AutoCloner

Multiple sequence alignment - TraesCS1B01G058800

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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	TraesCS1B01G058800	chr1B	100.000	2842	0	0	1	2842	41368444	41365603	0.000000e+00	5249.0
1	TraesCS1B01G058800	chr1B	80.107	1121	140	50	826	1895	41414240	41413152	0.000000e+00	758.0
2	TraesCS1B01G058800	chr1B	97.701	87	2	0	2073	2159	354227939	354228025	1.760000e-32	150.0
3	TraesCS1B01G058800	chr1A	95.871	2083	78	6	1	2076	27056200	27054119	0.000000e+00	3363.0
4	TraesCS1B01G058800	chr1A	94.883	469	18	4	2156	2619	27054122	27053655	0.000000e+00	728.0
5	TraesCS1B01G058800	chr1A	79.095	995	110	49	1073	2000	27137276	27136313	1.880000e-166	595.0
6	TraesCS1B01G058800	chr1A	90.438	251	23	1	2563	2812	27053670	27053420	2.110000e-86	329.0
7	TraesCS1B01G058800	chr1A	94.845	97	5	0	2061	2157	239904148	239904052	4.900000e-33	152.0
8	TraesCS1B01G058800	chr1D	94.502	1728	74	13	1	1717	25773630	25771913	0.000000e+00	2645.0
9	TraesCS1B01G058800	chr1D	92.532	616	39	5	2204	2812	25771450	25770835	0.000000e+00	876.0
10	TraesCS1B01G058800	chr1D	96.330	327	11	1	1750	2076	25771915	25771590	1.160000e-148	536.0
11	TraesCS1B01G058800	chr1D	82.042	568	76	17	1073	1616	25766960	25766395	7.170000e-126	460.0
12	TraesCS1B01G058800	chr1D	77.138	608	74	33	1382	1951	25784504	25783924	2.770000e-75	292.0
13	TraesCS1B01G058800	chr1D	75.367	682	112	36	61	724	25789826	25789183	7.750000e-71	278.0
14	TraesCS1B01G058800	chr1D	92.000	50	3	1	1668	1717	25766364	25766316	5.080000e-08	69.4
15	TraesCS1B01G058800	chr4A	96.667	90	3	0	2073	2162	621812560	621812471	1.760000e-32	150.0
16	TraesCS1B01G058800	chr4A	92.857	98	6	1	2073	2169	743279137	743279040	1.060000e-29	141.0
17	TraesCS1B01G058800	chr3B	95.652	92	4	0	2068	2159	805351601	805351692	6.340000e-32	148.0
18	TraesCS1B01G058800	chr3B	95.604	91	4	0	2068	2158	173097632	173097722	2.280000e-31	147.0
19	TraesCS1B01G058800	chr3B	81.188	101	18	1	2651	2750	809222279	809222379	2.350000e-11	80.5
20	TraesCS1B01G058800	chr7A	90.265	113	9	2	2051	2162	36527890	36528001	2.280000e-31	147.0
21	TraesCS1B01G058800	chr2D	96.591	88	3	0	2073	2160	475134509	475134422	2.280000e-31	147.0
22	TraesCS1B01G058800	chr5D	95.556	90	4	0	2070	2159	490869244	490869155	8.210000e-31	145.0
23	TraesCS1B01G058800	chr5D	87.500	88	9	2	2665	2750	315162045	315162132	1.800000e-17	100.0
