AutoCloner

Multiple sequence alignment - TraesCS1A01G159500

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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	TraesCS1A01G159500	chr1A	100.000	7832	0	0	1	7832	285979870	285987701	0.000000e+00	14464.0
1	TraesCS1A01G159500	chr1A	88.616	571	59	5	1	566	572682197	572681628	0.000000e+00	689.0
2	TraesCS1A01G159500	chr1A	88.556	568	61	3	1	564	447640041	447639474	0.000000e+00	686.0
3	TraesCS1A01G159500	chr1A	88.829	555	58	4	1	551	347675447	347674893	0.000000e+00	678.0
4	TraesCS1A01G159500	chr1A	97.368	38	1	0	6522	6559	285986362	285986399	1.820000e-06	65.8
5	TraesCS1A01G159500	chr1A	97.368	38	1	0	6493	6530	285986391	285986428	1.820000e-06	65.8
6	TraesCS1A01G159500	chr1D	97.108	5533	122	17	2325	7832	221096433	221101952	0.000000e+00	9297.0
7	TraesCS1A01G159500	chr1D	94.730	1537	45	9	579	2084	221094449	221095980	0.000000e+00	2357.0
8	TraesCS1A01G159500	chr1D	93.925	214	11	2	2084	2296	221096228	221096440	9.800000e-84	322.0
9	TraesCS1A01G159500	chr1D	94.737	38	2	0	6522	6559	221100612	221100649	8.490000e-05	60.2
10	TraesCS1A01G159500	chr1B	96.145	4799	117	23	3044	7832	317419930	317424670	0.000000e+00	7775.0
11	TraesCS1A01G159500	chr1B	94.233	1023	27	11	566	1564	317417116	317418130	0.000000e+00	1533.0
12	TraesCS1A01G159500	chr1B	97.215	754	16	4	2334	3082	317419182	317419935	0.000000e+00	1271.0
13	TraesCS1A01G159500	chr1B	93.929	280	10	3	1675	1950	317418129	317418405	4.370000e-112	416.0
14	TraesCS1A01G159500	chr1B	96.226	212	7	1	2084	2295	317418968	317419178	5.820000e-91	346.0
15	TraesCS1A01G159500	chr1B	92.414	145	8	2	1942	2084	317418578	317418721	3.710000e-48	204.0
16	TraesCS1A01G159500	chr1B	84.783	92	9	4	1998	2084	317418875	317418784	3.890000e-13	87.9
17	TraesCS1A01G159500	chr1B	94.737	38	2	0	6522	6559	317423367	317423404	8.490000e-05	60.2
18	TraesCS1A01G159500	chr3D	87.143	840	97	9	940	1774	8509163	8508330	0.000000e+00	942.0
19	TraesCS1A01G159500	chr3D	84.364	825	97	22	4754	5571	8520586	8519787	0.000000e+00	780.0
20	TraesCS1A01G159500	chr3D	83.918	827	103	19	4724	5545	8501971	8501170	0.000000e+00	763.0
21	TraesCS1A01G159500	chr3D	81.408	909	135	27	3787	4684	8503145	8502260	0.000000e+00	712.0
22	TraesCS1A01G159500	chr3D	81.851	843	127	17	933	1771	8534263	8533443	0.000000e+00	686.0
23	TraesCS1A01G159500	chr3D	86.610	590	61	14	4093	4677	8521500	8520924	3.080000e-178	636.0
24	TraesCS1A01G159500	chr3D	81.275	737	107	19	5628	6344	8499951	8499226	1.140000e-157	568.0
25	TraesCS1A01G159500	chr3D	86.364	176	24	0	2449	2624	8522978	8522803	8.020000e-45	193.0
26	TraesCS1A01G159500	chr3A	86.768	854	102	10	916	1765	12376054	12376900	0.000000e+00	941.0
27	TraesCS1A01G159500	chr3A	85.119	840	92	25	4724	5555	12380480	12381294	0.000000e+00	828.0
28	TraesCS1A01G159500	chr3A	81.737	783	102	23	3910	4681	12379424	12380176	4.020000e-172	616.0
29	TraesCS1A01G159500	chr3B	86.396	838	102	10	940	1774	10309026	10308198	0.000000e+00	905.0
30	TraesCS1A01G159500	chr3B	83.995	831	91	26	4751	5564	10327968	10327163	0.000000e+00	760.0
