AutoCloner

Multiple sequence alignment - TraesCS4A01G120200

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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	TraesCS4A01G120200	chr4A	100.000	2225	0	0	1	2225	147976697	147978921	0.000000e+00	4109
1	TraesCS4A01G120200	chr4A	95.186	1828	66	4	135	1961	147990133	147991939	0.000000e+00	2868
2	TraesCS4A01G120200	chr4A	92.647	340	24	1	106	445	496578539	496578877	2.570000e-134	488
3	TraesCS4A01G120200	chr3A	94.807	1964	68	9	1	1963	404460904	404458974	0.000000e+00	3031
4	TraesCS4A01G120200	chr3A	94.364	1455	51	5	1	1454	404469284	404467860	0.000000e+00	2204
5	TraesCS4A01G120200	chr3A	91.932	880	59	9	1303	2174	537116715	537115840	0.000000e+00	1221
6	TraesCS4A01G120200	chr3A	79.200	500	91	13	1731	2225	331708081	331708572	3.540000e-88	335
7	TraesCS4A01G120200	chr6D	94.498	1145	61	2	822	1965	17866752	17865609	0.000000e+00	1764
8	TraesCS4A01G120200	chr6D	81.081	333	21	21	463	789	136743223	136743519	6.180000e-56	228
9	TraesCS4A01G120200	chr7A	95.421	1092	44	2	872	1963	66124548	66123463	0.000000e+00	1735
10	TraesCS4A01G120200	chr7A	89.737	419	29	11	60	470	391787472	391787884	7.040000e-145	523
11	TraesCS4A01G120200	chrUn	96.321	761	28	0	1203	1963	257349800	257350560	0.000000e+00	1251
12	TraesCS4A01G120200	chrUn	96.321	761	28	0	1203	1963	332695996	332695236	0.000000e+00	1251
13	TraesCS4A01G120200	chr5A	91.818	880	61	9	1303	2174	119193788	119192912	0.000000e+00	1216
14	TraesCS4A01G120200	chr5A	94.437	791	40	4	1	789	396288122	396287334	0.000000e+00	1214
15	TraesCS4A01G120200	chr5A	95.626	663	27	2	1303	1963	119179933	119179271	0.000000e+00	1062
16	TraesCS4A01G120200	chr5A	93.629	518	28	5	274	789	396270714	396270200	0.000000e+00	769
17	TraesCS4A01G120200	chr1A	95.370	324	15	0	10	333	149253106	149252783	1.180000e-142	516
18	TraesCS4A01G120200	chr1A	93.333	330	22	0	4	333	149244584	149244255	2.570000e-134	488
19	TraesCS4A01G120200	chr1A	83.333	354	27	16	446	789	371408374	371408705	4.640000e-77	298
20	TraesCS4A01G120200	chr6A	89.203	389	32	8	59	446	276778731	276779110	5.560000e-131	477
21	TraesCS4A01G120200	chr6A	93.103	290	20	0	1936	2225	447196945	447197234	2.040000e-115	425
22	TraesCS4A01G120200	chr3D	91.640	311	20	3	853	1163	123152860	123152556	2.040000e-115	425
23	TraesCS4A01G120200	chr3D	81.030	427	75	6	1800	2225	55912665	55912244	3.540000e-88	335
24	TraesCS4A01G120200	chr2D	87.534	369	33	9	796	1163	198616186	198615830	4.420000e-112	414
