AutoCloner

Multiple sequence alignment - TraesCS4A01G051100

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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	TraesCS4A01G051100	chr4A	100.000	8724	0	0	1	8724	41967227	41975950	0.000000e+00	16111.0
1	TraesCS4A01G051100	chr4A	95.745	235	10	0	8013	8247	425964986	425964752	6.390000e-101	379.0
2	TraesCS4A01G051100	chr4A	81.982	111	15	3	475	580	24033344	24033234	1.210000e-13	89.8
3	TraesCS4A01G051100	chr4D	97.092	3507	95	5	3024	6530	422084740	422081241	0.000000e+00	5904.0
4	TraesCS4A01G051100	chr4D	94.503	1146	30	14	711	1855	422085846	422084733	0.000000e+00	1736.0
5	TraesCS4A01G051100	chr4D	93.273	773	34	7	7184	7954	422080644	422079888	0.000000e+00	1123.0
6	TraesCS4A01G051100	chr4D	95.414	567	21	1	6623	7189	422081236	422080675	0.000000e+00	898.0
7	TraesCS4A01G051100	chr4D	83.534	249	22	3	1308	1552	418520790	418520557	1.910000e-51	215.0
8	TraesCS4A01G051100	chr4B	97.066	3510	94	7	3024	6530	519050899	519047396	0.000000e+00	5903.0
9	TraesCS4A01G051100	chr4B	91.881	1281	58	19	6614	7870	519047397	519046139	0.000000e+00	1748.0
10	TraesCS4A01G051100	chr4B	92.492	999	26	16	869	1855	519051853	519050892	0.000000e+00	1384.0
11	TraesCS4A01G051100	chr4B	84.739	249	36	2	8276	8523	568607657	568607410	1.880000e-61	248.0
12	TraesCS4A01G051100	chr4B	96.842	95	3	0	7860	7954	519044896	519044802	9.070000e-35	159.0
13	TraesCS4A01G051100	chr3D	93.858	3517	195	12	3024	6530	89903063	89899558	0.000000e+00	5278.0
14	TraesCS4A01G051100	chr3D	81.075	2679	449	37	3041	5670	468759456	468762125	0.000000e+00	2085.0
15	TraesCS4A01G051100	chr3D	88.526	1194	115	15	6614	7796	89899559	89898377	0.000000e+00	1426.0
16	TraesCS4A01G051100	chr3D	88.837	851	50	12	1035	1855	89903891	89903056	0.000000e+00	1003.0
17	TraesCS4A01G051100	chr3D	79.899	796	96	49	1068	1849	468758692	468759437	7.760000e-145	525.0
18	TraesCS4A01G051100	chr3D	88.073	327	21	5	2140	2448	427055171	427055497	1.070000e-98	372.0
19	TraesCS4A01G051100	chr3D	86.709	316	40	2	5735	6049	468762701	468763015	5.010000e-92	350.0
20	TraesCS4A01G051100	chr3D	85.141	249	33	4	8278	8526	400274799	400274555	1.450000e-62	252.0
21	TraesCS4A01G051100	chr3D	95.918	147	6	0	8276	8422	496739960	496740106	1.130000e-58	239.0
22	TraesCS4A01G051100	chr3D	83.333	222	37	0	6136	6357	468763191	468763412	1.150000e-48	206.0
23	TraesCS4A01G051100	chr3D	85.263	95	4	4	6528	6618	459078916	459078828	1.210000e-13	89.8
24	TraesCS4A01G051100	chr3D	85.417	96	3	4	6529	6619	546330041	546329952	1.210000e-13	89.8
25	TraesCS4A01G051100	chr3D	100.000	29	0	0	475	503	551515579	551515607	4.000000e-03	54.7
26	TraesCS4A01G051100	chr3A	93.780	3521	191	13	3024	6530	106439909	106436403	0.000000e+00	5264.0