31	TraesCS1A01G159500	chr3B	82.706	850	126	16	933	1771	10344486	10343647	0.000000e+00	736.0
32	TraesCS1A01G159500	chr3B	86.615	650	72	10	4733	5380	10304477	10303841	0.000000e+00	704.0
33	TraesCS1A01G159500	chr3B	81.010	911	134	31	3787	4681	10305847	10304960	0.000000e+00	688.0
34	TraesCS1A01G159500	chr3B	80.735	898	133	30	3794	4677	10329194	10328323	0.000000e+00	664.0
35	TraesCS1A01G159500	chr3B	85.088	456	65	2	5712	6164	10302000	10301545	5.540000e-126	462.0
36	TraesCS1A01G159500	chr5D	89.104	569	55	6	1	564	505372127	505371561	0.000000e+00	701.0
37	TraesCS1A01G159500	chr5D	88.693	566	59	4	1	562	318867379	318867943	0.000000e+00	686.0
38	TraesCS1A01G159500	chr5D	85.938	64	7	1	1994	2055	106808503	106808566	5.070000e-07	67.6
39	TraesCS1A01G159500	chr7B	88.616	571	55	8	4	567	104298893	104298326	0.000000e+00	686.0
40	TraesCS1A01G159500	chr4D	88.328	574	62	5	1	569	417415523	417414950	0.000000e+00	684.0
41	TraesCS1A01G159500	chr2B	88.194	576	59	8	3	572	570063498	570064070	0.000000e+00	678.0
42	TraesCS1A01G159500	chr2A	88.112	572	56	10	1	565	66767760	66767194	0.000000e+00	669.0
43	TraesCS1A01G159500	chr7D	90.604	298	26	2	5182	5479	611273384	611273089	2.050000e-105	394.0

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	TraesCS1A01G159500	chr1A	285979870	285987701	7831	False	4865.200000	14464	98.245333	1	7832	3	chr1A.!!$F1	7831
1	TraesCS1A01G159500	chr1A	572681628	572682197	569	True	689.000000	689	88.616000	1	566	1	chr1A.!!$R3	565
2	TraesCS1A01G159500	chr1A	447639474	447640041	567	True	686.000000	686	88.556000	1	564	1	chr1A.!!$R2	563
3	TraesCS1A01G159500	chr1A	347674893	347675447	554	True	678.000000	678	88.829000	1	551	1	chr1A.!!$R1	550
4	TraesCS1A01G159500	chr1D	221094449	221101952	7503	False	3009.050000	9297	95.125000	579	7832	4	chr1D.!!$F1	7253
5	TraesCS1A01G159500	chr1B	317417116	317424670	7554	False	1657.885714	7775	94.985571	566	7832	7	chr1B.!!$F1	7266
6	TraesCS1A01G159500	chr3D	8508330	8509163	833	True	942.000000	942	87.143000	940	1774	1	chr3D.!!$R1	834
7	TraesCS1A01G159500	chr3D	8533443	8534263	820	True	686.000000	686	81.851000	933	1771	1	chr3D.!!$R2	838
8	TraesCS1A01G159500	chr3D	8499226	8503145	3919	True	681.000000	763	82.200333	3787	6344	3	chr3D.!!$R3	2557
9	TraesCS1A01G159500	chr3D	8519787	8522978	3191	True	536.333333	780	85.779333	2449	5571	3	chr3D.!!$R4	3122
10	TraesCS1A01G159500	chr3A	12376054	12381294	5240	False	795.000000	941	84.541333	916	5555	3	chr3A.!!$F1	4639
11	TraesCS1A01G159500	chr3B	10343647	10344486	839	True	736.000000	736	82.706000	933	1771	1	chr3B.!!$R1	838
12	TraesCS1A01G159500	chr3B	10327163	10329194	2031	True	712.000000	760	82.365000	3794	5564	2	chr3B.!!$R3	1770
13	TraesCS1A01G159500	chr3B	10301545	10309026	7481	True	689.750000	905	84.777250	940	6164	4	chr3B.!!$R2	5224
14	TraesCS1A01G159500	chr5D	505371561	505372127	566	True	701.000000	701	89.104000	1	564	1	chr5D.!!$R1	563
15	TraesCS1A01G159500	chr5D	318867379	318867943	564	False	686.000000	686	88.693000	1	562	1	chr5D.!!$F2	561
16	TraesCS1A01G159500	chr7B	104298326	104298893	567	True	686.000000	686	88.616000	4	567	1	chr7B.!!$R1	563
