AutoCloner

Multiple sequence alignment - TraesCS2A01G321800

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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	TraesCS2A01G321800	chr2A	100.000	6931	0	0	1	6931	551452571	551445641	0.000000e+00	12800.0
1	TraesCS2A01G321800	chr2A	98.365	3303	53	1	2360	5661	101854859	101858161	0.000000e+00	5799.0
2	TraesCS2A01G321800	chr2A	87.261	628	40	20	943	1540	551373439	551372822	0.000000e+00	680.0
3	TraesCS2A01G321800	chr2A	88.522	575	31	12	5662	6233	551462096	551461554	0.000000e+00	664.0
4	TraesCS2A01G321800	chr2A	89.979	479	24	8	932	1400	551463210	551462746	1.290000e-166	597.0
5	TraesCS2A01G321800	chr2A	84.041	589	52	18	5662	6233	551372342	551371779	4.760000e-146	529.0
6	TraesCS2A01G321800	chr2A	85.797	521	37	15	935	1420	551469288	551468770	1.030000e-142	518.0
7	TraesCS2A01G321800	chr2A	93.464	306	14	1	988	1293	551482425	551482126	3.810000e-122	449.0
8	TraesCS2A01G321800	chr2A	90.379	343	27	3	1881	2217	551468403	551468061	4.930000e-121	446.0
9	TraesCS2A01G321800	chr2A	85.393	445	34	14	5659	6098	551467987	551467569	3.840000e-117	433.0
10	TraesCS2A01G321800	chr2A	90.476	315	28	1	5662	5974	551481452	551481138	1.390000e-111	414.0
11	TraesCS2A01G321800	chr2A	83.438	477	19	21	1755	2216	551462562	551462131	8.430000e-104	388.0
12	TraesCS2A01G321800	chr2A	98.450	129	2	0	6273	6401	551379252	551379124	1.940000e-55	228.0
13	TraesCS2A01G321800	chr2A	97.321	112	3	0	719	830	551373661	551373550	2.550000e-44	191.0
14	TraesCS2A01G321800	chr2A	86.538	156	11	5	1486	1635	551468770	551468619	5.560000e-36	163.0
15	TraesCS2A01G321800	chr2A	90.598	117	9	1	6111	6225	551481033	551480917	3.350000e-33	154.0
16	TraesCS2A01G321800	chr2A	100.000	70	0	0	6164	6233	551467567	551467498	5.640000e-26	130.0
17	TraesCS2A01G321800	chr2A	90.164	61	2	2	1696	1756	551468596	551468540	7.450000e-10	76.8
18	TraesCS2A01G321800	chr2A	97.619	42	1	0	839	880	551463257	551463216	9.640000e-09	73.1
19	TraesCS2A01G321800	chr2A	95.556	45	1	1	6233	6277	551461538	551461495	3.470000e-08	71.3
20	TraesCS2A01G321800	chr2A	83.117	77	8	5	6233	6308	551467483	551467411	1.610000e-06	65.8
21	TraesCS2A01G321800	chr3A	98.336	3306	52	2	2359	5661	217717334	217720639	0.000000e+00	5797.0
22	TraesCS2A01G321800	chr3A	98.005	3308	64	2	2359	5664	633853194	633849887	0.000000e+00	5742.0
23	TraesCS2A01G321800	chr3A	94.655	580	22	6	1	571	11512588	11513167	0.000000e+00	891.0
24	TraesCS2A01G321800	chr3A	90.909	308	26	2	6625	6931	636563654	636563348	5.000000e-111	412.0
25	TraesCS2A01G321800	chr1A	98.061	3301	63	1	2362	5661	252517257	252513957	0.000000e+00	5740.0
26	TraesCS2A01G321800	chr1A	97.766	3312	70	4	2355	5664	106827693	106824384	0.000000e+00	5703.0
27	TraesCS2A01G321800	chr1A	97.731	3306	72	2	2367	5670	64565609	64562305	0.000000e+00	5686.0
