AutoCloner

Multiple sequence alignment - TraesCS6D01G231000

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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	TraesCS6D01G231000	chr6D	100.000	4353	0	0	567	4919	324519136	324523488	0.000000e+00	8039.0
1	TraesCS6D01G231000	chr6D	100.000	232	0	0	1	232	324518570	324518801	3.520000e-116	429.0
2	TraesCS6D01G231000	chr6D	88.485	165	18	1	4755	4919	324554572	324554735	1.080000e-46	198.0
3	TraesCS6D01G231000	chr6D	87.500	152	19	0	4768	4919	201008407	201008256	5.060000e-40	176.0
4	TraesCS6D01G231000	chr6D	85.455	165	22	2	4755	4919	273807203	273807365	2.350000e-38	171.0
5	TraesCS6D01G231000	chr6D	96.000	75	1	2	4320	4394	324522817	324522889	2.400000e-23	121.0
6	TraesCS6D01G231000	chr6D	96.000	75	1	2	4248	4320	324522889	324522963	2.400000e-23	121.0
7	TraesCS6D01G231000	chr3A	86.497	1496	138	33	621	2092	46616589	46615134	0.000000e+00	1585.0
8	TraesCS6D01G231000	chr3A	89.968	937	64	16	3234	4157	108921257	108922176	0.000000e+00	1182.0
9	TraesCS6D01G231000	chr3A	89.890	910	58	8	567	1468	108918445	108919328	0.000000e+00	1140.0
10	TraesCS6D01G231000	chr3A	90.658	653	45	8	1467	2112	108919403	108920046	0.000000e+00	854.0
11	TraesCS6D01G231000	chr3A	86.224	784	68	17	2740	3501	46612018	46611253	0.000000e+00	813.0
12	TraesCS6D01G231000	chr3A	83.276	879	110	17	3255	4114	271639715	271640575	0.000000e+00	774.0
13	TraesCS6D01G231000	chr3A	87.072	642	64	13	2970	3604	209642392	209643021	0.000000e+00	708.0
14	TraesCS6D01G231000	chr3A	88.565	446	20	13	2742	3171	108920664	108921094	3.400000e-141	512.0
15	TraesCS6D01G231000	chr3A	88.647	414	35	6	3611	4020	209650947	209651352	1.230000e-135	494.0
16	TraesCS6D01G231000	chr3A	86.562	320	18	6	2439	2733	108920293	108920612	3.670000e-86	329.0
17	TraesCS6D01G231000	chr3A	88.372	129	8	2	2614	2735	271639329	271639457	1.100000e-31	148.0
18	TraesCS6D01G231000	chr3A	87.218	133	14	2	2745	2876	271639511	271639641	1.100000e-31	148.0
19	TraesCS6D01G231000	chr3A	88.776	98	6	4	2111	2205	130843835	130843930	1.120000e-21	115.0
20	TraesCS6D01G231000	chr3A	98.387	62	1	0	17	78	108918222	108918283	5.210000e-20	110.0
21	TraesCS6D01G231000	chr3A	95.833	48	2	0	2382	2429	46614946	46614899	1.470000e-10	78.7
22	TraesCS6D01G231000	chr3A	95.238	42	2	0	4162	4203	359661792	359661833	3.180000e-07	67.6
23	TraesCS6D01G231000	chrUn	87.109	1373	118	25	620	1979	39272903	39274229	0.000000e+00	1500.0
24	TraesCS6D01G231000	chrUn	87.821	780	64	20	2741	3499	39275278	39276047	0.000000e+00	885.0
25	TraesCS6D01G231000	chrUn	88.608	237	21	2	2505	2735	39274988	39275224	2.900000e-72	283.0
26	TraesCS6D01G231000	chrUn	88.000	100	8	3	2110	2205	42338443	42338344	1.120000e-21	115.0
27	TraesCS6D01G231000	chrUn	88.000	100	8	3	2110	2205	42530506	42530605	1.120000e-21	115.0
28	TraesCS6D01G231000	chrUn	88.000	100	8	3	2110	2205	474064159	474064258	1.120000e-21	115.0
29	TraesCS6D01G231000	chrUn	91.892	74	6	0	2019	2092	39274568	39274641	2.420000e-18	104.0
30	TraesCS6D01G231000	chr6B	91.429	1085	74	9	3234	4310	499015353	499014280	0.000000e+00	1471.0
