AutoCloner

Multiple sequence alignment - TraesCS6D01G370700

Loading Multiple Alignment...

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	TraesCS6D01G370700	chr6D	100.000	2849	0	0	1	2849	456517687	456520535	0.000000e+00	5262.0
1	TraesCS6D01G370700	chr6B	89.372	2070	103	36	206	2238	694249674	694251663	0.000000e+00	2495.0
2	TraesCS6D01G370700	chr6A	91.366	1691	69	33	582	2252	603242433	603244066	0.000000e+00	2242.0
3	TraesCS6D01G370700	chr6A	91.887	604	32	9	1	596	603240709	603241303	0.000000e+00	828.0
4	TraesCS6D01G370700	chr2D	97.246	581	15	1	2270	2849	572662450	572663030	0.000000e+00	983.0
5	TraesCS6D01G370700	chr2D	96.913	583	16	2	2268	2849	522239777	522240358	0.000000e+00	976.0
6	TraesCS6D01G370700	chr7D	96.558	581	18	2	2270	2849	460841782	460841203	0.000000e+00	961.0
7	TraesCS6D01G370700	chr3D	96.386	581	19	2	2270	2849	456243619	456243040	0.000000e+00	955.0
8	TraesCS6D01G370700	chr3D	96.213	581	20	2	2270	2849	364683032	364683611	0.000000e+00	950.0
9	TraesCS6D01G370700	chr3D	96.048	582	21	2	2269	2849	159556946	159557526	0.000000e+00	946.0
10	TraesCS6D01G370700	chr3D	96.200	579	20	2	2272	2849	250981280	250981857	0.000000e+00	946.0
11	TraesCS6D01G370700	chr3D	96.048	582	21	2	2269	2849	456251711	456251131	0.000000e+00	946.0
12	TraesCS6D01G370700	chr4D	96.194	578	22	0	2270	2847	104800701	104800124	0.000000e+00	946.0
13	TraesCS6D01G370700	chr5D	88.312	77	8	1	242	317	487979551	487979475	1.090000e-14	91.6
14	TraesCS6D01G370700	chr3B	85.714	84	6	5	226	306	452726435	452726515	1.820000e-12	84.2

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	TraesCS6D01G370700	chr6D	456517687	456520535	2848	False	5262	5262	100.0000	1	2849	1	chr6D.!!$F1	2848
1	TraesCS6D01G370700	chr6B	694249674	694251663	1989	False	2495	2495	89.3720	206	2238	1	chr6B.!!$F1	2032
2	TraesCS6D01G370700	chr6A	603240709	603244066	3357	False	1535	2242	91.6265	1	2252	2	chr6A.!!$F1	2251
3	TraesCS6D01G370700	chr2D	572662450	572663030	580	False	983	983	97.2460	2270	2849	1	chr2D.!!$F2	579
4	TraesCS6D01G370700	chr2D	522239777	522240358	581	False	976	976	96.9130	2268	2849	1	chr2D.!!$F1	581
5	TraesCS6D01G370700	chr7D	460841203	460841782	579	True	961	961	96.5580	2270	2849	1	chr7D.!!$R1	579
6	TraesCS6D01G370700	chr3D	456243040	456243619	579	True	955	955	96.3860	2270	2849	1	chr3D.!!$R1	579