28	TraesCS2A01G321800	chr1A	96.409	557	17	3	1	554	536672293	536671737	0.000000e+00	915.0
29	TraesCS2A01G321800	chr1A	96.403	556	17	3	2	554	3978172	3978727	0.000000e+00	913.0
30	TraesCS2A01G321800	chr1A	96.230	557	17	4	1	554	497342611	497342056	0.000000e+00	909.0
31	TraesCS2A01G321800	chr1A	94.921	571	27	1	1	571	23170692	23171260	0.000000e+00	893.0
32	TraesCS2A01G321800	chr1A	82.051	273	36	8	6271	6535	90014372	90014639	3.250000e-53	220.0
33	TraesCS2A01G321800	chr1A	79.762	168	31	2	6616	6781	188185220	188185054	1.220000e-22	119.0
34	TraesCS2A01G321800	chr5A	97.791	3304	72	1	2359	5661	359107125	359110428	0.000000e+00	5696.0
35	TraesCS2A01G321800	chr5A	97.557	3316	78	3	2348	5661	574791280	574794594	0.000000e+00	5672.0
36	TraesCS2A01G321800	chr5A	81.098	328	26	19	6272	6590	277834677	277834377	5.410000e-56	230.0
37	TraesCS2A01G321800	chr5A	96.471	85	3	0	2216	2300	7109640	7109724	2.610000e-29	141.0
38	TraesCS2A01G321800	chr2D	97.669	3304	76	1	2359	5661	106332698	106329395	0.000000e+00	5674.0
39	TraesCS2A01G321800	chr2D	95.000	580	20	1	1	571	73126157	73125578	0.000000e+00	902.0
40	TraesCS2A01G321800	chr2D	88.358	481	30	9	932	1400	435221837	435222303	7.850000e-154	555.0
41	TraesCS2A01G321800	chr2D	91.209	364	18	5	932	1293	435196765	435197116	3.760000e-132	483.0
42	TraesCS2A01G321800	chr2D	91.813	342	17	3	1881	2217	435224259	435224594	3.790000e-127	466.0
43	TraesCS2A01G321800	chr2D	82.074	569	59	16	5662	6226	435224637	435225166	4.930000e-121	446.0
44	TraesCS2A01G321800	chr2D	81.754	570	63	26	5662	6225	435197446	435197980	8.250000e-119	438.0
45	TraesCS2A01G321800	chr2D	91.111	315	28	0	6617	6931	130891962	130891648	1.790000e-115	427.0
46	TraesCS2A01G321800	chr2D	90.093	323	22	6	1902	2217	435308215	435308534	1.800000e-110	411.0
47	TraesCS2A01G321800	chr2D	82.533	458	39	18	5831	6274	435325704	435326134	1.420000e-96	364.0
48	TraesCS2A01G321800	chr2D	89.494	257	21	1	1400	1650	435290249	435290505	3.120000e-83	320.0
49	TraesCS2A01G321800	chr2D	95.431	197	6	3	1211	1405	435275714	435275909	1.880000e-80	311.0
50	TraesCS2A01G321800	chr2D	93.514	185	11	1	5662	5845	435308576	435308760	2.460000e-69	274.0
51	TraesCS2A01G321800	chr2D	86.301	219	24	5	6400	6616	498809445	498809659	4.180000e-57	233.0
52	TraesCS2A01G321800	chr2D	84.286	140	19	3	2070	2207	435197230	435197368	4.360000e-27	134.0
53	TraesCS2A01G321800	chr2D	93.023	86	6	0	2215	2300	587734732	587734817	7.300000e-25	126.0
54	TraesCS2A01G321800	chr2D	92.045	88	7	0	2215	2302	495785963	495786050	2.620000e-24	124.0
55	TraesCS2A01G321800	chr2D	96.296	54	2	0	776	829	435196608	435196661	9.580000e-14	89.8
56	TraesCS2A01G321800	chr2D	96.078	51	2	0	830	880	435221781	435221831	4.450000e-12	84.2
