Multiple sequence alignment - TraesCS3B01G515600

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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 TraesCS3B01G515600 chr3B 100.000 1575 0 0 943 2517 757832794 757831220 0 2909
1 TraesCS3B01G515600 chr3B 97.843 1576 32 2 943 2517 201571124 201569550 0 2721
2 TraesCS3B01G515600 chr3B 100.000 700 0 0 1 700 757833736 757833037 0 1293
3 TraesCS3B01G515600 chr2A 98.033 1576 29 2 943 2517 726902792 726901218 0 2737
4 TraesCS3B01G515600 chr2A 97.143 700 20 0 1 700 726903547 726902848 0 1182
5 TraesCS3B01G515600 chr3D 97.970 1576 30 2 943 2517 589259865 589258291 0 2732
6 TraesCS3B01G515600 chr2D 97.779 1576 32 2 943 2517 591989336 591990909 0 2713
7 TraesCS3B01G515600 chr7B 97.716 1576 33 2 943 2517 663095762 663094189 0 2708
8 TraesCS3B01G515600 chr7B 97.587 1575 35 2 944 2517 662730578 662732150 0 2695
9 TraesCS3B01G515600 chr7B 96.844 697 22 0 1 697 662729822 662730518 0 1166
10 TraesCS3B01G515600 chr7B 96.714 700 23 0 1 700 663096517 663095818 0 1166
11 TraesCS3B01G515600 chr1D 97.589 1576 36 2 943 2517 254529269 254530843 0 2699
12 TraesCS3B01G515600 chr1D 96.700 697 23 0 1 697 254528514 254529210 0 1160
13 TraesCS3B01G515600 chr7A 97.462 1576 38 2 943 2517 258307151 258305577 0 2687
14 TraesCS3B01G515600 chr6B 97.462 1576 38 2 943 2517 450083465 450085039 0 2687
15 TraesCS3B01G515600 chr5D 97.274 697 19 0 1 697 503248179 503248875 0 1182
16 TraesCS3B01G515600 chr5D 97.143 700 20 0 1 700 503261869 503261170 0 1182
17 TraesCS3B01G515600 chr7D 97.000 700 21 0 1 700 231605010 231604311 0 1177
18 TraesCS3B01G515600 chr4A 96.857 700 22 0 1 700 583865998 583865299 0 1171
19 TraesCS3B01G515600 chr3A 96.857 700 22 0 1 700 66002225 66001526 0 1171


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 TraesCS3B01G515600 chr3B 757831220 757833736 2516 True 2101.0 2909 100.0000 1 2517 2 chr3B.!!$R2 2516
1 TraesCS3B01G515600 chr3B 201569550 201571124 1574 True 2721.0 2721 97.8430 943 2517 1 chr3B.!!$R1 1574
2 TraesCS3B01G515600 chr2A 726901218 726903547 2329 True 1959.5 2737 97.5880 1 2517 2 chr2A.!!$R1 2516
3 TraesCS3B01G515600 chr3D 589258291 589259865 1574 True 2732.0 2732 97.9700 943 2517 1 chr3D.!!$R1 1574
4 TraesCS3B01G515600 chr2D 591989336 591990909 1573 False 2713.0 2713 97.7790 943 2517 1 chr2D.!!$F1 1574
5 TraesCS3B01G515600 chr7B 663094189 663096517 2328 True 1937.0 2708 97.2150 1 2517 2 chr7B.!!$R1 2516
6 TraesCS3B01G515600 chr7B 662729822 662732150 2328 False 1930.5 2695 97.2155 1 2517 2 chr7B.!!$F1 2516
7 TraesCS3B01G515600 chr1D 254528514 254530843 2329 False 1929.5 2699 97.1445 1 2517 2 chr1D.!!$F1 2516
8 TraesCS3B01G515600 chr7A 258305577 258307151 1574 True 2687.0 2687 97.4620 943 2517 1 chr7A.!!$R1 1574
9 TraesCS3B01G515600 chr6B 450083465 450085039 1574 False 2687.0 2687 97.4620 943 2517 1 chr6B.!!$F1 1574
10 TraesCS3B01G515600 chr5D 503248179 503248875 696 False 1182.0 1182 97.2740 1 697 1 chr5D.!!$F1 696
11 TraesCS3B01G515600 chr5D 503261170 503261869 699 True 1182.0 1182 97.1430 1 700 1 chr5D.!!$R1 699
12 TraesCS3B01G515600 chr7D 231604311 231605010 699 True 1177.0 1177 97.0000 1 700 1 chr7D.!!$R1 699
13 TraesCS3B01G515600 chr4A 583865299 583865998 699 True 1171.0 1171 96.8570 1 700 1 chr4A.!!$R1 699
14 TraesCS3B01G515600 chr3A 66001526 66002225 699 True 1171.0 1171 96.8570 1 700 1 chr3A.!!$R1 699

