AutoCloner

Multiple sequence alignment - TraesCS3B01G028200

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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	TraesCS3B01G028200	chr3B	100.000	2533	0	0	1	2533	12141281	12143813	0.000000e+00	4678.0
1	TraesCS3B01G028200	chr3B	91.390	1475	104	11	383	1845	12304068	12302605	0.000000e+00	1999.0
2	TraesCS3B01G028200	chr3B	99.430	1053	6	0	381	1433	12122348	12123400	0.000000e+00	1912.0
3	TraesCS3B01G028200	chr3B	88.671	1324	133	13	383	1699	27873997	27875310	0.000000e+00	1598.0
4	TraesCS3B01G028200	chr3B	88.889	558	23	16	1974	2531	27877441	27877959	0.000000e+00	651.0
5	TraesCS3B01G028200	chr3B	99.668	301	1	0	1	301	12122031	12122331	3.680000e-153	551.0
6	TraesCS3B01G028200	chr3B	89.369	301	30	2	2	301	12304386	12304087	6.610000e-101	377.0
7	TraesCS3B01G028200	chr3B	91.732	254	19	2	1974	2225	12302576	12302323	4.010000e-93	351.0
8	TraesCS3B01G028200	chr3B	87.333	300	38	0	2	301	27873679	27873978	6.710000e-91	344.0
9	TraesCS3B01G028200	chr3B	95.500	200	9	0	1695	1894	27877244	27877443	1.130000e-83	320.0
10	TraesCS3B01G028200	chr3B	90.955	199	14	1	2059	2253	12297860	12297662	5.370000e-67	265.0
11	TraesCS3B01G028200	chr3B	91.791	134	10	1	1761	1894	12298048	12297916	4.300000e-43	185.0
12	TraesCS3B01G028200	chr3B	96.552	87	3	0	294	380	11210953	11211039	7.300000e-31	145.0
13	TraesCS3B01G028200	chr3B	88.430	121	12	1	2413	2533	12297089	12296971	7.300000e-31	145.0
14	TraesCS3B01G028200	chrUn	99.334	1351	9	0	381	1731	382717799	382719149	0.000000e+00	2446.0
15	TraesCS3B01G028200	chrUn	90.647	1529	106	13	383	1894	260889898	260888390	0.000000e+00	1997.0
16	TraesCS3B01G028200	chrUn	90.647	1529	106	13	383	1894	263768867	263770375	0.000000e+00	1997.0
17	TraesCS3B01G028200	chrUn	89.373	1468	134	13	383	1845	319812086	319810636	0.000000e+00	1827.0
18	TraesCS3B01G028200	chrUn	99.634	273	1	0	29	301	382717510	382717782	1.350000e-137	499.0
19	TraesCS3B01G028200	chrUn	91.667	300	25	0	2	301	319812404	319812105	1.400000e-112	416.0
20	TraesCS3B01G028200	chrUn	89.123	285	29	2	10	293	260890208	260889925	1.110000e-93	353.0
21	TraesCS3B01G028200	chrUn	88.889	288	30	2	7	293	263768554	263768840	1.110000e-93	353.0
22	TraesCS3B01G028200	chrUn	91.339	254	20	2	1974	2225	319810607	319810354	1.870000e-91	346.0
23	TraesCS3B01G028200	chrUn	91.053	190	13	1	2059	2244	36009676	36009487	1.160000e-63	254.0
24	TraesCS3B01G028200	chrUn	91.053	190	13	1	2059	2244	260888334	260888145	1.160000e-63	254.0
25	TraesCS3B01G028200	chrUn	91.444	187	12	1	2059	2241	263770431	263770617	1.160000e-63	254.0
26	TraesCS3B01G028200	chrUn	86.932	176	17	3	2239	2409	260886795	260886621	2.570000e-45	193.0
27	TraesCS3B01G028200	chrUn	86.932	176	17	3	2239	2409	263771970	263772144	2.570000e-45	193.0
28	TraesCS3B01G028200	chrUn	90.299	134	10	2	1761	1894	36009862	36009732	3.350000e-39	172.0
29	TraesCS3B01G028200	chrUn	91.057	123	9	1	2411	2533	260886565	260886445	5.610000e-37	165.0
