Multiple sequence alignment - TraesCS5B01G051700

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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 TraesCS5B01G051700 chr5B 100.000 1560 0 0 876 2435 56361471 56363030 0.000000e+00 2881.0
1 TraesCS5B01G051700 chr5B 93.756 977 50 5 891 1862 517572355 517571385 0.000000e+00 1456.0
2 TraesCS5B01G051700 chr5B 94.208 915 46 3 948 1861 297042230 297043138 0.000000e+00 1389.0
3 TraesCS5B01G051700 chr5B 100.000 376 0 0 1 376 56360596 56360971 0.000000e+00 695.0
4 TraesCS5B01G051700 chr5D 96.711 1520 31 6 917 2435 53756522 53758023 0.000000e+00 2512.0
5 TraesCS5B01G051700 chr5D 94.574 903 40 6 966 1865 397098263 397099159 0.000000e+00 1387.0
6 TraesCS5B01G051700 chr5D 91.755 376 26 4 1 376 53755547 53755917 3.590000e-143 518.0
7 TraesCS5B01G051700 chr5D 88.856 341 32 5 36 376 497306142 497305808 4.840000e-112 414.0
8 TraesCS5B01G051700 chr3D 94.521 949 34 7 921 1864 486147212 486146277 0.000000e+00 1448.0
9 TraesCS5B01G051700 chr3D 94.030 938 35 10 932 1861 124070379 124071303 0.000000e+00 1402.0
10 TraesCS5B01G051700 chr3D 96.362 852 26 3 1012 1862 363854795 363853948 0.000000e+00 1397.0
11 TraesCS5B01G051700 chr3D 89.869 306 21 10 38 343 486147833 486147538 3.800000e-103 385.0
12 TraesCS5B01G051700 chr7A 93.622 925 48 9 940 1861 700256705 700257621 0.000000e+00 1371.0
13 TraesCS5B01G051700 chr6D 92.644 938 51 6 931 1863 424649069 424648145 0.000000e+00 1334.0
14 TraesCS5B01G051700 chr4A 91.971 959 50 13 911 1867 274645253 274646186 0.000000e+00 1319.0
15 TraesCS5B01G051700 chr4A 89.655 87 9 0 2349 2435 11997409 11997323 7.120000e-21 111.0
16 TraesCS5B01G051700 chr4A 89.655 87 9 0 2349 2435 576363962 576363876 7.120000e-21 111.0
17 TraesCS5B01G051700 chrUn 88.201 339 35 5 38 376 470687619 470687952 1.360000e-107 399.0
18 TraesCS5B01G051700 chrUn 88.415 328 33 5 38 365 427412138 427412460 8.160000e-105 390.0
19 TraesCS5B01G051700 chr3A 87.500 336 37 5 41 376 308673628 308673958 1.370000e-102 383.0
20 TraesCS5B01G051700 chr3A 89.655 87 9 0 2349 2435 59680099 59680185 7.120000e-21 111.0
21 TraesCS5B01G051700 chr3B 89.967 299 25 3 38 336 207205132 207204839 4.910000e-102 381.0
22 TraesCS5B01G051700 chr3B 86.916 107 12 2 1859 1963 271740107 271740213 4.250000e-23 119.0
23 TraesCS5B01G051700 chr1D 86.550 342 36 8 38 376 441580055 441580389 3.820000e-98 368.0
24 TraesCS5B01G051700 chr2D 86.310 336 41 5 40 375 109401116 109401446 6.400000e-96 361.0
25 TraesCS5B01G051700 chr2B 90.805 87 8 0 2349 2435 312399462 312399376 1.530000e-22 117.0
26 TraesCS5B01G051700 chr2B 85.567 97 14 0 2338 2434 382672373 382672469 4.280000e-18 102.0
27 TraesCS5B01G051700 chr1A 90.805 87 8 0 2349 2435 282830044 282829958 1.530000e-22 117.0
28 TraesCS5B01G051700 chr2A 89.412 85 9 0 2351 2435 625768586 625768502 9.210000e-20 108.0
29 TraesCS5B01G051700 chr2A 92.537 67 4 1 1865 1930 283529214 283529148 7.170000e-16 95.3
30 TraesCS5B01G051700 chr4D 88.506 87 10 0 2349 2435 235448098 235448012 3.310000e-19 106.0