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
104 105 0.107945 GCTTCTCCACGAGGCTCATT 60.108 55.0 15.95 0.0 41.2 2.57 F
697 698 0.690762 AGCTTAGGTGGAAGGCGAAA 59.309 50.0 0.00 0.0 0.0 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1309 1310 0.107606 ACGTACCGCATTAATGGGCA 60.108 50.0 23.35 12.47 39.17 5.36 R
1969 1971 0.917533 TCCTCTACGCCTAGGACACT 59.082 55.0 14.75 0.00 36.97 3.55 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
27 28 2.159028 GGTAGAGAAAATGCCTCGAGCT 60.159 50.000 6.99 0.00 44.23 4.09
83 84 4.208686 GCCCCGTGGACTAGCGAG 62.209 72.222 0.00 0.00 0.00 5.03
104 105 0.107945 GCTTCTCCACGAGGCTCATT 60.108 55.000 15.95 0.00 41.20 2.57
129 130 2.973420 GCTACGGCGCTGAAGTATT 58.027 52.632 25.98 0.71 0.00 1.89
198 199 2.837532 GGTACTTGTACCCGAAACCA 57.162 50.000 16.80 0.00 34.06 3.67
428 429 3.884037 AGGTCAAGGAAGTTGGTGAAT 57.116 42.857 0.00 0.00 36.71 2.57
429 430 3.490348 AGGTCAAGGAAGTTGGTGAATG 58.510 45.455 0.00 0.00 36.71 2.67
448 449 3.329542 GATGACAGGGAAGCCGGCA 62.330 63.158 31.54 4.05 0.00 5.69
499 500 7.389053 CGTAACTATAACGGTCCTAAGGTAGAT 59.611 40.741 0.00 0.00 36.71 1.98
522 523 2.443887 TTCCTTGTCGGGTAAGTTCG 57.556 50.000 0.00 0.00 0.00 3.95
697 698 0.690762 AGCTTAGGTGGAAGGCGAAA 59.309 50.000 0.00 0.00 0.00 3.46
1004 1005 7.397476 ACATTCTCAGGTAGACAGTTTCTATGA 59.603 37.037 0.00 0.00 39.13 2.15
1108 1109 3.522750 AGAAGGGAGATTGACTGCAAGAT 59.477 43.478 0.00 0.00 38.74 2.40
1169 1170 3.637273 GGTGCCGAGTGGAAGGGT 61.637 66.667 0.00 0.00 37.49 4.34
1279 1280 2.586792 GCTCTTCGCCACCTGGAT 59.413 61.111 0.00 0.00 37.39 3.41
1429 1430 1.455959 CGAGAGGACCGGGAAGGAT 60.456 63.158 6.32 0.00 45.00 3.24
1539 1540 1.852157 GCCCACCCCAAGATGAGTGA 61.852 60.000 0.00 0.00 31.79 3.41
1591 1592 4.057428 ACAGCCGAGACAGCGACC 62.057 66.667 0.00 0.00 34.64 4.79
1700 1701 3.008375 AGTGGAAGTGCAGTGATGTATGT 59.992 43.478 0.00 0.00 0.00 2.29
1775 1776 3.057969 TCAAATCGATCAGGCACTTGT 57.942 42.857 0.00 0.00 34.60 3.16
1787 1788 3.801050 CAGGCACTTGTCATCTATCTTCG 59.199 47.826 0.00 0.00 34.60 3.79
1969 1971 5.533528 TCCTCGTTCATGGTTCGATATTCTA 59.466 40.000 7.85 0.00 33.26 2.10
2069 2071 1.680338 GAGGTCCTGCGGCAAAATAT 58.320 50.000 3.44 0.00 0.00 1.28
