AutoCloner

Multiple sequence alignment - TraesCS2A01G095700

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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	TraesCS2A01G095700	chr2A	100.000	3023	0	0	1	3023	49220108	49223130	0.000000e+00	5583.0
1	TraesCS2A01G095700	chr2A	90.217	184	18	0	435	618	49220447	49220630	1.080000e-59	241.0
2	TraesCS2A01G095700	chr2A	90.217	184	18	0	340	523	49220542	49220725	1.080000e-59	241.0
3	TraesCS2A01G095700	chr2A	92.157	102	8	0	525	626	367649268	367649167	8.730000e-31	145.0
4	TraesCS2A01G095700	chr2B	92.016	2981	136	42	1	2935	72894181	72897105	0.000000e+00	4093.0
5	TraesCS2A01G095700	chr2B	86.525	141	16	1	426	566	72894498	72894635	5.220000e-33	152.0
6	TraesCS2A01G095700	chr2B	92.233	103	6	2	525	626	17398857	17398958	8.730000e-31	145.0
7	TraesCS2A01G095700	chr2D	92.674	2375	106	35	400	2751	45798602	45800931	0.000000e+00	3360.0
8	TraesCS2A01G095700	chr2D	85.305	524	48	12	1	522	45798325	45798821	5.780000e-142	514.0
9	TraesCS2A01G095700	chr2D	87.241	290	20	5	2476	2749	45802950	45803238	6.290000e-82	315.0
10	TraesCS2A01G095700	chr2D	89.881	168	9	5	2773	2933	45803318	45803484	3.050000e-50	209.0
11	TraesCS2A01G095700	chr2D	83.099	142	20	4	280	420	10748375	10748513	3.160000e-25	126.0
12	TraesCS2A01G095700	chr2D	83.459	133	20	1	295	427	187042884	187042754	4.090000e-24	122.0
13	TraesCS2A01G095700	chr2D	91.549	71	2	3	2773	2839	45801539	45801609	8.920000e-16	95.3
14	TraesCS2A01G095700	chr2D	92.982	57	4	0	2967	3023	45803479	45803535	1.930000e-12	84.2
15	TraesCS2A01G095700	chr2D	89.655	58	5	1	225	282	158790964	158790908	4.180000e-09	73.1
16	TraesCS2A01G095700	chr7B	81.726	197	24	12	321	509	253688592	253688784	1.450000e-33	154.0
17	TraesCS2A01G095700	chr7B	81.208	149	24	3	280	427	550876792	550876937	1.900000e-22	117.0
18	TraesCS2A01G095700	chr6A	93.204	103	5	2	525	626	609593005	609593106	1.880000e-32	150.0
19	TraesCS2A01G095700	chr4B	93.878	98	3	3	525	621	601790257	601790352	8.730000e-31	145.0
20	TraesCS2A01G095700	chr1A	92.233	103	6	2	525	626	39438945	39438844	8.730000e-31	145.0
21	TraesCS2A01G095700	chr1A	83.824	136	20	2	292	427	496629329	496629196	8.800000e-26	128.0
22	TraesCS2A01G095700	chr1B	92.708	96	7	0	426	521	171034401	171034306	4.060000e-29	139.0
23	TraesCS2A01G095700	chr1B	83.108	148	23	2	280	427	643058618	643058763	1.890000e-27	134.0
