AutoCloner

Multiple sequence alignment - TraesCS3A01G308700

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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	TraesCS3A01G308700	chr3A	100.000	2777	0	0	1	2777	546719511	546716735	0.000000e+00	5129.0
1	TraesCS3A01G308700	chr3A	100.000	31	0	0	2419	2449	13131834	13131804	1.070000e-04	58.4
2	TraesCS3A01G308700	chr3D	92.974	2804	156	19	1	2777	93175199	93177988	0.000000e+00	4048.0
3	TraesCS3A01G308700	chr3B	89.363	1523	107	18	1259	2777	143175482	143174011	0.000000e+00	1864.0
4	TraesCS3A01G308700	chr3B	92.141	1247	77	11	1	1233	143176974	143175735	0.000000e+00	1740.0
5	TraesCS3A01G308700	chr3B	81.148	366	49	7	9	360	730699087	730699446	2.720000e-70	276.0
6	TraesCS3A01G308700	chr1B	85.151	1192	159	13	983	2165	118488684	118487502	0.000000e+00	1205.0
7	TraesCS3A01G308700	chr1B	83.621	464	64	5	9	461	64824631	64825093	2.560000e-115	425.0
8	TraesCS3A01G308700	chr1B	81.800	500	72	14	9	497	64016835	64017326	4.310000e-108	401.0
9	TraesCS3A01G308700	chr1B	77.570	535	79	23	781	1279	64825584	64826113	4.530000e-73	285.0
10	TraesCS3A01G308700	chr1B	77.672	524	75	18	781	1266	64017786	64018305	5.860000e-72	281.0
11	TraesCS3A01G308700	chr1B	77.230	527	81	25	787	1279	64928953	64929474	3.520000e-69	272.0
12	TraesCS3A01G308700	chr1B	77.087	515	79	23	781	1258	64288746	64289258	7.630000e-66	261.0
13	TraesCS3A01G308700	chr1A	82.213	1220	159	21	983	2165	75256313	75255115	0.000000e+00	998.0
14	TraesCS3A01G308700	chr1A	84.000	125	12	4	496	615	547578101	547578222	2.260000e-21	113.0
15	TraesCS3A01G308700	chr1D	79.616	1094	160	36	781	1835	45080244	45079175	0.000000e+00	726.0
16	TraesCS3A01G308700	chr1D	78.654	1129	173	38	781	1871	45114181	45113083	0.000000e+00	688.0
17	TraesCS3A01G308700	chr1D	82.411	705	91	14	1490	2165	74928553	74927853	3.990000e-163	584.0
18	TraesCS3A01G308700	chr1D	85.934	519	64	3	983	1492	74930157	74929639	1.880000e-151	545.0
19	TraesCS3A01G308700	chr1D	84.418	507	66	7	1	497	45083044	45082541	1.160000e-133	486.0
20	TraesCS3A01G308700	chr1D	84.252	508	66	6	1	497	44973978	44973474	1.500000e-132	483.0
21	TraesCS3A01G308700	chr1D	84.024	507	63	10	1	497	45077568	45078066	3.240000e-129	472.0
22	TraesCS3A01G308700	chr1D	82.446	507	71	10	1	497	44968517	44969015	7.110000e-116	427.0
23	TraesCS3A01G308700	chr1D	84.726	419	54	6	86	497	45116894	45116479	7.160000e-111	411.0
24	TraesCS3A01G308700	chr1D	81.818	66	12	0	2384	2449	17340683	17340748	3.860000e-04	56.5
25	TraesCS3A01G308700	chr7A	89.565	115	10	1	496	610	246120294	246120406	8.020000e-31	145.0
26	TraesCS3A01G308700	chr4B	88.333	120	6	5	496	610	620467170	620467054	1.340000e-28	137.0
27	TraesCS3A01G308700	chr5D	86.555	119	10	2	496	610	497141575	497141459	2.900000e-25	126.0
