AutoCloner

Multiple sequence alignment - TraesCS3A01G448700

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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	TraesCS3A01G448700	chr3A	100.000	2832	0	0	1	2832	688613393	688610562	0.000000e+00	5230.0
1	TraesCS3A01G448700	chr3A	96.020	1759	29	8	524	2277	264036093	264037815	0.000000e+00	2822.0
2	TraesCS3A01G448700	chr3A	97.333	75	2	0	2758	2832	41614474	41614400	8.230000e-26	128.0
3	TraesCS3A01G448700	chr3A	97.101	69	2	0	2764	2832	510009190	510009122	1.780000e-22	117.0
4	TraesCS3A01G448700	chr4A	97.796	2631	36	5	1	2621	44781632	44784250	0.000000e+00	4518.0
5	TraesCS3A01G448700	chr4A	97.485	2624	36	5	1	2621	44650158	44652754	0.000000e+00	4453.0
6	TraesCS3A01G448700	chr4A	97.424	1475	13	2	1151	2622	44645359	44643907	0.000000e+00	2490.0
7	TraesCS3A01G448700	chr4A	97.925	964	16	1	1	964	44646309	44645350	0.000000e+00	1666.0
8	TraesCS3A01G448700	chr4A	94.946	554	26	2	2069	2621	730679902	730679350	0.000000e+00	867.0
9	TraesCS3A01G448700	chr4A	91.096	146	9	3	2617	2762	567686063	567686204	8.010000e-46	195.0
10	TraesCS3A01G448700	chr4A	91.034	145	9	3	2618	2762	518118115	518118255	2.880000e-45	193.0
11	TraesCS3A01G448700	chr6A	91.781	2044	114	22	1	2016	85351461	85353478	0.000000e+00	2795.0
12	TraesCS3A01G448700	chr6A	93.401	1091	64	7	931	2016	31024602	31025689	0.000000e+00	1609.0
13	TraesCS3A01G448700	chr6A	90.989	455	37	3	2167	2620	85353484	85353935	6.710000e-171	610.0
14	TraesCS3A01G448700	chr6A	91.489	141	9	3	2119	2259	502540954	502541091	1.040000e-44	191.0
15	TraesCS3A01G448700	chr6A	85.393	89	12	1	2530	2618	49499447	49499534	1.080000e-14	91.6
16	TraesCS3A01G448700	chr3D	91.594	2058	103	22	1	2016	50895086	50897115	0.000000e+00	2778.0
17	TraesCS3A01G448700	chr3D	92.373	472	32	3	2152	2622	50897144	50897612	0.000000e+00	669.0
18	TraesCS3A01G448700	chr7B	90.949	2055	126	22	2	2016	471226741	471224707	0.000000e+00	2710.0
19	TraesCS3A01G448700	chr7B	85.624	473	45	9	2154	2625	471189091	471188641	2.550000e-130	475.0
20	TraesCS3A01G448700	chr7B	97.297	74	2	0	2759	2832	640260926	640260853	2.960000e-25	126.0
21	TraesCS3A01G448700	chr1D	94.763	1585	52	13	1042	2622	202978686	202980243	0.000000e+00	2438.0
22	TraesCS3A01G448700	chr1D	91.459	1487	73	15	1	1456	456809867	456811330	0.000000e+00	1993.0
23	TraesCS3A01G448700	chr6B	94.964	1370	49	5	1	1369	708191273	708192623	0.000000e+00	2130.0
24	TraesCS3A01G448700	chr6B	95.270	740	27	6	1661	2397	708205279	708206013	0.000000e+00	1166.0
25	TraesCS3A01G448700	chr2B	87.356	1906	166	34	1	1862	730525808	730527682	0.000000e+00	2115.0
