AutoCloner

Multiple sequence alignment - TraesCS7A01G307300

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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	TraesCS7A01G307300	chr7A	100.000	2822	0	0	1	2822	433742186	433745007	0.000000e+00	5212.0
1	TraesCS7A01G307300	chr7D	93.576	2086	82	24	1	2047	385716942	385719014	0.000000e+00	3062.0
2	TraesCS7A01G307300	chr7D	91.429	70	5	1	2753	2822	385719114	385719182	8.320000e-16	95.3
3	TraesCS7A01G307300	chr7B	93.754	1537	51	21	541	2047	380079197	380080718	0.000000e+00	2265.0
4	TraesCS7A01G307300	chr7B	86.076	553	43	23	1	523	380076254	380076802	5.280000e-157	564.0
5	TraesCS7A01G307300	chr5B	96.491	684	21	3	2044	2726	20129170	20128489	0.000000e+00	1127.0
6	TraesCS7A01G307300	chr5B	96.224	662	21	2	2055	2713	581218306	581218966	0.000000e+00	1081.0
7	TraesCS7A01G307300	chr3B	97.001	667	19	1	2047	2713	586472969	586472304	0.000000e+00	1120.0
8	TraesCS7A01G307300	chr1B	96.813	659	20	1	2061	2719	599317798	599317141	0.000000e+00	1099.0
9	TraesCS7A01G307300	chr1B	96.499	657	22	1	2058	2714	57805676	57805021	0.000000e+00	1085.0
10	TraesCS7A01G307300	chr2B	95.976	671	23	4	2055	2724	409328390	409327723	0.000000e+00	1086.0
11	TraesCS7A01G307300	chr2B	96.218	661	23	2	2055	2715	95792993	95792335	0.000000e+00	1081.0
12	TraesCS7A01G307300	chr4A	96.353	658	23	1	2056	2713	661815878	661815222	0.000000e+00	1081.0
13	TraesCS7A01G307300	chr4A	96.353	658	22	2	2058	2715	733340227	733340882	0.000000e+00	1081.0

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	TraesCS7A01G307300	chr7A	433742186	433745007	2821	False	5212.00	5212	100.0000	1	2822	1	chr7A.!!$F1	2821
1	TraesCS7A01G307300	chr7D	385716942	385719182	2240	False	1578.65	3062	92.5025	1	2822	2	chr7D.!!$F1	2821
2	TraesCS7A01G307300	chr7B	380076254	380080718	4464	False	1414.50	2265	89.9150	1	2047	2	chr7B.!!$F1	2046
3	TraesCS7A01G307300	chr5B	20128489	20129170	681	True	1127.00	1127	96.4910	2044	2726	1	chr5B.!!$R1	682
4	TraesCS7A01G307300	chr5B	581218306	581218966	660	False	1081.00	1081	96.2240	2055	2713	1	chr5B.!!$F1	658
5	TraesCS7A01G307300	chr3B	586472304	586472969	665	True	1120.00	1120	97.0010	2047	2713	1	chr3B.!!$R1	666
6	TraesCS7A01G307300	chr1B	599317141	599317798	657	True	1099.00	1099	96.8130	2061	2719	1	chr1B.!!$R2	658
7	TraesCS7A01G307300	chr1B	57805021	57805676	655	True	1085.00	1085	96.4990	2058	2714	1	chr1B.!!$R1	656
8	TraesCS7A01G307300	chr2B	409327723	409328390	667	True	1086.00	1086	95.9760	2055	2724	1	chr2B.!!$R2	669
9	TraesCS7A01G307300	chr2B	95792335	95792993	658	True	1081.00	1081	96.2180	2055	2715	1	chr2B.!!$R1	660
10	TraesCS7A01G307300	chr4A	661815222	661815878	656	True	1081.00	1081	96.3530	2056	2713	1	chr4A.!!$R1	657
11	TraesCS7A01G307300	chr4A	733340227	733340882	655	False	1081.00	1081	96.3530	2058	2715	1	chr4A.!!$F1	657