7	TraesCS6D01G370700	chr3D	364683032	364683611	579	False	950	950	96.2130	2270	2849	1	chr3D.!!$F3	579
8	TraesCS6D01G370700	chr3D	159556946	159557526	580	False	946	946	96.0480	2269	2849	1	chr3D.!!$F1	580
9	TraesCS6D01G370700	chr3D	250981280	250981857	577	False	946	946	96.2000	2272	2849	1	chr3D.!!$F2	577
10	TraesCS6D01G370700	chr3D	456251131	456251711	580	True	946	946	96.0480	2269	2849	1	chr3D.!!$R2	580
11	TraesCS6D01G370700	chr4D	104800124	104800701	577	True	946	946	96.1940	2270	2847	1	chr4D.!!$R1	577

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
80	81	0.036105	TCAAGAGTGGCGCACATGAT	60.036	50.0	10.83	0.0	36.74	2.45	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1889	3049	1.832608	ATCCTGCCAGCCATGCATG	60.833	57.895	20.19	20.19	38.22	4.06	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
72	73	2.146342	AGTTGTTGATCAAGAGTGGCG	58.854	47.619	8.80	0.00	36.66	5.69
76	77	0.250252	TTGATCAAGAGTGGCGCACA	60.250	50.000	10.83	1.22	36.74	4.57
80	81	0.036105	TCAAGAGTGGCGCACATGAT	60.036	50.000	10.83	0.00	36.74	2.45
110	111	3.255725	CATGGTCCAATTGTTGCATCAC	58.744	45.455	4.43	0.00	0.00	3.06
115	116	4.232221	GTCCAATTGTTGCATCACAAGAG	58.768	43.478	9.64	4.90	40.01	2.85
116	117	3.890756	TCCAATTGTTGCATCACAAGAGT	59.109	39.130	9.64	0.00	40.01	3.24
119	120	0.953727	TGTTGCATCACAAGAGTGGC	59.046	50.000	0.00	0.00	45.91	5.01
167	168	2.119495	GTCCTTGATAGAGGCAGGGAA	58.881	52.381	0.00	0.00	42.25	3.97
269	270	7.817418	TGCTTTGAGATTGGTACTACTTTTT	57.183	32.000	0.00	0.00	0.00	1.94
273	274	9.280174	CTTTGAGATTGGTACTACTTTTTGGTA	57.720	33.333	0.00	0.00	0.00	3.25
322	323	0.464013	TTTTGTTCGGGTTCCTCGCA	60.464	50.000	0.00	0.00	0.00	5.10
323	324	0.464013	TTTGTTCGGGTTCCTCGCAA	60.464	50.000	0.00	0.00	0.00	4.85
324	325	0.882927	TTGTTCGGGTTCCTCGCAAG	60.883	55.000	0.00	0.00	0.00	4.01
325	326	2.358247	TTCGGGTTCCTCGCAAGC	60.358	61.111	0.00	0.00	37.18	4.01
352	354	6.862711	TTGTTTTGTTCGGGTTTTTCTTTT	57.137	29.167	0.00	0.00	0.00	2.27
362	364	7.114866	TCGGGTTTTTCTTTTCTGGTTTTAT	57.885	32.000	0.00	0.00	0.00	1.40
524	533	6.342111	TCAAGACAAAATTTAACAACCACCC	58.658	36.000	0.00	0.00	0.00	4.61
529	538	7.665974	AGACAAAATTTAACAACCACCCAAAAA	59.334	29.630	0.00	0.00	0.00	1.94
555	564	9.454859	AAATAGTAGAATCTTAAAGCAAGCACT	57.545	29.630	0.00	0.00	33.94	4.40
654	1807	1.730064	CCACCAAATAGACGAACGTGG	59.270	52.381	4.19	1.30	33.91	4.94
674	1827	2.036604	GGAACGGGCAATCCAAGAAAAA	59.963	45.455	0.00	0.00	35.71	1.94
