AutoCloner

Multiple sequence alignment - TraesCS1A01G223600

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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	TraesCS1A01G223600	chr1A	100.000	2438	0	0	1	2438	394249171	394251608	0.000000e+00	4503.0
1	TraesCS1A01G223600	chr1A	100.000	289	0	0	2708	2996	394251878	394252166	4.400000e-148	534.0
2	TraesCS1A01G223600	chr1D	89.297	2504	105	66	2	2438	313848741	313851148	0.000000e+00	2988.0
3	TraesCS1A01G223600	chr1D	89.562	297	21	7	2708	2996	313851226	313851520	4.720000e-98	368.0
4	TraesCS1A01G223600	chr1B	88.748	1662	70	49	645	2248	423943772	423945374	0.000000e+00	1925.0
5	TraesCS1A01G223600	chr1B	90.182	275	16	5	329	595	423943493	423943764	6.150000e-92	348.0
6	TraesCS1A01G223600	chr1B	96.447	197	6	1	2243	2438	423945561	423945757	1.040000e-84	324.0
7	TraesCS1A01G223600	chr1B	84.775	289	28	8	2708	2986	423945834	423946116	2.940000e-70	276.0
8	TraesCS1A01G223600	chr1B	92.537	67	3	2	123	188	423943356	423943421	8.840000e-16	95.3
9	TraesCS1A01G223600	chr4B	79.530	298	53	8	1126	1419	585024411	585024118	3.910000e-49	206.0
10	TraesCS1A01G223600	chr4B	79.348	92	13	5	2820	2906	64395878	64395968	3.230000e-05	60.2
11	TraesCS1A01G223600	chr4D	78.859	298	55	8	1126	1419	467225576	467225283	8.470000e-46	195.0
12	TraesCS1A01G223600	chr4D	73.841	302	60	18	1144	1435	426643198	426643490	5.280000e-18	102.0
13	TraesCS1A01G223600	chr4D	78.022	91	16	2	2820	2906	305475017	305474927	2.000000e-03	54.7
14	TraesCS1A01G223600	chr4A	79.070	301	49	13	1126	1419	3799022	3799315	8.470000e-46	195.0
15	TraesCS1A01G223600	chr4A	74.679	312	66	11	1131	1435	38805643	38805338	3.140000e-25	126.0
16	TraesCS1A01G223600	chr5D	95.370	108	5	0	1241	1348	420026219	420026326	3.970000e-39	172.0
17	TraesCS1A01G223600	chr5D	94.495	109	6	0	1243	1351	444893885	444893993	5.140000e-38	169.0
18	TraesCS1A01G223600	chr5D	100.000	35	0	0	1129	1163	444893491	444893525	6.930000e-07	65.8
19	TraesCS1A01G223600	chr7D	79.439	107	16	5	2808	2908	360342954	360343060	1.490000e-08	71.3
20	TraesCS1A01G223600	chr7D	78.261	92	15	3	2820	2906	534027090	534026999	2.000000e-03	54.7
21	TraesCS1A01G223600	chr3D	79.121	91	15	2	2820	2906	303100412	303100502	3.230000e-05	60.2
22	TraesCS1A01G223600	chr2D	78.495	93	15	3	2819	2906	442809307	442809399	4.170000e-04	56.5
23	TraesCS1A01G223600	chr6D	78.495	93	13	5	2820	2906	445750840	445750749	2.000000e-03	54.7
24	TraesCS1A01G223600	chr2A	96.774	31	1	0	1137	1167	421243534	421243564	5.000000e-03	52.8

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	TraesCS1A01G223600	chr1A	394249171	394252166	2995	False	2518.50	4503	100.0000	1	2996	2	chr1A.!!$F1	2995