30	TraesCS3B01G028200	chrUn	91.057	123	9	1	2411	2533	263772200	263772320	5.610000e-37	165.0
31	TraesCS3B01G028200	chrUn	92.473	93	4	3	1889	1980	71667177	71667087	2.050000e-26	130.0
32	TraesCS3B01G028200	chr3D	89.809	1521	125	20	383	1894	5650323	5651822	0.000000e+00	1923.0
33	TraesCS3B01G028200	chr3D	89.438	445	34	7	1974	2410	5651820	5652259	1.320000e-152	549.0
34	TraesCS3B01G028200	chr3D	91.554	296	23	2	7	301	5650010	5650304	8.440000e-110	407.0
35	TraesCS3B01G028200	chr3D	92.800	125	4	2	2411	2533	5652314	5652435	2.590000e-40	176.0
36	TraesCS3B01G028200	chr3D	94.253	87	5	0	294	380	9105251	9105337	1.580000e-27	134.0
37	TraesCS3B01G028200	chr3D	92.308	91	6	1	1886	1975	455100665	455100575	7.360000e-26	128.0
38	TraesCS3B01G028200	chr3A	88.665	1438	128	19	383	1802	15619054	15617634	0.000000e+00	1720.0
39	TraesCS3B01G028200	chr3A	87.028	424	36	9	1974	2393	15617501	15617093	6.380000e-126	460.0
40	TraesCS3B01G028200	chr3A	89.527	296	29	2	7	301	15619367	15619073	8.560000e-100	374.0
41	TraesCS3B01G028200	chr3A	88.968	281	25	3	1354	1632	11617582	11617306	2.410000e-90	342.0
42	TraesCS3B01G028200	chr3A	92.453	106	5	2	2429	2533	15616662	15616559	5.650000e-32	148.0
43	TraesCS3B01G028200	chr7A	95.402	87	3	1	1890	1975	290919950	290920036	1.220000e-28	137.0
44	TraesCS3B01G028200	chr7D	93.548	93	3	3	1887	1976	403810454	403810546	4.400000e-28	135.0
45	TraesCS3B01G028200	chr2A	93.407	91	5	1	1892	1981	550865001	550864911	1.580000e-27	134.0
46	TraesCS3B01G028200	chr4D	93.333	90	5	1	1887	1975	31338440	31338351	5.690000e-27	132.0
47	TraesCS3B01G028200	chr2D	93.333	90	4	2	1892	1980	236654335	236654247	5.690000e-27	132.0
48	TraesCS3B01G028200	chr2D	87.736	106	9	3	1892	1995	649753814	649753711	1.230000e-23	121.0
49	TraesCS3B01G028200	chr1B	87.736	106	12	1	1871	1975	323632875	323632980	3.420000e-24	122.0
50	TraesCS3B01G028200	chr7B	90.909	44	4	0	2437	2480	446136180	446136223	2.720000e-05	60.2

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	TraesCS3B01G028200	chr3B	12141281	12143813	2532	False	4678.00	4678	100.000000	1	2533	1	chr3B.!!$F2	2532
1	TraesCS3B01G028200	chr3B	12122031	12123400	1369	False	1231.50	1912	99.549000	1	1433	2	chr3B.!!$F3	1432
2	TraesCS3B01G028200	chr3B	12302323	12304386	2063	True	909.00	1999	90.830333	2	2225	3	chr3B.!!$R2	2223
3	TraesCS3B01G028200	chr3B	27873679	27877959	4280	False	728.25	1598	90.098250	2	2531	4	chr3B.!!$F4	2529
4	TraesCS3B01G028200	chrUn	382717510	382719149	1639	False	1472.50	2446	99.484000	29	1731	2	chrUn.!!$F2	1702
5	TraesCS3B01G028200	chrUn	319810354	319812404	2050	True	863.00	1827	90.793000	2	2225	3	chrUn.!!$R4	2223
6	TraesCS3B01G028200	chrUn	260886445	260890208	3763	True	592.40	1997	89.762400	10	2533	5	chrUn.!!$R3	2523
7	TraesCS3B01G028200	chrUn	263768554	263772320	3766	False	592.40	1997	89.793800	7	2533	5	chrUn.!!$F1	2526
8	TraesCS3B01G028200	chr3D	5650010	5652435	2425	False	763.75	1923	90.900250	7	2533	4	chr3D.!!$F2	2526