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
835	3258	0.316524	GACGCGATCGGTACCTACAC	60.317	60.0	15.93	0.0	40.69	2.9	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2485	4943	1.074775	TGCTAAGGCCCCGTAGGAT	60.075	57.895	0.0	0.0	45.58	3.24	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
52	53	6.968904	GTGAACATGCACCTAGATAAACATTG	59.031	38.462	0.00	0.00	32.68	2.82
77	78	9.784531	TGAAATGGGTGAAATAGCAAAAATAAA	57.215	25.926	0.00	0.00	0.00	1.40
194	196	8.687824	TTTGAACAAAGAAGAGAAAATGTGTC	57.312	30.769	0.00	0.00	0.00	3.67
212	217	6.917217	TGTGTCCCAAAAAGCAATTTTTAG	57.083	33.333	0.00	0.00	39.20	1.85
225	230	5.836358	AGCAATTTTTAGGTAGTTTGGTGGA	59.164	36.000	0.00	0.00	0.00	4.02
232	237	3.705051	AGGTAGTTTGGTGGAGACGATA	58.295	45.455	0.00	0.00	0.00	2.92
240	245	5.873179	TTGGTGGAGACGATATTGTTTTC	57.127	39.130	0.00	0.00	0.00	2.29
255	261	2.758979	TGTTTTCCGCCCAAAACACTAA	59.241	40.909	13.89	0.00	46.51	2.24
261	267	2.556622	CCGCCCAAAACACTAAGAATGT	59.443	45.455	0.00	0.00	0.00	2.71
271	277	9.681692	CAAAACACTAAGAATGTCATTTCATCA	57.318	29.630	0.00	0.00	0.00	3.07
277	283	7.817478	ACTAAGAATGTCATTTCATCACGTGTA	59.183	33.333	16.51	2.58	0.00	2.90
416	454	4.949856	ACCCATGTTCACTGATGTAATTCC	59.050	41.667	0.00	0.00	0.00	3.01
417	455	4.035558	CCCATGTTCACTGATGTAATTCCG	59.964	45.833	0.00	0.00	0.00	4.30
418	456	4.635765	CCATGTTCACTGATGTAATTCCGT	59.364	41.667	0.00	0.00	0.00	4.69
419	457	5.447683	CCATGTTCACTGATGTAATTCCGTG	60.448	44.000	0.00	0.00	33.60	4.94
420	458	4.888917	TGTTCACTGATGTAATTCCGTGA	58.111	39.130	0.00	0.00	37.86	4.35
421	459	5.487433	TGTTCACTGATGTAATTCCGTGAT	58.513	37.500	0.00	0.00	38.89	3.06
422	460	5.580691	TGTTCACTGATGTAATTCCGTGATC	59.419	40.000	0.00	0.00	38.89	2.92
573	2989	2.603021	ACCTGATGGAGTCTCGCATAT	58.397	47.619	4.40	0.00	37.04	1.78
575	2991	2.560105	CCTGATGGAGTCTCGCATATCA	59.440	50.000	4.40	5.95	34.57	2.15
576	2992	3.573598	CTGATGGAGTCTCGCATATCAC	58.426	50.000	4.40	0.00	0.00	3.06
577	2993	3.225940	TGATGGAGTCTCGCATATCACT	58.774	45.455	4.40	0.00	0.00	3.41
578	2994	3.254411	TGATGGAGTCTCGCATATCACTC	59.746	47.826	4.40	0.00	35.49	3.51
579	2995	2.654863	TGGAGTCTCGCATATCACTCA	58.345	47.619	0.00	0.00	37.59	3.41
606	3025	6.942576	ACAGTTCATTCTGCTACTTGGTTTAT	59.057	34.615	0.00	0.00	38.84	1.40
612	3031	4.627015	TCTGCTACTTGGTTTATCCCCTA	58.373	43.478	0.00	0.00	34.77	3.53
656	3077	3.254903	ACTCCACCGGTAAAGCATTTTTC	59.745	43.478	6.87	0.00	40.09	2.29
816	3239	3.864686	GCCACCTGCATACGCACG	61.865	66.667	0.00	0.00	45.36	5.34
835	3258	0.316524	GACGCGATCGGTACCTACAC	60.317	60.000	15.93	0.00	40.69	2.90
858	3281	1.850441	CGACGTCGACTGAACTTTTGT	59.150	47.619	33.35	0.00	43.02	2.83
907	3332	1.153086	CCCTCTACTGCATGGCACC	60.153	63.158	0.00	0.00	33.79	5.01
1009	3435	0.825410	TCCGCGAACCCTATAAAGCA	59.175	50.000	8.23	0.00	0.00	3.91
