Multiple sequence alignment - TraesCS5B01G038000

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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 TraesCS5B01G038000 chr5B 100.000 2528 0 0 1 2528 42683014 42680487 0.000000e+00 4669
1 TraesCS5B01G038000 chr5B 95.842 1948 76 5 1 1946 419839609 419837665 0.000000e+00 3144
2 TraesCS5B01G038000 chr5B 95.825 1916 78 2 1 1915 511451051 511452965 0.000000e+00 3094
3 TraesCS5B01G038000 chr5B 94.967 1947 89 3 1 1946 620674125 620676063 0.000000e+00 3044
4 TraesCS5B01G038000 chr5B 94.407 590 27 2 1944 2528 683473384 683472796 0.000000e+00 902
5 TraesCS5B01G038000 chr5B 93.624 596 27 2 1944 2528 511464482 511465077 0.000000e+00 880
6 TraesCS5B01G038000 chr5B 89.091 605 34 17 1944 2528 538732278 538732870 0.000000e+00 723
7 TraesCS5B01G038000 chr5B 88.127 598 52 9 1946 2528 396142883 396143476 0.000000e+00 693
8 TraesCS5B01G038000 chr5B 86.824 592 60 13 1946 2528 419836494 419835912 0.000000e+00 645
9 TraesCS5B01G038000 chr5B 92.483 439 29 3 2091 2528 558743882 558743447 2.140000e-175 625
10 TraesCS5B01G038000 chr7B 97.072 1947 56 1 1 1946 679984865 679982919 0.000000e+00 3278
11 TraesCS5B01G038000 chr7B 94.426 592 20 5 1944 2528 143194903 143195488 0.000000e+00 898
12 TraesCS5B01G038000 chr7B 93.909 591 22 5 1944 2528 679972742 679972160 0.000000e+00 880
13 TraesCS5B01G038000 chr7B 88.742 604 48 10 1940 2528 39609049 39609647 0.000000e+00 721
14 TraesCS5B01G038000 chr7B 88.648 599 48 10 1946 2528 668267639 668267045 0.000000e+00 712
15 TraesCS5B01G038000 chr2B 96.302 1947 71 1 1 1946 152573532 152575478 0.000000e+00 3195
16 TraesCS5B01G038000 chr2B 95.223 1947 92 1 1 1946 2477324 2475378 0.000000e+00 3079
17 TraesCS5B01G038000 chr2B 95.018 1947 96 1 1 1946 119784241 119786187 0.000000e+00 3057
18 TraesCS5B01G038000 chr2B 89.094 596 41 5 1944 2528 152586883 152587465 0.000000e+00 719
19 TraesCS5B01G038000 chr4B 95.431 1948 83 5 1 1946 412186968 412188911 0.000000e+00 3099
20 TraesCS5B01G038000 chr4B 94.813 1947 99 2 1 1946 493789587 493787642 0.000000e+00 3035
21 TraesCS5B01G038000 chr4B 82.625 259 23 8 1940 2177 474329045 474329302 2.550000e-50 209
22 TraesCS5B01G038000 chr6B 92.694 438 29 3 2091 2528 170976743 170977177 1.650000e-176 628


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 TraesCS5B01G038000 chr5B 42680487 42683014 2527 True 4669.0 4669 100.000 1 2528 1 chr5B.!!$R1 2527
1 TraesCS5B01G038000 chr5B 511451051 511452965 1914 False 3094.0 3094 95.825 1 1915 1 chr5B.!!$F2 1914
2 TraesCS5B01G038000 chr5B 620674125 620676063 1938 False 3044.0 3044 94.967 1 1946 1 chr5B.!!$F5 1945
3 TraesCS5B01G038000 chr5B 419835912 419839609 3697 True 1894.5 3144 91.333 1 2528 2 chr5B.!!$R4 2527
4 TraesCS5B01G038000 chr5B 683472796 683473384 588 True 902.0 902 94.407 1944 2528 1 chr5B.!!$R3 584
5 TraesCS5B01G038000 chr5B 511464482 511465077 595 False 880.0 880 93.624 1944 2528 1 chr5B.!!$F3 584
6 TraesCS5B01G038000 chr5B 538732278 538732870 592 False 723.0 723 89.091 1944 2528 1 chr5B.!!$F4 584
7 TraesCS5B01G038000 chr5B 396142883 396143476 593 False 693.0 693 88.127 1946 2528 1 chr5B.!!$F1 582
8 TraesCS5B01G038000 chr7B 679982919 679984865 1946 True 3278.0 3278 97.072 1 1946 1 chr7B.!!$R3 1945
9 TraesCS5B01G038000 chr7B 143194903 143195488 585 False 898.0 898 94.426 1944 2528 1 chr7B.!!$F2 584
10 TraesCS5B01G038000 chr7B 679972160 679972742 582 True 880.0 880 93.909 1944 2528 1 chr7B.!!$R2 584
11 TraesCS5B01G038000 chr7B 39609049 39609647 598 False 721.0 721 88.742 1940 2528 1 chr7B.!!$F1 588
12 TraesCS5B01G038000 chr7B 668267045 668267639 594 True 712.0 712 88.648 1946 2528 1 chr7B.!!$R1 582
13 TraesCS5B01G038000 chr2B 152573532 152575478 1946 False 3195.0 3195 96.302 1 1946 1 chr2B.!!$F2 1945
14 TraesCS5B01G038000 chr2B 2475378 2477324 1946 True 3079.0 3079 95.223 1 1946 1 chr2B.!!$R1 1945
15 TraesCS5B01G038000 chr2B 119784241 119786187 1946 False 3057.0 3057 95.018 1 1946 1 chr2B.!!$F1 1945
16 TraesCS5B01G038000 chr2B 152586883 152587465 582 False 719.0 719 89.094 1944 2528 1 chr2B.!!$F3 584
17 TraesCS5B01G038000 chr4B 412186968 412188911 1943 False 3099.0 3099 95.431 1 1946 1 chr4B.!!$F1 1945
18 TraesCS5B01G038000 chr4B 493787642 493789587 1945 True 3035.0 3035 94.813 1 1946 1 chr4B.!!$R1 1945

