Multiple sequence alignment - TraesCS3B01G068600

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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 TraesCS3B01G068600 chr3B 100.000 2555 0 0 1 2555 40848918 40846364 0.000000e+00 4719.0
1 TraesCS3B01G068600 chr3B 81.879 1043 161 10 560 1589 39142017 39140990 0.000000e+00 854.0
2 TraesCS3B01G068600 chr3B 74.026 154 40 0 1798 1951 68282545 68282698 2.120000e-06 63.9
3 TraesCS3B01G068600 chr3D 97.019 1476 38 4 393 1864 23145657 23144184 0.000000e+00 2477.0
4 TraesCS3B01G068600 chr3D 94.813 694 31 2 1862 2555 23144026 23143338 0.000000e+00 1077.0
5 TraesCS3B01G068600 chr3D 96.708 243 8 0 4 246 23147801 23147559 3.060000e-109 405.0
6 TraesCS3B01G068600 chr3D 99.048 105 1 0 393 497 23145933 23145829 3.360000e-44 189.0
7 TraesCS3B01G068600 chr3A 95.479 1128 39 11 4 1125 32224173 32223052 0.000000e+00 1790.0
8 TraesCS3B01G068600 chr3A 92.806 1126 63 9 1436 2550 32223062 32221944 0.000000e+00 1615.0
9 TraesCS3B01G068600 chr3A 80.103 774 137 9 816 1589 31788858 31788102 6.170000e-156 560.0
10 TraesCS3B01G068600 chr5A 82.407 216 33 5 1756 1967 546711457 546711243 1.560000e-42 183.0


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 TraesCS3B01G068600 chr3B 40846364 40848918 2554 True 4719.0 4719 100.0000 1 2555 1 chr3B.!!$R2 2554
1 TraesCS3B01G068600 chr3B 39140990 39142017 1027 True 854.0 854 81.8790 560 1589 1 chr3B.!!$R1 1029
2 TraesCS3B01G068600 chr3D 23143338 23147801 4463 True 1037.0 2477 96.8970 4 2555 4 chr3D.!!$R1 2551
3 TraesCS3B01G068600 chr3A 32221944 32224173 2229 True 1702.5 1790 94.1425 4 2550 2 chr3A.!!$R2 2546
4 TraesCS3B01G068600 chr3A 31788102 31788858 756 True 560.0 560 80.1030 816 1589 1 chr3A.!!$R1 773

