AutoCloner

Multiple sequence alignment - TraesCS5A01G201000

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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	TraesCS5A01G201000	chr5A	100.000	3141	0	0	1	3141	407124313	407127453	0.000000e+00	5801.0
1	TraesCS5A01G201000	chr5A	90.760	1039	85	8	1024	2051	407154564	407153526	0.000000e+00	1376.0
2	TraesCS5A01G201000	chr5A	86.402	956	92	24	1	932	407157452	407156511	0.000000e+00	1011.0
3	TraesCS5A01G201000	chr5A	86.154	65	9	0	2913	2977	617951540	617951604	1.560000e-08	71.3
4	TraesCS5A01G201000	chr5B	91.999	2712	151	27	1	2667	360860327	360863017	0.000000e+00	3746.0
5	TraesCS5A01G201000	chr5B	87.981	624	72	1	21	644	360925625	360925005	0.000000e+00	734.0
6	TraesCS5A01G201000	chr5B	90.045	442	37	4	1613	2052	360922588	360922152	1.640000e-157	566.0
7	TraesCS5A01G201000	chr5B	85.865	474	56	4	2668	3141	360863110	360863572	7.830000e-136	494.0
8	TraesCS5A01G201000	chr5B	85.882	85	10	2	2372	2456	655806582	655806500	4.310000e-14	89.8
9	TraesCS5A01G201000	chr5B	92.857	56	3	1	2651	2705	360863034	360863089	2.600000e-11	80.5
10	TraesCS5A01G201000	chr5D	92.749	1710	81	21	1011	2704	313151963	313153645	0.000000e+00	2431.0
11	TraesCS5A01G201000	chr5D	90.544	1047	75	5	1011	2048	313333002	313331971	0.000000e+00	1363.0
12	TraesCS5A01G201000	chr5D	88.301	983	77	19	1	974	313334038	313333085	0.000000e+00	1144.0
13	TraesCS5A01G201000	chr5D	88.903	784	84	3	1	783	313150852	313151633	0.000000e+00	963.0
14	TraesCS5A01G201000	chr5D	85.084	476	53	12	2668	3141	313153667	313154126	1.320000e-128	470.0
15	TraesCS5A01G201000	chr5D	88.811	286	32	0	1	286	313284581	313284296	4.980000e-93	351.0
16	TraesCS5A01G201000	chr5D	85.542	83	10	1	2435	2515	538162118	538162200	5.580000e-13	86.1
17	TraesCS5A01G201000	chr2B	78.766	551	98	15	2518	3055	754776662	754777206	4.980000e-93	351.0
18	TraesCS5A01G201000	chr2B	86.239	109	10	3	2415	2521	146906995	146907100	2.560000e-21	113.0
19	TraesCS5A01G201000	chr6D	79.521	376	57	12	2668	3040	166749141	166749499	1.870000e-62	250.0
20	TraesCS5A01G201000	chr7A	84.615	221	32	2	544	763	581040028	581040247	5.270000e-53	219.0
21	TraesCS5A01G201000	chr4D	84.862	218	31	2	2790	3005	108205176	108204959	5.270000e-53	219.0
22	TraesCS5A01G201000	chr4D	83.007	153	20	5	2555	2706	42096847	42096700	1.970000e-27	134.0
23	TraesCS5A01G201000	chr3A	78.704	324	56	8	2668	2980	595958499	595958820	1.480000e-48	204.0
24	TraesCS5A01G201000	chr4B	84.946	186	23	4	2331	2514	108665678	108665496	1.920000e-42	183.0