1241	2398	4.452733	GGACGCCGGGTTCCTCAG	62.453	72.222	2.18	0.00	0.00	3.35
1530	2690	2.608059	TACCACATGCCGGGGTCA	60.608	61.111	2.18	0.00	36.14	4.02
1629	2789	2.851071	CGAGGCGAGGGATCTGGAC	61.851	68.421	0.00	0.00	0.00	4.02
1944	3104	1.895131	AGGTCGATTGCTTGCCAAATT	59.105	42.857	0.00	0.00	36.92	1.82
2018	3178	2.143008	TCACGTCGTGTAGCACAAAT	57.857	45.000	23.82	0.00	34.79	2.32
2019	3179	3.285816	TCACGTCGTGTAGCACAAATA	57.714	42.857	23.82	0.00	34.79	1.40
2020	3180	3.239254	TCACGTCGTGTAGCACAAATAG	58.761	45.455	23.82	0.00	34.79	1.73
2021	3181	1.990563	ACGTCGTGTAGCACAAATAGC	59.009	47.619	0.00	0.00	33.40	2.97
2022	3182	1.989864	CGTCGTGTAGCACAAATAGCA	59.010	47.619	0.14	0.00	33.40	3.49
2023	3183	2.410392	CGTCGTGTAGCACAAATAGCAA	59.590	45.455	0.14	0.00	33.40	3.91
2024	3184	3.062099	CGTCGTGTAGCACAAATAGCAAT	59.938	43.478	0.14	0.00	33.40	3.56
2066	3226	5.747951	ATTTTAGACCCTACGACTACTCG	57.252	43.478	0.00	0.00	46.06	4.18
2080	3240	7.564044	ACGACTACTCGAAATTTACTTTCAG	57.436	36.000	0.00	0.00	42.91	3.02
2084	3244	5.613358	ACTCGAAATTTACTTTCAGCCAG	57.387	39.130	0.00	0.00	42.91	4.85
2086	3246	5.179555	ACTCGAAATTTACTTTCAGCCAGAC	59.820	40.000	0.00	0.00	42.91	3.51
2089	3258	5.049405	CGAAATTTACTTTCAGCCAGACACT	60.049	40.000	0.00	0.00	42.91	3.55
2094	3263	0.690762	TTTCAGCCAGACACTACCCC	59.309	55.000	0.00	0.00	0.00	4.95
2096	3265	1.613630	CAGCCAGACACTACCCCCT	60.614	63.158	0.00	0.00	0.00	4.79
2099	3268	1.198759	GCCAGACACTACCCCCTTCA	61.199	60.000	0.00	0.00	0.00	3.02
2100	3269	1.584724	CCAGACACTACCCCCTTCAT	58.415	55.000	0.00	0.00	0.00	2.57
2111	3280	2.301346	CCCCCTTCATTTCTCCGAATG	58.699	52.381	0.00	0.00	38.16	2.67
2147	3321	6.534934	GCAAACGTACTTAAGAGAAAGATGG	58.465	40.000	10.09	0.00	0.00	3.51
2164	3338	0.892755	TGGTCGTTGTAGGTAGGCTG	59.107	55.000	0.00	0.00	0.00	4.85
2165	3339	1.180029	GGTCGTTGTAGGTAGGCTGA	58.820	55.000	0.00	0.00	0.00	4.26
2172	3346	4.863131	CGTTGTAGGTAGGCTGAAACTTAG	59.137	45.833	0.00	0.00	0.00	2.18
2174	3348	6.461640	GTTGTAGGTAGGCTGAAACTTAGAA	58.538	40.000	0.00	0.00	0.00	2.10
2175	3349	6.282199	TGTAGGTAGGCTGAAACTTAGAAG	57.718	41.667	0.00	0.00	0.00	2.85
2176	3350	4.209307	AGGTAGGCTGAAACTTAGAAGC	57.791	45.455	0.00	0.00	34.86	3.86
2177	3351	3.841255	AGGTAGGCTGAAACTTAGAAGCT	59.159	43.478	0.00	0.00	35.93	3.74
2178	3352	5.024118	AGGTAGGCTGAAACTTAGAAGCTA	58.976	41.667	0.00	0.00	35.93	3.32
