AutoCloner

Multiple sequence alignment - TraesCS5A01G145000

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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	TraesCS5A01G145000	chr5A	100.000	3187	0	0	1	3187	321018521	321021707	0.000000e+00	5886
1	TraesCS5A01G145000	chr5A	89.305	187	17	3	1409	1593	321001440	321001625	6.880000e-57	231
2	TraesCS5A01G145000	chr5D	90.798	2206	102	43	1032	3187	233742816	233740662	0.000000e+00	2856
3	TraesCS5A01G145000	chr5D	86.207	232	26	6	1364	1593	233748953	233748726	2.460000e-61	246
4	TraesCS5A01G145000	chr5B	90.430	2184	90	48	1032	3187	271140618	271142710	0.000000e+00	2765
5	TraesCS5A01G145000	chr5B	89.305	187	17	3	1409	1593	271110178	271110363	6.880000e-57	231
6	TraesCS5A01G145000	chr4A	98.015	1058	15	6	1	1057	738866971	738865919	0.000000e+00	1832
7	TraesCS5A01G145000	chr2D	95.404	631	24	5	1	630	129149485	129150111	0.000000e+00	1000
8	TraesCS5A01G145000	chr7B	90.596	755	66	4	276	1028	73006068	73006819	0.000000e+00	996
9	TraesCS5A01G145000	chr7B	93.015	272	18	1	1	271	73005709	73005980	2.300000e-106	396
10	TraesCS5A01G145000	chr1B	87.893	636	66	8	403	1031	520407059	520406428	0.000000e+00	737
11	TraesCS5A01G145000	chr7A	95.272	423	19	1	606	1028	28987836	28988257	0.000000e+00	669
12	TraesCS5A01G145000	chr7A	95.261	422	19	1	606	1027	28894265	28894685	0.000000e+00	667
13	TraesCS5A01G145000	chr7A	95.261	422	19	1	606	1027	28935341	28935761	0.000000e+00	667
14	TraesCS5A01G145000	chr7A	95.024	422	20	1	606	1027	28865364	28865784	0.000000e+00	662
15	TraesCS5A01G145000	chr7A	93.721	430	26	1	606	1034	28824235	28824664	0.000000e+00	643
16	TraesCS5A01G145000	chr2B	94.614	427	23	0	606	1032	788187113	788186687	0.000000e+00	662
17	TraesCS5A01G145000	chr3D	76.534	1027	206	30	13	1027	129697066	129696063	2.180000e-146	529
18	TraesCS5A01G145000	chr1D	88.664	247	19	4	403	644	387190139	387189897	3.110000e-75	292

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	TraesCS5A01G145000	chr5A	321018521	321021707	3186	False	5886	5886	100.0000	1	3187	1	chr5A.!!$F2	3186
1	TraesCS5A01G145000	chr5D	233740662	233742816	2154	True	2856	2856	90.7980	1032	3187	1	chr5D.!!$R1	2155
2	TraesCS5A01G145000	chr5B	271140618	271142710	2092	False	2765	2765	90.4300	1032	3187	1	chr5B.!!$F2	2155
3	TraesCS5A01G145000	chr4A	738865919	738866971	1052	True	1832	1832	98.0150	1	1057	1	chr4A.!!$R1	1056