25	TraesCS5A01G201000	chr7B	85.987	157	15	6	2368	2521	591526196	591526348	9.020000e-36	161.0
26	TraesCS5A01G201000	chr7B	86.885	122	14	2	643	763	538574875	538574995	5.460000e-28	135.0
27	TraesCS5A01G201000	chr2A	83.333	156	24	2	2913	3068	448296994	448296841	3.270000e-30	143.0
28	TraesCS5A01G201000	chr3D	86.111	108	10	4	2415	2520	43241398	43241502	9.210000e-21	111.0
29	TraesCS5A01G201000	chr7D	85.321	109	11	2	2415	2521	78118718	78118613	1.190000e-19	108.0
30	TraesCS5A01G201000	chr3B	84.259	108	12	4	2415	2520	67375815	67375919	1.990000e-17	100.0
31	TraesCS5A01G201000	chr1D	82.524	103	17	1	2541	2642	212076344	212076446	4.310000e-14	89.8

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	TraesCS5A01G201000	chr5A	407124313	407127453	3140	False	5801.000000	5801	100.000000	1	3141	1	chr5A.!!$F1	3140
1	TraesCS5A01G201000	chr5A	407153526	407157452	3926	True	1193.500000	1376	88.581000	1	2051	2	chr5A.!!$R1	2050
2	TraesCS5A01G201000	chr5B	360860327	360863572	3245	False	1440.166667	3746	90.240333	1	3141	3	chr5B.!!$F1	3140
3	TraesCS5A01G201000	chr5B	360922152	360925625	3473	True	650.000000	734	89.013000	21	2052	2	chr5B.!!$R2	2031
4	TraesCS5A01G201000	chr5D	313150852	313154126	3274	False	1288.000000	2431	88.912000	1	3141	3	chr5D.!!$F2	3140
5	TraesCS5A01G201000	chr5D	313331971	313334038	2067	True	1253.500000	1363	89.422500	1	2048	2	chr5D.!!$R2	2047
6	TraesCS5A01G201000	chr2B	754776662	754777206	544	False	351.000000	351	78.766000	2518	3055	1	chr2B.!!$F2	537

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
785	3038	0.250124	TTTGTTCCTGCGACATCCGT	60.25	50.0	0.0	0.0	41.15	4.69	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2766	7104	0.744771	TGTGTTGCAACCTACACGCA	60.745	50.0	26.14	11.47	46.26	5.24	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
24	25	3.420893	TCTTGTCCCATTCCATTGTGTC	58.579	45.455	0.00	0.00	0.00	3.67
133	134	3.259876	AGCTGTCTTCGTATACAAACCCA	59.740	43.478	3.32	0.00	0.00	4.51
174	175	7.584987	TCAAGAATTTCAAATCCTTCTTCGTC	58.415	34.615	0.00	0.00	36.16	4.20
352	353	2.555757	GCAACAACCAATCTCTTGAGCT	59.444	45.455	0.00	0.00	34.04	4.09
382	383	0.527113	CAATGCCGAACATCTTGCCA	59.473	50.000	0.00	0.00	38.34	4.92
767	3020	1.827969	CTGGGAGAGACGACCAATCTT	59.172	52.381	0.00	0.00	33.13	2.40
783	3036	1.808411	TCTTTGTTCCTGCGACATCC	58.192	50.000	0.00	0.00	0.00	3.51
784	3037	0.443869	CTTTGTTCCTGCGACATCCG	59.556	55.000	0.00	0.00	42.21	4.18
785	3038	0.250124	TTTGTTCCTGCGACATCCGT	60.250	50.000	0.00	0.00	41.15	4.69
786	3039	0.669318	TTGTTCCTGCGACATCCGTC	60.669	55.000	0.00	0.00	41.15	4.79