27	TraesCS4A01G051100	chr3A	79.688	2693	437	63	3041	5670	610541869	610544514	0.000000e+00	1842.0
28	TraesCS4A01G051100	chr3A	86.971	875	63	14	1008	1855	106440752	106439902	0.000000e+00	937.0
29	TraesCS4A01G051100	chr3A	92.361	576	43	1	6614	7189	106436404	106435830	0.000000e+00	819.0
30	TraesCS4A01G051100	chr3A	88.493	617	55	8	7187	7796	106435796	106435189	0.000000e+00	732.0
31	TraesCS4A01G051100	chr3A	83.427	531	63	18	1324	1849	610541340	610541850	3.690000e-128	470.0
32	TraesCS4A01G051100	chr3A	85.449	323	45	2	5728	6049	610545395	610545716	1.400000e-87	335.0
33	TraesCS4A01G051100	chr3A	79.633	491	80	15	6648	7135	610546224	610546697	1.400000e-87	335.0
34	TraesCS4A01G051100	chr3A	88.043	184	19	2	71	253	535716376	535716557	1.910000e-51	215.0
35	TraesCS4A01G051100	chr3B	93.821	3512	190	15	3026	6524	139414490	139410993	0.000000e+00	5258.0
36	TraesCS4A01G051100	chr3B	80.903	2681	448	38	3041	5670	622395526	622398193	0.000000e+00	2056.0
37	TraesCS4A01G051100	chr3B	86.480	858	57	18	1038	1855	139415323	139414485	0.000000e+00	887.0
38	TraesCS4A01G051100	chr3B	97.189	498	13	1	2526	3023	59891794	59892290	0.000000e+00	841.0
39	TraesCS4A01G051100	chr3B	92.721	577	41	1	6614	7190	139410960	139410385	0.000000e+00	832.0
40	TraesCS4A01G051100	chr3B	97.545	448	11	0	2083	2530	644316279	644315832	0.000000e+00	767.0
41	TraesCS4A01G051100	chr3B	89.251	614	52	9	7187	7796	139410260	139409657	0.000000e+00	756.0
42	TraesCS4A01G051100	chr3B	82.519	532	65	21	1323	1849	622394999	622395507	8.040000e-120	442.0
43	TraesCS4A01G051100	chr3B	84.615	312	47	1	5738	6049	622398569	622398879	8.510000e-80	309.0
44	TraesCS4A01G051100	chr3B	86.667	225	28	2	8302	8525	807599252	807599029	1.880000e-61	248.0
45	TraesCS4A01G051100	chr3B	86.139	101	11	3	2082	2180	782684340	782684241	1.200000e-18	106.0
46	TraesCS4A01G051100	chr3B	86.139	101	11	3	2082	2180	782685972	782685873	1.200000e-18	106.0
47	TraesCS4A01G051100	chr3B	83.838	99	11	3	2082	2180	52619087	52618994	1.210000e-13	89.8
48	TraesCS4A01G051100	chr3B	84.375	96	10	3	2082	2177	53038252	53038342	1.210000e-13	89.8
49	TraesCS4A01G051100	chr2B	97.595	1164	23	4	1864	3024	678386278	678387439	0.000000e+00	1989.0
50	TraesCS4A01G051100	chr2B	97.425	1165	25	3	1859	3023	113272444	113273603	0.000000e+00	1980.0
51	TraesCS4A01G051100	chr2B	97.395	499	12	1	2526	3024	374245067	374245564	0.000000e+00	848.0
52	TraesCS4A01G051100	chr2B	97.071	239	6	1	1862	2100	374244567	374244804	1.360000e-107	401.0
53	TraesCS4A01G051100	chr2B	95.763	236	10	0	2790	3025	374244801	374244566	1.780000e-101	381.0
54	TraesCS4A01G051100	chr2B	86.139	101	11	3	2082	2180	699215707	699215608	1.200000e-18	106.0
55	TraesCS4A01G051100	chr2B	83.696	92	13	2	6272	6362	706797663	706797573	1.560000e-12	86.1