31	TraesCS6D01G231000	chr6B	89.670	910	62	7	567	1468	499018155	499017270	0.000000e+00	1131.0
32	TraesCS6D01G231000	chr6B	89.449	635	40	9	1470	2100	499017184	499016573	0.000000e+00	776.0
33	TraesCS6D01G231000	chr6B	83.107	882	108	18	3255	4114	605767146	605766284	0.000000e+00	765.0
34	TraesCS6D01G231000	chr6B	89.238	446	17	17	2746	3174	499015944	499015513	3.370000e-146	529.0
35	TraesCS6D01G231000	chr6B	86.076	316	21	15	2439	2733	499016317	499016004	7.950000e-83	318.0
36	TraesCS6D01G231000	chr6B	90.710	183	13	2	2256	2435	499016534	499016353	1.770000e-59	241.0
37	TraesCS6D01G231000	chr6B	89.474	133	10	2	2745	2876	605767347	605767218	1.100000e-36	165.0
38	TraesCS6D01G231000	chr6B	80.702	171	8	7	17	187	499018378	499018233	5.210000e-20	110.0
39	TraesCS6D01G231000	chr6A	90.968	919	58	11	3234	4144	461838803	461839704	0.000000e+00	1214.0
40	TraesCS6D01G231000	chr6A	89.901	911	55	9	567	1468	461835988	461836870	0.000000e+00	1138.0
41	TraesCS6D01G231000	chr6A	90.505	653	46	8	1467	2112	461836949	461837592	0.000000e+00	848.0
42	TraesCS6D01G231000	chr6A	88.367	447	19	14	2742	3171	461838210	461838640	1.580000e-139	507.0
43	TraesCS6D01G231000	chr6A	86.562	320	18	6	2439	2733	461837839	461838158	3.670000e-86	329.0
44	TraesCS6D01G231000	chr6A	84.211	323	45	6	4410	4728	587734099	587733779	4.780000e-80	309.0
45	TraesCS6D01G231000	chr6A	86.441	59	4	3	4170	4225	507116521	507116464	1.480000e-05	62.1
46	TraesCS6D01G231000	chr2B	83.172	1242	135	37	2867	4059	62995554	62994338	0.000000e+00	1068.0
47	TraesCS6D01G231000	chr2B	86.408	721	67	18	923	1631	62996367	62995666	0.000000e+00	760.0
48	TraesCS6D01G231000	chr2B	90.816	98	6	3	2108	2205	622914108	622914014	1.440000e-25	128.0
49	TraesCS6D01G231000	chr2B	90.625	96	6	2	2111	2205	97569865	97569958	1.860000e-24	124.0
50	TraesCS6D01G231000	chr7D	84.960	1004	75	26	809	1768	72448015	72447044	0.000000e+00	948.0
51	TraesCS6D01G231000	chr7D	84.511	368	39	9	4416	4767	334869909	334870274	1.010000e-91	348.0
52	TraesCS6D01G231000	chr7D	88.591	149	17	0	4771	4919	370683460	370683312	1.090000e-41	182.0
53	TraesCS6D01G231000	chr7D	100.000	35	0	0	4169	4203	128787638	128787672	1.140000e-06	65.8
54	TraesCS6D01G231000	chr2A	81.111	1260	151	46	611	1834	40561329	40560121	0.000000e+00	928.0
55	TraesCS6D01G231000	chr2A	81.733	1073	114	37	2752	3769	40560072	40559027	0.000000e+00	821.0
56	TraesCS6D01G231000	chr2A	92.857	42	2	1	4157	4198	657531706	657531746	5.320000e-05	60.2
57	TraesCS6D01G231000	chr7A	85.114	880	92	15	3255	4114	165528857	165529717	0.000000e+00	863.0
58	TraesCS6D01G231000	chr7A	87.879	165	19	1	4755	4919	330444083	330444246	5.020000e-45	193.0
59	TraesCS6D01G231000	chr7A	82.759	203	15	7	2745	2931	165528655	165528853	3.940000e-36	163.0
60	TraesCS6D01G231000	chr1D	84.518	872	111	17	3255	4114	28959755	28958896	0.000000e+00	841.0
61	TraesCS6D01G231000	chr3D	86.701	782	72	22	2740	3501	35669894	35669125	0.000000e+00	839.0
62	TraesCS6D01G231000	chr3D	91.644	371	24	5	1101	1468	35694926	35694560	1.580000e-139	507.0