787	3040	1.810030	GTTCCTGCGACATCCGTCC	60.810	63.158	0.00	0.00	39.11	4.79
788	3041	3.014085	TTCCTGCGACATCCGTCCC	62.014	63.158	0.00	0.00	39.11	4.46
892	3207	9.640963	CCTTTACGCTACTATATATCTTTGCTT	57.359	33.333	0.00	0.00	0.00	3.91
986	3329	1.141254	TGACCCGAAACCTAAACTGCA	59.859	47.619	0.00	0.00	0.00	4.41
987	3330	2.223745	GACCCGAAACCTAAACTGCAA	58.776	47.619	0.00	0.00	0.00	4.08
1040	5254	2.702270	AGAAAACTTTGCAGGGGGAT	57.298	45.000	0.00	0.00	0.00	3.85
1085	5307	1.153549	GCGAGGCGGAGAACTTGAT	60.154	57.895	0.00	0.00	0.00	2.57
1172	5394	2.325082	AACATGACGGCGAGGCAAC	61.325	57.895	16.62	0.00	44.01	4.17
1305	5527	0.464916	TGCTGCATCTGGAATCGCAT	60.465	50.000	0.00	0.00	33.15	4.73
1313	5535	4.084118	GCATCTGGAATCGCATAAGTCTTC	60.084	45.833	0.00	0.00	0.00	2.87
1382	5604	2.682155	GAGAATCTTCTCCAAGCCGT	57.318	50.000	8.47	0.00	46.20	5.68
1459	5681	1.446272	GTAGCAGACCTCGCACACC	60.446	63.158	0.00	0.00	0.00	4.16
1533	5755	0.031178	AGCACGGCAAAAGCTTCAAG	59.969	50.000	0.00	0.00	34.37	3.02
1573	5797	1.479323	GTGGGAGGTTCTACGCATACA	59.521	52.381	0.00	0.00	0.00	2.29
1580	5804	2.277084	GTTCTACGCATACAACCCCTG	58.723	52.381	0.00	0.00	0.00	4.45
1593	5826	3.000727	CAACCCCTGTAAACGTCAGATC	58.999	50.000	4.41	0.00	35.20	2.75
1633	5866	2.290260	CCATACCCAGAGTTCAGCACAA	60.290	50.000	0.00	0.00	0.00	3.33
1727	5960	6.066054	AGAGCTGTTTGTTCTAAGCTTTTC	57.934	37.500	3.20	0.00	45.74	2.29
1886	6119	2.894387	GGATGCACTCCAGCTCGC	60.894	66.667	9.50	0.00	44.26	5.03
2078	6311	5.545588	CACAACCATCTATTCGAGATCCAT	58.454	41.667	0.00	0.00	43.52	3.41
2098	6331	6.306199	TCCATTTCAGACTTTGATCCTTGAA	58.694	36.000	0.00	0.00	35.27	2.69
2260	6497	3.301274	TGATATGGTCGTGTGGGTATGA	58.699	45.455	0.00	0.00	0.00	2.15
2275	6512	5.185828	GTGGGTATGAATTTTGCCTTCTCTT	59.814	40.000	0.00	0.00	0.00	2.85
2276	6513	5.779771	TGGGTATGAATTTTGCCTTCTCTTT	59.220	36.000	0.00	0.00	0.00	2.52
2314	6551	5.744171	TGTGGCAGATGTGTGTATCTTAAT	58.256	37.500	0.00	0.00	35.28	1.40
2386	6626	2.802816	GCTGTGTGTCAGTTTAGTCCTG	59.197	50.000	0.00	0.00	45.23	3.86
2404	6644	5.531287	AGTCCTGTTACTTTAAAACTGCAGG	59.469	40.000	19.93	16.27	42.43	4.85
2431	6671	6.137559	TGGGTTTTAAAACTATTGGAGGTGT	58.862	36.000	25.89	0.00	38.89	4.16
2432	6672	6.041069	TGGGTTTTAAAACTATTGGAGGTGTG	59.959	38.462	25.89	0.00	38.89	3.82
2433	6673	6.041182	GGGTTTTAAAACTATTGGAGGTGTGT	59.959	38.462	25.89	0.00	38.89	3.72
2444	6684	6.723298	ATTGGAGGTGTGTTGTCATTTTAA	57.277	33.333	0.00	0.00	0.00	1.52
2497	6737	7.227910	GTCCTAAAACTATTGAAGGTGTGTCAA	59.772	37.037	0.00	0.00	39.24	3.18