56	TraesCS4A01G051100	chr6D	84.901	1510	182	23	3964	5467	138806259	138804790	0.000000e+00	1483.0
57	TraesCS4A01G051100	chr6D	96.653	239	7	1	1862	2099	17447039	17447277	6.350000e-106	396.0
58	TraesCS4A01G051100	chr6D	95.319	235	10	1	2790	3024	17448006	17448239	1.070000e-98	372.0
59	TraesCS4A01G051100	chr6D	84.000	250	31	6	8278	8526	149647163	149646922	1.890000e-56	231.0
60	TraesCS4A01G051100	chr6D	82.143	112	16	4	6272	6380	283465137	283465027	9.330000e-15	93.5
61	TraesCS4A01G051100	chr6B	86.411	964	108	15	4575	5532	714810221	714811167	0.000000e+00	1033.0
62	TraesCS4A01G051100	chr6B	93.162	234	16	0	8013	8246	113783409	113783176	2.330000e-90	344.0
63	TraesCS4A01G051100	chr6B	94.340	212	11	1	2529	2740	694680875	694680665	3.040000e-84	324.0
64	TraesCS4A01G051100	chr6B	93.333	90	5	1	8418	8507	580305336	580305424	1.980000e-26	132.0
65	TraesCS4A01G051100	chr6B	96.154	52	2	0	2736	2787	694680642	694680591	1.560000e-12	86.1
66	TraesCS4A01G051100	chr5A	88.250	400	47	0	3964	4363	144940025	144939626	6.130000e-131	479.0
67	TraesCS4A01G051100	chr5A	93.162	234	16	0	8013	8246	386169755	386169522	2.330000e-90	344.0
68	TraesCS4A01G051100	chr5A	92.766	235	17	0	8013	8247	548500883	548500649	3.020000e-89	340.0
69	TraesCS4A01G051100	chr5A	86.022	93	3	3	6528	6616	330196306	330196392	3.350000e-14	91.6
70	TraesCS4A01G051100	chr5A	84.694	98	5	4	6524	6617	419210214	419210123	1.210000e-13	89.8
71	TraesCS4A01G051100	chrUn	97.490	239	5	1	1862	2100	306830720	306830483	2.930000e-109	407.0
72	TraesCS4A01G051100	chrUn	96.170	235	9	0	2790	3024	306830486	306830720	1.370000e-102	385.0
73	TraesCS4A01G051100	chrUn	85.870	92	3	2	6529	6616	197752395	197752480	1.210000e-13	89.8
74	TraesCS4A01G051100	chrUn	84.946	93	4	2	6528	6616	378270567	378270653	1.560000e-12	86.1
75	TraesCS4A01G051100	chrUn	84.946	93	4	2	6528	6616	447954347	447954261	1.560000e-12	86.1
76	TraesCS4A01G051100	chrUn	83.673	98	5	4	6529	6622	336469297	336469387	2.020000e-11	82.4
77	TraesCS4A01G051100	chrUn	100.000	29	0	0	6588	6616	94223229	94223201	4.000000e-03	54.7
78	TraesCS4A01G051100	chrUn	100.000	28	0	0	6589	6616	49143782	49143755	1.600000e-02	52.8
79	TraesCS4A01G051100	chrUn	96.875	32	0	1	6588	6619	87200169	87200139	1.600000e-02	52.8
80	TraesCS4A01G051100	chr7D	96.680	241	6	2	1859	2099	65757822	65757584	4.910000e-107	399.0
81	TraesCS4A01G051100	chr7D	94.811	212	10	1	2529	2740	543731313	543731103	6.530000e-86	329.0
82	TraesCS4A01G051100	chr7D	85.841	226	29	1	2165	2390	130766543	130766321	4.070000e-58	237.0
83	TraesCS4A01G051100	chr7D	84.848	99	3	5	6521	6615	362365296	362365386	1.210000e-13	89.8
84	TraesCS4A01G051100	chr7D	93.182	44	3	0	2405	2448	130766324	130766281	2.030000e-06	65.8
85	TraesCS4A01G051100	chr2D	96.218	238	7	2	1863	2099	596991620	596991384	1.060000e-103	388.0
