AutoCloner

Multiple sequence alignment - TraesCS6A01G115800

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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	TraesCS6A01G115800	chr6A	100.000	3257	0	0	1	3257	85593278	85590022	0.000000e+00	6015.0
1	TraesCS6A01G115800	chr6A	91.795	585	45	2	1	584	85698044	85697462	0.000000e+00	811.0
2	TraesCS6A01G115800	chr6D	96.328	2887	74	16	378	3257	68105334	68102473	0.000000e+00	4715.0
3	TraesCS6A01G115800	chr6B	95.773	2886	97	10	378	3257	143206209	143203343	0.000000e+00	4630.0
4	TraesCS6A01G115800	chr6B	100.000	44	0	0	2958	3001	408625528	408625571	7.490000e-12	82.4
5	TraesCS6A01G115800	chr6B	91.228	57	3	2	2957	3011	203686753	203686809	3.480000e-10	76.8
6	TraesCS6A01G115800	chr6B	93.750	48	3	0	2953	3000	38077889	38077936	4.510000e-09	73.1
7	TraesCS6A01G115800	chr3B	82.234	1289	150	37	981	2251	63392227	63393454	0.000000e+00	1038.0
8	TraesCS6A01G115800	chr3A	88.757	507	45	6	981	1485	51404824	51404328	7.730000e-171	610.0
9	TraesCS6A01G115800	chr3A	85.240	542	71	2	1747	2279	51404129	51403588	1.710000e-152	549.0
10	TraesCS6A01G115800	chr3A	93.878	49	2	1	2962	3010	729116925	729116878	4.510000e-09	73.1
11	TraesCS6A01G115800	chr3D	88.129	497	48	5	981	1475	39596674	39597161	6.060000e-162	580.0
12	TraesCS6A01G115800	chr7D	97.872	47	1	0	2956	3002	506679479	506679433	7.490000e-12	82.4
13	TraesCS6A01G115800	chr5B	97.872	47	1	0	2956	3002	589116868	589116914	7.490000e-12	82.4
14	TraesCS6A01G115800	chr7A	97.826	46	1	0	2956	3001	68236004	68236049	2.690000e-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	TraesCS6A01G115800	chr6A	85590022	85593278	3256	True	6015.0	6015	100.0000	1	3257	1	chr6A.!!$R1	3256
1	TraesCS6A01G115800	chr6A	85697462	85698044	582	True	811.0	811	91.7950	1	584	1	chr6A.!!$R2	583
2	TraesCS6A01G115800	chr6D	68102473	68105334	2861	True	4715.0	4715	96.3280	378	3257	1	chr6D.!!$R1	2879
3	TraesCS6A01G115800	chr6B	143203343	143206209	2866	True	4630.0	4630	95.7730	378	3257	1	chr6B.!!$R1	2879
4	TraesCS6A01G115800	chr3B	63392227	63393454	1227	False	1038.0	1038	82.2340	981	2251	1	chr3B.!!$F1	1270
5	TraesCS6A01G115800	chr3A	51403588	51404824	1236	True	579.5	610	86.9985	981	2279	2	chr3A.!!$R2	1298