25	TraesCS4A01G120200	chr2D	86.992	369	35	9	796	1163	198601260	198600904	9.570000e-109	403
26	TraesCS4A01G120200	chr2D	84.713	314	20	7	474	780	435633590	435633298	2.800000e-74	289
27	TraesCS4A01G120200	chr7D	86.944	360	39	7	805	1163	452789513	452789161	4.450000e-107	398
28	TraesCS4A01G120200	chr2A	94.581	203	10	1	246	448	59640837	59641038	1.660000e-81	313
29	TraesCS4A01G120200	chr7B	79.953	424	80	5	1803	2225	704907349	704906930	7.720000e-80	307
30	TraesCS4A01G120200	chr5D	85.135	296	21	3	497	789	208605574	208605849	4.680000e-72	281

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	TraesCS4A01G120200	chr4A	147976697	147978921	2224	False	4109	4109	100.000	1	2225	1	chr4A.!!$F1	2224
1	TraesCS4A01G120200	chr4A	147990133	147991939	1806	False	2868	2868	95.186	135	1961	1	chr4A.!!$F2	1826
2	TraesCS4A01G120200	chr3A	404458974	404460904	1930	True	3031	3031	94.807	1	1963	1	chr3A.!!$R1	1962
3	TraesCS4A01G120200	chr3A	404467860	404469284	1424	True	2204	2204	94.364	1	1454	1	chr3A.!!$R2	1453
4	TraesCS4A01G120200	chr3A	537115840	537116715	875	True	1221	1221	91.932	1303	2174	1	chr3A.!!$R3	871
5	TraesCS4A01G120200	chr6D	17865609	17866752	1143	True	1764	1764	94.498	822	1965	1	chr6D.!!$R1	1143
6	TraesCS4A01G120200	chr7A	66123463	66124548	1085	True	1735	1735	95.421	872	1963	1	chr7A.!!$R1	1091
7	TraesCS4A01G120200	chrUn	257349800	257350560	760	False	1251	1251	96.321	1203	1963	1	chrUn.!!$F1	760
8	TraesCS4A01G120200	chrUn	332695236	332695996	760	True	1251	1251	96.321	1203	1963	1	chrUn.!!$R1	760
9	TraesCS4A01G120200	chr5A	119192912	119193788	876	True	1216	1216	91.818	1303	2174	1	chr5A.!!$R2	871
10	TraesCS4A01G120200	chr5A	396287334	396288122	788	True	1214	1214	94.437	1	789	1	chr5A.!!$R4	788
11	TraesCS4A01G120200	chr5A	119179271	119179933	662	True	1062	1062	95.626	1303	1963	1	chr5A.!!$R1	660
12	TraesCS4A01G120200	chr5A	396270200	396270714	514	True	769	769	93.629	274	789	1	chr5A.!!$R3	515

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
701	707	1.439644	GCAGTTCGCTAGGAGGAGG	59.56	63.158	0.0	0.0	37.77	4.3	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2015	2051	0.90818	CGTAACCAGAACCCTCCCCT	60.908	60.0	0.0	0.0	0.0	4.79	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
202	203	3.354948	TGCATTATGTGAAGCAGGTCT	57.645	42.857	0.00	0.00	32.48	3.85
216	217	4.142038	AGCAGGTCTAACGGAACAAAATT	58.858	39.130	0.00	0.00	33.21	1.82
321	322	7.203910	AGAAGGCTAGTCATTGTAGAAATACG	58.796	38.462	0.00	0.00	0.00	3.06
