AutoCloner

Multiple sequence alignment - TraesCS7D01G460500

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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	TraesCS7D01G460500	chr7D	100.000	2799	0	0	1	2799	577200010	577202808	0.000000e+00	5169
1	TraesCS7D01G460500	chr7A	94.063	2813	118	17	3	2799	669292238	669295017	0.000000e+00	4224
2	TraesCS7D01G460500	chr7A	93.047	1769	102	8	576	2341	669214729	669216479	0.000000e+00	2566
3	TraesCS7D01G460500	chr7A	91.334	577	24	5	1	575	669214145	669214697	0.000000e+00	765
4	TraesCS7D01G460500	chr7A	95.076	264	13	0	2338	2601	48824797	48825060	1.550000e-112	416
5	TraesCS7D01G460500	chr7A	88.690	168	16	3	52	216	669328301	669328134	4.730000e-48	202
6	TraesCS7D01G460500	chr7B	93.311	2063	87	20	19	2032	639925051	639927111	0.000000e+00	2998
7	TraesCS7D01G460500	chr7B	93.311	2063	87	20	19	2032	639944697	639946757	0.000000e+00	2998
8	TraesCS7D01G460500	chr7B	86.122	245	26	5	2561	2799	99683146	99682904	9.950000e-65	257
9	TraesCS7D01G460500	chr3A	80.797	828	132	25	990	1798	9572494	9571675	8.510000e-175	623
10	TraesCS7D01G460500	chr3A	85.563	568	82	0	1231	1798	9556246	9556813	1.860000e-166	595
11	TraesCS7D01G460500	chr3A	83.505	582	96	0	1231	1812	9573496	9574077	6.820000e-151	544
12	TraesCS7D01G460500	chr3A	96.212	264	10	0	2338	2601	702593795	702594058	1.540000e-117	433
13	TraesCS7D01G460500	chr3A	87.755	245	20	8	2561	2799	107649050	107648810	7.640000e-71	278
14	TraesCS7D01G460500	chr3D	85.587	562	79	2	1232	1792	4046235	4046795	3.110000e-164	588
15	TraesCS7D01G460500	chr3D	84.737	570	87	0	1242	1811	4012403	4012972	3.130000e-159	571
16	TraesCS7D01G460500	chr2A	96.154	260	10	0	2342	2601	34312380	34312639	2.580000e-115	425
17	TraesCS7D01G460500	chr1B	94.615	260	14	0	2342	2601	580210534	580210793	1.210000e-108	403
18	TraesCS7D01G460500	chrUn	93.962	265	12	3	2338	2601	243149872	243149611	5.620000e-107	398
19	TraesCS7D01G460500	chrUn	93.962	265	12	3	2338	2601	243162745	243162484	5.620000e-107	398
20	TraesCS7D01G460500	chrUn	93.962	265	12	3	2338	2601	270190776	270191037	5.620000e-107	398
21	TraesCS7D01G460500	chr3B	93.962	265	12	3	2338	2601	5867610	5867349	5.620000e-107	398
22	TraesCS7D01G460500	chr6A	85.772	246	26	6	2561	2799	27562091	27562334	4.630000e-63	252
23	TraesCS7D01G460500	chr1A	82.390	159	21	5	2645	2799	288079845	288080000	6.290000e-27	132

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	TraesCS7D01G460500	chr7D	577200010	577202808	2798	False	5169.0	5169	100.0000	1	2799	1	chr7D.!!$F1	2798
1	TraesCS7D01G460500	chr7A	669292238	669295017	2779	False	4224.0	4224	94.0630	3	2799	1	chr7A.!!$F2	2796
2	TraesCS7D01G460500	chr7A	669214145	669216479	2334	False	1665.5	2566	92.1905	1	2341	2	chr7A.!!$F3	2340
3	TraesCS7D01G460500	chr7B	639925051	639927111	2060	False	2998.0	2998	93.3110	19	2032	1	chr7B.!!$F1	2013