1032	3458	1.643292	CAACACGTGACACTGCAGG	59.357	57.895	25.01	9.66	0.00	4.85
1160	3586	2.807472	CGCCGGAGAGTGTAGAGTAGAT	60.807	54.545	5.05	0.00	0.00	1.98
1193	3619	5.431765	AGAATTGTTAGCTGTGTATCAGGG	58.568	41.667	0.00	0.00	43.78	4.45
1231	3657	2.719705	GGGAGGGGAGATCTAGAGAGAA	59.280	54.545	0.00	0.00	34.61	2.87
1581	4035	2.105006	TACAGGTACGCGTCTCTCTT	57.895	50.000	18.63	6.35	0.00	2.85
1585	4039	2.676839	CAGGTACGCGTCTCTCTTTCTA	59.323	50.000	18.63	0.00	0.00	2.10
1586	4040	2.677337	AGGTACGCGTCTCTCTTTCTAC	59.323	50.000	18.63	3.52	0.00	2.59
1587	4041	2.677337	GGTACGCGTCTCTCTTTCTACT	59.323	50.000	18.63	0.00	0.00	2.57
1588	4042	3.868077	GGTACGCGTCTCTCTTTCTACTA	59.132	47.826	18.63	0.00	0.00	1.82
1589	4043	4.025813	GGTACGCGTCTCTCTTTCTACTAG	60.026	50.000	18.63	0.00	0.00	2.57
1595	4049	6.129009	CGCGTCTCTCTTTCTACTAGTAGATC	60.129	46.154	28.79	13.05	41.37	2.75
1622	4076	6.375377	TGTGGTGCAAATAATCGAAGTTAAC	58.625	36.000	0.00	0.00	0.00	2.01
1717	4171	1.079819	CTGTTCTGATGACGGCGGT	60.080	57.895	13.24	0.00	0.00	5.68
2086	4544	3.717294	GCCGCCTCCTCCTCCAAA	61.717	66.667	0.00	0.00	0.00	3.28
2107	4565	0.400594	AAAGCTAGGGTTCGTGCCTT	59.599	50.000	0.00	0.00	0.00	4.35
2120	4578	4.736896	GCCTTTCGTCGGCTCCGT	62.737	66.667	8.28	0.00	44.17	4.69
2213	4671	1.505425	GGCTCCGTTGTTAGTCGTTT	58.495	50.000	0.00	0.00	0.00	3.60
2287	4745	5.383476	CAGCTCCCTGAAGATGGAATAAAT	58.617	41.667	0.00	0.00	41.77	1.40
2485	4943	2.666190	GCTGTTCTGGTGCGCTGA	60.666	61.111	9.73	0.00	0.00	4.26
2679	5141	2.147958	GTTGTACTGCCGTGATGGAAA	58.852	47.619	0.00	0.00	42.00	3.13
2809	5301	0.112412	TTTTCCTCCTCCCCACAAGC	59.888	55.000	0.00	0.00	0.00	4.01
2810	5302	2.124507	TTTCCTCCTCCCCACAAGCG	62.125	60.000	0.00	0.00	0.00	4.68
2811	5303	4.101448	CCTCCTCCCCACAAGCGG	62.101	72.222	0.00	0.00	0.00	5.52
2812	5304	3.003173	CTCCTCCCCACAAGCGGA	61.003	66.667	0.00	0.00	0.00	5.54
2813	5305	3.316573	CTCCTCCCCACAAGCGGAC	62.317	68.421	0.00	0.00	0.00	4.79
2814	5306	3.322466	CCTCCCCACAAGCGGACT	61.322	66.667	0.00	0.00	0.00	3.85
2816	5308	3.316573	CTCCCCACAAGCGGACTCC	62.317	68.421	0.00	0.00	0.00	3.85
2817	5309	3.636231	CCCCACAAGCGGACTCCA	61.636	66.667	0.00	0.00	0.00	3.86
2818	5310	2.046892	CCCACAAGCGGACTCCAG	60.047	66.667	0.00	0.00	0.00	3.86
2819	5311	2.743928	CCACAAGCGGACTCCAGC	60.744	66.667	0.00	0.02	0.00	4.85
2820	5312	3.114616	CACAAGCGGACTCCAGCG	61.115	66.667	0.00	0.00	38.61	5.18

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
212	217	4.667519	ATATCGTCTCCACCAAACTACC	57.332	45.455	0.00	0.00	0.00	3.18
225	230	2.285977	GGGCGGAAAACAATATCGTCT	58.714	47.619	0.00	0.00	0.00	4.18
240	245	2.556622	ACATTCTTAGTGTTTTGGGCGG	59.443	45.455	0.00	0.00	0.00	6.13
255	261	7.334171	TGAATACACGTGATGAAATGACATTCT	59.666	33.333	25.01	0.00	25.53	2.40
493	531	7.307337	CCAATTTGTTGGTAGATTGTTTGCTTC	60.307	37.037	0.00	0.00	37.32	3.86
