AutoCloner

Multiple sequence alignment - TraesCS6A01G339000

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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	TraesCS6A01G339000	chr6A	100.000	2930	0	0	1	2930	572217572	572220501	0.000000e+00	5411
1	TraesCS6A01G339000	chr1D	94.597	2943	135	20	1	2930	218968349	218965418	0.000000e+00	4532
2	TraesCS6A01G339000	chr1D	94.303	2949	130	32	1	2927	108777908	108780840	0.000000e+00	4481
3	TraesCS6A01G339000	chr1D	94.040	2953	138	28	1	2930	58456797	58459734	0.000000e+00	4444
4	TraesCS6A01G339000	chr1D	93.966	2950	147	28	1	2930	10792711	10795649	0.000000e+00	4433
5	TraesCS6A01G339000	chr1D	93.932	2950	138	30	1	2930	466334700	466337628	0.000000e+00	4418
6	TraesCS6A01G339000	chr7D	94.573	2948	114	28	1	2930	135390922	135388003	0.000000e+00	4516
7	TraesCS6A01G339000	chr4D	94.036	2951	139	30	1	2930	65864900	65867834	0.000000e+00	4440
8	TraesCS6A01G339000	chr3D	94.012	2939	138	25	1	2930	175410702	175413611	0.000000e+00	4418
9	TraesCS6A01G339000	chr5B	93.299	2940	164	26	1	2930	12567641	12564725	0.000000e+00	4307
10	TraesCS6A01G339000	chr7B	90.918	3006	181	65	1	2930	5947408	5950397	0.000000e+00	3954
11	TraesCS6A01G339000	chr4A	92.143	140	8	2	1	137	66555685	66555546	8.290000e-46	195

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	TraesCS6A01G339000	chr6A	572217572	572220501	2929	False	5411	5411	100.000	1	2930	1	chr6A.!!$F1	2929
1	TraesCS6A01G339000	chr1D	218965418	218968349	2931	True	4532	4532	94.597	1	2930	1	chr1D.!!$R1	2929
2	TraesCS6A01G339000	chr1D	108777908	108780840	2932	False	4481	4481	94.303	1	2927	1	chr1D.!!$F3	2926
3	TraesCS6A01G339000	chr1D	58456797	58459734	2937	False	4444	4444	94.040	1	2930	1	chr1D.!!$F2	2929
4	TraesCS6A01G339000	chr1D	10792711	10795649	2938	False	4433	4433	93.966	1	2930	1	chr1D.!!$F1	2929
5	TraesCS6A01G339000	chr1D	466334700	466337628	2928	False	4418	4418	93.932	1	2930	1	chr1D.!!$F4	2929
6	TraesCS6A01G339000	chr7D	135388003	135390922	2919	True	4516	4516	94.573	1	2930	1	chr7D.!!$R1	2929
7	TraesCS6A01G339000	chr4D	65864900	65867834	2934	False	4440	4440	94.036	1	2930	1	chr4D.!!$F1	2929
8	TraesCS6A01G339000	chr3D	175410702	175413611	2909	False	4418	4418	94.012	1	2930	1	chr3D.!!$F1	2929
9	TraesCS6A01G339000	chr5B	12564725	12567641	2916	True	4307	4307	93.299	1	2930	1	chr5B.!!$R1	2929
10	TraesCS6A01G339000	chr7B	5947408	5950397	2989	False	3954	3954	90.918	1	2930	1	chr7B.!!$F1	2929

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
703	747	0.541863	CAACGCCTCTCTAACCCCAT	59.458	55.0	0.0	0.0	0.0	4.0	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2271	2347	0.109597	GCCAACTACACATGCACTGC	60.11	55.0	0.0	0.0	0.0	4.4	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
111	142	6.714810	AGTTGACATTAGTTGGCATTAGTTGA	59.285	34.615	0.00	0.00	44.92	3.18