28	TraesCS3A01G308700	chr5D	85.000	120	11	4	498	612	128659026	128659143	6.290000e-22	115.0
29	TraesCS3A01G308700	chr2D	85.366	123	13	3	496	617	37395502	37395384	3.760000e-24	122.0
30	TraesCS3A01G308700	chr6B	84.000	125	12	5	496	615	308299088	308298967	2.260000e-21	113.0
31	TraesCS3A01G308700	chrUn	81.818	66	12	0	2384	2449	356303042	356303107	3.860000e-04	56.5

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	TraesCS3A01G308700	chr3A	546716735	546719511	2776	True	5129.0	5129	100.0000	1	2777	1	chr3A.!!$R2	2776
1	TraesCS3A01G308700	chr3D	93175199	93177988	2789	False	4048.0	4048	92.9740	1	2777	1	chr3D.!!$F1	2776
2	TraesCS3A01G308700	chr3B	143174011	143176974	2963	True	1802.0	1864	90.7520	1	2777	2	chr3B.!!$R1	2776
3	TraesCS3A01G308700	chr1B	118487502	118488684	1182	True	1205.0	1205	85.1510	983	2165	1	chr1B.!!$R1	1182
4	TraesCS3A01G308700	chr1B	64824631	64826113	1482	False	355.0	425	80.5955	9	1279	2	chr1B.!!$F4	1270
5	TraesCS3A01G308700	chr1B	64016835	64018305	1470	False	341.0	401	79.7360	9	1266	2	chr1B.!!$F3	1257
6	TraesCS3A01G308700	chr1B	64928953	64929474	521	False	272.0	272	77.2300	787	1279	1	chr1B.!!$F2	492
7	TraesCS3A01G308700	chr1B	64288746	64289258	512	False	261.0	261	77.0870	781	1258	1	chr1B.!!$F1	477
8	TraesCS3A01G308700	chr1A	75255115	75256313	1198	True	998.0	998	82.2130	983	2165	1	chr1A.!!$R1	1182
9	TraesCS3A01G308700	chr1D	45079175	45083044	3869	True	606.0	726	82.0170	1	1835	2	chr1D.!!$R2	1834
10	TraesCS3A01G308700	chr1D	74927853	74930157	2304	True	564.5	584	84.1725	983	2165	2	chr1D.!!$R4	1182
11	TraesCS3A01G308700	chr1D	45113083	45116894	3811	True	549.5	688	81.6900	86	1871	2	chr1D.!!$R3	1785
12	TraesCS3A01G308700	chr1D	44973474	44973978	504	True	483.0	483	84.2520	1	497	1	chr1D.!!$R1	496

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
245	251	0.036732	ACATGATGTTCGGTGGCTGT	59.963	50.0	0.0	0.0	0.0	4.4	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1939	7263	0.552848	ACATCCCATGGAAGCGGAAT	59.447	50.0	15.22	0.0	34.34	3.01	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
136	142	3.547746	TGTTTCCTATGGTTTATCGCCC	58.452	45.455	0.00	0.00	0.00	6.13
154	160	1.659233	CCGTTGAGTTGGCATTGCA	59.341	52.632	11.39	0.00	0.00	4.08
224	230	5.880054	AAATCATTAAGACCGAGTTGTGG	57.120	39.130	0.00	0.00	0.00	4.17
245	251	0.036732	ACATGATGTTCGGTGGCTGT	59.963	50.000	0.00	0.00	0.00	4.40
303	314	8.277197	AGGGATATTCAAAAGTCTTCATCATGA	58.723	33.333	0.00	0.00	0.00	3.07
360	371	0.471591	TTGCCATTGCCTGGGTCTTT	60.472	50.000	4.72	0.00	46.06	2.52
365	376	3.635591	CCATTGCCTGGGTCTTTTAGAT	58.364	45.455	0.00	0.00	41.82	1.98
371	382	7.387265	TTGCCTGGGTCTTTTAGATATCATA	57.613	36.000	5.32	0.00	0.00	2.15
376	387	9.627123	CCTGGGTCTTTTAGATATCATACAAAA	57.373	33.333	5.32	5.23	0.00	2.44