17	TraesCS1A01G159500	chr4D	417414950	417415523	573	True	684.000000	684	88.328000	1	569	1	chr4D.!!$R1	568
18	TraesCS1A01G159500	chr2B	570063498	570064070	572	False	678.000000	678	88.194000	3	572	1	chr2B.!!$F1	569
19	TraesCS1A01G159500	chr2A	66767194	66767760	566	True	669.000000	669	88.112000	1	565	1	chr2A.!!$R1	564

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
406	410	0.468226	AGTTTTGTCCGACTCCAGCA	59.532	50.000	0.00	0.00	0.00	4.41	F
674	681	0.598065	CCAAGCTAGTGCCCAACAAC	59.402	55.000	0.00	0.00	40.80	3.32	F
908	925	0.912487	ACTTCCCGACCTGGCCATTA	60.912	55.000	5.51	0.00	35.87	1.90	F
1735	1784	1.137086	CAGCTAATGCCACCGTAGACT	59.863	52.381	0.00	0.00	40.80	3.24	F
2363	3135	2.543641	GCATTTATTTGCTCCAGTGGC	58.456	47.619	3.51	0.00	39.57	5.01	F
4038	5225	2.223157	TGCCGTATTTTGCGCACTAATC	60.223	45.455	11.12	6.68	0.00	1.75	F
4772	6427	5.957842	ATCTTGCAAACCGAGTTGATTAA	57.042	34.783	0.00	0.00	0.00	1.40	F
6619	9961	0.107831	AGGCGGTGCTAACAAGTGAA	59.892	50.000	0.00	0.00	0.00	3.18	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1751	1800	2.095461	CGAGGATGAACTCACCAGAGA	58.905	52.381	0.00	0.0	44.98	3.10	R
2363	3135	3.701532	TTAAAGTTCAAGCCAACACGG	57.298	42.857	0.00	0.0	38.11	4.94	R
2826	3712	6.005066	TGATTGATGACCATTGGTGATAGT	57.995	37.500	14.44	0.0	35.25	2.12	R
2971	3990	5.238432	TGCGATTAATTACATACCTGCCTTG	59.762	40.000	0.00	0.0	0.00	3.61	R
4088	5275	3.609853	GGCATATGAGGAAACACAGACA	58.390	45.455	6.97	0.0	33.32	3.41	R
4849	6504	1.079503	GCTTCCAGCTAAGTGTTCCG	58.920	55.000	0.00	0.0	38.45	4.30	R
6686	10031	0.909623	TAAGGGCTTCCTGTAGGTGC	59.090	55.000	0.00	4.3	40.74	5.01	R
7660	11010	1.675641	GCACCCGTGGCATTTCTCT	60.676	57.895	0.00	0.0	0.00	3.10	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
93	94	8.149647	TCTCTTCGTGTTTTGTTAGGGTTTATA	58.850	33.333	0.00	0.00	0.00	0.98
121	122	4.415332	GAAGACGAGACGGCGGCA	62.415	66.667	18.30	0.00	43.13	5.69
144	145	3.505293	GCTCCCTGAAGATGGAATAATGC	59.495	47.826	0.00	0.00	0.00	3.56
190	192	2.099405	TGGTGTGTCTAGCATCATCGA	58.901	47.619	0.00	0.00	0.00	3.59
284	286	4.712122	ACGTTCATGTGTTTTCAGGTTT	57.288	36.364	0.00	0.00	0.00	3.27
315	317	3.429207	CGATCTACGCTACTCTTCATCGA	59.571	47.826	0.00	0.00	35.08	3.59
348	350	2.010145	TCTGTTGCGCTGGTTCTATC	57.990	50.000	9.73	0.00	0.00	2.08
356	358	0.815615	GCTGGTTCTATCGGGCCTTG	60.816	60.000	0.84	0.00	0.00	3.61
406	410	0.468226	AGTTTTGTCCGACTCCAGCA	59.532	50.000	0.00	0.00	0.00	4.41
538	544	8.291191	TGTACTGCCATGATTGAAATGAATAA	57.709	30.769	0.00	0.00	0.00	1.40
596	602	1.086696	CTACAATCGTTGCACCCCTG	58.913	55.000	0.00	0.00	0.00	4.45
597	603	0.958382	TACAATCGTTGCACCCCTGC	60.958	55.000	0.00	0.00	44.52	4.85
641	648	3.034721	AGTTCGCATAGACGGTCAAAA	57.965	42.857	11.27	0.00	0.00	2.44
674	681	0.598065	CCAAGCTAGTGCCCAACAAC	59.402	55.000	0.00	0.00	40.80	3.32
715	722	2.125065	AACACGTTCACGCCACCA	60.125	55.556	0.00	0.00	44.43	4.17
720	727	1.298041	CGTTCACGCCACCAAACAC	60.298	57.895	0.00	0.00	0.00	3.32
754	765	7.700656	CGTTTTCAGTTCTGATTAAACAAAGGT	59.299	33.333	20.30	0.00	0.00	3.50
865	882	7.845537	TCCCTCATCCCAATATTTATACCAT	57.154	36.000	0.00	0.00	0.00	3.55
