AutoCloner

Multiple sequence alignment - TraesCS7A01G072300

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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	TraesCS7A01G072300	chr7A	100.000	2999	0	0	1	2999	37848225	37851223	0.000000e+00	5539.0
1	TraesCS7A01G072300	chr7A	80.763	1965	289	60	8	1942	25360114	25358209	0.000000e+00	1452.0
2	TraesCS7A01G072300	chr7D	94.863	2044	90	5	1	2040	24919921	24917889	0.000000e+00	3179.0
3	TraesCS7A01G072300	chr7D	86.490	866	75	24	2136	2999	430489898	430489073	0.000000e+00	913.0
4	TraesCS7A01G072300	chr7D	92.798	361	19	3	2231	2591	540796617	540796970	1.590000e-142	516.0
5	TraesCS7A01G072300	chr7D	91.866	209	13	3	2792	2999	540843477	540843682	3.780000e-74	289.0
6	TraesCS7A01G072300	chr7D	95.376	173	7	1	2632	2804	540843081	540843252	1.060000e-69	274.0
7	TraesCS7A01G072300	chr7D	89.222	167	8	4	2042	2198	540796137	540796303	1.820000e-47	200.0
8	TraesCS7A01G072300	chr7D	85.567	97	10	4	2745	2839	565241306	565241212	6.840000e-17	99.0
9	TraesCS7A01G072300	chr7D	85.366	82	4	2	2042	2115	430490037	430489956	8.910000e-11	78.7
10	TraesCS7A01G072300	chr4A	95.374	1297	44	7	1	1293	708626077	708624793	0.000000e+00	2049.0
11	TraesCS7A01G072300	chr4A	90.135	517	33	4	1413	1914	708623730	708623217	0.000000e+00	656.0
12	TraesCS7A01G072300	chr6D	93.278	967	29	11	2042	2999	122523811	122522872	0.000000e+00	1393.0
13	TraesCS7A01G072300	chr6D	85.961	406	45	7	2556	2958	304294555	304294159	9.940000e-115	424.0
14	TraesCS7A01G072300	chr7B	84.244	933	106	24	2088	2999	448004786	448003874	0.000000e+00	870.0
15	TraesCS7A01G072300	chr7B	100.000	53	0	0	2106	2158	448004869	448004817	6.840000e-17	99.0
16	TraesCS7A01G072300	chr7B	88.732	71	8	0	2077	2147	526868420	526868490	1.480000e-13	87.9
17	TraesCS7A01G072300	chr2A	88.854	323	25	7	2312	2631	196501762	196502076	1.300000e-103	387.0
18	TraesCS7A01G072300	chr2A	85.061	328	31	12	2674	2999	196502340	196502651	4.820000e-83	318.0
19	TraesCS7A01G072300	chr2A	87.027	185	13	5	2042	2217	196501598	196501780	6.560000e-47	198.0
20	TraesCS7A01G072300	chr2A	74.595	370	63	24	2482	2838	23949805	23950156	1.880000e-27	134.0
21	TraesCS7A01G072300	chr1D	84.483	116	18	0	939	1054	20344383	20344498	6.790000e-22	115.0
22	TraesCS7A01G072300	chr1B	81.890	127	10	6	2050	2163	666982318	666982444	8.850000e-16	95.3
23	TraesCS7A01G072300	chr5D	92.857	56	3	1	2354	2409	520655251	520655305	2.480000e-11	80.5
24	TraesCS7A01G072300	chr6A	82.609	92	13	3	2350	2439	602582280	602582190	8.910000e-11	78.7

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	TraesCS7A01G072300	chr7A	37848225	37851223	2998	False	5539.00	5539	100.000000	1	2999	1	chr7A.!!$F1	2998
