AutoCloner

Multiple sequence alignment - TraesCS7D01G515000

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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	TraesCS7D01G515000	chr7D	100.000	3136	0	0	1	3136	615764446	615767581	0.000000e+00	5792.0
1	TraesCS7D01G515000	chr7D	96.939	980	25	4	1	976	266018680	266019658	0.000000e+00	1639.0
2	TraesCS7D01G515000	chr7D	89.914	1160	72	20	1067	2205	615559446	615558311	0.000000e+00	1452.0
3	TraesCS7D01G515000	chr7D	88.723	940	72	17	1063	1992	615774913	615775828	0.000000e+00	1118.0
4	TraesCS7D01G515000	chr7D	84.706	170	25	1	2863	3032	615554839	615554671	5.380000e-38	169.0
5	TraesCS7D01G515000	chr7D	86.726	113	14	1	2956	3068	615554916	615554805	1.180000e-24	124.0
6	TraesCS7D01G515000	chr7B	85.222	2118	210	46	1045	3095	708529415	708531496	0.000000e+00	2082.0
7	TraesCS7D01G515000	chr7B	85.455	1650	154	45	1067	2675	708511615	708513219	0.000000e+00	1639.0
8	TraesCS7D01G515000	chr7B	83.984	1536	168	46	1067	2547	708446069	708447581	0.000000e+00	1402.0
9	TraesCS7D01G515000	chr7B	86.052	932	86	24	1067	1992	708552460	708553353	0.000000e+00	961.0
10	TraesCS7D01G515000	chr7B	86.762	491	47	15	2580	3062	708513168	708513648	5.960000e-147	531.0
11	TraesCS7D01G515000	chr5D	99.481	964	4	1	1	963	560417111	560418074	0.000000e+00	1751.0
12	TraesCS7D01G515000	chr5D	97.727	968	15	7	1	963	47084284	47083319	0.000000e+00	1659.0
13	TraesCS7D01G515000	chr5D	97.626	969	17	6	1	964	499746651	499745684	0.000000e+00	1657.0
14	TraesCS7D01G515000	chr4D	98.033	966	14	5	1	963	111583311	111582348	0.000000e+00	1674.0
15	TraesCS7D01G515000	chr6D	97.624	968	17	6	1	964	453649262	453650227	0.000000e+00	1655.0
16	TraesCS7D01G515000	chr6D	97.622	967	17	5	1	963	373375304	373374340	0.000000e+00	1653.0
17	TraesCS7D01G515000	chr6D	87.188	320	41	0	1075	1394	142139101	142138782	6.390000e-97	364.0
18	TraesCS7D01G515000	chr7A	90.539	1279	67	18	964	2200	708318976	708320242	0.000000e+00	1642.0
19	TraesCS7D01G515000	chr7A	85.410	939	90	25	1066	1992	708326520	708327423	0.000000e+00	931.0
20	TraesCS7D01G515000	chr7A	80.400	500	72	22	2612	3099	708320398	708320883	1.070000e-94	357.0
21	TraesCS7D01G515000	chr7A	84.894	331	38	6	2414	2736	708320237	708320563	1.080000e-84	324.0
22	TraesCS7D01G515000	chr1D	97.415	967	20	5	1	964	62938217	62937253	0.000000e+00	1642.0
23	TraesCS7D01G515000	chr2D	97.208	967	22	4	1	963	3028621	3029586	0.000000e+00	1631.0
