AutoCloner

Multiple sequence alignment - TraesCS5D01G452000

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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	TraesCS5D01G452000	chr5D	100.000	2985	0	0	1	2985	499957296	499954312	0.000000e+00	5513.0
1	TraesCS5D01G452000	chr5D	82.300	2000	235	66	4	1976	499446978	499448885	0.000000e+00	1622.0
2	TraesCS5D01G452000	chr5D	82.451	1134	169	23	5	1116	499652120	499653245	0.000000e+00	965.0
3	TraesCS5D01G452000	chr5D	85.550	436	39	11	1340	1766	499653393	499653813	4.570000e-118	435.0
4	TraesCS5D01G452000	chr5A	92.784	2647	114	31	3	2599	624476314	624473695	0.000000e+00	3759.0
5	TraesCS5D01G452000	chr5A	82.692	1976	226	63	54	1976	623684200	623686112	0.000000e+00	1648.0
6	TraesCS5D01G452000	chr5A	83.422	1128	164	21	3	1116	623954018	623955136	0.000000e+00	1026.0
7	TraesCS5D01G452000	chr5A	86.453	406	33	8	2601	2985	624473664	624473260	2.750000e-115	425.0
8	TraesCS5D01G452000	chr5A	83.133	498	50	16	1281	1766	623955234	623955709	9.890000e-115	424.0
9	TraesCS5D01G452000	chr5A	100.000	28	0	0	2146	2173	473114359	473114332	5.000000e-03	52.8
10	TraesCS5D01G452000	chr5B	93.612	2348	110	19	1	2323	621399932	621397600	0.000000e+00	3469.0
11	TraesCS5D01G452000	chr5B	82.271	2008	247	65	3	1976	620305954	620307886	0.000000e+00	1635.0
12	TraesCS5D01G452000	chr5B	81.682	1736	206	62	42	1734	620668469	620670135	0.000000e+00	1341.0
13	TraesCS5D01G452000	chr5B	81.996	1122	164	26	25	1116	620825428	620826541	0.000000e+00	918.0
14	TraesCS5D01G452000	chr5B	85.903	681	38	13	2343	2985	621397530	621396870	0.000000e+00	673.0
15	TraesCS5D01G452000	chr5B	80.431	649	66	34	1129	1766	620826515	620827113	3.530000e-119	438.0
16	TraesCS5D01G452000	chr6B	96.875	32	1	0	2145	2176	164028516	164028485	1.000000e-03	54.7
17	TraesCS5D01G452000	chr2B	100.000	29	0	0	2145	2173	295365969	295365997	1.000000e-03	54.7
18	TraesCS5D01G452000	chr4B	100.000	28	0	0	2146	2173	663639967	663639940	5.000000e-03	52.8
19	TraesCS5D01G452000	chr3D	100.000	28	0	0	2146	2173	15452863	15452836	5.000000e-03	52.8
20	TraesCS5D01G452000	chr2D	100.000	28	0	0	2146	2173	159600260	159600287	5.000000e-03	52.8
21	TraesCS5D01G452000	chr1A	100.000	28	0	0	2146	2173	551882195	551882168	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	TraesCS5D01G452000	chr5D	499954312	499957296	2984	True	5513	5513	100.0000	1	2985	1	chr5D.!!$R1	2984
1	TraesCS5D01G452000	chr5D	499446978	499448885	1907	False	1622	1622	82.3000	4	1976	1	chr5D.!!$F1	1972
2	TraesCS5D01G452000	chr5D	499652120	499653813	1693	False	700	965	84.0005	5	1766	2	chr5D.!!$F2	1761