4	TraesCS5A01G145000	chr2D	129149485	129150111	626	False	1000	1000	95.4040	1	630	1	chr2D.!!$F1	629
5	TraesCS5A01G145000	chr7B	73005709	73006819	1110	False	696	996	91.8055	1	1028	2	chr7B.!!$F1	1027
6	TraesCS5A01G145000	chr1B	520406428	520407059	631	True	737	737	87.8930	403	1031	1	chr1B.!!$R1	628
7	TraesCS5A01G145000	chr3D	129696063	129697066	1003	True	529	529	76.5340	13	1027	1	chr3D.!!$R1	1014

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
882	977	0.605319	TTGAAGGGCGCGAGACAAAT	60.605	50.0	12.1	0.0	45.4	2.32	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2613	2755	0.467804	ACGGCAAAGGCAACCATTTT	59.532	45.0	0.0	0.0	43.71	1.82	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
288	374	3.215151	CTGAGCCTGATACGAAGAGGTA	58.785	50.000	0.00	0.00	0.00	3.08
294	380	4.382793	GCCTGATACGAAGAGGTAGGTTTT	60.383	45.833	0.00	0.00	0.00	2.43
578	673	1.197910	GGCTACTTCGCGTACATCAC	58.802	55.000	5.77	0.00	0.00	3.06
597	692	6.528321	CATCACATGATGGGTCTATAAGTGT	58.472	40.000	13.15	0.00	46.09	3.55
599	694	4.984785	CACATGATGGGTCTATAAGTGTCG	59.015	45.833	0.00	0.00	0.00	4.35
600	695	4.649674	ACATGATGGGTCTATAAGTGTCGT	59.350	41.667	0.00	0.00	0.00	4.34
854	949	3.491447	GGTTCACAGTTTTCAGCATGCTT	60.491	43.478	19.98	0.00	34.76	3.91
882	977	0.605319	TTGAAGGGCGCGAGACAAAT	60.605	50.000	12.10	0.00	45.40	2.32
883	978	1.298157	TGAAGGGCGCGAGACAAATG	61.298	55.000	12.10	0.00	45.40	2.32
1097	1202	1.228306	CCCCTACTCCTCGCTCGAT	60.228	63.158	0.00	0.00	0.00	3.59
1098	1203	0.036448	CCCCTACTCCTCGCTCGATA	59.964	60.000	0.00	0.00	0.00	2.92
1113	1218	1.272715	GATACATTCCACACGCGCG	59.727	57.895	30.96	30.96	0.00	6.86
1130	1235	2.428902	GCGCACACGTACACGGTA	60.429	61.111	0.30	0.00	44.95	4.02
1131	1236	2.709999	GCGCACACGTACACGGTAC	61.710	63.158	0.30	0.00	44.95	3.34
1132	1237	1.370293	CGCACACGTACACGGTACA	60.370	57.895	6.72	0.00	44.95	2.90
1133	1238	1.599422	CGCACACGTACACGGTACAC	61.599	60.000	6.72	0.00	44.95	2.90
1225	1334	1.994885	TTCCCGCCCATCTCATTCCC	61.995	60.000	0.00	0.00	0.00	3.97
1229	1338	1.696063	CGCCCATCTCATTCCCATTT	58.304	50.000	0.00	0.00	0.00	2.32
1230	1339	1.338973	CGCCCATCTCATTCCCATTTG	59.661	52.381	0.00	0.00	0.00	2.32
1633	1742	2.105006	TGATCACAGCAGCTTCTTCC	57.895	50.000	0.00	0.00	0.00	3.46
1640	1749	0.685097	AGCAGCTTCTTCCCACGTAA	59.315	50.000	0.00	0.00	0.00	3.18
