Multiple sequence alignment - TraesCS4B01G258900

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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 TraesCS4B01G258900 chr4B 100.000 2893 0 0 1 2893 525305990 525308882 0 5343
1 TraesCS4B01G258900 chr4B 96.937 1959 59 1 1 1958 525388663 525386705 0 3284
2 TraesCS4B01G258900 chr4B 96.592 939 23 4 1957 2893 525321417 525322348 0 1548
3 TraesCS4B01G258900 chr4B 94.036 939 46 9 1959 2893 634721798 634720866 0 1415
4 TraesCS4B01G258900 chr4B 93.936 940 48 7 1957 2893 614194228 614195161 0 1411
5 TraesCS4B01G258900 chr5D 95.814 1959 77 3 1 1958 363005581 363007535 0 3158
6 TraesCS4B01G258900 chr2D 95.554 1957 78 4 4 1958 114668228 114666279 0 3123
7 TraesCS4B01G258900 chr5A 95.313 1963 79 5 4 1958 573662464 573660507 0 3103
8 TraesCS4B01G258900 chr5A 95.151 1959 90 3 1 1958 524632905 524630951 0 3086
9 TraesCS4B01G258900 chr5A 94.838 1763 80 4 203 1958 673390640 673388882 0 2741
10 TraesCS4B01G258900 chr1A 94.518 1970 92 12 4 1958 50971146 50969178 0 3025
11 TraesCS4B01G258900 chr2A 94.538 1959 95 3 1 1958 676711159 676713106 0 3014
12 TraesCS4B01G258900 chr2A 87.401 2024 177 42 8 1958 772245772 772243754 0 2254
13 TraesCS4B01G258900 chr7A 94.734 1861 89 7 1 1855 610421464 610423321 0 2885
14 TraesCS4B01G258900 chr2B 94.362 940 45 6 1957 2893 355346337 355345403 0 1435
15 TraesCS4B01G258900 chr2B 94.030 938 48 6 1959 2893 175950492 175951424 0 1415
16 TraesCS4B01G258900 chr7B 94.155 941 45 8 1957 2893 138948291 138949225 0 1424
17 TraesCS4B01G258900 chr5B 94.143 939 45 8 1958 2893 286888726 286889657 0 1421
18 TraesCS4B01G258900 chr3B 94.043 940 46 7 1957 2893 129223274 129222342 0 1417
19 TraesCS4B01G258900 chr3B 93.936 940 46 8 1957 2893 693299916 693298985 0 1410


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 TraesCS4B01G258900 chr4B 525305990 525308882 2892 False 5343 5343 100.000 1 2893 1 chr4B.!!$F1 2892
1 TraesCS4B01G258900 chr4B 525386705 525388663 1958 True 3284 3284 96.937 1 1958 1 chr4B.!!$R1 1957
2 TraesCS4B01G258900 chr4B 525321417 525322348 931 False 1548 1548 96.592 1957 2893 1 chr4B.!!$F2 936
3 TraesCS4B01G258900 chr4B 634720866 634721798 932 True 1415 1415 94.036 1959 2893 1 chr4B.!!$R2 934
4 TraesCS4B01G258900 chr4B 614194228 614195161 933 False 1411 1411 93.936 1957 2893 1 chr4B.!!$F3 936
5 TraesCS4B01G258900 chr5D 363005581 363007535 1954 False 3158 3158 95.814 1 1958 1 chr5D.!!$F1 1957
6 TraesCS4B01G258900 chr2D 114666279 114668228 1949 True 3123 3123 95.554 4 1958 1 chr2D.!!$R1 1954
7 TraesCS4B01G258900 chr5A 573660507 573662464 1957 True 3103 3103 95.313 4 1958 1 chr5A.!!$R2 1954
8 TraesCS4B01G258900 chr5A 524630951 524632905 1954 True 3086 3086 95.151 1 1958 1 chr5A.!!$R1 1957
9 TraesCS4B01G258900 chr5A 673388882 673390640 1758 True 2741 2741 94.838 203 1958 1 chr5A.!!$R3 1755
10 TraesCS4B01G258900 chr1A 50969178 50971146 1968 True 3025 3025 94.518 4 1958 1 chr1A.!!$R1 1954
11 TraesCS4B01G258900 chr2A 676711159 676713106 1947 False 3014 3014 94.538 1 1958 1 chr2A.!!$F1 1957
12 TraesCS4B01G258900 chr2A 772243754 772245772 2018 True 2254 2254 87.401 8 1958 1 chr2A.!!$R1 1950
13 TraesCS4B01G258900 chr7A 610421464 610423321 1857 False 2885 2885 94.734 1 1855 1 chr7A.!!$F1 1854
14 TraesCS4B01G258900 chr2B 355345403 355346337 934 True 1435 1435 94.362 1957 2893 1 chr2B.!!$R1 936
15 TraesCS4B01G258900 chr2B 175950492 175951424 932 False 1415 1415 94.030 1959 2893 1 chr2B.!!$F1 934
16 TraesCS4B01G258900 chr7B 138948291 138949225 934 False 1424 1424 94.155 1957 2893 1 chr7B.!!$F1 936
17 TraesCS4B01G258900 chr5B 286888726 286889657 931 False 1421 1421 94.143 1958 2893 1 chr5B.!!$F1 935
18 TraesCS4B01G258900 chr3B 129222342 129223274 932 True 1417 1417 94.043 1957 2893 1 chr3B.!!$R1 936
19 TraesCS4B01G258900 chr3B 693298985 693299916 931 True 1410 1410 93.936 1957 2893 1 chr3B.!!$R2 936