86	TraesCS4A01G051100	chr2D	84.694	98	6	4	6524	6619	579191495	579191585	1.210000e-13	89.8
87	TraesCS4A01G051100	chr2A	96.218	238	8	1	1863	2100	378847178	378847414	1.060000e-103	388.0
88	TraesCS4A01G051100	chr2A	95.455	242	9	2	1859	2099	378848274	378848034	1.370000e-102	385.0
89	TraesCS4A01G051100	chr2A	95.726	234	10	0	2790	3023	378847411	378847178	2.300000e-100	377.0
90	TraesCS4A01G051100	chr2A	95.339	236	11	0	2790	3025	378848036	378848271	8.270000e-100	375.0
91	TraesCS4A01G051100	chr2A	95.299	234	10	1	8013	8246	55163607	55163839	3.850000e-98	370.0
92	TraesCS4A01G051100	chr2A	92.771	249	15	2	8013	8259	604005508	604005755	3.000000e-94	357.0
93	TraesCS4A01G051100	chr2A	93.191	235	16	0	8013	8247	658771755	658771989	6.480000e-91	346.0
94	TraesCS4A01G051100	chr2A	92.405	237	16	2	8013	8247	715403663	715403899	3.900000e-88	337.0
95	TraesCS4A01G051100	chr2A	85.641	195	28	0	2537	2731	701848439	701848633	1.150000e-48	206.0
96	TraesCS4A01G051100	chr6A	94.191	241	12	2	8013	8251	128448885	128448645	4.980000e-97	366.0
97	TraesCS4A01G051100	chr6A	88.538	253	24	4	8276	8527	134548793	134548545	1.420000e-77	302.0
98	TraesCS4A01G051100	chr7A	97.642	212	4	1	2529	2740	625642080	625641870	6.440000e-96	363.0
99	TraesCS4A01G051100	chr7A	96.226	212	7	1	2529	2740	625674853	625674643	6.480000e-91	346.0
100	TraesCS4A01G051100	chr7A	88.400	250	26	3	8278	8525	513541065	513541313	1.840000e-76	298.0
101	TraesCS4A01G051100	chr7A	86.752	234	29	2	8292	8525	123271006	123271237	8.690000e-65	259.0
102	TraesCS4A01G051100	chr7A	86.408	103	6	4	6518	6615	590778472	590778373	1.200000e-18	106.0
103	TraesCS4A01G051100	chr7A	93.651	63	3	1	2725	2787	625641857	625641796	9.330000e-15	93.5
104	TraesCS4A01G051100	chr7A	93.651	63	3	1	2725	2787	625674630	625674569	9.330000e-15	93.5
105	TraesCS4A01G051100	chr7A	83.908	87	9	3	2110	2196	16738839	16738920	2.610000e-10	78.7
106	TraesCS4A01G051100	chr1D	95.283	212	9	1	2529	2740	110905070	110904860	1.400000e-87	335.0
107	TraesCS4A01G051100	chr1D	87.665	227	22	3	1423	1649	3173714	3173934	8.690000e-65	259.0
108	TraesCS4A01G051100	chr1D	83.240	179	26	2	72	249	198752351	198752526	2.520000e-35	161.0
109	TraesCS4A01G051100	chr1D	84.694	98	6	4	6526	6616	354500690	354500785	1.210000e-13	89.8
110	TraesCS4A01G051100	chr1D	95.122	41	2	0	7254	7294	490119714	490119754	2.030000e-06	65.8
111	TraesCS4A01G051100	chr1D	100.000	30	0	0	474	503	12066470	12066499	1.000000e-03	56.5
112	TraesCS4A01G051100	chr7B	82.869	251	40	3	8276	8525	84394336	84394088	1.140000e-53	222.0
113	TraesCS4A01G051100	chr7B	83.193	119	17	2	71	188	709190606	709190722	1.200000e-18	106.0
114	TraesCS4A01G051100	chr7B	85.149	101	12	3	2082	2180	510722662	510722563	5.570000e-17	100.0
