AutoCloner

Multiple sequence alignment - TraesCS3A01G514700

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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	TraesCS3A01G514700	chr3A	100.000	3297	0	0	1	3297	733410678	733413974	0.000000e+00	6089.0
1	TraesCS3A01G514700	chr3A	98.552	2693	33	4	1	2689	733435473	733438163	0.000000e+00	4752.0
2	TraesCS3A01G514700	chr3A	90.240	2080	137	24	647	2687	733465233	733467285	0.000000e+00	2656.0
3	TraesCS3A01G514700	chr3A	89.443	2084	168	16	649	2687	733332997	733335073	0.000000e+00	2582.0
4	TraesCS3A01G514700	chr3A	85.643	2006	203	38	730	2686	733039218	733041187	0.000000e+00	2030.0
5	TraesCS3A01G514700	chr3A	82.452	1835	271	24	703	2502	733860375	733858557	0.000000e+00	1557.0
6	TraesCS3A01G514700	chr3A	82.417	1837	272	23	696	2503	733726104	733724290	0.000000e+00	1555.0
7	TraesCS3A01G514700	chr3A	79.065	1605	281	29	791	2361	733732452	733730869	0.000000e+00	1051.0
8	TraesCS3A01G514700	chr3A	94.497	527	25	4	2773	3297	422841700	422841176	0.000000e+00	809.0
9	TraesCS3A01G514700	chr3A	83.505	194	31	1	118	311	484106676	484106484	2.610000e-41	180.0
10	TraesCS3A01G514700	chr3A	97.183	71	2	0	2705	2775	733413267	733413337	1.610000e-23	121.0
11	TraesCS3A01G514700	chr3A	97.183	71	2	0	2590	2660	733413382	733413452	1.610000e-23	121.0
12	TraesCS3A01G514700	chr3A	97.183	71	2	0	2705	2775	733467190	733467260	1.610000e-23	121.0
13	TraesCS3A01G514700	chr3B	93.732	2728	115	15	1	2687	810969559	810972271	0.000000e+00	4039.0
14	TraesCS3A01G514700	chr3B	89.517	2070	137	41	647	2687	811040638	811042656	0.000000e+00	2547.0
15	TraesCS3A01G514700	chr3B	88.418	2029	172	26	647	2618	810977750	810979772	0.000000e+00	2386.0
16	TraesCS3A01G514700	chr3B	85.500	2000	212	30	730	2684	810948009	810949975	0.000000e+00	2015.0
17	TraesCS3A01G514700	chr3B	78.865	1727	282	39	799	2483	811128607	811126922	0.000000e+00	1090.0
18	TraesCS3A01G514700	chr3B	76.157	432	66	17	118	535	473185514	473185106	3.360000e-45	193.0
19	TraesCS3A01G514700	chr3B	94.737	38	2	0	2559	2596	810979822	810979859	3.550000e-05	60.2
20	TraesCS3A01G514700	chr3D	93.789	2560	108	18	1	2536	602782377	602779845	0.000000e+00	3799.0
21	TraesCS3A01G514700	chr3D	90.765	2079	123	32	647	2687	603943418	603945465	0.000000e+00	2712.0
22	TraesCS3A01G514700	chr1A	95.810	525	22	0	2773	3297	357573868	357573344	0.000000e+00	848.0
23	TraesCS3A01G514700	chr1A	94.307	527	26	4	2773	3297	161761086	161761610	0.000000e+00	804.0