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
875 957 1.329906 CGAGATGGCACTTGATTCAGC 59.67 52.381 0.0 0.0 0.0 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2425 2537 0.251916 CTTACCGGAGTGATTGGGCA 59.748 55.0 9.46 0.0 0.0 5.36 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
93 95 1.777199 GCGTCGTCGAAAAATCGGT 59.223 52.632 6.17 0.00 39.71 4.69
383 405 3.761897 TCCTTCTAGCTAGATCTGAGCC 58.238 50.000 23.81 0.00 41.06 4.70
695 777 3.111853 ACCATGTACATGTATGCTCCG 57.888 47.619 29.25 16.32 37.11 4.63
740 822 2.376808 GTGTGCTATGCTCACTGTCT 57.623 50.000 14.81 0.00 45.66 3.41
751 833 2.544694 GCTCACTGTCTATGCGTGCTAT 60.545 50.000 0.00 0.00 0.00 2.97
772 854 2.565391 TGATTGTAGGACATGACCACGT 59.435 45.455 16.63 5.82 0.00 4.49
875 957 1.329906 CGAGATGGCACTTGATTCAGC 59.670 52.381 0.00 0.00 0.00 4.26
1006 1097 3.326747 AGTAGGTCGAACAACATGAAGC 58.673 45.455 1.87 0.00 0.00 3.86
1098 1190 1.000396 GGGCTTCAAGGAGGTGCAT 60.000 57.895 0.00 0.00 0.00 3.96
1163 1255 0.179045 GTGTCTGCCACTCAGGTGTT 60.179 55.000 0.00 0.00 43.06 3.32
1201 1293 2.168521 TGGAGAAGTCGATGGATCCAAC 59.831 50.000 20.67 15.91 34.02 3.77
1421 1514 1.371467 TCCTCAACACACCCATCCAT 58.629 50.000 0.00 0.00 0.00 3.41
1445 1538 4.144297 ACTACAACCAGATGCAACACATT 58.856 39.130 0.00 0.00 39.84 2.71
1663 1760 3.617284 TCAATGTCTTCTGCAGCATGAT 58.383 40.909 9.47 0.00 39.69 2.45
1764 1861 3.970410 CCCAGGGTGGCTTCAGCA 61.970 66.667 0.00 0.00 44.36 4.41
1766 1863 1.304713 CCAGGGTGGCTTCAGCAAT 60.305 57.895 0.30 0.00 44.36 3.56
2438 2550 0.329596 AGTCCTTGCCCAATCACTCC 59.670 55.000 0.00 0.00 0.00 3.85
2530 2642 1.064296 CTCAGAACGCGACGCCTAT 59.936 57.895 15.93 0.00 0.00 2.57
2850 2964 4.351192 GGTCAGATTTCAAACACACACAC 58.649 43.478 0.00 0.00 0.00 3.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
81 83 0.978151 TCCTCCCACCGATTTTTCGA 59.022 50.000 0.00 0.00 34.64 3.71
93 95 0.469917 GATGAGCCGAAATCCTCCCA 59.530 55.000 0.00 0.00 0.00 4.37
262 281 3.394836 GGCCGGTGAAGGAGCTCT 61.395 66.667 14.64 0.00 0.00 4.09
383 405 4.386867 TCTAGATCAAACCCTAGTTGCG 57.613 45.455 0.00 0.00 35.97 4.85
695 777 1.818674 ACCGAACAATCCATGAAAGCC 59.181 47.619 0.00 0.00 0.00 4.35
740 822 4.038642 TGTCCTACAATCATAGCACGCATA 59.961 41.667 0.00 0.00 0.00 3.14
751 833 2.565391 ACGTGGTCATGTCCTACAATCA 59.435 45.455 10.43 0.00 0.00 2.57
772 854 3.066900 GCCTGACTAAGATCTTGCGTCTA 59.933 47.826 26.41 17.60 0.00 2.59
875 957 1.630148 GGAATCAGACTCGAACACCG 58.370 55.000 0.00 0.00 40.25 4.94
1098 1190 0.248296 GCTTCGCAACGGTGTTCAAA 60.248 50.000 0.66 0.00 0.00 2.69
1163 1255 0.764890 CCACTTCCTCAGGTGGTTGA 59.235 55.000 4.18 0.00 45.52 3.18
1201 1293 1.265236 AGGTCTCTCAGCTTGGACAG 58.735 55.000 0.00 0.00 0.00 3.51
1421 1514 4.709250 TGTGTTGCATCTGGTTGTAGTTA 58.291 39.130 0.00 0.00 0.00 2.24
1663 1760 1.841556 ACCTCCTTCACCGCCTCAA 60.842 57.895 0.00 0.00 0.00 3.02
1766 1863 1.969200 GAGCTGCCATGAGAGCCTCA 61.969 60.000 11.16 7.26 44.99 3.86
1813 1910 2.852180 GCAACGAACCCAACACCCC 61.852 63.158 0.00 0.00 0.00 4.95
2326 2438 4.453478 CAGATGTACAGTTGTCACAGCAAT 59.547 41.667 0.33 0.00 31.16 3.56
2425 2537 0.251916 CTTACCGGAGTGATTGGGCA 59.748 55.000 9.46 0.00 0.00 5.36
2530 2642 0.613260 CTGTGAATCCTCCAACCGGA 59.387 55.000 9.46 0.00 39.79 5.14
2649 2761 4.934602 CGAAGCCTTTGAGAGAGAGAAATT 59.065 41.667 0.00 0.00 0.00 1.82
2850 2964 3.395639 TGTAGCCCAAGTAAAGTTGTCG 58.604 45.455 0.00 0.00 0.00 4.35


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

AutoCloner maintained by Alex Coulton.