AutoCloner

Multiple sequence alignment - TraesCS6D01G355600

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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	TraesCS6D01G355600	chr6D	100.000	4537	0	0	1	4537	450213533	450208997	0.000000e+00	8379.0
1	TraesCS6D01G355600	chr6D	81.858	915	132	18	1875	2773	450168347	450167451	0.000000e+00	739.0
2	TraesCS6D01G355600	chr6D	79.805	614	114	7	1055	1666	450168952	450168347	5.390000e-119	438.0
3	TraesCS6D01G355600	chr6D	71.866	1731	372	82	1030	2716	449818349	449816690	4.250000e-105	392.0
4	TraesCS6D01G355600	chr6D	72.637	1312	283	54	1438	2716	449844116	449842848	9.280000e-97	364.0
5	TraesCS6D01G355600	chr6D	76.554	563	102	16	2162	2716	452081642	452081102	9.610000e-72	281.0
6	TraesCS6D01G355600	chr6D	93.750	64	4	0	3575	3638	450334953	450334890	3.740000e-16	97.1
7	TraesCS6D01G355600	chr6B	93.656	2396	109	13	1	2369	682743776	682741397	0.000000e+00	3542.0
8	TraesCS6D01G355600	chr6B	87.151	1790	206	18	207	1980	682712819	682711038	0.000000e+00	2010.0
9	TraesCS6D01G355600	chr6B	97.031	1145	34	0	1895	3039	682707930	682706786	0.000000e+00	1927.0
10	TraesCS6D01G355600	chr6B	88.072	1442	160	10	544	1980	682676407	682674973	0.000000e+00	1700.0
11	TraesCS6D01G355600	chr6B	97.342	978	20	6	3563	4537	682696599	682695625	0.000000e+00	1657.0
12	TraesCS6D01G355600	chr6B	97.032	977	24	5	3563	4537	682740444	682739471	0.000000e+00	1639.0
13	TraesCS6D01G355600	chr6B	96.515	947	22	2	2654	3600	682741400	682740465	0.000000e+00	1555.0
14	TraesCS6D01G355600	chr6B	81.093	1756	292	30	960	2703	682662161	682660434	0.000000e+00	1367.0
15	TraesCS6D01G355600	chr6B	97.350	566	14	1	3035	3600	682697184	682696620	0.000000e+00	961.0
16	TraesCS6D01G355600	chr6B	72.582	1313	283	54	1438	2716	682418333	682419602	4.320000e-95	359.0
17	TraesCS6D01G355600	chr6B	78.870	478	63	21	2264	2716	683226696	683226232	5.740000e-74	289.0
18	TraesCS6D01G355600	chr6B	76.525	541	110	8	2189	2716	681929508	681928972	3.460000e-71	279.0
19	TraesCS6D01G355600	chr6B	93.103	58	2	1	3575	3630	683470620	683470563	2.910000e-12	84.2
20	TraesCS6D01G355600	chr6B	86.667	60	8	0	4440	4499	400091117	400091058	2.930000e-07	67.6
21	TraesCS6D01G355600	chr6B	97.368	38	1	0	4500	4537	682674973	682674936	1.050000e-06	65.8
22	TraesCS6D01G355600	chr6A	80.664	1898	305	43	912	2781	595664948	595663085	0.000000e+00	1415.0
23	TraesCS6D01G355600	chr6A	86.267	1085	120	15	182	1261	595679612	595678552	0.000000e+00	1151.0
24	TraesCS6D01G355600	chr6A	87.311	993	79	25	3563	4537	595677985	595677022	0.000000e+00	1092.0
25	TraesCS6D01G355600	chr6A	90.619	533	44	4	3072	3600	595678536	595678006	0.000000e+00	702.0

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	TraesCS6D01G355600	chr6D	450208997	450213533	4536	True	8379.000000	8379	100.000000	1	4537	1	chr6D.!!$R3	4536