231	262	1.813092	GCAGATGCTGAGGTATGTGGG	60.813	57.143	0.00	0.00	38.21	4.61
349	384	6.485648	ACATCCGCTAGAACTTTTTGTAGTTT	59.514	34.615	0.00	0.00	38.43	2.66
362	397	4.778534	TTGTAGTTTCCAGGTCTCGTAG	57.221	45.455	0.00	0.00	0.00	3.51
463	502	7.005902	ACATCATATTAGTTGGCATGATCCAA	58.994	34.615	0.00	0.00	43.36	3.53
464	503	7.672660	ACATCATATTAGTTGGCATGATCCAAT	59.327	33.333	7.90	1.75	46.64	3.16
604	648	2.035442	GCCAGCGGTGAAGGAGTTC	61.035	63.158	17.83	0.00	0.00	3.01
703	747	0.541863	CAACGCCTCTCTAACCCCAT	59.458	55.000	0.00	0.00	0.00	4.00
783	828	1.275291	CTTCCAGCGGACCTCACTAAA	59.725	52.381	0.00	0.00	0.00	1.85
802	847	1.958288	ATTCCTGGTGCAGTCCTACT	58.042	50.000	0.00	0.00	0.00	2.57
815	860	4.475345	CAGTCCTACTAGCCATAGACCTT	58.525	47.826	0.00	0.00	32.93	3.50
826	871	4.706962	AGCCATAGACCTTTGAAATGGTTC	59.293	41.667	2.47	0.00	39.45	3.62
1096	1141	3.977244	CACCAACCACGGCCTTGC	61.977	66.667	3.07	0.00	0.00	4.01
1195	1240	6.208204	AGCAGAACACATTAATGAAGCTTTCT	59.792	34.615	22.16	15.83	0.00	2.52
1200	1245	7.472334	ACACATTAATGAAGCTTTCTGGAAT	57.528	32.000	22.16	0.00	0.00	3.01
1224	1269	2.576615	GACCAGGAGAAGCAAACTGTT	58.423	47.619	0.00	0.00	0.00	3.16
1281	1327	3.181454	ACGACCACTTCCATCTGTTCTTT	60.181	43.478	0.00	0.00	0.00	2.52
1379	1429	5.511373	GGTGCAGATACTATACCTTGATGCA	60.511	44.000	0.00	0.00	38.70	3.96
1435	1485	3.401033	ACGATCGAATGCATGGGATAA	57.599	42.857	24.34	0.00	0.00	1.75
1495	1545	0.240945	CCTGGTGTGTTCGGCAAATC	59.759	55.000	0.00	0.00	0.00	2.17
1500	1550	2.480416	GGTGTGTTCGGCAAATCACAAA	60.480	45.455	5.80	0.00	41.39	2.83
1668	1729	7.503991	CATCTGCACACATGTTCATTTTAAAC	58.496	34.615	0.00	0.00	0.00	2.01
1844	1910	5.581085	CCTAGTATCTTGTTGTAGTTGCACC	59.419	44.000	0.00	0.00	0.00	5.01
1879	1945	5.562506	TGGTTTCGTTCAACACACAAATA	57.437	34.783	0.00	0.00	0.00	1.40
2075	2150	9.674068	AAATTTGTACCACTTACCAACATTTTT	57.326	25.926	0.00	0.00	0.00	1.94
2119	2194	8.841300	TGTTCAGTTGCACATGTATAACTTTTA	58.159	29.630	18.91	9.15	31.47	1.52
2271	2347	6.531240	AGAATGCATATTTTTAGTTTGTGCCG	59.469	34.615	0.00	0.00	0.00	5.69
2292	2368	1.198408	CAGTGCATGTGTAGTTGGCTG	59.802	52.381	0.00	0.00	0.00	4.85
2339	2415	7.010738	CAGAAAGTGTGTCTTAGTCGGTTTTTA	59.989	37.037	0.00	0.00	35.02	1.52
2343	2419	6.257193	AGTGTGTCTTAGTCGGTTTTTACTTG	59.743	38.462	0.00	0.00	0.00	3.16
2353	2429	6.262273	AGTCGGTTTTTACTTGTCACATCATT	59.738	34.615	0.00	0.00	0.00	2.57
2411	2492	9.798994	TTCTAACTGAATCGGTACTAAATCTTC	57.201	33.333	0.00	0.00	0.00	2.87
2412	2493	9.186837	TCTAACTGAATCGGTACTAAATCTTCT	57.813	33.333	0.00	0.00	0.00	2.85
2413	2494	9.804758	CTAACTGAATCGGTACTAAATCTTCTT	57.195	33.333	0.00	0.00	0.00	2.52
2414	2495	8.705048	AACTGAATCGGTACTAAATCTTCTTC	57.295	34.615	0.00	0.00	0.00	2.87
2419	2501	9.974750	GAATCGGTACTAAATCTTCTTCTTTTG	57.025	33.333	0.00	0.00	0.00	2.44
2541	2623	2.100197	TCGATGACGAGGAACCAGATT	58.900	47.619	0.00	0.00	43.81	2.40