63	TraesCS6D01G231000	chr3D	88.489	278	30	2	1470	1747	35694477	35694202	7.890000e-88	335.0
64	TraesCS6D01G231000	chr3D	84.091	352	35	14	1742	2086	35689494	35689157	2.210000e-83	320.0
65	TraesCS6D01G231000	chr3D	83.288	365	43	8	4408	4757	479054282	479054643	2.210000e-83	320.0
66	TraesCS6D01G231000	chr3D	79.026	534	46	30	2256	2735	35670468	35669947	6.190000e-79	305.0
67	TraesCS6D01G231000	chr3D	100.000	36	0	0	4168	4203	279201044	279201009	3.180000e-07	67.6
68	TraesCS6D01G231000	chr5A	84.187	879	102	17	3255	4114	237942087	237941227	0.000000e+00	819.0
69	TraesCS6D01G231000	chr5A	88.158	152	18	0	4768	4919	419263705	419263856	1.090000e-41	182.0
70	TraesCS6D01G231000	chr5A	83.251	203	16	6	2745	2931	237942291	237942091	2.350000e-38	171.0
71	TraesCS6D01G231000	chr5A	87.597	129	8	6	2614	2735	237942472	237942345	5.130000e-30	143.0
72	TraesCS6D01G231000	chr2D	87.556	450	44	7	1001	1447	36584578	36584138	1.220000e-140	510.0
73	TraesCS6D01G231000	chr2D	80.519	231	27	10	2746	2959	36583550	36583321	1.420000e-35	161.0
74	TraesCS6D01G231000	chr2D	91.579	95	8	0	2111	2205	363977841	363977935	1.110000e-26	132.0
75	TraesCS6D01G231000	chr4B	85.559	367	39	10	4408	4770	127726131	127726487	6.010000e-99	372.0
76	TraesCS6D01G231000	chr4A	85.627	327	34	9	4408	4724	735048166	735048489	1.020000e-86	331.0
77	TraesCS6D01G231000	chr4A	97.368	38	1	0	4162	4199	590945822	590945785	1.140000e-06	65.8
78	TraesCS6D01G231000	chr4D	86.379	301	34	4	4434	4727	30749867	30749567	6.140000e-84	322.0
79	TraesCS6D01G231000	chr4D	84.709	327	34	10	4410	4724	223633420	223633742	3.700000e-81	313.0
80	TraesCS6D01G231000	chr4D	88.816	152	17	0	4768	4919	261680004	261680155	2.340000e-43	187.0
81	TraesCS6D01G231000	chr4D	86.957	161	20	1	4759	4919	194354438	194354597	3.910000e-41	180.0
82	TraesCS6D01G231000	chr4D	88.421	95	10	1	2110	2203	385735001	385735095	4.020000e-21	113.0
83	TraesCS6D01G231000	chr1B	84.802	329	36	8	4402	4728	307433264	307433580	7.950000e-83	318.0
84	TraesCS6D01G231000	chr1A	84.226	336	38	10	4406	4731	403383111	403383441	3.700000e-81	313.0
85	TraesCS6D01G231000	chr1A	100.000	35	0	0	4169	4203	471324214	471324180	1.140000e-06	65.8
86	TraesCS6D01G231000	chr7B	87.975	158	16	3	4763	4919	363560696	363560851	3.020000e-42	183.0
87	TraesCS6D01G231000	chr5D	87.368	95	11	1	2111	2205	11305263	11305356	1.870000e-19	108.0
88	TraesCS6D01G231000	chr3B	95.238	42	2	0	4162	4203	370931962	370932003	3.180000e-07	67.6

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	TraesCS6D01G231000	chr6D	324518570	324523488	4918	False	2177.500000	8039	98.000000	1	4919	4	chr6D.!!$F3	4918
1	TraesCS6D01G231000	chr3A	46611253	46616589	5336	True	825.566667	1585	89.518000	621	3501	3	chr3A.!!$R1	2880
2	TraesCS6D01G231000	chr3A	209642392	209643021	629	False	708.000000	708	87.072000	2970	3604	1	chr3A.!!$F2	634
3	TraesCS6D01G231000	chr3A	108918222	108922176	3954	False	687.833333	1182	90.671667	17	4157	6	chr3A.!!$F5	4140
4	TraesCS6D01G231000	chr3A	271639329	271640575	1246	False	356.666667	774	86.288667	2614	4114	3	chr3A.!!$F6	1500