9	TraesCS3B01G028200	chr3A	15616559	15619367	2808	True	675.50	1720	89.418250	7	2533	4	chr3A.!!$R2	2526

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
365	366	0.249405	CTCCAGATTCGAGCAGGAGC	60.249	60.0	13.29	0.0	39.39	4.7	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1990	4017	0.53578	CTCAGCTTGCAACCAGGACA	60.536	55.0	0.0	0.0	0.0	4.02	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
309	310	8.970859	CTGTCTTCCAGGATAATAAATCAACT	57.029	34.615	0.00	0.00	37.54	3.16
310	311	9.401058	CTGTCTTCCAGGATAATAAATCAACTT	57.599	33.333	0.00	0.00	37.54	2.66
311	312	9.177608	TGTCTTCCAGGATAATAAATCAACTTG	57.822	33.333	0.00	0.00	0.00	3.16
314	315	5.833131	TCCAGGATAATAAATCAACTTGGCC	59.167	40.000	0.00	0.00	0.00	5.36
315	316	5.598005	CCAGGATAATAAATCAACTTGGCCA	59.402	40.000	0.00	0.00	0.00	5.36
317	318	7.149973	CAGGATAATAAATCAACTTGGCCATG	58.850	38.462	16.76	16.76	0.00	3.66
318	319	6.840705	AGGATAATAAATCAACTTGGCCATGT	59.159	34.615	18.18	18.18	0.00	3.21
319	320	8.004215	AGGATAATAAATCAACTTGGCCATGTA	58.996	33.333	23.40	10.44	0.00	2.29
320	321	8.806146	GGATAATAAATCAACTTGGCCATGTAT	58.194	33.333	23.40	12.26	0.00	2.29
322	323	9.985730	ATAATAAATCAACTTGGCCATGTATTG	57.014	29.630	23.40	18.44	0.00	1.90
323	324	3.806625	ATCAACTTGGCCATGTATTGC	57.193	42.857	23.40	0.00	0.00	3.56
324	325	2.523245	TCAACTTGGCCATGTATTGCA	58.477	42.857	23.40	7.77	0.00	4.08
325	326	2.230992	TCAACTTGGCCATGTATTGCAC	59.769	45.455	23.40	0.00	0.00	4.57
326	327	1.921982	ACTTGGCCATGTATTGCACA	58.078	45.000	22.02	0.00	42.69	4.57
328	329	2.833338	ACTTGGCCATGTATTGCACATT	59.167	40.909	22.02	0.00	46.01	2.71
329	330	2.963548	TGGCCATGTATTGCACATTG	57.036	45.000	0.00	0.00	46.01	2.82
330	331	1.481363	TGGCCATGTATTGCACATTGG	59.519	47.619	0.00	0.00	46.01	3.16
331	332	1.755959	GGCCATGTATTGCACATTGGA	59.244	47.619	0.00	0.00	46.01	3.53
332	333	2.481795	GGCCATGTATTGCACATTGGAC	60.482	50.000	0.00	0.00	46.01	4.02
333	334	2.481795	GCCATGTATTGCACATTGGACC	60.482	50.000	0.00	0.00	46.01	4.46
334	335	2.759535	CCATGTATTGCACATTGGACCA	59.240	45.455	0.00	0.00	46.01	4.02
335	336	3.385433	CCATGTATTGCACATTGGACCAT	59.615	43.478	0.00	0.00	46.01	3.55
336	337	4.141892	CCATGTATTGCACATTGGACCATT	60.142	41.667	0.00	0.00	46.01	3.16
337	338	4.453177	TGTATTGCACATTGGACCATTG	57.547	40.909	13.65	13.65	30.04	2.82
338	339	3.195182	TGTATTGCACATTGGACCATTGG	59.805	43.478	18.27	0.00	30.04	3.16
339	340	2.006805	TTGCACATTGGACCATTGGA	57.993	45.000	18.27	5.10	0.00	3.53
340	341	1.255882	TGCACATTGGACCATTGGAC	58.744	50.000	18.27	2.62	0.00	4.02
341	342	1.203038	TGCACATTGGACCATTGGACT	60.203	47.619	18.27	0.00	0.00	3.85
342	343	1.474077	GCACATTGGACCATTGGACTC	59.526	52.381	18.27	0.00	0.00	3.36
343	344	2.094675	CACATTGGACCATTGGACTCC	58.905	52.381	18.27	7.56	0.00	3.85
344	345	1.995542	ACATTGGACCATTGGACTCCT	59.004	47.619	18.27	0.00	0.00	3.69
345	346	2.379907	ACATTGGACCATTGGACTCCTT	59.620	45.455	18.27	0.00	0.00	3.36