496	535	5.334028	GCCAATTTGTTGGTAGATTGTTTGC	60.334	40.000	8.79	0.00	43.90	3.68
524	1214	5.221244	GCCCAACTAGCCCAATTATAAGTTG	60.221	44.000	6.13	6.13	42.05	3.16
539	1229	2.859165	TCAGGTTTGAGCCCAACTAG	57.141	50.000	0.00	0.00	30.88	2.57
573	2989	3.133691	GCAGAATGAACTGTGTGAGTGA	58.866	45.455	0.00	0.00	39.69	3.41
575	2991	3.482156	AGCAGAATGAACTGTGTGAGT	57.518	42.857	0.00	0.00	39.69	3.41
576	2992	4.564041	AGTAGCAGAATGAACTGTGTGAG	58.436	43.478	0.00	0.00	39.69	3.51
577	2993	4.607293	AGTAGCAGAATGAACTGTGTGA	57.393	40.909	0.00	0.00	39.69	3.58
578	2994	4.083643	CCAAGTAGCAGAATGAACTGTGTG	60.084	45.833	0.00	0.00	39.69	3.82
579	2995	4.067896	CCAAGTAGCAGAATGAACTGTGT	58.932	43.478	0.00	0.00	39.69	3.72
620	3039	3.003480	GGTGGAGTAGCAGAATGAACAC	58.997	50.000	0.00	0.00	39.69	3.32
621	3040	2.353704	CGGTGGAGTAGCAGAATGAACA	60.354	50.000	0.00	0.00	39.69	3.18
656	3077	1.304134	GGTGGGCCTGGGTTAACAG	60.304	63.158	4.53	0.00	38.21	3.16
816	3239	0.316524	GTGTAGGTACCGATCGCGTC	60.317	60.000	10.32	1.94	35.23	5.19
821	3244	2.349249	CGTCGATGTGTAGGTACCGATC	60.349	54.545	6.18	3.87	0.00	3.69
858	3281	8.047911	TCGGTGGGAACAAAAATAATACTATCA	58.952	33.333	0.00	0.00	46.06	2.15
907	3332	3.056304	ACGTGGAAATTGCCATTTTTCG	58.944	40.909	8.88	9.64	40.68	3.46
966	3391	0.038618	GGCAAATGTCCGAAACACCC	60.039	55.000	0.00	0.00	41.75	4.61
1009	3435	2.203153	GTGTCACGTGTTGGGGCT	60.203	61.111	16.51	0.00	0.00	5.19
1032	3458	1.065436	GCTAACGGGGAGAGCGTAC	59.935	63.158	0.00	0.00	0.00	3.67
1091	3517	1.021968	GTATTCACGGGAATGCCACC	58.978	55.000	23.14	2.02	43.47	4.61
1160	3586	6.646653	CACAGCTAACAATTCTCTCTGTACAA	59.353	38.462	0.00	0.00	32.73	2.41
1193	3619	3.496331	CTCCCCTGTCTCTAATCTCTCC	58.504	54.545	0.00	0.00	0.00	3.71
1581	4035	6.436218	TGCACCACAAAGATCTACTAGTAGAA	59.564	38.462	31.11	17.56	44.44	2.10
1585	4039	5.483685	TTGCACCACAAAGATCTACTAGT	57.516	39.130	0.00	0.00	34.56	2.57
1622	4076	3.125146	CACGTTCACACCCATGTAATCAG	59.875	47.826	0.00	0.00	36.72	2.90
1717	4171	4.124351	GTCGTCATCGCCGGTCCA	62.124	66.667	1.90	0.00	36.96	4.02
1869	4327	4.197750	GCGCATATAGGCTAGTAGGAGTA	58.802	47.826	0.30	0.00	0.00	2.59
2086	4544	1.202891	AGGCACGAACCCTAGCTTTTT	60.203	47.619	0.00	0.00	0.00	1.94
2287	4745	2.043248	GGACTAGGCGGGGAGACA	60.043	66.667	0.00	0.00	0.00	3.41
2485	4943	1.074775	TGCTAAGGCCCCGTAGGAT	60.075	57.895	0.00	0.00	45.58	3.24
2649	5111	3.247442	CGGCAGTACAACGAACATTAGA	58.753	45.455	0.00	0.00	0.00	2.10
2653	5115	1.144969	CACGGCAGTACAACGAACAT	58.855	50.000	10.19	0.00	0.00	2.71
2679	5141	8.514594	TGCGAGAAAACTTTCAATCTATTCATT	58.485	29.630	5.07	0.00	39.61	2.57
2747	5209	2.301346	GGATTCGCCCACAGATTGATT	58.699	47.619	0.00	0.00	0.00	2.57
2748	5210	1.972872	GGATTCGCCCACAGATTGAT	58.027	50.000	0.00	0.00	0.00	2.57
2774	5266	1.600485	GAAAACCTTTCGGCTTGACGA	59.400	47.619	0.00	0.00	41.76	4.20

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.