AutoCloner

Multiple sequence alignment - TraesCS3D01G488900

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	TraesCS3D01G488900	chr3D	100.000	2675	0	0	1	2675	583225622	583222948	0.000000e+00	4940.0
1	TraesCS3D01G488900	chr3D	92.549	1973	108	24	1	1951	583170773	583168818	0.000000e+00	2793.0
2	TraesCS3D01G488900	chr3D	87.460	1890	153	50	123	1940	583182226	583180349	0.000000e+00	2100.0
3	TraesCS3D01G488900	chr3D	85.919	2024	177	60	123	2055	583278831	583276825	0.000000e+00	2060.0
4	TraesCS3D01G488900	chr3D	85.986	1841	175	49	171	1940	583188165	583186337	0.000000e+00	1893.0
5	TraesCS3D01G488900	chr3D	90.762	1418	96	21	551	1940	583284625	583283215	0.000000e+00	1860.0
6	TraesCS3D01G488900	chr3D	78.765	1474	203	61	773	2175	583028957	583027523	0.000000e+00	887.0
7	TraesCS3D01G488900	chr3D	87.805	410	38	7	2268	2675	583282757	583282358	1.120000e-128	470.0
8	TraesCS3D01G488900	chr3D	86.829	410	42	4	2268	2675	583185877	583185478	5.250000e-122	448.0
9	TraesCS3D01G488900	chr3D	85.338	266	28	8	2282	2545	583179644	583179388	5.680000e-67	265.0
10	TraesCS3D01G488900	chr3D	85.772	246	25	3	2268	2513	583179886	583179651	4.420000e-63	252.0
11	TraesCS3D01G488900	chr3D	84.615	169	23	3	157	323	583030167	583030000	5.920000e-37	165.0
12	TraesCS3D01G488900	chr3B	87.818	2159	158	45	167	2239	780322080	780319941	0.000000e+00	2433.0
13	TraesCS3D01G488900	chr3B	87.790	2154	168	43	167	2239	780326685	780324546	0.000000e+00	2433.0
14	TraesCS3D01G488900	chr3B	87.726	2159	160	45	167	2239	780316706	780314567	0.000000e+00	2422.0
15	TraesCS3D01G488900	chr3B	86.380	2210	199	51	123	2239	780330480	780328280	0.000000e+00	2320.0
16	TraesCS3D01G488900	chr3B	88.913	1840	124	39	167	1940	780302619	780300794	0.000000e+00	2194.0
17	TraesCS3D01G488900	chr3B	81.112	1726	213	67	123	1768	780296445	780294753	0.000000e+00	1277.0
18	TraesCS3D01G488900	chr3B	84.899	1192	104	42	1540	2675	780340174	780339003	0.000000e+00	1134.0
19	TraesCS3D01G488900	chr3B	95.359	237	6	5	2440	2675	780314294	780314062	3.250000e-99	372.0
20	TraesCS3D01G488900	chr3B	95.359	237	6	5	2440	2675	780324273	780324041	3.250000e-99	372.0
21	TraesCS3D01G488900	chr3B	95.359	237	6	5	2440	2675	780328007	780327775	3.250000e-99	372.0
22	TraesCS3D01G488900	chr3B	92.254	142	11	0	2268	2409	780314437	780314296	4.520000e-48	202.0
23	TraesCS3D01G488900	chr3B	92.254	142	11	0	2268	2409	780328150	780328009	4.520000e-48	202.0
24	TraesCS3D01G488900	chr3B	91.549	142	12	0	2268	2409	780324416	780324275	2.100000e-46	196.0