1	TraesCS1A01G223600	chr1D	313848741	313851520	2779	False	1678.00	2988	89.4295	2	2996	2	chr1D.!!$F1	2994
2	TraesCS1A01G223600	chr1B	423943356	423946116	2760	False	593.66	1925	90.5378	123	2986	5	chr1B.!!$F1	2863

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
187	195	0.538584	CCATGAGACTGCAGCCTGTA	59.461	55.000	15.27	0.00	0.00	2.74	F
666	709	1.080434	AGCACTCGAGAGAAACGGC	60.080	57.895	21.68	10.23	41.32	5.68	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1049	1150	0.112412	GCCTCCTCTCCCCTCTCTAG	59.888	65.0	0.0	0.0	0.00	2.43	R
2009	2122	0.455633	CAATGCAGCCGCTTCTTGAC	60.456	55.0	0.0	0.0	39.64	3.18	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
26	27	1.063166	GCAACAAGATAGCGCCAGC	59.937	57.895	2.29	0.00	45.58	4.85
61	62	2.956964	CGATCTTCCCTCGCACGC	60.957	66.667	0.00	0.00	0.00	5.34
62	63	2.184322	GATCTTCCCTCGCACGCA	59.816	61.111	0.00	0.00	0.00	5.24
139	141	0.814812	GAGCATGCAGAGCCCTTCTC	60.815	60.000	21.98	0.00	42.21	2.87
174	176	3.305403	CGTATACCACTACCAGCCATGAG	60.305	52.174	0.00	0.00	0.00	2.90
183	191	2.113433	CAGCCATGAGACTGCAGCC	61.113	63.158	15.27	1.42	0.00	4.85
187	195	0.538584	CCATGAGACTGCAGCCTGTA	59.461	55.000	15.27	0.00	0.00	2.74
198	208	2.304470	TGCAGCCTGTAGTACATGGAAA	59.696	45.455	17.82	0.00	0.00	3.13
199	209	2.939103	GCAGCCTGTAGTACATGGAAAG	59.061	50.000	17.82	10.03	0.00	2.62
205	223	5.680151	GCCTGTAGTACATGGAAAGAGACTC	60.680	48.000	17.82	0.00	0.00	3.36
235	253	7.312899	ACGCCAAACCTTTAATCTTTAAGATG	58.687	34.615	8.34	0.00	34.65	2.90
402	420	8.706322	ACATAAAACCAGTATCAGAAACCTTT	57.294	30.769	0.00	0.00	0.00	3.11
429	447	5.120674	TCAGATAAACACAAGAAGCATCGTG	59.879	40.000	3.27	3.27	40.40	4.35
546	570	1.520787	CCCGACGGCACCAGTATTC	60.521	63.158	8.86	0.00	0.00	1.75
624	667	2.094338	GGAGATAACAGGAAACGGACGT	60.094	50.000	0.00	0.00	0.00	4.34
666	709	1.080434	AGCACTCGAGAGAAACGGC	60.080	57.895	21.68	10.23	41.32	5.68
1422	1523	1.446272	GAACTCCACGCTCCGGAAG	60.446	63.158	5.23	5.19	30.33	3.46
2035	2148	1.665599	GCGGCTGCATTGCAAGTTT	60.666	52.632	14.08	0.00	38.41	2.66
2038	2151	1.142474	GGCTGCATTGCAAGTTTCAC	58.858	50.000	13.18	0.00	38.41	3.18
2068	2181	1.525596	GTTGTCACTCGTCGATCTCG	58.474	55.000	0.00	0.00	41.45	4.04
2096	2209	1.539065	CCGTCTCCATCTCCATTTCCG	60.539	57.143	0.00	0.00	0.00	4.30
2196	2316	1.202110	GCATTTCGGATGAGCACTGTG	60.202	52.381	2.76	2.76	0.00	3.66
2235	2355	4.827481	CGGTTGGATCGACGGATT	57.173	55.556	0.00	0.00	31.51	3.01
2239	2359	1.006832	GTTGGATCGACGGATTGGTG	58.993	55.000	0.00	0.00	31.51	4.17
2251	2563	2.223572	CGGATTGGTGCTATTTTCCTGC	60.224	50.000	0.00	0.00	0.00	4.85
2266	2578	1.738099	CTGCTGGGGAGTTCGTTCG	60.738	63.158	0.00	0.00	0.00	3.95
2419	2732	3.804036	CTGGTGGTTTCAAGTGAGTACA	58.196	45.455	0.00	0.00	0.00	2.90