2179	3353	5.128008	AGGTAGGCTGAAACTTAGAAGCTAG	59.872	44.000	0.00	0.00	35.93	3.42
2247	3430	5.065859	CACGAAATTATAGTCATTGCACCCA	59.934	40.000	0.00	0.00	0.00	4.51
2252	3435	7.902920	AATTATAGTCATTGCACCCATTTCT	57.097	32.000	0.00	0.00	0.00	2.52
2253	3436	6.942532	TTATAGTCATTGCACCCATTTCTC	57.057	37.500	0.00	0.00	0.00	2.87
2254	3437	2.086869	AGTCATTGCACCCATTTCTCG	58.913	47.619	0.00	0.00	0.00	4.04
2255	3438	0.810648	TCATTGCACCCATTTCTCGC	59.189	50.000	0.00	0.00	0.00	5.03
2256	3439	0.813184	CATTGCACCCATTTCTCGCT	59.187	50.000	0.00	0.00	0.00	4.93
2257	3440	1.098050	ATTGCACCCATTTCTCGCTC	58.902	50.000	0.00	0.00	0.00	5.03
2258	3441	0.250684	TTGCACCCATTTCTCGCTCA	60.251	50.000	0.00	0.00	0.00	4.26
2259	3442	0.035152	TGCACCCATTTCTCGCTCAT	60.035	50.000	0.00	0.00	0.00	2.90
2260	3443	0.659957	GCACCCATTTCTCGCTCATC	59.340	55.000	0.00	0.00	0.00	2.92
2261	3444	1.745141	GCACCCATTTCTCGCTCATCT	60.745	52.381	0.00	0.00	0.00	2.90
2262	3445	1.938577	CACCCATTTCTCGCTCATCTG	59.061	52.381	0.00	0.00	0.00	2.90
2263	3446	1.556911	ACCCATTTCTCGCTCATCTGT	59.443	47.619	0.00	0.00	0.00	3.41
2264	3447	2.208431	CCCATTTCTCGCTCATCTGTC	58.792	52.381	0.00	0.00	0.00	3.51
2265	3448	2.158986	CCCATTTCTCGCTCATCTGTCT	60.159	50.000	0.00	0.00	0.00	3.41
2266	3449	3.529533	CCATTTCTCGCTCATCTGTCTT	58.470	45.455	0.00	0.00	0.00	3.01
2313	3496	4.293648	CCCACGTGTCGAGGCACA	62.294	66.667	15.65	0.00	39.19	4.57
2514	3697	6.929049	CCAAAAGAAAAGAAGATAACCCAACC	59.071	38.462	0.00	0.00	0.00	3.77
2605	3788	1.228337	TCCTCGTCGAACTCCCACA	60.228	57.895	0.00	0.00	0.00	4.17
2645	3828	1.214325	CACTGGTATCGTCGGCACA	59.786	57.895	0.00	0.00	0.00	4.57
2721	3904	5.282510	CCGCGAGATCAAGACTATTTAAGT	58.717	41.667	8.23	0.00	42.80	2.24
2753	3936	2.361085	AAGGGGTAATGAGGTGGAGT	57.639	50.000	0.00	0.00	0.00	3.85

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
72	73	2.286595	CCATGCTCAACGTATCATGTGC	60.287	50.000	14.07	10.31	35.72	4.57
76	77	2.170397	TGGACCATGCTCAACGTATCAT	59.830	45.455	0.00	0.00	0.00	2.45
80	81	2.746904	CAATTGGACCATGCTCAACGTA	59.253	45.455	0.00	0.00	0.00	3.57
110	111	0.656259	CATCTCATGCGCCACTCTTG	59.344	55.000	4.18	0.00	0.00	3.02
167	168	7.955918	ACAATTTAGATCTTGCTGGTTTTCTT	58.044	30.769	0.00	0.00	0.00	2.52
529	538	9.454859	AGTGCTTGCTTTAAGATTCTACTATTT	57.545	29.630	0.00	0.00	38.76	1.40
533	542	8.887717	CATTAGTGCTTGCTTTAAGATTCTACT	58.112	33.333	0.00	0.00	38.76	2.57
