Multiple sequence alignment - TraesCS3B01G179000

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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 TraesCS3B01G179000 chr3B 100.000 3080 0 0 1 3080 186096221 186093142 0.000000e+00 5688.0
1 TraesCS3B01G179000 chr3B 98.734 3080 30 3 1 3080 184964383 184961313 0.000000e+00 5463.0
2 TraesCS3B01G179000 chr3B 82.075 1272 193 17 1134 2378 248248685 248249948 0.000000e+00 1053.0
3 TraesCS3B01G179000 chr3B 82.646 922 152 4 1457 2378 248580937 248581850 0.000000e+00 809.0
4 TraesCS3B01G179000 chr3B 85.246 244 30 4 1134 1374 248580489 248580729 2.370000e-61 246.0
5 TraesCS3B01G179000 chr3D 91.952 1665 110 16 1107 2765 553426932 553425286 0.000000e+00 2311.0
6 TraesCS3B01G179000 chr3D 88.827 179 14 3 2765 2943 553424278 553424106 6.690000e-52 215.0
7 TraesCS3B01G179000 chr3D 95.714 70 1 2 86 154 175663782 175663850 9.030000e-21 111.0
8 TraesCS3B01G179000 chr3D 89.333 75 2 3 763 837 553427188 553427120 4.230000e-14 89.8
9 TraesCS3B01G179000 chr3A 89.414 973 68 17 1841 2804 690024276 690023330 0.000000e+00 1194.0
10 TraesCS3B01G179000 chr3A 93.343 691 42 4 1107 1796 690024961 690024274 0.000000e+00 1018.0
11 TraesCS3B01G179000 chr3A 88.353 249 20 4 473 721 690025490 690025251 1.080000e-74 291.0
12 TraesCS3B01G179000 chr1D 95.775 71 3 0 86 156 203264936 203264866 6.980000e-22 115.0
13 TraesCS3B01G179000 chr5D 92.500 80 4 2 78 156 375170841 375170919 2.510000e-21 113.0
14 TraesCS3B01G179000 chrUn 93.243 74 5 0 86 159 89803051 89802978 3.250000e-20 110.0
15 TraesCS3B01G179000 chr7D 94.444 72 2 2 86 156 58135021 58135091 3.250000e-20 110.0
16 TraesCS3B01G179000 chr7A 93.243 74 5 0 86 159 17210369 17210296 3.250000e-20 110.0
17 TraesCS3B01G179000 chr6A 91.250 80 5 2 78 156 78477159 78477081 1.170000e-19 108.0
18 TraesCS3B01G179000 chr4D 89.024 82 9 0 86 167 454449879 454449798 5.430000e-18 102.0


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 TraesCS3B01G179000 chr3B 186093142 186096221 3079 True 5688.000000 5688 100.000000 1 3080 1 chr3B.!!$R2 3079
1 TraesCS3B01G179000 chr3B 184961313 184964383 3070 True 5463.000000 5463 98.734000 1 3080 1 chr3B.!!$R1 3079
2 TraesCS3B01G179000 chr3B 248248685 248249948 1263 False 1053.000000 1053 82.075000 1134 2378 1 chr3B.!!$F1 1244
3 TraesCS3B01G179000 chr3B 248580489 248581850 1361 False 527.500000 809 83.946000 1134 2378 2 chr3B.!!$F2 1244
4 TraesCS3B01G179000 chr3D 553424106 553427188 3082 True 871.933333 2311 90.037333 763 2943 3 chr3D.!!$R1 2180
5 TraesCS3B01G179000 chr3A 690023330 690025490 2160 True 834.333333 1194 90.370000 473 2804 3 chr3A.!!$R1 2331