346	347	2.879103	TTGGACCATTGGACTCCTTC	57.121	50.000	10.37	0.00	0.00	3.46
347	348	2.044793	TGGACCATTGGACTCCTTCT	57.955	50.000	10.37	0.00	0.00	2.85
348	349	1.909302	TGGACCATTGGACTCCTTCTC	59.091	52.381	10.37	0.00	0.00	2.87
349	350	1.210722	GGACCATTGGACTCCTTCTCC	59.789	57.143	10.37	0.00	0.00	3.71
350	351	1.909302	GACCATTGGACTCCTTCTCCA	59.091	52.381	10.37	0.00	35.91	3.86
351	352	1.912043	ACCATTGGACTCCTTCTCCAG	59.088	52.381	10.37	0.00	39.06	3.86
352	353	2.191400	CCATTGGACTCCTTCTCCAGA	58.809	52.381	0.00	0.00	39.06	3.86
353	354	2.776536	CCATTGGACTCCTTCTCCAGAT	59.223	50.000	0.00	0.00	39.06	2.90
354	355	3.201708	CCATTGGACTCCTTCTCCAGATT	59.798	47.826	0.00	0.00	39.06	2.40
355	356	4.450053	CATTGGACTCCTTCTCCAGATTC	58.550	47.826	0.00	0.00	39.06	2.52
356	357	2.103373	TGGACTCCTTCTCCAGATTCG	58.897	52.381	0.00	0.00	32.52	3.34
357	358	2.291605	TGGACTCCTTCTCCAGATTCGA	60.292	50.000	0.00	0.00	32.52	3.71
358	359	2.360801	GGACTCCTTCTCCAGATTCGAG	59.639	54.545	0.00	0.00	0.00	4.04
359	360	1.754226	ACTCCTTCTCCAGATTCGAGC	59.246	52.381	0.00	0.00	0.00	5.03
360	361	1.753649	CTCCTTCTCCAGATTCGAGCA	59.246	52.381	0.00	0.00	0.00	4.26
361	362	1.753649	TCCTTCTCCAGATTCGAGCAG	59.246	52.381	0.00	0.00	0.00	4.24
362	363	1.202510	CCTTCTCCAGATTCGAGCAGG	60.203	57.143	0.00	0.00	35.00	4.85
363	364	1.753649	CTTCTCCAGATTCGAGCAGGA	59.246	52.381	2.40	2.40	0.00	3.86
364	365	1.397672	TCTCCAGATTCGAGCAGGAG	58.602	55.000	17.34	17.34	45.64	3.69
365	366	0.249405	CTCCAGATTCGAGCAGGAGC	60.249	60.000	13.29	0.00	39.39	4.70
366	367	0.972471	TCCAGATTCGAGCAGGAGCA	60.972	55.000	0.00	0.00	45.49	4.26
367	368	0.530211	CCAGATTCGAGCAGGAGCAG	60.530	60.000	0.00	0.00	45.49	4.24
368	369	0.530211	CAGATTCGAGCAGGAGCAGG	60.530	60.000	0.00	0.00	45.49	4.85
369	370	0.685785	AGATTCGAGCAGGAGCAGGA	60.686	55.000	0.00	0.00	45.49	3.86
370	371	0.249405	GATTCGAGCAGGAGCAGGAG	60.249	60.000	0.00	0.00	45.49	3.69
371	372	0.975040	ATTCGAGCAGGAGCAGGAGT	60.975	55.000	0.00	0.00	45.49	3.85
372	373	1.881903	TTCGAGCAGGAGCAGGAGTG	61.882	60.000	0.00	0.00	45.49	3.51
373	374	2.583520	GAGCAGGAGCAGGAGTGG	59.416	66.667	0.00	0.00	45.49	4.00
374	375	3.007920	AGCAGGAGCAGGAGTGGG	61.008	66.667	0.00	0.00	45.49	4.61
375	376	3.005539	GCAGGAGCAGGAGTGGGA	61.006	66.667	0.00	0.00	41.58	4.37
376	377	2.373707	GCAGGAGCAGGAGTGGGAT	61.374	63.158	0.00	0.00	41.58	3.85
377	378	1.050988	GCAGGAGCAGGAGTGGGATA	61.051	60.000	0.00	0.00	41.58	2.59
378	379	1.727062	CAGGAGCAGGAGTGGGATAT	58.273	55.000	0.00	0.00	0.00	1.63
379	380	1.347050	CAGGAGCAGGAGTGGGATATG	59.653	57.143	0.00	0.00	0.00	1.78
490	495	2.355363	CGACGACCGCCACAAGAA	60.355	61.111	0.00	0.00	0.00	2.52
643	659	3.325135	ACCAAGGAAGATCTTCTTGTCGT	59.675	43.478	29.64	21.01	36.73	4.34
1753	3734	5.826208	AGTTTATGTCCCTTTTTGTTCGACT	59.174	36.000	0.00	0.00	0.00	4.18
1846	3873	5.818136	AGGTGTTATGTTGATGTACATGC	57.182	39.130	14.43	5.76	39.06	4.06
1852	3879	7.594758	GTGTTATGTTGATGTACATGCAAAAGT	59.405	33.333	14.43	8.88	39.06	2.66