4	TraesCS7D01G460500	chr7B	639944697	639946757	2060	False	2998.0	2998	93.3110	19	2032	1	chr7B.!!$F2	2013
5	TraesCS7D01G460500	chr3A	9571675	9572494	819	True	623.0	623	80.7970	990	1798	1	chr3A.!!$R1	808
6	TraesCS7D01G460500	chr3A	9556246	9556813	567	False	595.0	595	85.5630	1231	1798	1	chr3A.!!$F1	567
7	TraesCS7D01G460500	chr3A	9573496	9574077	581	False	544.0	544	83.5050	1231	1812	1	chr3A.!!$F2	581
8	TraesCS7D01G460500	chr3D	4046235	4046795	560	False	588.0	588	85.5870	1232	1792	1	chr3D.!!$F2	560
9	TraesCS7D01G460500	chr3D	4012403	4012972	569	False	571.0	571	84.7370	1242	1811	1	chr3D.!!$F1	569

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
779	829	2.300152	TGAAGTGGACGATGAAGCTTCT	59.7	45.455	26.09	12.48	34.96	2.85	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2748	2837	0.391597	TCGTTTCGTTTGCTCCCTCT	59.608	50.0	0.0	0.0	0.0	3.69	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
34	35	4.219288	ACAAGGCTGAAATGGTCTTGATTC	59.781	41.667	13.72	0.00	45.79	2.52
159	162	3.041211	TGGGATCTCCAACCATGACTAG	58.959	50.000	0.00	0.00	43.84	2.57
170	173	7.398829	TCCAACCATGACTAGTTATTTGCTTA	58.601	34.615	0.00	0.00	0.00	3.09
187	190	4.682787	TGCTTAAGACTCGGTCACATATG	58.317	43.478	6.67	0.00	34.60	1.78
665	712	4.458397	CAGAGGTATCACGTAACTAGGGA	58.542	47.826	0.00	0.00	27.86	4.20
704	754	6.095860	ACGCATACATGTCCAGTAGTTTACTA	59.904	38.462	0.00	0.00	37.23	1.82
779	829	2.300152	TGAAGTGGACGATGAAGCTTCT	59.700	45.455	26.09	12.48	34.96	2.85
796	846	3.376546	GCTTCTTAATGCTGCAGCTAGTT	59.623	43.478	36.61	28.08	42.66	2.24
895	946	7.274468	CCAACTCTTTCTGCTGCTATATATACG	59.726	40.741	0.00	0.00	0.00	3.06
909	960	7.926018	TGCTATATATACGCATACATCCTTTGG	59.074	37.037	10.83	0.00	0.00	3.28
1528	1604	4.265073	GCTTTGTCACATCTAACCCAGAT	58.735	43.478	0.00	0.00	45.35	2.90
1966	2046	1.802960	GCACATGAGACCACACTTGAG	59.197	52.381	0.00	0.00	0.00	3.02
2021	2103	5.257082	TGAAAACAAGGCTAGGTTTTGAC	57.743	39.130	25.37	16.34	44.64	3.18
2039	2121	8.311109	GGTTTTGACCTGTTCCAAACATAATAT	58.689	33.333	4.71	0.00	40.23	1.28
2057	2139	7.512746	ACATAATATTTGAGTACTAGGCAGGGA	59.487	37.037	0.00	0.00	0.00	4.20
2122	2204	5.507149	CGGTGACTTTTCATTTGGACAATGA	60.507	40.000	0.00	0.00	33.11	2.57
2138	2220	8.171164	TGGACAATGAAACACATACAATGTAA	57.829	30.769	0.00	0.00	42.70	2.41
2139	2221	8.633561	TGGACAATGAAACACATACAATGTAAA	58.366	29.630	0.00	0.00	42.70	2.01
2216	2300	6.495872	TGGCGGTACAGGATTTTATCTATAGT	59.504	38.462	0.00	0.00	0.00	2.12
2346	2434	6.539649	AATCTCGTTTCGAAATCTCAAACA	57.460	33.333	14.69	0.00	34.74	2.83
2348	2436	5.286438	TCTCGTTTCGAAATCTCAAACAGA	58.714	37.500	14.69	4.34	34.74	3.41
2350	2438	5.286438	TCGTTTCGAAATCTCAAACAGAGA	58.714	37.500	14.69	0.00	44.74	3.10
2369	2457	2.087646	GACCTGGAAGCATGGAGAAAC	58.912	52.381	0.00	0.00	0.00	2.78
2376	2464	2.486796	GCATGGAGAAACAGGCCTC	58.513	57.895	0.00	0.00	41.89	4.70
2391	2479	4.598894	CTCGCCCATCCCGCTCAG	62.599	72.222	0.00	0.00	0.00	3.35