24	TraesCS7D01G515000	chrUn	100.000	28	0	0	999	1026	121822750	121822723	6.000000e-03	52.8
25	TraesCS7D01G515000	chrUn	100.000	28	0	0	999	1026	132361820	132361793	6.000000e-03	52.8
26	TraesCS7D01G515000	chrUn	100.000	28	0	0	999	1026	133814175	133814148	6.000000e-03	52.8
27	TraesCS7D01G515000	chrUn	100.000	28	0	0	999	1026	195197648	195197675	6.000000e-03	52.8
28	TraesCS7D01G515000	chrUn	100.000	28	0	0	999	1026	348043584	348043557	6.000000e-03	52.8
29	TraesCS7D01G515000	chrUn	100.000	28	0	0	999	1026	348045922	348045895	6.000000e-03	52.8
30	TraesCS7D01G515000	chr5B	100.000	28	0	0	999	1026	176940416	176940389	6.000000e-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	TraesCS7D01G515000	chr7D	615764446	615767581	3135	False	5792.000000	5792	100.000000	1	3136	1	chr7D.!!$F2	3135
1	TraesCS7D01G515000	chr7D	266018680	266019658	978	False	1639.000000	1639	96.939000	1	976	1	chr7D.!!$F1	975
2	TraesCS7D01G515000	chr7D	615774913	615775828	915	False	1118.000000	1118	88.723000	1063	1992	1	chr7D.!!$F3	929
3	TraesCS7D01G515000	chr7D	615554671	615559446	4775	True	581.666667	1452	87.115333	1067	3068	3	chr7D.!!$R1	2001
4	TraesCS7D01G515000	chr7B	708529415	708531496	2081	False	2082.000000	2082	85.222000	1045	3095	1	chr7B.!!$F2	2050
5	TraesCS7D01G515000	chr7B	708446069	708447581	1512	False	1402.000000	1402	83.984000	1067	2547	1	chr7B.!!$F1	1480
6	TraesCS7D01G515000	chr7B	708511615	708513648	2033	False	1085.000000	1639	86.108500	1067	3062	2	chr7B.!!$F4	1995
7	TraesCS7D01G515000	chr7B	708552460	708553353	893	False	961.000000	961	86.052000	1067	1992	1	chr7B.!!$F3	925
8	TraesCS7D01G515000	chr5D	560417111	560418074	963	False	1751.000000	1751	99.481000	1	963	1	chr5D.!!$F1	962
9	TraesCS7D01G515000	chr5D	47083319	47084284	965	True	1659.000000	1659	97.727000	1	963	1	chr5D.!!$R1	962
10	TraesCS7D01G515000	chr5D	499745684	499746651	967	True	1657.000000	1657	97.626000	1	964	1	chr5D.!!$R2	963
11	TraesCS7D01G515000	chr4D	111582348	111583311	963	True	1674.000000	1674	98.033000	1	963	1	chr4D.!!$R1	962
12	TraesCS7D01G515000	chr6D	453649262	453650227	965	False	1655.000000	1655	97.624000	1	964	1	chr6D.!!$F1	963
13	TraesCS7D01G515000	chr6D	373374340	373375304	964	True	1653.000000	1653	97.622000	1	963	1	chr6D.!!$R2	962
14	TraesCS7D01G515000	chr7A	708326520	708327423	903	False	931.000000	931	85.410000	1066	1992	1	chr7A.!!$F1	926
15	TraesCS7D01G515000	chr7A	708318976	708320883	1907	False	774.333333	1642	85.277667	964	3099	3	chr7A.!!$F2	2135
