Multiple sequence alignment - TraesCS4B01G158700

Loading Multiple Alignment...

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 TraesCS4B01G158700 chr4B 100.000 2105 0 0 1 2105 308674841 308672737 0.000000e+00 3888.0
1 TraesCS4B01G158700 chr4B 100.000 46 0 0 2060 2105 429228703 429228658 3.720000e-13 86.1
2 TraesCS4B01G158700 chr5D 96.741 2117 46 9 7 2105 503296839 503298950 0.000000e+00 3506.0
3 TraesCS4B01G158700 chr5D 96.174 2117 56 11 7 2105 6271042 6268933 0.000000e+00 3437.0
4 TraesCS4B01G158700 chr5D 95.409 2113 55 17 7 2105 6171977 6169893 0.000000e+00 3326.0
5 TraesCS4B01G158700 chr5D 96.059 1218 29 7 901 2105 329162135 329160924 0.000000e+00 1965.0
6 TraesCS4B01G158700 chr5D 96.881 481 13 2 7 485 512414207 512414687 0.000000e+00 804.0
7 TraesCS4B01G158700 chr1D 96.459 2118 49 12 7 2105 254439973 254442083 0.000000e+00 3472.0
8 TraesCS4B01G158700 chr1D 95.445 1427 36 4 9 1431 51866992 51865591 0.000000e+00 2248.0
9 TraesCS4B01G158700 chr1D 96.881 481 13 2 7 485 491423457 491422977 0.000000e+00 804.0
10 TraesCS4B01G158700 chr2D 96.268 2117 50 10 7 2105 638429369 638431474 0.000000e+00 3445.0
11 TraesCS4B01G158700 chr4D 95.784 2111 58 11 7 2105 19873448 19875539 0.000000e+00 3376.0
12 TraesCS4B01G158700 chr3D 93.920 1842 69 13 298 2105 235644625 235646457 0.000000e+00 2741.0
13 TraesCS4B01G158700 chr4A 96.126 1678 45 8 442 2105 309484656 309482985 0.000000e+00 2721.0
14 TraesCS4B01G158700 chr3B 98.505 669 10 0 475 1143 796325651 796324983 0.000000e+00 1181.0
15 TraesCS4B01G158700 chr5A 98.693 153 2 0 1953 2105 186939306 186939458 2.660000e-69 272.0


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 TraesCS4B01G158700 chr4B 308672737 308674841 2104 True 3888 3888 100.000 1 2105 1 chr4B.!!$R1 2104
1 TraesCS4B01G158700 chr5D 503296839 503298950 2111 False 3506 3506 96.741 7 2105 1 chr5D.!!$F1 2098
2 TraesCS4B01G158700 chr5D 6268933 6271042 2109 True 3437 3437 96.174 7 2105 1 chr5D.!!$R2 2098
3 TraesCS4B01G158700 chr5D 6169893 6171977 2084 True 3326 3326 95.409 7 2105 1 chr5D.!!$R1 2098
4 TraesCS4B01G158700 chr5D 329160924 329162135 1211 True 1965 1965 96.059 901 2105 1 chr5D.!!$R3 1204
5 TraesCS4B01G158700 chr1D 254439973 254442083 2110 False 3472 3472 96.459 7 2105 1 chr1D.!!$F1 2098
6 TraesCS4B01G158700 chr1D 51865591 51866992 1401 True 2248 2248 95.445 9 1431 1 chr1D.!!$R1 1422
7 TraesCS4B01G158700 chr2D 638429369 638431474 2105 False 3445 3445 96.268 7 2105 1 chr2D.!!$F1 2098
8 TraesCS4B01G158700 chr4D 19873448 19875539 2091 False 3376 3376 95.784 7 2105 1 chr4D.!!$F1 2098
9 TraesCS4B01G158700 chr3D 235644625 235646457 1832 False 2741 2741 93.920 298 2105 1 chr3D.!!$F1 1807
10 TraesCS4B01G158700 chr4A 309482985 309484656 1671 True 2721 2721 96.126 442 2105 1 chr4A.!!$R1 1663
11 TraesCS4B01G158700 chr3B 796324983 796325651 668 True 1181 1181 98.505 475 1143 1 chr3B.!!$R1 668