1	TraesCS7A01G072300	chr7A	25358209	25360114	1905	True	1452.00	1452	80.763000	8	1942	1	chr7A.!!$R1	1934
2	TraesCS7A01G072300	chr7D	24917889	24919921	2032	True	3179.00	3179	94.863000	1	2040	1	chr7D.!!$R1	2039
3	TraesCS7A01G072300	chr7D	430489073	430490037	964	True	495.85	913	85.928000	2042	2999	2	chr7D.!!$R3	957
4	TraesCS7A01G072300	chr7D	540796137	540796970	833	False	358.00	516	91.010000	2042	2591	2	chr7D.!!$F1	549
5	TraesCS7A01G072300	chr7D	540843081	540843682	601	False	281.50	289	93.621000	2632	2999	2	chr7D.!!$F2	367
6	TraesCS7A01G072300	chr4A	708623217	708626077	2860	True	1352.50	2049	92.754500	1	1914	2	chr4A.!!$R1	1913
7	TraesCS7A01G072300	chr6D	122522872	122523811	939	True	1393.00	1393	93.278000	2042	2999	1	chr6D.!!$R1	957
8	TraesCS7A01G072300	chr7B	448003874	448004869	995	True	484.50	870	92.122000	2088	2999	2	chr7B.!!$R1	911
9	TraesCS7A01G072300	chr2A	196501598	196502651	1053	False	301.00	387	86.980667	2042	2999	3	chr2A.!!$F2	957

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
170	171	1.070786	GCCAAGTTCGTGTGGAGGA	59.929	57.895	0.00	0.00	37.03	3.71	F
370	371	1.526917	CCTTATGCTGAAGCCCGGG	60.527	63.158	19.09	19.09	41.18	5.73	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1103	1123	0.390860	GCTACTGATCCAGGCGATGT	59.609	55.0	0.0	0.0	35.51	3.06	R
2240	3587	0.179121	GTGTCTCACACGGTCACACA	60.179	55.0	0.0	0.0	39.53	3.72	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
165	166	4.368808	CGCCGCCAAGTTCGTGTG	62.369	66.667	0.00	0.00	0.00	3.82
170	171	1.070786	GCCAAGTTCGTGTGGAGGA	59.929	57.895	0.00	0.00	37.03	3.71
235	236	3.591835	GCTCGCCTCCTCTCCTCG	61.592	72.222	0.00	0.00	0.00	4.63
242	243	2.024825	GCCTCCTCTCCTCGTACATGT	61.025	57.143	2.69	2.69	0.00	3.21
370	371	1.526917	CCTTATGCTGAAGCCCGGG	60.527	63.158	19.09	19.09	41.18	5.73
523	530	1.605058	TAAGCCTCTCCTTCGCGCTT	61.605	55.000	5.56	0.00	42.21	4.68
832	851	1.798735	CGACATGCTCTTGGCCTTG	59.201	57.895	3.32	0.00	40.92	3.61
834	853	2.262471	GACATGCTCTTGGCCTTGCG	62.262	60.000	3.32	0.00	40.92	4.85
970	990	3.184382	TCACCTACCTCCTGTTCATCA	57.816	47.619	0.00	0.00	0.00	3.07
1233	1253	0.239347	CAAGGCAAGCAAAGAGGTCG	59.761	55.000	0.00	0.00	0.00	4.79
1313	1333	5.961395	AGCAACGGAAAATACGTACTATG	57.039	39.130	0.00	0.00	44.83	2.23
1353	1373	1.195448	CACTTGTCATGGTTCTGCGAC	59.805	52.381	0.00	0.00	0.00	5.19
1427	2390	1.076923	AGGCGACGTATCCAGGACT	60.077	57.895	8.11	0.00	0.00	3.85
1430	2393	0.248949	GCGACGTATCCAGGACTTCC	60.249	60.000	0.00	0.00	0.00	3.46
1433	2396	1.409427	GACGTATCCAGGACTTCCCAG	59.591	57.143	0.00	0.00	37.41	4.45