1642	1751	1.197036	GCAGCTTCTTCCCACGTAAAC	59.803	52.381	0.00	0.00	0.00	2.01
1656	1765	2.222445	ACGTAAACACGCCATCAAACTC	59.778	45.455	0.00	0.00	36.44	3.01
1663	1772	1.796796	GCCATCAAACTCTGCGTCC	59.203	57.895	0.00	0.00	0.00	4.79
1672	1781	1.513586	CTCTGCGTCCGGTCGTTAC	60.514	63.158	21.70	6.61	0.00	2.50
1709	1818	2.421775	TCTCTGCTCGTGACAGATCTTC	59.578	50.000	10.52	0.00	42.99	2.87
1760	1869	1.415672	TTGCACCGGGAGAAGAAGGT	61.416	55.000	6.32	0.00	37.49	3.50
1769	1878	0.391793	GAGAAGAAGGTTGCCCGGAG	60.392	60.000	0.73	0.00	35.12	4.63
1859	1968	1.293179	CGCAGAGGTCCACATGTCA	59.707	57.895	0.00	0.00	0.00	3.58
1860	1969	0.320683	CGCAGAGGTCCACATGTCAA	60.321	55.000	0.00	0.00	0.00	3.18
1863	1972	1.000843	CAGAGGTCCACATGTCAACGA	59.999	52.381	0.00	0.00	0.00	3.85
1869	1978	1.014044	CCACATGTCAACGACCTCGG	61.014	60.000	0.00	0.00	44.95	4.63
2178	2287	2.872557	CACCAATGGCGTGCTCTG	59.127	61.111	0.00	0.00	0.00	3.35
2265	2374	2.988010	TGGTTGGATGAATCGGAGAG	57.012	50.000	0.00	0.00	43.63	3.20
2266	2375	1.486310	TGGTTGGATGAATCGGAGAGG	59.514	52.381	0.00	0.00	43.63	3.69
2322	2440	3.181536	CGATGTCGAAGAGCTGTTCTTTG	60.182	47.826	20.17	13.56	46.12	2.77
2335	2453	8.778358	AGAGCTGTTCTTTGTCTGTTTTATTAG	58.222	33.333	0.00	0.00	29.61	1.73
2336	2454	8.451908	AGCTGTTCTTTGTCTGTTTTATTAGT	57.548	30.769	0.00	0.00	0.00	2.24
2348	2466	8.803799	GTCTGTTTTATTAGTGTGTGGTTTTTG	58.196	33.333	0.00	0.00	0.00	2.44
2371	2489	5.008811	TGGTCATTTGTACGGGTTGTAAAAG	59.991	40.000	0.00	0.00	31.91	2.27
2426	2547	4.488126	TGCTGTCATTTTGTAAGCTGAC	57.512	40.909	0.00	0.00	38.74	3.51
2479	2600	2.736144	AAAATCTGGTCGAGTGCGTA	57.264	45.000	0.00	0.00	38.98	4.42
2480	2601	2.961526	AAATCTGGTCGAGTGCGTAT	57.038	45.000	0.00	0.00	38.98	3.06
2481	2602	4.380841	AAAATCTGGTCGAGTGCGTATA	57.619	40.909	0.00	0.00	38.98	1.47
2482	2603	3.627732	AATCTGGTCGAGTGCGTATAG	57.372	47.619	0.00	0.00	38.98	1.31
2483	2604	2.320745	TCTGGTCGAGTGCGTATAGA	57.679	50.000	0.00	0.00	38.98	1.98
2484	2605	2.635714	TCTGGTCGAGTGCGTATAGAA	58.364	47.619	0.00	0.00	38.98	2.10
2486	2607	3.441222	TCTGGTCGAGTGCGTATAGAAAA	59.559	43.478	0.00	0.00	38.98	2.29
2487	2608	4.097437	TCTGGTCGAGTGCGTATAGAAAAT	59.903	41.667	0.00	0.00	38.98	1.82
2489	2610	4.097437	TGGTCGAGTGCGTATAGAAAATCT	59.903	41.667	0.00	0.00	38.98	2.40