2663	2746	2.251818	TGTTGAGGAGGAGTCAGAAGG	58.748	52.381	0.00	0.00	0.00	3.46
2673	2756	3.207321	AGGAGTCAGAAGGAGATGAGGAT	59.793	47.826	0.00	0.00	0.00	3.24
2676	2759	6.276806	AGGAGTCAGAAGGAGATGAGGATATA	59.723	42.308	0.00	0.00	0.00	0.86
2679	2762	7.943076	AGTCAGAAGGAGATGAGGATATAGAT	58.057	38.462	0.00	0.00	0.00	1.98
2684	2767	5.210430	AGGAGATGAGGATATAGATGCAGG	58.790	45.833	0.00	0.00	0.00	4.85
2692	2775	8.061890	TGAGGATATAGATGCAGGGATAGATA	57.938	38.462	0.00	0.00	0.00	1.98
2742	2825	3.520696	TGAATCAGAGGAGGAGGACAAA	58.479	45.455	0.00	0.00	0.00	2.83
2745	2828	3.260269	TCAGAGGAGGAGGACAAAGAA	57.740	47.619	0.00	0.00	0.00	2.52
2748	2831	3.580458	CAGAGGAGGAGGACAAAGAAGAA	59.420	47.826	0.00	0.00	0.00	2.52
2752	2835	5.594777	AGGAGGAGGACAAAGAAGAAGATA	58.405	41.667	0.00	0.00	0.00	1.98
2753	2836	6.209026	AGGAGGAGGACAAAGAAGAAGATAT	58.791	40.000	0.00	0.00	0.00	1.63
2803	2928	2.907042	GAGGAGGAGGAGGACAAAGAAA	59.093	50.000	0.00	0.00	0.00	2.52
2828	2953	1.199615	GACAAAGGAGAGGAGGAGGG	58.800	60.000	0.00	0.00	0.00	4.30
2891	3019	1.544917	AGGCCAAAGAGGGGGACAT	60.545	57.895	5.01	0.00	38.09	3.06

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
182	213	2.575993	CGACACCTCCTCCAGCAG	59.424	66.667	0.00	0.00	0.00	4.24
194	225	0.457853	TGCTACGGAAGATGCGACAC	60.458	55.000	0.00	0.00	34.49	3.67
238	270	6.149474	ACTGTTCAATAGCTCATAAACACACC	59.851	38.462	0.00	0.00	0.00	4.16
349	384	4.950205	AAGAAAAACTACGAGACCTGGA	57.050	40.909	0.00	0.00	0.00	3.86
395	433	3.643320	TCATGAGGACAACTGAAGACTGT	59.357	43.478	0.00	0.00	0.00	3.55
604	648	3.933048	CTTCCCCTGCAGCCACCTG	62.933	68.421	8.66	0.00	42.13	4.00
703	747	4.320567	CGAAACTAGCTCTGACTTCTGTGA	60.321	45.833	0.00	0.00	0.00	3.58
783	828	1.958288	AGTAGGACTGCACCAGGAAT	58.042	50.000	0.00	0.00	35.51	3.01
802	847	5.450818	ACCATTTCAAAGGTCTATGGCTA	57.549	39.130	0.00	0.00	39.46	3.93
833	878	0.618981	GACACGGATCCTTCCCCTTT	59.381	55.000	10.75	0.00	39.01	3.11
1096	1141	0.321919	TAGCACTTTGGGCTGAGCTG	60.322	55.000	3.72	0.00	42.62	4.24
1195	1240	2.439507	GCTTCTCCTGGTCCATATTCCA	59.560	50.000	0.00	0.00	0.00	3.53
1200	1245	2.912956	AGTTTGCTTCTCCTGGTCCATA	59.087	45.455	0.00	0.00	0.00	2.74
1224	1269	2.189594	AGTGATACAAGCAGCAGCAA	57.810	45.000	3.17	0.00	45.49	3.91
1281	1327	7.434897	CAGCAAACTATAACTGCACAAAAGAAA	59.565	33.333	0.00	0.00	38.58	2.52
1379	1429	2.457598	ACTGGGATGTCATGTACGAGT	58.542	47.619	0.00	0.00	0.00	4.18
1435	1485	6.252599	TGATCACCTTGGCAATTAGAGTAT	57.747	37.500	0.00	0.00	0.00	2.12
1587	1647	1.317613	TGTTGTGCCAACTGATGACC	58.682	50.000	15.91	0.00	0.00	4.02
1622	1682	6.940298	AGATGCCAAACTTAAAGCTACAACTA	59.060	34.615	0.00	0.00	0.00	2.24
1808	1874	7.973048	ACAAGATACTAGGGTAGACAATTCA	57.027	36.000	0.00	0.00	0.00	2.57
1822	1888	5.165676	CGGTGCAACTACAACAAGATACTA	58.834	41.667	0.00	0.00	36.74	1.82
1844	1910	6.372185	TGAACGAAACCAAACATTATAACCG	58.628	36.000	0.00	0.00	0.00	4.44