908	925	0.912487	ACTTCCCGACCTGGCCATTA	60.912	55.000	5.51	0.00	35.87	1.90
1735	1784	1.137086	CAGCTAATGCCACCGTAGACT	59.863	52.381	0.00	0.00	40.80	3.24
1816	1865	7.828712	ACATACTACTAGCTTCGAGAAGTTTT	58.171	34.615	13.58	3.99	40.45	2.43
1817	1866	8.305317	ACATACTACTAGCTTCGAGAAGTTTTT	58.695	33.333	13.58	2.39	40.45	1.94
2260	3030	6.268617	TGGTACATTTGGAATCCAATGTTTGA	59.731	34.615	24.28	9.15	43.55	2.69
2300	3070	9.921637	TTTGAAGTTCTCTATTTTTGTTGTTGT	57.078	25.926	4.17	0.00	0.00	3.32
2301	3071	9.921637	TTGAAGTTCTCTATTTTTGTTGTTGTT	57.078	25.926	4.17	0.00	0.00	2.83
2302	3072	9.352784	TGAAGTTCTCTATTTTTGTTGTTGTTG	57.647	29.630	4.17	0.00	0.00	3.33
2303	3073	9.353999	GAAGTTCTCTATTTTTGTTGTTGTTGT	57.646	29.630	0.00	0.00	0.00	3.32
2304	3074	9.705290	AAGTTCTCTATTTTTGTTGTTGTTGTT	57.295	25.926	0.00	0.00	0.00	2.83
2305	3075	9.139174	AGTTCTCTATTTTTGTTGTTGTTGTTG	57.861	29.630	0.00	0.00	0.00	3.33
2306	3076	8.921670	GTTCTCTATTTTTGTTGTTGTTGTTGT	58.078	29.630	0.00	0.00	0.00	3.32
2307	3077	9.482627	TTCTCTATTTTTGTTGTTGTTGTTGTT	57.517	25.926	0.00	0.00	0.00	2.83
2308	3078	8.920665	TCTCTATTTTTGTTGTTGTTGTTGTTG	58.079	29.630	0.00	0.00	0.00	3.33
2309	3079	8.594881	TCTATTTTTGTTGTTGTTGTTGTTGT	57.405	26.923	0.00	0.00	0.00	3.32
2310	3080	9.046296	TCTATTTTTGTTGTTGTTGTTGTTGTT	57.954	25.926	0.00	0.00	0.00	2.83
2311	3081	7.905031	ATTTTTGTTGTTGTTGTTGTTGTTG	57.095	28.000	0.00	0.00	0.00	3.33
2312	3082	6.422776	TTTTGTTGTTGTTGTTGTTGTTGT	57.577	29.167	0.00	0.00	0.00	3.32
2313	3083	6.422776	TTTGTTGTTGTTGTTGTTGTTGTT	57.577	29.167	0.00	0.00	0.00	2.83
2314	3084	5.395325	TGTTGTTGTTGTTGTTGTTGTTG	57.605	34.783	0.00	0.00	0.00	3.33
2315	3085	4.870426	TGTTGTTGTTGTTGTTGTTGTTGT	59.130	33.333	0.00	0.00	0.00	3.32
2316	3086	5.351465	TGTTGTTGTTGTTGTTGTTGTTGTT	59.649	32.000	0.00	0.00	0.00	2.83
2317	3087	5.395325	TGTTGTTGTTGTTGTTGTTGTTG	57.605	34.783	0.00	0.00	0.00	3.33
2318	3088	4.870426	TGTTGTTGTTGTTGTTGTTGTTGT	59.130	33.333	0.00	0.00	0.00	3.32
2319	3089	5.351465	TGTTGTTGTTGTTGTTGTTGTTGTT	59.649	32.000	0.00	0.00	0.00	2.83
2320	3090	5.395325	TGTTGTTGTTGTTGTTGTTGTTG	57.605	34.783	0.00	0.00	0.00	3.33
2321	3091	4.870426	TGTTGTTGTTGTTGTTGTTGTTGT	59.130	33.333	0.00	0.00	0.00	3.32
2322	3092	5.351465	TGTTGTTGTTGTTGTTGTTGTTGTT	59.649	32.000	0.00	0.00	0.00	2.83
2323	3093	5.395325	TGTTGTTGTTGTTGTTGTTGTTG	57.605	34.783	0.00	0.00	0.00	3.33
2324	3094	4.870426	TGTTGTTGTTGTTGTTGTTGTTGT	59.130	33.333	0.00	0.00	0.00	3.32
2325	3095	5.351465	TGTTGTTGTTGTTGTTGTTGTTGTT	59.649	32.000	0.00	0.00	0.00	2.83
2326	3096	5.395325	TGTTGTTGTTGTTGTTGTTGTTG	57.605	34.783	0.00	0.00	0.00	3.33
2327	3097	4.870426	TGTTGTTGTTGTTGTTGTTGTTGT	59.130	33.333	0.00	0.00	0.00	3.32
2328	3098	5.351465	TGTTGTTGTTGTTGTTGTTGTTGTT	59.649	32.000	0.00	0.00	0.00	2.83
2329	3099	5.395325	TGTTGTTGTTGTTGTTGTTGTTG	57.605	34.783	0.00	0.00	0.00	3.33
2330	3100	4.870426	TGTTGTTGTTGTTGTTGTTGTTGT	59.130	33.333	0.00	0.00	0.00	3.32
2331	3101	5.351465	TGTTGTTGTTGTTGTTGTTGTTGTT	59.649	32.000	0.00	0.00	0.00	2.83
2363	3135	2.543641	GCATTTATTTGCTCCAGTGGC	58.456	47.619	3.51	0.00	39.57	5.01