3	TraesCS5D01G452000	chr5A	624473260	624476314	3054	True	2092	3759	89.6185	3	2985	2	chr5A.!!$R2	2982
4	TraesCS5D01G452000	chr5A	623684200	623686112	1912	False	1648	1648	82.6920	54	1976	1	chr5A.!!$F1	1922
5	TraesCS5D01G452000	chr5A	623954018	623955709	1691	False	725	1026	83.2775	3	1766	2	chr5A.!!$F2	1763
6	TraesCS5D01G452000	chr5B	621396870	621399932	3062	True	2071	3469	89.7575	1	2985	2	chr5B.!!$R1	2984
7	TraesCS5D01G452000	chr5B	620305954	620307886	1932	False	1635	1635	82.2710	3	1976	1	chr5B.!!$F1	1973
8	TraesCS5D01G452000	chr5B	620668469	620670135	1666	False	1341	1341	81.6820	42	1734	1	chr5B.!!$F2	1692
9	TraesCS5D01G452000	chr5B	620825428	620827113	1685	False	678	918	81.2135	25	1766	2	chr5B.!!$F3	1741

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
120	133	0.466555	TTTCCCCAACCACAGGAACG	60.467	55.0	0.0	0.0	39.36	3.95	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2011	2219	0.392595	GGGGAAAACTGCTACGGGAG	60.393	60.0	0.0	0.0	36.93	4.3	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
51	52	9.751542	ATCGAGAAACTATCTGAAATTACGATT	57.248	29.630	0.00	0.00	38.96	3.34
52	53	9.020813	TCGAGAAACTATCTGAAATTACGATTG	57.979	33.333	0.00	0.00	38.96	2.67
120	133	0.466555	TTTCCCCAACCACAGGAACG	60.467	55.000	0.00	0.00	39.36	3.95
418	435	1.924524	CGTTAACCAGCTACATGACCG	59.075	52.381	0.00	0.00	0.00	4.79
437	454	0.867329	GCGCCGGAAAATCTCATTGC	60.867	55.000	5.05	0.00	0.00	3.56
536	553	1.153086	CCGGCTCATTTCTCCCAGG	60.153	63.158	0.00	0.00	0.00	4.45
576	593	8.849168	TCACACAAACTCAATCTCATTACAAAT	58.151	29.630	0.00	0.00	0.00	2.32
580	597	8.299570	ACAAACTCAATCTCATTACAAATCCAC	58.700	33.333	0.00	0.00	0.00	4.02
804	822	4.160635	GGTTTGATGACGGCCGCG	62.161	66.667	28.58	1.99	0.00	6.46
1272	1349	1.126846	CATTGTCGTTCTCTGTTCGCC	59.873	52.381	0.00	0.00	0.00	5.54
1352	1433	1.028130	TGTTTTTGCGCAGATGGTGA	58.972	45.000	11.31	0.00	0.00	4.02
1383	1464	2.573869	CGCGCTGAAGGAGAGGAA	59.426	61.111	5.56	0.00	0.00	3.36
1489	1570	0.644331	CGCAGATCAAGAAGCTCGTG	59.356	55.000	0.00	0.00	0.00	4.35
1567	1648	2.335712	GCCCAAGAAGCCCAAGACG	61.336	63.158	0.00	0.00	0.00	4.18
1993	2200	1.474879	GCCAAGAAGTAGAGCGTCTCT	59.525	52.381	12.81	12.81	43.83	3.10
2011	2219	0.951040	CTGTCCTCCCGCAACAAGTC	60.951	60.000	0.00	0.00	0.00	3.01
2015	2223	1.376037	CTCCCGCAACAAGTCTCCC	60.376	63.158	0.00	0.00	0.00	4.30
2016	2224	2.742372	CCCGCAACAAGTCTCCCG	60.742	66.667	0.00	0.00	0.00	5.14
2335	2565	3.056322	GCCCTGCAATTCTTGTGATTTCT	60.056	43.478	0.00	0.00	0.00	2.52
2336	2566	4.491676	CCCTGCAATTCTTGTGATTTCTG	58.508	43.478	0.00	0.00	0.00	3.02
