Multiple sequence alignment - TraesCS2B01G279900

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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 TraesCS2B01G279900 chr2B 100.000 2993 0 0 1 2993 386132397 386135389 0.000000e+00 5528
1 TraesCS2B01G279900 chr2B 93.614 2709 154 18 66 2764 320940748 320938049 0.000000e+00 4026
2 TraesCS2B01G279900 chr2B 93.721 1513 91 4 242 1752 115619392 115617882 0.000000e+00 2265
3 TraesCS2B01G279900 chr1B 96.897 2997 86 5 1 2993 348700074 348697081 0.000000e+00 5012
4 TraesCS2B01G279900 chr1B 95.900 2756 101 10 242 2993 60863612 60860865 0.000000e+00 4453
5 TraesCS2B01G279900 chr1B 95.745 329 12 2 1 328 617351604 617351931 2.040000e-146 529
6 TraesCS2B01G279900 chr7B 95.660 2926 109 13 78 2993 393237320 393234403 0.000000e+00 4684
7 TraesCS2B01G279900 chr7B 94.909 2927 135 14 74 2993 319716422 319719341 0.000000e+00 4567
8 TraesCS2B01G279900 chr7B 96.046 2504 74 9 492 2993 240199659 240202139 0.000000e+00 4052
9 TraesCS2B01G279900 chr4B 94.342 2934 152 13 67 2993 559209651 559206725 0.000000e+00 4486
10 TraesCS2B01G279900 chr4B 95.570 2528 105 7 242 2764 277835002 277832477 0.000000e+00 4041
11 TraesCS2B01G279900 chr4B 95.965 347 13 1 1 346 411562267 411562613 2.010000e-156 562
12 TraesCS2B01G279900 chr4B 87.926 323 32 7 2 322 349355389 349355072 1.010000e-99 374
13 TraesCS2B01G279900 chr6B 95.492 2573 106 8 197 2764 48901246 48903813 0.000000e+00 4100
14 TraesCS2B01G279900 chr5A 89.812 1011 71 19 1993 2993 606428560 606427572 0.000000e+00 1267
15 TraesCS2B01G279900 chr4A 95.796 333 10 3 2664 2993 487351063 487350732 4.390000e-148 534


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 TraesCS2B01G279900 chr2B 386132397 386135389 2992 False 5528 5528 100.000 1 2993 1 chr2B.!!$F1 2992
1 TraesCS2B01G279900 chr2B 320938049 320940748 2699 True 4026 4026 93.614 66 2764 1 chr2B.!!$R2 2698
2 TraesCS2B01G279900 chr2B 115617882 115619392 1510 True 2265 2265 93.721 242 1752 1 chr2B.!!$R1 1510
3 TraesCS2B01G279900 chr1B 348697081 348700074 2993 True 5012 5012 96.897 1 2993 1 chr1B.!!$R2 2992
4 TraesCS2B01G279900 chr1B 60860865 60863612 2747 True 4453 4453 95.900 242 2993 1 chr1B.!!$R1 2751
5 TraesCS2B01G279900 chr7B 393234403 393237320 2917 True 4684 4684 95.660 78 2993 1 chr7B.!!$R1 2915
6 TraesCS2B01G279900 chr7B 319716422 319719341 2919 False 4567 4567 94.909 74 2993 1 chr7B.!!$F2 2919
7 TraesCS2B01G279900 chr7B 240199659 240202139 2480 False 4052 4052 96.046 492 2993 1 chr7B.!!$F1 2501
8 TraesCS2B01G279900 chr4B 559206725 559209651 2926 True 4486 4486 94.342 67 2993 1 chr4B.!!$R3 2926
9 TraesCS2B01G279900 chr4B 277832477 277835002 2525 True 4041 4041 95.570 242 2764 1 chr4B.!!$R1 2522
10 TraesCS2B01G279900 chr6B 48901246 48903813 2567 False 4100 4100 95.492 197 2764 1 chr6B.!!$F1 2567
11 TraesCS2B01G279900 chr5A 606427572 606428560 988 True 1267 1267 89.812 1993 2993 1 chr5A.!!$R1 1000

