Multiple sequence alignment - TraesCS5B01G409200

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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 TraesCS5B01G409200 chr5B 100.000 2579 0 0 1 2579 584816878 584814300 0.000000e+00 4763
1 TraesCS5B01G409200 chr5B 96.644 1728 58 0 1 1728 64293482 64295209 0.000000e+00 2870
2 TraesCS5B01G409200 chr5B 97.381 1489 36 3 672 2158 234884883 234883396 0.000000e+00 2531
3 TraesCS5B01G409200 chr5B 95.072 487 23 1 2094 2579 234883695 234883209 0.000000e+00 765
4 TraesCS5B01G409200 chr5B 95.683 417 16 2 1860 2275 584814902 584814487 0.000000e+00 669
5 TraesCS5B01G409200 chr5B 95.683 417 16 2 1977 2392 584815019 584814604 0.000000e+00 669
6 TraesCS5B01G409200 chr5B 83.922 510 55 8 2094 2579 709184880 709184374 1.810000e-126 462
7 TraesCS5B01G409200 chr5B 94.850 233 10 1 2347 2579 701831218 701830988 1.890000e-96 363
8 TraesCS5B01G409200 chr4A 90.588 2093 170 19 4 2088 564697244 564699317 0.000000e+00 2748
9 TraesCS5B01G409200 chr2A 92.674 1911 127 8 1 1907 48624185 48622284 0.000000e+00 2741
10 TraesCS5B01G409200 chr3A 90.720 2015 160 23 177 2181 497386153 497388150 0.000000e+00 2660
11 TraesCS5B01G409200 chr2B 96.389 1606 55 3 672 2276 549353568 549355171 0.000000e+00 2641
12 TraesCS5B01G409200 chr2B 93.864 603 36 1 1977 2579 549354756 549355357 0.000000e+00 907
13 TraesCS5B01G409200 chr2B 93.827 486 30 0 2094 2579 68147204 68147689 0.000000e+00 732
14 TraesCS5B01G409200 chr2B 95.652 115 5 0 2465 2579 71641154 71641040 4.380000e-43 185
15 TraesCS5B01G409200 chr6B 88.842 2151 196 29 1 2143 281223361 281221247 0.000000e+00 2603
16 TraesCS5B01G409200 chr6B 93.416 486 32 0 2094 2579 679253505 679253990 0.000000e+00 721
17 TraesCS5B01G409200 chr6B 83.071 254 34 7 2329 2579 522428533 522428286 3.340000e-54 222
18 TraesCS5B01G409200 chr2D 89.274 2107 184 29 1 2089 632766191 632768273 0.000000e+00 2601
19 TraesCS5B01G409200 chr1D 89.272 2088 170 31 1 2067 14674815 14672761 0.000000e+00 2566
20 TraesCS5B01G409200 chr3B 87.494 2159 197 46 1 2122 809559686 809557564 0.000000e+00 2423
21 TraesCS5B01G409200 chr3B 93.878 490 26 1 2094 2579 604264132 604263643 0.000000e+00 736
22 TraesCS5B01G409200 chr5A 93.959 1109 64 3 1 1108 599230979 599232085 0.000000e+00 1674
23 TraesCS5B01G409200 chr4B 94.215 484 27 1 2096 2579 310258071 310258553 0.000000e+00 737


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 TraesCS5B01G409200 chr5B 584814300 584816878 2578 True 2033.666667 4763 97.1220 1 2579 3 chr5B.!!$R4 2578
1 TraesCS5B01G409200 chr5B 64293482 64295209 1727 False 2870.000000 2870 96.6440 1 1728 1 chr5B.!!$F1 1727
2 TraesCS5B01G409200 chr5B 234883209 234884883 1674 True 1648.000000 2531 96.2265 672 2579 2 chr5B.!!$R3 1907
3 TraesCS5B01G409200 chr5B 709184374 709184880 506 True 462.000000 462 83.9220 2094 2579 1 chr5B.!!$R2 485
4 TraesCS5B01G409200 chr4A 564697244 564699317 2073 False 2748.000000 2748 90.5880 4 2088 1 chr4A.!!$F1 2084
5 TraesCS5B01G409200 chr2A 48622284 48624185 1901 True 2741.000000 2741 92.6740 1 1907 1 chr2A.!!$R1 1906
6 TraesCS5B01G409200 chr3A 497386153 497388150 1997 False 2660.000000 2660 90.7200 177 2181 1 chr3A.!!$F1 2004
7 TraesCS5B01G409200 chr2B 549353568 549355357 1789 False 1774.000000 2641 95.1265 672 2579 2 chr2B.!!$F2 1907
8 TraesCS5B01G409200 chr6B 281221247 281223361 2114 True 2603.000000 2603 88.8420 1 2143 1 chr6B.!!$R1 2142
9 TraesCS5B01G409200 chr2D 632766191 632768273 2082 False 2601.000000 2601 89.2740 1 2089 1 chr2D.!!$F1 2088
10 TraesCS5B01G409200 chr1D 14672761 14674815 2054 True 2566.000000 2566 89.2720 1 2067 1 chr1D.!!$R1 2066
11 TraesCS5B01G409200 chr3B 809557564 809559686 2122 True 2423.000000 2423 87.4940 1 2122 1 chr3B.!!$R2 2121
12 TraesCS5B01G409200 chr5A 599230979 599232085 1106 False 1674.000000 1674 93.9590 1 1108 1 chr5A.!!$F1 1107

