Multiple sequence alignment - TraesCS4B01G222000

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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 TraesCS4B01G222000 chr4B 100.000 2346 0 0 1 2346 466639181 466641526 0.000000e+00 4333
1 TraesCS4B01G222000 chr4D 94.006 1785 39 17 1 1724 379361752 379363529 0.000000e+00 2641
2 TraesCS4B01G222000 chr4A 93.426 1080 21 11 438 1469 85146727 85145650 0.000000e+00 1555
3 TraesCS4B01G222000 chr4A 91.964 336 23 2 1 336 85147063 85146732 3.530000e-128 468
4 TraesCS4B01G222000 chr4A 92.636 258 15 3 1471 1726 85142329 85142074 3.680000e-98 368
5 TraesCS4B01G222000 chr4A 80.711 394 48 17 1735 2112 7163353 7162972 4.940000e-72 281
6 TraesCS4B01G222000 chr4A 79.545 352 48 9 1735 2083 632784243 632783913 1.810000e-56 230
7 TraesCS4B01G222000 chr4A 83.534 249 23 11 1726 1959 607239998 607239753 1.410000e-52 217
8 TraesCS4B01G222000 chr4A 85.795 176 23 2 1003 1177 608990467 608990641 3.980000e-43 185
9 TraesCS4B01G222000 chr3B 92.200 641 21 11 1725 2346 30446487 30445857 0.000000e+00 880
10 TraesCS4B01G222000 chr1B 91.186 624 33 9 1735 2346 430089954 430090567 0.000000e+00 828
11 TraesCS4B01G222000 chr1B 84.255 235 26 7 1763 1991 662820839 662820610 3.930000e-53 219
12 TraesCS4B01G222000 chr5D 90.909 363 24 4 1991 2346 46616163 46615803 1.630000e-131 479
13 TraesCS4B01G222000 chr5D 94.714 227 9 3 1727 1951 46616394 46616169 1.330000e-92 350
14 TraesCS4B01G222000 chr7D 80.392 459 55 23 1720 2156 47109930 47110375 1.350000e-82 316
15 TraesCS4B01G222000 chr1A 81.006 358 46 15 1727 2074 557994559 557994214 4.970000e-67 265
16 TraesCS4B01G222000 chr2A 84.585 253 22 11 1723 1959 769557044 769557295 3.900000e-58 235
17 TraesCS4B01G222000 chr5B 86.364 176 20 2 1003 1176 705796934 705796761 3.080000e-44 189


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 TraesCS4B01G222000 chr4B 466639181 466641526 2345 False 4333.0 4333 100.000000 1 2346 1 chr4B.!!$F1 2345
1 TraesCS4B01G222000 chr4D 379361752 379363529 1777 False 2641.0 2641 94.006000 1 1724 1 chr4D.!!$F1 1723
2 TraesCS4B01G222000 chr4A 85142074 85147063 4989 True 797.0 1555 92.675333 1 1726 3 chr4A.!!$R4 1725
3 TraesCS4B01G222000 chr3B 30445857 30446487 630 True 880.0 880 92.200000 1725 2346 1 chr3B.!!$R1 621
4 TraesCS4B01G222000 chr1B 430089954 430090567 613 False 828.0 828 91.186000 1735 2346 1 chr1B.!!$F1 611
5 TraesCS4B01G222000 chr5D 46615803 46616394 591 True 414.5 479 92.811500 1727 2346 2 chr5D.!!$R1 619

