AutoCloner

Multiple sequence alignment - TraesCS1D01G311100

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	TraesCS1D01G311100	chr1D	100.000	2909	0	0	1	2909	407210146	407207238	0.000000e+00	5373.0
1	TraesCS1D01G311100	chr1B	91.684	1972	73	32	1	1928	547579401	547577477	0.000000e+00	2649.0
2	TraesCS1D01G311100	chr4D	92.836	1005	51	9	1924	2909	468858754	468857752	0.000000e+00	1437.0
3	TraesCS1D01G311100	chr4D	92.520	1016	45	12	1923	2909	416864281	416863268	0.000000e+00	1426.0
4	TraesCS1D01G311100	chr4D	95.414	894	30	2	2027	2909	337961341	337960448	0.000000e+00	1413.0
5	TraesCS1D01G311100	chr7D	95.349	903	28	5	2019	2909	625243410	625244310	0.000000e+00	1423.0
6	TraesCS1D01G311100	chr7D	95.323	898	32	3	2022	2909	187250851	187249954	0.000000e+00	1417.0
7	TraesCS1D01G311100	chr7D	91.929	1016	52	8	1923	2909	261870816	261871830	0.000000e+00	1395.0
8	TraesCS1D01G311100	chr2D	92.110	1014	51	8	1924	2909	394573958	394574970	0.000000e+00	1402.0
9	TraesCS1D01G311100	chr2D	94.321	898	38	3	2022	2909	429382447	429381553	0.000000e+00	1363.0
10	TraesCS1D01G311100	chr2D	81.685	273	21	8	1925	2168	5664933	5665205	1.770000e-47	200.0
11	TraesCS1D01G311100	chr2D	77.895	190	19	11	2019	2195	608741667	608741488	2.390000e-16	97.1
12	TraesCS1D01G311100	chr2D	100.000	30	0	0	1920	1949	61321883	61321912	4.050000e-04	56.5
13	TraesCS1D01G311100	chr5D	92.004	1013	47	12	1927	2909	454491269	454492277	0.000000e+00	1391.0
14	TraesCS1D01G311100	chr1A	93.950	843	30	7	997	1818	502824545	502823703	0.000000e+00	1254.0
15	TraesCS1D01G311100	chr1A	87.612	1001	75	24	1	978	502825599	502824625	0.000000e+00	1116.0
16	TraesCS1D01G311100	chr1A	88.889	99	2	4	1839	1928	502823712	502823614	2.370000e-21	113.0
17	TraesCS1D01G311100	chr7A	87.365	926	71	19	2022	2909	136423230	136422313	0.000000e+00	1020.0
18	TraesCS1D01G311100	chr7A	86.157	903	92	20	2022	2909	163160281	163159397	0.000000e+00	944.0
19	TraesCS1D01G311100	chr7A	90.244	41	2	1	1922	1962	517573651	517573613	5.000000e-03	52.8
20	TraesCS1D01G311100	chr4A	85.979	756	88	9	1081	1824	625686023	625685274	0.000000e+00	793.0
21	TraesCS1D01G311100	chr4A	90.361	83	5	3	2018	2098	717638794	717638713	3.960000e-19	106.0
22	TraesCS1D01G311100	chr3B	81.594	690	75	15	1927	2574	90979343	90980022	9.240000e-145	523.0
23	TraesCS1D01G311100	chr3A	80.190	737	96	28	1107	1800	575612973	575613702	9.300000e-140	507.0
24	TraesCS1D01G311100	chr3D	81.312	503	68	15	1325	1812	437670016	437670507	4.550000e-103	385.0
25	TraesCS1D01G311100	chr2B	77.778	198	20	10	1924	2098	760147895	760147699	1.840000e-17	100.0
26	TraesCS1D01G311100	chr2B	80.741	135	11	6	2019	2139	729776525	729776392	1.110000e-14	91.6
27	TraesCS1D01G311100	chr4B	96.364	55	1	1	2022	2075	17653489	17653435	3.990000e-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	TraesCS1D01G311100	chr1D	407207238	407210146	2908	True	5373.000000	5373	100.000000	1	2909	1	chr1D.!!$R1	2908