26	TraesCS3A01G448700	chr6D	91.961	821	44	7	1201	2016	28691870	28691067	0.000000e+00	1131.0
27	TraesCS3A01G448700	chr6D	92.128	470	33	3	2152	2620	28691038	28690572	0.000000e+00	660.0
28	TraesCS3A01G448700	chr6D	97.297	74	2	0	2759	2832	467806076	467806003	2.960000e-25	126.0
29	TraesCS3A01G448700	chr1A	90.989	455	37	3	2167	2620	516651982	516651531	6.710000e-171	610.0
30	TraesCS3A01G448700	chr1A	89.510	143	11	1	2620	2762	399234612	399234750	8.060000e-41	178.0
31	TraesCS3A01G448700	chr1A	88.966	145	12	3	2618	2762	218758092	218757952	2.900000e-40	176.0
32	TraesCS3A01G448700	chrUn	79.777	628	87	27	1676	2294	108609209	108609805	1.210000e-113	420.0
33	TraesCS3A01G448700	chr7A	91.034	145	9	3	2618	2762	185196977	185196837	2.880000e-45	193.0
34	TraesCS3A01G448700	chr2A	90.345	145	10	3	2618	2762	369167876	369168016	1.340000e-43	187.0
35	TraesCS3A01G448700	chr2A	90.141	142	10	3	2618	2759	278463768	278463905	6.230000e-42	182.0
36	TraesCS3A01G448700	chr2A	89.583	144	11	3	2618	2761	71550654	71550793	2.240000e-41	180.0
37	TraesCS3A01G448700	chr2A	88.889	144	12	3	2618	2761	71564818	71564957	1.040000e-39	174.0
38	TraesCS3A01G448700	chr2A	96.000	75	3	0	2758	2832	50059157	50059083	3.830000e-24	122.0
39	TraesCS3A01G448700	chr3B	100.000	69	0	0	2764	2832	616891698	616891630	8.230000e-26	128.0
40	TraesCS3A01G448700	chr5D	96.000	75	3	0	2758	2832	72498890	72498964	3.830000e-24	122.0
41	TraesCS3A01G448700	chr5D	97.101	69	2	0	2764	2832	360747440	360747372	1.780000e-22	117.0
42	TraesCS3A01G448700	chr1B	95.946	74	3	0	2759	2832	27238048	27237975	1.380000e-23	121.0
43	TraesCS3A01G448700	chr2D	72.901	262	55	15	1458	1711	360284521	360284268	3.030000e-10	76.8

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	TraesCS3A01G448700	chr3A	688610562	688613393	2831	True	5230.0	5230	100.0000	1	2832	1	chr3A.!!$R3	2831
1	TraesCS3A01G448700	chr3A	264036093	264037815	1722	False	2822.0	2822	96.0200	524	2277	1	chr3A.!!$F1	1753
2	TraesCS3A01G448700	chr4A	44781632	44784250	2618	False	4518.0	4518	97.7960	1	2621	1	chr4A.!!$F2	2620
3	TraesCS3A01G448700	chr4A	44650158	44652754	2596	False	4453.0	4453	97.4850	1	2621	1	chr4A.!!$F1	2620
4	TraesCS3A01G448700	chr4A	44643907	44646309	2402	True	2078.0	2490	97.6745	1	2622	2	chr4A.!!$R2	2621
5	TraesCS3A01G448700	chr4A	730679350	730679902	552	True	867.0	867	94.9460	2069	2621	1	chr4A.!!$R1	552
6	TraesCS3A01G448700	chr6A	85351461	85353935	2474	False	1702.5	2795	91.3850	1	2620	2	chr6A.!!$F4	2619
7	TraesCS3A01G448700	chr6A	31024602	31025689	1087	False	1609.0	1609	93.4010	931	2016	1	chr6A.!!$F1	1085
8	TraesCS3A01G448700	chr3D	50895086	50897612	2526	False	1723.5	2778	91.9835	1	2622	2	chr3D.!!$F1	2621