115	TraesCS4A01G051100	chr7B	84.946	93	8	4	6528	6617	632792240	632792151	1.210000e-13	89.8
116	TraesCS4A01G051100	chr7B	83.696	92	13	2	6272	6362	322659926	322660016	1.560000e-12	86.1
117	TraesCS4A01G051100	chr7B	93.750	48	2	1	2725	2772	587090176	587090130	4.370000e-08	71.3
118	TraesCS4A01G051100	chr7B	100.000	33	0	0	7976	8008	651494384	651494416	2.630000e-05	62.1
119	TraesCS4A01G051100	chr1A	76.101	318	72	4	6648	6963	500828866	500828551	7.010000e-36	163.0
120	TraesCS4A01G051100	chr5D	85.714	84	8	3	2114	2197	61650466	61650545	1.560000e-12	86.1

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	TraesCS4A01G051100	chr4A	41967227	41975950	8723	False	16111.000000	16111	100.00000	1	8724	1	chr4A.!!$F1	8723
1	TraesCS4A01G051100	chr4D	422079888	422085846	5958	True	2415.250000	5904	95.07050	711	7954	4	chr4D.!!$R2	7243
2	TraesCS4A01G051100	chr4B	519044802	519051853	7051	True	2298.500000	5903	94.57025	869	7954	4	chr4B.!!$R2	7085
3	TraesCS4A01G051100	chr3D	89898377	89903891	5514	True	2569.000000	5278	90.40700	1035	7796	3	chr3D.!!$R4	6761
4	TraesCS4A01G051100	chr3D	468758692	468763412	4720	False	791.500000	2085	82.75400	1068	6357	4	chr3D.!!$F4	5289
5	TraesCS4A01G051100	chr3A	106435189	106440752	5563	True	1938.000000	5264	90.40125	1008	7796	4	chr3A.!!$R1	6788
6	TraesCS4A01G051100	chr3A	610541340	610546697	5357	False	745.500000	1842	82.04925	1324	7135	4	chr3A.!!$F2	5811
7	TraesCS4A01G051100	chr3B	139409657	139415323	5666	True	1933.250000	5258	90.56825	1038	7796	4	chr3B.!!$R4	6758
8	TraesCS4A01G051100	chr3B	622394999	622398879	3880	False	935.666667	2056	82.67900	1323	6049	3	chr3B.!!$F3	4726
9	TraesCS4A01G051100	chr2B	678386278	678387439	1161	False	1989.000000	1989	97.59500	1864	3024	1	chr2B.!!$F2	1160
10	TraesCS4A01G051100	chr2B	113272444	113273603	1159	False	1980.000000	1980	97.42500	1859	3023	1	chr2B.!!$F1	1164
11	TraesCS4A01G051100	chr2B	374244567	374245564	997	False	624.500000	848	97.23300	1862	3024	2	chr2B.!!$F3	1162
12	TraesCS4A01G051100	chr6D	138804790	138806259	1469	True	1483.000000	1483	84.90100	3964	5467	1	chr6D.!!$R1	1503
13	TraesCS4A01G051100	chr6D	17447039	17448239	1200	False	384.000000	396	95.98600	1862	3024	2	chr6D.!!$F1	1162
14	TraesCS4A01G051100	chr6B	714810221	714811167	946	False	1033.000000	1033	86.41100	4575	5532	1	chr6B.!!$F2	957
15	TraesCS4A01G051100	chr2A	378847178	378848271	1093	False	381.500000	388	95.77850	1863	3025	2	chr2A.!!$F6	1162
16	TraesCS4A01G051100	chr2A	378847178	378848274	1096	True	381.000000	385	95.59050	1859	3023	2	chr2A.!!$R1	1164

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
37	38	0.031178	GCGGAATTCACCATGCCATC	59.969	55.000	7.93	27.02	3.51	F
302	303	0.036671	GCGTAGTTGCTAGGGTGGTT	60.037	55.000	0.00	0.00	3.67	F