24	TraesCS3A01G514700	chr5A	94.877	527	23	4	2773	3297	325502103	325502627	0.000000e+00	821.0
25	TraesCS3A01G514700	chr6A	94.867	526	23	4	2774	3297	432189282	432188759	0.000000e+00	819.0
26	TraesCS3A01G514700	chr6A	94.497	527	25	4	2773	3297	211220580	211220056	0.000000e+00	809.0
27	TraesCS3A01G514700	chr7A	94.497	527	25	4	2773	3297	32568587	32568063	0.000000e+00	809.0
28	TraesCS3A01G514700	chr2A	94.487	526	27	2	2773	3297	446346255	446346779	0.000000e+00	809.0
29	TraesCS3A01G514700	chr2A	94.508	528	23	5	2773	3297	687224678	687224154	0.000000e+00	809.0
30	TraesCS3A01G514700	chr4D	78.913	460	65	16	16	455	75049153	75049600	1.940000e-72	283.0
31	TraesCS3A01G514700	chr7B	92.958	71	5	0	575	645	426540495	426540565	1.620000e-18	104.0
32	TraesCS3A01G514700	chrUn	100.000	28	0	0	2624	2651	42262266	42262293	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	TraesCS3A01G514700	chr3A	733410678	733413974	3296	False	2110.333333	6089	98.1220	1	3297	3	chr3A.!!$F4	3296
1	TraesCS3A01G514700	chr3A	733435473	733438163	2690	False	4752.000000	4752	98.5520	1	2689	1	chr3A.!!$F3	2688
2	TraesCS3A01G514700	chr3A	733332997	733335073	2076	False	2582.000000	2582	89.4430	649	2687	1	chr3A.!!$F2	2038
3	TraesCS3A01G514700	chr3A	733039218	733041187	1969	False	2030.000000	2030	85.6430	730	2686	1	chr3A.!!$F1	1956
4	TraesCS3A01G514700	chr3A	733858557	733860375	1818	True	1557.000000	1557	82.4520	703	2502	1	chr3A.!!$R5	1799
5	TraesCS3A01G514700	chr3A	733724290	733726104	1814	True	1555.000000	1555	82.4170	696	2503	1	chr3A.!!$R3	1807
6	TraesCS3A01G514700	chr3A	733465233	733467285	2052	False	1388.500000	2656	93.7115	647	2775	2	chr3A.!!$F5	2128
7	TraesCS3A01G514700	chr3A	733730869	733732452	1583	True	1051.000000	1051	79.0650	791	2361	1	chr3A.!!$R4	1570
8	TraesCS3A01G514700	chr3A	422841176	422841700	524	True	809.000000	809	94.4970	2773	3297	1	chr3A.!!$R1	524
9	TraesCS3A01G514700	chr3B	810969559	810972271	2712	False	4039.000000	4039	93.7320	1	2687	1	chr3B.!!$F2	2686
10	TraesCS3A01G514700	chr3B	811040638	811042656	2018	False	2547.000000	2547	89.5170	647	2687	1	chr3B.!!$F3	2040
11	TraesCS3A01G514700	chr3B	810948009	810949975	1966	False	2015.000000	2015	85.5000	730	2684	1	chr3B.!!$F1	1954
12	TraesCS3A01G514700	chr3B	810977750	810979859	2109	False	1223.100000	2386	91.5775	647	2618	2	chr3B.!!$F4	1971