24	TraesCS2A01G095700	chr6D	90.385	104	8	2	420	522	431160711	431160813	5.260000e-28	135.0
25	TraesCS2A01G095700	chr3A	87.603	121	9	4	521	637	562879667	562879549	5.260000e-28	135.0
26	TraesCS2A01G095700	chr1D	88.393	112	10	2	411	522	410457715	410457823	6.800000e-27	132.0
27	TraesCS2A01G095700	chr5D	82.000	150	24	3	266	415	394099487	394099633	1.140000e-24	124.0

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	TraesCS2A01G095700	chr2A	49220108	49223130	3022	False	2021.666667	5583	93.478000	1	3023	3	chr2A.!!$F1	3022
1	TraesCS2A01G095700	chr2B	72894181	72897105	2924	False	2122.500000	4093	89.270500	1	2935	2	chr2B.!!$F2	2934
2	TraesCS2A01G095700	chr2D	45798325	45803535	5210	False	762.916667	3360	89.938667	1	3023	6	chr2D.!!$F2	3022

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
76	77	1.072489	TGCCGGAAGATACAAACACCA	59.928	47.619	5.05	0.0	0.0	4.17	F
906	914	1.134848	GCCTCCATCACTCACTCTCAC	60.135	57.143	0.00	0.0	0.0	3.51	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1605	1616	0.388134	CCAGGAACACCACGTCGTAG	60.388	60.0	0.0	0.0	0.0	3.51	R
2536	2569	0.104855	TCGGAGGGCAAATCGAGATG	59.895	55.0	0.0	0.0	0.0	2.90	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
45	46	2.865551	AGAATGTGTTTTGCCGCTTTTG	59.134	40.909	0.00	0.00	0.00	2.44
71	72	4.020039	TCCTACTTTGCCGGAAGATACAAA	60.020	41.667	5.05	3.83	0.00	2.83
72	73	4.094442	CCTACTTTGCCGGAAGATACAAAC	59.906	45.833	5.05	0.00	0.00	2.93
73	74	3.482436	ACTTTGCCGGAAGATACAAACA	58.518	40.909	5.05	0.00	0.00	2.83
75	76	1.816074	TGCCGGAAGATACAAACACC	58.184	50.000	5.05	0.00	0.00	4.16
76	77	1.072489	TGCCGGAAGATACAAACACCA	59.928	47.619	5.05	0.00	0.00	4.17
77	78	1.467342	GCCGGAAGATACAAACACCAC	59.533	52.381	5.05	0.00	0.00	4.16
79	80	2.482721	CCGGAAGATACAAACACCACAC	59.517	50.000	0.00	0.00	0.00	3.82
102	103	1.136529	CACACACAAGATGCGACTTCG	60.137	52.381	0.00	0.00	43.27	3.79
121	122	2.671619	TTTCTTTCCTGCCGCCGG	60.672	61.111	0.00	0.00	0.00	6.13
122	123	4.715523	TTCTTTCCTGCCGCCGGG	62.716	66.667	4.77	0.00	38.98	5.73
152	153	4.084849	GGTGAATTCGAAGCTGATACGATG	60.085	45.833	3.35	0.00	36.02	3.84
258	259	8.734386	CCCTTCATTCCTAAATATAATGTCTGC	58.266	37.037	0.00	0.00	33.35	4.26
288	289	8.517323	AGATTCCAATATGAATTACTCCCTCT	57.483	34.615	0.00	0.00	35.15	3.69
383	384	8.804204	ACACTCTAAACTATGGCTATATACACC	58.196	37.037	0.00	0.00	0.00	4.16