57	TraesCS2A01G321800	chr7D	95.972	571	21	2	1	571	637694851	637694283	0.000000e+00	926.0
58	TraesCS2A01G321800	chr6D	96.558	552	18	1	1	551	142135977	142135426	0.000000e+00	913.0
59	TraesCS2A01G321800	chr6D	88.172	186	18	3	5697	5880	269806540	269806723	1.170000e-52	219.0
60	TraesCS2A01G321800	chr6D	84.663	163	23	2	6616	6777	160853157	160852996	2.000000e-35	161.0
61	TraesCS2A01G321800	chr6D	88.235	119	10	3	6617	6733	13738877	13738761	9.370000e-29	139.0
62	TraesCS2A01G321800	chr6D	92.391	92	6	1	2209	2300	381355406	381355496	5.640000e-26	130.0
63	TraesCS2A01G321800	chr6D	93.258	89	5	1	2212	2300	455718103	455718016	5.640000e-26	130.0
64	TraesCS2A01G321800	chr1D	95.000	580	20	1	1	571	60171101	60170522	0.000000e+00	902.0
65	TraesCS2A01G321800	chr1D	82.609	161	28	0	6617	6777	477231565	477231405	7.250000e-30	143.0
66	TraesCS2A01G321800	chr1D	88.136	118	14	0	6616	6733	465352381	465352498	2.610000e-29	141.0
67	TraesCS2A01G321800	chr1D	90.476	105	10	0	6616	6720	12065294	12065398	9.370000e-29	139.0
68	TraesCS2A01G321800	chr2B	90.351	570	29	7	932	1485	513695260	513695819	0.000000e+00	725.0
69	TraesCS2A01G321800	chr2B	88.850	574	22	14	5662	6233	513696536	513697069	0.000000e+00	667.0
70	TraesCS2A01G321800	chr2B	85.248	644	46	24	932	1537	513706468	513707100	9.880000e-173	617.0
71	TraesCS2A01G321800	chr2B	92.484	306	20	1	988	1293	513680838	513681140	1.070000e-117	435.0
72	TraesCS2A01G321800	chr2B	91.083	314	27	1	5662	5974	513681467	513681780	2.310000e-114	424.0
73	TraesCS2A01G321800	chr2B	90.221	317	30	1	6616	6931	562725652	562725968	5.000000e-111	412.0
74	TraesCS2A01G321800	chr2B	86.571	350	17	11	1881	2217	513696161	513696493	6.610000e-95	359.0
75	TraesCS2A01G321800	chr2B	89.928	139	14	0	582	720	513705133	513705271	5.520000e-41	180.0
76	TraesCS2A01G321800	chr2B	82.941	170	18	5	6062	6226	513708736	513708899	7.250000e-30	143.0
77	TraesCS2A01G321800	chr2B	92.135	89	7	0	2215	2303	545253110	545253022	7.300000e-25	126.0
78	TraesCS2A01G321800	chr2B	88.235	102	10	2	2212	2312	682915933	682915833	3.400000e-23	121.0
79	TraesCS2A01G321800	chr2B	87.850	107	6	2	723	829	513706275	513706374	1.220000e-22	119.0
80	TraesCS2A01G321800	chr2B	81.560	141	19	4	2070	2207	513681257	513681393	7.350000e-20	110.0
81	TraesCS2A01G321800	chr2B	98.148	54	1	0	776	829	513695083	513695136	2.060000e-15	95.3
82	TraesCS2A01G321800	chr2B	98.039	51	1	0	830	880	513706412	513706462	9.580000e-14	89.8
83	TraesCS2A01G321800	chr2B	100.000	37	0	0	1838	1874	513696132	513696168	1.250000e-07	69.4
84	TraesCS2A01G321800	chr1B	91.111	315	27	1	6616	6929	653207408	653207722	6.430000e-115	425.0
85	TraesCS2A01G321800	chr1B	91.083	314	27	1	6617	6929	625917332	625917645	2.310000e-114	424.0
86	TraesCS2A01G321800	chr1B	91.579	285	21	2	6616	6899	625925915	625925633	2.340000e-104	390.0