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 TraesCS5B01G051700 chr5B 56360596 56363030 2434 False 1788.0 2881 100.000 1 2435 2 chr5B.!!$F2 2434
1 TraesCS5B01G051700 chr5B 517571385 517572355 970 True 1456.0 1456 93.756 891 1862 1 chr5B.!!$R1 971
2 TraesCS5B01G051700 chr5B 297042230 297043138 908 False 1389.0 1389 94.208 948 1861 1 chr5B.!!$F1 913
3 TraesCS5B01G051700 chr5D 53755547 53758023 2476 False 1515.0 2512 94.233 1 2435 2 chr5D.!!$F2 2434
4 TraesCS5B01G051700 chr5D 397098263 397099159 896 False 1387.0 1387 94.574 966 1865 1 chr5D.!!$F1 899
5 TraesCS5B01G051700 chr3D 124070379 124071303 924 False 1402.0 1402 94.030 932 1861 1 chr3D.!!$F1 929
6 TraesCS5B01G051700 chr3D 363853948 363854795 847 True 1397.0 1397 96.362 1012 1862 1 chr3D.!!$R1 850
7 TraesCS5B01G051700 chr3D 486146277 486147833 1556 True 916.5 1448 92.195 38 1864 2 chr3D.!!$R2 1826
8 TraesCS5B01G051700 chr7A 700256705 700257621 916 False 1371.0 1371 93.622 940 1861 1 chr7A.!!$F1 921
9 TraesCS5B01G051700 chr6D 424648145 424649069 924 True 1334.0 1334 92.644 931 1863 1 chr6D.!!$R1 932
10 TraesCS5B01G051700 chr4A 274645253 274646186 933 False 1319.0 1319 91.971 911 1867 1 chr4A.!!$F1 956