24	TraesCS1B01G058800	chr7D	77.876	113	24	1	2638	2749	634604029	634603917	5.080000e-08	69.4
25	TraesCS1B01G058800	chr6A	81.928	83	14	1	2665	2746	16353175	16353093	5.080000e-08	69.4
26	TraesCS1B01G058800	chr6B	89.130	46	4	1	2681	2725	517112909	517112954	3.960000e-04	56.5

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	TraesCS1B01G058800	chr1B	41365603	41368444	2841	True	5249.000000	5249	100.000000	1	2842	1	chr1B.!!$R1	2841
1	TraesCS1B01G058800	chr1B	41413152	41414240	1088	True	758.000000	758	80.107000	826	1895	1	chr1B.!!$R2	1069
2	TraesCS1B01G058800	chr1A	27053420	27056200	2780	True	1473.333333	3363	93.730667	1	2812	3	chr1A.!!$R3	2811
3	TraesCS1B01G058800	chr1A	27136313	27137276	963	True	595.000000	595	79.095000	1073	2000	1	chr1A.!!$R1	927
4	TraesCS1B01G058800	chr1D	25766316	25773630	7314	True	917.280000	2645	91.481200	1	2812	5	chr1D.!!$R3	2811
5	TraesCS1B01G058800	chr1D	25783924	25784504	580	True	292.000000	292	77.138000	1382	1951	1	chr1D.!!$R1	569
6	TraesCS1B01G058800	chr1D	25789183	25789826	643	True	278.000000	278	75.367000	61	724	1	chr1D.!!$R2	663

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
410	417	2.105821	CCCAGTACCACCTTTGACTTGA	59.894	50.0	0.0	0.0	0.0	3.02	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2150	2256	1.206371	TCGCTGCCTTTTAGTACTCCC	59.794	52.381	0.0	0.0	0.0	4.3	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
30	31	8.771286	TGCAGATCTAGATCTAGACTATCTCAT	58.229	37.037	30.31	14.87	45.78	2.90
127	129	7.254522	GCCAATTACATAGGAACATGCAAATTG	60.255	37.037	0.00	12.80	39.45	2.32
196	198	8.970691	AAGTGTCTAAAACAACATTATGCATC	57.029	30.769	0.19	0.00	40.31	3.91
235	238	8.915871	ATTGCAATGAAATGAACATAGTGTAC	57.084	30.769	12.09	0.00	0.00	2.90
404	411	2.951229	AGAACCCAGTACCACCTTTG	57.049	50.000	0.00	0.00	0.00	2.77
410	417	2.105821	CCCAGTACCACCTTTGACTTGA	59.894	50.000	0.00	0.00	0.00	3.02
432	439	4.881920	ACCATGCAAGGTAAATGTTGTTC	58.118	39.130	12.93	0.00	40.98	3.18
510	519	2.452295	AGATATCTGCATGCTCGTGG	57.548	50.000	20.33	4.23	0.00	4.94
591	610	4.262808	GCGTGACCTATACTAGAGGGTCTA	60.263	50.000	19.81	10.24	45.85	2.59
609	628	6.954102	AGGGTCTAATCTTTGGCAATAAAACT	59.046	34.615	0.00	0.00	0.00	2.66
645	665	5.928976	AGGAAAAAGCAATTAATATGGGGC	58.071	37.500	0.00	0.00	0.00	5.80
720	740	7.684937	AGTTACTACTAGCAGATATTACGGG	57.315	40.000	0.00	0.00	31.21	5.28
767	787	5.912149	ATCCCCAGCAAAACTATGATCTA	57.088	39.130	0.00	0.00	0.00	1.98
808	828	6.182627	TGCAGATGTAAGAATTCAGGTCATT	58.817	36.000	8.44	0.00	0.00	2.57