2854	3180	9.820725	ATGCATTGCAATTAATACAGTTGTAAT	57.179	25.926	16.46	0.00	43.62	1.89
2892	3221	7.287050	ACGAACGTATTGATTAGGTTCTTTC	57.713	36.000	14.19	0.00	46.36	2.62

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	2.222819	CGCTATCTTGTTGCCTTCGAAC	60.223	50.000	0.00	0.00	0.00	3.95
3	4	0.026803	GCGCTATCTTGTTGCCTTCG	59.973	55.000	0.00	0.00	0.00	3.79
26	27	1.068474	CGCAACCTTCGTACCAGAAG	58.932	55.000	4.11	4.11	45.26	2.85
35	36	0.108138	AGGGAAGATCGCAACCTTCG	60.108	55.000	0.00	0.00	39.60	3.79
59	60	3.429043	AAAAAGATGGCTGCATGCG	57.571	47.368	14.09	9.16	44.05	4.73
82	83	2.202743	GTGAGCATGCGCGTAGGA	60.203	61.111	14.26	0.00	45.49	2.94
83	84	3.620428	CGTGAGCATGCGCGTAGG	61.620	66.667	16.86	6.12	45.49	3.18
114	115	0.532417	GGCTCTGCATGCTCCTGTAG	60.532	60.000	20.33	6.69	0.00	2.74
139	141	2.613595	TGGTATACGTGTAGGTGTAGCG	59.386	50.000	0.00	0.00	35.56	4.26
174	176	2.544685	CATGTACTACAGGCTGCAGTC	58.455	52.381	23.17	11.28	0.00	3.51
183	191	5.419155	TGGAGTCTCTTTCCATGTACTACAG	59.581	44.000	0.00	0.00	39.74	2.74
198	208	0.976641	TTTGGCGTCATGGAGTCTCT	59.023	50.000	0.00	0.00	0.00	3.10
199	209	1.079503	GTTTGGCGTCATGGAGTCTC	58.920	55.000	0.00	0.00	0.00	3.36
205	223	3.443681	AGATTAAAGGTTTGGCGTCATGG	59.556	43.478	0.00	0.00	0.00	3.66
296	314	9.838339	CAAGTAAGTATTATCACAATCTTCCCT	57.162	33.333	0.00	0.00	30.46	4.20
297	315	9.614792	ACAAGTAAGTATTATCACAATCTTCCC	57.385	33.333	0.00	0.00	30.46	3.97
311	329	9.971922	ACGACTACAACTTTACAAGTAAGTATT	57.028	29.630	0.00	0.00	41.91	1.89
314	332	9.801873	TTTACGACTACAACTTTACAAGTAAGT	57.198	29.630	0.00	0.00	41.91	2.24
373	391	7.328493	GGTTTCTGATACTGGTTTTATGTTTGC	59.672	37.037	0.00	0.00	0.00	3.68
402	420	7.077605	CGATGCTTCTTGTGTTTATCTGAAAA	58.922	34.615	0.00	0.00	0.00	2.29
406	424	5.120674	TCACGATGCTTCTTGTGTTTATCTG	59.879	40.000	6.07	0.00	34.08	2.90
415	433	1.291877	GCCGTCACGATGCTTCTTGT	61.292	55.000	0.00	0.00	0.00	3.16
416	434	1.421485	GCCGTCACGATGCTTCTTG	59.579	57.895	0.00	0.10	0.00	3.02
417	435	2.094659	CGCCGTCACGATGCTTCTT	61.095	57.895	0.00	0.00	34.06	2.52
429	447	0.737715	ATCTGAAGCTTGTCGCCGTC	60.738	55.000	2.10	0.00	40.39	4.79
642	685	2.125753	CTCTCGAGTGCTGTGGGC	60.126	66.667	13.13	0.00	42.22	5.36
649	692	1.347817	CTGCCGTTTCTCTCGAGTGC	61.348	60.000	13.13	5.81	0.00	4.40
805	890	2.750237	GTGGGACGGATGGTTGCC	60.750	66.667	0.00	0.00	0.00	4.52
806	891	3.124921	CGTGGGACGGATGGTTGC	61.125	66.667	0.00	0.00	38.08	4.17
807	892	3.124921	GCGTGGGACGGATGGTTG	61.125	66.667	0.00	0.00	42.82	3.77
808	893	3.632080	TGCGTGGGACGGATGGTT	61.632	61.111	0.00	0.00	42.82	3.67
992	1093	2.810400	CGGGGGTTGTGCATATAAGGAG	60.810	54.545	0.00	0.00	0.00	3.69
1029	1130	3.735029	GCGTCGGTCTCGGTCTGT	61.735	66.667	0.00	0.00	36.95	3.41