2491	2612	5.173492	GGTCGAGTGCGTATAGAAAATCTTC	59.827	44.000	0.00	0.00	38.98	2.87
2492	2613	5.742453	GTCGAGTGCGTATAGAAAATCTTCA	59.258	40.000	0.00	0.00	38.98	3.02
2493	2614	6.252869	GTCGAGTGCGTATAGAAAATCTTCAA	59.747	38.462	0.00	0.00	38.98	2.69
2494	2615	6.978659	TCGAGTGCGTATAGAAAATCTTCAAT	59.021	34.615	0.00	0.00	38.98	2.57
2495	2616	7.491372	TCGAGTGCGTATAGAAAATCTTCAATT	59.509	33.333	0.00	0.00	38.98	2.32
2496	2617	8.752254	CGAGTGCGTATAGAAAATCTTCAATTA	58.248	33.333	0.00	0.00	33.64	1.40
2497	2618	9.851043	GAGTGCGTATAGAAAATCTTCAATTAC	57.149	33.333	0.00	0.00	33.64	1.89
2540	2682	0.106708	GCACACTGTGACCTCAGGAA	59.893	55.000	15.86	0.00	39.48	3.36
2604	2746	4.650972	AGTGGATACCCAAAGCACTAAA	57.349	40.909	0.00	0.00	45.59	1.85
2605	2747	4.993028	AGTGGATACCCAAAGCACTAAAA	58.007	39.130	0.00	0.00	45.59	1.52
2606	2748	4.765339	AGTGGATACCCAAAGCACTAAAAC	59.235	41.667	0.00	0.00	45.59	2.43
2607	2749	4.765339	GTGGATACCCAAAGCACTAAAACT	59.235	41.667	0.00	0.00	45.59	2.66
2608	2750	5.941647	GTGGATACCCAAAGCACTAAAACTA	59.058	40.000	0.00	0.00	45.59	2.24
2609	2751	6.431852	GTGGATACCCAAAGCACTAAAACTAA	59.568	38.462	0.00	0.00	45.59	2.24
2611	2753	4.848562	ACCCAAAGCACTAAAACTAAGC	57.151	40.909	0.00	0.00	0.00	3.09
2612	2754	3.572682	ACCCAAAGCACTAAAACTAAGCC	59.427	43.478	0.00	0.00	0.00	4.35
2613	2755	3.572255	CCCAAAGCACTAAAACTAAGCCA	59.428	43.478	0.00	0.00	0.00	4.75
2706	2860	0.803380	GCAGGCGAACAATGAATGGC	60.803	55.000	0.00	0.00	0.00	4.40
2818	2972	2.829720	CTGGTGCAGGTTACCTAGTACA	59.170	50.000	2.52	0.77	39.01	2.90
2836	2990	0.443869	CAGAGGCAACGAATCCAACG	59.556	55.000	0.00	0.00	46.39	4.10
2841	2995	0.237235	GCAACGAATCCAACGCTGAA	59.763	50.000	0.00	0.00	0.00	3.02
2861	3015	1.898574	ACTCACCGCTTGGCAAAGG	60.899	57.895	16.87	16.87	35.53	3.11
2896	3050	1.796617	GCGAATTGCAATCCAGAGCAC	60.797	52.381	13.38	0.00	45.45	4.40
2902	3056	1.855213	GCAATCCAGAGCACGCACAA	61.855	55.000	0.00	0.00	0.00	3.33
2904	3058	0.035317	AATCCAGAGCACGCACAAGA	59.965	50.000	0.00	0.00	0.00	3.02
2916	3070	4.651994	CACGCACAAGACAGAAATATTCC	58.348	43.478	0.00	0.00	0.00	3.01
2917	3071	3.370978	ACGCACAAGACAGAAATATTCCG	59.629	43.478	0.00	0.00	0.00	4.30
2918	3072	3.370978	CGCACAAGACAGAAATATTCCGT	59.629	43.478	0.00	0.00	0.00	4.69
2993	3147	0.310854	ACAAAAGCCTTCTTTCCGCG	59.689	50.000	0.00	0.00	41.40	6.46
3034	3188	0.325272	TTTGGCGTACATACCAGGCA	59.675	50.000	0.00	0.00	37.24	4.75