1	TraesCS6D01G355600	chr6D	450167451	450168952	1501	True	588.500000	739	80.831500	1055	2773	2	chr6D.!!$R6	1718
2	TraesCS6D01G355600	chr6D	449816690	449818349	1659	True	392.000000	392	71.866000	1030	2716	1	chr6D.!!$R1	1686
3	TraesCS6D01G355600	chr6D	449842848	449844116	1268	True	364.000000	364	72.637000	1438	2716	1	chr6D.!!$R2	1278
4	TraesCS6D01G355600	chr6D	452081102	452081642	540	True	281.000000	281	76.554000	2162	2716	1	chr6D.!!$R5	554
5	TraesCS6D01G355600	chr6B	682739471	682743776	4305	True	2245.333333	3542	95.734333	1	4537	3	chr6B.!!$R9	4536
6	TraesCS6D01G355600	chr6B	682706786	682712819	6033	True	1968.500000	2010	92.091000	207	3039	2	chr6B.!!$R8	2832
7	TraesCS6D01G355600	chr6B	682660434	682662161	1727	True	1367.000000	1367	81.093000	960	2703	1	chr6B.!!$R3	1743
8	TraesCS6D01G355600	chr6B	682695625	682697184	1559	True	1309.000000	1657	97.346000	3035	4537	2	chr6B.!!$R7	1502
9	TraesCS6D01G355600	chr6B	682674936	682676407	1471	True	882.900000	1700	92.720000	544	4537	2	chr6B.!!$R6	3993
10	TraesCS6D01G355600	chr6B	682418333	682419602	1269	False	359.000000	359	72.582000	1438	2716	1	chr6B.!!$F1	1278
11	TraesCS6D01G355600	chr6B	681928972	681929508	536	True	279.000000	279	76.525000	2189	2716	1	chr6B.!!$R2	527
12	TraesCS6D01G355600	chr6A	595663085	595664948	1863	True	1415.000000	1415	80.664000	912	2781	1	chr6A.!!$R1	1869
13	TraesCS6D01G355600	chr6A	595677022	595679612	2590	True	981.666667	1151	88.065667	182	4537	3	chr6A.!!$R2	4355

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
164	165	0.303191	TTTCATCACACACACACGCG	59.697	50.000	3.53	3.53	0.00	6.01	F
875	922	1.141881	CAAGTCATCTAGCGGCGGT	59.858	57.895	18.21	18.21	0.00	5.68	F
1366	1417	0.038343	CCAACAAATGAAGCCGTGGG	60.038	55.000	0.00	0.00	0.00	4.61	F
1497	1550	0.674581	TGCACTTTGAGGGATGCTCG	60.675	55.000	0.00	0.00	38.90	5.03	F
2707	6031	0.251916	CCCATGGAGTGCCTTACGAA	59.748	55.000	15.22	0.00	34.31	3.85	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1312	1360	0.179056	CATTCGGGGTAATCAGCCGT	60.179	55.000	0.0	0.00	43.74	5.68	R
1768	1824	4.662179	ACATCCCTCACATGATGGATTACT	59.338	41.667	14.1	0.77	43.92	2.24	R
2707	6031	5.004922	TGCGAACTTCAACCTCAATTTTT	57.995	34.783	0.0	0.00	0.00	1.94	R
3478	6827	4.780815	AGATCGAAATTGAACCCTGCATA	58.219	39.130	0.0	0.00	0.00	3.14	R
3657	7064	0.859232	CCACGACACTTCAAACCTCG	59.141	55.000	0.0	0.00	0.00	4.63	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	0.886490	CAGCAGTGGTTGGAGGTCAC	60.886	60.000	0.00	0.00	0.00	3.67
71	72	2.203408	GCCCCTGATAGCCTTGCC	60.203	66.667	0.00	0.00	0.00	4.52
77	78	2.107204	CCCTGATAGCCTTGCCTGTTAT	59.893	50.000	0.00	0.00	0.00	1.89
102	103	1.226128	GCTTTTTCGCTAGCCGCTG	60.226	57.895	9.66	0.00	36.73	5.18
