AutoCloner

Multiple sequence alignment - TraesCS5A01G257800

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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	TraesCS5A01G257800	chr5A	100.000	4187	0	0	1	4187	472921778	472917592	0.000000e+00	7733
1	TraesCS5A01G257800	chr5A	89.116	147	15	1	645	790	634467722	634467576	9.250000e-42	182
2	TraesCS5A01G257800	chr5D	97.994	3390	50	5	812	4187	370453126	370449741	0.000000e+00	5867
3	TraesCS5A01G257800	chr5D	89.655	145	14	1	645	788	482166592	482166736	2.570000e-42	183
4	TraesCS5A01G257800	chr2B	96.183	2279	65	10	931	3193	143824839	143822567	0.000000e+00	3707
5	TraesCS5A01G257800	chr2D	95.908	2273	76	7	931	3193	90818804	90816539	0.000000e+00	3666
6	TraesCS5A01G257800	chr2D	89.189	148	15	1	645	791	222850912	222850765	2.570000e-42	183
7	TraesCS5A01G257800	chr2A	97.134	1919	55	0	1275	3193	90578064	90576146	0.000000e+00	3240
8	TraesCS5A01G257800	chr6D	92.228	772	41	11	20	788	448352824	448353579	0.000000e+00	1075
9	TraesCS5A01G257800	chr6D	94.595	629	31	3	20	645	433920614	433921242	0.000000e+00	970
10	TraesCS5A01G257800	chr6D	88.667	150	16	1	643	791	433921275	433921424	9.250000e-42	182
11	TraesCS5A01G257800	chr4A	94.277	629	32	4	20	645	11100039	11100666	0.000000e+00	959
12	TraesCS5A01G257800	chr1D	94.277	629	32	4	20	645	41306462	41307089	0.000000e+00	959
13	TraesCS5A01G257800	chr1D	89.796	147	14	1	645	790	451134656	451134802	1.990000e-43	187
14	TraesCS5A01G257800	chr3A	94.118	629	34	3	20	645	749477563	749476935	0.000000e+00	953
15	TraesCS5A01G257800	chr3A	89.726	146	14	1	646	790	682238789	682238644	7.150000e-43	185
16	TraesCS5A01G257800	chr1A	94.108	628	35	2	20	645	535306450	535307077	0.000000e+00	953
17	TraesCS5A01G257800	chr7D	93.949	628	35	3	20	645	392825826	392825200	0.000000e+00	946
18	TraesCS5A01G257800	chr7D	93.959	629	32	6	20	645	560251933	560252558	0.000000e+00	946
19	TraesCS5A01G257800	chr7D	91.275	149	12	1	645	792	83851519	83851371	7.100000e-48	202
20	TraesCS5A01G257800	chr7D	90.345	145	13	1	645	788	593680840	593680696	5.530000e-44	189
21	TraesCS5A01G257800	chr6B	93.790	628	36	3	20	645	45531066	45531692	0.000000e+00	941
22	TraesCS5A01G257800	chr6B	95.631	206	8	1	3969	4174	317753525	317753321	3.120000e-86	329
23	TraesCS5A01G257800	chr6B	95.146	206	8	2	3969	4174	455142312	455142515	1.450000e-84	324
24	TraesCS5A01G257800	chr3B	94.366	213	9	3	3964	4174	696947882	696948093	1.450000e-84	324