1897	3924	7.981102	ATTGTCAGTTAAGAAAACTACTCCC	57.019	36.000	0.00	0.00	0.00	4.30
1898	3925	6.742559	TGTCAGTTAAGAAAACTACTCCCT	57.257	37.500	0.00	0.00	0.00	4.20
1899	3926	6.756221	TGTCAGTTAAGAAAACTACTCCCTC	58.244	40.000	0.00	0.00	0.00	4.30
1900	3927	6.164876	GTCAGTTAAGAAAACTACTCCCTCC	58.835	44.000	0.00	0.00	0.00	4.30
1901	3928	5.047519	TCAGTTAAGAAAACTACTCCCTCCG	60.048	44.000	0.00	0.00	0.00	4.63
1902	3929	4.837298	AGTTAAGAAAACTACTCCCTCCGT	59.163	41.667	0.00	0.00	0.00	4.69
1903	3930	3.957591	AAGAAAACTACTCCCTCCGTC	57.042	47.619	0.00	0.00	0.00	4.79
1904	3931	2.177734	AGAAAACTACTCCCTCCGTCC	58.822	52.381	0.00	0.00	0.00	4.79
1905	3932	1.206610	GAAAACTACTCCCTCCGTCCC	59.793	57.143	0.00	0.00	0.00	4.46
1906	3933	0.115745	AAACTACTCCCTCCGTCCCA	59.884	55.000	0.00	0.00	0.00	4.37
1907	3934	0.338814	AACTACTCCCTCCGTCCCAT	59.661	55.000	0.00	0.00	0.00	4.00
1908	3935	1.229131	ACTACTCCCTCCGTCCCATA	58.771	55.000	0.00	0.00	0.00	2.74
1909	3936	1.572415	ACTACTCCCTCCGTCCCATAA	59.428	52.381	0.00	0.00	0.00	1.90
1910	3937	2.179424	ACTACTCCCTCCGTCCCATAAT	59.821	50.000	0.00	0.00	0.00	1.28
1911	3938	3.400322	ACTACTCCCTCCGTCCCATAATA	59.600	47.826	0.00	0.00	0.00	0.98
1912	3939	3.562108	ACTCCCTCCGTCCCATAATAT	57.438	47.619	0.00	0.00	0.00	1.28
1913	3940	4.687262	ACTCCCTCCGTCCCATAATATA	57.313	45.455	0.00	0.00	0.00	0.86
1914	3941	5.019657	ACTCCCTCCGTCCCATAATATAA	57.980	43.478	0.00	0.00	0.00	0.98
1915	3942	5.024118	ACTCCCTCCGTCCCATAATATAAG	58.976	45.833	0.00	0.00	0.00	1.73
1916	3943	5.222484	ACTCCCTCCGTCCCATAATATAAGA	60.222	44.000	0.00	0.00	0.00	2.10
1917	3944	5.657446	TCCCTCCGTCCCATAATATAAGAA	58.343	41.667	0.00	0.00	0.00	2.52
1918	3945	5.482878	TCCCTCCGTCCCATAATATAAGAAC	59.517	44.000	0.00	0.00	0.00	3.01
1919	3946	5.408356	CCTCCGTCCCATAATATAAGAACG	58.592	45.833	0.00	0.00	0.00	3.95
1920	3947	5.047519	CCTCCGTCCCATAATATAAGAACGT	60.048	44.000	0.00	0.00	0.00	3.99
1921	3948	6.409524	TCCGTCCCATAATATAAGAACGTT	57.590	37.500	0.00	0.00	0.00	3.99
1922	3949	6.819284	TCCGTCCCATAATATAAGAACGTTT	58.181	36.000	0.46	0.00	0.00	3.60
1923	3950	7.274447	TCCGTCCCATAATATAAGAACGTTTT	58.726	34.615	0.46	0.00	0.00	2.43
1924	3951	7.769970	TCCGTCCCATAATATAAGAACGTTTTT	59.230	33.333	9.22	9.22	0.00	1.94
1925	3952	9.044150	CCGTCCCATAATATAAGAACGTTTTTA	57.956	33.333	13.02	13.02	0.00	1.52
1990	4017	7.229506	CAGAGGGAGTACATTTTTGTTCTTCTT	59.770	37.037	0.00	0.00	0.00	2.52
1998	4025	5.422012	ACATTTTTGTTCTTCTTGTCCTGGT	59.578	36.000	0.00	0.00	0.00	4.00
2013	4040	0.170561	CTGGTTGCAAGCTGAGATGC	59.829	55.000	27.31	1.00	42.86	3.91
2052	4107	3.003275	GGTTCAAATTTGTGAGAGCGACA	59.997	43.478	17.47	0.00	0.00	4.35
2135	4194	9.937175	GAAGGTTGAACATAATCAGTTATTAGC	57.063	33.333	0.00	0.00	33.56	3.09
2169	4230	1.211457	AGCTCTGGCCTTGACCATAAG	59.789	52.381	3.32	0.00	39.54	1.73
2271	5688	8.328758	ACATATTATTTGAGTTCAAGGGAGACA	58.671	33.333	0.00	0.00	37.15	3.41
2341	5763	2.070783	CAACATCAATGCAACAAGGGC	58.929	47.619	0.00	0.00	0.00	5.19