512	1827	3.838244	TTTATATGCCGGCTCAGTCTT	57.162	42.857	29.70	7.85	0.00	3.01
514	1829	2.717639	ATATGCCGGCTCAGTCTTTT	57.282	45.000	29.70	3.51	0.00	2.27
529	1844	3.054802	AGTCTTTTGAGGGTGCTCATAGG	60.055	47.826	0.00	0.00	32.91	2.57
535	1850	0.642710	AGGGTGCTCATAGGGGTAGT	59.357	55.000	0.00	0.00	0.00	2.73
567	3312	7.530010	GTGCATTCATAAAAGTGAGTGTATGT	58.470	34.615	0.00	0.00	37.92	2.29
570	3315	7.482743	GCATTCATAAAAGTGAGTGTATGTGTG	59.517	37.037	0.00	0.00	37.92	3.82
571	3316	8.506437	CATTCATAAAAGTGAGTGTATGTGTGT	58.494	33.333	0.00	0.00	32.90	3.72
779	4695	3.537580	GGGATATACAGTGCGGTTTCAA	58.462	45.455	0.00	0.00	0.00	2.69
1013	4966	1.003355	AGGCCATGGACGTCAAGTG	60.003	57.895	18.40	11.98	0.00	3.16
1075	5037	0.450983	GGTGGAAGAGGAGACGTACG	59.549	60.000	15.01	15.01	0.00	3.67
1172	5134	4.715523	CCACAACCCCGCCGACAT	62.716	66.667	0.00	0.00	0.00	3.06
1215	5177	3.605664	GGCTGCCACCGCAACTTT	61.606	61.111	15.17	0.00	46.66	2.66
1304	5497	2.188994	GCAGCGCAGGGAGAAGAT	59.811	61.111	11.47	0.00	0.00	2.40
1306	5499	1.220206	CAGCGCAGGGAGAAGATGT	59.780	57.895	11.47	0.00	0.00	3.06
1399	5614	1.672030	TACGACTCGGAAGGCACGA	60.672	57.895	2.98	0.00	38.79	4.35
1407	5622	1.546923	TCGGAAGGCACGAAGTATGAA	59.453	47.619	0.00	0.00	41.61	2.57
1410	5625	3.738281	CGGAAGGCACGAAGTATGAAGAT	60.738	47.826	0.00	0.00	41.61	2.40
1426	5643	3.069980	GATGAGCGCTCCGTGTCCT	62.070	63.158	33.23	9.93	0.00	3.85
1495	6800	1.299468	CCGCCAGCGTACATCTCTC	60.299	63.158	11.55	0.00	37.81	3.20
1533	6838	0.179000	CGCTAGGGGAACTGCAGATT	59.821	55.000	23.35	11.07	0.00	2.40
1623	6928	0.602638	GGTCTCGCACCATGTTCACA	60.603	55.000	0.00	0.00	45.98	3.58
1626	6931	0.952497	CTCGCACCATGTTCACAGCT	60.952	55.000	0.00	0.00	0.00	4.24
1723	7047	1.965930	GCAAGGTGCCACGACATCA	60.966	57.895	0.00	0.00	37.42	3.07
1776	7100	3.002246	TGAACAACAAGAAGCGCAAGTAG	59.998	43.478	11.47	0.00	41.68	2.57
1899	7223	3.728076	TGTCTGTGCGTCTAGTTTCTT	57.272	42.857	0.00	0.00	0.00	2.52
1900	7224	3.381045	TGTCTGTGCGTCTAGTTTCTTG	58.619	45.455	0.00	0.00	0.00	3.02
1927	7251	1.406539	GCAACATTGAGCTACCATGGG	59.593	52.381	18.09	0.00	0.00	4.00
1939	7263	3.498481	GCTACCATGGGAGCATTTATCCA	60.498	47.826	39.28	0.00	38.70	3.41
1947	7298	2.887152	GGAGCATTTATCCATTCCGCTT	59.113	45.455	0.00	0.00	36.79	4.68
1980	7331	2.749044	CGGCTGCCATGACAAGCT	60.749	61.111	20.29	0.00	0.00	3.74
2138	7491	6.890979	AAGGAGGTGAAAGAAATGAGAAAG	57.109	37.500	0.00	0.00	0.00	2.62
2167	7520	1.859398	CACGCGCTGCAGAAAACTA	59.141	52.632	20.43	0.00	0.00	2.24
2186	7539	7.954788	AAACTATCTGTGTCTCTTTGTTCTC	57.045	36.000	0.00	0.00	0.00	2.87
2210	7563	0.881796	TTCATCGAGCGAGTGTGAGT	59.118	50.000	0.00	0.00	0.00	3.41
2234	7587	4.130118	GTTTGTGTGTGAGAGGAGATTGT	58.870	43.478	0.00	0.00	0.00	2.71
2312	7665	2.668457	GACAACACCGTGAGCTAAGATG	59.332	50.000	5.28	0.00	0.00	2.90