9	TraesCS3A01G448700	chr7B	471224707	471226741	2034	True	2710.0	2710	90.9490	2	2016	1	chr7B.!!$R2	2014
10	TraesCS3A01G448700	chr1D	202978686	202980243	1557	False	2438.0	2438	94.7630	1042	2622	1	chr1D.!!$F1	1580
11	TraesCS3A01G448700	chr1D	456809867	456811330	1463	False	1993.0	1993	91.4590	1	1456	1	chr1D.!!$F2	1455
12	TraesCS3A01G448700	chr6B	708191273	708192623	1350	False	2130.0	2130	94.9640	1	1369	1	chr6B.!!$F1	1368
13	TraesCS3A01G448700	chr6B	708205279	708206013	734	False	1166.0	1166	95.2700	1661	2397	1	chr6B.!!$F2	736
14	TraesCS3A01G448700	chr2B	730525808	730527682	1874	False	2115.0	2115	87.3560	1	1862	1	chr2B.!!$F1	1861
15	TraesCS3A01G448700	chr6D	28690572	28691870	1298	True	895.5	1131	92.0445	1201	2620	2	chr6D.!!$R2	1419
16	TraesCS3A01G448700	chrUn	108609209	108609805	596	False	420.0	420	79.7770	1676	2294	1	chrUn.!!$F1	618

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
480	486	1.139439	TGCAAGGGATAGGCAGCATA	58.861	50.000	0.0	0.0	32.95	3.14	F
891	949	1.671845	TGTTTCAACTTACACGCACCC	59.328	47.619	0.0	0.0	0.00	4.61	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1375	1500	0.454285	GCACACACACACACACACAC	60.454	55.0	0.00	0.0	0.00	3.82	R
2752	2969	0.167470	CGAACGCGGTCTAAGACTCA	59.833	55.0	23.62	0.0	32.47	3.41	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
191	192	4.990257	TCGACTCGGTATCACTTAAAAGG	58.010	43.478	0.00	0.00	0.00	3.11
357	358	4.657814	AAAGGACCAGGTATGATGTGTT	57.342	40.909	0.00	0.00	0.00	3.32
480	486	1.139439	TGCAAGGGATAGGCAGCATA	58.861	50.000	0.00	0.00	32.95	3.14
885	943	6.858993	TGTTGTCTTTGTGTTTCAACTTACAC	59.141	34.615	0.00	0.00	43.76	2.90
891	949	1.671845	TGTTTCAACTTACACGCACCC	59.328	47.619	0.00	0.00	0.00	4.61
1255	1314	6.882610	ACAAGCTGTCAATTGATAGTGAAA	57.117	33.333	26.86	0.00	35.94	2.69
1364	1489	5.185454	TGACAATTCTCTCTTTGTGTGTGT	58.815	37.500	0.00	0.00	36.25	3.72
1365	1490	5.065090	TGACAATTCTCTCTTTGTGTGTGTG	59.935	40.000	0.00	0.00	36.25	3.82
1366	1491	4.943705	ACAATTCTCTCTTTGTGTGTGTGT	59.056	37.500	0.00	0.00	34.87	3.72
1367	1492	5.163723	ACAATTCTCTCTTTGTGTGTGTGTG	60.164	40.000	0.00	0.00	34.87	3.82
1368	1493	3.610040	TCTCTCTTTGTGTGTGTGTGT	57.390	42.857	0.00	0.00	0.00	3.72
1369	1494	3.261580	TCTCTCTTTGTGTGTGTGTGTG	58.738	45.455	0.00	0.00	0.00	3.82
1370	1495	3.002791	CTCTCTTTGTGTGTGTGTGTGT	58.997	45.455	0.00	0.00	0.00	3.72
1371	1496	2.741517	TCTCTTTGTGTGTGTGTGTGTG	59.258	45.455	0.00	0.00	0.00	3.82
1372	1497	2.483877	CTCTTTGTGTGTGTGTGTGTGT	59.516	45.455	0.00	0.00	0.00	3.72
1373	1498	2.225255	TCTTTGTGTGTGTGTGTGTGTG	59.775	45.455	0.00	0.00	0.00	3.82