25	TraesCS5A01G257800	chr7A	89.333	150	15	1	645	793	682268385	682268236	1.990000e-43	187

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	TraesCS5A01G257800	chr5A	472917592	472921778	4186	True	7733	7733	100.000	1	4187	1	chr5A.!!$R1	4186
1	TraesCS5A01G257800	chr5D	370449741	370453126	3385	True	5867	5867	97.994	812	4187	1	chr5D.!!$R1	3375
2	TraesCS5A01G257800	chr2B	143822567	143824839	2272	True	3707	3707	96.183	931	3193	1	chr2B.!!$R1	2262
3	TraesCS5A01G257800	chr2D	90816539	90818804	2265	True	3666	3666	95.908	931	3193	1	chr2D.!!$R1	2262
4	TraesCS5A01G257800	chr2A	90576146	90578064	1918	True	3240	3240	97.134	1275	3193	1	chr2A.!!$R1	1918
5	TraesCS5A01G257800	chr6D	448352824	448353579	755	False	1075	1075	92.228	20	788	1	chr6D.!!$F1	768
6	TraesCS5A01G257800	chr6D	433920614	433921424	810	False	576	970	91.631	20	791	2	chr6D.!!$F2	771
7	TraesCS5A01G257800	chr4A	11100039	11100666	627	False	959	959	94.277	20	645	1	chr4A.!!$F1	625
8	TraesCS5A01G257800	chr1D	41306462	41307089	627	False	959	959	94.277	20	645	1	chr1D.!!$F1	625
9	TraesCS5A01G257800	chr3A	749476935	749477563	628	True	953	953	94.118	20	645	1	chr3A.!!$R2	625
10	TraesCS5A01G257800	chr1A	535306450	535307077	627	False	953	953	94.108	20	645	1	chr1A.!!$F1	625
11	TraesCS5A01G257800	chr7D	392825200	392825826	626	True	946	946	93.949	20	645	1	chr7D.!!$R2	625
12	TraesCS5A01G257800	chr7D	560251933	560252558	625	False	946	946	93.959	20	645	1	chr7D.!!$F1	625
13	TraesCS5A01G257800	chr6B	45531066	45531692	626	False	941	941	93.790	20	645	1	chr6B.!!$F1	625

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	Hairpin	End Stability	Orientation
797	855	0.036294	AAGTTGCTCTTAGGTCGGCC	60.036	55.0	0.00	34.23	6.13	F
806	864	0.687098	TTAGGTCGGCCCGTTGGATA	60.687	55.0	0.08	38.74	2.59	F
1982	2064	0.712979	AGAGTGTGGGAGGAGATGGA	59.287	55.0	0.00	0.00	3.41	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1982	2064	0.252421	TGGCTCCACACCATCTCTCT	60.252	55.000	0.00	30.29	3.10	R
2205	2287	0.950555	ATGTTTTGAGCTCAGCGCGA	60.951	50.000	17.43	45.59	5.87	R
3694	3777	1.346068	ACTGGTGCCTTCTCTCACTTC	59.654	52.381	0.00	33.91	3.01	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
112	113	3.807538	GAGTCGGCGGCGTACTCA	61.808	66.667	35.44	18.70	39.54	3.41
117	118	4.752879	GGCGGCGTACTCAGGCAA	62.753	66.667	9.37	0.00	37.28	4.52