2394	3166	9.434420	TTGGCTTGAACTTTAATGATAATTTGG	57.566	29.630	0.00	0.00	0.00	3.28
2826	3712	3.940852	GGATGATGACATGCAGTGTGTAA	59.059	43.478	6.52	0.00	42.36	2.41
2899	3914	6.115446	AGATTTTCAGTGCTATCCGAATCAA	58.885	36.000	0.00	0.00	0.00	2.57
3487	4604	5.664294	AATGAGCACCTGCAAAATTCATA	57.336	34.783	0.00	0.00	45.16	2.15
3547	4664	9.950680	ATAGTGTTCAACTTATTGTTTGAACAG	57.049	29.630	23.38	0.00	45.49	3.16
3548	4665	7.826690	AGTGTTCAACTTATTGTTTGAACAGT	58.173	30.769	23.38	23.07	45.49	3.55
3574	4693	7.122055	TGTGACTACAACCATTTGTCTCTTTTT	59.878	33.333	0.00	0.00	42.67	1.94
4038	5225	2.223157	TGCCGTATTTTGCGCACTAATC	60.223	45.455	11.12	6.68	0.00	1.75
4772	6427	5.957842	ATCTTGCAAACCGAGTTGATTAA	57.042	34.783	0.00	0.00	0.00	1.40
4849	6504	2.426024	TGGTATAACAGGTGAGAGACGC	59.574	50.000	0.00	0.00	0.00	5.19
4860	6515	1.199327	TGAGAGACGCGGAACACTTAG	59.801	52.381	12.47	0.00	0.00	2.18
5491	7155	5.814188	TCACTCTATGCACTGCTGATTTAAG	59.186	40.000	1.98	0.00	0.00	1.85
5804	9129	4.625742	CGTTGGATCGTGAAGAATACAAGT	59.374	41.667	0.00	0.00	0.00	3.16
6272	9612	3.181496	CGACGATCTGAGACCATTCTTCA	60.181	47.826	0.00	0.00	29.47	3.02
6282	9622	2.424956	GACCATTCTTCATGTCCCTTGC	59.575	50.000	0.00	0.00	0.00	4.01
6326	9668	8.885494	TTTTCACAATCAAGAATTTACCTTGG	57.115	30.769	5.75	0.00	40.88	3.61
6352	9694	4.022242	TCAAGGTATTCTAGCTCGTATGCC	60.022	45.833	4.27	4.27	35.05	4.40
6358	9700	1.065102	TCTAGCTCGTATGCCGTGAAC	59.935	52.381	0.00	0.00	37.94	3.18
6382	9724	6.208007	ACATGAATTCTGATTTCTGAGTTGCA	59.792	34.615	7.05	0.00	0.00	4.08
6447	9789	7.217200	CCACTCATCTAAATCGAAATAGGGAA	58.783	38.462	7.70	0.00	0.00	3.97
6590	9932	4.947388	TGTGGTTCAAGAAACTTTAGCTGT	59.053	37.500	0.00	0.00	38.02	4.40
6592	9934	5.297029	GTGGTTCAAGAAACTTTAGCTGTCT	59.703	40.000	0.00	0.00	38.02	3.41
6619	9961	0.107831	AGGCGGTGCTAACAAGTGAA	59.892	50.000	0.00	0.00	0.00	3.18
6686	10031	0.737715	GTCGTACAAGCCTCAGCCAG	60.738	60.000	0.00	0.00	41.25	4.85
6707	10052	2.092375	GCACCTACAGGAAGCCCTTAAT	60.092	50.000	1.29	0.00	42.02	1.40
6715	10060	6.041423	ACAGGAAGCCCTTAATTTTGATTG	57.959	37.500	0.00	0.00	42.02	2.67
6760	10105	5.915196	GCTGTACTTTCCAGTTTTCATGAAC	59.085	40.000	7.89	0.00	34.06	3.18
6784	10129	5.103687	GTCTACAGAAAGTAAGCTACAGCC	58.896	45.833	0.00	0.00	43.38	4.85
6892	10237	5.695851	ACAAAAAGTACATGAAGCTCCAG	57.304	39.130	0.00	0.00	0.00	3.86
6893	10238	4.520492	ACAAAAAGTACATGAAGCTCCAGG	59.480	41.667	0.00	0.00	0.00	4.45
6898	10243	2.789409	ACATGAAGCTCCAGGTAACC	57.211	50.000	0.00	0.00	37.17	2.85
6899	10244	1.066143	ACATGAAGCTCCAGGTAACCG	60.066	52.381	0.00	0.00	37.17	4.44
6912	10257	1.664873	GTAACCGCATCCCCTCTTTC	58.335	55.000	0.00	0.00	0.00	2.62
6920	10265	3.181493	CGCATCCCCTCTTTCTTGAATTG	60.181	47.826	0.00	0.00	0.00	2.32
7055	10400	9.167311	GGAAACCAATATATAGAGGCTTATGTG	57.833	37.037	0.00	0.00	0.00	3.21
7311	10659	4.320494	GCGTTGGTCAAGAAATTCTGACAT	60.320	41.667	19.40	0.00	31.05	3.06
7440	10789	3.819564	AGCTGACTTCACTACACAACA	57.180	42.857	0.00	0.00	0.00	3.33
7643	10992	2.038952	TGAACTCTCCTGTTGATGGTGG	59.961	50.000	0.00	0.00	0.00	4.61
7648	10997	0.112218	TCCTGTTGATGGTGGTTGGG	59.888	55.000	0.00	0.00	0.00	4.12