701	707	1.439644	GCAGTTCGCTAGGAGGAGG	59.560	63.158	0.00	0.00	37.77	4.30
1159	1191	0.608640	CGAACTGGAGGTTGTAGGCT	59.391	55.000	0.00	0.00	38.41	4.58
1205	1237	0.608035	GGTCATCTTCCCAAACGCCA	60.608	55.000	0.00	0.00	0.00	5.69
1237	1269	1.542030	GGCCATGAGTACGAGATCGAT	59.458	52.381	9.58	0.00	43.02	3.59
1245	1277	1.197036	GTACGAGATCGATCATGGCGA	59.803	52.381	26.47	12.66	43.02	5.54
1915	1949	4.072131	ACAACAGTAATTGCGATGACCTT	58.928	39.130	0.00	0.00	32.47	3.50
1977	2013	3.430929	GCGTCACAATTCTCCTCCACTAT	60.431	47.826	0.00	0.00	0.00	2.12
2006	2042	1.407979	TCGTCCCGAGATTTAAGAGGC	59.592	52.381	0.00	0.00	0.00	4.70
2007	2043	1.136305	CGTCCCGAGATTTAAGAGGCA	59.864	52.381	0.00	0.00	0.00	4.75
2008	2044	2.799917	CGTCCCGAGATTTAAGAGGCAG	60.800	54.545	0.00	0.00	0.00	4.85
2009	2045	2.431057	GTCCCGAGATTTAAGAGGCAGA	59.569	50.000	0.00	0.00	0.00	4.26
2010	2046	2.695666	TCCCGAGATTTAAGAGGCAGAG	59.304	50.000	0.00	0.00	0.00	3.35
2011	2047	2.432510	CCCGAGATTTAAGAGGCAGAGT	59.567	50.000	0.00	0.00	0.00	3.24
2014	2050	5.395324	CCCGAGATTTAAGAGGCAGAGTAAA	60.395	44.000	0.00	0.00	0.00	2.01
2015	2051	6.106673	CCGAGATTTAAGAGGCAGAGTAAAA	58.893	40.000	0.00	0.00	0.00	1.52
2024	2061	0.992695	GCAGAGTAAAAGGGGAGGGT	59.007	55.000	0.00	0.00	0.00	4.34
2028	2065	2.913617	AGAGTAAAAGGGGAGGGTTCTG	59.086	50.000	0.00	0.00	0.00	3.02
2039	2076	3.268330	GGAGGGTTCTGGTTACGAAATC	58.732	50.000	0.00	0.00	0.00	2.17
2043	2080	4.161754	AGGGTTCTGGTTACGAAATCCTAG	59.838	45.833	0.00	0.00	29.93	3.02
2044	2081	4.081254	GGGTTCTGGTTACGAAATCCTAGT	60.081	45.833	0.00	0.00	0.00	2.57
2047	2084	5.578005	TCTGGTTACGAAATCCTAGTGAG	57.422	43.478	0.00	0.00	0.00	3.51
2049	2086	5.068234	TGGTTACGAAATCCTAGTGAGTG	57.932	43.478	0.00	0.00	0.00	3.51
2059	2096	2.040012	TCCTAGTGAGTGTTCTCGGTCT	59.960	50.000	0.00	0.00	43.09	3.85
2067	2104	2.067013	GTGTTCTCGGTCTTAGTTGCC	58.933	52.381	0.00	0.00	0.00	4.52
2071	2108	2.811410	TCTCGGTCTTAGTTGCCCTTA	58.189	47.619	0.00	0.00	0.00	2.69
2101	2138	5.661458	AGGTCGATCTATTTCGTTGATGTT	58.339	37.500	0.00	0.00	40.03	2.71
2103	2140	6.594159	AGGTCGATCTATTTCGTTGATGTTTT	59.406	34.615	0.00	0.00	40.03	2.43
2114	2153	8.795786	TTTCGTTGATGTTTTTATTTCTCTGG	57.204	30.769	0.00	0.00	0.00	3.86
2118	2157	7.326063	CGTTGATGTTTTTATTTCTCTGGTTCC	59.674	37.037	0.00	0.00	0.00	3.62
2119	2158	6.908825	TGATGTTTTTATTTCTCTGGTTCCG	58.091	36.000	0.00	0.00	0.00	4.30
2120	2159	6.712998	TGATGTTTTTATTTCTCTGGTTCCGA	59.287	34.615	0.00	0.00	0.00	4.55