305	306	0.036765	TAGTTGCTAGGGTGGTTGCG	60.037	55.000	0.00	0.00	4.85	F
703	704	0.039074	ACAGCTCAGTTTCCGTCGAG	60.039	55.000	0.00	0.00	4.04	F
805	806	0.170561	CTCAACCAGGTCGTCCGTAG	59.829	60.000	0.00	39.05	3.51	F
811	812	0.802222	CAGGTCGTCCGTAGCATGTG	60.802	60.000	0.00	39.05	3.21	F
1452	1493	1.762708	CGCTCTTCCTTCTCCTCTCT	58.237	55.000	0.00	0.00	3.10	F
2874	3999	1.386533	GGTCGGGTAGTCAGATTCGA	58.613	55.000	0.00	0.00	3.71	F
3626	4757	0.620556	AAGGATGTGCGGATGAAGGT	59.379	50.000	0.00	0.00	3.50	F
4206	5350	0.257039	AGGTGCCAAAGCTATCAGGG	59.743	55.000	0.00	40.80	4.45	F
5236	6455	1.802960	ACGTCGACACTGATCTACGTT	59.197	47.619	17.16	45.46	3.99	F
6663	8868	0.253044	TTCTGCAGGTGAGGTATGCC	59.747	55.000	15.13	39.22	4.40	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1273	1281	1.016130	TCGAGGTACCACGAGACGAC	61.016	60.000	27.50	1.16	33.48	4.34	R
2003	2062	2.093783	GCAGTCAGATTCGGGTTTAACG	59.906	50.000	0.00	0.00	0.00	3.18	R
2331	2624	0.756442	CCAGCAGAGAGGAGGAGGAG	60.756	65.000	0.00	0.00	0.00	3.69	R
2332	2625	1.309347	CCAGCAGAGAGGAGGAGGA	59.691	63.158	0.00	0.00	0.00	3.71	R
2395	2691	2.938539	CTAGCTTAGCTTCGCGCCGT	62.939	60.000	13.44	0.00	40.44	5.68	R
2874	3999	2.616842	CACGCTTTGACTGGGTTAAACT	59.383	45.455	0.00	0.00	0.00	2.66	R
2989	4114	1.161843	AAACTACCACAATTCGCGGG	58.838	50.000	6.13	0.00	0.00	6.13	R
4206	5350	1.376037	CCCGCAAGTCTTGACCTCC	60.376	63.158	16.99	0.00	0.00	4.30	R
5236	6455	1.950828	CAACAGCCAATGCCACAAAA	58.049	45.000	0.00	0.00	38.69	2.44	R
5762	7837	1.303074	CCTTTGCAGCTCTCTGGCA	60.303	57.895	0.00	0.00	40.65	4.92	R
7090	9299	0.174617	GCTCCTTCTTCCTGACCTCG	59.825	60.000	0.00	0.00	0.00	4.63	R
8558	12163	0.039798	CGACGGAGGTTGAAGACGAA	60.040	55.000	0.00	0.00	0.00	3.85	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
18	19	2.012237	CAGAGCACAATGGCTAGCG	58.988	57.895	9.00	0.00	45.99	4.26
19	20	1.817099	AGAGCACAATGGCTAGCGC	60.817	57.895	9.00	0.00	45.99	5.92
20	21	3.160557	GAGCACAATGGCTAGCGCG	62.161	63.158	9.00	0.00	45.99	6.86
21	22	4.241999	GCACAATGGCTAGCGCGG	62.242	66.667	8.83	0.00	36.88	6.46
22	23	2.511373	CACAATGGCTAGCGCGGA	60.511	61.111	8.83	0.00	36.88	5.54
23	24	2.106074	CACAATGGCTAGCGCGGAA	61.106	57.895	8.83	0.00	36.88	4.30
24	25	1.153168	ACAATGGCTAGCGCGGAAT	60.153	52.632	8.83	0.00	36.88	3.01
25	26	0.748005	ACAATGGCTAGCGCGGAATT	60.748	50.000	8.83	0.85	36.88	2.17
26	27	0.040958	CAATGGCTAGCGCGGAATTC	60.041	55.000	8.83	0.00	36.88	2.17
27	28	0.463654	AATGGCTAGCGCGGAATTCA	60.464	50.000	8.83	0.00	36.88	2.57
28	29	1.160329	ATGGCTAGCGCGGAATTCAC	61.160	55.000	8.83	0.00	36.88	3.18
29	30	2.534903	GGCTAGCGCGGAATTCACC	61.535	63.158	8.83	0.00	36.88	4.02
30	31	1.813753	GCTAGCGCGGAATTCACCA	60.814	57.895	8.83	0.00	0.00	4.17
31	32	1.160329	GCTAGCGCGGAATTCACCAT	61.160	55.000	8.83	0.00	0.00	3.55