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
55 56 1.853250 AAGGGCTAGTCCTGGTTGGC 61.853 60.000 18.80 0.0 37.20 4.52 F
352 2061 3.055385 GGGCGCCCATGTAGAGATATAAA 60.055 47.826 40.73 0.0 35.81 1.40 F
1176 2946 2.100749 GCTTACCACAAAGCCACAAAGT 59.899 45.455 0.00 0.0 44.98 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1045 2815 0.250770 ATGGCTGCGAGCATGATGAT 60.251 50.000 0.00 0.0 44.75 2.45 R
1491 3261 0.595588 AGTGCTCTATCATCTCGCGG 59.404 55.000 6.13 0.0 0.00 6.46 R
2140 4080 1.202348 GTGACAAATAAGGGTGCTGCC 59.798 52.381 0.00 0.0 0.00 4.85 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
55 56 1.853250 AAGGGCTAGTCCTGGTTGGC 61.853 60.000 18.80 0.00 37.20 4.52
97 98 9.331282 GATGTCTAGTTAGCATGAAAATTACCT 57.669 33.333 0.00 0.00 0.00 3.08
324 2008 8.824781 ACAGATCTCACATCATAAAGAATTTCG 58.175 33.333 0.00 0.00 40.09 3.46
331 2015 5.125417 ACATCATAAAGAATTTCGGTGGTGG 59.875 40.000 9.65 0.00 40.09 4.61
352 2061 3.055385 GGGCGCCCATGTAGAGATATAAA 60.055 47.826 40.73 0.00 35.81 1.40
551 2307 3.254060 GCGAACGTGCATATGGAGATAT 58.746 45.455 4.56 0.00 34.15 1.63
749 2507 5.802465 TCTCCGGTGAACGTATATAGAGAT 58.198 41.667 3.14 0.00 42.24 2.75
1059 2829 4.152938 GCTATGTTTATCATCATGCTCGCA 59.847 41.667 0.00 0.00 37.91 5.10
1176 2946 2.100749 GCTTACCACAAAGCCACAAAGT 59.899 45.455 0.00 0.00 44.98 2.66
1362 3132 3.659183 AGTGCCCTTGAGATTTATGCT 57.341 42.857 0.00 0.00 0.00 3.79
1380 3150 2.807967 TGCTGTCTCGAACTTCCAAATG 59.192 45.455 0.00 0.00 0.00 2.32
1491 3261 3.028094 TCCCCAGTGTCCTACATAGAC 57.972 52.381 0.00 0.00 34.72 2.59
1502 3272 2.750166 CCTACATAGACCGCGAGATGAT 59.250 50.000 8.23 0.00 0.00 2.45
1578 3348 2.691526 ACATTGCATTCCTGGCACATAG 59.308 45.455 0.00 0.00 41.75 2.23
1614 3387 9.152595 GCTAATAACAAGATAATACCCTACTGC 57.847 37.037 0.00 0.00 0.00 4.40
1641 3414 4.968259 TGCGGGAATTTGTAGCACTATAT 58.032 39.130 0.00 0.00 32.43 0.86
1739 3512 8.782137 AAGCCAGGAAAATTGGTATATTGTAT 57.218 30.769 0.00 0.00 38.02 2.29
1779 3552 9.120538 TGAATTAGCTTCCATTTTCCACTATAC 57.879 33.333 0.00 0.00 32.49 1.47
1911 3845 9.567776 TCCAACATAGAACAATTGAAGTAAAGA 57.432 29.630 13.59 0.00 0.00 2.52
1925 3859 6.169094 TGAAGTAAAGAAGAATCAGAGCAGG 58.831 40.000 0.00 0.00 0.00 4.85
1949 3885 2.399916 ACTTGATCCTCTCAGCAAGC 57.600 50.000 0.00 0.00 40.94 4.01
2055 3995 8.589335 TTAGAGAAGACTGTTTATTCACACAC 57.411 34.615 4.80 0.00 0.00 3.82
2056 3996 6.582636 AGAGAAGACTGTTTATTCACACACA 58.417 36.000 4.80 0.00 0.00 3.72
2140 4080 3.125316 GCTATCTCCAAACCAGAAACACG 59.875 47.826 0.00 0.00 0.00 4.49
2141 4081 1.961793 TCTCCAAACCAGAAACACGG 58.038 50.000 0.00 0.00 0.00 4.94
2144 4084 0.030638 CCAAACCAGAAACACGGCAG 59.969 55.000 0.00 0.00 0.00 4.85
2218 4158 7.039504 AGGTTGAATATTCAGCTGAACAAACAT 60.040 33.333 31.13 23.84 38.32 2.71