13	TraesCS3A01G514700	chr3B	811126922	811128607	1685	True	1090.000000	1090	78.8650	799	2483	1	chr3B.!!$R2	1684
14	TraesCS3A01G514700	chr3D	602779845	602782377	2532	True	3799.000000	3799	93.7890	1	2536	1	chr3D.!!$R1	2535
15	TraesCS3A01G514700	chr3D	603943418	603945465	2047	False	2712.000000	2712	90.7650	647	2687	1	chr3D.!!$F1	2040
16	TraesCS3A01G514700	chr1A	357573344	357573868	524	True	848.000000	848	95.8100	2773	3297	1	chr1A.!!$R1	524
17	TraesCS3A01G514700	chr1A	161761086	161761610	524	False	804.000000	804	94.3070	2773	3297	1	chr1A.!!$F1	524
18	TraesCS3A01G514700	chr5A	325502103	325502627	524	False	821.000000	821	94.8770	2773	3297	1	chr5A.!!$F1	524
19	TraesCS3A01G514700	chr6A	432188759	432189282	523	True	819.000000	819	94.8670	2774	3297	1	chr6A.!!$R2	523
20	TraesCS3A01G514700	chr6A	211220056	211220580	524	True	809.000000	809	94.4970	2773	3297	1	chr6A.!!$R1	524
21	TraesCS3A01G514700	chr7A	32568063	32568587	524	True	809.000000	809	94.4970	2773	3297	1	chr7A.!!$R1	524
22	TraesCS3A01G514700	chr2A	446346255	446346779	524	False	809.000000	809	94.4870	2773	3297	1	chr2A.!!$F1	524
23	TraesCS3A01G514700	chr2A	687224154	687224678	524	True	809.000000	809	94.5080	2773	3297	1	chr2A.!!$R1	524

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
147	148	1.830279	CATCACAGGAACAGCATGGT	58.170	50.0	0.00	0.0	42.46	3.55	F
1541	1623	4.340950	TCGCCTCAACCTGAAAAATTTCTT	59.659	37.5	7.36	0.0	38.02	2.52	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1887	1980	1.902938	AGTCAGGAGCCAAAAGAAGC	58.097	50.0	0.0	0.0	0.0	3.86	R
2512	2668	0.107017	AAAGTGATGGGGGATGCTCG	60.107	55.0	0.0	0.0	0.0	5.03	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
147	148	1.830279	CATCACAGGAACAGCATGGT	58.170	50.000	0.00	0.00	42.46	3.55
773	797	8.677300	GTTGCTATTCAAGATCACAAATTAGGA	58.323	33.333	0.00	0.00	34.91	2.94
1011	1083	7.056635	CCTGTATTCTGGAAATGTTAGGACAT	58.943	38.462	0.00	0.00	40.04	3.06
1220	1296	9.196552	GACTAATATGCCAAAAATATTTCTGCC	57.803	33.333	0.10	0.00	33.38	4.85
1541	1623	4.340950	TCGCCTCAACCTGAAAAATTTCTT	59.659	37.500	7.36	0.00	38.02	2.52
1553	1635	7.857885	CCTGAAAAATTTCTTGTCTACAGACAC	59.142	37.037	11.54	0.00	43.08	3.67
1931	2038	9.831737	CTAATCTGTATTGACACTTCCTTTTTG	57.168	33.333	0.00	0.00	0.00	2.44
2152	2261	3.102972	TCTCCCTTCCTCAGTCATTCAG	58.897	50.000	0.00	0.00	0.00	3.02
2504	2660	3.370840	TTGATAAGCTTGCATCCCTGT	57.629	42.857	9.86	0.00	0.00	4.00