2358	7711	0.809385	GATCGTGAAGACTCGGGTGA	59.191	55.000	0.00	0.00	34.43	4.02
2451	7804	1.220206	CAAGTGATGCTCGAGGGCT	59.780	57.895	15.58	0.00	0.00	5.19
2453	7806	1.548357	AAGTGATGCTCGAGGGCTGT	61.548	55.000	15.58	0.00	0.00	4.40
2462	7815	3.650950	GAGGGCTGTTGGGAGGCA	61.651	66.667	0.00	0.00	40.29	4.75
2466	7819	1.304381	GGCTGTTGGGAGGCAATCA	60.304	57.895	0.00	0.00	38.40	2.57
2485	7838	1.561769	AAGATCGGCACCACCATCCA	61.562	55.000	0.00	0.00	39.03	3.41
2494	7847	1.375396	CCACCATCCAAAGCGACGA	60.375	57.895	0.00	0.00	0.00	4.20
2520	7873	0.106116	AGCCCCTAAGGTAGTCCTCG	60.106	60.000	0.00	0.00	44.35	4.63
2526	7879	3.181436	CCCTAAGGTAGTCCTCGATGGTA	60.181	52.174	0.00	0.00	44.35	3.25
2529	7882	5.539193	CCTAAGGTAGTCCTCGATGGTATTT	59.461	44.000	0.00	0.00	44.35	1.40
2534	7887	5.533903	GGTAGTCCTCGATGGTATTTCACTA	59.466	44.000	0.00	0.00	37.07	2.74
2633	7986	0.246360	CACATGTCTACGAGGCCACA	59.754	55.000	5.01	0.00	0.00	4.17
2637	7990	0.538746	TGTCTACGAGGCCACACTCA	60.539	55.000	5.01	0.00	37.34	3.41
2643	7996	1.293498	GAGGCCACACTCACGACAT	59.707	57.895	5.01	0.00	37.44	3.06
2661	8014	3.156293	ACATTGTCCAAGCATTACAGCA	58.844	40.909	0.00	0.00	36.85	4.41
2754	8107	1.901948	AGCTCAACGAGACGACCCA	60.902	57.895	0.00	0.00	0.00	4.51
2757	8110	2.214181	CTCAACGAGACGACCCAGGG	62.214	65.000	2.85	2.85	0.00	4.45
2758	8111	2.116772	AACGAGACGACCCAGGGA	59.883	61.111	14.54	0.00	0.00	4.20
2771	8124	0.962356	CCAGGGAAAGCGCATTGTCT	60.962	55.000	11.47	0.22	0.00	3.41

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
7	8	7.398024	AGCTCAAGGTTATCTTCTATGTGTTT	58.602	34.615	0.00	0.00	32.41	2.83
61	62	9.625747	TTTAGGATTGCAATATCATGACAAGTA	57.374	29.630	12.97	0.00	0.00	2.24
136	142	0.031857	TTGCAATGCCAACTCAACGG	59.968	50.000	1.53	0.00	0.00	4.44
154	160	5.452917	GCTATTGTCCTCATTACCGGTAGTT	60.453	44.000	15.20	3.77	0.00	2.24
245	251	8.226819	TCAACACACCATCAAATAGTTAAACA	57.773	30.769	0.00	0.00	0.00	2.83
387	398	8.997621	TTTTACTCGATAAGCTGAAACATACT	57.002	30.769	0.00	0.00	0.00	2.12
477	489	4.319694	GCATATAAATCTCACGCATGTGCA	60.320	41.667	6.08	0.00	46.01	4.57
529	1844	1.234615	AATGCACGCACACACTACCC	61.235	55.000	0.00	0.00	0.00	3.69
535	1850	3.004210	ACTTTTATGAATGCACGCACACA	59.996	39.130	0.00	0.00	0.00	3.72
567	3312	4.798387	CGCAAGCGCTCATATATATACACA	59.202	41.667	12.06	0.00	35.30	3.72
570	3315	5.274718	AGACGCAAGCGCTCATATATATAC	58.725	41.667	12.06	0.00	44.19	1.47
571	3316	5.500645	AGACGCAAGCGCTCATATATATA	57.499	39.130	12.06	0.00	44.19	0.86
1067	5029	2.559840	CGCACTCCACGTACGTCT	59.440	61.111	19.94	0.00	0.00	4.18
1075	5037	2.617274	GGTTTCTGCCGCACTCCAC	61.617	63.158	0.00	0.00	0.00	4.02
1171	5133	1.415374	GCACACTTGTACGACGACAT	58.585	50.000	0.00	0.00	0.00	3.06
1172	5134	0.931202	CGCACACTTGTACGACGACA	60.931	55.000	0.00	0.00	36.98	4.35
1300	5493	1.280421	GAGCTGGTCCTCCAACATCTT	59.720	52.381	0.00	0.00	43.81	2.40