2271 2274 6.570571 GCTTTCCCATCTTCTTAACCTGAAAC 60.571 42.308 0.00 0.00 0.00 2.78
2426 2429 1.354705 GCCTTTACTTTCCCCCTGAGT 59.645 52.381 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 1.592400 CGCTTGGTACTCGGACCTCA 61.592 60.000 0.00 0.00 40.46 3.86
55 56 0.469917 CCACGGGGCTCATACTTCAT 59.530 55.000 0.00 0.00 0.00 2.57
83 84 1.446966 GAGCCTCGTGGAGAAGCAC 60.447 63.158 7.92 0.00 38.75 4.40
129 130 3.136443 CCTGGGAGTATGGCATCAGTTAA 59.864 47.826 1.65 0.00 0.00 2.01
184 185 2.290464 CTGTGTTGGTTTCGGGTACAA 58.710 47.619 0.00 0.00 0.00 2.41
198 199 2.111255 TCTCTACCTACCCACCTGTGTT 59.889 50.000 0.00 0.00 0.00 3.32
336 337 4.096682 CGGAGACCTGTGTTTTTGGTAAAA 59.903 41.667 0.00 0.00 33.74 1.52
428 429 2.669133 CCGGCTTCCCTGTCATCCA 61.669 63.158 0.00 0.00 0.00 3.41
429 430 2.190578 CCGGCTTCCCTGTCATCC 59.809 66.667 0.00 0.00 0.00 3.51
499 500 4.931002 CGAACTTACCCGACAAGGAATTTA 59.069 41.667 0.00 0.00 45.00 1.40
549 550 0.679640 CTCTCTCCGAGACAGTGCCT 60.680 60.000 0.00 0.00 42.62 4.75
981 982 6.378564 CCTCATAGAAACTGTCTACCTGAGAA 59.621 42.308 12.46 0.00 43.13 2.87
1095 1096 2.086869 CGGGTGAATCTTGCAGTCAAT 58.913 47.619 0.00 0.00 0.00 2.57
1108 1109 1.602605 TCTCTGCTCGACGGGTGAA 60.603 57.895 0.00 0.00 0.00 3.18
1169 1170 2.256174 CTTTTATCCGTTGAGCGACGA 58.744 47.619 11.61 0.00 45.47 4.20
1207 1208 1.556911 GACTCTTGGGGAAGATCAGCA 59.443 52.381 0.00 0.00 0.00 4.41
1279 1280 1.358152 CCCTTGGAACCACCTACAGA 58.642 55.000 0.00 0.00 39.86 3.41
1306 1307 2.034053 CGTACCGCATTAATGGGCAAAT 59.966 45.455 23.35 12.47 39.17 2.32
1309 1310 0.107606 ACGTACCGCATTAATGGGCA 60.108 50.000 23.35 12.47 39.17 5.36
1539 1540 0.930726 AGGGAAGTCGGAGGAGAGAT 59.069 55.000 0.00 0.00 0.00 2.75
1700 1701 2.067365 TCGTTAGGATGCCTCAGCTA 57.933 50.000 0.00 0.00 40.80 3.32
1775 1776 6.925211 AGAGTTGAACAACGAAGATAGATGA 58.075 36.000 11.21 0.00 45.50 2.92
1828 1830 3.730269 AGAGATGGAAGGGTAGAGCTTT 58.270 45.455 0.00 0.00 0.00 3.51
1969 1971 0.917533 TCCTCTACGCCTAGGACACT 59.082 55.000 14.75 0.00 36.97 3.55
2069 2071 5.008019 GCTTTTTATCATTCTGGCATCGAGA 59.992 40.000 0.00 0.00 0.00 4.04
2426 2429 5.567037 ATCCCGATCATGATTTTCCTACA 57.433 39.130 10.14 0.00 0.00 2.74


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

AutoCloner maintained by Alex Coulton.