472	477	1.072331	GTGAGGAAGCAAAGGGAGTGA	59.928	52.381	0.00	0.00	0.00	3.41
561	568	3.984749	TGCACTGGCTGACGCGTA	61.985	61.111	13.97	0.00	41.91	4.42
621	628	3.948719	GGTTGGGTGTCCGCCAGA	61.949	66.667	0.00	0.00	35.24	3.86
633	640	3.838271	GCCAGATGAGGACGCGGA	61.838	66.667	12.47	0.00	0.00	5.54
635	642	2.121538	CCAGATGAGGACGCGGAGA	61.122	63.158	12.47	0.00	0.00	3.71
648	655	2.125106	GGAGAACGGCGAGGCAAT	60.125	61.111	16.62	0.00	0.00	3.56
649	656	1.745489	GGAGAACGGCGAGGCAATT	60.745	57.895	16.62	0.00	0.00	2.32
650	657	1.305930	GGAGAACGGCGAGGCAATTT	61.306	55.000	16.62	0.00	0.00	1.82
651	658	0.521735	GAGAACGGCGAGGCAATTTT	59.478	50.000	16.62	0.00	0.00	1.82
652	659	1.735571	GAGAACGGCGAGGCAATTTTA	59.264	47.619	16.62	0.00	0.00	1.52
653	660	1.737793	AGAACGGCGAGGCAATTTTAG	59.262	47.619	16.62	0.00	0.00	1.85
654	661	0.808755	AACGGCGAGGCAATTTTAGG	59.191	50.000	16.62	0.00	0.00	2.69
655	662	1.064134	CGGCGAGGCAATTTTAGGC	59.936	57.895	0.00	0.00	0.00	3.93
664	671	2.935849	GGCAATTTTAGGCCGAAAATGG	59.064	45.455	29.88	27.92	40.93	3.16
665	672	2.935849	GCAATTTTAGGCCGAAAATGGG	59.064	45.455	29.88	25.19	38.67	4.00
666	673	3.618752	GCAATTTTAGGCCGAAAATGGGT	60.619	43.478	29.88	16.37	38.67	4.51
707	764	2.139917	CACGATTTGAGTTTGGGTCGA	58.860	47.619	0.00	0.00	33.68	4.20
729	786	1.281566	CGTTGGGCCGTCATTTTTGC	61.282	55.000	0.00	0.00	0.00	3.68
736	793	2.258286	GTCATTTTTGCCCGCGCT	59.742	55.556	5.56	0.00	35.36	5.92
747	804	3.283684	CCGCGCTGACCCAAACAA	61.284	61.111	5.56	0.00	0.00	2.83
791	849	2.424956	GCCCATTGAAGTTGCTCTTAGG	59.575	50.000	0.00	0.00	36.40	2.69
792	850	3.690460	CCCATTGAAGTTGCTCTTAGGT	58.310	45.455	0.00	0.00	36.40	3.08
793	851	3.691609	CCCATTGAAGTTGCTCTTAGGTC	59.308	47.826	0.00	0.00	36.40	3.85
794	852	3.372206	CCATTGAAGTTGCTCTTAGGTCG	59.628	47.826	0.00	0.00	36.40	4.79
795	853	2.743636	TGAAGTTGCTCTTAGGTCGG	57.256	50.000	0.00	0.00	36.40	4.79
796	854	1.337823	TGAAGTTGCTCTTAGGTCGGC	60.338	52.381	0.00	0.00	36.40	5.54
797	855	0.036294	AAGTTGCTCTTAGGTCGGCC	60.036	55.000	0.00	0.00	34.23	6.13
798	856	1.449778	GTTGCTCTTAGGTCGGCCC	60.450	63.158	0.08	0.00	34.57	5.80
799	857	3.014085	TTGCTCTTAGGTCGGCCCG	62.014	63.158	0.08	0.00	38.74	6.13
800	858	3.459063	GCTCTTAGGTCGGCCCGT	61.459	66.667	0.08	0.00	38.74	5.28
801	859	3.015312	GCTCTTAGGTCGGCCCGTT	62.015	63.158	0.08	0.00	38.74	4.44
802	860	1.153628	CTCTTAGGTCGGCCCGTTG	60.154	63.158	0.08	0.00	38.74	4.10
803	861	2.125269	CTTAGGTCGGCCCGTTGG	60.125	66.667	0.08	0.00	38.74	3.77
