AutoCloner

Multiple sequence alignment - TraesCS1D01G450000

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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	TraesCS1D01G450000	chr1D	100.000	3315	0	0	1	3315	492502596	492499282	0.000000e+00	6122.0
1	TraesCS1D01G450000	chr1D	88.115	976	97	10	1447	2413	492513556	492512591	0.000000e+00	1142.0
2	TraesCS1D01G450000	chr1D	73.675	566	123	20	1696	2251	7129630	7129081	2.610000e-46	196.0
3	TraesCS1D01G450000	chr1D	73.179	563	113	27	1696	2242	7653452	7653992	5.690000e-38	169.0
4	TraesCS1D01G450000	chr1B	94.925	2916	108	15	420	3315	685170489	685167594	0.000000e+00	4529.0
5	TraesCS1D01G450000	chr1B	89.073	723	72	5	1695	2413	685179537	685178818	0.000000e+00	891.0
6	TraesCS1D01G450000	chr1B	91.919	198	11	4	228	422	685170712	685170517	4.210000e-69	272.0
7	TraesCS1D01G450000	chr1B	94.406	143	8	0	3	145	685170883	685170741	1.550000e-53	220.0
8	TraesCS1D01G450000	chr1A	94.542	2913	108	14	420	3315	590833910	590831032	0.000000e+00	4451.0
9	TraesCS1D01G450000	chr1A	87.219	978	105	13	1447	2413	590863337	590862369	0.000000e+00	1096.0
10	TraesCS1D01G450000	chr1A	95.952	420	12	1	3	422	590834352	590833938	0.000000e+00	676.0
11	TraesCS1D01G450000	chr1A	86.179	123	15	2	2130	2251	8675559	8675438	7.460000e-27	132.0
12	TraesCS1D01G450000	chr3A	89.583	48	4	1	3263	3310	383694341	383694387	3.570000e-05	60.2

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	TraesCS1D01G450000	chr1D	492499282	492502596	3314	True	6122.000000	6122	100.000	1	3315	1	chr1D.!!$R2	3314
1	TraesCS1D01G450000	chr1D	492512591	492513556	965	True	1142.000000	1142	88.115	1447	2413	1	chr1D.!!$R3	966
2	TraesCS1D01G450000	chr1B	685167594	685170883	3289	True	1673.666667	4529	93.750	3	3315	3	chr1B.!!$R2	3312
3	TraesCS1D01G450000	chr1B	685178818	685179537	719	True	891.000000	891	89.073	1695	2413	1	chr1B.!!$R1	718
4	TraesCS1D01G450000	chr1A	590831032	590834352	3320	True	2563.500000	4451	95.247	3	3315	2	chr1A.!!$R3	3312
5	TraesCS1D01G450000	chr1A	590862369	590863337	968	True	1096.000000	1096	87.219	1447	2413	1	chr1A.!!$R2	966

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	Hairpin	End Stability	Orientation
677	718	0.665369	GTTCAAGTGCCATGTGCTGC	60.665	55.000	7.54	42.00	5.25	F
734	775	0.965439	TTCTTTGGTTCCATTGCCCG	59.035	50.000	0.00	0.00	6.13	F
770	811	1.194772	GTTGAGGTTGCACTCGCTTAC	59.805	52.381	0.00	40.39	2.34	F