2490	6310	8.978874	TTGTATGTTTCATGCCACTATCTTAT	57.021	30.769	0.00	0.00	0.00	1.73
2491	6311	8.978874	TGTATGTTTCATGCCACTATCTTATT	57.021	30.769	0.00	0.00	0.00	1.40
2526	6346	7.481798	GCAAACTTCGATATTTGTTTGGACTAG	59.518	37.037	18.08	0.00	45.21	2.57

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
301	302	4.020396	TGCAATACATGGCCAAGTTGATTT	60.020	37.500	20.29	5.77	0.00	2.17
303	304	3.098377	TGCAATACATGGCCAAGTTGAT	58.902	40.909	20.29	4.61	0.00	2.57
305	306	2.029200	TGTGCAATACATGGCCAAGTTG	60.029	45.455	20.29	13.46	33.42	3.16
306	307	2.246469	TGTGCAATACATGGCCAAGTT	58.754	42.857	20.29	3.97	33.42	2.66
307	308	1.921982	TGTGCAATACATGGCCAAGT	58.078	45.000	18.99	18.99	33.42	3.16
317	318	3.446873	TCCAATGGTCCAATGTGCAATAC	59.553	43.478	6.19	0.00	0.00	1.89
318	319	3.446873	GTCCAATGGTCCAATGTGCAATA	59.553	43.478	6.19	0.00	0.00	1.90
319	320	2.234414	GTCCAATGGTCCAATGTGCAAT	59.766	45.455	6.19	0.00	0.00	3.56
320	321	1.617850	GTCCAATGGTCCAATGTGCAA	59.382	47.619	6.19	0.00	0.00	4.08
321	322	1.203038	AGTCCAATGGTCCAATGTGCA	60.203	47.619	6.19	0.00	0.00	4.57
322	323	1.474077	GAGTCCAATGGTCCAATGTGC	59.526	52.381	6.19	0.00	0.00	4.57
323	324	2.094675	GGAGTCCAATGGTCCAATGTG	58.905	52.381	3.60	0.41	0.00	3.21
324	325	1.995542	AGGAGTCCAATGGTCCAATGT	59.004	47.619	12.86	0.00	32.23	2.71
325	326	2.814805	AGGAGTCCAATGGTCCAATG	57.185	50.000	12.86	0.00	32.23	2.82
326	327	2.922283	AGAAGGAGTCCAATGGTCCAAT	59.078	45.455	12.86	0.29	32.23	3.16
327	328	2.305927	GAGAAGGAGTCCAATGGTCCAA	59.694	50.000	12.86	0.00	32.23	3.53
328	329	1.909302	GAGAAGGAGTCCAATGGTCCA	59.091	52.381	12.86	0.00	32.23	4.02
329	330	1.210722	GGAGAAGGAGTCCAATGGTCC	59.789	57.143	12.86	6.15	33.84	4.46
330	331	1.909302	TGGAGAAGGAGTCCAATGGTC	59.091	52.381	12.86	0.00	41.32	4.02
331	332	1.912043	CTGGAGAAGGAGTCCAATGGT	59.088	52.381	12.86	0.00	43.68	3.55
332	333	2.191400	TCTGGAGAAGGAGTCCAATGG	58.809	52.381	12.86	0.00	43.68	3.16
333	334	4.450053	GAATCTGGAGAAGGAGTCCAATG	58.550	47.826	12.86	0.00	43.68	2.82
334	335	3.133721	CGAATCTGGAGAAGGAGTCCAAT	59.866	47.826	12.86	0.00	43.68	3.16
335	336	2.497675	CGAATCTGGAGAAGGAGTCCAA	59.502	50.000	12.86	0.00	43.68	3.53
336	337	2.103373	CGAATCTGGAGAAGGAGTCCA	58.897	52.381	12.86	0.00	42.06	4.02
337	338	2.360801	CTCGAATCTGGAGAAGGAGTCC	59.639	54.545	0.00	0.00	33.27	3.85
338	339	2.223711	GCTCGAATCTGGAGAAGGAGTC	60.224	54.545	0.00	0.00	33.27	3.36
339	340	1.754226	GCTCGAATCTGGAGAAGGAGT	59.246	52.381	0.00	0.00	33.27	3.85
340	341	1.753649	TGCTCGAATCTGGAGAAGGAG	59.246	52.381	0.00	0.00	33.27	3.69
341	342	1.753649	CTGCTCGAATCTGGAGAAGGA	59.246	52.381	0.00	0.00	34.13	3.36
342	343	2.222007	CTGCTCGAATCTGGAGAAGG	57.778	55.000	0.00	0.00	34.13	3.46
343	344	1.753649	TCCTGCTCGAATCTGGAGAAG	59.246	52.381	8.32	0.00	37.00	2.85
344	345	1.753649	CTCCTGCTCGAATCTGGAGAA	59.246	52.381	24.03	0.00	46.41	2.87
345	346	1.397672	CTCCTGCTCGAATCTGGAGA	58.602	55.000	24.03	4.06	46.41	3.71