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
258 263 0.553612 AAGGGGCAGGGAGGAAGATT 60.554 55.0 0.0 0.0 0.0 2.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2057 2136 4.873746 TCCTATTCCCGCTTCTTCTATG 57.126 45.455 0.0 0.0 0.0 2.23 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
39 40 7.094075 TGTGGGTATGTAGTATATGATTCGTCC 60.094 40.741 0.00 0.00 0.00 4.79
156 157 4.643387 GCACCGCCCTGTCAAGGT 62.643 66.667 0.00 0.00 42.74 3.50
216 217 6.940430 AGGGTTCAATGAATGGAGAAATTT 57.060 33.333 0.00 0.00 0.00 1.82
258 263 0.553612 AAGGGGCAGGGAGGAAGATT 60.554 55.000 0.00 0.00 0.00 2.40
268 273 5.458215 GCAGGGAGGAAGATTAAATACCCAT 60.458 44.000 0.00 0.00 38.62 4.00
317 322 2.915349 TGCATCTCTCATGAAAGAGGC 58.085 47.619 24.97 24.97 46.54 4.70
332 337 0.756903 GAGGCAGGGAAGGCGTATAA 59.243 55.000 0.00 0.00 39.37 0.98
843 879 8.012957 ACTCTCATCCGTGAAATATAACTCTT 57.987 34.615 0.00 0.00 33.05 2.85
1489 1550 4.141824 TGTGATATGCCGTGAATAGTTCCA 60.142 41.667 0.00 0.00 0.00 3.53
1498 1559 4.572389 CCGTGAATAGTTCCATGGAAGAAG 59.428 45.833 27.73 12.25 40.92 2.85
1549 1612 7.972832 TTTGTACCATTCGTCATTTCTAGTT 57.027 32.000 0.00 0.00 0.00 2.24
1633 1701 8.749354 ACAGGAGTGAAACAAAACTAAAGAAAT 58.251 29.630 0.00 0.00 41.43 2.17
1742 1815 5.998128 AGTAGTATCCCTAGAGTCCACTT 57.002 43.478 0.00 0.00 0.00 3.16
2057 2136 1.139058 AGTACGGGAATGATGTCCTGC 59.861 52.381 0.00 0.00 46.63 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.754946 ACCCACATATTATACGCGGG 57.245 50.000 12.47 0.00 38.23 6.13
1 2 4.751060 ACATACCCACATATTATACGCGG 58.249 43.478 12.47 0.00 0.00 6.46
2 3 6.558009 ACTACATACCCACATATTATACGCG 58.442 40.000 3.53 3.53 0.00 6.01
39 40 7.792383 TTCGTCTTTCGTACTCTAAGAAATG 57.208 36.000 0.00 0.00 36.02 2.32
156 157 3.589654 CTCGAACCCGCAGCTTCCA 62.590 63.158 0.00 0.00 35.37 3.53
252 257 5.710567 GGTGCCCTATGGGTATTTAATCTTC 59.289 44.000 4.42 0.00 46.51 2.87
258 263 3.083573 AGGGTGCCCTATGGGTATTTA 57.916 47.619 8.24 0.00 46.51 1.40
309 314 1.746991 CGCCTTCCCTGCCTCTTTC 60.747 63.158 0.00 0.00 0.00 2.62
317 322 6.451064 AAAAATTCTTATACGCCTTCCCTG 57.549 37.500 0.00 0.00 0.00 4.45
1489 1550 9.981460 ACATAAGAAAATTAGACCTTCTTCCAT 57.019 29.630 5.54 0.00 39.50 3.41
1528 1590 7.591006 TTCAACTAGAAATGACGAATGGTAC 57.409 36.000 0.00 0.00 32.05 3.34
1549 1612 8.537728 AGCCATTATACCAATTCAGAATTTCA 57.462 30.769 5.58 0.00 0.00 2.69
1742 1815 6.738635 TCTTTCACTAGTAGTATGGGGAAGA 58.261 40.000 1.57 3.95 0.00 2.87
1867 1945 9.574516 GTACCCTTGATTCCACTATGATTATTT 57.425 33.333 0.00 0.00 0.00 1.40
2057 2136 4.873746 TCCTATTCCCGCTTCTTCTATG 57.126 45.455 0.00 0.00 0.00 2.23



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

AutoCloner maintained by Alex Coulton.