2512	2668	2.483889	GCTTGCATCCCTGTAGTCTACC	60.484	54.545	7.56	0.00	0.00	3.18
2691	2871	3.253955	CACAAGCCGCTGTGGTAC	58.746	61.111	9.31	0.00	42.52	3.34
2692	2872	2.357034	ACAAGCCGCTGTGGTACG	60.357	61.111	9.31	0.02	41.21	3.67
2693	2873	2.048597	CAAGCCGCTGTGGTACGA	60.049	61.111	9.31	0.00	41.21	3.43
2694	2874	1.666553	CAAGCCGCTGTGGTACGAA	60.667	57.895	9.31	0.00	41.21	3.85
2695	2875	1.019278	CAAGCCGCTGTGGTACGAAT	61.019	55.000	9.31	0.00	41.21	3.34
2696	2876	0.321298	AAGCCGCTGTGGTACGAATT	60.321	50.000	9.31	0.00	41.21	2.17
2697	2877	0.739813	AGCCGCTGTGGTACGAATTC	60.740	55.000	9.31	0.00	41.21	2.17
2698	2878	0.739813	GCCGCTGTGGTACGAATTCT	60.740	55.000	9.31	0.00	41.21	2.40
2699	2879	1.722011	CCGCTGTGGTACGAATTCTT	58.278	50.000	3.52	0.00	0.00	2.52
2700	2880	2.073816	CCGCTGTGGTACGAATTCTTT	58.926	47.619	3.52	0.00	0.00	2.52
2701	2881	2.159707	CCGCTGTGGTACGAATTCTTTG	60.160	50.000	3.52	0.00	0.00	2.77
2702	2882	2.724839	CGCTGTGGTACGAATTCTTTGC	60.725	50.000	3.52	0.00	0.00	3.68
2703	2883	2.225491	GCTGTGGTACGAATTCTTTGCA	59.775	45.455	3.52	0.00	0.00	4.08
2704	2884	3.304391	GCTGTGGTACGAATTCTTTGCAA	60.304	43.478	3.52	0.00	0.00	4.08
2705	2885	4.615912	GCTGTGGTACGAATTCTTTGCAAT	60.616	41.667	0.00	0.00	0.00	3.56
2706	2886	4.793071	TGTGGTACGAATTCTTTGCAATG	58.207	39.130	0.00	2.27	0.00	2.82
2707	2887	4.277174	TGTGGTACGAATTCTTTGCAATGT	59.723	37.500	11.67	0.00	0.00	2.71
2708	2888	4.616802	GTGGTACGAATTCTTTGCAATGTG	59.383	41.667	11.67	0.82	0.00	3.21
2709	2889	4.277174	TGGTACGAATTCTTTGCAATGTGT	59.723	37.500	11.67	7.03	0.00	3.72
2710	2890	4.616802	GGTACGAATTCTTTGCAATGTGTG	59.383	41.667	11.67	2.82	0.00	3.82
2728	2908	3.615496	GTGTGCATTTGAGGCAAATCATC	59.385	43.478	2.62	0.00	41.40	2.92
2730	2910	3.863424	GTGCATTTGAGGCAAATCATCAG	59.137	43.478	2.62	0.00	41.40	2.90
2733	2913	2.219080	TTGAGGCAAATCATCAGGCA	57.781	45.000	0.00	0.00	36.78	4.75
2734	2914	1.758936	TGAGGCAAATCATCAGGCAG	58.241	50.000	0.00	0.00	31.11	4.85
2737	2917	1.030457	GGCAAATCATCAGGCAGAGG	58.970	55.000	0.00	0.00	0.00	3.69
2738	2918	1.030457	GCAAATCATCAGGCAGAGGG	58.970	55.000	0.00	0.00	0.00	4.30
2739	2919	1.409241	GCAAATCATCAGGCAGAGGGA	60.409	52.381	0.00	0.00	0.00	4.20
2740	2920	2.573369	CAAATCATCAGGCAGAGGGAG	58.427	52.381	0.00	0.00	0.00	4.30
2741	2921	1.890552	AATCATCAGGCAGAGGGAGT	58.109	50.000	0.00	0.00	0.00	3.85
2742	2922	2.783379	ATCATCAGGCAGAGGGAGTA	57.217	50.000	0.00	0.00	0.00	2.59
2743	2923	1.781786	TCATCAGGCAGAGGGAGTAC	58.218	55.000	0.00	0.00	0.00	2.73
