Multiple sequence alignment - TraesCS3B01G211900

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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 TraesCS3B01G211900 chr3B 100.000 4387 0 0 1 4387 251180561 251184947 0.000000e+00 8102.0
1 TraesCS3B01G211900 chr3B 97.674 3827 73 3 576 4387 251267083 251270908 0.000000e+00 6560.0
2 TraesCS3B01G211900 chr3B 85.947 2761 305 45 1075 3785 798551813 798549086 0.000000e+00 2872.0
3 TraesCS3B01G211900 chr3B 85.185 216 21 6 1113 1319 798557347 798557134 1.240000e-50 211.0
4 TraesCS3B01G211900 chr3B 80.000 165 24 7 3784 3941 828115215 828115053 3.590000e-21 113.0
5 TraesCS3B01G211900 chr3B 81.416 113 12 5 634 737 137779921 137779809 2.810000e-12 84.2
6 TraesCS3B01G211900 chr3A 85.786 2807 316 45 1037 3790 726141963 726139187 0.000000e+00 2896.0
7 TraesCS3B01G211900 chr3A 86.014 286 26 5 291 576 303553130 303553401 1.190000e-75 294.0
8 TraesCS3B01G211900 chr3A 86.408 206 21 4 1121 1320 726146066 726145862 7.390000e-53 219.0
9 TraesCS3B01G211900 chr3A 86.408 206 21 4 1121 1320 726147452 726147248 7.390000e-53 219.0
10 TraesCS3B01G211900 chr3A 86.408 206 21 4 1121 1320 726148838 726148634 7.390000e-53 219.0
11 TraesCS3B01G211900 chr3D 85.760 2809 312 48 1039 3790 595112292 595109515 0.000000e+00 2891.0
12 TraesCS3B01G211900 chr3D 84.749 459 38 12 118 576 263345927 263346353 8.720000e-117 431.0
13 TraesCS3B01G211900 chr3D 86.695 233 30 1 1088 1320 595187909 595187678 1.570000e-64 257.0
14 TraesCS3B01G211900 chr3D 82.036 167 24 6 3780 3941 610547639 610547474 2.130000e-28 137.0
15 TraesCS3B01G211900 chr6B 96.220 582 20 2 1 582 708587309 708586730 0.000000e+00 952.0
16 TraesCS3B01G211900 chr6B 86.404 456 34 17 136 575 634569740 634570183 1.430000e-129 473.0
17 TraesCS3B01G211900 chr4A 92.566 417 14 3 145 559 83322922 83322521 2.270000e-162 582.0
18 TraesCS3B01G211900 chr4A 89.024 164 10 1 1 156 83323368 83323205 3.460000e-46 196.0
19 TraesCS3B01G211900 chr7B 97.015 335 10 0 242 576 103889854 103890188 8.240000e-157 564.0
20 TraesCS3B01G211900 chr7B 93.627 204 10 1 1 201 721313778 721313575 7.130000e-78 302.0
21 TraesCS3B01G211900 chr7B 96.591 176 3 1 1 176 103889296 103889468 5.550000e-74 289.0
22 TraesCS3B01G211900 chr7B 94.798 173 9 0 408 580 721311583 721311411 2.010000e-68 270.0
23 TraesCS3B01G211900 chr7B 98.319 119 2 0 302 420 721313230 721313112 4.450000e-50 209.0
24 TraesCS3B01G211900 chr7B 79.630 162 19 10 3813 3970 162624084 162623933 2.160000e-18 104.0
25 TraesCS3B01G211900 chr6D 84.683 457 32 19 136 575 421033642 421034077 5.250000e-114 422.0
26 TraesCS3B01G211900 chr2A 87.310 197 24 1 3791 3986 10409253 10409057 1.590000e-54 224.0
27 TraesCS3B01G211900 chr6A 78.710 155 20 8 3816 3970 454480628 454480487 1.680000e-14 91.6
28 TraesCS3B01G211900 chr1B 87.013 77 3 6 3841 3912 656201869 656201795 3.640000e-11 80.5