7660	11010	3.053544	TGGTGGTTGGGTGTTCTTCTAAA	60.054	43.478	0.00	0.00	0.00	1.85
7804	11156	6.823689	TGATCTTTGTTCTAGGTTATTGAGGC	59.176	38.462	0.00	0.00	0.00	4.70

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
93	94	3.623960	CGTCTCGTCTTCCTGAGTAGAAT	59.376	47.826	0.00	0.00	33.88	2.40
121	122	4.749166	GCATTATTCCATCTTCAGGGAGCT	60.749	45.833	0.00	0.00	34.02	4.09
144	145	2.522193	GGGACTAGGCGGGGAGAG	60.522	72.222	0.00	0.00	0.00	3.20
190	192	3.249189	ACACCTCCACACGCCCAT	61.249	61.111	0.00	0.00	0.00	4.00
315	317	1.027792	AACAGAACAACAACCGCCGT	61.028	50.000	0.00	0.00	0.00	5.68
356	358	4.047059	TCGGGAAGTCGTCGTGCC	62.047	66.667	0.00	0.00	0.00	5.01
403	407	0.613012	GTCATTGCCCCTTCCTTGCT	60.613	55.000	0.00	0.00	0.00	3.91
406	410	1.000896	CCGTCATTGCCCCTTCCTT	60.001	57.895	0.00	0.00	0.00	3.36
574	580	1.654023	GGGTGCAACGATTGTAGGGC	61.654	60.000	0.00	0.00	38.12	5.19
576	582	0.035439	AGGGGTGCAACGATTGTAGG	60.035	55.000	0.00	0.00	38.12	3.18
596	602	1.338020	CCAAGATTATTGGGGAAGCGC	59.662	52.381	0.00	0.00	35.96	5.92
597	603	2.880890	CTCCAAGATTATTGGGGAAGCG	59.119	50.000	3.73	0.00	42.70	4.68
641	648	5.183904	CACTAGCTTGGTTCCTTGCTAAAAT	59.816	40.000	0.00	4.65	37.53	1.82
674	681	1.869767	GATCGGCTGCTATTCTTGTGG	59.130	52.381	0.00	0.00	0.00	4.17
703	710	1.065109	GGTGTTTGGTGGCGTGAAC	59.935	57.895	0.00	0.00	0.00	3.18
715	722	1.029681	GAAAACGGCTGAGGGTGTTT	58.970	50.000	0.00	0.00	36.17	2.83
720	727	0.875059	GAACTGAAAACGGCTGAGGG	59.125	55.000	0.00	0.00	0.00	4.30
754	765	0.943673	CATTGCATGTCGCCGGAATA	59.056	50.000	5.05	0.00	41.33	1.75
865	882	2.612972	GGAACAGCTGATTGGTTCGAGA	60.613	50.000	23.35	0.00	41.31	4.04
908	925	1.603455	CGGCAAGGGTGGTGTGATT	60.603	57.895	0.00	0.00	0.00	2.57
1751	1800	2.095461	CGAGGATGAACTCACCAGAGA	58.905	52.381	0.00	0.00	44.98	3.10
1817	1866	6.952743	TCGGTACAACGCAAAACTATAAAAA	58.047	32.000	0.00	0.00	0.00	1.94
1818	1867	6.347563	CCTCGGTACAACGCAAAACTATAAAA	60.348	38.462	0.00	0.00	0.00	1.52
2296	3066	5.396750	ACAACAACAACAACAACAACAAC	57.603	34.783	0.00	0.00	0.00	3.32
2297	3067	5.351465	ACAACAACAACAACAACAACAACAA	59.649	32.000	0.00	0.00	0.00	2.83
2298	3068	4.870426	ACAACAACAACAACAACAACAACA	59.130	33.333	0.00	0.00	0.00	3.33
2299	3069	5.396750	ACAACAACAACAACAACAACAAC	57.603	34.783	0.00	0.00	0.00	3.32
2300	3070	5.351465	ACAACAACAACAACAACAACAACAA	59.649	32.000	0.00	0.00	0.00	2.83
2301	3071	4.870426	ACAACAACAACAACAACAACAACA	59.130	33.333	0.00	0.00	0.00	3.33
2302	3072	5.396750	ACAACAACAACAACAACAACAAC	57.603	34.783	0.00	0.00	0.00	3.32
2303	3073	5.351465	ACAACAACAACAACAACAACAACAA	59.649	32.000	0.00	0.00	0.00	2.83
2304	3074	4.870426	ACAACAACAACAACAACAACAACA	59.130	33.333	0.00	0.00	0.00	3.33
2305	3075	5.396750	ACAACAACAACAACAACAACAAC	57.603	34.783	0.00	0.00	0.00	3.32
2306	3076	5.351465	ACAACAACAACAACAACAACAACAA	59.649	32.000	0.00	0.00	0.00	2.83
2307	3077	4.870426	ACAACAACAACAACAACAACAACA	59.130	33.333	0.00	0.00	0.00	3.33
2308	3078	5.396750	ACAACAACAACAACAACAACAAC	57.603	34.783	0.00	0.00	0.00	3.32
2309	3079	5.351465	ACAACAACAACAACAACAACAACAA	59.649	32.000	0.00	0.00	0.00	2.83
2310	3080	4.870426	ACAACAACAACAACAACAACAACA	59.130	33.333	0.00	0.00	0.00	3.33