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
935 937 1.788229 TGAAGATGGCCGGAGATACA 58.212 50.0 5.05 0.0 0.0 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2291 3584 4.955811 ATACACACCTGAAGACTTCACA 57.044 40.909 13.99 0.0 35.46 3.58 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
134 135 5.819991 ACTCAATATCCACACTTCCAACAT 58.180 37.500 0.00 0.00 0.00 2.71
313 314 2.282887 ACAAACCCGGGCATGGTC 60.283 61.111 24.08 0.00 34.15 4.02
742 743 5.873179 TTTGTTCAAACTTCTATAGGGCG 57.127 39.130 0.00 0.00 0.00 6.13
891 893 6.994421 TCTCCATAGGCACATTCAATACTA 57.006 37.500 0.00 0.00 0.00 1.82
935 937 1.788229 TGAAGATGGCCGGAGATACA 58.212 50.000 5.05 0.00 0.00 2.29
985 988 3.274288 CTCAATAGGGTGCTCAAAGGAC 58.726 50.000 0.00 0.00 35.67 3.85
1040 1043 8.795513 TCAATACACATTTGACAAGATGAATGT 58.204 29.630 13.71 6.89 41.85 2.71
1305 1308 2.176045 TGTGATTGCTCTTACGGGAGA 58.824 47.619 6.52 0.00 35.52 3.71
1384 1387 1.705337 GGACATCAATCACCCACGCG 61.705 60.000 3.53 3.53 0.00 6.01
1526 1530 5.867330 TCCGGAGTTGAAGGTTGTTAAATA 58.133 37.500 0.00 0.00 0.00 1.40
1539 1543 7.906327 AGGTTGTTAAATAGGGTAGACGTAAA 58.094 34.615 0.00 0.00 0.00 2.01
1662 1666 0.896940 AGTGCAAAGGTCATGGCCAG 60.897 55.000 20.74 9.15 0.00 4.85
1772 1776 0.474184 AGTGGTAGCCAACAAGTGCT 59.526 50.000 0.00 0.00 41.57 4.40
2095 3372 5.720041 AGCTACAACCTAGAGTGACCATTAA 59.280 40.000 0.00 0.00 0.00 1.40
2261 3554 1.033746 CATCCAAAGCTGCCATCCGT 61.034 55.000 0.00 0.00 0.00 4.69
2291 3584 1.318576 CCGTCCTTTTGCCTCTTTGT 58.681 50.000 0.00 0.00 0.00 2.83
2340 3633 4.079958 TGATTCCCTTCCTAGGCTTTAACC 60.080 45.833 2.96 0.00 40.50 2.85
2465 3768 5.986741 TGCAATGCATCAACAATTGGATATC 59.013 36.000 2.72 0.00 31.71 1.63
2480 3783 3.583966 TGGATATCTGCTCATGCCATACA 59.416 43.478 2.05 0.00 38.71 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 1.462731 TTGGCACATGTGAGTTGGCC 61.463 55.000 29.80 21.27 39.30 5.36
134 135 2.183478 ATGACATGTTGGACGCTCAA 57.817 45.000 0.00 0.00 0.00 3.02
313 314 1.524002 ATGAGGCTCGACCACATGG 59.476 57.895 10.42 0.00 46.71 3.66
742 743 1.534729 CCAACTCCTTAAGGCCACAC 58.465 55.000 17.32 0.00 34.44 3.82
891 893 2.186826 GCACGTGCCCACTTGTTCT 61.187 57.895 30.12 0.00 33.66 3.01
935 937 4.142093 GGCCATATTGCTTGTCATTTGACT 60.142 41.667 11.67 0.00 44.99 3.41
1059 1062 2.198827 TCTGTGCATCCGTTTCCATT 57.801 45.000 0.00 0.00 0.00 3.16
1305 1308 3.499338 TGGAAGATGAAGCAACAATGGT 58.501 40.909 0.00 0.00 39.43 3.55
1384 1387 3.827898 CTCCGACTCCCTCACGGC 61.828 72.222 0.00 0.00 45.25 5.68
1526 1530 3.062042 CGCTTTGTTTTACGTCTACCCT 58.938 45.455 0.00 0.00 0.00 4.34
1539 1543 1.000506 TCGCCTCTAAGACGCTTTGTT 59.999 47.619 0.00 0.00 0.00 2.83
1588 1592 2.970324 GTCGTTGCCCGCTTCACA 60.970 61.111 0.00 0.00 36.19 3.58
1612 1616 1.746220 GAAGCTCTCACGAGGCTCTTA 59.254 52.381 13.50 0.00 37.75 2.10
1631 1635 3.705934 TTGCACTGCCCACAACGGA 62.706 57.895 0.00 0.00 36.56 4.69
2095 3372 6.608002 AGGAACTAGTCATCGTCCTCTATTTT 59.392 38.462 7.17 0.00 36.02 1.82
2261 3554 4.988716 AGGACGGTCGGCACCTCA 62.989 66.667 1.43 0.00 41.17 3.86
2291 3584 4.955811 ATACACACCTGAAGACTTCACA 57.044 40.909 13.99 0.00 35.46 3.58


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

AutoCloner maintained by Alex Coulton.