2140	2179	2.985957	TCATCATGATGAAGCCGTCA	57.014	45.000	31.46	10.26	44.14	4.35
2151	2190	2.038426	TGAAGCCGTCATCCTTTCTTCA	59.962	45.455	0.00	0.00	37.97	3.02
2168	2208	4.537751	TCTTCAGGATCTCCATCGTACTT	58.462	43.478	0.00	0.00	38.89	2.24
2223	2263	4.964593	ACGGAGTTTAACACATGTTAGGT	58.035	39.130	0.00	0.00	37.78	3.08
2224	2264	6.100404	ACGGAGTTTAACACATGTTAGGTA	57.900	37.500	0.00	0.00	37.78	3.08

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
202	203	6.394025	AACAAGCCTAATTTTGTTCCGTTA	57.606	33.333	1.04	0.00	42.17	3.18
216	217	5.156355	CGAAAAGTAGACGTAACAAGCCTA	58.844	41.667	0.00	0.00	0.00	3.93
255	256	5.681437	GCGATAAGACAAGTCCTAACATGGA	60.681	44.000	0.00	0.00	0.00	3.41
291	292	6.875076	TCTACAATGACTAGCCTTCTAAACC	58.125	40.000	0.00	0.00	0.00	3.27
321	322	3.447944	ACTGTAGTGGGTAGCTAGCTTTC	59.552	47.826	24.88	16.00	0.00	2.62
890	916	4.112341	GCTGCTGCTTCTTGCCGG	62.112	66.667	8.53	0.00	42.00	6.13
1159	1191	3.638484	CTTCATCGCCGACATGTACATA	58.362	45.455	8.32	0.00	0.00	2.29
1205	1237	3.025599	ATGGCCACCATGCTCCCT	61.026	61.111	8.16	0.00	43.39	4.20
1334	1368	1.748879	GCCCTGCGTGCTGGATAAA	60.749	57.895	18.13	0.00	37.23	1.40
1441	1475	1.341913	GGCCCAACCCAAAAACACCT	61.342	55.000	0.00	0.00	0.00	4.00
1915	1949	5.820423	ACAGTAATCTTATGTTAATGGCGCA	59.180	36.000	10.83	0.00	32.96	6.09
2001	2037	2.192263	CTCCCCTTTTACTCTGCCTCT	58.808	52.381	0.00	0.00	0.00	3.69
2005	2041	0.992695	ACCCTCCCCTTTTACTCTGC	59.007	55.000	0.00	0.00	0.00	4.26
2006	2042	2.913617	AGAACCCTCCCCTTTTACTCTG	59.086	50.000	0.00	0.00	0.00	3.35
2007	2043	2.913617	CAGAACCCTCCCCTTTTACTCT	59.086	50.000	0.00	0.00	0.00	3.24
2008	2044	2.026169	CCAGAACCCTCCCCTTTTACTC	60.026	54.545	0.00	0.00	0.00	2.59
2009	2045	1.993301	CCAGAACCCTCCCCTTTTACT	59.007	52.381	0.00	0.00	0.00	2.24
2010	2046	1.709115	ACCAGAACCCTCCCCTTTTAC	59.291	52.381	0.00	0.00	0.00	2.01
2011	2047	2.143231	ACCAGAACCCTCCCCTTTTA	57.857	50.000	0.00	0.00	0.00	1.52
2014	2050	1.369403	GTAACCAGAACCCTCCCCTT	58.631	55.000	0.00	0.00	0.00	3.95
2015	2051	0.908180	CGTAACCAGAACCCTCCCCT	60.908	60.000	0.00	0.00	0.00	4.79
2024	2061	5.479375	ACTCACTAGGATTTCGTAACCAGAA	59.521	40.000	0.00	0.00	0.00	3.02
2028	2065	5.069501	ACACTCACTAGGATTTCGTAACC	57.930	43.478	0.00	0.00	0.00	2.85
2039	2076	2.438411	AGACCGAGAACACTCACTAGG	58.562	52.381	0.00	0.00	35.56	3.02
2043	2080	3.919223	ACTAAGACCGAGAACACTCAC	57.081	47.619	0.00	0.00	0.00	3.51
2044	2081	3.552273	GCAACTAAGACCGAGAACACTCA	60.552	47.826	0.00	0.00	0.00	3.41