804	862	2.604079	TTAGGTCGGCCCGTTGGA	60.604	61.111	0.08	0.00	38.74	3.53
805	863	1.968050	CTTAGGTCGGCCCGTTGGAT	61.968	60.000	0.08	0.00	38.74	3.41
806	864	0.687098	TTAGGTCGGCCCGTTGGATA	60.687	55.000	0.08	0.00	38.74	2.59
807	865	1.394266	TAGGTCGGCCCGTTGGATAC	61.394	60.000	0.08	0.00	38.74	2.24
808	866	2.202974	GTCGGCCCGTTGGATACC	60.203	66.667	1.63	0.00	0.00	2.73
809	867	2.364579	TCGGCCCGTTGGATACCT	60.365	61.111	1.63	0.00	0.00	3.08
810	868	2.108362	CGGCCCGTTGGATACCTC	59.892	66.667	0.00	0.00	0.00	3.85
869	927	8.187913	TCCAAATGTTTTCCAATCATGAAGTA	57.812	30.769	0.00	0.00	0.00	2.24
877	935	0.814010	AATCATGAAGTACCGCCGGC	60.814	55.000	19.07	19.07	0.00	6.13
896	954	3.134127	GTTGGATGTGCCGGAGCC	61.134	66.667	5.05	0.00	40.66	4.70
936	998	1.524849	GCTCGCATTTCTCCCCTCC	60.525	63.158	0.00	0.00	0.00	4.30
1254	1336	3.628280	GACTCCGTCGCACTCCACC	62.628	68.421	0.00	0.00	0.00	4.61
1773	1855	2.119801	AGCTGTTCGATGAAATGGCT	57.880	45.000	0.00	0.00	0.00	4.75
1891	1973	1.003476	ATGCGTGATGAGGTGTGCA	60.003	52.632	0.00	0.00	36.69	4.57
1982	2064	0.712979	AGAGTGTGGGAGGAGATGGA	59.287	55.000	0.00	0.00	0.00	3.41
2087	2169	5.185635	CAGCTAAATTGTTTGAGGGGATGAA	59.814	40.000	0.00	0.00	0.00	2.57
2108	2190	2.503765	AGAAAAAGGGGTTGTTGGTTGG	59.496	45.455	0.00	0.00	0.00	3.77
2205	2287	1.350351	GAGATGGTGGATGCTGGCTAT	59.650	52.381	0.00	0.00	0.00	2.97
2214	2296	3.034923	GCTGGCTATCGCGCTGAG	61.035	66.667	5.56	0.12	36.88	3.35
2422	2504	3.914579	GAGCTGAGCTTGCCTGCCA	62.915	63.158	9.00	0.00	39.88	4.92
2526	2608	3.255642	TGAGACAAAAAGGGTATTGCAGC	59.744	43.478	0.00	0.00	0.00	5.25
2740	2822	4.473196	TGAAGGCTGAATGGATACCAAGTA	59.527	41.667	0.00	0.00	36.95	2.24
2886	2968	2.778299	ACTGTTATTGAAGCTTGCCGA	58.222	42.857	2.10	0.00	0.00	5.54
3180	3262	7.816031	TCAAAATTGAAATGGAGAAGCAGAATC	59.184	33.333	0.00	0.00	33.55	2.52
3567	3649	5.590259	AGTGTGTCTTTTACAAGCATCAGTT	59.410	36.000	0.00	0.00	40.63	3.16
3694	3777	2.097466	GGGCAAATGTGGTATCGTTGAG	59.903	50.000	0.00	0.00	0.00	3.02
3716	3799	2.609747	AGTGAGAGAAGGCACCAGTAA	58.390	47.619	0.00	0.00	35.67	2.24
3933	4016	4.402851	GTGAATCCACAGCCTGCA	57.597	55.556	0.00	0.00	42.72	4.41
4030	4113	7.387673	TGTTGTACTATGGAATGTTCAGACTTG	59.612	37.037	0.00	0.00	0.00	3.16
4074	4157	7.488205	AGAATACCACCATATATCCTGTAGGT	58.512	38.462	0.00	0.00	36.34	3.08

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