2744	2924	0.755686	CATCAGGCAGAGGGAGTACC	59.244	60.000	0.00	0.00	40.67	3.34
2759	2939	5.480205	GGGAGTACCTAATGTGCTATAAGC	58.520	45.833	0.00	0.00	40.31	3.09
2760	2940	5.011738	GGGAGTACCTAATGTGCTATAAGCA	59.988	44.000	0.00	0.00	42.39	3.91
2761	2941	6.463897	GGGAGTACCTAATGTGCTATAAGCAA	60.464	42.308	2.64	0.00	44.70	3.91
2762	2942	8.218876	GGGAGTACCTAATGTGCTATAAGCAAG	61.219	44.444	2.64	0.00	44.70	4.01
3039	3219	7.655236	TTGCAATGAACATGGTCATTTAAAG	57.345	32.000	31.76	22.32	44.09	1.85
3113	3293	5.359009	ACTTGATTTCCCTTGCACATCATAG	59.641	40.000	0.00	0.00	0.00	2.23
3122	3302	5.824624	CCCTTGCACATCATAGTGAACTTAT	59.175	40.000	0.00	0.00	42.05	1.73
3268	3448	9.743057	TTGAAAATCCTTATATTGCCAATTACG	57.257	29.630	0.00	0.00	0.00	3.18

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
147	148	0.670162	GCTGCTTCCTTGTTGCTTCA	59.330	50.000	0.00	0.00	0.00	3.02
373	374	5.816258	TCGACGCCACAAAATATATGGTTTA	59.184	36.000	0.00	0.00	35.79	2.01
379	380	3.799366	TGGTCGACGCCACAAAATATAT	58.201	40.909	9.92	0.00	32.81	0.86
1011	1083	7.564793	TCATTTCTTCAGAATCCGGATTAAGA	58.435	34.615	29.28	27.58	33.54	2.10
1220	1296	3.679502	GGTTCTTGCAAAATTTCCATCGG	59.320	43.478	0.00	0.00	0.00	4.18
1541	1623	2.290705	TGGATCTCCGTGTCTGTAGACA	60.291	50.000	10.51	10.51	45.14	3.41
1887	1980	1.902938	AGTCAGGAGCCAAAAGAAGC	58.097	50.000	0.00	0.00	0.00	3.86
1931	2038	8.324163	AGATACTACACCATGAACAGAAAAAC	57.676	34.615	0.00	0.00	0.00	2.43
2152	2261	9.846248	GCCATAAATATAAGAATGAACATGGAC	57.154	33.333	0.00	0.00	32.69	4.02
2504	2660	0.178970	GGGGGATGCTCGGTAGACTA	60.179	60.000	0.00	0.00	0.00	2.59
2512	2668	0.107017	AAAGTGATGGGGGATGCTCG	60.107	55.000	0.00	0.00	0.00	5.03
2701	2881	5.861571	ATTTGCCTCAAATGCACACATTGC	61.862	41.667	4.20	0.00	45.90	3.56
2702	2882	2.442212	TGCCTCAAATGCACACATTG	57.558	45.000	0.00	0.00	45.90	2.82
2704	2884	3.007074	TGATTTGCCTCAAATGCACACAT	59.993	39.130	9.24	0.00	43.05	3.21
2705	2885	2.364647	TGATTTGCCTCAAATGCACACA	59.635	40.909	9.24	0.00	43.05	3.72
2706	2886	3.029320	TGATTTGCCTCAAATGCACAC	57.971	42.857	9.24	0.00	43.05	3.82
2707	2887	3.258622	TGATGATTTGCCTCAAATGCACA	59.741	39.130	9.24	2.91	43.05	4.57
2708	2888	3.852286	TGATGATTTGCCTCAAATGCAC	58.148	40.909	9.24	2.33	43.05	4.57
2709	2889	3.118920	CCTGATGATTTGCCTCAAATGCA	60.119	43.478	9.24	0.00	43.05	3.96
2710	2890	3.454375	CCTGATGATTTGCCTCAAATGC	58.546	45.455	9.24	3.23	43.05	3.56