1374	1499	1.598882	TTGTGTGTGTGTGTGTGTGT	58.401	45.000	0.00	0.00	0.00	3.72
1375	1500	0.871057	TGTGTGTGTGTGTGTGTGTG	59.129	50.000	0.00	0.00	0.00	3.82
1954	2087	4.751600	CACAAGACTTGCTATGTGTTCTGA	59.248	41.667	15.24	0.00	38.62	3.27
2474	2691	4.347583	TCCAAACAAGATTTGGCATTCCTT	59.652	37.500	12.62	0.00	46.40	3.36
2622	2839	1.398390	CATCCAAACAGAGCGTAAGGC	59.602	52.381	0.00	0.00	44.05	4.35
2623	2840	0.321298	TCCAAACAGAGCGTAAGGCC	60.321	55.000	0.00	0.00	45.17	5.19
2624	2841	0.321653	CCAAACAGAGCGTAAGGCCT	60.322	55.000	0.00	0.00	45.17	5.19
2625	2842	1.079503	CAAACAGAGCGTAAGGCCTC	58.920	55.000	5.23	0.00	45.17	4.70
2626	2843	0.036294	AAACAGAGCGTAAGGCCTCC	60.036	55.000	5.23	0.00	45.17	4.30
2627	2844	0.905337	AACAGAGCGTAAGGCCTCCT	60.905	55.000	5.23	0.00	45.17	3.69
2628	2845	0.905337	ACAGAGCGTAAGGCCTCCTT	60.905	55.000	5.23	3.40	46.63	3.36
2629	2846	0.250513	CAGAGCGTAAGGCCTCCTTT	59.749	55.000	5.23	0.00	41.69	3.11
2630	2847	0.250513	AGAGCGTAAGGCCTCCTTTG	59.749	55.000	5.23	0.00	41.69	2.77
2631	2848	0.249398	GAGCGTAAGGCCTCCTTTGA	59.751	55.000	5.23	0.00	41.69	2.69
2632	2849	0.912486	AGCGTAAGGCCTCCTTTGAT	59.088	50.000	5.23	0.00	41.69	2.57
2633	2850	1.282157	AGCGTAAGGCCTCCTTTGATT	59.718	47.619	5.23	0.00	41.69	2.57
2634	2851	1.671328	GCGTAAGGCCTCCTTTGATTC	59.329	52.381	5.23	0.00	41.69	2.52
2635	2852	2.681097	GCGTAAGGCCTCCTTTGATTCT	60.681	50.000	5.23	0.00	41.69	2.40
2636	2853	2.939103	CGTAAGGCCTCCTTTGATTCTG	59.061	50.000	5.23	0.00	41.69	3.02
2637	2854	3.369471	CGTAAGGCCTCCTTTGATTCTGA	60.369	47.826	5.23	0.00	41.69	3.27
2638	2855	2.797177	AGGCCTCCTTTGATTCTGAC	57.203	50.000	0.00	0.00	0.00	3.51
2639	2856	1.988107	AGGCCTCCTTTGATTCTGACA	59.012	47.619	0.00	0.00	0.00	3.58
2640	2857	2.087646	GGCCTCCTTTGATTCTGACAC	58.912	52.381	0.00	0.00	0.00	3.67
2641	2858	2.553028	GGCCTCCTTTGATTCTGACACA	60.553	50.000	0.00	0.00	0.00	3.72
2642	2859	3.350833	GCCTCCTTTGATTCTGACACAT	58.649	45.455	0.00	0.00	0.00	3.21
2643	2860	3.128242	GCCTCCTTTGATTCTGACACATG	59.872	47.826	0.00	0.00	0.00	3.21
2644	2861	4.582869	CCTCCTTTGATTCTGACACATGA	58.417	43.478	0.00	0.00	0.00	3.07
2645	2862	5.191426	CCTCCTTTGATTCTGACACATGAT	58.809	41.667	0.00	0.00	0.00	2.45
2646	2863	6.351711	CCTCCTTTGATTCTGACACATGATA	58.648	40.000	0.00	0.00	0.00	2.15
2647	2864	6.825213	CCTCCTTTGATTCTGACACATGATAA	59.175	38.462	0.00	0.00	0.00	1.75
2648	2865	7.337689	CCTCCTTTGATTCTGACACATGATAAA	59.662	37.037	0.00	0.00	0.00	1.40
2649	2866	8.634335	TCCTTTGATTCTGACACATGATAAAA	57.366	30.769	0.00	0.00	0.00	1.52
2650	2867	9.076781	TCCTTTGATTCTGACACATGATAAAAA	57.923	29.630	0.00	0.00	0.00	1.94
2651	2868	9.865321	CCTTTGATTCTGACACATGATAAAAAT	57.135	29.630	0.00	0.00	0.00	1.82