1399	5614	2.544694	CGGAGCGCTCATCTTCATACTT	60.545	50.000	36.27	0.00	0.00	2.24
1407	5622	2.492090	GACACGGAGCGCTCATCT	59.508	61.111	36.27	16.85	0.00	2.90
1410	5625	4.056125	CAGGACACGGAGCGCTCA	62.056	66.667	36.27	0.00	0.00	4.26
1426	5643	2.848679	TGGAGGCTGCAGTGGTCA	60.849	61.111	16.64	6.71	0.00	4.02
1623	6928	1.302033	CCGCAACTTCTGGTCAGCT	60.302	57.895	0.00	0.00	0.00	4.24
1626	6931	0.955428	GCATCCGCAACTTCTGGTCA	60.955	55.000	0.00	0.00	38.36	4.02
1723	7047	2.175878	AAGACGTTCTTGCTGATGCT	57.824	45.000	0.00	0.00	34.98	3.79
1899	7223	1.890625	GCTCAATGTTGCCATGGCCA	61.891	55.000	33.44	24.66	41.09	5.36
1900	7224	1.153509	GCTCAATGTTGCCATGGCC	60.154	57.895	33.44	19.61	41.09	5.36
1915	7239	2.355010	AAATGCTCCCATGGTAGCTC	57.645	50.000	27.45	3.07	39.53	4.09
1927	7251	3.057946	GGAAGCGGAATGGATAAATGCTC	60.058	47.826	0.00	0.00	0.00	4.26
1939	7263	0.552848	ACATCCCATGGAAGCGGAAT	59.447	50.000	15.22	0.00	34.34	3.01
1947	7298	1.181786	GCCGAAAAACATCCCATGGA	58.818	50.000	15.22	0.00	35.55	3.41
2027	7378	1.729131	CGAGCGCGCCACAAAAATT	60.729	52.632	30.33	5.17	0.00	1.82
2167	7520	3.322254	ACGGAGAACAAAGAGACACAGAT	59.678	43.478	0.00	0.00	0.00	2.90
2186	7539	1.154016	ACTCGCTCGATGAACACGG	60.154	57.895	0.00	0.00	0.00	4.94
2210	7563	3.904800	TCTCCTCTCACACACAAACAA	57.095	42.857	0.00	0.00	0.00	2.83
2234	7587	2.472059	GCTCCGATGCCAATTGCGA	61.472	57.895	0.00	0.00	45.60	5.10
2292	7645	2.299013	TCATCTTAGCTCACGGTGTTGT	59.701	45.455	8.17	0.00	0.00	3.32
2312	7665	1.444553	CTCTTCGTCGGCACTGGTC	60.445	63.158	0.00	0.00	0.00	4.02
2451	7804	2.726821	GATCTTGATTGCCTCCCAACA	58.273	47.619	0.00	0.00	35.99	3.33
2453	7806	1.408683	CCGATCTTGATTGCCTCCCAA	60.409	52.381	0.00	0.00	37.94	4.12
2462	7815	0.327924	TGGTGGTGCCGATCTTGATT	59.672	50.000	0.00	0.00	41.21	2.57
2466	7819	1.224592	GGATGGTGGTGCCGATCTT	59.775	57.895	0.00	0.00	41.21	2.40
2485	7838	2.181021	CTAGCCGGTCGTCGCTTT	59.819	61.111	1.90	0.00	37.59	3.51
2494	7847	1.953100	TACCTTAGGGGCTAGCCGGT	61.953	60.000	27.00	27.00	39.10	5.28
2529	7882	8.350722	GGTGAGTATCGTCATTATTTCTAGTGA	58.649	37.037	0.00	0.00	38.61	3.41
2534	7887	6.127168	TGGTGGTGAGTATCGTCATTATTTCT	60.127	38.462	0.00	0.00	38.61	2.52
2571	7924	2.593956	GGGTGTCCCAGGTGTCCTC	61.594	68.421	0.00	0.00	44.65	3.71
2618	7971	0.538746	TGAGTGTGGCCTCGTAGACA	60.539	55.000	3.32	0.00	34.04	3.41
2633	7986	1.202639	TGCTTGGACAATGTCGTGAGT	60.203	47.619	7.35	0.00	32.65	3.41
2637	7990	3.407698	TGTAATGCTTGGACAATGTCGT	58.592	40.909	7.35	0.00	32.65	4.34
2643	7996	2.954989	TGTTGCTGTAATGCTTGGACAA	59.045	40.909	0.00	0.00	0.00	3.18
2661	8014	1.812571	GCAGTTGGTGAATCGGATGTT	59.187	47.619	0.00	0.00	0.00	2.71
2754	8107	0.250901	ACAGACAATGCGCTTTCCCT	60.251	50.000	9.73	4.95	0.00	4.20

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.