2383	2647	7.576403	TGGAATGTGATGGAATTTGAGATCTA	58.424	34.615	0.00	0.00	0.00	1.98
2422	2687	9.646427	TGTTTGTATTTTAGTATGGAAAATGCC	57.354	29.630	4.09	0.00	37.80	4.40
2427	2692	9.476202	GTATTTTAGTATGGAAAATGCCAATCC	57.524	33.333	4.09	0.00	42.16	3.01
2428	2693	6.478512	TTTAGTATGGAAAATGCCAATCCC	57.521	37.500	0.00	0.00	42.16	3.85
2479	2751	0.179073	AGTACGTGGCTGGCATCATC	60.179	55.000	7.33	0.00	0.00	2.92
2480	2752	0.461870	GTACGTGGCTGGCATCATCA	60.462	55.000	7.33	0.00	0.00	3.07
2481	2753	0.469494	TACGTGGCTGGCATCATCAT	59.531	50.000	7.33	0.00	0.00	2.45
2482	2754	0.469494	ACGTGGCTGGCATCATCATA	59.531	50.000	7.33	0.00	0.00	2.15
2483	2755	1.072806	ACGTGGCTGGCATCATCATAT	59.927	47.619	7.33	0.00	0.00	1.78
2484	2756	1.736126	CGTGGCTGGCATCATCATATC	59.264	52.381	7.33	0.00	0.00	1.63
2485	2757	2.786777	GTGGCTGGCATCATCATATCA	58.213	47.619	7.33	0.00	0.00	2.15
2486	2758	3.353557	GTGGCTGGCATCATCATATCAT	58.646	45.455	7.33	0.00	0.00	2.45
2544	2820	3.463585	TACATGACCGGGGCGTCC	61.464	66.667	6.32	0.00	31.35	4.79
2564	2840	3.188460	TCCGTTACTGCTGCTGAAATTTC	59.812	43.478	13.69	11.41	0.00	2.17
2599	2929	4.157840	GCGATTTTGGATGGACCTACTTTT	59.842	41.667	0.00	0.00	39.86	2.27
2636	2966	5.585047	ACGCATGGTTTTTAGGTAGATCTTC	59.415	40.000	0.00	0.00	0.00	2.87
2678	3009	6.258287	GTCTTGGAGAGATGAATGTGATCTTG	59.742	42.308	0.00	0.00	36.61	3.02
2679	3010	4.449131	TGGAGAGATGAATGTGATCTTGC	58.551	43.478	0.00	0.00	29.97	4.01
2708	3058	3.943381	AGTAAGCTAATTGGCCCGTTAAC	59.057	43.478	10.54	0.00	0.00	2.01
2767	3126	2.689471	TGCAGGAAAATGAATGGGATCG	59.311	45.455	0.00	0.00	0.00	3.69
2811	3170	1.226974	CGATGCCTGTAGTGTCGGG	60.227	63.158	0.00	0.00	36.96	5.14
2815	3174	2.181021	CCTGTAGTGTCGGGCGTC	59.819	66.667	0.00	0.00	0.00	5.19
2842	3202	0.170339	GGGTACGCCTGTTTTGCATC	59.830	55.000	0.00	0.00	34.45	3.91
2919	3285	2.835895	GTGGCCGTTTTGGGTGGT	60.836	61.111	0.00	0.00	38.63	4.16
2920	3286	2.835431	TGGCCGTTTTGGGTGGTG	60.835	61.111	0.00	0.00	38.63	4.17
2921	3287	3.611674	GGCCGTTTTGGGTGGTGG	61.612	66.667	0.00	0.00	38.63	4.61
2922	3288	2.835895	GCCGTTTTGGGTGGTGGT	60.836	61.111	0.00	0.00	38.63	4.16
2923	3289	3.124686	CCGTTTTGGGTGGTGGTG	58.875	61.111	0.00	0.00	0.00	4.17
2924	3290	2.494530	CCGTTTTGGGTGGTGGTGG	61.495	63.158	0.00	0.00	0.00	4.61
2968	3334	2.747855	GGGTTCTGCCGCCTGAAG	60.748	66.667	0.00	0.00	38.44	3.02

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
51	52	7.244886	TGTTCTACCTCTCAGATCAAATTCA	57.755	36.000	0.00	0.00	0.00	2.57
52	53	7.201600	GCTTGTTCTACCTCTCAGATCAAATTC	60.202	40.741	0.00	0.00	0.00	2.17