2706	2923	8.755696	GAGATGACATGTATCTCAATTCCTAC	57.244	38.462	24.95	3.52	46.22	3.18
2707	2924	7.374272	AGATGACATGTATCTCAATTCCTACG	58.626	38.462	0.00	0.00	29.05	3.51
2708	2925	5.842907	TGACATGTATCTCAATTCCTACGG	58.157	41.667	0.00	0.00	0.00	4.02
2709	2926	5.596772	TGACATGTATCTCAATTCCTACGGA	59.403	40.000	0.00	0.00	0.00	4.69
2710	2927	6.090483	ACATGTATCTCAATTCCTACGGAG	57.910	41.667	0.00	0.00	31.21	4.63
2711	2928	5.833667	ACATGTATCTCAATTCCTACGGAGA	59.166	40.000	0.00	0.00	40.37	3.71
2712	2929	6.323996	ACATGTATCTCAATTCCTACGGAGAA	59.676	38.462	0.00	0.00	39.60	2.87
2713	2930	6.785337	TGTATCTCAATTCCTACGGAGAAA	57.215	37.500	0.00	0.00	39.60	2.52
2714	2931	6.806751	TGTATCTCAATTCCTACGGAGAAAG	58.193	40.000	0.00	0.00	39.60	2.62
2715	2932	6.605995	TGTATCTCAATTCCTACGGAGAAAGA	59.394	38.462	0.00	0.00	39.60	2.52
2716	2933	5.584253	TCTCAATTCCTACGGAGAAAGAG	57.416	43.478	0.00	3.89	33.73	2.85
2717	2934	5.262009	TCTCAATTCCTACGGAGAAAGAGA	58.738	41.667	0.00	6.08	36.73	3.10
2718	2935	5.894393	TCTCAATTCCTACGGAGAAAGAGAT	59.106	40.000	0.00	0.00	35.41	2.75
2719	2936	5.907207	TCAATTCCTACGGAGAAAGAGATG	58.093	41.667	0.00	0.00	31.21	2.90
2720	2937	5.422331	TCAATTCCTACGGAGAAAGAGATGT	59.578	40.000	0.00	0.00	31.21	3.06
2721	2938	4.985538	TTCCTACGGAGAAAGAGATGTC	57.014	45.455	0.00	0.00	31.21	3.06
2722	2939	3.964411	TCCTACGGAGAAAGAGATGTCA	58.036	45.455	0.00	0.00	0.00	3.58
2723	2940	4.537751	TCCTACGGAGAAAGAGATGTCAT	58.462	43.478	0.00	0.00	0.00	3.06
2724	2941	4.956700	TCCTACGGAGAAAGAGATGTCATT	59.043	41.667	0.00	0.00	0.00	2.57
2725	2942	5.422331	TCCTACGGAGAAAGAGATGTCATTT	59.578	40.000	0.00	0.00	0.00	2.32
2726	2943	5.521735	CCTACGGAGAAAGAGATGTCATTTG	59.478	44.000	0.00	0.00	0.00	2.32
2727	2944	5.152623	ACGGAGAAAGAGATGTCATTTGA	57.847	39.130	0.00	0.00	0.00	2.69
2728	2945	5.738909	ACGGAGAAAGAGATGTCATTTGAT	58.261	37.500	0.00	0.00	0.00	2.57
2729	2946	5.583854	ACGGAGAAAGAGATGTCATTTGATG	59.416	40.000	0.00	0.00	0.00	3.07
2730	2947	5.503683	CGGAGAAAGAGATGTCATTTGATGC	60.504	44.000	0.00	0.00	0.00	3.91
2731	2948	5.356190	GGAGAAAGAGATGTCATTTGATGCA	59.644	40.000	0.00	0.00	0.00	3.96
2732	2949	6.039493	GGAGAAAGAGATGTCATTTGATGCAT	59.961	38.462	0.00	0.00	32.43	3.96
2733	2950	7.228108	GGAGAAAGAGATGTCATTTGATGCATA	59.772	37.037	0.00	0.00	30.80	3.14
2734	2951	8.155821	AGAAAGAGATGTCATTTGATGCATAG	57.844	34.615	0.00	0.00	30.80	2.23
2735	2952	6.879276	AAGAGATGTCATTTGATGCATAGG	57.121	37.500	0.00	0.00	30.80	2.57
2736	2953	6.183810	AGAGATGTCATTTGATGCATAGGA	57.816	37.500	0.00	0.00	30.80	2.94
2737	2954	6.780901	AGAGATGTCATTTGATGCATAGGAT	58.219	36.000	0.00	0.00	30.80	3.24