267	270	1.003718	GGTGGCACTGGGAGTACAC	60.004	63.158	18.45	0.00	35.69	2.90
343	346	3.795924	CTCCCCCTCCCCCTCCAT	61.796	72.222	0.00	0.00	0.00	3.41
472	477	2.287117	TCCACATCTGGCCCCCAT	60.287	61.111	0.00	0.00	37.49	4.00
599	606	2.345991	CGGACACCCAACCGTCAT	59.654	61.111	0.00	0.00	43.53	3.06
613	620	3.838271	GCGTCCTCATCTGGCGGA	61.838	66.667	0.00	0.00	0.00	5.54
621	628	2.490217	CGTTCTCCGCGTCCTCAT	59.510	61.111	4.92	0.00	0.00	2.90
633	640	1.737793	CTAAAATTGCCTCGCCGTTCT	59.262	47.619	0.00	0.00	0.00	3.01
635	642	0.808755	CCTAAAATTGCCTCGCCGTT	59.191	50.000	0.00	0.00	0.00	4.44
645	652	4.180817	GACCCATTTTCGGCCTAAAATTG	58.819	43.478	21.87	18.60	37.03	2.32
646	653	3.119280	CGACCCATTTTCGGCCTAAAATT	60.119	43.478	21.87	10.69	37.03	1.82
648	655	1.813786	CGACCCATTTTCGGCCTAAAA	59.186	47.619	16.67	16.67	32.66	1.52
649	656	1.455248	CGACCCATTTTCGGCCTAAA	58.545	50.000	0.00	0.00	32.66	1.85
650	657	3.162448	CGACCCATTTTCGGCCTAA	57.838	52.632	0.00	0.00	32.66	2.69
651	658	4.946038	CGACCCATTTTCGGCCTA	57.054	55.556	0.00	0.00	32.66	3.93
656	663	2.478746	CACGCCGACCCATTTTCG	59.521	61.111	0.00	0.00	36.20	3.46
657	664	1.673009	TCCACGCCGACCCATTTTC	60.673	57.895	0.00	0.00	0.00	2.29
658	665	1.969589	GTCCACGCCGACCCATTTT	60.970	57.895	0.00	0.00	0.00	1.82
659	666	2.359478	GTCCACGCCGACCCATTT	60.359	61.111	0.00	0.00	0.00	2.32
660	667	4.752879	CGTCCACGCCGACCCATT	62.753	66.667	0.00	0.00	0.00	3.16
720	777	2.257980	CAGCGCGGGCAAAAATGA	59.742	55.556	27.20	0.00	43.41	2.57
723	780	3.972276	GGTCAGCGCGGGCAAAAA	61.972	61.111	27.20	5.62	43.41	1.94
736	793	1.096416	GTCCGTGTTTGTTTGGGTCA	58.904	50.000	0.00	0.00	0.00	4.02
746	803	0.863144	CATTTCGTCCGTCCGTGTTT	59.137	50.000	0.00	0.00	0.00	2.83
747	804	0.947180	CCATTTCGTCCGTCCGTGTT	60.947	55.000	0.00	0.00	0.00	3.32
778	836	0.036294	GGCCGACCTAAGAGCAACTT	60.036	55.000	0.00	2.10	42.04	2.66
791	849	2.202974	GGTATCCAACGGGCCGAC	60.203	66.667	35.78	19.06	0.00	4.79
792	850	2.364579	AGGTATCCAACGGGCCGA	60.365	61.111	35.78	10.94	0.00	5.54
793	851	2.108362	GAGGTATCCAACGGGCCG	59.892	66.667	27.06	27.06	0.00	6.13
794	852	1.146263	CAGAGGTATCCAACGGGCC	59.854	63.158	0.00	0.00	0.00	5.80
795	853	0.105039	CTCAGAGGTATCCAACGGGC	59.895	60.000	0.00	0.00	0.00	6.13
796	854	0.105039	GCTCAGAGGTATCCAACGGG	59.895	60.000	0.00	0.00	0.00	5.28
797	855	0.105039	GGCTCAGAGGTATCCAACGG	59.895	60.000	0.00	0.00	0.00	4.44
798	856	0.824109	TGGCTCAGAGGTATCCAACG	59.176	55.000	0.00	0.00	0.00	4.10