94	107	2.105821	CTGTGGTTGGGGAAAGTCTACA	59.894	50.000	0.00	0.00	0.00	2.74
201	214	3.000819	TGCTCCGGTAGGTGTGGG	61.001	66.667	0.00	0.00	39.05	4.61
271	284	4.980805	TGTGTGAGTTCGGCCGGC	62.981	66.667	27.83	21.18	0.00	6.13
418	435	0.867329	GCAATGAGATTTTCCGGCGC	60.867	55.000	0.00	0.00	0.00	6.53
536	553	6.503524	AGTTTGTGTGATTTGGTTGTGTATC	58.496	36.000	0.00	0.00	0.00	2.24
576	593	0.535335	GTGTAGGCAAGGATCGTGGA	59.465	55.000	0.00	0.00	0.00	4.02
580	597	1.067060	TCATCGTGTAGGCAAGGATCG	59.933	52.381	0.00	0.00	0.00	3.69
830	848	1.377202	GCGCTGATTGGTCAAGGGA	60.377	57.895	0.00	0.00	33.05	4.20
1105	1162	1.745489	CCTTGGTAGCCTTGGTCGC	60.745	63.158	0.00	0.00	0.00	5.19
1116	1173	1.076549	CTTGGCCTTGGCCTTGGTA	59.923	57.895	28.37	7.84	0.00	3.25
1136	1211	4.740822	CCTTGGGGGTCTTGGCGG	62.741	72.222	0.00	0.00	0.00	6.13
1139	1214	3.204467	TTCGCCTTGGGGGTCTTGG	62.204	63.158	3.89	0.00	36.95	3.61
1140	1215	1.675641	CTTCGCCTTGGGGGTCTTG	60.676	63.158	3.89	0.00	36.95	3.02
1141	1216	1.423794	TTCTTCGCCTTGGGGGTCTT	61.424	55.000	3.89	0.00	36.95	3.01
1142	1217	1.842381	CTTCTTCGCCTTGGGGGTCT	61.842	60.000	3.89	0.00	36.95	3.85
1143	1218	1.377333	CTTCTTCGCCTTGGGGGTC	60.377	63.158	3.89	0.00	36.95	4.46
1144	1219	2.757077	CTTCTTCGCCTTGGGGGT	59.243	61.111	3.89	0.00	36.95	4.95
1145	1220	2.751837	GCTTCTTCGCCTTGGGGG	60.752	66.667	3.89	0.00	36.96	5.40
1146	1221	2.751837	GGCTTCTTCGCCTTGGGG	60.752	66.667	0.00	0.00	46.63	4.96
1239	1316	1.142778	GACAATGGAGCGAGCGAGAC	61.143	60.000	0.00	0.00	0.00	3.36
1272	1349	1.797933	CGAACAGAGAGCACGACGG	60.798	63.158	0.00	0.00	0.00	4.79
1877	2081	3.984732	GGCCTTCTTGGGGGTGCT	61.985	66.667	0.00	0.00	36.00	4.40
1993	2200	1.070786	GACTTGTTGCGGGAGGACA	59.929	57.895	0.00	0.00	0.00	4.02
2011	2219	0.392595	GGGGAAAACTGCTACGGGAG	60.393	60.000	0.00	0.00	36.93	4.30
2015	2223	1.804748	GAACAGGGGAAAACTGCTACG	59.195	52.381	0.00	0.00	39.55	3.51
2016	2224	2.814336	CAGAACAGGGGAAAACTGCTAC	59.186	50.000	0.00	0.00	39.55	3.58
2100	2310	1.448893	TACGCCGGATTGAACCAGC	60.449	57.895	5.05	0.00	0.00	4.85
2243	2454	2.857483	TGTTTTCGACACCCATCACAT	58.143	42.857	0.00	0.00	32.00	3.21
2245	2456	3.701532	TTTGTTTTCGACACCCATCAC	57.298	42.857	0.00	0.00	38.18	3.06
2246	2457	5.049060	CACTATTTGTTTTCGACACCCATCA	60.049	40.000	0.00	0.00	38.18	3.07
2247	2458	5.390613	CACTATTTGTTTTCGACACCCATC	58.609	41.667	0.00	0.00	38.18	3.51
2248	2459	4.320935	GCACTATTTGTTTTCGACACCCAT	60.321	41.667	0.00	0.00	38.18	4.00
2249	2460	3.003897	GCACTATTTGTTTTCGACACCCA	59.996	43.478	0.00	0.00	38.18	4.51
2250	2461	3.003897	TGCACTATTTGTTTTCGACACCC	59.996	43.478	0.00	0.00	38.18	4.61
