AutoCloner

Multiple sequence alignment - TraesCS4B01G146800

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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	TraesCS4B01G146800	chr4B	100.000	2960	0	0	1	2960	209241135	209244094	0.000000e+00	5467
1	TraesCS4B01G146800	chr6A	97.331	2960	79	0	1	2960	155855877	155858836	0.000000e+00	5029
2	TraesCS4B01G146800	chr6A	96.793	2962	92	3	1	2960	375862183	375859223	0.000000e+00	4940
3	TraesCS4B01G146800	chr3B	97.028	2961	84	4	1	2960	483331791	483334748	0.000000e+00	4977
4	TraesCS4B01G146800	chr3B	96.860	2962	91	2	1	2960	575841165	575838204	0.000000e+00	4953
5	TraesCS4B01G146800	chr2A	96.993	2960	87	2	1	2960	750455011	750452054	0.000000e+00	4972
6	TraesCS4B01G146800	chr7A	98.424	2729	41	2	1	2729	60083516	60086242	0.000000e+00	4800
7	TraesCS4B01G146800	chr7A	98.316	2732	46	0	1	2732	60170189	60167458	0.000000e+00	4791
8	TraesCS4B01G146800	chr7B	98.280	2732	47	0	1	2732	742950160	742947429	0.000000e+00	4785
9	TraesCS4B01G146800	chr4A	95.711	2961	123	4	1	2960	350170820	350173777	0.000000e+00	4761
10	TraesCS4B01G146800	chrUn	99.408	338	2	0	2623	2960	261512824	261512487	5.420000e-172	614
11	TraesCS4B01G146800	chr5B	99.408	338	2	0	2623	2960	130537519	130537856	5.420000e-172	614
12	TraesCS4B01G146800	chr5B	99.408	338	2	0	2623	2960	130568515	130568178	5.420000e-172	614

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	TraesCS4B01G146800	chr4B	209241135	209244094	2959	False	5467	5467	100.000	1	2960	1	chr4B.!!$F1	2959
1	TraesCS4B01G146800	chr6A	155855877	155858836	2959	False	5029	5029	97.331	1	2960	1	chr6A.!!$F1	2959
2	TraesCS4B01G146800	chr6A	375859223	375862183	2960	True	4940	4940	96.793	1	2960	1	chr6A.!!$R1	2959
3	TraesCS4B01G146800	chr3B	483331791	483334748	2957	False	4977	4977	97.028	1	2960	1	chr3B.!!$F1	2959
4	TraesCS4B01G146800	chr3B	575838204	575841165	2961	True	4953	4953	96.860	1	2960	1	chr3B.!!$R1	2959
5	TraesCS4B01G146800	chr2A	750452054	750455011	2957	True	4972	4972	96.993	1	2960	1	chr2A.!!$R1	2959
6	TraesCS4B01G146800	chr7A	60083516	60086242	2726	False	4800	4800	98.424	1	2729	1	chr7A.!!$F1	2728
7	TraesCS4B01G146800	chr7A	60167458	60170189	2731	True	4791	4791	98.316	1	2732	1	chr7A.!!$R1	2731
8	TraesCS4B01G146800	chr7B	742947429	742950160	2731	True	4785	4785	98.280	1	2732	1	chr7B.!!$R1	2731
9	TraesCS4B01G146800	chr4A	350170820	350173777	2957	False	4761	4761	95.711	1	2960	1	chr4A.!!$F1	2959