117	118	1.675714	CCGCTGTTAGTCATTCCTGCA	60.676	52.381	0.00	0.00	0.00	4.41
139	140	0.534412	AGTGACTCCTTCGATGGCAG	59.466	55.000	12.42	12.33	0.00	4.85
140	141	0.460987	GTGACTCCTTCGATGGCAGG	60.461	60.000	12.42	3.38	0.00	4.85
162	163	3.097910	GTTGTTTCATCACACACACACG	58.902	45.455	0.00	0.00	0.00	4.49
164	165	0.303191	TTTCATCACACACACACGCG	59.697	50.000	3.53	3.53	0.00	6.01
166	167	3.701530	ATCACACACACACGCGCG	61.702	61.111	30.96	30.96	0.00	6.86
204	205	2.403186	CGCACACACACACACACC	59.597	61.111	0.00	0.00	0.00	4.16
291	293	1.555075	GTAGTTGCTCCACCATCCTCA	59.445	52.381	0.00	0.00	0.00	3.86
359	363	1.526917	AGTGCCGCCATTATGCTCC	60.527	57.895	0.00	0.00	0.00	4.70
378	382	4.036852	GCTCCCATGGTAAAACTGATAAGC	59.963	45.833	11.73	0.00	0.00	3.09
483	488	5.734855	ATCAGTTATAAACCATGACGTGC	57.265	39.130	0.00	0.00	0.00	5.34
516	523	8.758829	TGTTGTATTTTCTAATGGCTCTCTCTA	58.241	33.333	0.00	0.00	0.00	2.43
572	579	8.549548	CAGTGAATGCAAAGATAATCTAGACTG	58.450	37.037	0.00	0.00	0.00	3.51
771	779	2.943036	TTCCTGTCCCACCAAGTTAC	57.057	50.000	0.00	0.00	0.00	2.50
859	906	1.203187	AGGAGGTAGAGGAGCACACAA	60.203	52.381	0.00	0.00	0.00	3.33
875	922	1.141881	CAAGTCATCTAGCGGCGGT	59.858	57.895	18.21	18.21	0.00	5.68
941	988	3.092301	CTCCATGTGACTGGTCTCACTA	58.908	50.000	7.50	0.00	41.15	2.74
1015	1062	3.801050	CGACATAATGTCTGAGAGGCTTG	59.199	47.826	0.00	0.00	44.85	4.01
1090	1138	2.092212	GCCCTCCCAAATGATCTTCTCA	60.092	50.000	0.00	0.00	38.53	3.27
1312	1360	1.135199	GTTCGGATTGCGTGGAGACTA	60.135	52.381	0.00	0.00	0.00	2.59
1366	1417	0.038343	CCAACAAATGAAGCCGTGGG	60.038	55.000	0.00	0.00	0.00	4.61
1497	1550	0.674581	TGCACTTTGAGGGATGCTCG	60.675	55.000	0.00	0.00	38.90	5.03
1768	1824	4.280174	GTGAGGAGGAACTGTGTTACTGTA	59.720	45.833	0.00	0.00	41.55	2.74
2160	5443	6.844696	ACAAATCGTGGTATATGCTAACTG	57.155	37.500	0.00	0.00	0.00	3.16
2247	5550	6.809630	AAAGGAGCTTGTACTTCTGAATTC	57.190	37.500	0.00	0.00	0.00	2.17
2275	5582	7.272037	TCTTGAATTGTGGTTTAACCTTCTC	57.728	36.000	15.68	5.69	39.58	2.87
2449	5756	3.681897	ACTTACGCTTCAGCTTGATCTTG	59.318	43.478	0.00	0.00	39.32	3.02
2458	5765	6.551385	TTCAGCTTGATCTTGAAAGTTCTC	57.449	37.500	0.00	0.00	0.00	2.87
2512	5823	7.469456	GCTTGTCTTTGAAGTTACCATTTACCA	60.469	37.037	0.00	0.00	0.00	3.25
2518	5829	9.541143	CTTTGAAGTTACCATTTACCATTTGTT	57.459	29.630	0.00	0.00	0.00	2.83
2519	5830	8.879342	TTGAAGTTACCATTTACCATTTGTTG	57.121	30.769	0.00	0.00	0.00	3.33
2520	5831	8.239038	TGAAGTTACCATTTACCATTTGTTGA	57.761	30.769	0.00	0.00	0.00	3.18
2521	5832	8.138712	TGAAGTTACCATTTACCATTTGTTGAC	58.861	33.333	0.00	0.00	0.00	3.18
2522	5833	6.988522	AGTTACCATTTACCATTTGTTGACC	58.011	36.000	0.00	0.00	0.00	4.02
2523	5834	6.780522	AGTTACCATTTACCATTTGTTGACCT	59.219	34.615	0.00	0.00	0.00	3.85
2524	5835	7.945664	AGTTACCATTTACCATTTGTTGACCTA	59.054	33.333	0.00	0.00	0.00	3.08