2335	2565	2.466846	TCTCACCCGATTTCAGATCCA	58.533	47.619	0.00	0.00	0.00	3.41
2336	2566	3.323403	AGATCTCACCCGATTTCAGATCC	59.677	47.826	0.00	0.00	40.21	3.36
2389	2654	8.018520	TCCATACTAAAATACAAACAAGCAACG	58.981	33.333	0.00	0.00	0.00	4.10
2418	2683	0.625849	AAAGACGAGGGGATTGGCAT	59.374	50.000	0.00	0.00	0.00	4.40
2419	2684	1.281419	TAAAGACGAGGGGATTGGCA	58.719	50.000	0.00	0.00	0.00	4.92
2420	2685	2.413310	TTAAAGACGAGGGGATTGGC	57.587	50.000	0.00	0.00	0.00	4.52
2422	2687	4.399303	AGCAAATTAAAGACGAGGGGATTG	59.601	41.667	0.00	0.00	0.00	2.67
2424	2689	4.236527	AGCAAATTAAAGACGAGGGGAT	57.763	40.909	0.00	0.00	0.00	3.85
2425	2690	3.713826	AGCAAATTAAAGACGAGGGGA	57.286	42.857	0.00	0.00	0.00	4.81
2426	2691	3.128764	GGAAGCAAATTAAAGACGAGGGG	59.871	47.826	0.00	0.00	0.00	4.79
2427	2692	3.181510	CGGAAGCAAATTAAAGACGAGGG	60.182	47.826	0.00	0.00	0.00	4.30
2428	2693	3.435671	ACGGAAGCAAATTAAAGACGAGG	59.564	43.478	0.00	0.00	0.00	4.63
2482	2754	8.689972	CCTTTTCCTTTCATTTACAGCTATGAT	58.310	33.333	0.00	0.00	31.34	2.45
2483	2755	7.362920	GCCTTTTCCTTTCATTTACAGCTATGA	60.363	37.037	0.00	0.00	0.00	2.15
2484	2756	6.753744	GCCTTTTCCTTTCATTTACAGCTATG	59.246	38.462	0.00	0.00	0.00	2.23
2485	2757	6.665248	AGCCTTTTCCTTTCATTTACAGCTAT	59.335	34.615	0.00	0.00	0.00	2.97
2486	2758	6.010219	AGCCTTTTCCTTTCATTTACAGCTA	58.990	36.000	0.00	0.00	0.00	3.32
2544	2820	3.120683	TCGAAATTTCAGCAGCAGTAACG	60.121	43.478	17.99	0.31	0.00	3.18
2551	2827	7.553034	CATTGAATATTCGAAATTTCAGCAGC	58.447	34.615	17.99	2.07	30.45	5.25
2564	2840	6.088483	CCATCCAAAATCGCATTGAATATTCG	59.912	38.462	10.80	0.00	0.00	3.34
2599	2929	2.691526	ACCATGCGTACGAAGGAAGATA	59.308	45.455	21.65	0.00	0.00	1.98
2636	2966	4.083271	CCAAGACCGCCTTTCTTTCTAAAG	60.083	45.833	0.00	0.00	36.43	1.85
2652	2983	4.478206	TCACATTCATCTCTCCAAGACC	57.522	45.455	0.00	0.00	36.65	3.85
2678	3009	3.247886	GCCAATTAGCTTACTCCGTTAGC	59.752	47.826	0.00	0.00	38.30	3.09
2679	3010	3.808174	GGCCAATTAGCTTACTCCGTTAG	59.192	47.826	0.00	0.00	0.00	2.34
2708	3058	2.046023	TCCAAGCCTGCATCACCG	60.046	61.111	0.00	0.00	0.00	4.94
2767	3126	0.944788	GCGGGCCGATTAGCTAAGAC	60.945	60.000	33.44	2.51	0.00	3.01
2800	3159	2.669229	TCGACGCCCGACACTACA	60.669	61.111	0.00	0.00	43.23	2.74
2828	3188	1.135315	CTCCGATGCAAAACAGGCG	59.865	57.895	0.00	0.00	0.00	5.52
2831	3191	1.135315	CCGCTCCGATGCAAAACAG	59.865	57.895	0.00	0.00	0.00	3.16
2940	3306	2.035832	CGGCAGAACCCAAAAACTGAAT	59.964	45.455	0.00	0.00	33.26	2.57
2944	3310	1.739667	GCGGCAGAACCCAAAAACT	59.260	52.632	0.00	0.00	33.26	2.66

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.