5	TraesCS6D01G231000	chrUn	39272903	39276047	3144	False	693.000000	1500	88.857500	620	3499	4	chrUn.!!$F3	2879
6	TraesCS6D01G231000	chr6B	499014280	499018378	4098	True	653.714286	1471	88.182000	17	4310	7	chr6B.!!$R1	4293
7	TraesCS6D01G231000	chr6B	605766284	605767347	1063	True	465.000000	765	86.290500	2745	4114	2	chr6B.!!$R2	1369
8	TraesCS6D01G231000	chr6A	461835988	461839704	3716	False	807.200000	1214	89.260600	567	4144	5	chr6A.!!$F1	3577
9	TraesCS6D01G231000	chr2B	62994338	62996367	2029	True	914.000000	1068	84.790000	923	4059	2	chr2B.!!$R2	3136
10	TraesCS6D01G231000	chr7D	72447044	72448015	971	True	948.000000	948	84.960000	809	1768	1	chr7D.!!$R1	959
11	TraesCS6D01G231000	chr2A	40559027	40561329	2302	True	874.500000	928	81.422000	611	3769	2	chr2A.!!$R1	3158
12	TraesCS6D01G231000	chr7A	165528655	165529717	1062	False	513.000000	863	83.936500	2745	4114	2	chr7A.!!$F2	1369
13	TraesCS6D01G231000	chr1D	28958896	28959755	859	True	841.000000	841	84.518000	3255	4114	1	chr1D.!!$R1	859
14	TraesCS6D01G231000	chr3D	35669125	35670468	1343	True	572.000000	839	82.863500	2256	3501	2	chr3D.!!$R3	1245
15	TraesCS6D01G231000	chr3D	35694202	35694926	724	True	421.000000	507	90.066500	1101	1747	2	chr3D.!!$R4	646
16	TraesCS6D01G231000	chr5A	237941227	237942472	1245	True	377.666667	819	85.011667	2614	4114	3	chr5A.!!$R1	1500
17	TraesCS6D01G231000	chr2D	36583321	36584578	1257	True	335.500000	510	84.037500	1001	2959	2	chr2D.!!$R1	1958

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
751	756	0.106894	GTGCTACCTGGGGCAGATAC	59.893	60.0	15.05	2.67	39.22	2.24	F
2017	2567	0.179200	GTTATGTTCACTTGCCCGCG	60.179	55.0	0.00	0.00	0.00	6.46	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2189	2740	0.031111	TTCCACTCCCTCCGATCCAT	60.031	55.0	0.00	0.0	0.00	3.41	R
3945	7321	0.037326	TGCTTCTGGGTGTAAGCTCG	60.037	55.0	8.36	0.0	46.57	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)

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
78	79	5.619220	TGGGATTGATTTTTCAAAAGGTGG	58.381	37.500	0.00	0.00	32.94	4.61
79	80	5.003160	GGGATTGATTTTTCAAAAGGTGGG	58.997	41.667	0.00	0.00	32.94	4.61
80	81	4.455533	GGATTGATTTTTCAAAAGGTGGGC	59.544	41.667	0.00	0.00	32.94	5.36
81	82	4.494091	TTGATTTTTCAAAAGGTGGGCA	57.506	36.364	0.00	0.00	0.00	5.36
84	85	4.637977	TGATTTTTCAAAAGGTGGGCAAAC	59.362	37.500	0.00	0.00	0.00	2.93
96	97	3.616343	TGGGCAAACCATATCCATCAT	57.384	42.857	0.00	0.00	46.80	2.45
97	98	3.926198	TGGGCAAACCATATCCATCATT	58.074	40.909	0.00	0.00	46.80	2.57
98	99	4.296912	TGGGCAAACCATATCCATCATTT	58.703	39.130	0.00	0.00	46.80	2.32
99	100	4.720773	TGGGCAAACCATATCCATCATTTT	59.279	37.500	0.00	0.00	46.80	1.82
100	101	5.163322	TGGGCAAACCATATCCATCATTTTC	60.163	40.000	0.00	0.00	46.80	2.29
101	102	5.070847	GGGCAAACCATATCCATCATTTTCT	59.929	40.000	0.00	0.00	39.85	2.52
102	103	5.987347	GGCAAACCATATCCATCATTTTCTG	59.013	40.000	0.00	0.00	35.26	3.02
103	104	6.183360	GGCAAACCATATCCATCATTTTCTGA	60.183	38.462	0.00	0.00	35.27	3.27