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
287 288 0.522626 CATTTGATGACCGCAGCACA 59.477 50.0 0.0 0.0 40.65 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2057 2108 1.860676 CGTTCTTGGGTTCTTCGTCA 58.139 50.0 0.0 0.0 0.0 4.35 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
188 189 0.620556 AGGGACGGTAGGTCTTACGA 59.379 55.000 0.00 0.00 45.35 3.43
287 288 0.522626 CATTTGATGACCGCAGCACA 59.477 50.000 0.00 0.00 40.65 4.57
296 297 2.031516 CCGCAGCACAGGTGAGAAG 61.032 63.158 3.10 0.00 32.98 2.85
349 350 4.498345 GGTTGCACGAGTTTACATTGGAAA 60.498 41.667 0.00 0.00 0.00 3.13
519 520 4.745351 TGGATGATCTAGCTGGATACACT 58.255 43.478 13.16 0.00 46.17 3.55
618 619 2.946329 ACACAACGTTAGGACATGCAAA 59.054 40.909 0.00 0.00 0.00 3.68
663 664 1.593209 TCAAACACGTGGACGGAGC 60.593 57.895 21.57 0.00 44.95 4.70
983 1006 1.195442 TCCATGACAAGGCCACCGTA 61.195 55.000 5.01 0.00 0.00 4.02
1315 1339 6.244552 ACTTCAGCTGGATAGATCATGAAA 57.755 37.500 15.13 0.00 0.00 2.69
1910 1960 2.240162 CTGGAACCTACCGCCAGGAC 62.240 65.000 7.47 2.00 44.24 3.85
1964 2015 1.172812 AAGAACCCAAGAACGCTGGC 61.173 55.000 0.00 0.00 0.00 4.85
1965 2016 2.966309 GAACCCAAGAACGCTGGCG 61.966 63.158 13.56 13.56 46.03 5.69
1968 2019 2.047655 CCAAGAACGCTGGCGGTA 60.048 61.111 18.99 0.00 40.58 4.02
1969 2020 2.100631 CCAAGAACGCTGGCGGTAG 61.101 63.158 18.99 6.31 40.58 3.18
1970 2021 2.100631 CAAGAACGCTGGCGGTAGG 61.101 63.158 18.99 2.14 40.58 3.18
1971 2022 2.280552 AAGAACGCTGGCGGTAGGA 61.281 57.895 18.99 0.00 40.58 2.94
1972 2023 2.502692 AAGAACGCTGGCGGTAGGAC 62.503 60.000 18.99 0.72 40.58 3.85
1973 2024 4.078516 AACGCTGGCGGTAGGACC 62.079 66.667 18.99 0.00 44.69 4.46
2025 2076 3.470888 CTGGACCCTACCGCCAGG 61.471 72.222 0.00 0.00 44.24 4.45
2027 2078 2.446036 GGACCCTACCGCCAGGAT 60.446 66.667 0.00 0.00 41.02 3.24
2028 2079 2.808206 GGACCCTACCGCCAGGATG 61.808 68.421 0.00 0.00 41.02 3.51
2070 2121 2.234300 GTTCTGTGACGAAGAACCCA 57.766 50.000 4.89 0.00 45.10 4.51
2072 2123 2.526304 TCTGTGACGAAGAACCCAAG 57.474 50.000 0.00 0.00 0.00 3.61
2073 2124 2.036387 TCTGTGACGAAGAACCCAAGA 58.964 47.619 0.00 0.00 0.00 3.02
2074 2125 2.432874 TCTGTGACGAAGAACCCAAGAA 59.567 45.455 0.00 0.00 0.00 2.52
2075 2126 2.544267 CTGTGACGAAGAACCCAAGAAC 59.456 50.000 0.00 0.00 0.00 3.01
2076 2127 1.525619 GTGACGAAGAACCCAAGAACG 59.474 52.381 0.00 0.00 0.00 3.95
2077 2128 0.511653 GACGAAGAACCCAAGAACGC 59.488 55.000 0.00 0.00 0.00 4.84