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
838	841	0.400213	TGTCGAAGTGAAAGCCCCAT	59.600	50.0	0.0	0.0	0.00	4.00	F
1146	1151	0.744414	TTCTTGTAGCAGCCATCGCC	60.744	55.0	0.0	0.0	34.57	5.54	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1658	1666	0.035630	GGCAGCATCAAGGTCTGACT	60.036	55.0	7.85	0.0	36.69	3.41	R
2484	2492	0.098728	GGACATTTCCAATGCCGACG	59.901	55.0	0.00	0.0	42.30	5.12	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
168	171	2.122783	TGTTTGGGCCGATTCCTTAG	57.877	50.000	0.00	0.0	0.00	2.18
213	216	7.327518	CGCCCATAAAAAGAGTAAATCGTTTTT	59.672	33.333	7.35	1.9	44.06	1.94
225	228	6.941436	AGTAAATCGTTTTTGGTATGGGTACA	59.059	34.615	0.00	0.0	32.25	2.90
461	464	1.220206	CCAGAGCTGCGGAACTCAT	59.780	57.895	10.09	0.0	35.28	2.90
554	557	1.106285	GTTGGAGATGGGATTGCACC	58.894	55.000	0.00	0.0	0.00	5.01
605	608	3.007831	GGAGAAATGGTGGAATTTGCCAA	59.992	43.478	0.00	0.0	40.20	4.52
838	841	0.400213	TGTCGAAGTGAAAGCCCCAT	59.600	50.000	0.00	0.0	0.00	4.00
1044	1048	5.928264	TGAGAGTGAGACATTGTATTGTGTG	59.072	40.000	0.00	0.0	0.00	3.82
1081	1085	0.884704	AAAACGCTCGACTGTGGCAT	60.885	50.000	0.00	0.0	0.00	4.40
1142	1147	3.370840	TTCCATTCTTGTAGCAGCCAT	57.629	42.857	0.00	0.0	0.00	4.40
1146	1151	0.744414	TTCTTGTAGCAGCCATCGCC	60.744	55.000	0.00	0.0	34.57	5.54
1175	1181	1.352017	TGCTCCTCTGCAATTTCTGGA	59.648	47.619	0.00	0.0	40.29	3.86
1373	1380	4.530710	TCTTAGAAAGAGCCGCTAAACA	57.469	40.909	0.00	0.0	32.71	2.83
1388	1395	3.616560	GCTAAACAATCGGACCAGACAGA	60.617	47.826	0.00	0.0	0.00	3.41
1658	1666	1.922135	GCCGCCTTCGCTCAATTTGA	61.922	55.000	0.00	0.0	0.00	2.69
1677	1685	0.035630	AGTCAGACCTTGATGCTGCC	60.036	55.000	0.00	0.0	38.29	4.85
1704	1712	2.802816	GGCATTACTGAATAGAGGTGCG	59.197	50.000	0.00	0.0	32.68	5.34
2396	2404	1.597663	ACAGCGAAGGAAAAACGTGAG	59.402	47.619	0.00	0.0	0.00	3.51
2531	2539	0.957888	TTGATTCATTCCGTGGCGCA	60.958	50.000	10.83	0.0	0.00	6.09
2896	2905	7.094508	GCTAGAAGCTATATCATGACTGCTA	57.905	40.000	0.00	0.0	38.45	3.49

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
168	171	0.868177	GCTTTCGACTAGGCTCTCGC	60.868	60.000	9.13	0.00	0.00	5.03
213	216	1.276140	GGGCCAGTGTACCCATACCA	61.276	60.000	4.39	0.00	46.22	3.25
461	464	9.475620	TGGTCATTCTACTTTCTAATAGAGTCA	57.524	33.333	0.00	0.00	0.00	3.41
554	557	7.307493	TGAATCTCGTTCAATCCATAAACAG	57.693	36.000	0.00	0.00	43.64	3.16
605	608	0.953960	GGCGATTCCTTTCACACCGT	60.954	55.000	0.00	0.00	0.00	4.83
838	841	8.190122	GTGCACAGATTTACATTCAATAATCCA	58.810	33.333	13.17	0.00	0.00	3.41
1044	1048	4.087930	CGTTTTTGTCCAATCGCAACATAC	59.912	41.667	0.00	0.00	0.00	2.39
1142	1147	3.219928	GAGCAGGATCCGAGGCGA	61.220	66.667	16.84	0.00	0.00	5.54
1146	1151	2.040330	CAGAGGAGCAGGATCCGAG	58.960	63.158	5.98	4.36	44.65	4.63
1324	1331	6.320164	CGGGAATGTAAATAGAAAACATCCCA	59.680	38.462	15.84	0.00	38.98	4.37
1373	1380	0.904649	TGCATCTGTCTGGTCCGATT	59.095	50.000	0.00	0.00	0.00	3.34
1407	1414	4.320935	GCTTGTGTTTCAATCACGGGTAAT	60.321	41.667	0.00	0.00	38.48	1.89
1658	1666	0.035630	GGCAGCATCAAGGTCTGACT	60.036	55.000	7.85	0.00	36.69	3.41
1677	1685	5.163364	ACCTCTATTCAGTAATGCCTGAGTG	60.163	44.000	0.00	0.00	42.16	3.51
1692	1700	2.100916	TGTAAGCCTCGCACCTCTATTC	59.899	50.000	0.00	0.00	0.00	1.75
1704	1712	0.324943	TGGGCACTTCTGTAAGCCTC	59.675	55.000	0.00	0.00	46.23	4.70
1792	1800	2.306341	AGTGGCATTCGATCACAGAG	57.694	50.000	0.00	0.00	34.17	3.35
2446	2454	2.184020	ATTGTAGCAGCTCCGGCACA	62.184	55.000	0.00	0.00	41.70	4.57
2484	2492	0.098728	GGACATTTCCAATGCCGACG	59.901	55.000	0.00	0.00	42.30	5.12
2490	2498	5.972107	AAGAACTGAGGACATTTCCAATG	57.028	39.130	0.00	0.00	45.72	2.82
2499	2507	5.707298	GGAATGAATCAAAGAACTGAGGACA	59.293	40.000	0.00	0.00	0.00	4.02
2531	2539	7.622713	TGATTGTTTAGCCAATGATGGATTTT	58.377	30.769	0.00	0.00	44.90	1.82
2896	2905	1.893801	ACTCATCGGGTCTTTCGTTCT	59.106	47.619	0.00	0.00	0.00	3.01

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.