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
189	190	0.028902	GCGCGTTTGTCTGTTCCTTT	59.971	50.0	8.43	0.0	0.0	3.11	F
746	751	0.317160	TGTTAGCCACCGTGTCAGAG	59.683	55.0	0.00	0.0	0.0	3.35	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1715	1740	0.107831	ATTAATCTTAGGCGGCGGCA	59.892	50.000	34.87	18.16	42.47	5.69	R
2460	2494	4.430137	TCAGATGATCTTTTTGCAGTGC	57.570	40.909	8.58	8.58	0.00	4.40	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
55	56	1.200948	GGACATCTTGTTGCTCCTTGC	59.799	52.381	0.00	0.00	43.25	4.01
69	70	1.628340	TCCTTGCGGGAATCTTTCAGA	59.372	47.619	0.00	0.00	41.91	3.27
100	101	0.397254	GGATCTCCTCGGGTTCCTCA	60.397	60.000	0.00	0.00	0.00	3.86
120	121	1.282382	TGGAGGGTTAGGTACTTGCC	58.718	55.000	0.00	0.00	41.75	4.52
124	125	1.266867	GGGTTAGGTACTTGCCCCGA	61.267	60.000	7.85	0.00	42.66	5.14
125	126	0.614812	GGTTAGGTACTTGCCCCGAA	59.385	55.000	0.00	0.00	41.75	4.30
188	189	0.814010	AGCGCGTTTGTCTGTTCCTT	60.814	50.000	8.43	0.00	0.00	3.36
189	190	0.028902	GCGCGTTTGTCTGTTCCTTT	59.971	50.000	8.43	0.00	0.00	3.11
267	268	6.889722	ACACTTTACAATAGCAACCCATACAT	59.110	34.615	0.00	0.00	0.00	2.29
307	308	3.664025	TTGCGGGATGCTCTCGTGG	62.664	63.158	7.18	0.00	43.50	4.94
316	317	0.984230	TGCTCTCGTGGGGAAAAGAT	59.016	50.000	0.00	0.00	0.00	2.40
363	364	9.159364	GAAAGTATATATGCTGAGATGAATGCA	57.841	33.333	3.90	0.00	39.83	3.96
365	366	7.618137	AGTATATATGCTGAGATGAATGCACA	58.382	34.615	2.13	0.00	38.29	4.57
454	457	4.780815	TGACCTATATCTGTGCCCTTTTG	58.219	43.478	0.00	0.00	0.00	2.44
466	469	0.684153	CCCTTTTGCATCATCCGGGT	60.684	55.000	0.00	0.00	0.00	5.28
479	482	2.281091	CGGGTAGCCCTAGGTCCA	59.719	66.667	8.29	0.00	42.67	4.02
583	586	6.000891	TCGTTCTTGAATTTGGAGATGTTG	57.999	37.500	0.00	0.00	0.00	3.33
611	614	4.272504	TCGTGTTGATTCAGGTTGTTTCTC	59.727	41.667	0.00	0.00	0.00	2.87
613	616	5.277974	CGTGTTGATTCAGGTTGTTTCTCAT	60.278	40.000	0.00	0.00	0.00	2.90
626	629	4.641396	TGTTTCTCATGGATCGTTGAACT	58.359	39.130	0.00	0.00	0.00	3.01
636	639	7.867909	TCATGGATCGTTGAACTCATTCTATAC	59.132	37.037	0.00	0.00	35.69	1.47
746	751	0.317160	TGTTAGCCACCGTGTCAGAG	59.683	55.000	0.00	0.00	0.00	3.35
948	953	4.659172	CAGCCCCTCGCAAACCCA	62.659	66.667	0.00	0.00	41.38	4.51
951	956	2.359975	CCCCTCGCAAACCCACTC	60.360	66.667	0.00	0.00	0.00	3.51
1524	1531	1.153086	GGAGCTCATGATTGCCCGT	60.153	57.895	17.19	0.00	0.00	5.28
1539	1546	2.202479	CGTCAGATCGAGCGTGCA	60.202	61.111	0.00	0.00	0.00	4.57
1580	1596	3.116300	GCGAAGAAGACGATGATGCTAA	58.884	45.455	0.00	0.00	0.00	3.09
1659	1684	3.102972	TCAGGAAGAACATCAGGAGGAG	58.897	50.000	0.00	0.00	0.00	3.69
1674	1699	0.553612	AGGAGGGGAAAGAGGCCAAT	60.554	55.000	5.01	0.00	0.00	3.16
1695	1720	0.613012	AGCCAACTGGGAAGATTGCC	60.613	55.000	0.00	0.00	40.01	4.52
2460	2494	3.909776	TCATTCTTGCTGCTGAAAGTG	57.090	42.857	10.84	3.81	35.30	3.16
2638	2672	2.030805	GGACTGGAAATATCATTGCGGC	60.031	50.000	0.00	0.00	30.83	6.53
2690	2724	3.953612	TGGACTGGAAATATCATTGTGGC	59.046	43.478	0.00	0.00	0.00	5.01
2765	2799	6.456501	TGACTTCTACCTTAAGAAAGCTGAC	58.543	40.000	3.36	0.00	35.14	3.51
3061	3096	1.747444	ACCTTGTCCATCTTCCCAGT	58.253	50.000	0.00	0.00	0.00	4.00
3114	3150	7.662669	TGTTACCTTAATTCTGTCCACCTTAAC	59.337	37.037	0.00	0.00	0.00	2.01
3198	3237	7.465353	TTTTGACATAGATTGCTTCCATTCA	57.535	32.000	0.00	0.00	0.00	2.57
3200	3239	7.649533	TTGACATAGATTGCTTCCATTCAAT	57.350	32.000	0.00	0.00	35.79	2.57