32	33	0.583438	CTAGCGCGGAATTCACCATG	59.417	55.000	8.83	0.00	0.00	3.66
33	34	1.436195	TAGCGCGGAATTCACCATGC	61.436	55.000	8.83	3.74	0.00	4.06
34	35	2.408835	CGCGGAATTCACCATGCC	59.591	61.111	7.93	0.00	0.00	4.40
35	36	2.405805	CGCGGAATTCACCATGCCA	61.406	57.895	7.93	0.00	27.02	4.92
36	37	1.727511	CGCGGAATTCACCATGCCAT	61.728	55.000	7.93	0.00	27.02	4.40
37	38	0.031178	GCGGAATTCACCATGCCATC	59.969	55.000	7.93	0.00	27.02	3.51
38	39	1.683943	CGGAATTCACCATGCCATCT	58.316	50.000	7.93	0.00	27.02	2.90
39	40	1.605710	CGGAATTCACCATGCCATCTC	59.394	52.381	7.93	0.00	27.02	2.75
40	41	1.605710	GGAATTCACCATGCCATCTCG	59.394	52.381	7.93	0.00	28.86	4.04
41	42	2.564771	GAATTCACCATGCCATCTCGA	58.435	47.619	0.00	0.00	0.00	4.04
42	43	2.945080	ATTCACCATGCCATCTCGAT	57.055	45.000	0.00	0.00	0.00	3.59

Showing 1 to 25 of 838 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	2.012237	CGCTAGCCATTGTGCTCTG	58.988	57.895	9.66	1.20	41.68	3.35
1	2	1.817099	GCGCTAGCCATTGTGCTCT	60.817	57.895	9.66	0.00	41.68	4.09
3	4	3.197790	CGCGCTAGCCATTGTGCT	61.198	61.111	9.66	5.23	45.38	4.40
4	5	4.241999	CCGCGCTAGCCATTGTGC	62.242	66.667	9.66	4.45	41.18	4.57
5	6	1.439353	ATTCCGCGCTAGCCATTGTG	61.439	55.000	9.66	1.28	41.18	3.33
6	7	0.748005	AATTCCGCGCTAGCCATTGT	60.748	50.000	9.66	0.00	41.18	2.71
7	8	0.040958	GAATTCCGCGCTAGCCATTG	60.041	55.000	9.66	0.00	41.18	2.82
8	9	0.463654	TGAATTCCGCGCTAGCCATT	60.464	50.000	9.66	0.00	41.18	3.16
9	10	1.146041	TGAATTCCGCGCTAGCCAT	59.854	52.632	9.66	0.00	41.18	4.40
10	11	1.813753	GTGAATTCCGCGCTAGCCA	60.814	57.895	9.66	0.00	41.18	4.75
11	12	2.534903	GGTGAATTCCGCGCTAGCC	61.535	63.158	9.66	0.79	41.18	3.93
12	13	1.160329	ATGGTGAATTCCGCGCTAGC	61.160	55.000	5.56	4.06	40.74	3.42
13	14	0.583438	CATGGTGAATTCCGCGCTAG	59.417	55.000	5.56	0.00	0.00	3.42
14	15	1.436195	GCATGGTGAATTCCGCGCTA	61.436	55.000	5.56	0.00	0.00	4.26
15	16	2.764314	GCATGGTGAATTCCGCGCT	61.764	57.895	5.56	0.00	0.00	5.92
16	17	2.278142	GCATGGTGAATTCCGCGC	60.278	61.111	0.00	0.00	0.00	6.86
17	18	1.727511	ATGGCATGGTGAATTCCGCG	61.728	55.000	0.00	0.00	0.00	6.46
18	19	0.031178	GATGGCATGGTGAATTCCGC	59.969	55.000	3.81	0.00	0.00	5.54
19	20	1.605710	GAGATGGCATGGTGAATTCCG	59.394	52.381	3.81	0.00	0.00	4.30
20	21	1.605710	CGAGATGGCATGGTGAATTCC	59.394	52.381	3.81	0.00	0.00	3.01
21	22	2.564771	TCGAGATGGCATGGTGAATTC	58.435	47.619	3.81	0.00	0.00	2.17
22	23	2.715749	TCGAGATGGCATGGTGAATT	57.284	45.000	3.81	0.00	0.00	2.17
23	24	2.105306	TCATCGAGATGGCATGGTGAAT	59.895	45.455	3.81	0.00	39.24	2.57
24	25	1.485895	TCATCGAGATGGCATGGTGAA	59.514	47.619	3.81	0.00	39.24	3.18
25	26	1.122227	TCATCGAGATGGCATGGTGA	58.878	50.000	3.81	0.00	39.24	4.02

Showing 1 to 25 of 841 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.