389	390	8.827832	AAACTATGGCTATATACACCCGTATA	57.172	34.615	0.00	0.00	43.16	1.47
666	671	2.653890	CAGCCAGAAAACGTTGATGTG	58.346	47.619	0.00	2.92	0.00	3.21
829	834	4.803426	CCCCAGCACGCTCTCGAC	62.803	72.222	0.00	0.00	39.41	4.20
834	839	2.101380	GCACGCTCTCGACTCCTC	59.899	66.667	0.00	0.00	39.41	3.71
838	843	2.795297	GCTCTCGACTCCTCCGTG	59.205	66.667	0.00	0.00	0.00	4.94
906	914	1.134848	GCCTCCATCACTCACTCTCAC	60.135	57.143	0.00	0.00	0.00	3.51
931	941	1.745264	CCAGCTAGCTAGTGCCCTC	59.255	63.158	18.86	4.26	40.80	4.30
959	970	2.355132	TCGTGCTCGGAGAACTTAGATC	59.645	50.000	14.10	0.00	34.09	2.75
2078	2089	2.821366	CCCAGAGCACGGTGATGC	60.821	66.667	13.29	0.00	46.50	3.91
2085	2096	2.174334	GCACGGTGATGCATGAACT	58.826	52.632	13.29	0.00	45.39	3.01
2086	2097	0.097674	GCACGGTGATGCATGAACTC	59.902	55.000	13.29	0.00	45.39	3.01
2117	2128	7.392113	ACCGATTAATATTTGCCCGATTAATCA	59.608	33.333	15.57	0.00	44.99	2.57
2118	2129	7.696453	CCGATTAATATTTGCCCGATTAATCAC	59.304	37.037	15.57	4.94	44.99	3.06
2149	2160	9.706846	CGATACATACATGCATGGTAATAATTG	57.293	33.333	29.41	14.91	0.00	2.32
2291	2309	1.737029	GCAATCGTCTGACAGCTGCTA	60.737	52.381	15.27	1.41	0.00	3.49
2292	2310	2.819115	CAATCGTCTGACAGCTGCTAT	58.181	47.619	15.27	0.00	0.00	2.97
2320	2338	2.104281	CCGGGTTTAACATAGAGGAGGG	59.896	54.545	0.00	0.00	0.00	4.30
2343	2361	3.309682	GGATGATATGTGTCGTGTTGTGG	59.690	47.826	0.00	0.00	0.00	4.17
2382	2400	2.265739	CGAGTTGCCTGCCTGCTA	59.734	61.111	0.00	0.00	0.00	3.49
2383	2401	1.812922	CGAGTTGCCTGCCTGCTAG	60.813	63.158	0.00	0.00	0.00	3.42
2384	2402	2.045536	AGTTGCCTGCCTGCTAGC	60.046	61.111	8.10	8.10	0.00	3.42
2385	2403	2.045536	GTTGCCTGCCTGCTAGCT	60.046	61.111	17.23	0.00	0.00	3.32
2386	2404	2.045634	TTGCCTGCCTGCTAGCTG	60.046	61.111	17.23	15.65	0.00	4.24
2387	2405	2.898933	TTGCCTGCCTGCTAGCTGT	61.899	57.895	17.23	0.00	0.00	4.40
2388	2406	2.045536	GCCTGCCTGCTAGCTGTT	60.046	61.111	17.23	0.00	0.00	3.16
2431	2449	7.935520	TGACACTCTATATGACTCAAGTGATC	58.064	38.462	12.72	8.23	37.97	2.92
2432	2450	7.013750	TGACACTCTATATGACTCAAGTGATCC	59.986	40.741	12.72	4.73	37.97	3.36
2448	2468	3.548770	TGATCCATCATCACCAAGAAGC	58.451	45.455	0.00	0.00	36.51	3.86
2465	2485	0.038892	AGCAGTGTAACACCGTACCG	60.039	55.000	0.00	0.00	41.43	4.02
2474	2502	0.390735	ACACCGTACCGATGCTTTCC	60.391	55.000	0.00	0.00	0.00	3.13
2507	2535	4.495844	CCCTTGTTTCAACGACTTGTCTTC	60.496	45.833	0.00	0.00	0.00	2.87