534	543	8.125448	CCATTAGTGCTTGCTTTAAGATTCTAC	58.875	37.037	0.00	0.00	38.76	2.59
535	544	7.829211	ACCATTAGTGCTTGCTTTAAGATTCTA	59.171	33.333	0.00	0.00	38.76	2.10
537	546	6.749118	CACCATTAGTGCTTGCTTTAAGATTC	59.251	38.462	0.00	0.00	40.28	2.52
538	547	6.350445	CCACCATTAGTGCTTGCTTTAAGATT	60.350	38.462	0.00	0.00	45.83	2.40
539	548	5.126061	CCACCATTAGTGCTTGCTTTAAGAT	59.874	40.000	0.00	0.00	45.83	2.40
540	549	4.458989	CCACCATTAGTGCTTGCTTTAAGA	59.541	41.667	0.00	0.00	45.83	2.10
541	550	4.458989	TCCACCATTAGTGCTTGCTTTAAG	59.541	41.667	0.00	0.00	45.83	1.85
542	551	4.402829	TCCACCATTAGTGCTTGCTTTAA	58.597	39.130	0.00	0.00	45.83	1.52
551	560	2.689471	TGCATGAATCCACCATTAGTGC	59.311	45.455	0.00	0.00	45.83	4.40
555	564	2.997980	ACGTGCATGAATCCACCATTA	58.002	42.857	14.17	0.00	0.00	1.90
654	1807	3.378911	TTTTTCTTGGATTGCCCGTTC	57.621	42.857	0.00	0.00	37.93	3.95
774	1928	1.268265	GCGCGATCAAATTTGGAACC	58.732	50.000	17.90	4.43	0.00	3.62
1851	3011	2.286595	CCGCCTTGATTGATTGATCACG	60.287	50.000	0.00	0.00	35.86	4.35
1882	3042	2.443952	AGCCATGCATGCAGCCAT	60.444	55.556	26.69	6.06	44.83	4.40
1883	3043	3.457263	CAGCCATGCATGCAGCCA	61.457	61.111	26.69	1.47	44.83	4.75
1884	3044	4.221422	CCAGCCATGCATGCAGCC	62.221	66.667	26.69	15.74	44.83	4.85
1885	3045	4.891727	GCCAGCCATGCATGCAGC	62.892	66.667	26.69	23.56	45.96	5.25
1886	3046	3.430565	CTGCCAGCCATGCATGCAG	62.431	63.158	26.69	19.69	44.23	4.41
1887	3047	3.457263	CTGCCAGCCATGCATGCA	61.457	61.111	25.04	25.04	38.22	3.96
1888	3048	4.221422	CCTGCCAGCCATGCATGC	62.221	66.667	21.69	11.82	38.22	4.06
1889	3049	1.832608	ATCCTGCCAGCCATGCATG	60.833	57.895	20.19	20.19	38.22	4.06
1890	3050	1.832608	CATCCTGCCAGCCATGCAT	60.833	57.895	0.00	0.00	38.22	3.96
1891	3051	2.441348	CATCCTGCCAGCCATGCA	60.441	61.111	0.00	0.00	37.17	3.96
1994	3154	2.182825	GTGCTACACGACGTGATAAGG	58.817	52.381	33.12	17.37	36.96	2.69
2003	3163	4.600012	ATTGCTATTTGTGCTACACGAC	57.400	40.909	0.00	0.00	37.14	4.34
2066	3226	6.319141	AGTGTCTGGCTGAAAGTAAATTTC	57.681	37.500	0.00	0.00	46.37	2.17
2080	3240	1.198759	TGAAGGGGGTAGTGTCTGGC	61.199	60.000	0.00	0.00	0.00	4.85
2084	3244	3.370633	GGAGAAATGAAGGGGGTAGTGTC	60.371	52.174	0.00	0.00	0.00	3.67
2086	3246	2.420129	CGGAGAAATGAAGGGGGTAGTG	60.420	54.545	0.00	0.00	0.00	2.74
2089	3258	2.257391	TCGGAGAAATGAAGGGGGTA	57.743	50.000	0.00	0.00	0.00	3.69
