Multiple sequence alignment - TraesCS1B01G081100

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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 TraesCS1B01G081100 chr1B 100.000 2401 0 0 1 2401 63758503 63760903 0.000000e+00 4434.0
1 TraesCS1B01G081100 chr1B 92.854 2421 147 14 1 2401 63479096 63481510 0.000000e+00 3489.0
2 TraesCS1B01G081100 chr1B 92.387 2417 153 15 3 2401 63467866 63470269 0.000000e+00 3415.0
3 TraesCS1B01G081100 chr1B 92.387 2417 152 14 1 2399 63808107 63810509 0.000000e+00 3415.0
4 TraesCS1B01G081100 chr1B 95.654 1933 69 3 1 1918 63613506 63615438 0.000000e+00 3090.0
5 TraesCS1B01G081100 chr1B 93.451 1695 93 5 1 1677 63888395 63890089 0.000000e+00 2499.0
6 TraesCS1B01G081100 chr1A 90.890 2426 177 27 2 2401 43272334 43269927 0.000000e+00 3216.0
7 TraesCS1B01G081100 chr1A 89.720 2432 173 25 2 2401 43392951 43390565 0.000000e+00 3035.0
8 TraesCS1B01G081100 chr1A 80.870 460 59 22 247 690 42718627 42719073 3.820000e-88 335.0
9 TraesCS1B01G081100 chr1D 90.534 1891 133 25 535 2401 43823100 43824968 0.000000e+00 2459.0
10 TraesCS1B01G081100 chr1D 90.479 1880 135 14 535 2401 44275018 44276866 0.000000e+00 2440.0
11 TraesCS1B01G081100 chr1D 90.395 1593 118 28 408 1987 44628791 44630361 0.000000e+00 2061.0
12 TraesCS1B01G081100 chr1D 90.034 592 45 11 1818 2401 44160031 44160616 0.000000e+00 754.0
13 TraesCS1B01G081100 chr1D 85.765 281 26 6 254 520 43822414 43822694 3.910000e-73 285.0
14 TraesCS1B01G081100 chr4B 86.420 81 5 4 2200 2275 50463843 50463922 1.530000e-12 84.2


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 TraesCS1B01G081100 chr1B 63758503 63760903 2400 False 4434 4434 100.0000 1 2401 1 chr1B.!!$F4 2400
1 TraesCS1B01G081100 chr1B 63479096 63481510 2414 False 3489 3489 92.8540 1 2401 1 chr1B.!!$F2 2400
2 TraesCS1B01G081100 chr1B 63467866 63470269 2403 False 3415 3415 92.3870 3 2401 1 chr1B.!!$F1 2398
3 TraesCS1B01G081100 chr1B 63808107 63810509 2402 False 3415 3415 92.3870 1 2399 1 chr1B.!!$F5 2398
4 TraesCS1B01G081100 chr1B 63613506 63615438 1932 False 3090 3090 95.6540 1 1918 1 chr1B.!!$F3 1917
5 TraesCS1B01G081100 chr1B 63888395 63890089 1694 False 2499 2499 93.4510 1 1677 1 chr1B.!!$F6 1676
6 TraesCS1B01G081100 chr1A 43269927 43272334 2407 True 3216 3216 90.8900 2 2401 1 chr1A.!!$R1 2399
7 TraesCS1B01G081100 chr1A 43390565 43392951 2386 True 3035 3035 89.7200 2 2401 1 chr1A.!!$R2 2399
8 TraesCS1B01G081100 chr1D 44275018 44276866 1848 False 2440 2440 90.4790 535 2401 1 chr1D.!!$F2 1866
9 TraesCS1B01G081100 chr1D 44628791 44630361 1570 False 2061 2061 90.3950 408 1987 1 chr1D.!!$F3 1579
10 TraesCS1B01G081100 chr1D 43822414 43824968 2554 False 1372 2459 88.1495 254 2401 2 chr1D.!!$F4 2147
11 TraesCS1B01G081100 chr1D 44160031 44160616 585 False 754 754 90.0340 1818 2401 1 chr1D.!!$F1 583