2707	6031	0.251916	CCCATGGAGTGCCTTACGAA	59.748	55.000	15.22	0.00	34.31	3.85
2748	6092	3.004002	CGCATGTAAGTTGCCATCATCAT	59.996	43.478	0.00	0.00	36.75	2.45
2749	6093	4.498513	CGCATGTAAGTTGCCATCATCATT	60.499	41.667	0.00	0.00	36.75	2.57
2750	6094	4.980434	GCATGTAAGTTGCCATCATCATTC	59.020	41.667	0.00	0.00	33.95	2.67
2751	6095	5.221185	GCATGTAAGTTGCCATCATCATTCT	60.221	40.000	0.00	0.00	33.95	2.40
2752	6096	6.682113	GCATGTAAGTTGCCATCATCATTCTT	60.682	38.462	0.00	0.00	33.95	2.52
2753	6097	6.441093	TGTAAGTTGCCATCATCATTCTTC	57.559	37.500	0.00	0.00	0.00	2.87
2754	6098	5.945191	TGTAAGTTGCCATCATCATTCTTCA	59.055	36.000	0.00	0.00	0.00	3.02
2755	6099	6.604396	TGTAAGTTGCCATCATCATTCTTCAT	59.396	34.615	0.00	0.00	0.00	2.57
2756	6100	5.769484	AGTTGCCATCATCATTCTTCATC	57.231	39.130	0.00	0.00	0.00	2.92
2757	6101	5.198207	AGTTGCCATCATCATTCTTCATCA	58.802	37.500	0.00	0.00	0.00	3.07
2881	6225	1.916273	TAGCCCACCATGACACCGT	60.916	57.895	0.00	0.00	0.00	4.83
3165	6509	9.327578	GACTAATGTAGGTAGTACCGAAGGCAG	62.328	48.148	13.76	10.63	44.90	4.85
3252	6596	2.486592	GTGTAAGCGCTACCCAAAATGT	59.513	45.455	12.05	0.00	0.00	2.71
3478	6827	4.081752	TGCTCATTGTGTCCTTTGTTGTTT	60.082	37.500	0.00	0.00	0.00	2.83
3657	7064	9.669353	GGATGTTGTCATAAATCATAACATGTC	57.331	33.333	0.00	0.00	38.45	3.06
3966	7374	0.898326	TGTCACCGCCTCTAGCTTCA	60.898	55.000	0.00	0.00	40.39	3.02
4058	7466	2.268920	GCGGTGAAGGCTGATGGA	59.731	61.111	0.00	0.00	0.00	3.41
4117	7525	9.947433	TTCTCTGTATTTTTATTTTCCTCGGTA	57.053	29.630	0.00	0.00	0.00	4.02
4371	7794	2.037121	TCTCGCCACAATGAGTCTTTGA	59.963	45.455	21.87	2.26	33.88	2.69

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
71	72	3.244976	CGAAAAAGCCCAGCAATAACAG	58.755	45.455	0.00	0.00	0.00	3.16
77	78	0.881118	CTAGCGAAAAAGCCCAGCAA	59.119	50.000	0.00	0.00	38.01	3.91
99	100	2.704572	ACTGCAGGAATGACTAACAGC	58.295	47.619	19.93	0.00	30.84	4.40
102	103	4.865365	GTCACTACTGCAGGAATGACTAAC	59.135	45.833	28.93	7.20	34.86	2.34
117	118	1.751924	GCCATCGAAGGAGTCACTACT	59.248	52.381	11.67	0.00	39.21	2.57
139	140	2.425312	TGTGTGTGTGATGAAACAACCC	59.575	45.455	0.00	0.00	0.00	4.11
140	141	3.434637	GTGTGTGTGTGATGAAACAACC	58.565	45.455	0.00	0.00	0.00	3.77
285	287	2.230025	CGTATCGGCTGAGATTGAGGAT	59.770	50.000	0.00	0.00	32.39	3.24
291	293	1.661821	GCGCGTATCGGCTGAGATT	60.662	57.895	8.43	0.00	38.94	2.40
359	363	4.704540	TGGTGCTTATCAGTTTTACCATGG	59.295	41.667	11.19	11.19	32.26	3.66
378	382	0.890683	GGCTCCAAGGTTTGATGGTG	59.109	55.000	0.00	0.00	37.94	4.17
483	488	6.472163	GCCATTAGAAAATACAACACCGAATG	59.528	38.462	0.00	0.00	0.00	2.67
516	523	3.582208	GGATATGTGCCATCCTCTCTTCT	59.418	47.826	0.00	0.00	39.17	2.85
572	579	2.538132	CGAACCGAAAGTGGTGACAAAC	60.538	50.000	0.00	0.00	46.06	2.93