Position	MSA Position	Penalty	Sequence	TM	GC	Hairpin	End Stability	Orientation
1924	1980	1.021202	CTTCGTTCACCTTGCAACCA	58.979	50.000	0.0	3.67	R
1999	2055	1.871772	CTTTGCAACAGCCTCCTCG	59.128	57.895	0.0	4.63	R
2743	2822	1.220206	CTTCTCACAGCTCCGGCAT	59.780	57.895	41.7	4.40	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
79	80	2.089201	CCTTCCCCACCACGAAAATAC	58.911	52.381	0.00	0.00	0.00	1.89
222	223	3.441163	CATAATACCTGTGCACGTACGT	58.559	45.455	16.72	16.72	0.00	3.57
296	304	6.774170	TGGGAGAAGTAGCGTACTAATTATCA	59.226	38.462	9.28	0.00	43.17	2.15
340	348	5.178797	CCAGCCTATATAGAACCAATTCCG	58.821	45.833	11.53	0.00	35.18	4.30
341	349	4.631813	CAGCCTATATAGAACCAATTCCGC	59.368	45.833	11.53	2.19	35.18	5.54
345	353	1.583054	ATAGAACCAATTCCGCGAGC	58.417	50.000	8.23	0.00	35.18	5.03
632	673	1.373570	GGCTTCTTTCCGAGGTGATG	58.626	55.000	0.00	0.00	0.00	3.07
677	718	0.665369	GTTCAAGTGCCATGTGCTGC	60.665	55.000	7.54	0.00	42.00	5.25
718	759	5.126061	GTGGATGTCTAACATTGCCAATTCT	59.874	40.000	2.97	0.00	39.27	2.40
720	761	6.211184	TGGATGTCTAACATTGCCAATTCTTT	59.789	34.615	0.00	0.00	39.27	2.52
734	775	0.965439	TTCTTTGGTTCCATTGCCCG	59.035	50.000	0.00	0.00	0.00	6.13
751	792	2.292292	GCCCGGCGTAATGAATTATTGT	59.708	45.455	6.01	0.00	0.00	2.71
770	811	1.194772	GTTGAGGTTGCACTCGCTTAC	59.805	52.381	0.00	0.00	40.39	2.34
776	817	1.727335	GTTGCACTCGCTTACTCCTTC	59.273	52.381	0.00	0.00	39.64	3.46
786	827	3.084786	GCTTACTCCTTCCTGCAATTGT	58.915	45.455	7.40	0.00	0.00	2.71
794	835	4.344679	TCCTTCCTGCAATTGTGATGTTTT	59.655	37.500	7.40	0.00	0.00	2.43
800	841	9.941325	TTCCTGCAATTGTGATGTTTTTATATT	57.059	25.926	7.40	0.00	0.00	1.28
1023	1068	5.122512	TGATTATAGCTACGTTCTCTGCC	57.877	43.478	0.00	0.00	0.00	4.85
1074	1119	3.772025	AGAACCATACTGAGAGGGAACAG	59.228	47.826	0.00	0.00	39.65	3.16
1089	1134	5.006386	AGGGAACAGTTTGTTGATGAGATC	58.994	41.667	0.00	0.00	41.28	2.75
1284	1329	4.938080	AGACATAAGGCTCATACAGTTCG	58.062	43.478	0.00	0.00	0.00	3.95
