Multiple sequence alignment - TraesCS4B01G287500

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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 TraesCS4B01G287500 chr4B 100.000 2549 0 0 1 2549 570972482 570975030 0.000000e+00 4708
1 TraesCS4B01G287500 chr4B 94.508 2549 109 17 6 2549 560117487 560120009 0.000000e+00 3903
2 TraesCS4B01G287500 chr7B 96.075 2548 92 5 6 2549 143955296 143957839 0.000000e+00 4145
3 TraesCS4B01G287500 chr7B 93.404 2547 127 24 13 2549 188093990 188091475 0.000000e+00 3735
4 TraesCS4B01G287500 chr3B 94.331 2540 120 15 13 2549 741944323 741946841 0.000000e+00 3871
5 TraesCS4B01G287500 chr3B 94.221 1886 86 9 6 1886 729307624 729309491 0.000000e+00 2857
6 TraesCS4B01G287500 chr2B 94.328 2539 116 15 13 2549 488119930 488122442 0.000000e+00 3866
7 TraesCS4B01G287500 chr2B 94.289 1891 81 10 3 1886 791277813 791275943 0.000000e+00 2868
8 TraesCS4B01G287500 chr2B 93.590 156 7 3 6 160 177315540 177315693 1.970000e-56 230
9 TraesCS4B01G287500 chr1B 93.968 2553 123 21 6 2549 678965665 678963135 0.000000e+00 3832
10 TraesCS4B01G287500 chr1B 93.821 2541 127 20 13 2549 101777036 101779550 0.000000e+00 3795
11 TraesCS4B01G287500 chr1B 93.448 2549 131 18 6 2549 445288068 445285551 0.000000e+00 3749
12 TraesCS4B01G287500 chr5B 94.458 2418 123 9 136 2549 584508320 584510730 0.000000e+00 3712
13 TraesCS4B01G287500 chr5B 94.303 1457 65 11 13 1465 230958543 230959985 0.000000e+00 2215
14 TraesCS4B01G287500 chr6B 92.301 1130 60 11 6 1133 698265474 698266578 0.000000e+00 1580
15 TraesCS4B01G287500 chr6B 93.275 922 39 10 13 930 692905468 692906370 0.000000e+00 1338


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 TraesCS4B01G287500 chr4B 570972482 570975030 2548 False 4708 4708 100.000 1 2549 1 chr4B.!!$F2 2548
1 TraesCS4B01G287500 chr4B 560117487 560120009 2522 False 3903 3903 94.508 6 2549 1 chr4B.!!$F1 2543
2 TraesCS4B01G287500 chr7B 143955296 143957839 2543 False 4145 4145 96.075 6 2549 1 chr7B.!!$F1 2543
3 TraesCS4B01G287500 chr7B 188091475 188093990 2515 True 3735 3735 93.404 13 2549 1 chr7B.!!$R1 2536
4 TraesCS4B01G287500 chr3B 741944323 741946841 2518 False 3871 3871 94.331 13 2549 1 chr3B.!!$F2 2536
5 TraesCS4B01G287500 chr3B 729307624 729309491 1867 False 2857 2857 94.221 6 1886 1 chr3B.!!$F1 1880
6 TraesCS4B01G287500 chr2B 488119930 488122442 2512 False 3866 3866 94.328 13 2549 1 chr2B.!!$F2 2536
7 TraesCS4B01G287500 chr2B 791275943 791277813 1870 True 2868 2868 94.289 3 1886 1 chr2B.!!$R1 1883
8 TraesCS4B01G287500 chr1B 678963135 678965665 2530 True 3832 3832 93.968 6 2549 1 chr1B.!!$R2 2543
9 TraesCS4B01G287500 chr1B 101777036 101779550 2514 False 3795 3795 93.821 13 2549 1 chr1B.!!$F1 2536