2518	2551	6.532365	ACGACTTGTCTTCATTTCTTCTTC	57.468	37.500	0.00	0.00	0.00	2.87
2552	2589	6.566197	AAATAATCATCTCGATTTGCCCTC	57.434	37.500	0.00	0.00	41.83	4.30
2577	2614	3.316071	TTACCCGATCGTTGCAGTTAA	57.684	42.857	15.09	0.00	0.00	2.01
2668	2715	2.026641	CAAATGATTGGAGTGCGGGAT	58.973	47.619	0.00	0.00	32.69	3.85
2669	2716	2.428171	CAAATGATTGGAGTGCGGGATT	59.572	45.455	0.00	0.00	32.69	3.01
2706	2753	2.765250	AAACGACCGTGCTGCTCGAT	62.765	55.000	23.74	8.35	0.00	3.59
2808	5222	4.105486	GTTTCTGTTTTCACCTGCAGAAC	58.895	43.478	17.39	11.75	44.47	3.01
2809	5223	2.997980	TCTGTTTTCACCTGCAGAACA	58.002	42.857	17.39	15.84	35.36	3.18
2818	5233	0.318955	CCTGCAGAACAAAAAGGCCG	60.319	55.000	17.39	0.00	0.00	6.13
2901	5318	1.686355	ACGAACAGCCCAATGACAAA	58.314	45.000	0.00	0.00	0.00	2.83
2915	5332	2.156917	TGACAAAGAGGAGCAATGCTG	58.843	47.619	14.48	0.00	39.88	4.41
2935	5352	4.763793	GCTGTAGGGATGCAATATGTGATT	59.236	41.667	0.00	0.00	0.00	2.57
2936	5353	5.242393	GCTGTAGGGATGCAATATGTGATTT	59.758	40.000	0.00	0.00	0.00	2.17
2937	5354	6.239120	GCTGTAGGGATGCAATATGTGATTTT	60.239	38.462	0.00	0.00	0.00	1.82
2938	5355	7.658525	TGTAGGGATGCAATATGTGATTTTT	57.341	32.000	0.00	0.00	0.00	1.94
3008	5425	0.319297	AAACTAGACGGGTGCACGAC	60.319	55.000	11.45	5.37	37.61	4.34
3013	5430	4.969196	ACGGGTGCACGACTGCTG	62.969	66.667	11.45	3.97	44.57	4.41

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
45	46	1.549170	TCTTCCGGCAAAGTAGGAGTC	59.451	52.381	0.00	0.00	35.23	3.36
71	72	0.250945	TTGTGTGTGGTGTGTGGTGT	60.251	50.000	0.00	0.00	0.00	4.16
72	73	0.451383	CTTGTGTGTGGTGTGTGGTG	59.549	55.000	0.00	0.00	0.00	4.17
73	74	0.326595	TCTTGTGTGTGGTGTGTGGT	59.673	50.000	0.00	0.00	0.00	4.16
75	76	1.268692	GCATCTTGTGTGTGGTGTGTG	60.269	52.381	0.00	0.00	0.00	3.82
76	77	1.024271	GCATCTTGTGTGTGGTGTGT	58.976	50.000	0.00	0.00	0.00	3.72
77	78	0.041047	CGCATCTTGTGTGTGGTGTG	60.041	55.000	0.00	0.00	33.61	3.82
79	80	0.235665	GTCGCATCTTGTGTGTGGTG	59.764	55.000	0.00	0.00	39.38	4.17
102	103	2.568612	GGCGGCAGGAAAGAAAGC	59.431	61.111	3.07	0.00	0.00	3.51
122	123	1.644786	CTTCGAATTCACCCGGGCAC	61.645	60.000	24.08	4.71	0.00	5.01
123	124	1.376683	CTTCGAATTCACCCGGGCA	60.377	57.895	24.08	3.91	0.00	5.36
124	125	2.761195	GCTTCGAATTCACCCGGGC	61.761	63.158	24.08	0.89	0.00	6.13
125	126	1.078426	AGCTTCGAATTCACCCGGG	60.078	57.895	22.25	22.25	0.00	5.73