2311	3081	5.396750	ACAACAACAACAACAACAACAAC	57.603	34.783	0.00	0.00	0.00	3.32
2312	3082	7.224753	ACATTACAACAACAACAACAACAACAA	59.775	29.630	0.00	0.00	0.00	2.83
2313	3083	6.701841	ACATTACAACAACAACAACAACAACA	59.298	30.769	0.00	0.00	0.00	3.33
2314	3084	7.111353	ACATTACAACAACAACAACAACAAC	57.889	32.000	0.00	0.00	0.00	3.32
2315	3085	8.812147	TTACATTACAACAACAACAACAACAA	57.188	26.923	0.00	0.00	0.00	2.83
2316	3086	8.812147	TTTACATTACAACAACAACAACAACA	57.188	26.923	0.00	0.00	0.00	3.33
2317	3087	8.376942	CCTTTACATTACAACAACAACAACAAC	58.623	33.333	0.00	0.00	0.00	3.32
2318	3088	7.063544	GCCTTTACATTACAACAACAACAACAA	59.936	33.333	0.00	0.00	0.00	2.83
2319	3089	6.531948	GCCTTTACATTACAACAACAACAACA	59.468	34.615	0.00	0.00	0.00	3.33
2320	3090	6.531948	TGCCTTTACATTACAACAACAACAAC	59.468	34.615	0.00	0.00	0.00	3.32
2321	3091	6.631016	TGCCTTTACATTACAACAACAACAA	58.369	32.000	0.00	0.00	0.00	2.83
2322	3092	6.208988	TGCCTTTACATTACAACAACAACA	57.791	33.333	0.00	0.00	0.00	3.33
2323	3093	7.707774	AATGCCTTTACATTACAACAACAAC	57.292	32.000	0.00	0.00	38.48	3.32
2324	3094	9.988815	ATAAATGCCTTTACATTACAACAACAA	57.011	25.926	0.00	0.00	39.32	2.83
2325	3095	9.988815	AATAAATGCCTTTACATTACAACAACA	57.011	25.926	0.00	0.00	39.32	3.33
2328	3098	8.930760	GCAAATAAATGCCTTTACATTACAACA	58.069	29.630	0.00	0.00	39.32	3.33
2363	3135	3.701532	TTAAAGTTCAAGCCAACACGG	57.298	42.857	0.00	0.00	38.11	4.94
2419	3191	9.898152	TGAATTGGAACCTTTTTCTTTATTTGT	57.102	25.926	0.00	0.00	0.00	2.83
2826	3712	6.005066	TGATTGATGACCATTGGTGATAGT	57.995	37.500	14.44	0.00	35.25	2.12
2971	3990	5.238432	TGCGATTAATTACATACCTGCCTTG	59.762	40.000	0.00	0.00	0.00	3.61
3056	4103	5.470098	TGAAAACATGTCTACTTCTGCCTTC	59.530	40.000	0.00	0.00	0.00	3.46
3263	4344	6.152379	GCATATAAAGGAGCCTAACATTTGC	58.848	40.000	0.00	0.00	0.00	3.68
4038	5225	8.940768	TTTTCCAATTAACTTTCCAGAAACAG	57.059	30.769	0.00	0.00	0.00	3.16
4088	5275	3.609853	GGCATATGAGGAAACACAGACA	58.390	45.455	6.97	0.00	33.32	3.41
4772	6427	2.283298	CAAGTCAGCACTGTCACAAGT	58.717	47.619	0.00	0.00	31.06	3.16
4849	6504	1.079503	GCTTCCAGCTAAGTGTTCCG	58.920	55.000	0.00	0.00	38.45	4.30
4860	6515	3.552604	TGTTAAATCGTTGCTTCCAGC	57.447	42.857	0.00	0.00	42.82	4.85
5533	7198	8.635765	ATTTTCTGGAGAAGCATAAACACTAA	57.364	30.769	0.00	0.00	35.21	2.24
6211	9540	3.507233	CACTTGTAACATGCATGAGGGTT	59.493	43.478	32.75	18.24	0.00	4.11
6326	9668	4.373348	ACGAGCTAGAATACCTTGACAC	57.627	45.455	0.00	0.00	0.00	3.67
6352	9694	6.834876	TCAGAAATCAGAATTCATGTTCACG	58.165	36.000	8.44	2.36	0.00	4.35
6358	9700	6.617879	TGCAACTCAGAAATCAGAATTCATG	58.382	36.000	8.44	3.57	0.00	3.07
6382	9724	8.059798	TCTAAGGTTGTTTTACTATAGCGACT	57.940	34.615	0.00	0.00	0.00	4.18
6447	9789	8.537016	TGGTAGCTAAGTTTCAGTTGTATATGT	58.463	33.333	0.00	0.00	0.00	2.29
6463	9805	8.589338	AGTATGGATTTATGTCTGGTAGCTAAG	58.411	37.037	0.00	0.00	0.00	2.18
6590	9932	1.789523	AGCACCGCCTAATTAGGAGA	58.210	50.000	31.78	0.00	46.63	3.71
6592	9934	2.767394	TGTTAGCACCGCCTAATTAGGA	59.233	45.455	31.78	9.03	46.63	2.94
6653	9995	5.980116	GCTTGTACGACACAATCTCTATCAT	59.020	40.000	7.59	0.00	45.96	2.45