2711	2891	3.118920	TGCCTGATGATTTGCCTCAAATG	60.119	43.478	9.24	0.00	43.05	2.32
2718	2898	1.030457	CCTCTGCCTGATGATTTGCC	58.970	55.000	0.00	0.00	0.00	4.52
2719	2899	1.030457	CCCTCTGCCTGATGATTTGC	58.970	55.000	0.00	0.00	0.00	3.68
2728	2908	2.160721	TTAGGTACTCCCTCTGCCTG	57.839	55.000	0.00	0.00	44.81	4.85
2730	2910	2.103263	CACATTAGGTACTCCCTCTGCC	59.897	54.545	0.00	0.00	44.81	4.85
2733	2913	3.406512	AGCACATTAGGTACTCCCTCT	57.593	47.619	0.00	0.00	44.81	3.69
2734	2914	6.572703	GCTTATAGCACATTAGGTACTCCCTC	60.573	46.154	0.00	0.00	41.62	4.30
2751	2931	5.346011	GCAAAGGAAAACACTTGCTTATAGC	59.654	40.000	0.00	0.00	42.82	2.97
2752	2932	6.446318	TGCAAAGGAAAACACTTGCTTATAG	58.554	36.000	7.12	0.00	29.82	1.31
2753	2933	6.398234	TGCAAAGGAAAACACTTGCTTATA	57.602	33.333	7.12	0.00	29.82	0.98
2754	2934	5.275067	TGCAAAGGAAAACACTTGCTTAT	57.725	34.783	7.12	0.00	29.82	1.73
2755	2935	4.727507	TGCAAAGGAAAACACTTGCTTA	57.272	36.364	7.12	0.00	29.82	3.09
2756	2936	3.608316	TGCAAAGGAAAACACTTGCTT	57.392	38.095	7.12	0.00	0.00	3.91
2757	2937	3.608316	TTGCAAAGGAAAACACTTGCT	57.392	38.095	0.00	0.00	0.00	3.91
2758	2938	3.622612	ACATTGCAAAGGAAAACACTTGC	59.377	39.130	1.71	0.00	0.00	4.01
2759	2939	5.122082	ACAACATTGCAAAGGAAAACACTTG	59.878	36.000	1.71	0.00	0.00	3.16
2760	2940	5.244755	ACAACATTGCAAAGGAAAACACTT	58.755	33.333	1.71	0.00	0.00	3.16
2761	2941	4.831107	ACAACATTGCAAAGGAAAACACT	58.169	34.783	1.71	0.00	0.00	3.55
2762	2942	5.544136	AACAACATTGCAAAGGAAAACAC	57.456	34.783	1.71	0.00	0.00	3.32
2763	2943	6.402222	ACTAACAACATTGCAAAGGAAAACA	58.598	32.000	1.71	0.00	0.00	2.83
2764	2944	6.902224	ACTAACAACATTGCAAAGGAAAAC	57.098	33.333	1.71	0.00	0.00	2.43
2765	2945	6.693545	CGTACTAACAACATTGCAAAGGAAAA	59.306	34.615	1.71	0.00	0.00	2.29
2766	2946	6.038382	TCGTACTAACAACATTGCAAAGGAAA	59.962	34.615	1.71	0.00	0.00	3.13
2767	2947	5.527951	TCGTACTAACAACATTGCAAAGGAA	59.472	36.000	1.71	0.00	0.00	3.36
2768	2948	5.057819	TCGTACTAACAACATTGCAAAGGA	58.942	37.500	1.71	0.00	0.00	3.36
2769	2949	5.351233	TCGTACTAACAACATTGCAAAGG	57.649	39.130	1.71	0.89	0.00	3.11
2770	2950	7.803189	AGAATTCGTACTAACAACATTGCAAAG	59.197	33.333	1.71	0.19	0.00	2.77
2771	2951	7.644490	AGAATTCGTACTAACAACATTGCAAA	58.356	30.769	1.71	0.00	0.00	3.68
3039	3219	4.691685	TCATGAAACAATTTGCATTGGAGC	59.308	37.500	5.11	0.00	43.82	4.70
3113	3293	8.840867	CATAACGAAAGAGCAAAATAAGTTCAC	58.159	33.333	0.00	0.00	0.00	3.18

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.