25	TraesCS3D01G488900	chr6B	86.073	1156	112	25	832	1951	62690882	62689740	0.000000e+00	1197.0
26	TraesCS3D01G488900	chr6B	82.333	300	43	6	2378	2675	62691238	62690947	4.420000e-63	252.0
27	TraesCS3D01G488900	chr7A	82.692	1144	157	26	832	1950	287848732	287849859	0.000000e+00	977.0
28	TraesCS3D01G488900	chr7A	80.716	1089	157	38	895	1945	287552241	287553314	0.000000e+00	798.0
29	TraesCS3D01G488900	chr7A	95.918	49	1	1	2582	2630	287816808	287816855	7.940000e-11	78.7
30	TraesCS3D01G488900	chr7D	82.214	551	37	28	235	769	39552972	39552467	4.120000e-113	418.0
31	TraesCS3D01G488900	chr4A	83.532	419	44	12	235	638	645784641	645784233	4.210000e-98	368.0
32	TraesCS3D01G488900	chr4A	79.151	542	53	27	235	769	645729063	645728575	1.190000e-83	320.0
33	TraesCS3D01G488900	chr4A	79.151	542	53	28	235	769	645762259	645761771	1.190000e-83	320.0
34	TraesCS3D01G488900	chr4A	90.000	110	10	1	240	348	645687077	645686968	9.980000e-30	141.0
35	TraesCS3D01G488900	chr6A	77.468	395	43	30	317	675	34388896	34388512	7.560000e-46	195.0
36	TraesCS3D01G488900	chrUn	91.667	72	6	0	235	306	41695926	41695997	1.690000e-17	100.0
37	TraesCS3D01G488900	chrUn	91.667	72	2	4	2300	2371	101990224	101990157	2.190000e-16	97.1
38	TraesCS3D01G488900	chr7B	95.918	49	1	1	2582	2630	244631380	244631427	7.940000e-11	78.7

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	TraesCS3D01G488900	chr3D	583222948	583225622	2674	True	4940.000000	4940	100.0000	1	2675	1	chr3D.!!$R2	2674
1	TraesCS3D01G488900	chr3D	583168818	583170773	1955	True	2793.000000	2793	92.5490	1	1951	1	chr3D.!!$R1	1950
2	TraesCS3D01G488900	chr3D	583276825	583284625	7800	True	1463.333333	2060	88.1620	123	2675	3	chr3D.!!$R5	2552
3	TraesCS3D01G488900	chr3D	583179388	583188165	8777	True	991.600000	2100	86.2770	123	2675	5	chr3D.!!$R4	2552
4	TraesCS3D01G488900	chr3D	583027523	583030167	2644	True	526.000000	887	81.6900	157	2175	2	chr3D.!!$R3	2018
5	TraesCS3D01G488900	chr3B	780300794	780302619	1825	True	2194.000000	2194	88.9130	167	1940	1	chr3B.!!$R2	1773
6	TraesCS3D01G488900	chr3B	780294753	780296445	1692	True	1277.000000	1277	81.1120	123	1768	1	chr3B.!!$R1	1645
7	TraesCS3D01G488900	chr3B	780339003	780340174	1171	True	1134.000000	1134	84.8990	1540	2675	1	chr3B.!!$R3	1135
8	TraesCS3D01G488900	chr3B	780314062	780330480	16418	True	1132.400000	2433	91.1848	123	2675	10	chr3B.!!$R4	2552
9	TraesCS3D01G488900	chr6B	62689740	62691238	1498	True	724.500000	1197	84.2030	832	2675	2	chr6B.!!$R1	1843
