Multiple sequence alignment - TraesCS5B01G050300

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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 TraesCS5B01G050300 chr5B 100.000 2336 0 0 1 2336 55377019 55374684 0.000000e+00 4314.0
1 TraesCS5B01G050300 chr5B 81.481 189 27 8 999 1179 55547858 55547670 5.200000e-32 148.0
2 TraesCS5B01G050300 chr5D 96.751 2339 69 5 1 2335 52290353 52288018 0.000000e+00 3892.0
3 TraesCS5B01G050300 chr5D 94.180 2079 71 19 269 2335 52286822 52284782 0.000000e+00 3123.0
4 TraesCS5B01G050300 chr5D 81.383 188 27 8 999 1179 52397923 52397737 1.870000e-31 147.0
5 TraesCS5B01G050300 chr5A 92.736 647 31 9 1694 2335 41428327 41427692 0.000000e+00 920.0
6 TraesCS5B01G050300 chr5A 89.982 549 45 8 708 1252 41429955 41429413 0.000000e+00 701.0
7 TraesCS5B01G050300 chr5A 90.549 455 36 6 1231 1680 41428840 41428388 1.550000e-166 595.0
8 TraesCS5B01G050300 chr5A 94.118 68 4 0 60 127 41432149 41432082 1.140000e-18 104.0
9 TraesCS5B01G050300 chr1A 91.935 62 5 0 1700 1761 527789634 527789695 1.150000e-13 87.9


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 TraesCS5B01G050300 chr5B 55374684 55377019 2335 True 4314.0 4314 100.00000 1 2336 1 chr5B.!!$R1 2335
1 TraesCS5B01G050300 chr5D 52284782 52290353 5571 True 3507.5 3892 95.46550 1 2335 2 chr5D.!!$R2 2334
2 TraesCS5B01G050300 chr5A 41427692 41432149 4457 True 580.0 920 91.84625 60 2335 4 chr5A.!!$R1 2275