1336	1381	1.699083	TCCAGATGAGGAAACAGCACA	59.301	47.619	0.00	0.00	33.93	4.57
1416	1466	7.290248	ACAAAGAGTATAGGGCTGCTTTAGATA	59.710	37.037	0.00	0.00	0.00	1.98
1513	1564	3.131046	CCTGTTGTGAGGAAACAAAAGCT	59.869	43.478	2.33	0.00	42.00	3.74
1778	1834	8.543774	ACTATATGAAGACCAAACAGTCAATCT	58.456	33.333	0.00	0.00	39.34	2.40
1904	1960	4.202131	GGAGTGAATCTTCCTACCCTTACG	60.202	50.000	0.00	0.00	0.00	3.18
1924	1980	5.479124	ACGTGGACCAGAGTAATAGTTTT	57.521	39.130	0.00	0.00	0.00	2.43
1940	1996	1.923864	GTTTTGGTTGCAAGGTGAACG	59.076	47.619	0.00	0.00	0.00	3.95
1963	2019	5.278512	CGAAGCAGTAGTAGCAAGGATATCA	60.279	44.000	4.83	0.00	0.00	2.15
1999	2055	1.338579	CCCACAACAGAGGAAGCTCTC	60.339	57.143	0.00	0.00	0.00	3.20
2048	2104	6.038161	CGTGATTATCTATTTGAAGTGGCCAA	59.962	38.462	7.24	0.00	0.00	4.52
2269	2343	1.750778	GTCCATAATGGGCAAGGTGTG	59.249	52.381	0.00	0.00	42.98	3.82
2522	2601	6.183360	GCCACGCCAAAATGTTTTTCTTATAG	60.183	38.462	0.00	0.00	0.00	1.31
2573	2652	2.798976	TGTGCAGCAACCTTTTCATC	57.201	45.000	0.00	0.00	0.00	2.92
2693	2772	4.720775	TGTACAATATGATCCATGGCCA	57.279	40.909	8.56	8.56	0.00	5.36
2743	2822	4.162320	AGACAAGCCAAGAGAATATTCCGA	59.838	41.667	11.92	0.00	0.00	4.55
2786	2865	9.778741	AGTGTAATTCAGTTTGAAGATACAGAA	57.221	29.630	14.99	0.00	40.28	3.02
2831	2910	9.824216	ATACACCTGGTATTACTCTATGTACAT	57.176	33.333	13.93	13.93	39.73	2.29
2862	2941	5.819991	AGGACCTGATCAATTACACACAAT	58.180	37.500	0.00	0.00	0.00	2.71
2946	3025	4.284550	TTCCTGGTGTGCTGCCCC	62.285	66.667	0.00	0.00	0.00	5.80
2960	3039	2.814336	GCTGCCCCGAGGATATTTTTAG	59.186	50.000	0.00	0.00	33.47	1.85
2963	3042	3.203487	TGCCCCGAGGATATTTTTAGGTT	59.797	43.478	0.00	0.00	33.47	3.50
2971	3050	6.538742	CGAGGATATTTTTAGGTTTGCTCTCA	59.461	38.462	0.00	0.00	0.00	3.27
2986	3065	1.696336	CTCTCATCGGGGGAACATCAT	59.304	52.381	0.00	0.00	0.00	2.45
3159	3247	5.470437	CGCTACAAGATCTACATCAGACCTA	59.530	44.000	0.00	0.00	35.62	3.08
3183	3271	0.879090	GCTTCAACGGGGTAAACCAG	59.121	55.000	0.81	0.00	42.91	4.00