126	127	0.391130	TCAGCTTCGAATTCACCCGG	60.391	55.000	6.22	0.00	0.00	5.73
127	128	1.656652	ATCAGCTTCGAATTCACCCG	58.343	50.000	6.22	0.00	0.00	5.28
128	129	2.540101	CGTATCAGCTTCGAATTCACCC	59.460	50.000	6.22	0.00	0.00	4.61
522	525	7.750229	AGATTCACTCATTTTGCTTTGTAGA	57.250	32.000	0.00	0.00	0.00	2.59
527	530	7.516198	AGTGTAGATTCACTCATTTTGCTTT	57.484	32.000	0.00	0.00	44.07	3.51
617	622	1.416243	ACAACCACCTACTCCGTTCA	58.584	50.000	0.00	0.00	0.00	3.18
618	623	2.140717	CAACAACCACCTACTCCGTTC	58.859	52.381	0.00	0.00	0.00	3.95
666	671	6.136541	CCAGCTGATTATTTGGGAGTTTAC	57.863	41.667	17.39	0.00	0.00	2.01
691	696	7.334171	GGGTAACGGTTGTGTATTTATGTACTT	59.666	37.037	3.07	0.00	37.60	2.24
829	834	4.982916	GTGTTTATATAGCACACGGAGGAG	59.017	45.833	10.10	0.00	32.03	3.69
834	839	3.799366	TGGGTGTTTATATAGCACACGG	58.201	45.455	15.79	0.00	41.54	4.94
838	843	4.315803	AGCGATGGGTGTTTATATAGCAC	58.684	43.478	9.66	9.66	0.00	4.40
959	970	2.125753	GACCCTCGCTCTGTGCTG	60.126	66.667	0.00	0.00	40.11	4.41
1006	1017	3.368571	GTTGCAGCAGCCCTCCAC	61.369	66.667	0.00	0.00	41.13	4.02
1605	1616	0.388134	CCAGGAACACCACGTCGTAG	60.388	60.000	0.00	0.00	0.00	3.51
2048	2059	2.509336	CTGGGCGATGACGGTGAC	60.509	66.667	0.00	0.00	40.15	3.67
2049	2060	2.678580	TCTGGGCGATGACGGTGA	60.679	61.111	0.00	0.00	40.15	4.02
2052	2063	4.147449	TGCTCTGGGCGATGACGG	62.147	66.667	0.00	0.00	45.43	4.79
2078	2089	2.113860	AATCGGTGGGTGAGTTCATG	57.886	50.000	0.00	0.00	0.00	3.07
2081	2092	6.725246	CAAATATTAATCGGTGGGTGAGTTC	58.275	40.000	0.00	0.00	0.00	3.01
2082	2093	5.067283	GCAAATATTAATCGGTGGGTGAGTT	59.933	40.000	0.00	0.00	0.00	3.01
2085	2096	3.886505	GGCAAATATTAATCGGTGGGTGA	59.113	43.478	0.00	0.00	0.00	4.02
2086	2097	3.005367	GGGCAAATATTAATCGGTGGGTG	59.995	47.826	0.00	0.00	0.00	4.61
2090	2101	5.371115	AATCGGGCAAATATTAATCGGTG	57.629	39.130	0.00	0.00	0.00	4.94
2117	2128	1.684450	TGCATGTATGTATCGGTCGGT	59.316	47.619	0.00	0.00	0.00	4.69
2118	2129	2.432206	TGCATGTATGTATCGGTCGG	57.568	50.000	0.00	0.00	0.00	4.79
2149	2160	1.838112	TCCATGCATGAGGACAAACC	58.162	50.000	28.31	0.00	39.35	3.27
2174	2185	4.127566	TGGTAAATAAGTAGCCACGTCC	57.872	45.455	0.00	0.00	0.00	4.79
2175	2186	7.958053	ATTATGGTAAATAAGTAGCCACGTC	57.042	36.000	0.00	0.00	31.47	4.34
2253	2271	4.335341	ATTGCTAAAACAAACACGGCACG	61.335	43.478	0.00	0.00	46.22	5.34
2320	2338	3.309682	CACAACACGACACATATCATCCC	59.690	47.826	0.00	0.00	0.00	3.85