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
945 958 3.370953 GGTACAATGAGGAGAGCCACAAT 60.371 47.826 0.0 0.0 38.29 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2793 2905 1.048601 ATGGTATACACCTGGCTCGG 58.951 55.0 5.01 0.0 45.98 4.63 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
157 159 5.491982 TCTGAACCTTCCTTTGCTTCTATC 58.508 41.667 0.00 0.0 0.00 2.08
238 242 3.953612 TGCCTTCATCACCCAATATTGTC 59.046 43.478 14.25 0.0 0.00 3.18
255 259 9.778741 CAATATTGTCTTACCTAGATTTAGCCA 57.221 33.333 7.32 0.0 34.79 4.75
341 350 5.989777 ACCCTGCTATATTACAAACGATCAC 59.010 40.000 0.00 0.0 0.00 3.06
545 557 5.840693 TGGCTTACTATTCAGATCATCAGGA 59.159 40.000 0.00 0.0 0.00 3.86
905 918 6.500041 AGATCTCATCGTTTGCTTCTAGTAC 58.500 40.000 0.00 0.0 0.00 2.73
913 926 7.096884 TCGTTTGCTTCTAGTACTCATATGT 57.903 36.000 0.00 0.0 0.00 2.29
945 958 3.370953 GGTACAATGAGGAGAGCCACAAT 60.371 47.826 0.00 0.0 38.29 2.71
1054 1067 1.748493 GTCAACCAACAACTCCAGCAA 59.252 47.619 0.00 0.0 0.00 3.91
1058 1071 0.031178 CCAACAACTCCAGCAACTGC 59.969 55.000 0.00 0.0 42.49 4.40
1637 1650 7.728847 TGCATTACATGATACCATCACTTAC 57.271 36.000 0.00 0.0 43.01 2.34
1641 1654 8.864024 CATTACATGATACCATCACTTACGATC 58.136 37.037 0.00 0.0 43.01 3.69
1716 1729 6.560711 CATTGCTCTCATTTGTGATGATCAA 58.439 36.000 0.00 0.0 0.00 2.57
1903 1916 5.236478 AGTTGTTTGTGTGAGTCCTATTTCG 59.764 40.000 0.00 0.0 0.00 3.46
2020 2033 3.862642 GCACAAACAGGGAACACAAACAA 60.863 43.478 0.00 0.0 0.00 2.83
2756 2782 2.484947 GGGATCGGTGGTATGTTCCTTC 60.485 54.545 0.00 0.0 0.00 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
157 159 7.273659 GGAAAAATCATCGACAAAAGAAAACG 58.726 34.615 0.00 0.00 0.00 3.60
219 223 7.056635 AGGTAAGACAATATTGGGTGATGAAG 58.943 38.462 19.37 0.00 0.00 3.02
238 242 4.694339 ACGCTTGGCTAAATCTAGGTAAG 58.306 43.478 0.00 0.00 0.00 2.34
442 451 1.209747 GAACAGGGGTTAGTGGCTAGG 59.790 57.143 0.00 0.00 37.36 3.02
545 557 4.454161 TGTTTGTAGTGTTGCTCGCATAAT 59.546 37.500 0.00 0.00 0.00 1.28
628 641 0.108585 AAAACTCCTTCTCGCTGCCA 59.891 50.000 0.00 0.00 0.00 4.92
905 918 9.658799 CATTGTACCTAAATCCCTACATATGAG 57.341 37.037 10.38 2.59 0.00 2.90
913 926 6.689561 TCTCCTCATTGTACCTAAATCCCTA 58.310 40.000 0.00 0.00 0.00 3.53
945 958 6.528321 TGAATGGAATTGTTTTGGTGCATAA 58.472 32.000 0.00 0.00 36.07 1.90
1058 1071 6.951336 GCACTTGCACATGAGATTGCTCAG 62.951 50.000 0.00 2.27 46.57 3.35
1637 1650 5.796935 AGCAAATGAGTTTTCAAATCGATCG 59.203 36.000 9.36 9.36 36.78 3.69
1641 1654 5.691305 TCCAAGCAAATGAGTTTTCAAATCG 59.309 36.000 0.00 0.00 36.78 3.34
1716 1729 8.103305 TCAAGACTAGCATGAGGAAAGTAATTT 58.897 33.333 0.00 0.00 0.00 1.82
1988 2001 1.281867 CCTGTTTGTGCTCCCCTCATA 59.718 52.381 0.00 0.00 0.00 2.15
2020 2033 6.210584 CCTACTTTCTTCTCTCCACTCTTCTT 59.789 42.308 0.00 0.00 0.00 2.52
2698 2723 8.974060 ATACACCTGGTTCGACAAATTATTAT 57.026 30.769 0.00 0.00 0.00 1.28
2793 2905 1.048601 ATGGTATACACCTGGCTCGG 58.951 55.000 5.01 0.00 45.98 4.63


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

AutoCloner maintained by Alex Coulton.