1	TraesCS1D01G311100	chr1B	547577477	547579401	1924	True	2649.000000	2649	91.684000	1	1928	1	chr1B.!!$R1	1927
2	TraesCS1D01G311100	chr4D	468857752	468858754	1002	True	1437.000000	1437	92.836000	1924	2909	1	chr4D.!!$R3	985
3	TraesCS1D01G311100	chr4D	416863268	416864281	1013	True	1426.000000	1426	92.520000	1923	2909	1	chr4D.!!$R2	986
4	TraesCS1D01G311100	chr4D	337960448	337961341	893	True	1413.000000	1413	95.414000	2027	2909	1	chr4D.!!$R1	882
5	TraesCS1D01G311100	chr7D	625243410	625244310	900	False	1423.000000	1423	95.349000	2019	2909	1	chr7D.!!$F2	890
6	TraesCS1D01G311100	chr7D	187249954	187250851	897	True	1417.000000	1417	95.323000	2022	2909	1	chr7D.!!$R1	887
7	TraesCS1D01G311100	chr7D	261870816	261871830	1014	False	1395.000000	1395	91.929000	1923	2909	1	chr7D.!!$F1	986
8	TraesCS1D01G311100	chr2D	394573958	394574970	1012	False	1402.000000	1402	92.110000	1924	2909	1	chr2D.!!$F3	985
9	TraesCS1D01G311100	chr2D	429381553	429382447	894	True	1363.000000	1363	94.321000	2022	2909	1	chr2D.!!$R1	887
10	TraesCS1D01G311100	chr5D	454491269	454492277	1008	False	1391.000000	1391	92.004000	1927	2909	1	chr5D.!!$F1	982
11	TraesCS1D01G311100	chr1A	502823614	502825599	1985	True	827.666667	1254	90.150333	1	1928	3	chr1A.!!$R1	1927
12	TraesCS1D01G311100	chr7A	136422313	136423230	917	True	1020.000000	1020	87.365000	2022	2909	1	chr7A.!!$R1	887
13	TraesCS1D01G311100	chr7A	163159397	163160281	884	True	944.000000	944	86.157000	2022	2909	1	chr7A.!!$R2	887
14	TraesCS1D01G311100	chr4A	625685274	625686023	749	True	793.000000	793	85.979000	1081	1824	1	chr4A.!!$R1	743
15	TraesCS1D01G311100	chr3B	90979343	90980022	679	False	523.000000	523	81.594000	1927	2574	1	chr3B.!!$F1	647
16	TraesCS1D01G311100	chr3A	575612973	575613702	729	False	507.000000	507	80.190000	1107	1800	1	chr3A.!!$F1	693

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
764	796	0.031449	TCGCAACCGCATCATCGATA	59.969	50.0	0.0	0.0	38.4	2.92	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2008	2201	1.268352	CAATTTCGACCGCTTTTGGGA	59.732	47.619	0.0	0.0	33.84	4.37	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
34	36	0.839946	ACATTTCCATCCCTCTCCCG	59.160	55.000	0.00	0.00	0.00	5.14
66	68	1.818674	AGAAAATGCAATCCCACCGTC	59.181	47.619	0.00	0.00	0.00	4.79
93	95	1.269621	GCAGCAGGATTGATGATTGGC	60.270	52.381	0.00	0.00	43.30	4.52
164	174	4.803426	GTGACCGAGCCAGCTCCG	62.803	72.222	13.83	9.96	39.77	4.63
223	233	2.617274	GCCCCAGATATTTCCGCGC	61.617	63.158	0.00	0.00	0.00	6.86
226	236	1.557443	CCCAGATATTTCCGCGCGTC	61.557	60.000	29.95	18.24	0.00	5.19
296	307	0.744771	GCCAACCGAATCCTGAGACC	60.745	60.000	0.00	0.00	0.00	3.85