814	834	8.814038	ATGTAAGAATTCAGGTCATTAAGCTT	57.186	30.769	8.44	3.48	31.91	3.74
1013	1037	7.016268	TGGTGATGTTCTCCTATAAATACTCCC	59.984	40.741	0.00	0.00	31.62	4.30
1267	1299	1.802365	ACAAATACCGTTTGACCGAGC	59.198	47.619	7.44	0.00	33.83	5.03
1390	1438	2.123018	ATGGCTGGAGACCATGGATA	57.877	50.000	21.47	0.00	46.27	2.59
1589	1645	2.426842	AGTAATCCTCCTTTGCAGGC	57.573	50.000	0.00	0.00	40.58	4.85
1596	1652	1.228552	TCCTTTGCAGGCCCTTGAC	60.229	57.895	0.00	0.00	40.58	3.18
1730	1790	5.935945	TGGACGATGATACCAATTACCAAT	58.064	37.500	0.00	0.00	0.00	3.16
1777	1850	3.644265	GTCTTTGTTACCCCCAATGGTTT	59.356	43.478	0.00	0.00	39.91	3.27
2020	2126	2.632537	AGACTTGGTTCCAGGTACCAT	58.367	47.619	18.26	4.93	44.70	3.55
2036	2142	3.350219	ACCATCGGAGTTTGTATGCTT	57.650	42.857	0.00	0.00	0.00	3.91
2037	2143	3.009723	ACCATCGGAGTTTGTATGCTTG	58.990	45.455	0.00	0.00	0.00	4.01
2063	2169	1.883732	CCTCGGAGTGTGTCGTGAT	59.116	57.895	4.02	0.00	0.00	3.06
2077	2183	9.095065	AGTGTGTCGTGATTTAATTAATACTCC	57.905	33.333	0.00	0.00	0.00	3.85
2078	2184	8.333186	GTGTGTCGTGATTTAATTAATACTCCC	58.667	37.037	0.00	0.00	0.00	4.30
2079	2185	8.262227	TGTGTCGTGATTTAATTAATACTCCCT	58.738	33.333	0.00	0.00	0.00	4.20
2080	2186	8.762426	GTGTCGTGATTTAATTAATACTCCCTC	58.238	37.037	0.00	0.00	0.00	4.30
2081	2187	8.701895	TGTCGTGATTTAATTAATACTCCCTCT	58.298	33.333	0.00	0.00	0.00	3.69
2082	2188	8.979574	GTCGTGATTTAATTAATACTCCCTCTG	58.020	37.037	0.00	0.00	0.00	3.35
2083	2189	8.701895	TCGTGATTTAATTAATACTCCCTCTGT	58.298	33.333	0.00	0.00	0.00	3.41
2084	2190	9.976511	CGTGATTTAATTAATACTCCCTCTGTA	57.023	33.333	0.00	0.00	0.00	2.74
2152	2258	8.617290	ACGCTTTTATATTAGTTTATGGAGGG	57.383	34.615	0.00	0.00	0.00	4.30
2153	2259	8.434392	ACGCTTTTATATTAGTTTATGGAGGGA	58.566	33.333	0.00	0.00	0.00	4.20
2154	2260	8.936864	CGCTTTTATATTAGTTTATGGAGGGAG	58.063	37.037	0.00	0.00	0.00	4.30
2155	2261	9.794719	GCTTTTATATTAGTTTATGGAGGGAGT	57.205	33.333	0.00	0.00	0.00	3.85
2260	2465	7.926555	CCTTTTGAGAACTTGAGTCTACTGTTA	59.073	37.037	0.00	0.00	0.00	2.41
2374	2580	6.772605	AGTACCCAGTTCGGTAAAAAGTAAT	58.227	36.000	0.00	0.00	40.09	1.89
2641	2890	3.450904	ACCAGGCTGAATCCAAGTACTA	58.549	45.455	17.94	0.00	0.00	1.82
2642	2891	4.040755	ACCAGGCTGAATCCAAGTACTAT	58.959	43.478	17.94	0.00	0.00	2.12
2645	2894	5.295950	CAGGCTGAATCCAAGTACTATCTG	58.704	45.833	9.42	0.00	0.00	2.90
2659	2908	4.913335	ACTATCTGTGTACCGGTACATG	57.087	45.455	41.46	34.58	46.36	3.21