1974	2046	2.029649	ACGAATGCTTCAGCTTGCAAAT	60.030	40.909	0.00	3.08	42.74	2.32
2075	2150	3.737559	ACATACATCCCAGCCAAAAGA	57.262	42.857	0.00	0.00	0.00	2.52
2119	2194	6.161855	TGAATCCTGTATTCTCGCAACTAT	57.838	37.500	0.00	0.00	43.83	2.12
2219	2295	5.021033	ACTTGATGTCAATGGTTGCAAAA	57.979	34.783	0.00	0.00	35.02	2.44
2255	2331	3.380142	CACTGCGGCACAAACTAAAAAT	58.620	40.909	0.00	0.00	0.00	1.82
2271	2347	0.109597	GCCAACTACACATGCACTGC	60.110	55.000	0.00	0.00	0.00	4.40
2292	2368	5.047377	TCTGGCCAACTAAAAACATGATTCC	60.047	40.000	7.01	0.00	0.00	3.01
2339	2415	6.054941	TGTAACTGACAATGATGTGACAAGT	58.945	36.000	0.00	0.00	40.74	3.16
2343	2419	5.696270	TGTCTGTAACTGACAATGATGTGAC	59.304	40.000	6.14	0.00	40.74	3.67
2398	2479	8.837389	ACACACAAAAGAAGAAGATTTAGTACC	58.163	33.333	0.00	0.00	0.00	3.34
2411	2492	4.923893	TCTGCATCAACACACAAAAGAAG	58.076	39.130	0.00	0.00	0.00	2.85
2412	2493	4.979943	TCTGCATCAACACACAAAAGAA	57.020	36.364	0.00	0.00	0.00	2.52
2413	2494	4.979943	TTCTGCATCAACACACAAAAGA	57.020	36.364	0.00	0.00	0.00	2.52
2414	2495	6.406093	TTTTTCTGCATCAACACACAAAAG	57.594	33.333	0.00	0.00	0.00	2.27
2419	2501	2.796593	GCCTTTTTCTGCATCAACACAC	59.203	45.455	0.00	0.00	0.00	3.82
2537	2619	7.094933	GGTTGTTGTACGTAAGGATCAAAATCT	60.095	37.037	0.00	0.00	46.39	2.40
2541	2623	5.366460	TGGTTGTTGTACGTAAGGATCAAA	58.634	37.500	0.00	0.00	46.39	2.69
2593	2675	3.219281	CCCCGTCTCTTTCTTTTTGGAA	58.781	45.455	0.00	0.00	0.00	3.53
2616	2699	9.825109	AACTCTTCTTCTTCTTATATAGTTGGC	57.175	33.333	0.00	0.00	0.00	4.52
2626	2709	7.792032	TCCTCAACAAACTCTTCTTCTTCTTA	58.208	34.615	0.00	0.00	0.00	2.10
2663	2746	5.207354	TCCCTGCATCTATATCCTCATCTC	58.793	45.833	0.00	0.00	0.00	2.75
2673	2756	7.998964	TCGTCAATATCTATCCCTGCATCTATA	59.001	37.037	0.00	0.00	0.00	1.31
2676	2759	5.019470	TCGTCAATATCTATCCCTGCATCT	58.981	41.667	0.00	0.00	0.00	2.90
2679	2762	4.772100	TCATCGTCAATATCTATCCCTGCA	59.228	41.667	0.00	0.00	0.00	4.41
2684	2767	5.354513	TCCTCGTCATCGTCAATATCTATCC	59.645	44.000	0.00	0.00	38.33	2.59
2692	2775	1.544246	TGTGTCCTCGTCATCGTCAAT	59.456	47.619	0.00	0.00	38.33	2.57
2742	2825	6.011628	CCTCCTCCTCCTCTATATCTTCTTCT	60.012	46.154	0.00	0.00	0.00	2.85
2745	2828	5.429518	TCCTCCTCCTCCTCTATATCTTCT	58.570	45.833	0.00	0.00	0.00	2.85
2748	2831	4.119155	CCTCCTCCTCCTCCTCTATATCT	58.881	52.174	0.00	0.00	0.00	1.98
2752	2835	2.358258	CTCCTCCTCCTCCTCCTCTAT	58.642	57.143	0.00	0.00	0.00	1.98
2753	2836	1.700907	CCTCCTCCTCCTCCTCCTCTA	60.701	61.905	0.00	0.00	0.00	2.43
2803	2928	2.909662	CCTCCTCTCCTTTGTCCTCTTT	59.090	50.000	0.00	0.00	0.00	2.52
2828	2953	3.202097	GCCTCACTATCTTCTTCCTTGC	58.798	50.000	0.00	0.00	0.00	4.01
2891	3019	1.955778	CAACTGATGCACCTTTGTCCA	59.044	47.619	0.00	0.00	0.00	4.02
2905	3033	1.277273	CCTCTCACTGCCATCAACTGA	59.723	52.381	0.00	0.00	0.00	3.41

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.