2738	2955	7.914859	AGAGATGTCATTTGATGCATAGGATA	58.085	34.615	0.00	0.00	30.80	2.59
2739	2956	8.041919	AGAGATGTCATTTGATGCATAGGATAG	58.958	37.037	0.00	0.00	30.80	2.08
2740	2957	7.110810	AGATGTCATTTGATGCATAGGATAGG	58.889	38.462	0.00	0.00	30.80	2.57
2741	2958	6.438186	TGTCATTTGATGCATAGGATAGGA	57.562	37.500	0.00	0.00	0.00	2.94
2742	2959	6.840527	TGTCATTTGATGCATAGGATAGGAA	58.159	36.000	0.00	0.00	0.00	3.36
2743	2960	7.464273	TGTCATTTGATGCATAGGATAGGAAT	58.536	34.615	0.00	0.00	0.00	3.01
2744	2961	7.946219	TGTCATTTGATGCATAGGATAGGAATT	59.054	33.333	0.00	0.00	0.00	2.17
2745	2962	8.800332	GTCATTTGATGCATAGGATAGGAATTT	58.200	33.333	0.00	0.00	0.00	1.82
2746	2963	9.370930	TCATTTGATGCATAGGATAGGAATTTT	57.629	29.630	0.00	0.00	0.00	1.82
2747	2964	9.991906	CATTTGATGCATAGGATAGGAATTTTT	57.008	29.630	0.00	0.00	0.00	1.94
2766	2983	5.607119	TTTTTCATTGAGTCTTAGACCGC	57.393	39.130	8.96	2.41	32.18	5.68
2767	2984	2.561733	TCATTGAGTCTTAGACCGCG	57.438	50.000	8.96	0.00	32.18	6.46
2768	2985	1.816835	TCATTGAGTCTTAGACCGCGT	59.183	47.619	8.96	0.00	32.18	6.01
2769	2986	2.230508	TCATTGAGTCTTAGACCGCGTT	59.769	45.455	8.96	0.00	32.18	4.84
2770	2987	2.342910	TTGAGTCTTAGACCGCGTTC	57.657	50.000	8.96	0.00	32.18	3.95
2771	2988	0.167470	TGAGTCTTAGACCGCGTTCG	59.833	55.000	8.96	0.00	32.18	3.95
2781	2998	4.856607	CGCGTTCGGCTCCTCTCC	62.857	72.222	0.00	0.00	40.44	3.71
2783	3000	4.856607	CGTTCGGCTCCTCTCCGC	62.857	72.222	0.00	0.00	46.05	5.54
2784	3001	3.453679	GTTCGGCTCCTCTCCGCT	61.454	66.667	0.00	0.00	46.05	5.52
2785	3002	3.141488	TTCGGCTCCTCTCCGCTC	61.141	66.667	0.00	0.00	46.05	5.03
2788	3005	4.851214	GGCTCCTCTCCGCTCCCT	62.851	72.222	0.00	0.00	0.00	4.20
2789	3006	3.223589	GCTCCTCTCCGCTCCCTC	61.224	72.222	0.00	0.00	0.00	4.30
2790	3007	2.520741	CTCCTCTCCGCTCCCTCC	60.521	72.222	0.00	0.00	0.00	4.30
2791	3008	3.347590	TCCTCTCCGCTCCCTCCA	61.348	66.667	0.00	0.00	0.00	3.86
2792	3009	3.151022	CCTCTCCGCTCCCTCCAC	61.151	72.222	0.00	0.00	0.00	4.02
2793	3010	2.043450	CTCTCCGCTCCCTCCACT	60.043	66.667	0.00	0.00	0.00	4.00
2794	3011	2.043852	TCTCCGCTCCCTCCACTC	60.044	66.667	0.00	0.00	0.00	3.51
2795	3012	3.151022	CTCCGCTCCCTCCACTCC	61.151	72.222	0.00	0.00	0.00	3.85
2799	3016	3.844090	GCTCCCTCCACTCCGCTC	61.844	72.222	0.00	0.00	0.00	5.03
2800	3017	3.151022	CTCCCTCCACTCCGCTCC	61.151	72.222	0.00	0.00	0.00	4.70
2818	3035	2.516460	GGAGCGGACGAGCCTCTA	60.516	66.667	0.00	0.00	38.01	2.43
2819	3036	2.548295	GGAGCGGACGAGCCTCTAG	61.548	68.421	0.00	0.00	38.01	2.43
2820	3037	3.189010	GAGCGGACGAGCCTCTAGC	62.189	68.421	0.00	0.00	44.25	3.42

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
191	192	3.482436	TGTTGTTGACTTGATACCCACC	58.518	45.455	0.00	0.00	0.00	4.61