2047	2084	2.067013	GGCAACTAAGACCGAGAACAC	58.933	52.381	0.00	0.00	0.00	3.32
2049	2086	1.275573	AGGGCAACTAAGACCGAGAAC	59.724	52.381	0.00	0.00	0.00	3.01
2059	2096	3.773119	ACCTCTTCGATAAGGGCAACTAA	59.227	43.478	15.76	0.00	36.95	2.24
2090	2127	7.936584	ACCAGAGAAATAAAAACATCAACGAA	58.063	30.769	0.00	0.00	0.00	3.85
2091	2128	7.504924	ACCAGAGAAATAAAAACATCAACGA	57.495	32.000	0.00	0.00	0.00	3.85
2093	2130	7.326063	CGGAACCAGAGAAATAAAAACATCAAC	59.674	37.037	0.00	0.00	0.00	3.18
2101	2138	7.109501	TGATGATCGGAACCAGAGAAATAAAA	58.890	34.615	0.00	0.00	0.00	1.52
2103	2140	6.233905	TGATGATCGGAACCAGAGAAATAA	57.766	37.500	0.00	0.00	0.00	1.40
2108	2147	3.299503	TCATGATGATCGGAACCAGAGA	58.700	45.455	0.00	0.00	0.00	3.10
2114	2153	3.188048	GGCTTCATCATGATGATCGGAAC	59.812	47.826	33.23	19.89	46.12	3.62
2118	2157	2.410939	ACGGCTTCATCATGATGATCG	58.589	47.619	33.23	32.39	46.12	3.69
2119	2158	3.396560	TGACGGCTTCATCATGATGATC	58.603	45.455	33.23	26.77	46.12	2.92
2120	2159	3.480505	TGACGGCTTCATCATGATGAT	57.519	42.857	33.23	21.04	46.12	2.45
2146	2185	4.171878	AGTACGATGGAGATCCTGAAGA	57.828	45.455	0.00	0.00	36.82	2.87
2186	2226	4.100279	ACTCCGTCCTTCCTGAATTTTT	57.900	40.909	0.00	0.00	0.00	1.94
2187	2227	3.790089	ACTCCGTCCTTCCTGAATTTT	57.210	42.857	0.00	0.00	0.00	1.82
2188	2228	3.790089	AACTCCGTCCTTCCTGAATTT	57.210	42.857	0.00	0.00	0.00	1.82
2189	2229	3.790089	AAACTCCGTCCTTCCTGAATT	57.210	42.857	0.00	0.00	0.00	2.17
2190	2230	4.041198	TGTTAAACTCCGTCCTTCCTGAAT	59.959	41.667	0.00	0.00	0.00	2.57
2191	2231	3.388676	TGTTAAACTCCGTCCTTCCTGAA	59.611	43.478	0.00	0.00	0.00	3.02
2192	2232	2.967201	TGTTAAACTCCGTCCTTCCTGA	59.033	45.455	0.00	0.00	0.00	3.86
2193	2233	3.064931	GTGTTAAACTCCGTCCTTCCTG	58.935	50.000	0.00	0.00	0.00	3.86
2194	2234	2.701951	TGTGTTAAACTCCGTCCTTCCT	59.298	45.455	0.00	0.00	0.00	3.36
2195	2235	3.116079	TGTGTTAAACTCCGTCCTTCC	57.884	47.619	0.00	0.00	0.00	3.46
2196	2236	4.062991	ACATGTGTTAAACTCCGTCCTTC	58.937	43.478	0.00	0.00	0.00	3.46
2197	2237	4.081322	ACATGTGTTAAACTCCGTCCTT	57.919	40.909	0.00	0.00	0.00	3.36
2198	2238	3.764237	ACATGTGTTAAACTCCGTCCT	57.236	42.857	0.00	0.00	0.00	3.85
2199	2239	4.390909	CCTAACATGTGTTAAACTCCGTCC	59.609	45.833	0.00	0.00	39.70	4.79
2200	2240	4.992951	ACCTAACATGTGTTAAACTCCGTC	59.007	41.667	0.00	0.00	39.70	4.79
2201	2241	4.964593	ACCTAACATGTGTTAAACTCCGT	58.035	39.130	0.00	0.00	39.70	4.69

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.