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	9.488762	ACCATCCTATTCCGTCTGATATATAAA	57.511	33.333	0.00	0.00	0.00	1.40
1	2	8.914011	CACCATCCTATTCCGTCTGATATATAA	58.086	37.037	0.00	0.00	0.00	0.98
79	80	0.182299	GCTCCCTTCCTTCCCTGATG	59.818	60.000	0.00	0.00	0.00	3.07
124	125	4.974368	ACTCGAGAGACCATCTAGTTTG	57.026	45.455	21.68	0.00	38.84	2.93
224	225	3.593551	GATGCACCCACACGCAACG	62.594	63.158	0.00	0.00	42.37	4.10
225	226	1.795170	AAGATGCACCCACACGCAAC	61.795	55.000	0.00	0.00	42.37	4.17
226	227	1.514678	GAAGATGCACCCACACGCAA	61.515	55.000	0.00	0.00	42.37	4.85
296	304	3.053619	GGGGTTCAGTTCATATTGGAGGT	60.054	47.826	0.00	0.00	0.00	3.85
473	511	7.449395	TGGATAAGGATTGCAAGATGAAATAGG	59.551	37.037	4.94	0.00	0.00	2.57
632	673	1.065854	TGCAAGGAAGAAGGCTAGAGC	60.066	52.381	0.00	0.00	41.14	4.09
677	718	7.554118	AGACATCCACTCACAAAACCATAATAG	59.446	37.037	0.00	0.00	0.00	1.73
718	759	2.578714	GCCGGGCAATGGAACCAAA	61.579	57.895	15.62	0.00	0.00	3.28
734	775	6.131544	ACCTCAACAATAATTCATTACGCC	57.868	37.500	0.00	0.00	0.00	5.68
738	779	8.121305	AGTGCAACCTCAACAATAATTCATTA	57.879	30.769	0.00	0.00	37.80	1.90
751	792	1.070134	AGTAAGCGAGTGCAACCTCAA	59.930	47.619	5.30	0.00	46.23	3.02
770	811	3.087031	ACATCACAATTGCAGGAAGGAG	58.913	45.455	5.05	0.00	0.00	3.69
800	841	3.516300	AGGGCATGATCAATGAGCAAAAA	59.484	39.130	4.96	0.00	38.72	1.94
1014	1059	0.670854	GACCTCCAACGGCAGAGAAC	60.671	60.000	0.00	0.00	31.43	3.01
1023	1068	2.360801	ACACCAAATTTGACCTCCAACG	59.639	45.455	19.86	1.99	33.85	4.10
1074	1119	4.082125	ACTTGGGGATCTCATCAACAAAC	58.918	43.478	0.00	0.00	0.00	2.93
1089	1134	0.321653	CCTTGGACGAAGACTTGGGG	60.322	60.000	2.09	0.00	32.82	4.96
1284	1329	2.693591	TGTATTCGTCCATCCACTCCTC	59.306	50.000	0.00	0.00	0.00	3.71
1336	1381	5.821995	GCCTTGAAGATAGAGAATTTGCTCT	59.178	40.000	0.00	0.00	46.47	4.09
1439	1489	1.071019	TTGATCGTCGAAGTGAGCGC	61.071	55.000	0.00	0.00	0.00	5.92
1513	1564	2.070783	GTCCGAGACAATTACCGCAAA	58.929	47.619	0.00	0.00	32.09	3.68
1904	1960	5.557866	ACCAAAACTATTACTCTGGTCCAC	58.442	41.667	0.00	0.00	31.52	4.02
1924	1980	1.021202	CTTCGTTCACCTTGCAACCA	58.979	50.000	0.00	0.00	0.00	3.67
1940	1996	6.090483	TGATATCCTTGCTACTACTGCTTC	57.910	41.667	0.00	0.00	0.00	3.86
1963	2019	2.775384	TGTGGGTACAGTCTCAAAACCT	59.225	45.455	0.00	0.00	31.91	3.50
1999	2055	1.871772	CTTTGCAACAGCCTCCTCG	59.128	57.895	0.00	0.00	0.00	4.63
2048	2104	7.553044	GCCTCCTTTGTAATTGTTCATACTAGT	59.447	37.037	0.00	0.00	0.00	2.57
2269	2343	3.429547	CCGGATATGTGCAGATACCTAGC	60.430	52.174	5.58	0.00	0.00	3.42
2421	2500	2.027653	TCACACACACCACAACTGAGAA	60.028	45.455	0.00	0.00	0.00	2.87
2573	2652	9.539825	AGACAATTGAGATAGCTACAATAACAG	57.460	33.333	13.59	3.53	34.48	3.16
2670	2749	5.643176	TGGCCATGGATCATATTGTACAAT	58.357	37.500	23.80	23.80	34.93	2.71
2743	2822	1.220206	CTTCTCACAGCTCCGGCAT	59.780	57.895	0.00	0.00	41.70	4.40
2789	2868	7.016268	ACCAGGTGTATTCGATATGAACCTATT	59.984	37.037	0.00	0.00	40.00	1.73
2797	2876	8.740906	AGAGTAATACCAGGTGTATTCGATATG	58.259	37.037	0.76	0.00	45.02	1.78
2801	2880	7.722728	ACATAGAGTAATACCAGGTGTATTCGA	59.277	37.037	0.76	0.00	45.02	3.71
2809	2888	8.548880	ACAATGTACATAGAGTAATACCAGGT	57.451	34.615	9.21	0.00	33.72	4.00
2831	2910	7.552687	GTGTAATTGATCAGGTCCTTATGACAA	59.447	37.037	0.00	0.00	46.38	3.18
2837	2916	6.367374	TGTGTGTAATTGATCAGGTCCTTA	57.633	37.500	0.00	0.00	0.00	2.69
2946	3025	6.538742	TGAGAGCAAACCTAAAAATATCCTCG	59.461	38.462	0.00	0.00	0.00	4.63
2960	3039	1.452108	CCCCCGATGAGAGCAAACC	60.452	63.158	0.00	0.00	0.00	3.27
2963	3042	1.198094	TGTTCCCCCGATGAGAGCAA	61.198	55.000	0.00	0.00	0.00	3.91
2971	3050	1.128200	TCGAATGATGTTCCCCCGAT	58.872	50.000	0.00	0.00	0.00	4.18
3063	3147	8.544622	TGATGGTTGTAGTATTTGGTTGAGATA	58.455	33.333	0.00	0.00	0.00	1.98
3159	3247	1.053424	TTACCCCGTTGAAGCAGACT	58.947	50.000	0.00	0.00	0.00	3.24

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.