87	TraesCS2A01G321800	chr1B	91.166	283	24	1	6617	6898	653215979	653215697	3.920000e-102	383.0
88	TraesCS2A01G321800	chr1B	97.872	47	1	0	886	932	553007916	553007870	1.600000e-11	82.4
89	TraesCS2A01G321800	chr5B	92.606	284	20	1	6617	6899	678334584	678334301	2.330000e-109	407.0
90	TraesCS2A01G321800	chr5B	89.590	317	30	2	6616	6931	678327367	678327681	3.890000e-107	399.0
91	TraesCS2A01G321800	chr5B	89.241	316	32	2	6616	6931	116690677	116690990	1.810000e-105	394.0
92	TraesCS2A01G321800	chr7B	92.199	282	21	1	6617	6898	99595799	99596079	1.400000e-106	398.0
93	TraesCS2A01G321800	chr7B	89.274	317	33	1	6616	6931	99600279	99599963	5.040000e-106	396.0
94	TraesCS2A01G321800	chr7B	87.402	127	16	0	6617	6743	619151028	619151154	5.600000e-31	147.0
95	TraesCS2A01G321800	chr7B	86.131	137	18	1	6607	6742	674976995	674976859	5.600000e-31	147.0
96	TraesCS2A01G321800	chr7B	82.716	162	28	0	6616	6777	33942218	33942379	2.010000e-30	145.0
97	TraesCS2A01G321800	chr7B	82.099	162	27	2	6617	6777	33949971	33949811	3.370000e-28	137.0
98	TraesCS2A01G321800	chr5D	88.994	318	32	3	6616	6931	107477441	107477757	2.340000e-104	390.0
99	TraesCS2A01G321800	chr7A	83.537	328	36	12	6269	6582	89781335	89781012	2.450000e-74	291.0
100	TraesCS2A01G321800	chr7A	79.878	328	48	11	6270	6582	655006526	655006202	2.520000e-54	224.0
101	TraesCS2A01G321800	chr6B	82.521	349	44	14	6271	6610	382511636	382511296	2.450000e-74	291.0
102	TraesCS2A01G321800	chr6B	88.587	184	21	0	5697	5880	422567406	422567589	2.520000e-54	224.0
103	TraesCS2A01G321800	chr3D	81.215	362	54	11	6261	6617	296161731	296161379	5.290000e-71	279.0
104	TraesCS2A01G321800	chr3D	84.649	228	27	7	6390	6616	537632032	537632252	3.250000e-53	220.0
105	TraesCS2A01G321800	chr3D	79.118	340	51	13	6268	6594	365522422	365522754	4.210000e-52	217.0
106	TraesCS2A01G321800	chr4A	79.870	308	42	13	6286	6583	653423246	653423543	2.530000e-49	207.0
107	TraesCS2A01G321800	chr4A	95.294	85	4	0	2216	2300	744188210	744188294	1.210000e-27	135.0
108	TraesCS2A01G321800	chr4A	92.222	90	6	1	2211	2300	640248417	640248505	7.300000e-25	126.0
109	TraesCS2A01G321800	chr6A	87.006	177	23	0	5697	5873	384315974	384316150	4.240000e-47	200.0
110	TraesCS2A01G321800	chr6A	83.007	153	26	0	6616	6768	484613631	484613783	9.370000e-29	139.0
111	TraesCS2A01G321800	chrUn	82.716	162	28	0	6616	6777	21249017	21249178	2.010000e-30	145.0
112	TraesCS2A01G321800	chrUn	82.609	161	28	0	6617	6777	21276959	21276799	7.250000e-30	143.0
113	TraesCS2A01G321800	chr4B	86.923	130	13	4	6616	6743	35183454	35183327	7.250000e-30	143.0
114	TraesCS2A01G321800	chr4B	78.818	203	39	4	6617	6817	119305592	119305792	4.360000e-27	134.0
115	TraesCS2A01G321800	chr4D	85.156	128	19	0	6616	6743	67291277	67291150	1.570000e-26	132.0
116	TraesCS2A01G321800	chr4D	82.203	118	21	0	6616	6733	12531739	12531856	1.230000e-17	102.0