16	TraesCS7D01G515000	chr1D	62937253	62938217	964	True	1642.000000	1642	97.415000	1	964	1	chr1D.!!$R1	963
17	TraesCS7D01G515000	chr2D	3028621	3029586	965	False	1631.000000	1631	97.208000	1	963	1	chr2D.!!$F1	962

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
935	948	1.686355	AAGTGAACATCGGTGGCAAA	58.314	45.0	0.0	0.0	0.0	3.68	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2263	5081	0.165944	CCGACGCTTGATGTTGTTCC	59.834	55.0	0.0	0.0	0.0	3.62	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
685	697	9.413048	ACGTGTCTCTTCTTTCTTATCTAAAAG	57.587	33.333	0.00	0.00	34.49	2.27
935	948	1.686355	AAGTGAACATCGGTGGCAAA	58.314	45.000	0.00	0.00	0.00	3.68
974	987	7.718525	TGTGATATTACCTCGCTACAAATACA	58.281	34.615	0.00	0.00	0.00	2.29
975	988	7.650504	TGTGATATTACCTCGCTACAAATACAC	59.349	37.037	0.00	0.00	0.00	2.90
976	989	7.866393	GTGATATTACCTCGCTACAAATACACT	59.134	37.037	0.00	0.00	0.00	3.55
977	990	8.080417	TGATATTACCTCGCTACAAATACACTC	58.920	37.037	0.00	0.00	0.00	3.51
978	991	3.146618	ACCTCGCTACAAATACACTCG	57.853	47.619	0.00	0.00	0.00	4.18
983	996	2.159282	CGCTACAAATACACTCGTCCCT	60.159	50.000	0.00	0.00	0.00	4.20
990	1003	2.599408	TACACTCGTCCCTTCTCCTT	57.401	50.000	0.00	0.00	0.00	3.36
1017	1036	3.484806	AACCACCACCACCGCTCA	61.485	61.111	0.00	0.00	0.00	4.26
1050	1082	3.611766	AGAATCAATCGTCTTCCCGTT	57.388	42.857	0.00	0.00	0.00	4.44
1081	1113	1.001120	TAGATGGAGGGGTGCGACA	59.999	57.895	0.00	0.00	0.00	4.35
1280	1312	3.823330	GGAGGACGCCGTCATCGT	61.823	66.667	23.33	3.21	43.16	3.73
1498	1542	2.444895	GATCGGGGTCTGGCTCCT	60.445	66.667	0.00	0.00	34.84	3.69
1625	1702	2.750637	GCGACACGAGGAGGAGGA	60.751	66.667	0.00	0.00	0.00	3.71
1627	1704	2.766400	CGACACGAGGAGGAGGAGC	61.766	68.421	0.00	0.00	0.00	4.70
1630	1707	2.757917	ACGAGGAGGAGGAGCAGC	60.758	66.667	0.00	0.00	0.00	5.25
1672	1755	3.347590	TCTCGCTCTCCCTCCCCA	61.348	66.667	0.00	0.00	0.00	4.96
1702	1797	2.032634	CACGGGTTCCACCACGATG	61.033	63.158	9.80	3.09	41.02	3.84
1857	1952	1.317431	ACGAGGTGCGCAGGTACATA	61.317	55.000	12.22	0.00	46.04	2.29
1868	1963	1.067974	CAGGTACATATCCGGCGTCAA	59.932	52.381	6.01	0.00	0.00	3.18
2054	2168	1.838715	ACTCTAGGACAGCCGAGTCTA	59.161	52.381	0.00	0.00	38.03	2.59
2138	2271	9.883142	ACAAACAAATGAAATGGAAAGAAACTA	57.117	25.926	0.00	0.00	0.00	2.24
2206	5016	5.817816	TCCTCCGAAAGCAAAAATCTATCTC	59.182	40.000	0.00	0.00	0.00	2.75
2239	5049	2.073816	TGAAGCGAAAAATCCCTCGTC	58.926	47.619	0.00	0.00	37.39	4.20