10 TraesCS4B01G287500 chr1B 445285551 445288068 2517 True 3749 3749 93.448 6 2549 1 chr1B.!!$R1 2543
11 TraesCS4B01G287500 chr5B 584508320 584510730 2410 False 3712 3712 94.458 136 2549 1 chr5B.!!$F2 2413
12 TraesCS4B01G287500 chr5B 230958543 230959985 1442 False 2215 2215 94.303 13 1465 1 chr5B.!!$F1 1452
13 TraesCS4B01G287500 chr6B 698265474 698266578 1104 False 1580 1580 92.301 6 1133 1 chr6B.!!$F2 1127
14 TraesCS4B01G287500 chr6B 692905468 692906370 902 False 1338 1338 93.275 13 930 1 chr6B.!!$F1 917

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
537 550 0.033405 CAGGGAGGAGGTTCTACGGA 60.033 60.0 0.0 0.0 0.0 4.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2138 2170 0.679505 AGACTGTACGTGCACATGGT 59.32 50.0 18.64 9.39 0.0 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
21 23 3.808834 AAAGAAAAAGAGGACGGGGAT 57.191 42.857 0.00 0.00 0.00 3.85
103 105 2.426738 CGAAGTCCTCTTGCTCTCTCAT 59.573 50.000 0.00 0.00 33.64 2.90
111 113 5.660417 TCCTCTTGCTCTCTCATTGTATCTT 59.340 40.000 0.00 0.00 0.00 2.40
135 140 3.721087 CCCCCTCTCTCTCTATCTCTC 57.279 57.143 0.00 0.00 0.00 3.20
141 146 6.256819 CCCTCTCTCTCTATCTCTCTCTCTA 58.743 48.000 0.00 0.00 0.00 2.43
142 147 6.153680 CCCTCTCTCTCTATCTCTCTCTCTAC 59.846 50.000 0.00 0.00 0.00 2.59
143 148 6.153680 CCTCTCTCTCTATCTCTCTCTCTACC 59.846 50.000 0.00 0.00 0.00 3.18
229 242 0.749049 CATCTGCTCACATCCTCCGA 59.251 55.000 0.00 0.00 0.00 4.55
299 312 4.520492 TGAACTTCCTTGAGCTGGATTTTC 59.480 41.667 0.00 0.00 33.09 2.29
418 431 2.320781 AGGAGAACCCTGATACCATCG 58.679 52.381 0.00 0.00 45.61 3.84
437 450 2.567169 TCGAGGACCATGATTTCTGTGT 59.433 45.455 0.00 0.00 0.00 3.72
451 464 1.957177 TCTGTGTCAAAGAGCTCGACT 59.043 47.619 17.58 1.67 0.00 4.18
537 550 0.033405 CAGGGAGGAGGTTCTACGGA 60.033 60.000 0.00 0.00 0.00 4.69
548 561 2.418746 GGTTCTACGGATGTGCTGTGAT 60.419 50.000 0.00 0.00 36.57 3.06
615 628 7.537715 TCAAACTGTTCGGATATACGACTTAA 58.462 34.615 10.24 0.00 43.37 1.85
778 791 7.995289 ACACTCTCATGTTTGTTTACAAATGA 58.005 30.769 10.87 10.29 46.12 2.57
1092 1112 7.778470 TTATTTTGTTCCTTTTTGTTCGCAT 57.222 28.000 0.00 0.00 0.00 4.73
1173 1194 0.107945 GGTGCCTACTCAAGCTCTGG 60.108 60.000 0.00 0.00 0.00 3.86
1461 1483 9.282569 CATAAGCTAAAGGAGAATAGAAGCAAT 57.717 33.333 0.00 0.00 0.00 3.56
1591 1614 2.482721 CGAAACGTTGCAAGGGATACTT 59.517 45.455 22.07 5.24 41.00 2.24
1771 1794 5.041951 TCCAACAATATTTCGTCTTGCAC 57.958 39.130 0.00 0.00 0.00 4.57
1859 1882 1.474143 GCCTCTGATAACCTGGCACTC 60.474 57.143 0.00 0.00 42.79 3.51
1873 1896 1.312815 GCACTCACTTGTCAAAGGCT 58.687 50.000 0.00 0.00 37.76 4.58
1899 1922 4.833380 GTCCTATGTGCCTCTGATAACCTA 59.167 45.833 0.00 0.00 0.00 3.08