10	TraesCS3D01G488900	chr7A	287848732	287849859	1127	False	977.000000	977	82.6920	832	1950	1	chr7A.!!$F3	1118
11	TraesCS3D01G488900	chr7A	287552241	287553314	1073	False	798.000000	798	80.7160	895	1945	1	chr7A.!!$F1	1050
12	TraesCS3D01G488900	chr7D	39552467	39552972	505	True	418.000000	418	82.2140	235	769	1	chr7D.!!$R1	534

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
374	6075	1.39944	CCTGGAACATGCGATGAAGTG	59.601	52.381	0.0	0.0	38.2	3.16	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1713	18001	0.606604	GGGGCGTCAAGAGTTACTCA	59.393	55.0	15.23	0.0	32.06	3.41	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
50	52	5.611374	ACACATGTAGCTAAGAAGTTGTGT	58.389	37.500	0.00	14.02	40.98	3.72
101	103	3.690460	ACATGGGTCCAGATCTCAAAAC	58.310	45.455	0.00	0.00	0.00	2.43
110	112	3.446161	CCAGATCTCAAAACCATGCATGT	59.554	43.478	24.58	10.59	0.00	3.21
111	113	4.081862	CCAGATCTCAAAACCATGCATGTT	60.082	41.667	24.58	15.63	0.00	2.71
114	116	5.421056	AGATCTCAAAACCATGCATGTTCAT	59.579	36.000	24.58	6.23	0.00	2.57
115	117	5.471556	TCTCAAAACCATGCATGTTCATT	57.528	34.783	24.58	11.37	0.00	2.57
116	118	6.587206	TCTCAAAACCATGCATGTTCATTA	57.413	33.333	24.58	5.96	0.00	1.90
117	119	6.389091	TCTCAAAACCATGCATGTTCATTAC	58.611	36.000	24.58	0.00	0.00	1.89
374	6075	1.399440	CCTGGAACATGCGATGAAGTG	59.601	52.381	0.00	0.00	38.20	3.16
387	6088	3.189080	CGATGAAGTGAATGACCAGCAAA	59.811	43.478	0.00	0.00	0.00	3.68
556	6312	6.252995	TGCCCCTGATAATTAAGACACTTTT	58.747	36.000	0.00	0.00	0.00	2.27
677	10169	3.364366	GCTTGAACTGACAAGATTCCACG	60.364	47.826	17.72	0.00	46.85	4.94
821	10958	3.554752	GGATCTCTATGCTTCTGCCAGAC	60.555	52.174	0.00	0.00	38.71	3.51
967	13268	2.494073	TCTTTCTTCCTCCTCTCTTCGC	59.506	50.000	0.00	0.00	0.00	4.70
977	13282	1.473434	CCTCTCTTCGCCCACAATACC	60.473	57.143	0.00	0.00	0.00	2.73
1086	13391	2.093235	GCAAGAACTCCACAGCCTAGAT	60.093	50.000	0.00	0.00	0.00	1.98
1113	13418	4.079327	AGCATCTCTTCCTCCAATTCCATT	60.079	41.667	0.00	0.00	0.00	3.16
1145	13450	2.685897	GCGATAGTCTCAGGAGTCTTGT	59.314	50.000	1.77	0.00	39.35	3.16
1160	13465	5.232414	GGAGTCTTGTAAACATCTACGATGC	59.768	44.000	3.88	0.00	0.00	3.91
1200	17479	2.693074	CCTACCAAGCAACCAAGTTTGT	59.307	45.455	0.00	0.00	0.00	2.83
1420	17699	0.865769	TCTTTTCAAGAAGACCGCGC	59.134	50.000	0.00	0.00	33.83	6.86
1563	17851	4.279169	TCTCTTGTTTCCAAGGCATTTCAG	59.721	41.667	2.88	0.00	46.65	3.02
1564	17852	4.214310	TCTTGTTTCCAAGGCATTTCAGA	58.786	39.130	2.88	0.00	46.65	3.27
1603	17891	1.202915	TGCAAGGAGGAGCAATTGTCA	60.203	47.619	7.40	0.00	37.90	3.58