6654	9996	5.340803	GCTTGTACGACACAATCTCTATCA	58.659	41.667	7.59	0.00	45.96	2.15
6655	9997	4.740695	GGCTTGTACGACACAATCTCTATC	59.259	45.833	7.59	0.00	45.96	2.08
6656	9998	4.402793	AGGCTTGTACGACACAATCTCTAT	59.597	41.667	7.59	0.00	45.96	1.98
6657	9999	3.762288	AGGCTTGTACGACACAATCTCTA	59.238	43.478	7.59	0.00	45.96	2.43
6658	10000	2.563179	AGGCTTGTACGACACAATCTCT	59.437	45.455	7.59	4.29	45.96	3.10
6659	10001	2.924290	GAGGCTTGTACGACACAATCTC	59.076	50.000	7.59	12.07	45.96	2.75
6660	10002	2.299013	TGAGGCTTGTACGACACAATCT	59.701	45.455	7.59	8.34	45.96	2.40
6661	10003	2.668457	CTGAGGCTTGTACGACACAATC	59.332	50.000	7.59	4.47	45.96	2.67
6662	10004	2.688507	CTGAGGCTTGTACGACACAAT	58.311	47.619	7.59	0.00	45.96	2.71
6686	10031	0.909623	TAAGGGCTTCCTGTAGGTGC	59.090	55.000	0.00	4.30	40.74	5.01
6707	10052	7.278875	ACATTTCCCTAAGTTTGCAATCAAAA	58.721	30.769	10.05	0.00	43.12	2.44
6715	10060	5.050159	CAGCAAAACATTTCCCTAAGTTTGC	60.050	40.000	9.55	9.55	34.70	3.68
6760	10105	4.794246	GCTGTAGCTTACTTTCTGTAGACG	59.206	45.833	0.00	0.00	38.21	4.18
6784	10129	0.323178	ATGCCTGCAGAGTTCCAAGG	60.323	55.000	17.39	0.00	0.00	3.61
6861	10206	9.226345	GCTTCATGTACTTTTTGTATTCTATGC	57.774	33.333	0.00	0.00	33.23	3.14
6892	10237	0.255033	AAAGAGGGGATGCGGTTACC	59.745	55.000	0.00	0.00	0.00	2.85
6893	10238	1.209747	AGAAAGAGGGGATGCGGTTAC	59.790	52.381	0.00	0.00	0.00	2.50
6898	10243	2.113860	TTCAAGAAAGAGGGGATGCG	57.886	50.000	0.00	0.00	0.00	4.73
6899	10244	3.131755	CCAATTCAAGAAAGAGGGGATGC	59.868	47.826	0.00	0.00	0.00	3.91
6912	10257	0.890683	GTCACCCCTGCCAATTCAAG	59.109	55.000	0.00	0.00	0.00	3.02
7055	10400	2.623416	GTTATTAGCCCATGCAGAACCC	59.377	50.000	0.00	0.00	41.13	4.11
7169	10514	8.978874	TTAATGATTACCTATGTGACAGCATT	57.021	30.769	0.00	0.00	0.00	3.56
7289	10637	4.811555	TGTCAGAATTTCTTGACCAACG	57.188	40.909	18.20	0.00	0.00	4.10
7332	10680	5.487433	CACTGACACCCACATAATAACAGA	58.513	41.667	0.00	0.00	0.00	3.41
7340	10688	2.024176	AGACCACTGACACCCACATA	57.976	50.000	0.00	0.00	0.00	2.29
7341	10689	1.902508	CTAGACCACTGACACCCACAT	59.097	52.381	0.00	0.00	0.00	3.21
7342	10690	1.338107	CTAGACCACTGACACCCACA	58.662	55.000	0.00	0.00	0.00	4.17
7343	10691	0.037232	GCTAGACCACTGACACCCAC	60.037	60.000	0.00	0.00	0.00	4.61
7344	10692	0.471022	TGCTAGACCACTGACACCCA	60.471	55.000	0.00	0.00	0.00	4.51
7345	10693	0.037232	GTGCTAGACCACTGACACCC	60.037	60.000	0.00	0.00	33.02	4.61
7346	10694	0.969894	AGTGCTAGACCACTGACACC	59.030	55.000	2.57	0.00	44.00	4.16
7440	10789	3.521126	ACTTGGATGCTCACTACCTGAAT	59.479	43.478	0.00	0.00	0.00	2.57
7610	10959	9.823647	CAACAGGAGAGTTCATATACAATAGTT	57.176	33.333	0.00	0.00	0.00	2.24
7643	10992	6.937436	TTTCTCTTTAGAAGAACACCCAAC	57.063	37.500	0.00	0.00	42.60	3.77
7648	10997	6.374578	GTGGCATTTCTCTTTAGAAGAACAC	58.625	40.000	0.00	0.00	42.60	3.32
7660	11010	1.675641	GCACCCGTGGCATTTCTCT	60.676	57.895	0.00	0.00	0.00	3.10
7757	11109	7.254227	TCAACTATTGTGGTTGTCAGTTTAC	57.746	36.000	6.17	0.00	42.97	2.01
7804	11156	7.119846	AGCTTAACCATAGCTAAGAACAACTTG	59.880	37.037	0.00	0.00	46.66	3.16

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.