357	358	5.623169	TGCATCTTATTCAGCACCATATGA	58.377	37.500	3.65	0.00	31.05	2.15
480	486	4.201657	TCGAGCAACAAATCATCCATCAT	58.798	39.130	0.00	0.00	0.00	2.45
885	943	2.095768	CACAAAGACAACATAGGGTGCG	60.096	50.000	0.00	0.00	0.00	5.34
1255	1314	4.495679	CGCGACATATTTAAGCCACACATT	60.496	41.667	0.00	0.00	0.00	2.71
1364	1489	0.871057	CACACACACACACACACACA	59.129	50.000	0.00	0.00	0.00	3.72
1365	1490	0.871722	ACACACACACACACACACAC	59.128	50.000	0.00	0.00	0.00	3.82
1366	1491	0.871057	CACACACACACACACACACA	59.129	50.000	0.00	0.00	0.00	3.72
1367	1492	0.871722	ACACACACACACACACACAC	59.128	50.000	0.00	0.00	0.00	3.82
1368	1493	0.871057	CACACACACACACACACACA	59.129	50.000	0.00	0.00	0.00	3.72
1369	1494	0.871722	ACACACACACACACACACAC	59.128	50.000	0.00	0.00	0.00	3.82
1370	1495	0.871057	CACACACACACACACACACA	59.129	50.000	0.00	0.00	0.00	3.72
1371	1496	0.871722	ACACACACACACACACACAC	59.128	50.000	0.00	0.00	0.00	3.82
1372	1497	0.871057	CACACACACACACACACACA	59.129	50.000	0.00	0.00	0.00	3.72
1373	1498	0.871722	ACACACACACACACACACAC	59.128	50.000	0.00	0.00	0.00	3.82
1374	1499	0.871057	CACACACACACACACACACA	59.129	50.000	0.00	0.00	0.00	3.72
1375	1500	0.454285	GCACACACACACACACACAC	60.454	55.000	0.00	0.00	0.00	3.82
1954	2087	9.851686	ACATATTATAACATGTCTCACACCATT	57.148	29.630	3.47	0.00	29.34	3.16
2622	2839	4.582869	TCATGTGTCAGAATCAAAGGAGG	58.417	43.478	0.00	0.00	0.00	4.30
2623	2840	7.854557	TTATCATGTGTCAGAATCAAAGGAG	57.145	36.000	0.00	0.00	0.00	3.69
2624	2841	8.634335	TTTTATCATGTGTCAGAATCAAAGGA	57.366	30.769	0.00	0.00	0.00	3.36
2625	2842	9.865321	ATTTTTATCATGTGTCAGAATCAAAGG	57.135	29.630	0.00	0.00	0.00	3.11
2681	2898	7.540400	CGTAGGAATTGAGATACATGTCATCTC	59.460	40.741	24.04	24.04	45.76	2.75
2682	2899	7.374272	CGTAGGAATTGAGATACATGTCATCT	58.626	38.462	0.00	9.42	35.43	2.90
2683	2900	7.573916	CGTAGGAATTGAGATACATGTCATC	57.426	40.000	0.00	4.47	29.66	2.92
2703	2920	6.333416	TCAAATGACATCTCTTTCTCCGTAG	58.667	40.000	0.00	0.00	0.00	3.51
2704	2921	6.280855	TCAAATGACATCTCTTTCTCCGTA	57.719	37.500	0.00	0.00	0.00	4.02
2705	2922	5.152623	TCAAATGACATCTCTTTCTCCGT	57.847	39.130	0.00	0.00	0.00	4.69
2706	2923	5.503683	GCATCAAATGACATCTCTTTCTCCG	60.504	44.000	0.00	0.00	0.00	4.63
2707	2924	5.356190	TGCATCAAATGACATCTCTTTCTCC	59.644	40.000	0.00	0.00	0.00	3.71
2708	2925	6.432607	TGCATCAAATGACATCTCTTTCTC	57.567	37.500	0.00	0.00	0.00	2.87
2709	2926	7.228906	CCTATGCATCAAATGACATCTCTTTCT	59.771	37.037	0.19	0.00	32.25	2.52
2710	2927	7.228108	TCCTATGCATCAAATGACATCTCTTTC	59.772	37.037	0.19	0.00	32.25	2.62
2711	2928	7.058525	TCCTATGCATCAAATGACATCTCTTT	58.941	34.615	0.19	0.00	32.25	2.52