3035	3189	0.107897	TTGGCGTACATACCAGGCAG	60.108	55.000	0.00	0.00	40.20	4.85
3036	3190	1.227556	GGCGTACATACCAGGCAGG	60.228	63.158	0.00	0.00	45.67	4.85
3037	3191	1.887707	GCGTACATACCAGGCAGGC	60.888	63.158	0.00	0.00	43.14	4.85
3102	3266	0.038166	TGCACAGGATGAAAGGGACC	59.962	55.000	0.00	0.00	39.69	4.46

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
288	374	3.006859	GCTATCCAACAAGGCAAAAACCT	59.993	43.478	0.00	0.00	43.91	3.50
294	380	3.010138	AGGTAAGCTATCCAACAAGGCAA	59.990	43.478	9.32	0.00	37.29	4.52
578	673	4.984785	CACGACACTTATAGACCCATCATG	59.015	45.833	0.00	0.00	0.00	3.07
597	692	0.107643	TGTCATCCCTGCAAACACGA	59.892	50.000	0.00	0.00	0.00	4.35
599	694	1.203052	CCATGTCATCCCTGCAAACAC	59.797	52.381	0.00	0.00	0.00	3.32
600	695	1.548081	CCATGTCATCCCTGCAAACA	58.452	50.000	0.00	0.00	0.00	2.83
1097	1202	3.483665	GCGCGCGTGTGGAATGTA	61.484	61.111	32.35	0.00	0.00	2.29
1113	1218	2.428902	TACCGTGTACGTGTGCGC	60.429	61.111	0.00	0.00	42.83	6.09
1127	1232	1.647346	TCGATTGCGATTGGTGTACC	58.353	50.000	1.05	0.00	42.51	3.34
1225	1334	0.317269	GCGCGATGGATGGACAAATG	60.317	55.000	12.10	0.00	0.00	2.32
1229	1338	2.511373	GTGCGCGATGGATGGACA	60.511	61.111	12.10	0.00	0.00	4.02
1230	1339	3.272334	GGTGCGCGATGGATGGAC	61.272	66.667	12.10	0.00	0.00	4.02
1404	1513	1.069090	CCACACCGTGTACACAGCT	59.931	57.895	24.98	4.12	0.00	4.24
1407	1516	1.067974	CTCTTCCACACCGTGTACACA	59.932	52.381	24.98	1.19	0.00	3.72
1622	1731	1.197036	GTTTACGTGGGAAGAAGCTGC	59.803	52.381	0.00	0.00	0.00	5.25
1640	1749	0.593128	GCAGAGTTTGATGGCGTGTT	59.407	50.000	0.00	0.00	0.00	3.32
1642	1751	1.133253	CGCAGAGTTTGATGGCGTG	59.867	57.895	0.00	0.00	42.51	5.34
1656	1765	0.168788	TTAGTAACGACCGGACGCAG	59.831	55.000	25.79	5.60	36.70	5.18
1663	1772	6.091986	AGAGTAAGAAGAGTTAGTAACGACCG	59.908	42.308	7.38	0.00	36.23	4.79
1672	1781	6.238103	CGAGCAGAGAGAGTAAGAAGAGTTAG	60.238	46.154	0.00	0.00	0.00	2.34
1709	1818	3.190849	CATCGGTCGTGCAGGCTG	61.191	66.667	10.94	10.94	0.00	4.85
1769	1878	1.513622	GGAGGAGCTCTTGTCCGTC	59.486	63.158	14.64	0.00	39.30	4.79
2178	2287	8.594881	ACAGTAGCTATTGATTATTACTGTGC	57.405	34.615	21.77	0.00	45.46	4.57
2187	2296	7.935755	ACCGTCTAGTACAGTAGCTATTGATTA	59.064	37.037	21.77	10.01	0.00	1.75
2188	2297	6.771749	ACCGTCTAGTACAGTAGCTATTGATT	59.228	38.462	21.77	9.46	0.00	2.57