2231 4171 5.512473 TGAACAAACATTAACACCGTAAGC 58.488 37.500 0.00 0.00 0.00 3.09
2267 4207 5.163426 TGCAATGTATCAGCAAATTAAGGGG 60.163 40.000 0.00 0.00 34.97 4.79
2529 4469 4.025360 AGCATGGGTGAATTGCATAAAGA 58.975 39.130 0.00 0.00 38.84 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.633193 TTTACAGAAGAAAGCAACCTAAACA 57.367 32.000 0.00 0.00 0.00 2.83
1 2 8.188799 ACTTTTACAGAAGAAAGCAACCTAAAC 58.811 33.333 0.00 0.00 36.56 2.01
2 3 8.288689 ACTTTTACAGAAGAAAGCAACCTAAA 57.711 30.769 0.00 0.00 36.56 1.85
97 98 4.764823 CCCCCGCATAGCTCATTATTTTTA 59.235 41.667 0.00 0.00 0.00 1.52
102 103 1.279271 GTCCCCCGCATAGCTCATTAT 59.721 52.381 0.00 0.00 0.00 1.28
331 2015 3.887621 TTATATCTCTACATGGGCGCC 57.112 47.619 21.18 21.18 0.00 6.53
533 2289 8.531982 AGTGTAATATATCTCCATATGCACGTT 58.468 33.333 0.00 0.00 35.25 3.99
784 2542 7.495934 CCCACCTAGTGAATAGATGTACAAAAG 59.504 40.741 0.00 0.00 35.23 2.27
1045 2815 0.250770 ATGGCTGCGAGCATGATGAT 60.251 50.000 0.00 0.00 44.75 2.45
1048 2818 1.153025 ACATGGCTGCGAGCATGAT 60.153 52.632 19.58 0.00 44.75 2.45
1075 2845 3.947834 GTGTTAGCATAGGCAACAAGGAT 59.052 43.478 15.42 0.00 44.61 3.24
1294 3064 1.196104 ATGGCCAGTGCAAATGCCTT 61.196 50.000 13.05 12.03 44.32 4.35
1362 3132 2.552155 CCCCATTTGGAAGTTCGAGACA 60.552 50.000 0.00 0.00 37.39 3.41
1491 3261 0.595588 AGTGCTCTATCATCTCGCGG 59.404 55.000 6.13 0.00 0.00 6.46
1610 3383 1.039856 AAATTCCCGCAACAAGCAGT 58.960 45.000 0.00 0.00 46.13 4.40
1614 3387 2.030363 TGCTACAAATTCCCGCAACAAG 60.030 45.455 0.00 0.00 0.00 3.16
1739 3512 9.026121 GGAAGCTAATTCAGTATGGAGATACTA 57.974 37.037 0.00 0.00 42.55 1.82
1911 3845 2.776536 AGTATGGCCTGCTCTGATTCTT 59.223 45.455 3.32 0.00 0.00 2.52
1925 3859 2.103771 TGCTGAGAGGATCAAGTATGGC 59.896 50.000 0.00 0.00 37.52 4.40
2009 3949 9.092876 CTCTAAGGCTATAACTTCACTTTCAAG 57.907 37.037 0.00 0.00 0.00 3.02
2017 3957 7.616150 ACAGTCTTCTCTAAGGCTATAACTTCA 59.384 37.037 0.00 0.00 45.99 3.02
2055 3995 5.174398 GTGATGTTCTGTTTTCAAGCATGTG 59.826 40.000 0.00 0.00 0.00 3.21
2056 3996 5.068198 AGTGATGTTCTGTTTTCAAGCATGT 59.932 36.000 0.00 0.00 0.00 3.21
2140 4080 1.202348 GTGACAAATAAGGGTGCTGCC 59.798 52.381 0.00 0.00 0.00 4.85
2141 4081 1.202348 GGTGACAAATAAGGGTGCTGC 59.798 52.381 0.00 0.00 0.00 5.25
2144 4084 2.030274 GTGTGGTGACAAATAAGGGTGC 60.030 50.000 0.00 0.00 46.06 5.01
2218 4158 3.196939 ACAGGTTGCTTACGGTGTTAA 57.803 42.857 0.00 0.00 0.00 2.01
2231 4171 6.254157 GCTGATACATTGCAATTTACAGGTTG 59.746 38.462 22.46 11.16 0.00 3.77
2303 4243 9.816354 GTAAAAATATAGGCCACAATCAAATGT 57.184 29.630 5.01 0.00 0.00 2.71
2304 4244 9.814899 TGTAAAAATATAGGCCACAATCAAATG 57.185 29.630 5.01 0.00 0.00 2.32
2464 4404 7.231317 ACAAATGTCACATGGTTTCATACTCTT 59.769 33.333 0.00 0.00 31.33 2.85


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

AutoCloner maintained by Alex Coulton.