1624	17912	1.538419	GGGTTAGAGTGCAGTATCGGC	60.538	57.143	0.00	0.00	0.00	5.54
1672	17960	5.544176	TCTGTTCAGGAAATTAGTCCAGAGT	59.456	40.000	0.00	0.00	40.48	3.24
1712	18000	7.947332	TCAACATCCTTAGCTCATAGATACTCT	59.053	37.037	0.00	0.00	0.00	3.24
1713	18001	8.584157	CAACATCCTTAGCTCATAGATACTCTT	58.416	37.037	0.00	0.00	0.00	2.85
1782	23461	7.291411	AGCCGATCTTCATACAACTATACTT	57.709	36.000	0.00	0.00	0.00	2.24
1888	23590	4.661222	TGTGATCCCAGTTTTTGATGCTA	58.339	39.130	0.00	0.00	0.00	3.49
1964	23682	6.127730	ACAAGGTCCCAATCGATCAATTTTAC	60.128	38.462	0.00	0.00	0.00	2.01
1976	23694	8.833231	TCGATCAATTTTACTATCCAGATTCC	57.167	34.615	0.00	0.00	0.00	3.01
2018	23744	2.288825	TGCACTACTCTGGCACTACAAC	60.289	50.000	0.00	0.00	31.58	3.32
2022	23748	3.508012	ACTACTCTGGCACTACAACTGAG	59.492	47.826	0.00	0.00	36.59	3.35
2085	23839	9.632638	ACTATATCATTTAAGCATTGAAGGTGT	57.367	29.630	0.00	0.00	0.00	4.16
2129	23886	3.320541	CCAGGACCACAACTTTTTGCATA	59.679	43.478	0.00	0.00	36.00	3.14
2178	23951	9.150348	TGAGAAAGAAACAATCCAAACTTTTTC	57.850	29.630	0.00	0.00	32.80	2.29
2198	24007	7.581213	TTTTCGTCCTTTCCATATAATGCAT	57.419	32.000	0.00	0.00	0.00	3.96
2239	24094	0.693049	ATATGCTCATTCCCGGGGTC	59.307	55.000	23.50	4.14	0.00	4.46
2413	24586	1.387295	GCCTAAACATGCCAGCTCCC	61.387	60.000	0.00	0.00	0.00	4.30
2445	24618	4.929211	GGCTTTAACCTGTAATTTGCAAGG	59.071	41.667	0.00	0.00	0.00	3.61
2476	24649	7.602265	CCACCAAGGAAAACACCTTATTAAATG	59.398	37.037	0.00	0.00	46.94	2.32
2477	24650	8.147704	CACCAAGGAAAACACCTTATTAAATGT	58.852	33.333	0.00	0.00	46.94	2.71
2478	24651	8.710239	ACCAAGGAAAACACCTTATTAAATGTT	58.290	29.630	0.00	1.63	46.94	2.71

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
101	103	6.566141	TGAATGAAGTAATGAACATGCATGG	58.434	36.000	29.41	12.50	0.00	3.66
116	118	9.561069	AGTGACAAGTTTATAGTTGAATGAAGT	57.439	29.630	7.63	0.00	37.97	3.01
178	5855	6.294120	GCCCAAAAATGCTTAAATTTTCTGCT	60.294	34.615	0.00	0.00	38.49	4.24
374	6075	2.545742	GGTTGGTGTTTGCTGGTCATTC	60.546	50.000	0.00	0.00	0.00	2.67
387	6088	0.182775	GAGGGTGTCTTGGTTGGTGT	59.817	55.000	0.00	0.00	0.00	4.16
556	6312	3.973305	TGAATGAGTATATGGGCCTGTCA	59.027	43.478	4.53	0.00	0.00	3.58
604	10096	0.097674	GTTTATGCCGCTCTGCTGTG	59.902	55.000	0.00	0.00	0.00	3.66
677	10169	4.928601	TGCATGCTCAAGCTATCATTTTC	58.071	39.130	20.33	0.00	42.66	2.29
821	10958	1.952296	GCCATTACATCAGCCTTGAGG	59.048	52.381	0.00	0.00	40.80	3.86
967	13268	2.643551	AGATTTGCTCGGTATTGTGGG	58.356	47.619	0.00	0.00	0.00	4.61
1086	13391	0.986527	TGGAGGAAGAGATGCTTGCA	59.013	50.000	0.00	0.00	46.32	4.08