859	906	1.141881	CAACCGCCGCTAGATGACT	59.858	57.895	0.00	0.00	0.00	3.41
875	922	0.107703	CCGGATTAGCTCACCTGCAA	60.108	55.000	0.00	0.00	34.99	4.08
941	988	1.466025	TTAGACGTGGTGAGCCGGTT	61.466	55.000	1.90	0.00	37.67	4.44
1015	1062	4.201950	CGTTTCCATGGTTTCCTCATCATC	60.202	45.833	12.58	0.00	0.00	2.92
1090	1138	4.835615	AGGCAGGAACGACATAAGATAGAT	59.164	41.667	0.00	0.00	0.00	1.98
1312	1360	0.179056	CATTCGGGGTAATCAGCCGT	60.179	55.000	0.00	0.00	43.74	5.68
1366	1417	3.315470	TGACACGATAGAGCATACCAGAC	59.685	47.826	0.00	0.00	41.38	3.51
1608	1661	4.495472	CGAATGCGGTCATCAATACAAAAC	59.505	41.667	0.00	0.00	31.27	2.43
1768	1824	4.662179	ACATCCCTCACATGATGGATTACT	59.338	41.667	14.10	0.77	43.92	2.24
1982	5239	4.771590	ATGCAACACATGTAAGGAACAG	57.228	40.909	0.00	0.00	42.70	3.16
2103	5364	9.796120	GCTGTACTATAATCTCAATCCTACATC	57.204	37.037	0.00	0.00	0.00	3.06
2160	5443	8.458843	TGGCTCTCTTTTTGTATAGCAATTAAC	58.541	33.333	0.00	0.00	36.89	2.01
2247	5550	7.219484	AGGTTAAACCACAATTCAAGATCTG	57.781	36.000	0.00	0.00	41.95	2.90
2476	5783	8.541133	AACTTCAAAGACAAGCTATCTTACTC	57.459	34.615	12.33	0.00	35.31	2.59
2542	5863	8.462016	GTTTTGCTCAAATGATAATCCTGTAGT	58.538	33.333	0.00	0.00	0.00	2.73
2707	6031	5.004922	TGCGAACTTCAACCTCAATTTTT	57.995	34.783	0.00	0.00	0.00	1.94
2749	6093	8.982685	GCGACTGAAAGATAATAATGATGAAGA	58.017	33.333	0.00	0.00	37.43	2.87
2750	6094	8.226448	GGCGACTGAAAGATAATAATGATGAAG	58.774	37.037	0.00	0.00	37.43	3.02
2751	6095	7.714813	TGGCGACTGAAAGATAATAATGATGAA	59.285	33.333	0.00	0.00	37.43	2.57
2752	6096	7.216494	TGGCGACTGAAAGATAATAATGATGA	58.784	34.615	0.00	0.00	37.43	2.92
2753	6097	7.425577	TGGCGACTGAAAGATAATAATGATG	57.574	36.000	0.00	0.00	37.43	3.07
2754	6098	7.041098	GGTTGGCGACTGAAAGATAATAATGAT	60.041	37.037	4.59	0.00	37.43	2.45
2755	6099	6.260050	GGTTGGCGACTGAAAGATAATAATGA	59.740	38.462	4.59	0.00	37.43	2.57
2756	6100	6.038161	TGGTTGGCGACTGAAAGATAATAATG	59.962	38.462	4.59	0.00	37.43	1.90
2757	6101	6.119536	TGGTTGGCGACTGAAAGATAATAAT	58.880	36.000	4.59	0.00	37.43	1.28
2822	6166	5.124138	GGTGTGGATATATCGTCCTACTCTG	59.876	48.000	6.64	0.00	36.68	3.35
2881	6225	6.630203	ACATTGTGGTTCCCAAGTATAGTA	57.370	37.500	0.00	0.00	34.18	1.82
3478	6827	4.780815	AGATCGAAATTGAACCCTGCATA	58.219	39.130	0.00	0.00	0.00	3.14
3657	7064	0.859232	CCACGACACTTCAAACCTCG	59.141	55.000	0.00	0.00	0.00	4.63
3966	7374	4.043310	TCCTTTCATGGACCTCAAGAATGT	59.957	41.667	0.00	0.00	33.75	2.71
4017	7425	2.810852	CCAGAGAAGAGAAGCAAACCAC	59.189	50.000	0.00	0.00	0.00	4.16
4058	7466	2.755876	TGAGCGACGGCCATCTCT	60.756	61.111	2.24	0.00	41.24	3.10
4145	7553	4.263374	CCTCTGCATCATTAGGATCCACAT	60.263	45.833	15.82	1.75	32.57	3.21
4371	7794	1.499007	ACAACCACCATTTCACCTCCT	59.501	47.619	0.00	0.00	0.00	3.69

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.