2712	2929	6.598503	TCCTATGCATCAAATGACATCTCTT	58.401	36.000	0.19	0.00	32.25	2.85
2713	2930	6.183810	TCCTATGCATCAAATGACATCTCT	57.816	37.500	0.19	0.00	32.25	3.10
2714	2931	7.280428	CCTATCCTATGCATCAAATGACATCTC	59.720	40.741	0.19	0.00	32.25	2.75
2715	2932	7.037802	TCCTATCCTATGCATCAAATGACATCT	60.038	37.037	0.19	0.00	32.25	2.90
2716	2933	7.108194	TCCTATCCTATGCATCAAATGACATC	58.892	38.462	0.19	0.00	32.25	3.06
2717	2934	7.024345	TCCTATCCTATGCATCAAATGACAT	57.976	36.000	0.19	0.00	33.67	3.06
2718	2935	6.438186	TCCTATCCTATGCATCAAATGACA	57.562	37.500	0.19	0.00	0.00	3.58
2719	2936	7.934855	ATTCCTATCCTATGCATCAAATGAC	57.065	36.000	0.19	0.00	0.00	3.06
2720	2937	8.945195	AAATTCCTATCCTATGCATCAAATGA	57.055	30.769	0.19	0.00	0.00	2.57
2721	2938	9.991906	AAAAATTCCTATCCTATGCATCAAATG	57.008	29.630	0.19	0.00	0.00	2.32
2744	2961	4.151689	CGCGGTCTAAGACTCAATGAAAAA	59.848	41.667	0.00	0.00	32.47	1.94
2745	2962	3.678072	CGCGGTCTAAGACTCAATGAAAA	59.322	43.478	0.00	0.00	32.47	2.29
2746	2963	3.250744	CGCGGTCTAAGACTCAATGAAA	58.749	45.455	0.00	0.00	32.47	2.69
2747	2964	2.230508	ACGCGGTCTAAGACTCAATGAA	59.769	45.455	12.47	0.00	32.47	2.57
2748	2965	1.816835	ACGCGGTCTAAGACTCAATGA	59.183	47.619	12.47	0.00	32.47	2.57
2749	2966	2.279582	ACGCGGTCTAAGACTCAATG	57.720	50.000	12.47	0.00	32.47	2.82
2750	2967	2.731341	CGAACGCGGTCTAAGACTCAAT	60.731	50.000	23.62	0.00	32.47	2.57
2751	2968	1.400629	CGAACGCGGTCTAAGACTCAA	60.401	52.381	23.62	0.00	32.47	3.02
2752	2969	0.167470	CGAACGCGGTCTAAGACTCA	59.833	55.000	23.62	0.00	32.47	3.41
2753	2970	2.927437	CGAACGCGGTCTAAGACTC	58.073	57.895	23.62	0.00	32.47	3.36
2764	2981	4.856607	GGAGAGGAGCCGAACGCG	62.857	72.222	3.53	3.53	44.76	6.01
2771	2988	4.851214	AGGGAGCGGAGAGGAGCC	62.851	72.222	0.00	0.00	0.00	4.70
2772	2989	3.223589	GAGGGAGCGGAGAGGAGC	61.224	72.222	0.00	0.00	0.00	4.70
2773	2990	2.520741	GGAGGGAGCGGAGAGGAG	60.521	72.222	0.00	0.00	0.00	3.69
2774	2991	3.347590	TGGAGGGAGCGGAGAGGA	61.348	66.667	0.00	0.00	0.00	3.71
2775	2992	3.151022	GTGGAGGGAGCGGAGAGG	61.151	72.222	0.00	0.00	0.00	3.69
2776	2993	2.043450	AGTGGAGGGAGCGGAGAG	60.043	66.667	0.00	0.00	0.00	3.20
2777	2994	2.043852	GAGTGGAGGGAGCGGAGA	60.044	66.667	0.00	0.00	0.00	3.71
2778	2995	3.151022	GGAGTGGAGGGAGCGGAG	61.151	72.222	0.00	0.00	0.00	4.63
2782	2999	3.844090	GAGCGGAGTGGAGGGAGC	61.844	72.222	0.00	0.00	0.00	4.70
2783	3000	3.151022	GGAGCGGAGTGGAGGGAG	61.151	72.222	0.00	0.00	0.00	4.30
2801	3018	2.516460	TAGAGGCTCGTCCGCTCC	60.516	66.667	9.22	0.00	41.47	4.70
2802	3019	3.027292	CTAGAGGCTCGTCCGCTC	58.973	66.667	9.22	0.00	41.47	5.03

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.