2343	2361	0.803117	TCGACTCGATCTCACCACAC	59.197	55.000	0.00	0.00	0.00	3.82
2382	2400	8.247562	TCAAAAACACTTATTACAACAACAGCT	58.752	29.630	0.00	0.00	0.00	4.24
2383	2401	8.318167	GTCAAAAACACTTATTACAACAACAGC	58.682	33.333	0.00	0.00	0.00	4.40
2384	2402	9.347934	TGTCAAAAACACTTATTACAACAACAG	57.652	29.630	0.00	0.00	31.20	3.16
2431	2449	2.422479	CACTGCTTCTTGGTGATGATGG	59.578	50.000	0.00	0.00	33.32	3.51
2432	2450	3.079578	ACACTGCTTCTTGGTGATGATG	58.920	45.455	0.00	0.00	35.28	3.07
2444	2462	2.064014	GGTACGGTGTTACACTGCTTC	58.936	52.381	22.63	13.17	43.84	3.86
2465	2485	6.097412	ACAAGGGAATCAATTAGGAAAGCATC	59.903	38.462	0.00	0.00	0.00	3.91
2474	2502	6.801862	GTCGTTGAAACAAGGGAATCAATTAG	59.198	38.462	0.00	0.00	34.62	1.73
2536	2569	0.104855	TCGGAGGGCAAATCGAGATG	59.895	55.000	0.00	0.00	0.00	2.90
2537	2570	1.051812	ATCGGAGGGCAAATCGAGAT	58.948	50.000	0.00	0.00	35.07	2.75
2676	2723	2.027625	GGTCGTTTCGGCACCAGAG	61.028	63.158	0.00	0.00	30.88	3.35
2678	2725	3.411351	CGGTCGTTTCGGCACCAG	61.411	66.667	0.00	0.00	30.88	4.00
2706	2753	3.827008	TTAAAATGGCTGGCACACAAA	57.173	38.095	5.88	0.00	0.00	2.83
2808	5222	1.506309	GCCCAAAAGCGGCCTTTTTG	61.506	55.000	24.48	24.48	46.33	2.44
2809	5223	1.227823	GCCCAAAAGCGGCCTTTTT	60.228	52.632	0.00	5.04	46.33	1.94
2818	5233	2.670939	AGGATCTAATGGCCCAAAAGC	58.329	47.619	0.00	0.00	0.00	3.51
2901	5318	0.835941	CCCTACAGCATTGCTCCTCT	59.164	55.000	8.54	0.00	36.40	3.69
2947	5364	9.880064	CAAACATTCACATATTTCATTGCAAAA	57.120	25.926	1.71	0.00	0.00	2.44
2948	5365	9.269453	TCAAACATTCACATATTTCATTGCAAA	57.731	25.926	1.71	0.00	0.00	3.68
2949	5366	8.828688	TCAAACATTCACATATTTCATTGCAA	57.171	26.923	0.00	0.00	0.00	4.08
2960	5377	9.330063	GTTCTCTCCATATCAAACATTCACATA	57.670	33.333	0.00	0.00	0.00	2.29
2961	5378	7.830697	TGTTCTCTCCATATCAAACATTCACAT	59.169	33.333	0.00	0.00	0.00	3.21
2962	5379	7.167535	TGTTCTCTCCATATCAAACATTCACA	58.832	34.615	0.00	0.00	0.00	3.58
2963	5380	7.615582	TGTTCTCTCCATATCAAACATTCAC	57.384	36.000	0.00	0.00	0.00	3.18
2964	5381	8.634335	TTTGTTCTCTCCATATCAAACATTCA	57.366	30.769	0.00	0.00	0.00	2.57
2965	5382	9.912634	TTTTTGTTCTCTCCATATCAAACATTC	57.087	29.630	0.00	0.00	0.00	2.67
2971	5388	9.436957	GTCTAGTTTTTGTTCTCTCCATATCAA	57.563	33.333	0.00	0.00	0.00	2.57
2979	5396	4.448060	CACCCGTCTAGTTTTTGTTCTCTC	59.552	45.833	0.00	0.00	0.00	3.20

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.