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
262 263 0.958091 CAACCGCCACTTCATTTCCA 59.042 50.000 0.0 0.0 0.00 3.53 F
1242 1323 1.580942 GAAGATGCTTGTGCCGCAA 59.419 52.632 0.0 0.0 41.26 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1339 1432 0.035439 GGATGCTCCCGAGAAAACCA 60.035 55.000 0.0 0.0 0.0 3.67 R
2102 2220 5.973899 TGTATGCCAGCAGAAAATGTTAA 57.026 34.783 0.0 0.0 0.0 2.01 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
34 35 7.326454 TGAACATTTTCTCAAATTCACAACCA 58.674 30.769 0.00 0.0 29.41 3.67
230 231 2.496817 GTGCAAAACCAACCGCCA 59.503 55.556 0.00 0.0 0.00 5.69
262 263 0.958091 CAACCGCCACTTCATTTCCA 59.042 50.000 0.00 0.0 0.00 3.53
365 366 2.664185 CTGCCCGCATCAGATCCG 60.664 66.667 0.00 0.0 33.54 4.18
370 371 4.957684 CGCATCAGATCCGGCGCT 62.958 66.667 7.64 0.0 43.14 5.92
1242 1323 1.580942 GAAGATGCTTGTGCCGCAA 59.419 52.632 0.00 0.0 41.26 4.85
1326 1419 2.184322 GCTGGCGAGACCGATGAA 59.816 61.111 0.00 0.0 43.94 2.57
1339 1432 1.227380 GATGAAGAGGCGATGGCGT 60.227 57.895 0.00 0.0 41.24 5.68
1345 1438 2.282180 AGGCGATGGCGTGGTTTT 60.282 55.556 0.00 0.0 41.24 2.43
1350 1443 1.794222 GATGGCGTGGTTTTCTCGG 59.206 57.895 0.00 0.0 0.00 4.63
1351 1444 1.644786 GATGGCGTGGTTTTCTCGGG 61.645 60.000 0.00 0.0 0.00 5.14
1352 1445 2.031465 GGCGTGGTTTTCTCGGGA 59.969 61.111 0.00 0.0 0.00 5.14
1432 1529 0.325272 GAAGAAGGGGCCGAAGAAGT 59.675 55.000 0.00 0.0 0.00 3.01
1515 1618 3.109847 CTTCTCGGAGGAGGAGGAG 57.890 63.158 5.32 0.0 41.54 3.69
1696 1801 7.817962 ACTAGTAGCATGTCGTTTTACATCTTT 59.182 33.333 0.00 0.0 38.01 2.52
1737 1855 4.565652 GGAGTTGCTCTTTTGGACCATCTA 60.566 45.833 0.00 0.0 0.00 1.98
1738 1856 5.184892 AGTTGCTCTTTTGGACCATCTAT 57.815 39.130 0.00 0.0 0.00 1.98
1739 1857 5.574188 AGTTGCTCTTTTGGACCATCTATT 58.426 37.500 0.00 0.0 0.00 1.73
1740 1858 6.012745 AGTTGCTCTTTTGGACCATCTATTT 58.987 36.000 0.00 0.0 0.00 1.40
1741 1859 5.902613 TGCTCTTTTGGACCATCTATTTG 57.097 39.130 0.00 0.0 0.00 2.32
1742 1860 4.706476 TGCTCTTTTGGACCATCTATTTGG 59.294 41.667 0.00 0.0 42.82 3.28
1743 1861 4.949856 GCTCTTTTGGACCATCTATTTGGA 59.050 41.667 0.00 0.0 39.25 3.53
1744 1862 5.163612 GCTCTTTTGGACCATCTATTTGGAC 60.164 44.000 0.00 0.0 39.25 4.02
1749 1867 3.756117 GGACCATCTATTTGGACCATCC 58.244 50.000 0.00 0.0 46.78 3.51
1913 2031 7.555087 TCATGTTGTTTTCCTGTCTGAAAAAT 58.445 30.769 0.93 0.0 43.64 1.82
1921 2039 8.504815 GTTTTCCTGTCTGAAAAATAGAGTACC 58.495 37.037 0.93 0.0 43.64 3.34
2078 2196 5.382303 GGAATGAACACGTGAACTTACATG 58.618 41.667 25.01 0.0 0.00 3.21
2130 2248 2.857186 TCTGCTGGCATACAAACTGA 57.143 45.000 0.00 0.0 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 7.492020 TGGTTGTGAATTTGAGAAAATGTTCAG 59.508 33.333 0.00 0.00 36.09 3.02
109 110 3.223435 CATATGGACCGTCTACTGGAGT 58.777 50.000 0.00 0.00 0.00 3.85
141 142 3.083997 GAGGAGGCCACGGTCCAT 61.084 66.667 5.01 0.00 35.02 3.41
149 150 3.426787 TTTTAAATCACGAGGAGGCCA 57.573 42.857 5.01 0.00 0.00 5.36
215 216 2.279851 GGTGGCGGTTGGTTTTGC 60.280 61.111 0.00 0.00 0.00 3.68
1136 1216 4.746951 CGTCGTAGGCACACGCGA 62.747 66.667 15.93 4.42 40.96 5.87
1225 1306 3.762293 TTGCGGCACAAGCATCTT 58.238 50.000 0.05 0.00 44.74 2.40
1242 1323 3.201487 TGATCTCCTTCATGTTGATGCCT 59.799 43.478 0.00 0.00 0.00 4.75
1326 1419 2.748058 AAAACCACGCCATCGCCTCT 62.748 55.000 0.00 0.00 39.84 3.69
1339 1432 0.035439 GGATGCTCCCGAGAAAACCA 60.035 55.000 0.00 0.00 0.00 3.67
1350 1443 1.359475 GACGTACTCCGGATGCTCC 59.641 63.158 3.57 0.00 42.24 4.70
1351 1444 1.359475 GGACGTACTCCGGATGCTC 59.641 63.158 3.57 0.00 42.24 4.26
1352 1445 1.379443 TGGACGTACTCCGGATGCT 60.379 57.895 3.57 0.00 43.03 3.79
1432 1529 2.122989 GGGACCGGCCTCATCCTA 60.123 66.667 14.47 0.00 36.66 2.94
1456 1553 1.148867 AGAGGACTCGATGGGGATCAT 59.851 52.381 0.00 0.00 39.13 2.45
1490 1587 0.682855 CTCCTCCGAGAAGTCTGCCT 60.683 60.000 0.00 0.00 38.52 4.75
1513 1616 2.766229 GCACCCCTCCTCCTCCTC 60.766 72.222 0.00 0.00 0.00 3.71
1514 1617 4.787280 CGCACCCCTCCTCCTCCT 62.787 72.222 0.00 0.00 0.00 3.69
1515 1618 4.779733 TCGCACCCCTCCTCCTCC 62.780 72.222 0.00 0.00 0.00 4.30
1745 1863 1.813513 AAGCTCAACTCCAACGGATG 58.186 50.000 0.00 0.00 0.00 3.51
1746 1864 2.568623 AAAGCTCAACTCCAACGGAT 57.431 45.000 0.00 0.00 0.00 4.18
1747 1865 2.341846 AAAAGCTCAACTCCAACGGA 57.658 45.000 0.00 0.00 0.00 4.69
1913 2031 4.223700 TCTTCAGTCAGTACGGGTACTCTA 59.776 45.833 8.48 0.00 43.98 2.43
1921 2039 1.920574 CGCAATCTTCAGTCAGTACGG 59.079 52.381 0.00 0.00 0.00 4.02
2102 2220 5.973899 TGTATGCCAGCAGAAAATGTTAA 57.026 34.783 0.00 0.00 0.00 2.01


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

AutoCloner maintained by Alex Coulton.