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
55	56	5.392380	CCACAAGAATTCTGAAAGATTCCCG	60.392	44.000	9.17	0.00	46.36	5.14
100	101	1.844497	GGCAAGTACCTAACCCTCCAT	59.156	52.381	0.00	0.00	0.00	3.41
120	121	1.067582	GCGAGTACATCCCTTCGGG	59.932	63.158	0.00	0.00	46.11	5.14
124	125	1.264749	TGCAGGCGAGTACATCCCTT	61.265	55.000	0.00	0.00	0.00	3.95
125	126	1.264749	TTGCAGGCGAGTACATCCCT	61.265	55.000	0.00	0.00	0.00	4.20
131	132	1.258982	CGAATGATTGCAGGCGAGTAC	59.741	52.381	0.00	0.00	0.00	2.73
168	169	0.814010	AGGAACAGACAAACGCGCTT	60.814	50.000	5.73	0.00	0.00	4.68
188	189	1.203287	CTCCTCACGAGATGCTCACAA	59.797	52.381	0.00	0.00	41.63	3.33
189	190	0.813821	CTCCTCACGAGATGCTCACA	59.186	55.000	0.00	0.00	41.63	3.58
257	258	7.883311	GGCTGAAACTGTATATATGTATGGGTT	59.117	37.037	0.00	0.00	0.00	4.11
267	268	4.252971	GCGAGGGCTGAAACTGTATATA	57.747	45.455	0.00	0.00	35.83	0.86
307	308	0.248094	GCGCGCAAGTATCTTTTCCC	60.248	55.000	29.10	0.00	41.68	3.97
316	317	1.446099	CTCAAGAGGCGCGCAAGTA	60.446	57.895	34.42	11.58	41.68	2.24
345	346	3.497262	CGTGTGCATTCATCTCAGCATAT	59.503	43.478	0.00	0.00	39.43	1.78
346	347	2.867975	CGTGTGCATTCATCTCAGCATA	59.132	45.455	0.00	0.00	39.43	3.14
365	366	1.229428	CAAGCATCCAACACACTCGT	58.771	50.000	0.00	0.00	0.00	4.18
411	414	2.172483	GACAGCGCCTCCAAGAAGGA	62.172	60.000	2.29	0.00	46.75	3.36
454	457	2.032681	GGGCTACCCGGATGATGC	59.967	66.667	0.73	0.00	32.13	3.91
466	469	0.042731	ACAAGCTGGACCTAGGGCTA	59.957	55.000	16.16	7.79	34.40	3.93
479	482	1.071471	CCGTCCAGTCCAACAAGCT	59.929	57.895	0.00	0.00	0.00	3.74
542	545	1.227853	AGAACGCCGCCAAGAAACT	60.228	52.632	0.00	0.00	0.00	2.66
583	586	2.607187	ACCTGAATCAACACGACGATC	58.393	47.619	0.00	0.00	0.00	3.69
611	614	7.869937	AGTATAGAATGAGTTCAACGATCCATG	59.130	37.037	0.00	0.00	36.79	3.66
613	616	7.348080	AGTATAGAATGAGTTCAACGATCCA	57.652	36.000	0.00	0.00	36.79	3.41
746	751	1.946267	CAAACCAGCACGTACCCAC	59.054	57.895	0.00	0.00	0.00	4.61
1386	1393	2.915659	TTGGGCGTGTCCTCGACT	60.916	61.111	0.00	0.00	39.03	4.18
1503	1510	0.822532	GGGCAATCATGAGCTCCTGG	60.823	60.000	17.59	4.75	0.00	4.45
1524	1531	1.153958	CTGTGCACGCTCGATCTGA	60.154	57.895	13.13	0.00	0.00	3.27
1580	1596	0.250209	GCCGAGGTCATCATCAGCAT	60.250	55.000	0.00	0.00	29.63	3.79
1659	1684	1.403814	GCTTATTGGCCTCTTTCCCC	58.596	55.000	3.32	0.00	0.00	4.81
1674	1699	2.446435	GCAATCTTCCCAGTTGGCTTA	58.554	47.619	0.00	0.00	0.00	3.09
1715	1740	0.107831	ATTAATCTTAGGCGGCGGCA	59.892	50.000	34.87	18.16	42.47	5.69
1845	1870	6.466038	CCTCCTCCTTCATCAGATCATCAATT	60.466	42.308	0.00	0.00	0.00	2.32
2460	2494	4.430137	TCAGATGATCTTTTTGCAGTGC	57.570	40.909	8.58	8.58	0.00	4.40
2605	2639	4.916041	TTTCCAGTCCAGAATGTCTCAT	57.084	40.909	0.00	0.00	0.00	2.90
2765	2799	5.782047	TCAATTACATGGAGTGCCTTTTTG	58.218	37.500	0.00	0.00	34.31	2.44
2980	3015	4.081309	TGGTACTCCCTCCGTAAAGAAATG	60.081	45.833	0.00	0.00	0.00	2.32
3061	3096	9.847224	AAGTTAACTTGGATGAGTTTCTTTAGA	57.153	29.630	19.94	0.00	40.24	2.10
3114	3150	9.780413	GTTATAAAGGAAGCTGAAGAAGATTTG	57.220	33.333	0.00	0.00	33.71	2.32
3198	3237	7.829725	TCAGATAAAAAGCACATACAGCAATT	58.170	30.769	0.00	0.00	0.00	2.32
3200	3239	6.816134	TCAGATAAAAAGCACATACAGCAA	57.184	33.333	0.00	0.00	0.00	3.91

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.