2557	6797	3.342627	CTTCGCGTTGTCCGGCAA	61.343	61.111	5.77	1.09	36.94	4.52
2689	6968	2.202756	GACGTCCTGCATCCCGAC	60.203	66.667	3.51	0.70	0.00	4.79
2695	7033	2.270205	CTGCATCCCGACTGGCTT	59.730	61.111	0.00	0.00	0.00	4.35
2715	7053	1.681327	GGTCTCCCCAGCGAGTGTA	60.681	63.158	0.00	0.00	0.00	2.90
2724	7062	1.542547	CCAGCGAGTGTACCAAACCTT	60.543	52.381	0.00	0.00	0.00	3.50
2731	7069	4.196971	GAGTGTACCAAACCTTTCAGTGT	58.803	43.478	0.00	0.00	0.00	3.55
2766	7104	3.228243	ATGGCCATGCAGGTGGTGT	62.228	57.895	20.04	0.00	41.47	4.16
2787	7126	1.010580	CGTGTAGGTTGCAACACACA	58.989	50.000	34.05	29.39	44.98	3.72
2788	7127	1.601903	CGTGTAGGTTGCAACACACAT	59.398	47.619	34.05	18.78	44.98	3.21
2833	7172	5.591472	ACCACTTTTAGGGAAGTAAACACAC	59.409	40.000	0.00	0.00	37.76	3.82
2872	7213	5.520376	AAAAATGTACCATAGATGCTGGC	57.480	39.130	0.00	0.00	37.27	4.85
2878	7219	1.583495	CCATAGATGCTGGCCATGCG	61.583	60.000	5.51	0.00	33.29	4.73
2886	7227	1.153289	CTGGCCATGCGAGCTTAGT	60.153	57.895	5.51	0.00	0.00	2.24
2895	7236	2.443416	TGCGAGCTTAGTACCTGAGAA	58.557	47.619	0.00	0.00	0.00	2.87
2910	7251	8.211629	AGTACCTGAGAAGAACAAACTTACATT	58.788	33.333	0.00	0.00	0.00	2.71
2964	7306	9.305555	AGTTATAGAACTAAACTGACACACCTA	57.694	33.333	0.00	0.00	44.36	3.08
2981	7324	8.937634	ACACACCTATAATAGTTTTAGAACCG	57.062	34.615	0.00	0.00	36.39	4.44
2995	7338	7.680982	GTTTTAGAACCGAAAACTGCAATTTT	58.319	30.769	5.41	5.41	41.50	1.82
3131	7474	8.786826	AATGTAATAAATGTCGTTCTCCTTCA	57.213	30.769	0.00	0.00	0.00	3.02

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
13	14	4.401022	AGCTCAATGAAGACACAATGGAA	58.599	39.130	0.00	0.00	0.00	3.53
133	134	2.158813	TCTTGAGAAGCCACGGAGTTTT	60.159	45.455	0.00	0.00	41.61	2.43
174	175	0.439985	CGCATGTGACGAGTCCAAAG	59.560	55.000	0.00	0.00	0.00	2.77
352	353	0.319986	TCGGCATTGACACGCTTGTA	60.320	50.000	0.00	0.00	35.47	2.41
409	413	3.009033	TCCCACCGATTTCTCAGATTTGT	59.991	43.478	0.00	0.00	0.00	2.83
767	3020	0.669318	GACGGATGTCGCAGGAACAA	60.669	55.000	0.00	0.00	43.89	2.83
788	3041	3.521529	CTATTGGGGAGAGGCGGCG	62.522	68.421	0.51	0.51	0.00	6.46
802	3056	0.960364	CCACCTGTTGTGCGGCTATT	60.960	55.000	0.00	0.00	44.01	1.73
986	3329	0.540830	TTATGTTGCCGGTTGCCCTT	60.541	50.000	1.90	0.00	40.16	3.95
987	3330	0.540830	TTTATGTTGCCGGTTGCCCT	60.541	50.000	1.90	0.00	40.16	5.19
1040	5254	3.822192	CCATCTCGTCGTCCGCCA	61.822	66.667	0.00	0.00	36.19	5.69
1313	5535	0.034089	GGTTGATGGGTTCCAGAGGG	60.034	60.000	0.00	0.00	36.75	4.30
1459	5681	3.801638	GCATGGCAGTAGTAGATGAGTGG	60.802	52.174	0.00	0.00	0.00	4.00
1533	5755	1.439679	CAAGCGTGGTAAGACCTTCC	58.560	55.000	0.00	0.00	39.58	3.46