458	470	5.940595	AGAGTACGTCAGCTAAGTAAACTG	58.059	41.667	0.00	0.00	0.00	3.16
488	503	4.848562	TGATACATGATCCAGTACGTCC	57.151	45.455	0.00	0.00	33.07	4.79
559	574	4.086178	GCGCTGTGCTGCAGTCTG	62.086	66.667	16.64	13.33	46.64	3.51
560	575	4.086178	CGCTGTGCTGCAGTCTGC	62.086	66.667	18.32	18.32	46.64	4.26
602	617	2.270205	CTCTGTCCGGGCAGCAAT	59.730	61.111	31.50	0.00	36.49	3.56
603	618	1.377725	CTCTGTCCGGGCAGCAATT	60.378	57.895	31.50	0.00	36.49	2.32
647	674	1.300388	GCTGCTGGCACTGTTTTGG	60.300	57.895	0.00	0.00	41.35	3.28
653	680	1.896660	GGCACTGTTTTGGCGGAGA	60.897	57.895	0.00	0.00	31.60	3.71
696	728	1.222115	GATTAGCGTGCGGGGATGAC	61.222	60.000	0.00	0.00	0.00	3.06
710	742	3.496870	GGGGATGACGGAGATATTTTGCT	60.497	47.826	0.00	0.00	0.00	3.91
714	746	2.351418	TGACGGAGATATTTTGCTTGCG	59.649	45.455	0.00	0.00	0.00	4.85
754	786	0.794605	GCTTTTCTGATCGCAACCGC	60.795	55.000	0.00	0.00	0.00	5.68
756	788	1.131126	CTTTTCTGATCGCAACCGCAT	59.869	47.619	0.00	0.00	38.40	4.73
758	790	0.390998	TTCTGATCGCAACCGCATCA	60.391	50.000	0.00	0.00	38.40	3.07
759	791	0.179076	TCTGATCGCAACCGCATCAT	60.179	50.000	0.00	0.00	36.08	2.45
760	792	0.234106	CTGATCGCAACCGCATCATC	59.766	55.000	0.00	0.00	36.08	2.92
761	793	1.202568	GATCGCAACCGCATCATCG	59.797	57.895	0.00	0.00	38.40	3.84
762	794	1.215014	GATCGCAACCGCATCATCGA	61.215	55.000	0.00	0.00	38.40	3.59
763	795	0.601046	ATCGCAACCGCATCATCGAT	60.601	50.000	0.00	0.00	38.40	3.59
764	796	0.031449	TCGCAACCGCATCATCGATA	59.969	50.000	0.00	0.00	38.40	2.92
769	802	3.304559	GCAACCGCATCATCGATAGTATC	59.695	47.826	0.00	0.00	38.36	2.24
778	811	3.767287	CGATAGTATCGCGGCTGAA	57.233	52.632	18.92	0.00	46.55	3.02
798	831	1.225637	CGTACAATTGTCACGCGCC	60.226	57.895	15.85	0.00	0.00	6.53
933	966	4.789075	GCTCGGGCACGCGAGTTA	62.789	66.667	29.70	3.02	46.40	2.24
951	984	1.166129	TACAGTCACGCTCAGAGTCC	58.834	55.000	0.00	0.00	0.00	3.85
952	985	0.823769	ACAGTCACGCTCAGAGTCCA	60.824	55.000	0.00	0.00	0.00	4.02
953	986	0.387878	CAGTCACGCTCAGAGTCCAC	60.388	60.000	0.00	0.00	0.00	4.02
954	987	0.823769	AGTCACGCTCAGAGTCCACA	60.824	55.000	0.00	0.00	0.00	4.17
955	988	0.244994	GTCACGCTCAGAGTCCACAT	59.755	55.000	0.00	0.00	0.00	3.21
962	995	1.206610	CTCAGAGTCCACATCCACCAG	59.793	57.143	0.00	0.00	0.00	4.00
978	1075	1.595357	CAGGTCGGGTAACTGGGTC	59.405	63.158	0.00	0.00	45.79	4.46
980	1077	1.978617	GGTCGGGTAACTGGGTCGA	60.979	63.158	0.00	0.00	45.79	4.20
981	1078	1.213799	GTCGGGTAACTGGGTCGAC	59.786	63.158	7.13	7.13	45.79	4.20
1807	1991	3.071206	GCCTCTCCTCCAGCGACA	61.071	66.667	0.00	0.00	0.00	4.35
1872	2056	2.378084	CGACTCTGACGACGACGGA	61.378	63.158	12.58	5.09	44.46	4.69
2138	2373	0.321741	ACTCGACTCTCTTCTCGCCA	60.322	55.000	0.00	0.00	0.00	5.69
2232	2485	0.178767	CTCCATTGATGCCTCACGGA	59.821	55.000	8.49	8.49	0.00	4.69
2577	2848	4.147449	CGTGGAGGATCAGCGCCA	62.147	66.667	2.29	0.00	36.25	5.69