1129	13434	5.777732	AGATGTTTACAAGACTCCTGAGACT	59.222	40.000	0.22	0.00	35.07	3.24
1145	13450	6.863275	TCTTCAAGAGCATCGTAGATGTTTA	58.137	36.000	11.12	0.00	45.12	2.01
1160	13465	7.050377	TGGTAGGCAAATAATCTCTTCAAGAG	58.950	38.462	8.27	8.27	43.64	2.85
1284	17563	3.400007	GCCTTCATCTCGGCGAAC	58.600	61.111	12.13	0.00	36.45	3.95
1420	17699	1.339824	ACAATCTGCAGGAGCCTTCTG	60.340	52.381	15.13	0.00	41.13	3.02
1603	17891	2.032620	CCGATACTGCACTCTAACCCT	58.967	52.381	0.00	0.00	0.00	4.34
1624	17912	2.251075	GCTCCGCTCTCGAGATCG	59.749	66.667	27.14	27.14	38.10	3.69
1672	17960	9.179909	CTAAGGATGTTGAGTAGAGAAACTCTA	57.820	37.037	4.64	4.64	45.12	2.43
1712	18000	1.001633	GGGGCGTCAAGAGTTACTCAA	59.998	52.381	15.23	0.00	32.06	3.02
1713	18001	0.606604	GGGGCGTCAAGAGTTACTCA	59.393	55.000	15.23	0.00	32.06	3.41
1806	23492	9.936759	TCAAAACTTTGGTTTCACTTTCTATTT	57.063	25.926	2.49	0.00	43.90	1.40
1816	23502	7.279758	GTCAAATGGATCAAAACTTTGGTTTCA	59.720	33.333	2.49	0.00	43.90	2.69
1888	23590	5.520748	AGGAACAAGATCCACTAACCATT	57.479	39.130	0.00	0.00	42.27	3.16
1964	23682	1.421646	GGTGGTGGGGAATCTGGATAG	59.578	57.143	0.00	0.00	0.00	2.08
1976	23694	2.283101	CCATGTGGTGGTGGTGGG	60.283	66.667	0.00	0.00	43.44	4.61
2059	23786	9.632638	ACACCTTCAATGCTTAAATGATATAGT	57.367	29.630	0.00	0.00	0.00	2.12
2111	23868	7.367285	TGTAGAATATGCAAAAAGTTGTGGTC	58.633	34.615	0.00	0.00	37.06	4.02
2161	23918	5.592104	AGGACGAAAAAGTTTGGATTGTT	57.408	34.783	0.00	0.00	0.00	2.83
2162	23919	5.592104	AAGGACGAAAAAGTTTGGATTGT	57.408	34.783	0.00	0.00	0.00	2.71
2163	23920	5.462068	GGAAAGGACGAAAAAGTTTGGATTG	59.538	40.000	0.00	0.00	0.00	2.67
2178	23951	4.216042	TGCATGCATTATATGGAAAGGACG	59.784	41.667	18.46	0.00	33.18	4.79
2198	24007	2.309528	AGTGTCGACTGTTCTTTGCA	57.690	45.000	17.92	0.00	0.00	4.08
2239	24094	8.199176	TTAGTCGTACTAACTGATTCTCAGAG	57.801	38.462	10.94	0.00	46.84	3.35
2329	24274	5.563592	TCAGCATGTTATCCCCATATTCTG	58.436	41.667	0.00	0.00	37.40	3.02
2331	24276	5.183904	GGTTCAGCATGTTATCCCCATATTC	59.816	44.000	0.00	0.00	37.40	1.75
2413	24586	3.214328	ACAGGTTAAAGCCTCAACAGTG	58.786	45.455	0.00	0.00	36.58	3.66
2476	24649	7.611213	AACATTTAGCTGTGACATACCTAAC	57.389	36.000	0.00	0.00	0.00	2.34
2477	24650	7.985184	CCTAACATTTAGCTGTGACATACCTAA	59.015	37.037	0.00	0.00	0.00	2.69
2478	24651	7.125204	ACCTAACATTTAGCTGTGACATACCTA	59.875	37.037	0.00	0.00	0.00	3.08
2545	24718	3.429135	GGTTTAGTCTGACGGTGGATCTC	60.429	52.174	1.52	0.00	0.00	2.75

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.