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
90 91 1.12820 TCCGGGATGTGATAACCAGG 58.872 55.0 0.0 0.0 39.67 4.45 F
1518 1646 0.46546 GTGAGTTTGGGCTGGTGTCA 60.465 55.0 0.0 0.0 0.00 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1680 1808 1.136085 CGTGCAACCTTGTATGTTCCG 60.136 52.381 0.00 0.00 0.0 4.30 R
2722 2873 5.099042 TGATGGTCTCCCTTTAAAGTAGC 57.901 43.478 14.03 6.85 0.0 3.58 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
22 23 4.448210 GCAATCACCGGTATTTCCTAGAA 58.552 43.478 6.87 0.0 0.00 2.10
24 25 5.355910 GCAATCACCGGTATTTCCTAGAAAA 59.644 40.000 6.87 0.0 0.00 2.29
90 91 1.128200 TCCGGGATGTGATAACCAGG 58.872 55.000 0.00 0.0 39.67 4.45
159 160 2.281484 ACAGGTTGGTTCGCGCAT 60.281 55.556 8.75 0.0 0.00 4.73
424 425 3.205056 TCCAGTAAGAACCCTACCCGATA 59.795 47.826 0.00 0.0 0.00 2.92
1026 1029 5.045797 GGACTTGAAGAGGGTTAATGGTACT 60.046 44.000 0.00 0.0 0.00 2.73
1518 1646 0.465460 GTGAGTTTGGGCTGGTGTCA 60.465 55.000 0.00 0.0 0.00 3.58
1680 1808 0.541764 TGGGCCTTGATGTTTCCACC 60.542 55.000 4.53 0.0 0.00 4.61
1891 2020 0.248621 GAAAAATCAGCGATGCCCCG 60.249 55.000 0.00 0.0 0.00 5.73
2242 2377 6.102897 AGAAGAGGATACGTTTGATATGGG 57.897 41.667 0.00 0.0 46.39 4.00
2519 2655 1.813178 GGGCACTTAAACAAGCTCCTC 59.187 52.381 0.00 0.0 0.00 3.71
2538 2675 4.037923 TCCTCTTCATGTTTTTCCTGTTGC 59.962 41.667 0.00 0.0 0.00 4.17
2681 2832 4.339748 TGTTGGATTATGTAGCCTGCAAA 58.660 39.130 0.00 0.0 0.00 3.68
2684 2835 5.772825 TGGATTATGTAGCCTGCAAATTC 57.227 39.130 0.00 0.0 0.00 2.17
2722 2873 3.825585 TCTGGATCTGCTATCTGCTAGTG 59.174 47.826 0.00 0.0 43.37 2.74
2723 2874 2.298446 TGGATCTGCTATCTGCTAGTGC 59.702 50.000 0.00 0.0 43.37 4.40
2724 2875 2.562298 GGATCTGCTATCTGCTAGTGCT 59.438 50.000 0.00 0.0 43.37 4.40
2725 2876 3.761218 GGATCTGCTATCTGCTAGTGCTA 59.239 47.826 0.00 0.0 43.37 3.49
2726 2877 4.380444 GGATCTGCTATCTGCTAGTGCTAC 60.380 50.000 0.00 0.0 43.37 3.58
2727 2878 3.826524 TCTGCTATCTGCTAGTGCTACT 58.173 45.455 0.00 0.0 43.37 2.57
3063 4222 9.601971 CTTTTTATGTTTGGATTTTGCAATCTG 57.398 29.630 0.00 0.0 39.17 2.90
3076 4235 9.717942 GATTTTGCAATCTGAGTATCTACCTAT 57.282 33.333 0.00 0.0 36.58 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
52 53 6.544564 TCCCGGATTTTTCTCAAATATGGTAC 59.455 38.462 0.73 0.00 0.00 3.34
159 160 6.242396 TCTTACTAACTAGCAAAAATGCCCA 58.758 36.000 0.00 0.00 34.90 5.36
424 425 5.776716 TGAGCTTCAGGATTTCAGGAAATTT 59.223 36.000 8.53 0.00 40.77 1.82
756 757 1.456544 ACACGCACCAAATTACGTACG 59.543 47.619 15.01 15.01 36.91 3.67
1026 1029 2.208132 TAGCCGGCATTTTTGGAGAA 57.792 45.000 31.54 0.00 0.00 2.87
1518 1646 1.614903 CCATCACAGTGTGCCATTTGT 59.385 47.619 18.80 0.00 32.98 2.83
1641 1769 1.720781 AACCAATTGGAAGGCAGCTT 58.279 45.000 31.22 9.14 38.94 3.74
1680 1808 1.136085 CGTGCAACCTTGTATGTTCCG 60.136 52.381 0.00 0.00 0.00 4.30
2036 2171 1.871039 ACCAATACTCGTTGCACACAC 59.129 47.619 0.00 0.00 0.00 3.82
2037 2172 2.139917 GACCAATACTCGTTGCACACA 58.860 47.619 0.00 0.00 0.00 3.72
2242 2377 1.328279 CCCAAGGAACCTTTGGTCAC 58.672 55.000 13.51 0.00 35.04 3.67
2248 2383 1.156095 CTGGGCCCAAGGAACCTTT 59.844 57.895 28.29 0.00 33.42 3.11
2519 2655 5.811613 TGAAAGCAACAGGAAAAACATGAAG 59.188 36.000 0.00 0.00 34.19 3.02
2538 2675 8.246180 ACCATAAGAATACAGTTTGCATGAAAG 58.754 33.333 0.00 0.00 0.00 2.62
2648 2799 8.499162 GCTACATAATCCAACAGATGACATAAC 58.501 37.037 0.00 0.00 34.56 1.89
2681 2832 7.067496 TCCAGAAACAAGAGAACTACAGAAT 57.933 36.000 0.00 0.00 0.00 2.40
2684 2835 6.589523 CAGATCCAGAAACAAGAGAACTACAG 59.410 42.308 0.00 0.00 0.00 2.74
2722 2873 5.099042 TGATGGTCTCCCTTTAAAGTAGC 57.901 43.478 14.03 6.85 0.00 3.58
2723 2874 7.130681 AGATGATGGTCTCCCTTTAAAGTAG 57.869 40.000 14.03 10.67 0.00 2.57
2724 2875 7.037586 ACAAGATGATGGTCTCCCTTTAAAGTA 60.038 37.037 14.03 1.35 0.00 2.24
2725 2876 6.183347 CAAGATGATGGTCTCCCTTTAAAGT 58.817 40.000 14.03 0.00 0.00 2.66
2726 2877 6.183347 ACAAGATGATGGTCTCCCTTTAAAG 58.817 40.000 8.32 8.32 0.00 1.85
2727 2878 6.139679 ACAAGATGATGGTCTCCCTTTAAA 57.860 37.500 0.00 0.00 0.00 1.52


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

AutoCloner maintained by Alex Coulton.