2246	5056	2.044123	AAAATCCCTCGTCCTGCATC	57.956	50.000	0.00	0.00	0.00	3.91
2254	5072	1.520120	CGTCCTGCATCTGACGCAT	60.520	57.895	17.00	0.00	46.41	4.73
2266	5084	3.056458	ACGCATGGACGTGAGGAA	58.944	55.556	0.00	0.00	46.28	3.36
2267	5085	1.374252	ACGCATGGACGTGAGGAAC	60.374	57.895	0.00	0.00	46.28	3.62
2282	5101	0.165944	GGAACAACATCAAGCGTCGG	59.834	55.000	0.00	0.00	0.00	4.79
2299	5118	1.660264	GGAAACGGCGTGGCAAAAG	60.660	57.895	15.70	0.00	0.00	2.27
2300	5119	1.065109	GAAACGGCGTGGCAAAAGT	59.935	52.632	15.70	0.00	0.00	2.66
2330	5152	4.015084	CAGGATGGAGAAGCAGAACAATT	58.985	43.478	0.00	0.00	0.00	2.32
2339	5161	7.068103	TGGAGAAGCAGAACAATTAGACAAAAA	59.932	33.333	0.00	0.00	0.00	1.94
2345	5167	6.460953	GCAGAACAATTAGACAAAAAGGTGGA	60.461	38.462	0.00	0.00	0.00	4.02
2358	5180	8.622948	ACAAAAAGGTGGACAAAACAAATTTA	57.377	26.923	0.00	0.00	0.00	1.40
2455	5294	5.983118	GGAAAATGTTCTGGACGTGAATTTT	59.017	36.000	0.00	0.00	33.92	1.82
2456	5295	7.142680	GGAAAATGTTCTGGACGTGAATTTTA	58.857	34.615	0.00	0.00	33.92	1.52
2531	5374	6.777580	AGAACTCCCAAATGTTTGTGAACTAT	59.222	34.615	4.92	0.00	36.45	2.12
2590	5488	8.728833	TCAAAGATTGTTTGCAAAAAGTTCATT	58.271	25.926	14.67	6.28	38.21	2.57
2601	5499	5.220681	GCAAAAAGTTCATTGCCCGTTTAAA	60.221	36.000	12.89	0.00	44.72	1.52
2692	5631	7.969387	ATGTTCACGTGTTTCAATAATATGC	57.031	32.000	16.51	0.00	0.00	3.14
2897	5846	9.152851	CCATTTTAAAAAGTGTTAACGCATTTG	57.847	29.630	19.58	9.31	29.33	2.32
2985	6020	9.483062	TTTCAAAATTTTGTTCACGCATTTAAG	57.517	25.926	25.98	0.00	39.18	1.85
3082	6117	3.088552	CGTATTTCCGAAATGTGTTCGC	58.911	45.455	15.37	0.00	40.30	4.70
3099	6134	8.508800	TGTGTTCGCGTCATTTTTATAAAATT	57.491	26.923	11.33	5.59	0.00	1.82
3100	6135	9.608617	TGTGTTCGCGTCATTTTTATAAAATTA	57.391	25.926	11.33	0.00	0.00	1.40

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
974	987	1.268066	GGAAAGGAGAAGGGACGAGT	58.732	55.000	0.00	0.00	0.00	4.18
975	988	0.537653	GGGAAAGGAGAAGGGACGAG	59.462	60.000	0.00	0.00	0.00	4.18
976	989	0.908180	GGGGAAAGGAGAAGGGACGA	60.908	60.000	0.00	0.00	0.00	4.20
977	990	1.602771	GGGGAAAGGAGAAGGGACG	59.397	63.158	0.00	0.00	0.00	4.79
978	991	1.911702	CGGGGGAAAGGAGAAGGGAC	61.912	65.000	0.00	0.00	0.00	4.46
983	996	0.399075	GTTGTCGGGGGAAAGGAGAA	59.601	55.000	0.00	0.00	0.00	2.87
990	1003	2.773053	TGGTGGTTGTCGGGGGAA	60.773	61.111	0.00	0.00	0.00	3.97
1017	1036	1.303317	GATTCTTGTGGGTGGCGGT	60.303	57.895	0.00	0.00	0.00	5.68
1050	1082	4.202336	CCCTCCATCTAGTACGAGTCTACA	60.202	50.000	2.75	0.00	0.00	2.74