1467	2430	1.317431	CGACGGACCACCATAGGACA	61.317	60.000	0.00	0.00	35.59	4.02
1480	2443	4.289672	ACCATAGGACAGTGGAGACAAAAT	59.710	41.667	0.00	0.00	46.06	1.82
1503	2466	8.706322	AATTGTCCAAGTATTGTTCTTACCTT	57.294	30.769	0.00	0.00	46.99	3.50
1615	2578	2.165234	GGGAGTCGTTGGAACTACTACC	59.835	54.545	9.14	9.14	45.13	3.18
1623	2589	4.347607	GTTGGAACTACTACCTAGGGTCA	58.652	47.826	14.81	0.00	37.09	4.02
1627	2593	4.463070	GAACTACTACCTAGGGTCAGAGG	58.537	52.174	14.81	7.88	37.09	3.69
1640	2606	3.138798	AGAGGACGCGCGGTACAT	61.139	61.111	35.22	21.74	0.00	2.29
1672	2638	1.802880	CGACGAACCAGGATAAGCTGG	60.803	57.143	0.00	0.00	45.70	4.85
1738	2710	4.142966	GGATAGTGCTTGGAAACGTGTTAC	60.143	45.833	0.00	0.00	0.00	2.50
1739	2711	2.634600	AGTGCTTGGAAACGTGTTACA	58.365	42.857	0.00	0.00	0.00	2.41
1742	2714	1.265905	GCTTGGAAACGTGTTACAGGG	59.734	52.381	9.87	0.00	0.00	4.45
1776	2752	0.629058	ACTATGGGGCCGTTTGGAAT	59.371	50.000	0.00	0.00	37.49	3.01
1811	2792	1.608055	TGGGTTGAGCTGATTGTGTG	58.392	50.000	0.00	0.00	0.00	3.82
1824	2805	0.396278	TTGTGTGTGTTGCCCCATCA	60.396	50.000	0.00	0.00	0.00	3.07
1833	2814	3.134127	GCCCCATCAAGCGGTGAC	61.134	66.667	0.00	0.00	39.72	3.67
1935	2916	4.006357	GTAACCCGCCCACCGTCA	62.006	66.667	0.00	0.00	34.38	4.35
1943	2924	2.388232	GCCCACCGTCAACATCGTC	61.388	63.158	0.00	0.00	0.00	4.20
1944	2925	1.740296	CCCACCGTCAACATCGTCC	60.740	63.158	0.00	0.00	0.00	4.79
1949	2930	1.129809	CGTCAACATCGTCCGTTGC	59.870	57.895	8.74	4.94	42.78	4.17
1952	2933	1.206578	CAACATCGTCCGTTGCCAC	59.793	57.895	0.00	0.00	37.53	5.01
1971	2952	4.143333	CCGGTCGGCGAGGATGTT	62.143	66.667	11.20	0.00	0.00	2.71
1974	2955	1.079405	GGTCGGCGAGGATGTTGAA	60.079	57.895	11.20	0.00	0.00	2.69
1994	2975	0.108756	GAGGGAGTACGTCCTTGTGC	60.109	60.000	10.62	0.00	46.06	4.57
2033	3014	7.672983	ATACCTTTCTTTATATGCACATCGG	57.327	36.000	0.00	0.00	0.00	4.18
2085	3074	2.804986	TCCTTTAGTCCATGCATGCA	57.195	45.000	25.04	25.04	0.00	3.96
2158	3183	1.227999	TGCCTGTACGCTGCACTTTC	61.228	55.000	0.00	0.00	0.00	2.62
2194	3541	4.615541	GTGCGTGTTAGTTTCTTTTATGCC	59.384	41.667	0.00	0.00	0.00	4.40
2229	3576	0.770008	GTTGTTTGTGCGCGTGAATC	59.230	50.000	8.43	0.00	0.00	2.52
2234	3581	2.202222	GTGCGCGTGAATCTGTGC	60.202	61.111	8.43	5.01	41.81	4.57
2237	3584	2.094539	CGCGTGAATCTGTGCGTG	59.905	61.111	0.00	0.00	45.12	5.34
2238	3585	2.371923	CGCGTGAATCTGTGCGTGA	61.372	57.895	0.00	0.00	45.12	4.35
2239	3586	1.859398	GCGTGAATCTGTGCGTGAA	59.141	52.632	0.00	0.00	0.00	3.18
2240	3587	0.443869	GCGTGAATCTGTGCGTGAAT	59.556	50.000	0.00	0.00	0.00	2.57
2241	3588	1.787989	GCGTGAATCTGTGCGTGAATG	60.788	52.381	0.00	0.00	0.00	2.67
2242	3589	1.460743	CGTGAATCTGTGCGTGAATGT	59.539	47.619	0.00	0.00	0.00	2.71