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
660 672 0.104855 CACGCTCTGGCTATGGCTAA 59.895 55.0 0.0 0.0 38.73 3.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2160 5578 0.323302 TGTTATCCTGCTTCACGGCA 59.677 50.0 0.0 0.0 40.15 5.69 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
91 94 3.982475 TCGTACATGATTGGCTCATCTC 58.018 45.455 0.00 0.00 42.91 2.75
110 113 8.821686 TCATCTCCTTTTCAATATAAGGCAAA 57.178 30.769 0.00 0.00 40.59 3.68
121 124 6.894654 TCAATATAAGGCAAACAATCCAGGAA 59.105 34.615 0.00 0.00 0.00 3.36
242 245 5.236282 CAGTTCCATCCATGCATCTACTAG 58.764 45.833 0.00 0.00 0.00 2.57
243 246 3.969287 TCCATCCATGCATCTACTAGC 57.031 47.619 0.00 0.00 0.00 3.42
244 247 3.514539 TCCATCCATGCATCTACTAGCT 58.485 45.455 0.00 0.00 0.00 3.32
245 248 4.677182 TCCATCCATGCATCTACTAGCTA 58.323 43.478 0.00 0.00 0.00 3.32
275 281 0.249657 GACTGCCGACCATGATCTCC 60.250 60.000 0.00 0.00 0.00 3.71
312 318 9.918630 TGTAAAAATACTAGTAACTCACACTCC 57.081 33.333 6.70 0.00 0.00 3.85
321 327 9.815306 ACTAGTAACTCACACTCCATCATATAT 57.185 33.333 0.00 0.00 0.00 0.86
344 351 4.892433 ACAGTTTGAGAATGACTGGAGAG 58.108 43.478 7.53 0.00 33.15 3.20
402 409 6.196535 GATCGAGTCGAAGATCTTCAAATG 57.803 41.667 29.93 16.57 39.99 2.32
413 420 7.587757 CGAAGATCTTCAAATGAAAACTTTCGT 59.412 33.333 29.93 0.00 38.43 3.85
553 563 8.595362 AGGCAGTTAAAATAAGGAGCTAATTT 57.405 30.769 0.00 0.00 0.00 1.82
660 672 0.104855 CACGCTCTGGCTATGGCTAA 59.895 55.000 0.00 0.00 38.73 3.09
1200 1234 4.334118 GGTTACCCCAACGGCGGT 62.334 66.667 13.24 0.00 38.09 5.68
1266 1300 1.909376 ACACGTGTACGATCATCAGC 58.091 50.000 21.98 0.00 43.02 4.26
1672 5061 1.096967 TCGCTGTTATGCATGCCTGG 61.097 55.000 16.68 0.65 0.00 4.45
1985 5380 6.654793 CTAATTCTTCATTAGGATAGGCGC 57.345 41.667 0.00 0.00 40.59 6.53
1986 5381 4.623932 ATTCTTCATTAGGATAGGCGCA 57.376 40.909 10.83 0.00 0.00 6.09
1987 5382 3.667497 TCTTCATTAGGATAGGCGCAG 57.333 47.619 10.83 0.00 0.00 5.18
1988 5383 2.300152 TCTTCATTAGGATAGGCGCAGG 59.700 50.000 10.83 0.00 0.00 4.85
2028 5423 1.141881 CAGCCCGCGTACAAGAGAT 59.858 57.895 4.92 0.00 0.00 2.75
2032 5427 1.030457 CCCGCGTACAAGAGATAGGT 58.970 55.000 4.92 0.00 0.00 3.08
2085 5488 4.699522 AGTGGGAAAGGTCGCCGC 62.700 66.667 0.00 0.00 35.87 6.53
2160 5578 3.815401 CTCGTTCAATTGGAAACTCACCT 59.185 43.478 5.42 0.00 37.23 4.00
2163 5581 2.238521 TCAATTGGAAACTCACCTGCC 58.761 47.619 5.42 0.00 0.00 4.85
2196 5614 3.854669 AAGGGCGAGGCAGGATCG 61.855 66.667 0.00 0.00 43.00 3.69
2209 5627 2.159421 GCAGGATCGTCAAACTAGTCGA 60.159 50.000 6.83 6.83 36.77 4.20
2316 5735 6.070881 ACTGCTTTGATTAGACTCTGTCAGAT 60.071 38.462 2.22 0.00 34.60 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
60 63 4.397730 CCAATCATGTACGATCCCACAAAA 59.602 41.667 0.00 0.00 0.00 2.44
91 94 8.040132 TGGATTGTTTGCCTTATATTGAAAAGG 58.960 33.333 0.00 0.00 44.32 3.11
110 113 4.968080 AGCTAGATCTTCTTCCTGGATTGT 59.032 41.667 0.00 0.00 0.00 2.71
121 124 4.141041 TCCAAGGAGCTAGCTAGATCTTCT 60.141 45.833 31.82 21.35 38.69 2.85
242 245 4.436998 AGTCGGCACCACGCTAGC 62.437 66.667 4.06 4.06 41.91 3.42
243 246 2.507102 CAGTCGGCACCACGCTAG 60.507 66.667 0.00 0.00 41.91 3.42
244 247 4.735132 GCAGTCGGCACCACGCTA 62.735 66.667 0.00 0.00 43.97 4.26
275 281 3.689649 AGTATTTTTACAGCCAAGAGCCG 59.310 43.478 0.00 0.00 45.47 5.52
321 327 5.775195 TCTCTCCAGTCATTCTCAAACTGTA 59.225 40.000 0.00 0.00 38.97 2.74
344 351 4.789012 TCATGCAAGAAACCAAGGATTC 57.211 40.909 0.00 1.22 0.00 2.52
354 361 4.405116 AAGCCAAACTTCATGCAAGAAA 57.595 36.364 5.79 0.00 35.82 2.52
402 409 4.034048 TCAGCTCTTCACACGAAAGTTTTC 59.966 41.667 0.00 0.00 46.40 2.29
413 420 3.309682 CGACAAGTTTTCAGCTCTTCACA 59.690 43.478 0.00 0.00 0.00 3.58
532 542 8.251026 GTGCCAAATTAGCTCCTTATTTTAACT 58.749 33.333 0.00 0.00 0.00 2.24
553 563 3.866379 ATCGCTGCTTTGGGTGCCA 62.866 57.895 0.00 0.00 0.00 4.92
650 662 2.072298 CGAGGAATGCTTAGCCATAGC 58.928 52.381 0.29 0.00 39.10 2.97
660 672 2.107141 GCGGCTACGAGGAATGCT 59.893 61.111 0.00 0.00 44.60 3.79
1207 1241 1.599606 TTGTTGCGGTTGGTGTTGCT 61.600 50.000 0.00 0.00 0.00 3.91
1266 1300 8.336806 AGTACTTAGTCTACTGATCGAAAATCG 58.663 37.037 0.00 0.00 42.10 3.34
1672 5061 3.339141 GTTCTTCATCCCCACTCAGAAC 58.661 50.000 0.00 0.00 34.92 3.01
2046 5441 4.522114 TCGATGCCATTCCAACTAATTCA 58.478 39.130 0.00 0.00 0.00 2.57
2160 5578 0.323302 TGTTATCCTGCTTCACGGCA 59.677 50.000 0.00 0.00 40.15 5.69
2163 5581 2.009774 CCCTTGTTATCCTGCTTCACG 58.990 52.381 0.00 0.00 0.00 4.35
2196 5614 6.629649 CGTGATAGATCTTCGACTAGTTTGAC 59.370 42.308 0.00 0.00 0.00 3.18
2209 5627 3.736433 GCAGTGCTGACGTGATAGATCTT 60.736 47.826 8.18 0.00 0.00 2.40
2316 5735 2.143122 GTTCGCTCAACACTTGATCCA 58.857 47.619 0.00 0.00 39.30 3.41


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

AutoCloner maintained by Alex Coulton.