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 TraesCS3B01G211900 chr3B 251180561 251184947 4386 False 8102.000000 8102 100.000000 1 4387 1 chr3B.!!$F1 4386
1 TraesCS3B01G211900 chr3B 251267083 251270908 3825 False 6560.000000 6560 97.674000 576 4387 1 chr3B.!!$F2 3811
2 TraesCS3B01G211900 chr3B 798549086 798551813 2727 True 2872.000000 2872 85.947000 1075 3785 1 chr3B.!!$R2 2710
3 TraesCS3B01G211900 chr3A 726139187 726148838 9651 True 888.250000 2896 86.252500 1037 3790 4 chr3A.!!$R1 2753
4 TraesCS3B01G211900 chr3D 595109515 595112292 2777 True 2891.000000 2891 85.760000 1039 3790 1 chr3D.!!$R1 2751
5 TraesCS3B01G211900 chr6B 708586730 708587309 579 True 952.000000 952 96.220000 1 582 1 chr6B.!!$R1 581
6 TraesCS3B01G211900 chr4A 83322521 83323368 847 True 389.000000 582 90.795000 1 559 2 chr4A.!!$R1 558
7 TraesCS3B01G211900 chr7B 103889296 103890188 892 False 426.500000 564 96.803000 1 576 2 chr7B.!!$F1 575
8 TraesCS3B01G211900 chr7B 721311411 721313778 2367 True 260.333333 302 95.581333 1 580 3 chr7B.!!$R2 579