799	857	1.474143	GCTGGCTCAGAGGTATCCAAC	60.474	57.143	0.00	0.00	32.44	3.77
800	858	0.833287	GCTGGCTCAGAGGTATCCAA	59.167	55.000	0.00	0.00	32.44	3.53
801	859	1.395045	CGCTGGCTCAGAGGTATCCA	61.395	60.000	0.00	0.00	32.44	3.41
802	860	1.365633	CGCTGGCTCAGAGGTATCC	59.634	63.158	0.00	0.00	32.44	2.59
803	861	0.249238	CACGCTGGCTCAGAGGTATC	60.249	60.000	0.00	0.00	35.65	2.24
804	862	1.680522	CCACGCTGGCTCAGAGGTAT	61.681	60.000	0.00	0.00	35.65	2.73
805	863	2.351244	CCACGCTGGCTCAGAGGTA	61.351	63.158	0.00	0.00	35.65	3.08
806	864	3.699894	CCACGCTGGCTCAGAGGT	61.700	66.667	0.00	1.19	35.65	3.85
835	893	1.535204	AAACATTTGGAGCCGGCAGG	61.535	55.000	31.54	12.02	41.62	4.85
850	908	4.083003	GCGGTACTTCATGATTGGAAAACA	60.083	41.667	0.00	0.00	31.51	2.83
984	1057	0.678950	TCATTCTCAGTGTGCGGTGA	59.321	50.000	0.00	0.00	0.00	4.02
1248	1330	1.621672	GGGAAGAGGCAGAGGTGGAG	61.622	65.000	0.00	0.00	0.00	3.86
1254	1336	4.521062	CGGCGGGAAGAGGCAGAG	62.521	72.222	0.00	0.00	0.00	3.35
1891	1973	2.030490	TACACAAACACGTCCGGCCT	62.030	55.000	0.00	0.00	0.00	5.19
1982	2064	0.252421	TGGCTCCACACCATCTCTCT	60.252	55.000	0.00	0.00	30.29	3.10
2087	2169	2.503765	CCAACCAACAACCCCTTTTTCT	59.496	45.455	0.00	0.00	0.00	2.52
2108	2190	2.279252	ACGCATACACGATCCGGC	60.279	61.111	0.00	0.00	36.70	6.13
2205	2287	0.950555	ATGTTTTGAGCTCAGCGCGA	60.951	50.000	17.43	0.00	45.59	5.87
2214	2296	7.485913	CCAATGAGTATGTTGTATGTTTTGAGC	59.514	37.037	0.00	0.00	0.00	4.26
2422	2504	9.171877	CCTCAAGAAGTCTGCTAAAAATTCTAT	57.828	33.333	0.00	0.00	0.00	1.98
2740	2822	2.474816	GAGCGAACGATAGGCTGAAAT	58.525	47.619	0.00	0.00	43.77	2.17
2886	2968	1.985895	ACCTTCTCCGGGTCTTTTGAT	59.014	47.619	0.00	0.00	30.15	2.57
3180	3262	8.539770	AGCAGATTGTACCTATATTTCAATCG	57.460	34.615	0.00	0.00	44.82	3.34
3567	3649	3.830744	ACTGCCAGTAAGTGTGTGTAA	57.169	42.857	0.00	0.00	0.00	2.41
3694	3777	1.346068	ACTGGTGCCTTCTCTCACTTC	59.654	52.381	0.00	0.00	33.91	3.01
3851	3934	6.379417	TCGCTCCTGTGATATGAATATGATCT	59.621	38.462	0.00	0.00	0.00	2.75
3857	3940	3.056536	GGCTCGCTCCTGTGATATGAATA	60.057	47.826	0.00	0.00	31.73	1.75
4001	4084	7.766278	GTCTGAACATTCCATAGTACAACAGAT	59.234	37.037	0.00	0.00	33.35	2.90
4030	4113	9.899226	GGTATTCTAAACATATTTCAAGGCATC	57.101	33.333	0.00	0.00	0.00	3.91
4074	4157	8.695456	AGCTTCTTGGTTTTCATTTCTTCTAAA	58.305	29.630	0.00	0.00	0.00	1.85

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.