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
923 1337 0.663153 GCCATAGCCATGACGAAACC 59.337 55.0 0.0 0.0 33.67 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2124 2589 5.703978 TTTGTAGATGTTGGTTCATGGTG 57.296 39.13 0.0 0.0 0.0 4.17 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
143 144 3.853330 CCGTGAGCGAATGCACCG 61.853 66.667 6.02 6.02 46.23 4.94
164 165 3.570550 CGGTGGGACAAAAATAGGTTTGA 59.429 43.478 4.76 0.00 44.16 2.69
189 190 5.517054 GCGAATCTTAAAGACAGACGAGATT 59.483 40.000 0.00 0.00 36.76 2.40
235 236 8.190888 GTGAAGTAGTTATTTCACATCTGGAG 57.809 38.462 17.46 0.00 46.10 3.86
413 429 5.163163 TGCAGTGCCATATCTTCCTATCTTT 60.163 40.000 13.72 0.00 0.00 2.52
469 485 4.013728 GTGGATGTGCAACTAATGGGTAA 58.986 43.478 0.00 0.00 38.04 2.85
691 1104 9.830186 AGAACTAATGTATGGTGTATCCTCTAT 57.170 33.333 0.00 0.00 37.07 1.98
923 1337 0.663153 GCCATAGCCATGACGAAACC 59.337 55.000 0.00 0.00 33.67 3.27
933 1347 0.950836 TGACGAAACCCATGTGCTTG 59.049 50.000 0.00 0.00 0.00 4.01
1044 1458 1.002201 CAACAATGGCCAGCAAATCCA 59.998 47.619 13.05 0.00 0.00 3.41
1047 1461 2.106166 ACAATGGCCAGCAAATCCAAAA 59.894 40.909 13.05 0.00 33.04 2.44
1070 1484 1.686587 AGATCCATCGGACGCATGTTA 59.313 47.619 0.00 0.00 32.98 2.41
1392 1831 2.504175 GCAGGTTACACATTCCCTCCTA 59.496 50.000 0.00 0.00 0.00 2.94
1892 2350 0.755686 GATGGACCCTACCTGAGCTG 59.244 60.000 0.00 0.00 0.00 4.24
1949 2410 2.964464 TCACGGTGTTTACCCTGACTAA 59.036 45.455 8.17 0.00 44.53 2.24
2077 2542 1.178276 TTTTGGGCTCAACGTTGTGT 58.822 45.000 26.47 0.00 31.78 3.72
2092 2557 5.801380 ACGTTGTGTAGATTATGGAAACCT 58.199 37.500 0.00 0.00 0.00 3.50
2126 2591 5.948348 CGACTCGCATGTACTAAATAACAC 58.052 41.667 0.00 0.00 0.00 3.32
2133 2598 6.905076 CGCATGTACTAAATAACACCATGAAC 59.095 38.462 0.00 0.00 32.07 3.18
2138 2603 7.720074 TGTACTAAATAACACCATGAACCAACA 59.280 33.333 0.00 0.00 0.00 3.33
2187 2656 5.997385 AGCAGGTTAGTTTTGTTCGTTATG 58.003 37.500 0.00 0.00 0.00 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 2.594303 TGGCAGGCCGTTTGTCTG 60.594 61.111 5.74 0.00 39.42 3.51
120 121 1.358725 GCATTCGCTCACGGCTGTTA 61.359 55.000 0.00 0.00 40.63 2.41
143 144 4.560716 GCTCAAACCTATTTTTGTCCCACC 60.561 45.833 0.00 0.00 37.66 4.61
164 165 4.156190 TCTCGTCTGTCTTTAAGATTCGCT 59.844 41.667 0.00 0.00 0.00 4.93
189 190 5.893824 TCACATCTAAGTCTAGAGCCATTGA 59.106 40.000 0.00 0.00 37.58 2.57
261 262 8.349568 ACATCTACAGACTACAACATTACAGA 57.650 34.615 0.00 0.00 0.00 3.41
449 465 5.852282 ATTTACCCATTAGTTGCACATCC 57.148 39.130 0.00 0.00 0.00 3.51
531 654 6.614160 TGAACTTCTCATCGACACGTTATAA 58.386 36.000 0.00 0.00 0.00 0.98
716 1129 2.945008 AGATATGGCACCATGTCAAACG 59.055 45.455 23.35 0.00 43.85 3.60
815 1229 5.104402 TCTGTGAATGTGTGGGATACATGAT 60.104 40.000 0.00 0.00 42.24 2.45
923 1337 3.646611 TGATGAAACACAAGCACATGG 57.353 42.857 0.00 0.00 0.00 3.66
933 1347 5.297776 CCCAATAGTGAGGATGATGAAACAC 59.702 44.000 0.00 0.00 0.00 3.32
994 1408 2.171237 CACACTCCTTGATCATGGCCTA 59.829 50.000 20.32 5.27 0.00 3.93
1044 1458 3.804036 TGCGTCCGATGGATCTATTTTT 58.196 40.909 0.00 0.00 32.73 1.94
1047 1461 2.300152 ACATGCGTCCGATGGATCTATT 59.700 45.455 0.00 0.00 32.73 1.73
1234 1648 5.187687 TGTATGCAATGGCGATCATCATAT 58.812 37.500 0.00 0.00 45.35 1.78
1288 1702 6.582295 GCATCACTAAAATCAAAATCGTGTGT 59.418 34.615 0.00 0.00 0.00 3.72
1392 1831 4.948621 ACTAAACTAGAGTCACTACGCCAT 59.051 41.667 0.00 0.00 0.00 4.40
2124 2589 5.703978 TTTGTAGATGTTGGTTCATGGTG 57.296 39.130 0.00 0.00 0.00 4.17
2126 2591 9.703892 TTTTTATTTGTAGATGTTGGTTCATGG 57.296 29.630 0.00 0.00 0.00 3.66
2334 2815 8.474025 TGTCCAGTATTTTGAAAAGATGTTTGT 58.526 29.630 0.00 0.00 0.00 2.83


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

AutoCloner maintained by Alex Coulton.