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
174 499 0.320858 TGCAACGTCTGGCGGAAATA 60.321 50.0 6.61 0.0 46.52 1.40 F
1180 2814 0.461548 TACAGCAGGATCTGAAGGCG 59.538 55.0 0.00 0.0 37.51 5.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1214 2848 0.105760 TTGGTCACCCTTGCATTGGT 60.106 50.000 1.93 1.93 34.40 3.67 R
2150 4434 3.769536 CAGGTGACTTGGTTTGTTTCAC 58.230 45.455 0.00 0.00 40.21 3.18 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
174 499 0.320858 TGCAACGTCTGGCGGAAATA 60.321 50.000 6.61 0.00 46.52 1.40
296 639 5.295431 TCAGCAACATTGTTTCCTAATCG 57.705 39.130 0.00 0.00 0.00 3.34
301 644 5.004726 GCAACATTGTTTCCTAATCGAATGC 59.995 40.000 0.00 0.00 0.00 3.56
314 657 4.891098 ATCGAATGCCCGATATGCTGGG 62.891 54.545 4.30 0.71 46.16 4.45
377 721 8.025243 AGTGGTACAAAACTACAAATATCACG 57.975 34.615 0.00 0.00 44.16 4.35
455 799 0.875059 GTCTCGGTGCCTTTTTCCAG 59.125 55.000 0.00 0.00 0.00 3.86
481 825 3.945981 AACACATTGCTGCATCATTCA 57.054 38.095 1.84 0.00 0.00 2.57
1005 2638 5.253330 GTGTTTATTCCTGGAGACATGGAA 58.747 41.667 0.00 0.00 45.36 3.53
1180 2814 0.461548 TACAGCAGGATCTGAAGGCG 59.538 55.000 0.00 0.00 37.51 5.52
1208 2842 0.609662 GGGTTAAGCCAGACGTACCA 59.390 55.000 18.84 0.00 39.65 3.25
1209 2843 1.002315 GGGTTAAGCCAGACGTACCAA 59.998 52.381 18.84 0.00 39.65 3.67
1214 2848 1.045407 AGCCAGACGTACCAAACTGA 58.955 50.000 1.53 0.00 32.90 3.41
1215 2849 1.145803 GCCAGACGTACCAAACTGAC 58.854 55.000 1.53 0.00 32.90 3.51
1258 3488 0.605083 AGAGCACTGCGAACATGAGA 59.395 50.000 0.00 0.00 0.00 3.27
1259 3489 1.001293 AGAGCACTGCGAACATGAGAA 59.999 47.619 0.00 0.00 0.00 2.87
1341 3571 3.181489 GCTTCTTTCCATGCTGATTCTGG 60.181 47.826 0.00 0.00 0.00 3.86
1672 3906 8.306761 ACTCAATTGGACTTTTAAAGCCATTAG 58.693 33.333 16.98 14.20 35.59 1.73
1733 4015 5.587289 GCCATGGCAATTCGTTTAAATCTA 58.413 37.500 32.08 0.00 41.49 1.98
1761 4043 4.323553 TTTTGGTCCAAAATTACCACCG 57.676 40.909 23.25 0.00 45.31 4.94
1770 4052 2.922740 AATTACCACCGTCACACACT 57.077 45.000 0.00 0.00 0.00 3.55
1930 4214 3.153919 TGTAACAAACCCTGCTGAATCC 58.846 45.455 0.00 0.00 0.00 3.01
1943 4227 0.471191 TGAATCCGATGCTGCCTCAT 59.529 50.000 5.78 0.00 0.00 2.90
2013 4297 5.506686 TGCACAACTTATAACTGCAACAA 57.493 34.783 0.00 0.00 34.97 2.83
2050 4334 6.306987 ACATACAATCTTTGAACTCCCAGTT 58.693 36.000 0.00 0.00 41.95 3.16
2056 4340 4.457466 TCTTTGAACTCCCAGTTACAACC 58.543 43.478 0.00 0.00 38.80 3.77
2150 4434 0.040067 GCCTTCTGAAGCAAACCACG 60.040 55.000 11.93 0.00 0.00 4.94
2168 4452 3.168193 CACGTGAAACAAACCAAGTCAC 58.832 45.455 10.90 0.00 35.74 3.67
2193 4482 7.459795 CTGCTATATCACAGGATCAGTTCTA 57.540 40.000 0.00 0.00 34.89 2.10
2258 7783 7.608153 TCTGTAAACTGCAAATGTAGTAGCTA 58.392 34.615 4.56 0.00 40.09 3.32
2335 7860 4.082081 CAGCAAGCTTTATTCATCAACCCA 60.082 41.667 0.00 0.00 0.00 4.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
79 80 8.653191 TCTAACTTTCTAAGGATAAACACACCA 58.347 33.333 0.00 0.00 0.00 4.17
174 499 6.183360 GGGCTTAAAAGATCATCTTCTGCAAT 60.183 38.462 0.00 0.00 35.27 3.56
296 639 2.559785 CCCAGCATATCGGGCATTC 58.440 57.895 0.00 0.00 35.09 2.67
543 1206 2.293399 GTGCCTTTGTTGGTTAGACAGG 59.707 50.000 0.00 0.00 0.00 4.00
683 2315 7.337689 GCATGGTATATATCCAGAAGATGCAAA 59.662 37.037 14.91 0.00 36.54 3.68
752 2384 1.133637 TGGTGCCTTTGTTGCTTAGGA 60.134 47.619 0.00 0.00 0.00 2.94
886 2519 7.410174 TGGATGATGGAACCTTACAATAAACT 58.590 34.615 0.00 0.00 0.00 2.66
1005 2638 1.271597 GCCATCTTGACCTTGTGGACT 60.272 52.381 0.00 0.00 37.04 3.85
1180 2814 2.755876 GCTTAACCCCCTGCAGGC 60.756 66.667 28.39 9.49 0.00 4.85
1189 2823 0.609662 TGGTACGTCTGGCTTAACCC 59.390 55.000 0.00 0.00 37.83 4.11
1208 2842 1.688197 CACCCTTGCATTGGTCAGTTT 59.312 47.619 4.75 0.00 30.70 2.66
1209 2843 1.133513 TCACCCTTGCATTGGTCAGTT 60.134 47.619 4.75 0.00 30.70 3.16
1214 2848 0.105760 TTGGTCACCCTTGCATTGGT 60.106 50.000 1.93 1.93 34.40 3.67
1215 2849 1.066716 CATTGGTCACCCTTGCATTGG 60.067 52.381 0.00 0.64 0.00 3.16
1341 3571 2.095364 CACATCCTGAAGCAACTTGAGC 60.095 50.000 0.00 0.00 0.00 4.26
1755 4037 1.405872 TTCTAGTGTGTGACGGTGGT 58.594 50.000 0.00 0.00 0.00 4.16
1761 4043 3.113260 AGCCAGTTTCTAGTGTGTGAC 57.887 47.619 0.00 0.00 0.00 3.67
1770 4052 4.967084 TTGGACAGTAAGCCAGTTTCTA 57.033 40.909 0.00 0.00 35.23 2.10
1911 4195 2.039216 TCGGATTCAGCAGGGTTTGTTA 59.961 45.455 0.00 0.00 0.00 2.41
1930 4214 1.002792 CAACATCATGAGGCAGCATCG 60.003 52.381 7.40 0.00 0.00 3.84
1943 4227 3.507924 GCATCGGCCGCAACATCA 61.508 61.111 23.51 0.16 0.00 3.07
2150 4434 3.769536 CAGGTGACTTGGTTTGTTTCAC 58.230 45.455 0.00 0.00 40.21 3.18
2193 4482 9.903682 CATTTCTGTGAGACATTGAATTACTTT 57.096 29.630 0.00 0.00 0.00 2.66


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

AutoCloner maintained by Alex Coulton.