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	TraesCS2A01G321800	chr2A	551445641	551452571	6930	True	12800.000000	12800	100.000000	1	6931	1	chr2A.!!$R2	6930
1	TraesCS2A01G321800	chr2A	101854859	101858161	3302	False	5799.000000	5799	98.365000	2360	5661	1	chr2A.!!$F1	3301
2	TraesCS2A01G321800	chr2A	551371779	551373661	1882	True	466.666667	680	89.541000	719	6233	3	chr2A.!!$R3	5514
3	TraesCS2A01G321800	chr2A	551461495	551463257	1762	True	358.680000	664	91.022800	839	6277	5	chr2A.!!$R4	5438
4	TraesCS2A01G321800	chr2A	551480917	551482425	1508	True	339.000000	449	91.512667	988	6225	3	chr2A.!!$R6	5237
5	TraesCS2A01G321800	chr2A	551467411	551469288	1877	True	261.800000	518	88.769714	935	6308	7	chr2A.!!$R5	5373
6	TraesCS2A01G321800	chr3A	217717334	217720639	3305	False	5797.000000	5797	98.336000	2359	5661	1	chr3A.!!$F2	3302
7	TraesCS2A01G321800	chr3A	633849887	633853194	3307	True	5742.000000	5742	98.005000	2359	5664	1	chr3A.!!$R1	3305
8	TraesCS2A01G321800	chr3A	11512588	11513167	579	False	891.000000	891	94.655000	1	571	1	chr3A.!!$F1	570
9	TraesCS2A01G321800	chr1A	252513957	252517257	3300	True	5740.000000	5740	98.061000	2362	5661	1	chr1A.!!$R4	3299
10	TraesCS2A01G321800	chr1A	106824384	106827693	3309	True	5703.000000	5703	97.766000	2355	5664	1	chr1A.!!$R2	3309
11	TraesCS2A01G321800	chr1A	64562305	64565609	3304	True	5686.000000	5686	97.731000	2367	5670	1	chr1A.!!$R1	3303
12	TraesCS2A01G321800	chr1A	536671737	536672293	556	True	915.000000	915	96.409000	1	554	1	chr1A.!!$R6	553
13	TraesCS2A01G321800	chr1A	3978172	3978727	555	False	913.000000	913	96.403000	2	554	1	chr1A.!!$F1	552
14	TraesCS2A01G321800	chr1A	497342056	497342611	555	True	909.000000	909	96.230000	1	554	1	chr1A.!!$R5	553
15	TraesCS2A01G321800	chr1A	23170692	23171260	568	False	893.000000	893	94.921000	1	571	1	chr1A.!!$F2	570
16	TraesCS2A01G321800	chr5A	359107125	359110428	3303	False	5696.000000	5696	97.791000	2359	5661	1	chr5A.!!$F2	3302
17	TraesCS2A01G321800	chr5A	574791280	574794594	3314	False	5672.000000	5672	97.557000	2348	5661	1	chr5A.!!$F3	3313
18	TraesCS2A01G321800	chr2D	106329395	106332698	3303	True	5674.000000	5674	97.669000	2359	5661	1	chr2D.!!$R2	3302
19	TraesCS2A01G321800	chr2D	73125578	73126157	579	True	902.000000	902	95.000000	1	571	1	chr2D.!!$R1	570
20	TraesCS2A01G321800	chr2D	435221781	435225166	3385	False	387.800000	555	89.580750	830	6226	4	chr2D.!!$F8	5396
21	TraesCS2A01G321800	chr2D	435308215	435308760	545	False	342.500000	411	91.803500	1902	5845	2	chr2D.!!$F9	3943
22	TraesCS2A01G321800	chr2D	435196608	435197980	1372	False	286.200000	483	88.386250	776	6225	4	chr2D.!!$F7	5449
23	TraesCS2A01G321800	chr7D	637694283	637694851	568	True	926.000000	926	95.972000	1	571	1	chr7D.!!$R1	570