2661	2910	4.951715	ACTATCTGTGTACCGGTACATGAA	59.048	41.667	41.46	30.30	46.36	2.57
2662	2911	3.581024	TCTGTGTACCGGTACATGAAC	57.419	47.619	41.46	30.52	46.36	3.18
2692	2941	0.457853	GGTGCATCGCGACTAAGACA	60.458	55.000	12.93	0.05	0.00	3.41
2791	3041	1.597195	GCACACACGTCTCACATTTCA	59.403	47.619	0.00	0.00	0.00	2.69
2801	3051	3.003689	GTCTCACATTTCATATTGGCCGG	59.996	47.826	0.00	0.00	0.00	6.13
2805	3055	4.221703	TCACATTTCATATTGGCCGGTTTT	59.778	37.500	1.90	0.00	0.00	2.43
2827	3077	3.477210	TTTTTGAATTTTCACCGGGGG	57.523	42.857	2.42	0.00	36.83	5.40

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
30	31	6.127758	GCACATAAATGGACACACTTTATCCA	60.128	38.462	0.00	0.00	46.36	3.41
127	129	6.590234	ATGAAATACTTCCTTTTCCACCAC	57.410	37.500	0.00	0.00	32.14	4.16
234	237	5.712917	TCAAGGAAAGTAAAGTTTGTGGTGT	59.287	36.000	0.00	0.00	0.00	4.16
235	238	6.202516	TCAAGGAAAGTAAAGTTTGTGGTG	57.797	37.500	0.00	0.00	0.00	4.17
404	411	4.218417	ACATTTACCTTGCATGGTCAAGTC	59.782	41.667	26.23	0.00	41.29	3.01
410	417	4.588528	AGAACAACATTTACCTTGCATGGT	59.411	37.500	25.80	25.80	43.66	3.55
424	431	8.621286	GGAAATATATTCCACGAAGAACAACAT	58.379	33.333	0.00	0.00	38.45	2.71
510	519	4.735662	TGTGTTGTTTCGTTGTATAGGC	57.264	40.909	0.00	0.00	0.00	3.93
645	665	2.853731	TGGTGCGTTTTGTTACCTTG	57.146	45.000	0.00	0.00	34.32	3.61
720	740	7.939784	ATGTACAAGTTCCTCCCTTTATTTC	57.060	36.000	0.00	0.00	0.00	2.17
767	787	1.406903	GCAGGATTGCCCTTTAGCAT	58.593	50.000	0.00	0.00	44.85	3.79
808	828	2.297880	TCCAGAACTACACGCAAGCTTA	59.702	45.455	0.00	0.00	45.62	3.09
814	834	0.830444	AGGGTCCAGAACTACACGCA	60.830	55.000	0.00	0.00	0.00	5.24
1013	1037	4.129380	TGCAAGATCGTTAGGAATGATGG	58.871	43.478	0.00	0.00	37.26	3.51
1240	1272	5.525199	GGTCAAACGGTATTTGTGAAATGT	58.475	37.500	0.00	0.00	32.38	2.71
1390	1438	9.369672	CTTACCATACTCCTTTAGGTCTTCTAT	57.630	37.037	0.00	0.00	36.34	1.98
1589	1645	4.464069	TGTTGTTTCTTTTGGTCAAGGG	57.536	40.909	0.00	0.00	0.00	3.95
1596	1652	5.237344	TGGTTGTTGTTGTTGTTTCTTTTGG	59.763	36.000	0.00	0.00	0.00	3.28
1777	1850	5.186409	AGCACTTTTCAGTACCGACCTATAA	59.814	40.000	0.00	0.00	0.00	0.98
1937	2039	2.256306	TGAGCTCCACAATAGGACACA	58.744	47.619	12.15	0.00	33.19	3.72
2020	2126	2.422597	CACCAAGCATACAAACTCCGA	58.577	47.619	0.00	0.00	0.00	4.55
2036	2142	4.954118	ACTCCGAGGCCACCACCA	62.954	66.667	5.01	0.00	0.00	4.17
2037	2143	4.394712	CACTCCGAGGCCACCACC	62.395	72.222	5.01	0.00	0.00	4.61