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
623 2790 0.613012 GGCCAGAAACCTCTTGGCAT 60.613 55.0 15.7 0.0 42.78 4.4 F
1672 7524 0.862490 CATGTTTGCCGACGTGTACA 59.138 50.0 0.0 0.0 33.01 2.9 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2406 8261 4.873259 GCATTAGAAACCTCTTCCTCAGTC 59.127 45.833 0.00 0.00 32.70 3.51 R
3425 9331 1.135721 GATGGCCATTGAAGCTTGGTC 59.864 52.381 21.84 0.54 38.13 4.02 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
96 97 4.483311 GTCTAGTCGTTTGGTCTCGAAAT 58.517 43.478 0.00 0.00 37.81 2.17
460 2625 6.020678 GGCGTAAACGAACAATTATACGTAGT 60.021 38.462 6.71 0.00 43.95 2.73
557 2722 2.250008 TCCACTAGGAGATTGGATCCCA 59.750 50.000 9.90 0.00 39.61 4.37
622 2789 1.228552 GGCCAGAAACCTCTTGGCA 60.229 57.895 15.70 0.00 42.78 4.92
623 2790 0.613012 GGCCAGAAACCTCTTGGCAT 60.613 55.000 15.70 0.00 42.78 4.40
672 2839 3.279875 GCCGAATGATGGGCCGTC 61.280 66.667 19.12 19.12 44.10 4.79
688 2855 2.342279 TCCCAAGTGGAAGCGACG 59.658 61.111 0.00 0.00 41.40 5.12
771 2938 1.132640 GTCAGCCGAAACACGCATC 59.867 57.895 0.00 0.00 41.07 3.91
803 2970 2.717139 GAATCGTCCCTGGCCGGATC 62.717 65.000 15.09 1.65 33.48 3.36
904 3071 3.827898 CACGCCTCCGGTCCTCTC 61.828 72.222 0.00 0.00 39.22 3.20
1672 7524 0.862490 CATGTTTGCCGACGTGTACA 59.138 50.000 0.00 0.00 33.01 2.90
1724 7576 1.864862 CACTGACAAAGGAGCTGCG 59.135 57.895 0.00 0.00 0.00 5.18
1920 7772 4.810033 GCAGATGATGAATATGAGGGGCTT 60.810 45.833 0.00 0.00 28.18 4.35
2406 8261 2.643551 AGGCCAGACATATTTGGAACG 58.356 47.619 5.01 0.00 36.55 3.95
2778 8657 1.402787 CCATGGGTCCTATGCCAAAC 58.597 55.000 9.71 0.00 0.00 2.93
2848 8730 1.858739 AAGGTTCCCTATGCCGCCAA 61.859 55.000 0.00 0.00 31.13 4.52
3058 8940 8.785101 CGGTAATGTTTCTTTTCATATGTTTCG 58.215 33.333 1.90 0.00 0.00 3.46
3197 9090 5.251764 CAAGTTTTGGAGATCTCTGTCCAT 58.748 41.667 21.81 2.79 43.83 3.41
3425 9331 2.896745 ACTTACGGGGGCTTATTACG 57.103 50.000 0.00 0.00 0.00 3.18
3696 9603 4.442472 GGCCGTATTAGCTTCTCCTGTTTA 60.442 45.833 0.00 0.00 0.00 2.01
3889 9796 5.099575 CGTATCCAAAAACCTAACAATGCC 58.900 41.667 0.00 0.00 0.00 4.40
3923 9830 0.535102 AAACCGAGTGAGCACCCAAG 60.535 55.000 0.00 0.00 0.00 3.61
4021 9928 5.841810 AGACACTGTCTCTCTCTTTTCAAG 58.158 41.667 5.82 0.00 38.71 3.02
4067 9974 8.947115 GTGGAAAGCTTATGTTGTAGTTCTAAT 58.053 33.333 0.00 0.00 0.00 1.73
4346 10253 6.726258 TTCATGGTGCTATTAATATCTGCG 57.274 37.500 0.00 0.00 0.00 5.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
96 97 3.945285 CCGCTCTTGCCCTCTTATTTTTA 59.055 43.478 0.00 0.00 35.36 1.52
207 511 1.198713 GATCTTCTGCTGGGGAGTGA 58.801 55.000 0.00 0.00 0.00 3.41
208 512 0.179936 GGATCTTCTGCTGGGGAGTG 59.820 60.000 0.00 0.00 0.00 3.51
243 867 1.141881 CTCGTGTCGGGATGGAAGG 59.858 63.158 0.00 0.00 0.00 3.46
460 2625 3.122480 TCCTTTCCTGCATAATCCCTGA 58.878 45.455 0.00 0.00 0.00 3.86
545 2710 2.041081 TCGGTTGTTTGGGATCCAATCT 59.959 45.455 15.23 0.00 43.55 2.40
557 2722 2.096248 TGAGGCTTTGTTCGGTTGTTT 58.904 42.857 0.00 0.00 0.00 2.83
622 2789 5.196695 GTTTCTTCCTTGCAGGATCCTTAT 58.803 41.667 13.00 0.00 45.34 1.73
623 2790 4.042809 TGTTTCTTCCTTGCAGGATCCTTA 59.957 41.667 13.00 0.65 45.34 2.69
647 2814 1.502163 CCATCATTCGGCTTCGCTCC 61.502 60.000 0.00 0.00 0.00 4.70
650 2817 3.025619 CCCATCATTCGGCTTCGC 58.974 61.111 0.00 0.00 0.00 4.70
672 2839 2.742372 CCGTCGCTTCCACTTGGG 60.742 66.667 0.00 0.00 35.41 4.12
897 3064 4.838486 CCTGCGACGCGAGAGGAC 62.838 72.222 15.93 0.00 32.20 3.85
2406 8261 4.873259 GCATTAGAAACCTCTTCCTCAGTC 59.127 45.833 0.00 0.00 32.70 3.51
2848 8730 4.722700 GGTCTGCATGTGCGGGGT 62.723 66.667 13.44 0.00 46.99 4.95
3197 9090 1.609072 CCGACTGTGTCTGAGAGTGAA 59.391 52.381 0.00 0.00 0.00 3.18
3425 9331 1.135721 GATGGCCATTGAAGCTTGGTC 59.864 52.381 21.84 0.54 38.13 4.02
3923 9830 7.041712 TGTCCTTTTTCCTTTTTGTGTTTGTTC 60.042 33.333 0.00 0.00 0.00 3.18
4021 9928 4.095483 CCACAGACCTTTCATGATAAGCAC 59.905 45.833 0.00 1.41 0.00 4.40
4067 9974 4.380843 ACATCACCCACAACTCCATTTA 57.619 40.909 0.00 0.00 0.00 1.40
4346 10253 8.325997 CGTGTAAAGACCTATGCTAAACATTAC 58.674 37.037 0.00 0.00 40.38 1.89


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

AutoCloner maintained by Alex Coulton.