2078 2129 0.106149 ACGAAGAACCCAAGAACGCT 59.894 50.000 0.00 0.00 0.00 5.07
2079 2130 0.512952 CGAAGAACCCAAGAACGCTG 59.487 55.000 0.00 0.00 0.00 5.18
2080 2131 0.875059 GAAGAACCCAAGAACGCTGG 59.125 55.000 0.00 0.00 0.00 4.85
2101 2152 1.307647 GTAGGACCGGACCCTACCA 59.692 63.158 30.38 12.91 46.52 3.25
2260 2314 3.976490 CTGGACCCTACCGCCAGGA 62.976 68.421 0.00 0.00 44.24 3.86
2531 2608 6.519761 CACGAATAGCACATGTTCAAACTAAC 59.480 38.462 0.00 0.00 0.00 2.34
2550 2627 3.495434 ACTAAAACATGACCCGGTTCA 57.505 42.857 3.36 3.36 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
188 189 1.676014 GCACCTCGTAAGCAACTCCAT 60.676 52.381 0.00 0.00 37.18 3.41
287 288 3.430929 GGATACGTTCATGCTTCTCACCT 60.431 47.826 0.00 0.00 0.00 4.00
349 350 1.620822 GCCCACATCAACCTTGTTCT 58.379 50.000 0.00 0.00 0.00 3.01
519 520 4.220382 CCACTACCAAATTGCTTCATTCCA 59.780 41.667 0.00 0.00 0.00 3.53
618 619 1.402613 CCCGTGTTGGTTCTTCGTTTT 59.597 47.619 0.00 0.00 35.15 2.43
663 664 1.616628 ACCCCCTCCAAGGCTACTG 60.617 63.158 0.00 0.00 32.73 2.74
1441 1465 4.382541 TGCCCTCTCCTCCTCGCA 62.383 66.667 0.00 0.00 0.00 5.10
1965 2016 4.266962 GTAGGGTCCGGTCCTACC 57.733 66.667 29.66 19.34 46.75 3.18
1967 2018 2.597340 CGGTAGGGTCCGGTCCTA 59.403 66.667 17.57 17.82 45.88 2.94
1974 2025 3.782443 CCTGTGGCGGTAGGGTCC 61.782 72.222 0.00 0.00 0.00 4.46
1975 2026 4.468689 GCCTGTGGCGGTAGGGTC 62.469 72.222 4.07 0.00 39.62 4.46
1994 2045 4.181010 CCAGCAGCCTACCGCCAT 62.181 66.667 0.00 0.00 38.78 4.40
2051 2102 2.234300 TGGGTTCTTCGTCACAGAAC 57.766 50.000 4.52 4.52 46.50 3.01
2057 2108 1.860676 CGTTCTTGGGTTCTTCGTCA 58.139 50.000 0.00 0.00 0.00 4.35
2067 2118 3.599285 TACCGCCAGCGTTCTTGGG 62.599 63.158 11.55 0.00 37.81 4.12
2068 2119 2.047655 TACCGCCAGCGTTCTTGG 60.048 61.111 11.55 0.00 37.81 3.61
2069 2120 2.100631 CCTACCGCCAGCGTTCTTG 61.101 63.158 11.55 0.00 37.81 3.02
2070 2121 2.264794 CCTACCGCCAGCGTTCTT 59.735 61.111 11.55 0.00 37.81 2.52
2072 2123 2.508663 GTCCTACCGCCAGCGTTC 60.509 66.667 11.55 0.00 37.81 3.95
2073 2124 4.078516 GGTCCTACCGCCAGCGTT 62.079 66.667 11.55 0.00 37.81 4.84
2366 2424 1.449601 CCACAGTCCATGGCGGTAC 60.450 63.158 6.96 0.00 35.57 3.34
2531 2608 4.839668 TTTGAACCGGGTCATGTTTTAG 57.160 40.909 25.78 0.00 0.00 1.85
2550 2627 9.236006 AGCTATTAGTTTGAACTGATGTCATTT 57.764 29.630 10.39 0.00 40.07 2.32


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

AutoCloner maintained by Alex Coulton.