2031 2058 0.900182 ATCTGTGCCTCCGTGACTCA 60.900 55.000 0.00 0.00 0.00 3.41
2138 2170 4.783764 TTGAGATTAAGCAGAGTCACGA 57.216 40.909 0.00 0.00 0.00 4.35
2203 2235 3.046087 CACTGCAGACGCACTGGG 61.046 66.667 23.35 0.00 45.36 4.45
2439 2472 5.895636 TGTTTGGCCATGTTTAGACATAG 57.104 39.130 6.09 0.00 44.55 2.23
2525 2558 0.896940 CCCAGCAGGCACAAGTGAAT 60.897 55.000 4.04 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 2.084546 CACATCCCCGTCCTCTTTTTC 58.915 52.381 0.00 0.00 0.00 2.29
21 23 2.277072 CACCAACCACCACCCACA 59.723 61.111 0.00 0.00 0.00 4.17
135 140 5.144100 AGAGAGAGAGAGAGAGGTAGAGAG 58.856 50.000 0.00 0.00 0.00 3.20
141 146 3.964031 GAGAGAGAGAGAGAGAGAGAGGT 59.036 52.174 0.00 0.00 0.00 3.85
142 147 4.222336 AGAGAGAGAGAGAGAGAGAGAGG 58.778 52.174 0.00 0.00 0.00 3.69
143 148 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
229 242 1.967319 ACTTTTGTGTCGACATGGCT 58.033 45.000 23.12 0.00 30.13 4.75
299 312 7.619050 AGCAGGATATCACCTACATAGAAATG 58.381 38.462 4.83 0.00 38.32 2.32
317 330 0.105593 CGCTCCACATGTAGCAGGAT 59.894 55.000 18.32 0.00 38.70 3.24
418 431 3.942829 TGACACAGAAATCATGGTCCTC 58.057 45.455 0.00 0.00 0.00 3.71
437 450 1.542030 GAGGACAGTCGAGCTCTTTGA 59.458 52.381 12.85 0.00 0.00 2.69
451 464 2.085320 GAGAACGCAGTAGAGAGGACA 58.915 52.381 0.00 0.00 45.00 4.02
548 561 6.680810 TCGGATTTTCGAAAGTGACTAACTA 58.319 36.000 10.93 0.00 35.06 2.24
600 613 8.583810 TTGGAAGATTTTAAGTCGTATATCCG 57.416 34.615 0.00 0.00 0.00 4.18
1092 1112 0.888619 CTCCACAGTTCACGCCTCTA 59.111 55.000 0.00 0.00 0.00 2.43
1173 1194 1.344114 TCCTTTGCTTGCAACATTCCC 59.656 47.619 7.60 0.00 0.00 3.97
1461 1483 5.737860 AGATCACAGATGACACTTTGCATA 58.262 37.500 0.00 0.00 37.79 3.14
1591 1614 8.755028 TGTCCAAGCATAAACTTATACTAGACA 58.245 33.333 0.00 9.40 32.81 3.41
1771 1794 0.680921 ACCCATGCCTCATTGAACGG 60.681 55.000 0.00 0.00 0.00 4.44
1817 1840 2.679642 TTCCCCATGCCAAAGCGG 60.680 61.111 0.00 0.00 44.31 5.52
1859 1882 1.876156 GGACTGAGCCTTTGACAAGTG 59.124 52.381 0.00 0.00 0.00 3.16
1873 1896 2.532250 TCAGAGGCACATAGGACTGA 57.468 50.000 0.00 0.00 33.06 3.41
1899 1922 1.312815 GCCTTTGACAAGTCAGTGCT 58.687 50.000 2.87 0.00 41.13 4.40
2031 2058 9.355215 CGAGTTTATGTCTGAGTACAAACTATT 57.645 33.333 0.00 0.00 32.97 1.73
2087 2114 0.881796 CAGCGACCTCAGACTGTACA 59.118 55.000 1.59 0.00 0.00 2.90
2138 2170 0.679505 AGACTGTACGTGCACATGGT 59.320 50.000 18.64 9.39 0.00 3.55
2203 2235 3.721625 TGCGTCTAGTGCATGAGAC 57.278 52.632 16.97 16.97 37.44 3.36
2439 2472 2.486966 GCCAATCCGAAGCTGTGC 59.513 61.111 0.00 0.00 0.00 4.57
2525 2558 1.554617 TGCCTCGATTTGTCAGATCCA 59.445 47.619 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.