2406	2494	4.475944	CCGCTCAGAAACGATTTGAAAAT	58.524	39.130	0.00	0.00	0.00	1.82
2416	2504	8.174422	AGAAACGATTTGAAAATTGGTTTGTTG	58.826	29.630	16.75	0.00	39.26	3.33
2478	2566	3.007398	TCGCTTTATTTTTGGGCATTGGT	59.993	39.130	0.00	0.00	0.00	3.67
2498	2586	3.435671	GGTGGTGTAAGATGGAAAGAACG	59.564	47.826	0.00	0.00	0.00	3.95
2531	2619	6.364976	TGATTGGCGTTGTATATCTGATTACG	59.635	38.462	0.00	0.00	0.00	3.18
2565	2653	5.353956	CGATTTGATTCCTGTTGTGTATGGA	59.646	40.000	0.00	0.00	0.00	3.41
2567	2655	6.573664	TTTGATTCCTGTTGTGTATGGAAG	57.426	37.500	0.00	0.00	41.20	3.46
2620	2708	3.893326	ATTTTATTGTGCAAGGGAGGC	57.107	42.857	0.00	0.00	0.00	4.70
2623	2711	0.676466	TATTGTGCAAGGGAGGCGTG	60.676	55.000	0.00	0.00	0.00	5.34
2666	2754	4.946478	TTGGTCTTTGTGGGGTTTATTG	57.054	40.909	0.00	0.00	0.00	1.90
2668	2756	2.565391	GGTCTTTGTGGGGTTTATTGGG	59.435	50.000	0.00	0.00	0.00	4.12
2676	2764	2.114506	TGGGGTTTATTGGGGGATTGTT	59.885	45.455	0.00	0.00	0.00	2.83
2743	2832	1.450312	GGTGGCCTCTCGTTGGATG	60.450	63.158	3.32	0.00	0.00	3.51
2748	2837	1.330655	GCCTCTCGTTGGATGGGAGA	61.331	60.000	0.00	0.00	35.63	3.71
2752	2841	0.749649	CTCGTTGGATGGGAGAGAGG	59.250	60.000	0.00	0.00	0.00	3.69
2754	2843	0.687757	CGTTGGATGGGAGAGAGGGA	60.688	60.000	0.00	0.00	0.00	4.20
2756	2845	0.692419	TTGGATGGGAGAGAGGGAGC	60.692	60.000	0.00	0.00	0.00	4.70
2758	2847	0.692419	GGATGGGAGAGAGGGAGCAA	60.692	60.000	0.00	0.00	0.00	3.91
2759	2848	1.207791	GATGGGAGAGAGGGAGCAAA	58.792	55.000	0.00	0.00	0.00	3.68
2760	2849	0.915364	ATGGGAGAGAGGGAGCAAAC	59.085	55.000	0.00	0.00	0.00	2.93
2771	2861	1.064357	GGGAGCAAACGAAACGAAACA	59.936	47.619	0.00	0.00	0.00	2.83
2777	2867	3.720328	GCAAACGAAACGAAACAACGTAT	59.280	39.130	0.00	0.00	45.83	3.06

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
46	49	8.862085	GCTCTATAATAGACCACTTAAACCTCT	58.138	37.037	0.00	0.00	0.00	3.69
47	50	7.808856	CGCTCTATAATAGACCACTTAAACCTC	59.191	40.741	0.00	0.00	0.00	3.85
53	56	8.859236	ATACACGCTCTATAATAGACCACTTA	57.141	34.615	0.00	0.00	0.00	2.24
56	59	9.504710	CATAATACACGCTCTATAATAGACCAC	57.495	37.037	0.00	0.00	0.00	4.16
115	118	2.290071	ACAAACTATGTGGAGAACCCGG	60.290	50.000	0.00	0.00	41.93	5.73
159	162	5.407387	TGTGACCGAGTCTTAAGCAAATAAC	59.593	40.000	0.00	0.00	33.15	1.89
170	173	3.096852	TGTCCATATGTGACCGAGTCTT	58.903	45.455	16.79	0.00	33.15	3.01
187	190	2.808543	GTCACTGTTGATGGAGTTGTCC	59.191	50.000	0.00	0.00	44.24	4.02
665	712	5.857471	TGTATGCGTATTTGGTAGTACCT	57.143	39.130	20.07	2.88	39.58	3.08
704	754	3.575256	ACTTGGTCATGCATGTGTGAAAT	59.425	39.130	25.43	5.51	0.00	2.17
779	829	1.745087	GCCAACTAGCTGCAGCATTAA	59.255	47.619	38.24	20.06	45.16	1.40
796	846	0.906066	TAAGCCGGTTGAGTATGCCA	59.094	50.000	1.90	0.00	0.00	4.92
895	946	3.221771	TGCCATACCAAAGGATGTATGC	58.778	45.455	0.00	0.00	0.00	3.14
1199	1273	9.787532	GCATAATAAAAAGAAGCATGTAAGTCA	57.212	29.630	0.00	0.00	0.00	3.41