2189	2298	6.205076	CACCGTCTAGTACAGTAGCTATTGAT	59.795	42.308	21.77	10.08	0.00	2.57
2190	2299	5.526479	CACCGTCTAGTACAGTAGCTATTGA	59.474	44.000	21.77	4.10	0.00	2.57
2322	2440	8.803799	CAAAAACCACACACTAATAAAACAGAC	58.196	33.333	0.00	0.00	0.00	3.51
2335	2453	4.249661	ACAAATGACCAAAAACCACACAC	58.750	39.130	0.00	0.00	0.00	3.82
2336	2454	4.543590	ACAAATGACCAAAAACCACACA	57.456	36.364	0.00	0.00	0.00	3.72
2348	2466	5.239087	TCTTTTACAACCCGTACAAATGACC	59.761	40.000	0.00	0.00	0.00	4.02
2371	2489	1.536284	GGCATGACGGTACTGCTACTC	60.536	57.143	0.23	0.00	36.18	2.59
2402	2523	5.173854	GTCAGCTTACAAAATGACAGCAAAC	59.826	40.000	0.00	3.25	41.32	2.93
2426	2547	9.756461	CGATTATCAAGATATTTGATGCTCAAG	57.244	33.333	16.73	6.16	37.70	3.02
2447	2568	6.759356	TCGACCAGATTTTATCAAAGCGATTA	59.241	34.615	0.00	0.00	33.25	1.75
2604	2746	3.401033	GGCAACCATTTTGGCTTAGTT	57.599	42.857	3.48	0.00	42.67	2.24
2611	2753	1.237533	GGCAAAGGCAACCATTTTGG	58.762	50.000	0.00	0.00	42.66	3.28
2612	2754	0.867086	CGGCAAAGGCAACCATTTTG	59.133	50.000	0.00	0.00	43.71	2.44
2613	2755	0.467804	ACGGCAAAGGCAACCATTTT	59.532	45.000	0.00	0.00	43.71	1.82
2706	2860	1.662446	CTTTGGCGCAGTTGCTTGG	60.662	57.895	10.83	0.00	39.32	3.61
2818	2972	1.298859	GCGTTGGATTCGTTGCCTCT	61.299	55.000	0.00	0.00	0.00	3.69
2836	2990	1.571460	CAAGCGGTGAGTGTTCAGC	59.429	57.895	0.00	0.00	45.96	4.26
2841	2995	1.447317	CTTTGCCAAGCGGTGAGTGT	61.447	55.000	0.00	0.00	33.28	3.55
2861	3015	3.807538	CGCCACATCTGCTGGTGC	61.808	66.667	3.41	0.00	32.64	5.01
2896	3050	3.370978	ACGGAATATTTCTGTCTTGTGCG	59.629	43.478	0.00	0.00	45.92	5.34
2916	3070	2.602257	TAGGATGTGCTGATGGAACG	57.398	50.000	0.00	0.00	0.00	3.95
2917	3071	4.077300	TGATAGGATGTGCTGATGGAAC	57.923	45.455	0.00	0.00	0.00	3.62
2918	3072	4.103627	ACATGATAGGATGTGCTGATGGAA	59.896	41.667	0.00	0.00	35.17	3.53
2993	3147	0.673985	GGACCTTTGTTCTTGTGGCC	59.326	55.000	0.00	0.00	0.00	5.36
3034	3188	1.806542	CATCTTTTACGCTGTGTGCCT	59.193	47.619	3.71	0.00	38.78	4.75
3035	3189	1.804151	TCATCTTTTACGCTGTGTGCC	59.196	47.619	3.71	0.00	38.78	5.01
3036	3190	3.536158	TTCATCTTTTACGCTGTGTGC	57.464	42.857	3.71	0.00	38.57	4.57
3037	3191	6.086765	GTCATTTTCATCTTTTACGCTGTGTG	59.913	38.462	3.71	0.00	0.00	3.82
3102	3266	2.629656	CGGAGCCTGGGCAACTTTG	61.630	63.158	14.39	0.00	44.88	2.77

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.