24	TraesCS2A01G321800	chr6D	142135426	142135977	551	True	913.000000	913	96.558000	1	551	1	chr6D.!!$R2	550
25	TraesCS2A01G321800	chr1D	60170522	60171101	579	True	902.000000	902	95.000000	1	571	1	chr1D.!!$R1	570
26	TraesCS2A01G321800	chr2B	513695083	513697069	1986	False	383.140000	725	92.784000	776	6233	5	chr2B.!!$F3	5457
27	TraesCS2A01G321800	chr2B	513680838	513681780	942	False	323.000000	435	88.375667	988	5974	3	chr2B.!!$F2	4986
28	TraesCS2A01G321800	chr2B	513705133	513708899	3766	False	229.760000	617	88.801200	582	6226	5	chr2B.!!$F4	5644

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	Hairpin	End Stability	Orientation
904	1984	0.107993	TCTTTCTGATGCAGAGGCCG	60.108	55.000	0.00	41.75	6.13	F
1421	2598	0.034477	TGATTCCTTTCGGGGCTTCC	60.034	55.000	0.00	35.33	3.46	F
2230	5861	0.039180	TTGCTACTCCCTCCGTCTCA	59.961	55.000	0.00	0.00	3.27	F
3217	6910	0.447801	CCGCAAAGAGCATACACCAC	59.552	55.000	0.00	46.13	4.16	F
3832	7526	1.075374	CCTTTCCACACCTCAATGGGA	59.925	52.381	0.00	41.11	4.37	F
4088	7782	0.472471	TTGGCCAATATCCCTCGTCC	59.528	55.000	16.05	0.00	4.79	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2212	5843	0.039180	TTGAGACGGAGGGAGTAGCA	59.961	55.000	0.00	0.00	0.00	3.49	R
3001	6691	1.618837	CCTCAGAAGGACACCTTTCGA	59.381	52.381	4.51	4.16	44.82	3.71	R
3726	7420	0.462759	GCCAGAAGAATGGAGACGGG	60.463	60.000	0.00	0.00	43.57	5.28	R
4088	7782	0.673437	GCCAAGATCCGAGAGAGGAG	59.327	60.000	0.00	0.00	44.55	3.69	R
5399	9094	0.674895	GTGGCAAGTGAGCGAGGATT	60.675	55.000	0.00	0.00	34.64	3.01	R
6052	9779	1.187974	CCATGCATCAGCTCCCAAAA	58.812	50.000	0.00	0.00	42.74	2.44	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
40	41	3.059386	GATGCCGGGCCGAAAACA	61.059	61.111	30.79	19.72	0.00	2.83
352	353	2.415843	CACCACCTCACGACACGT	59.584	61.111	0.00	0.00	42.36	4.49
554	555	4.144727	GGCGAGGGGAGGAGGAGA	62.145	72.222	0.00	0.00	0.00	3.71
555	556	2.835895	GCGAGGGGAGGAGGAGAC	60.836	72.222	0.00	0.00	0.00	3.36
566	567	2.360980	AGGAGACTCGAGGGGTGG	59.639	66.667	18.41	0.00	32.90	4.61
567	568	3.462678	GGAGACTCGAGGGGTGGC	61.463	72.222	18.41	0.00	0.00	5.01
568	569	3.827898	GAGACTCGAGGGGTGGCG	61.828	72.222	18.41	0.00	0.00	5.69
592	593	4.275936	GCGCTGTGGTAAGGATAAATTGAT	59.724	41.667	0.00	0.00	0.00	2.57
595	596	7.624344	GCGCTGTGGTAAGGATAAATTGATATC	60.624	40.741	0.00	0.00	0.00	1.63
624	625	2.675075	ACATTTCGTTGGGGCCCG	60.675	61.111	19.83	6.16	0.00	6.13
646	647	1.234821	TGTCATTGGCCGTCTGAAAC	58.765	50.000	0.00	0.00	0.00	2.78
660	661	3.921021	GTCTGAAACGATCTTGTGACGAT	59.079	43.478	0.00	0.00	0.00	3.73
670	671	2.292292	TCTTGTGACGATGTTGAGTCGA	59.708	45.455	2.28	0.00	41.40	4.20
706	707	3.499737	CGGCGTGGCTTCATGGAC	61.500	66.667	0.00	0.00	0.00	4.02
713	714	1.522580	GGCTTCATGGACGCTCTCC	60.523	63.158	0.00	0.00	39.97	3.71