2243	3590	2.722706	CGTGAATCTGTGCGTGAATGTG	60.723	50.000	0.00	0.00	0.00	3.21
2244	3591	2.224079	GTGAATCTGTGCGTGAATGTGT	59.776	45.455	0.00	0.00	0.00	3.72
2245	3592	2.223845	TGAATCTGTGCGTGAATGTGTG	59.776	45.455	0.00	0.00	0.00	3.82
2246	3593	2.168326	ATCTGTGCGTGAATGTGTGA	57.832	45.000	0.00	0.00	0.00	3.58
2247	3594	1.217001	TCTGTGCGTGAATGTGTGAC	58.783	50.000	0.00	0.00	0.00	3.67
2248	3595	0.235665	CTGTGCGTGAATGTGTGACC	59.764	55.000	0.00	0.00	0.00	4.02
2458	3806	9.846248	GTGAAAACTTCAGCAATCATATTTAGT	57.154	29.630	0.00	0.00	41.01	2.24
2555	3904	9.300681	AGTTGATTTTCTGACCATTGATTTCTA	57.699	29.630	0.00	0.00	0.00	2.10
2576	3925	3.866651	ACTCTAAGATTCGTGCTGCATT	58.133	40.909	5.27	0.00	0.00	3.56
2577	3926	4.256920	ACTCTAAGATTCGTGCTGCATTT	58.743	39.130	5.27	0.00	0.00	2.32
2790	4366	7.201453	CGTTCGGTTTTATTTTTCTTTTGTGGT	60.201	33.333	0.00	0.00	0.00	4.16
2851	4664	8.970293	CACATAAATATTATGCAATGTGTGTGG	58.030	33.333	13.32	0.00	39.39	4.17

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
22	23	4.342378	GTGATGATGTTAGAGTAGCCCTGA	59.658	45.833	0.00	0.00	0.00	3.86
164	165	2.669133	CGGTGAAGGCCATCCTCCA	61.669	63.158	5.01	0.00	43.40	3.86
165	166	2.190578	CGGTGAAGGCCATCCTCC	59.809	66.667	5.01	7.38	43.40	4.30
170	171	1.051812	CCTATCTCGGTGAAGGCCAT	58.948	55.000	5.01	0.00	0.00	4.40
235	236	5.122396	GTCCTTGACCATTTCAGACATGTAC	59.878	44.000	0.00	0.00	34.94	2.90
286	287	1.304952	CGGAGAGAGGTCCTGGTCT	59.695	63.158	0.00	0.00	34.00	3.85
523	530	2.746412	TAGGCCGCAGCAGCTTGAAA	62.746	55.000	0.00	0.00	42.56	2.69
773	792	1.406614	GGTCATGAAGCAGAGGACCAG	60.407	57.143	0.00	0.00	45.70	4.00
841	860	2.643232	GGCGTAGTTGTCGTCCCCT	61.643	63.158	0.00	0.00	0.00	4.79
1103	1123	0.390860	GCTACTGATCCAGGCGATGT	59.609	55.000	0.00	0.00	35.51	3.06
1313	1333	0.391130	TGAGTACCGTTGCATGGAGC	60.391	55.000	12.14	0.00	45.96	4.70
1480	2443	7.012894	CACAAGGTAAGAACAATACTTGGACAA	59.987	37.037	0.00	0.00	34.12	3.18
1600	2563	3.359950	ACCCTAGGTAGTAGTTCCAACG	58.640	50.000	8.29	0.00	32.11	4.10
1601	2564	4.347607	TGACCCTAGGTAGTAGTTCCAAC	58.652	47.826	8.29	0.00	35.25	3.77
1602	2565	4.293102	TCTGACCCTAGGTAGTAGTTCCAA	59.707	45.833	8.29	0.00	35.25	3.53
1615	2578	3.111939	CGCGTCCTCTGACCCTAG	58.888	66.667	0.00	0.00	38.32	3.02
1623	2589	3.138798	ATGTACCGCGCGTCCTCT	61.139	61.111	29.95	7.36	0.00	3.69
1627	2593	0.870307	ATCTTCATGTACCGCGCGTC	60.870	55.000	29.95	18.38	0.00	5.19
1640	2606	1.640428	GTTCGTCGCCATCATCTTCA	58.360	50.000	0.00	0.00	0.00	3.02
1672	2638	4.459089	GTCCCAGCAGTCGGAGCC	62.459	72.222	0.00	0.00	0.00	4.70
1738	2710	0.984961	TCTCCATTGGCCTCTCCCTG	60.985	60.000	3.32	0.00	0.00	4.45