346	347	0.249405	GCTCCTGCTCGAATCTGGAG	60.249	60.000	24.03	24.03	46.30	3.86
347	348	0.972471	TGCTCCTGCTCGAATCTGGA	60.972	55.000	10.92	10.92	40.48	3.86
348	349	0.530211	CTGCTCCTGCTCGAATCTGG	60.530	60.000	4.51	4.51	40.48	3.86
349	350	0.530211	CCTGCTCCTGCTCGAATCTG	60.530	60.000	0.00	0.00	40.48	2.90
350	351	0.685785	TCCTGCTCCTGCTCGAATCT	60.686	55.000	0.00	0.00	40.48	2.40
351	352	0.249405	CTCCTGCTCCTGCTCGAATC	60.249	60.000	0.00	0.00	40.48	2.52
352	353	0.975040	ACTCCTGCTCCTGCTCGAAT	60.975	55.000	0.00	0.00	40.48	3.34
353	354	1.607756	ACTCCTGCTCCTGCTCGAA	60.608	57.895	0.00	0.00	40.48	3.71
354	355	2.036414	ACTCCTGCTCCTGCTCGA	59.964	61.111	0.00	0.00	40.48	4.04
355	356	2.183811	CACTCCTGCTCCTGCTCG	59.816	66.667	0.00	0.00	40.48	5.03
356	357	2.583520	CCACTCCTGCTCCTGCTC	59.416	66.667	0.00	0.00	40.48	4.26
357	358	2.836672	ATCCCACTCCTGCTCCTGCT	62.837	60.000	0.00	0.00	40.48	4.24
358	359	1.050988	TATCCCACTCCTGCTCCTGC	61.051	60.000	0.00	0.00	40.20	4.85
359	360	1.347050	CATATCCCACTCCTGCTCCTG	59.653	57.143	0.00	0.00	0.00	3.86
360	361	1.221523	TCATATCCCACTCCTGCTCCT	59.778	52.381	0.00	0.00	0.00	3.69
361	362	1.722034	TCATATCCCACTCCTGCTCC	58.278	55.000	0.00	0.00	0.00	4.70
362	363	2.902486	TCATCATATCCCACTCCTGCTC	59.098	50.000	0.00	0.00	0.00	4.26
363	364	2.636893	GTCATCATATCCCACTCCTGCT	59.363	50.000	0.00	0.00	0.00	4.24
364	365	2.636893	AGTCATCATATCCCACTCCTGC	59.363	50.000	0.00	0.00	0.00	4.85
365	366	5.105023	CCATAGTCATCATATCCCACTCCTG	60.105	48.000	0.00	0.00	0.00	3.86
366	367	5.028802	CCATAGTCATCATATCCCACTCCT	58.971	45.833	0.00	0.00	0.00	3.69
367	368	4.780021	ACCATAGTCATCATATCCCACTCC	59.220	45.833	0.00	0.00	0.00	3.85
368	369	5.481824	TCACCATAGTCATCATATCCCACTC	59.518	44.000	0.00	0.00	0.00	3.51
369	370	5.247110	GTCACCATAGTCATCATATCCCACT	59.753	44.000	0.00	0.00	0.00	4.00
370	371	5.247110	AGTCACCATAGTCATCATATCCCAC	59.753	44.000	0.00	0.00	0.00	4.61
371	372	5.406163	AGTCACCATAGTCATCATATCCCA	58.594	41.667	0.00	0.00	0.00	4.37
372	373	6.212388	AGAAGTCACCATAGTCATCATATCCC	59.788	42.308	0.00	0.00	0.00	3.85
373	374	7.238486	AGAAGTCACCATAGTCATCATATCC	57.762	40.000	0.00	0.00	0.00	2.59
374	375	7.965655	CGTAGAAGTCACCATAGTCATCATATC	59.034	40.741	0.00	0.00	0.00	1.63
375	376	7.575909	GCGTAGAAGTCACCATAGTCATCATAT	60.576	40.741	0.00	0.00	0.00	1.78
376	377	6.294010	GCGTAGAAGTCACCATAGTCATCATA	60.294	42.308	0.00	0.00	0.00	2.15
377	378	5.508153	GCGTAGAAGTCACCATAGTCATCAT	60.508	44.000	0.00	0.00	0.00	2.45
378	379	4.202020	GCGTAGAAGTCACCATAGTCATCA	60.202	45.833	0.00	0.00	0.00	3.07
379	380	4.291783	GCGTAGAAGTCACCATAGTCATC	58.708	47.826	0.00	0.00	0.00	2.92
490	495	3.736224	CCTGGATGCTGGCCCAGT	61.736	66.667	13.35	0.00	46.47	4.00
643	659	4.399395	CAGCTGCCTCCCGCTTCA	62.399	66.667	0.00	0.00	38.78	3.02
1433	1466	2.808543	GCCATTGTTGAAGACGAAGAGT	59.191	45.455	0.00	0.00	0.00	3.24
1802	3790	7.385752	CACCTTAGAAAATGTGCATGTCAAAAT	59.614	33.333	0.00	0.00	0.00	1.82