1528	1604	4.141251	AGGACCTTCCAAAAGAGCTTGTTA	60.141	41.667	0.00	0.00	39.61	2.41
1845	1921	8.780249	ACAACAAACAATCTTATTAGTACGCTT	58.220	29.630	0.00	0.00	0.00	4.68
1846	1922	8.319143	ACAACAAACAATCTTATTAGTACGCT	57.681	30.769	0.00	0.00	0.00	5.07
1934	2014	5.109903	GGTCTCATGTGCGTAAAACTAGAT	58.890	41.667	0.00	0.00	0.00	1.98
2039	2121	3.039011	GGATCCCTGCCTAGTACTCAAA	58.961	50.000	0.00	0.00	0.00	2.69
2057	2139	5.046304	CGTAATACTGATCCTCATTGGGGAT	60.046	44.000	18.28	18.28	45.23	3.85
2187	2271	2.871096	AAATCCTGTACCGCCAAAGA	57.129	45.000	0.00	0.00	0.00	2.52
2216	2300	6.256819	TCTCAAATGACCTCTCTCTTTAGGA	58.743	40.000	0.00	0.00	36.66	2.94
2225	2309	9.558396	AGATTGATAATTCTCAAATGACCTCTC	57.442	33.333	9.97	2.01	38.55	3.20
2346	2434	1.202330	CTCCATGCTTCCAGGTCTCT	58.798	55.000	0.00	0.00	0.00	3.10
2348	2436	1.661463	TTCTCCATGCTTCCAGGTCT	58.339	50.000	0.00	0.00	0.00	3.85
2350	2438	1.425066	TGTTTCTCCATGCTTCCAGGT	59.575	47.619	0.00	0.00	0.00	4.00
2376	2464	3.680620	TTTCTGAGCGGGATGGGCG	62.681	63.158	0.00	0.00	35.00	6.13
2381	2469	2.009774	CAAATCGTTTCTGAGCGGGAT	58.990	47.619	4.40	0.00	0.00	3.85
2391	2479	7.960195	ACAACAAACCAATTTTCAAATCGTTTC	59.040	29.630	7.16	0.00	32.76	2.78
2406	2494	6.517529	GCCTTCCATATACAACAACAAACCAA	60.518	38.462	0.00	0.00	0.00	3.67
2416	2504	4.054780	TCTCACGCCTTCCATATACAAC	57.945	45.455	0.00	0.00	0.00	3.32
2478	2566	4.610605	TCGTTCTTTCCATCTTACACCA	57.389	40.909	0.00	0.00	0.00	4.17
2498	2586	8.345565	AGATATACAACGCCAATCAATCTTTTC	58.654	33.333	0.00	0.00	0.00	2.29
2531	2619	2.975851	GGAATCAAATCGCATCGCAATC	59.024	45.455	0.00	0.00	0.00	2.67
2620	2708	1.434696	GCATCCTTTCCATGCCACG	59.565	57.895	0.00	0.00	40.79	4.94
2666	2754	4.603989	TTTTTAACCGAAACAATCCCCC	57.396	40.909	0.00	0.00	0.00	5.40
2701	2790	4.339748	CTCGATCCCATCTCTCTTCCATA	58.660	47.826	0.00	0.00	0.00	2.74
2702	2791	3.164268	CTCGATCCCATCTCTCTTCCAT	58.836	50.000	0.00	0.00	0.00	3.41
2709	2798	0.470833	CACCCCTCGATCCCATCTCT	60.471	60.000	0.00	0.00	0.00	3.10
2711	2800	1.460305	CCACCCCTCGATCCCATCT	60.460	63.158	0.00	0.00	0.00	2.90
2735	2824	0.687757	TCCCTCTCTCCCATCCAACG	60.688	60.000	0.00	0.00	0.00	4.10
2743	2832	1.219393	CGTTTGCTCCCTCTCTCCC	59.781	63.158	0.00	0.00	0.00	4.30
2748	2837	0.391597	TCGTTTCGTTTGCTCCCTCT	59.608	50.000	0.00	0.00	0.00	3.69
2752	2841	2.461897	TGTTTCGTTTCGTTTGCTCC	57.538	45.000	0.00	0.00	0.00	4.70
2754	2843	2.170770	CGTTGTTTCGTTTCGTTTGCT	58.829	42.857	0.00	0.00	0.00	3.91
2756	2845	4.143374	CCATACGTTGTTTCGTTTCGTTTG	59.857	41.667	0.00	0.00	43.80	2.93
2758	2847	3.555139	TCCATACGTTGTTTCGTTTCGTT	59.445	39.130	0.00	0.00	43.80	3.85
2759	2848	3.060339	GTCCATACGTTGTTTCGTTTCGT	60.060	43.478	0.00	0.00	43.80	3.85
2760	2849	3.182972	AGTCCATACGTTGTTTCGTTTCG	59.817	43.478	0.00	0.00	43.80	3.46
2771	2861	4.954202	TCCTAATGTCTCAGTCCATACGTT	59.046	41.667	0.00	0.00	0.00	3.99

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.