1739	2711	0.985490	GTCTCCATTGGCCTCTCCCT	60.985	60.000	3.32	0.00	0.00	4.20
1742	2714	2.038295	CCATAGTCTCCATTGGCCTCTC	59.962	54.545	3.32	0.00	0.00	3.20
1776	2752	1.600636	CCAAAGGTCGGCAAGCAGA	60.601	57.895	0.00	0.00	0.00	4.26
1811	2792	2.568090	CGCTTGATGGGGCAACAC	59.432	61.111	0.00	0.00	44.44	3.32
1833	2814	3.334751	TGCCGTTTCACGTGCTCG	61.335	61.111	11.67	14.31	40.58	5.03
1935	2916	2.314647	CGTGGCAACGGACGATGTT	61.315	57.895	5.48	0.00	46.25	2.71
1959	2940	0.807667	CCTCTTCAACATCCTCGCCG	60.808	60.000	0.00	0.00	0.00	6.46
1971	2952	2.168496	CAAGGACGTACTCCCTCTTCA	58.832	52.381	0.00	0.00	40.53	3.02
1974	2955	1.546961	CACAAGGACGTACTCCCTCT	58.453	55.000	0.00	0.00	40.53	3.69
2010	2991	6.588204	ACCGATGTGCATATAAAGAAAGGTA	58.412	36.000	0.00	0.00	0.00	3.08
2012	2993	7.173218	ACATACCGATGTGCATATAAAGAAAGG	59.827	37.037	0.00	0.00	44.90	3.11
2013	2994	8.087982	ACATACCGATGTGCATATAAAGAAAG	57.912	34.615	0.00	0.00	44.90	2.62
2032	3013	4.332828	ACCAAACCTAGAAAGCACATACC	58.667	43.478	0.00	0.00	0.00	2.73
2033	3014	5.472137	TGAACCAAACCTAGAAAGCACATAC	59.528	40.000	0.00	0.00	0.00	2.39
2040	3021	4.628074	TCGACTGAACCAAACCTAGAAAG	58.372	43.478	0.00	0.00	0.00	2.62
2047	3028	3.568430	AGGAAAATCGACTGAACCAAACC	59.432	43.478	0.00	0.00	0.00	3.27
2085	3074	2.744202	CAGCTACTTCAAGGCAATTCGT	59.256	45.455	0.00	0.00	0.00	3.85
2158	3183	4.919677	AACACGCACAAAAAGGAAAAAG	57.080	36.364	0.00	0.00	0.00	2.27
2194	3541	2.536365	ACAACACAGACACACACGTAG	58.464	47.619	0.00	0.00	0.00	3.51
2229	3576	0.235665	GGTCACACATTCACGCACAG	59.764	55.000	0.00	0.00	0.00	3.66
2234	3581	0.232046	CACACGGTCACACATTCACG	59.768	55.000	0.00	0.00	0.00	4.35
2235	3582	1.526887	CTCACACGGTCACACATTCAC	59.473	52.381	0.00	0.00	0.00	3.18
2236	3583	1.410882	TCTCACACGGTCACACATTCA	59.589	47.619	0.00	0.00	0.00	2.57
2237	3584	1.792949	GTCTCACACGGTCACACATTC	59.207	52.381	0.00	0.00	0.00	2.67
2238	3585	1.138069	TGTCTCACACGGTCACACATT	59.862	47.619	0.00	0.00	0.00	2.71
2239	3586	0.750249	TGTCTCACACGGTCACACAT	59.250	50.000	0.00	0.00	0.00	3.21
2240	3587	0.179121	GTGTCTCACACGGTCACACA	60.179	55.000	0.00	0.00	39.53	3.72
2241	3588	2.589890	GTGTCTCACACGGTCACAC	58.410	57.895	0.00	0.00	39.53	3.82
2555	3904	3.533606	ATGCAGCACGAATCTTAGAGT	57.466	42.857	0.00	0.00	0.00	3.24
2676	4252	0.107456	AGGGCCAGATCGCATAGTTG	59.893	55.000	6.18	0.00	0.00	3.16
2764	4340	7.114289	CCACAAAAGAAAAATAAAACCGAACG	58.886	34.615	0.00	0.00	0.00	3.95
2790	4366	6.947733	ACACTCATCTGACATCCCAAAAATAA	59.052	34.615	0.00	0.00	0.00	1.40
2972	4787	8.520351	GTGACATTGCTACTACCCTTTAAAAAT	58.480	33.333	0.00	0.00	0.00	1.82

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.