2126	2232	9.063615	CCCTCCATAAACTAATATAAAAGCGTT	57.936	33.333	0.00	0.00	0.00	4.84
2127	2233	8.434392	TCCCTCCATAAACTAATATAAAAGCGT	58.566	33.333	0.00	0.00	0.00	5.07
2128	2234	8.842358	TCCCTCCATAAACTAATATAAAAGCG	57.158	34.615	0.00	0.00	0.00	4.68
2129	2235	9.794719	ACTCCCTCCATAAACTAATATAAAAGC	57.205	33.333	0.00	0.00	0.00	3.51
2138	2244	8.765517	CCTTTTAGTACTCCCTCCATAAACTAA	58.234	37.037	0.00	0.00	0.00	2.24
2139	2245	7.147602	GCCTTTTAGTACTCCCTCCATAAACTA	60.148	40.741	0.00	0.00	0.00	2.24
2140	2246	6.352823	GCCTTTTAGTACTCCCTCCATAAACT	60.353	42.308	0.00	0.00	0.00	2.66
2141	2247	5.821470	GCCTTTTAGTACTCCCTCCATAAAC	59.179	44.000	0.00	0.00	0.00	2.01
2142	2248	5.489637	TGCCTTTTAGTACTCCCTCCATAAA	59.510	40.000	0.00	0.00	0.00	1.40
2143	2249	5.034200	TGCCTTTTAGTACTCCCTCCATAA	58.966	41.667	0.00	0.00	0.00	1.90
2144	2250	4.627015	TGCCTTTTAGTACTCCCTCCATA	58.373	43.478	0.00	0.00	0.00	2.74
2145	2251	3.456277	CTGCCTTTTAGTACTCCCTCCAT	59.544	47.826	0.00	0.00	0.00	3.41
2146	2252	2.838202	CTGCCTTTTAGTACTCCCTCCA	59.162	50.000	0.00	0.00	0.00	3.86
2147	2253	2.420269	GCTGCCTTTTAGTACTCCCTCC	60.420	54.545	0.00	0.00	0.00	4.30
2148	2254	2.738964	CGCTGCCTTTTAGTACTCCCTC	60.739	54.545	0.00	0.00	0.00	4.30
2149	2255	1.207329	CGCTGCCTTTTAGTACTCCCT	59.793	52.381	0.00	0.00	0.00	4.20
2150	2256	1.206371	TCGCTGCCTTTTAGTACTCCC	59.794	52.381	0.00	0.00	0.00	4.30
2151	2257	2.667473	TCGCTGCCTTTTAGTACTCC	57.333	50.000	0.00	0.00	0.00	3.85
2152	2258	4.034163	GGAAATCGCTGCCTTTTAGTACTC	59.966	45.833	0.00	0.00	0.00	2.59
2153	2259	3.939592	GGAAATCGCTGCCTTTTAGTACT	59.060	43.478	0.00	0.00	0.00	2.73
2154	2260	3.687698	TGGAAATCGCTGCCTTTTAGTAC	59.312	43.478	0.00	0.00	0.00	2.73
2155	2261	3.945346	TGGAAATCGCTGCCTTTTAGTA	58.055	40.909	0.00	0.00	0.00	1.82
2156	2262	2.790433	TGGAAATCGCTGCCTTTTAGT	58.210	42.857	0.00	0.00	0.00	2.24
2157	2263	3.191371	AGTTGGAAATCGCTGCCTTTTAG	59.809	43.478	0.00	0.00	0.00	1.85
2158	2264	3.153919	AGTTGGAAATCGCTGCCTTTTA	58.846	40.909	0.00	0.00	0.00	1.52
2260	2465	6.012771	AGCAGTAAACACTCTACCCCTAAAAT	60.013	38.462	0.00	0.00	0.00	1.82
2374	2580	9.627123	CAAACTTATCTCCCAAATATCTAACCA	57.373	33.333	0.00	0.00	0.00	3.67
2612	2861	1.734465	GATTCAGCCTGGTCGAAACAG	59.266	52.381	10.56	10.56	35.74	3.16
2613	2862	1.610624	GGATTCAGCCTGGTCGAAACA	60.611	52.381	0.00	0.00	0.00	2.83
2662	2911	1.586422	CGATGCACCACCTAAGATGG	58.414	55.000	0.00	0.00	43.43	3.51

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.