1894	3921	5.279562	TCTTATATTATGGGACGGAGGGA	57.720	43.478	0.00	0.00	0.00	4.20
1895	3922	5.623824	CGTTCTTATATTATGGGACGGAGGG	60.624	48.000	0.00	0.00	0.00	4.30
1896	3923	5.047519	ACGTTCTTATATTATGGGACGGAGG	60.048	44.000	13.18	0.00	0.00	4.30
1897	3924	6.022163	ACGTTCTTATATTATGGGACGGAG	57.978	41.667	13.18	0.00	0.00	4.63
1898	3925	6.409524	AACGTTCTTATATTATGGGACGGA	57.590	37.500	0.00	0.00	0.00	4.69
1899	3926	7.486802	AAAACGTTCTTATATTATGGGACGG	57.513	36.000	0.00	1.76	0.00	4.79
1950	3977	9.976776	TGTACTCCCTCTGTCCTATAATATAAG	57.023	37.037	0.00	0.00	0.00	1.73
1953	3980	9.845214	AAATGTACTCCCTCTGTCCTATAATAT	57.155	33.333	0.00	0.00	0.00	1.28
1954	3981	9.670442	AAAATGTACTCCCTCTGTCCTATAATA	57.330	33.333	0.00	0.00	0.00	0.98
1955	3982	8.568617	AAAATGTACTCCCTCTGTCCTATAAT	57.431	34.615	0.00	0.00	0.00	1.28
1956	3983	7.989947	AAAATGTACTCCCTCTGTCCTATAA	57.010	36.000	0.00	0.00	0.00	0.98
1957	3984	7.402071	ACAAAAATGTACTCCCTCTGTCCTATA	59.598	37.037	0.00	0.00	0.00	1.31
1958	3985	6.215636	ACAAAAATGTACTCCCTCTGTCCTAT	59.784	38.462	0.00	0.00	0.00	2.57
1959	3986	5.546499	ACAAAAATGTACTCCCTCTGTCCTA	59.454	40.000	0.00	0.00	0.00	2.94
1960	3987	4.351111	ACAAAAATGTACTCCCTCTGTCCT	59.649	41.667	0.00	0.00	0.00	3.85
1961	3988	4.652822	ACAAAAATGTACTCCCTCTGTCC	58.347	43.478	0.00	0.00	0.00	4.02
1962	3989	5.998363	AGAACAAAAATGTACTCCCTCTGTC	59.002	40.000	0.00	0.00	0.00	3.51
1963	3990	5.941788	AGAACAAAAATGTACTCCCTCTGT	58.058	37.500	0.00	0.00	0.00	3.41
1964	3991	6.712547	AGAAGAACAAAAATGTACTCCCTCTG	59.287	38.462	0.00	0.00	0.00	3.35
1965	3992	6.842676	AGAAGAACAAAAATGTACTCCCTCT	58.157	36.000	0.00	0.00	0.00	3.69
1966	3993	7.013369	ACAAGAAGAACAAAAATGTACTCCCTC	59.987	37.037	0.00	0.00	0.00	4.30
1967	3994	6.833933	ACAAGAAGAACAAAAATGTACTCCCT	59.166	34.615	0.00	0.00	0.00	4.20
1968	3995	7.039313	ACAAGAAGAACAAAAATGTACTCCC	57.961	36.000	0.00	0.00	0.00	4.30
1969	3996	7.013369	AGGACAAGAAGAACAAAAATGTACTCC	59.987	37.037	0.00	0.00	0.00	3.85
1970	3997	7.857885	CAGGACAAGAAGAACAAAAATGTACTC	59.142	37.037	0.00	0.00	28.26	2.59
1971	3998	7.201821	CCAGGACAAGAAGAACAAAAATGTACT	60.202	37.037	0.00	0.00	30.82	2.73
1972	3999	6.918022	CCAGGACAAGAAGAACAAAAATGTAC	59.082	38.462	0.00	0.00	0.00	2.90
1990	4017	0.535780	CTCAGCTTGCAACCAGGACA	60.536	55.000	0.00	0.00	0.00	4.02
2013	4040	5.957842	TGAACCTATTGCTGGTTTAGTTG	57.042	39.130	0.00	0.00	46.59	3.16
2034	4089	3.885484	ACTGTCGCTCTCACAAATTTG	57.115	42.857	16.67	16.67	0.00	2.32
2052	4107	4.992951	ACTCCGCAGAAATTTTACGTTACT	59.007	37.500	0.00	0.00	0.00	2.24
2135	4194	3.182967	CCAGAGCTTCAAGTAAGTAGCG	58.817	50.000	0.00	0.00	37.06	4.26
2169	4230	3.621268	TGCTTGTACAAGATTATCACGGC	59.379	43.478	34.43	18.38	40.79	5.68
2271	5688	4.385754	GCTTTGGTGGAAATCCTAGATCCT	60.386	45.833	0.44	0.00	36.82	3.24
2368	5791	0.394488	CTCTGACTGAGGCCGGAGTA	60.394	60.000	5.05	0.00	39.08	2.59
2508	6328	6.281405	AGTAGGCTAGTCCAAACAAATATCG	58.719	40.000	0.00	0.00	37.29	2.92

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.