTCGGTGCCAGATA 59.793 52.381 0.00 0.0 0.00 1.98
2487 4606 4.577246 CCGACCTAGGCTGCTCGC 62.577 72.222 9.30 0.0 38.13 5.03
2498 4617 0.479815 TATGTCCCCGATACCGACCT 59.520 55.000 0.00 0.0 38.22 3.85
2579 4699 9.520204 AAATCACAATTTATGCAACTATGCTAC 57.480 29.630 0.00 0.0 41.99 3.58
2597 4717 5.189736 AGTGATCTAGGTAGGCAAATCACAA 59.810 40.000 15.35 0.0 43.32 3.33
2641 4761 5.467035 AAGAATTTTGCCGAGATGGAAAA 57.533 34.783 0.00 0.0 44.06 2.29


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

AutoCloner maintained by Alex Coulton.