1573	5797	2.353406	CGATCTGACGTTTACAGGGGTT	60.353	50.000	3.21	0.00	36.22	4.11
1580	5804	3.562505	AGTGTGACGATCTGACGTTTAC	58.437	45.455	0.00	0.00	46.52	2.01
1593	5826	2.552743	TGGTGAGAACTCTAGTGTGACG	59.447	50.000	0.00	0.00	0.00	4.35
1727	5960	2.030185	CGGACAGATATCCCGTGGTAAG	60.030	54.545	9.90	0.00	38.55	2.34
1886	6119	3.040147	TGCAGTCCCGTTTTCTTAGAG	57.960	47.619	0.00	0.00	0.00	2.43
2078	6311	6.356556	TCACTTCAAGGATCAAAGTCTGAAA	58.643	36.000	0.00	0.00	37.67	2.69
2098	6331	4.689612	TGTTCTAAAGACTTGCCTCACT	57.310	40.909	0.00	0.00	0.00	3.41
2230	6467	3.627577	ACACGACCATATCATGAAAAGGC	59.372	43.478	0.00	0.00	0.00	4.35
2247	6484	2.490115	GGCAAAATTCATACCCACACGA	59.510	45.455	0.00	0.00	0.00	4.35
2260	6497	4.122046	GCACACAAAGAGAAGGCAAAATT	58.878	39.130	0.00	0.00	0.00	1.82
2292	6529	6.683974	AATTAAGATACACACATCTGCCAC	57.316	37.500	0.00	0.00	35.42	5.01
2386	6626	5.751509	CCCAAACCTGCAGTTTTAAAGTAAC	59.248	40.000	13.81	0.00	46.79	2.50
2404	6644	7.439955	CACCTCCAATAGTTTTAAAACCCAAAC	59.560	37.037	24.06	2.63	39.71	2.93
2486	6726	8.603304	AGTTATAGGACTAAATTGACACACCTT	58.397	33.333	0.00	0.00	0.00	3.50
2589	6829	1.140452	TGCATGTTGTTGTTTGGGCAT	59.860	42.857	0.00	0.00	0.00	4.40
2649	6889	5.427806	TCATCCCAACTCTTTCTCTCATGAT	59.572	40.000	0.00	0.00	0.00	2.45
2705	7043	1.878953	AAGGTTTGGTACACTCGCTG	58.121	50.000	0.00	0.00	39.29	5.18
2706	7044	2.158871	TGAAAGGTTTGGTACACTCGCT	60.159	45.455	0.00	0.00	39.29	4.93
2707	7045	2.215196	TGAAAGGTTTGGTACACTCGC	58.785	47.619	0.00	0.00	39.29	5.03
2711	7049	3.066203	CCACACTGAAAGGTTTGGTACAC	59.934	47.826	0.00	0.00	36.22	2.90
2715	7053	1.111277	GCCACACTGAAAGGTTTGGT	58.889	50.000	0.00	0.00	38.77	3.67
2766	7104	0.744771	TGTGTTGCAACCTACACGCA	60.745	50.000	26.14	11.47	46.26	5.24
2787	7126	1.599071	CATACGCTTCCACATCGCAAT	59.401	47.619	0.00	0.00	0.00	3.56
2788	7127	1.006086	CATACGCTTCCACATCGCAA	58.994	50.000	0.00	0.00	0.00	4.85
2857	7198	1.271543	GCATGGCCAGCATCTATGGTA	60.272	52.381	13.05	0.00	40.17	3.25
2872	7213	1.409064	TCAGGTACTAAGCTCGCATGG	59.591	52.381	0.00	0.00	36.02	3.66
2878	7219	5.646577	TGTTCTTCTCAGGTACTAAGCTC	57.353	43.478	0.00	0.00	36.02	4.09
2886	7227	7.990886	ACAATGTAAGTTTGTTCTTCTCAGGTA	59.009	33.333	0.00	0.00	33.64	3.08
2977	7320	7.603963	AACTTTAAAATTGCAGTTTTCGGTT	57.396	28.000	21.48	19.22	33.62	4.44
3015	7358	8.706322	AGTCCTAAAATTATTGGAAGTGTGTT	57.294	30.769	0.00	0.00	0.00	3.32
3118	7461	2.095718	GCCAACAATGAAGGAGAACGAC	60.096	50.000	0.00	0.00	0.00	4.34

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.