1625	1702	3.715097	GGTCCTCCTGCTGCTGCT	61.715	66.667	17.00	0.00	40.48	4.24
1627	1704	2.207501	AATGGGTCCTCCTGCTGCTG	62.208	60.000	0.00	0.00	36.20	4.41
1630	1707	0.393537	GTGAATGGGTCCTCCTGCTG	60.394	60.000	0.00	0.00	36.20	4.41
1780	1875	1.470979	GCTGAACGGGTATGATGACGT	60.471	52.381	0.00	0.00	41.88	4.34
2054	2168	6.072199	AGTTCTTCTTTCTCCCATTGCTAT	57.928	37.500	0.00	0.00	0.00	2.97
2158	2291	4.510038	ACAAATTTGACATGAGTGAGCC	57.490	40.909	24.64	0.00	0.00	4.70
2239	5049	1.153309	TCCATGCGTCAGATGCAGG	60.153	57.895	21.76	21.01	44.19	4.85
2246	5056	1.807165	CCTCACGTCCATGCGTCAG	60.807	63.158	0.00	0.00	43.83	3.51
2254	5072	1.414550	TGATGTTGTTCCTCACGTCCA	59.585	47.619	0.00	0.00	0.00	4.02
2262	5080	1.148310	CGACGCTTGATGTTGTTCCT	58.852	50.000	0.00	0.00	0.00	3.36
2263	5081	0.165944	CCGACGCTTGATGTTGTTCC	59.834	55.000	0.00	0.00	0.00	3.62
2266	5084	1.263217	GTTTCCGACGCTTGATGTTGT	59.737	47.619	0.00	0.00	0.00	3.32
2267	5085	1.721489	CGTTTCCGACGCTTGATGTTG	60.721	52.381	0.00	0.00	45.86	3.33
2282	5101	0.526739	AACTTTTGCCACGCCGTTTC	60.527	50.000	0.00	0.00	0.00	2.78
2291	5110	2.170166	CCTGGAGCATAACTTTTGCCA	58.830	47.619	1.03	0.00	41.06	4.92
2321	5143	6.918022	GTCCACCTTTTTGTCTAATTGTTCTG	59.082	38.462	0.00	0.00	0.00	3.02
2322	5144	6.605594	TGTCCACCTTTTTGTCTAATTGTTCT	59.394	34.615	0.00	0.00	0.00	3.01
2330	5152	6.591750	TTGTTTTGTCCACCTTTTTGTCTA	57.408	33.333	0.00	0.00	0.00	2.59
2339	5161	5.105146	TGCTGTAAATTTGTTTTGTCCACCT	60.105	36.000	0.00	0.00	0.00	4.00
2345	5167	6.150140	TGCCTTTTGCTGTAAATTTGTTTTGT	59.850	30.769	0.00	0.00	42.00	2.83
2358	5180	4.463539	TCATACATGAATGCCTTTTGCTGT	59.536	37.500	0.00	0.00	35.74	4.40
2420	5259	4.150451	CAGAACATTTTCCGAATTTGTGCC	59.850	41.667	0.00	0.00	31.28	5.01
2431	5270	4.766404	ATTCACGTCCAGAACATTTTCC	57.234	40.909	0.00	0.00	31.28	3.13
2432	5271	8.568732	TTAAAATTCACGTCCAGAACATTTTC	57.431	30.769	0.00	0.00	0.00	2.29
2537	5380	6.983474	TCACGAATGCTTCTTGAATTCATA	57.017	33.333	9.40	0.00	40.07	2.15
2670	5609	7.240674	TGAGCATATTATTGAAACACGTGAAC	58.759	34.615	25.01	12.94	0.00	3.18
2962	5996	6.904011	TGCTTAAATGCGTGAACAAAATTTTG	59.096	30.769	25.73	25.73	38.76	2.44
2967	6001	6.408858	TTTTGCTTAAATGCGTGAACAAAA	57.591	29.167	0.00	0.00	34.44	2.44
2968	6002	6.417327	CATTTTGCTTAAATGCGTGAACAAA	58.583	32.000	10.49	0.00	44.69	2.83
2969	6003	5.972018	CATTTTGCTTAAATGCGTGAACAA	58.028	33.333	10.49	0.00	44.69	2.83

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.