1030	1131	4.813526	CGCGTCGGTCTCGGTCTG	62.814	72.222	0.00	0.00	36.95	3.51
1049	1150	0.112412	GCCTCCTCTCCCCTCTCTAG	59.888	65.000	0.00	0.00	0.00	2.43
1488	1589	2.434884	AACGACATGGCAGAGGCG	60.435	61.111	15.36	15.36	42.47	5.52
1492	1593	1.278985	AGATTGGAACGACATGGCAGA	59.721	47.619	0.00	0.00	0.00	4.26
1763	1876	2.037620	CTCCATCCAGGGCTCCTTCG	62.038	65.000	0.00	0.00	38.24	3.79
1771	1884	4.598894	CGCGCTCTCCATCCAGGG	62.599	72.222	5.56	0.00	38.24	4.45
1773	1886	2.027314	CTCGCGCTCTCCATCCAG	59.973	66.667	5.56	0.00	0.00	3.86
1872	1985	2.816360	CGCCATGATGGAGCACACG	61.816	63.158	17.22	3.94	40.96	4.49
1944	2057	2.452813	CGGGTGCGTTTCTGATCGG	61.453	63.158	0.00	0.00	0.00	4.18
1948	2061	4.243008	TGCCGGGTGCGTTTCTGA	62.243	61.111	2.18	0.00	45.60	3.27
2001	2114	2.768920	CGCTTCTTGACGCGTCTCG	61.769	63.158	36.27	26.52	44.01	4.04
2002	2115	3.065015	CGCTTCTTGACGCGTCTC	58.935	61.111	36.27	15.85	44.01	3.36
2007	2120	4.451652	GCAGCCGCTTCTTGACGC	62.452	66.667	0.00	0.00	34.30	5.19
2008	2121	1.915614	AATGCAGCCGCTTCTTGACG	61.916	55.000	0.00	0.00	39.64	4.35
2009	2122	0.455633	CAATGCAGCCGCTTCTTGAC	60.456	55.000	0.00	0.00	39.64	3.18
2010	2123	1.878070	CAATGCAGCCGCTTCTTGA	59.122	52.632	0.00	0.00	39.64	3.02
2011	2124	1.804326	GCAATGCAGCCGCTTCTTG	60.804	57.895	0.00	0.00	39.64	3.02
2012	2125	1.808531	TTGCAATGCAGCCGCTTCTT	61.809	50.000	8.31	0.00	40.61	2.52
2013	2126	2.209064	CTTGCAATGCAGCCGCTTCT	62.209	55.000	8.31	0.00	40.61	2.85
2014	2127	1.804326	CTTGCAATGCAGCCGCTTC	60.804	57.895	8.31	0.00	40.61	3.86
2019	2132	1.142474	GTGAAACTTGCAATGCAGCC	58.858	50.000	8.31	0.00	40.61	4.85
2054	2167	0.658368	ATGGACGAGATCGACGAGTG	59.342	55.000	18.74	0.00	43.02	3.51
2068	2181	1.067821	GAGATGGAGACGGACATGGAC	59.932	57.143	0.00	0.00	0.00	4.02
2157	2277	7.521871	AAATGCTTCTGTTTCTCTTGAAGAT	57.478	32.000	0.00	0.00	38.42	2.40
2158	2278	6.293081	CGAAATGCTTCTGTTTCTCTTGAAGA	60.293	38.462	0.00	0.00	38.42	2.87
2161	2281	4.214119	CCGAAATGCTTCTGTTTCTCTTGA	59.786	41.667	0.00	0.00	33.32	3.02
2196	2316	3.056821	GGCCCAACTAATTCACAGGAAAC	60.057	47.826	0.00	0.00	36.43	2.78
2235	2355	1.616725	CCCAGCAGGAAAATAGCACCA	60.617	52.381	0.00	0.00	38.24	4.17
2239	2359	1.064389	ACTCCCCAGCAGGAAAATAGC	60.064	52.381	0.00	0.00	38.24	2.97
2251	2563	2.264794	CCCGAACGAACTCCCCAG	59.735	66.667	0.00	0.00	0.00	4.45
2266	2578	1.400494	GTGATAATCGCAACCACACCC	59.600	52.381	0.00	0.00	0.00	4.61
2419	2732	1.149174	CAAGTGTGAGCCCACTGGT	59.851	57.895	0.00	0.00	44.74	4.00
2862	3191	7.662604	ACCTAATCAATACGTTCGTTTTCTT	57.337	32.000	2.62	1.79	0.00	2.52
2868	3197	6.034256	CGAAAGAACCTAATCAATACGTTCGT	59.966	38.462	0.00	2.91	35.75	3.85

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.