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
34	36	3.981211	TGCATTTTCTTTGTCCTCTTGC	58.019	40.909	0.00	0.00	0.00	4.01
72	74	1.001706	CCAATCATCAATCCTGCTGCG	60.002	52.381	0.00	0.00	0.00	5.18
458	470	2.928757	GGATCATGTATCATGCGAGCTC	59.071	50.000	2.73	2.73	36.20	4.09
488	503	5.003804	ACACTGCCCATCTTAGTTTACTTG	58.996	41.667	0.00	0.00	0.00	3.16
602	617	2.592287	GCCACCGACCGTCCAAAA	60.592	61.111	0.00	0.00	0.00	2.44
603	618	4.973055	CGCCACCGACCGTCCAAA	62.973	66.667	0.00	0.00	36.29	3.28
629	645	1.300388	CCAAAACAGTGCCAGCAGC	60.300	57.895	0.00	0.00	44.14	5.25
630	646	1.300388	GCCAAAACAGTGCCAGCAG	60.300	57.895	0.00	0.00	0.00	4.24
631	647	2.813901	GCCAAAACAGTGCCAGCA	59.186	55.556	0.00	0.00	0.00	4.41
632	648	2.355009	CGCCAAAACAGTGCCAGC	60.355	61.111	0.00	0.00	0.00	4.85
696	728	1.002468	CCCGCAAGCAAAATATCTCCG	60.002	52.381	0.00	0.00	0.00	4.63
761	793	1.699343	GGTTCAGCCGCGATACTATC	58.301	55.000	8.23	0.00	0.00	2.08
762	794	3.888093	GGTTCAGCCGCGATACTAT	57.112	52.632	8.23	0.00	0.00	2.12
778	811	1.893168	GCGCGTGACAATTGTACGGT	61.893	55.000	26.73	4.45	38.20	4.83
872	905	0.389757	TGGGCAGTTATATACGCGCA	59.610	50.000	5.73	11.48	42.25	6.09
930	963	2.586900	GACTCTGAGCGTGACTGTAAC	58.413	52.381	4.19	0.00	0.00	2.50
932	965	1.166129	GGACTCTGAGCGTGACTGTA	58.834	55.000	4.19	0.00	0.00	2.74
933	966	0.823769	TGGACTCTGAGCGTGACTGT	60.824	55.000	4.19	0.00	0.00	3.55
951	984	1.261938	TACCCGACCTGGTGGATGTG	61.262	60.000	10.71	0.00	39.53	3.21
952	985	0.545787	TTACCCGACCTGGTGGATGT	60.546	55.000	10.71	9.39	39.53	3.06
953	986	0.107848	GTTACCCGACCTGGTGGATG	60.108	60.000	10.71	3.81	39.53	3.51
954	987	0.252558	AGTTACCCGACCTGGTGGAT	60.253	55.000	10.71	0.00	39.53	3.41
955	988	1.156803	AGTTACCCGACCTGGTGGA	59.843	57.895	10.71	0.00	39.53	4.02
962	995	1.978617	TCGACCCAGTTACCCGACC	60.979	63.158	0.00	0.00	0.00	4.79
978	1075	4.111375	ACTACCAGCTGAATGTTAGTCG	57.889	45.455	17.39	1.06	0.00	4.18
980	1077	6.684111	GCTCATACTACCAGCTGAATGTTAGT	60.684	42.308	17.39	14.50	0.00	2.24
981	1078	5.694006	GCTCATACTACCAGCTGAATGTTAG	59.306	44.000	17.39	9.60	0.00	2.34
1305	1426	2.997897	GAGGAGCCCGTGGTGAGT	60.998	66.667	0.00	0.00	0.00	3.41
1872	2056	4.015406	TCGGCGGTGGCAGTGAAT	62.015	61.111	7.21	0.00	42.47	2.57
1898	2091	3.175240	CTTCGCGTCACAGCTCCG	61.175	66.667	5.77	0.00	34.40	4.63
2000	2193	4.445545	GCTTTTGGGAGCGCGACG	62.446	66.667	12.10	0.00	32.23	5.12
2008	2201	1.268352	CAATTTCGACCGCTTTTGGGA	59.732	47.619	0.00	0.00	33.84	4.37
2014	2207	2.867472	CGCCAATTTCGACCGCTT	59.133	55.556	0.00	0.00	0.00	4.68
2015	2208	3.799755	GCGCCAATTTCGACCGCT	61.800	61.111	0.00	0.00	41.28	5.52
2170	2405	2.413239	CGCAGCTTTGACATTGATTCGT	60.413	45.455	0.00	0.00	0.00	3.85
2554	2825	4.770362	TGATCCTCCACGCCCCGA	62.770	66.667	0.00	0.00	0.00	5.14

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.