721	1723	2.492090	GACGCTCTCCATCGCACT	59.508	61.111	0.00	0.00	0.00	4.40
830	1832	1.659098	CCTACGTTGACGCCTTTGATC	59.341	52.381	3.05	0.00	44.43	2.92
831	1833	1.659098	CTACGTTGACGCCTTTGATCC	59.341	52.381	3.05	0.00	44.43	3.36
837	1907	3.746045	TGACGCCTTTGATCCCTATAC	57.254	47.619	0.00	0.00	0.00	1.47
880	1960	1.355720	ACAGCAAAGCCCTGTTCCTAT	59.644	47.619	0.00	0.00	40.45	2.57
882	1962	3.010138	ACAGCAAAGCCCTGTTCCTATAA	59.990	43.478	0.00	0.00	40.45	0.98
884	1964	3.267031	AGCAAAGCCCTGTTCCTATAACT	59.733	43.478	0.00	0.00	0.00	2.24
885	1965	4.017126	GCAAAGCCCTGTTCCTATAACTT	58.983	43.478	0.00	0.00	0.00	2.66
886	1966	4.096532	GCAAAGCCCTGTTCCTATAACTTC	59.903	45.833	0.00	0.00	0.00	3.01
887	1967	5.501156	CAAAGCCCTGTTCCTATAACTTCT	58.499	41.667	0.00	0.00	0.00	2.85

Showing 1 to 25 of 597 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
37	38	2.294979	GAGGAAACTTTGGTCGGTGTT	58.705	47.619	0.00	0.00	44.43	3.32
40	41	0.250166	CGGAGGAAACTTTGGTCGGT	60.250	55.000	0.00	0.00	44.43	4.69
100	101	4.812476	CGGATCGTGGCTTGCCGA	62.812	66.667	7.18	1.95	44.43	5.54
537	538	4.144727	TCTCCTCCTCCCCTCGCC	62.145	72.222	0.00	0.00	0.00	5.54
538	539	2.835895	GTCTCCTCCTCCCCTCGC	60.836	72.222	0.00	0.00	0.00	5.03
539	540	1.152839	GAGTCTCCTCCTCCCCTCG	60.153	68.421	0.00	0.00	0.00	4.63
540	541	1.152839	CGAGTCTCCTCCTCCCCTC	60.153	68.421	0.00	0.00	33.93	4.30
541	542	1.619975	TCGAGTCTCCTCCTCCCCT	60.620	63.158	0.00	0.00	33.93	4.79
542	543	1.152839	CTCGAGTCTCCTCCTCCCC	60.153	68.421	3.62	0.00	33.93	4.81
543	544	1.152839	CCTCGAGTCTCCTCCTCCC	60.153	68.421	12.31	0.00	33.93	4.30
544	545	1.152839	CCCTCGAGTCTCCTCCTCC	60.153	68.421	12.31	0.00	33.93	4.30
545	546	1.152839	CCCCTCGAGTCTCCTCCTC	60.153	68.421	12.31	0.00	33.93	3.71
546	547	1.931705	ACCCCTCGAGTCTCCTCCT	60.932	63.158	12.31	0.00	33.93	3.69
547	548	1.755008	CACCCCTCGAGTCTCCTCC	60.755	68.421	12.31	0.00	33.93	4.30
548	549	1.755008	CCACCCCTCGAGTCTCCTC	60.755	68.421	12.31	0.00	0.00	3.71
549	550	2.360980	CCACCCCTCGAGTCTCCT	59.639	66.667	12.31	0.00	0.00	3.69
550	551	3.462678	GCCACCCCTCGAGTCTCC	61.463	72.222	12.31	0.00	0.00	3.71
551	552	3.827898	CGCCACCCCTCGAGTCTC	61.828	72.222	12.31	0.00	0.00	3.36
566	567	2.638330	TATCCTTACCACAGCGCCGC	62.638	60.000	2.29	0.00	0.00	6.53
567	568	0.179094	TTATCCTTACCACAGCGCCG	60.179	55.000	2.29	0.00	0.00	6.46
568	569	2.032680	TTTATCCTTACCACAGCGCC	57.967	50.000	2.29	0.00	0.00	6.53
569	570	3.625764	TCAATTTATCCTTACCACAGCGC	59.374	43.478	0.00	0.00	0.00	5.92
570	571	7.604164	AGATATCAATTTATCCTTACCACAGCG	59.396	37.037	5.32	0.00	30.29	5.18
571	572	8.725148	CAGATATCAATTTATCCTTACCACAGC	58.275	37.037	5.32	0.00	30.29	4.40
572	573	8.725148	GCAGATATCAATTTATCCTTACCACAG	58.275	37.037	5.32	0.00	30.29	3.66

Showing 1 to 25 of 603 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.