104	105	7.267128	GCAAACCATATCCATCATTTTCTGAA	58.733	34.615	0.00	0.00	37.44	3.02
105	106	7.765360	GCAAACCATATCCATCATTTTCTGAAA	59.235	33.333	0.00	0.00	37.44	2.69
106	107	9.309516	CAAACCATATCCATCATTTTCTGAAAG	57.690	33.333	2.75	0.00	37.44	2.62
107	108	7.592885	ACCATATCCATCATTTTCTGAAAGG	57.407	36.000	2.75	1.38	37.44	3.11
108	109	7.128077	ACCATATCCATCATTTTCTGAAAGGT	58.872	34.615	2.75	0.40	37.44	3.50
109	110	7.620888	ACCATATCCATCATTTTCTGAAAGGTT	59.379	33.333	2.75	0.00	37.44	3.50
110	111	8.480501	CCATATCCATCATTTTCTGAAAGGTTT	58.519	33.333	2.75	0.00	37.44	3.27
111	112	9.880157	CATATCCATCATTTTCTGAAAGGTTTT	57.120	29.630	2.75	0.00	37.44	2.43
178	179	2.704725	ACCGATGTGCAAATGTTCAC	57.295	45.000	0.00	0.00	0.00	3.18
179	180	2.229792	ACCGATGTGCAAATGTTCACT	58.770	42.857	0.00	0.00	34.49	3.41
180	181	2.622942	ACCGATGTGCAAATGTTCACTT	59.377	40.909	0.00	0.00	34.49	3.16
181	182	3.818210	ACCGATGTGCAAATGTTCACTTA	59.182	39.130	0.00	0.00	34.49	2.24

Showing 1 to 25 of 548 entries

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Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
4	5	5.219633	GGCTTTAACAACGTGATTGATGTT	58.780	37.500	6.33	6.33	41.23	2.71
5	6	4.277174	TGGCTTTAACAACGTGATTGATGT	59.723	37.500	0.00	0.00	41.23	3.06
6	7	4.616802	GTGGCTTTAACAACGTGATTGATG	59.383	41.667	0.00	0.00	41.23	3.07
7	8	4.277174	TGTGGCTTTAACAACGTGATTGAT	59.723	37.500	0.00	0.00	41.23	2.57
8	9	3.628032	TGTGGCTTTAACAACGTGATTGA	59.372	39.130	0.00	0.00	41.23	2.57
9	10	3.958704	TGTGGCTTTAACAACGTGATTG	58.041	40.909	0.00	0.00	44.60	2.67
10	11	3.880490	TCTGTGGCTTTAACAACGTGATT	59.120	39.130	0.00	0.00	0.00	2.57
11	12	3.472652	TCTGTGGCTTTAACAACGTGAT	58.527	40.909	0.00	0.00	0.00	3.06
12	13	2.907634	TCTGTGGCTTTAACAACGTGA	58.092	42.857	0.00	0.00	0.00	4.35
13	14	3.684103	TTCTGTGGCTTTAACAACGTG	57.316	42.857	0.00	0.00	0.00	4.49
14	15	3.692593	ACTTTCTGTGGCTTTAACAACGT	59.307	39.130	0.00	0.00	0.00	3.99
15	16	4.287238	ACTTTCTGTGGCTTTAACAACG	57.713	40.909	0.00	0.00	0.00	4.10
78	79	5.987347	CAGAAAATGATGGATATGGTTTGCC	59.013	40.000	0.00	0.00	0.00	4.52
79	80	6.808829	TCAGAAAATGATGGATATGGTTTGC	58.191	36.000	0.00	0.00	31.12	3.68
80	81	9.309516	CTTTCAGAAAATGATGGATATGGTTTG	57.690	33.333	0.00	0.00	37.89	2.93
81	82	8.480501	CCTTTCAGAAAATGATGGATATGGTTT	58.519	33.333	0.00	0.00	37.89	3.27
84	85	7.592885	ACCTTTCAGAAAATGATGGATATGG	57.407	36.000	5.36	0.00	37.89	2.74
164	165	4.826733	AGACCATAAGTGAACATTTGCACA	59.173	37.500	0.00	0.00	37.48	4.57
165	166	5.182001	AGAGACCATAAGTGAACATTTGCAC	59.818	40.000	0.00	0.00	35.30	4.57
178	179	6.166984	TCATAAGAAGGCAGAGACCATAAG	57.833	41.667	0.00	0.00	0.00	1.73
179	180	6.753913	ATCATAAGAAGGCAGAGACCATAA	57.246	37.500	0.00	0.00	0.00	1.90
180	181	7.855784	TTATCATAAGAAGGCAGAGACCATA	57.144	36.000	0.00	0.00	0.00	2.74
181	182	6.753913	TTATCATAAGAAGGCAGAGACCAT	57.246	37.500	0.00	0.00	0.00	3.55
182	183	6.753913	ATTATCATAAGAAGGCAGAGACCA	57.246	37.500	0.00	0.00	0.00	4.02
183	184	8.348507	CAAAATTATCATAAGAAGGCAGAGACC	58.651	37.037	0.00	0.00	0.00	3.85

Showing 1 to 25 of 506 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.