2111	3280	2.640684	CGTTTGCGTGCATCAATCC	58.359	52.632	0.00	0.49	0.00	3.01
2129	3298	6.867293	ACAACGACCATCTTTCTCTTAAGTAC	59.133	38.462	1.63	0.00	0.00	2.73
2141	3315	2.167900	GCCTACCTACAACGACCATCTT	59.832	50.000	0.00	0.00	0.00	2.40
2143	3317	1.755380	AGCCTACCTACAACGACCATC	59.245	52.381	0.00	0.00	0.00	3.51
2147	3321	2.991866	GTTTCAGCCTACCTACAACGAC	59.008	50.000	0.00	0.00	0.00	4.34
2226	3409	8.416329	AGAAATGGGTGCAATGACTATAATTTC	58.584	33.333	0.00	0.00	32.90	2.17
2238	3421	1.098050	GAGCGAGAAATGGGTGCAAT	58.902	50.000	0.00	0.00	0.00	3.56
2241	3424	0.659957	GATGAGCGAGAAATGGGTGC	59.340	55.000	0.00	0.00	0.00	5.01
2247	3430	4.462508	TCAAGACAGATGAGCGAGAAAT	57.537	40.909	0.00	0.00	0.00	2.17
2252	3435	4.424626	GTTACATCAAGACAGATGAGCGA	58.575	43.478	10.59	0.00	46.51	4.93
2253	3436	3.241553	CGTTACATCAAGACAGATGAGCG	59.758	47.826	10.59	7.68	46.51	5.03
2254	3437	3.000724	GCGTTACATCAAGACAGATGAGC	59.999	47.826	10.59	6.77	46.51	4.26
2255	3438	3.553511	GGCGTTACATCAAGACAGATGAG	59.446	47.826	10.59	1.51	46.51	2.90
2256	3439	3.521560	GGCGTTACATCAAGACAGATGA	58.478	45.455	10.59	0.00	46.51	2.92
2258	3441	2.236146	TGGGCGTTACATCAAGACAGAT	59.764	45.455	0.00	0.00	0.00	2.90
2259	3442	1.621317	TGGGCGTTACATCAAGACAGA	59.379	47.619	0.00	0.00	0.00	3.41
2260	3443	2.093306	TGGGCGTTACATCAAGACAG	57.907	50.000	0.00	0.00	0.00	3.51
2261	3444	2.027653	TCATGGGCGTTACATCAAGACA	60.028	45.455	0.00	0.00	0.00	3.41
2262	3445	2.627945	TCATGGGCGTTACATCAAGAC	58.372	47.619	0.00	0.00	0.00	3.01
2263	3446	3.205338	CATCATGGGCGTTACATCAAGA	58.795	45.455	0.00	0.00	0.00	3.02
2264	3447	2.287188	GCATCATGGGCGTTACATCAAG	60.287	50.000	0.00	0.00	0.00	3.02
2265	3448	1.675483	GCATCATGGGCGTTACATCAA	59.325	47.619	0.00	0.00	0.00	2.57
2266	3449	1.308047	GCATCATGGGCGTTACATCA	58.692	50.000	0.00	0.00	0.00	3.07
2313	3496	3.560636	ATGCGGTTATGCCTCTAAGTT	57.439	42.857	0.00	0.00	34.25	2.66
2385	3568	6.158695	AGCCAACTCTCTTTATCCCATTCTTA	59.841	38.462	0.00	0.00	0.00	2.10
2514	3697	1.502640	GACGATCGGGGATCTAGCG	59.497	63.158	20.98	0.00	36.96	4.26
2605	3788	2.362397	CAGGTGATGCTACCGTACTCAT	59.638	50.000	0.00	0.00	45.56	2.90
2645	3828	5.536161	ACAGATTCTACCAAAACAGTTGCAT	59.464	36.000	0.00	0.00	0.00	3.96
2721	3904	5.737113	TCATTACCCCTTTCCTACCCATAAA	59.263	40.000	0.00	0.00	0.00	1.40
2781	3964	5.637104	CGCTCTTATTTGCGTATGTTAGT	57.363	39.130	0.00	0.00	46.09	2.24

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.