AutoCloner

Multiple sequence alignment - TraesCS2D01G601800

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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	TraesCS2D01G601800	chr2D	100.000	5518	0	0	1	5518	651824192	651818675	0.000000e+00	10190.0
1	TraesCS2D01G601800	chr2D	81.638	1209	170	24	1044	2243	651782556	651781391	0.000000e+00	955.0
2	TraesCS2D01G601800	chr2D	83.710	884	128	12	1094	1970	651785539	651784665	0.000000e+00	821.0
3	TraesCS2D01G601800	chr2D	82.362	669	97	16	30	692	651742734	651742081	3.730000e-156	562.0
4	TraesCS2D01G601800	chr2D	83.062	614	58	20	4409	4987	651741066	651740464	2.950000e-142	516.0
5	TraesCS2D01G601800	chr2D	80.311	579	95	16	2	575	651778109	651777545	2.380000e-113	420.0
6	TraesCS2D01G601800	chr2D	80.138	579	93	15	2	575	651769298	651768737	3.980000e-111	412.0
7	TraesCS2D01G601800	chr2D	92.857	182	13	0	2239	2420	651781267	651781086	1.180000e-66	265.0
8	TraesCS2D01G601800	chrUn	96.643	1698	44	6	2239	3933	31422745	31424432	0.000000e+00	2808.0
9	TraesCS2D01G601800	chrUn	95.691	1439	36	11	4095	5518	31383827	31385254	0.000000e+00	2290.0
10	TraesCS2D01G601800	chrUn	95.549	1438	38	11	4095	5518	31424762	31426187	0.000000e+00	2278.0
11	TraesCS2D01G601800	chrUn	94.752	1410	61	8	835	2243	31421180	31422577	0.000000e+00	2182.0
12	TraesCS2D01G601800	chrUn	94.340	1325	48	14	2620	3933	31382193	31383501	0.000000e+00	2006.0
13	TraesCS2D01G601800	chrUn	91.343	1467	90	13	11	1473	31378869	31380302	0.000000e+00	1971.0
14	TraesCS2D01G601800	chrUn	93.844	796	47	2	1	795	31420396	31421190	0.000000e+00	1197.0
15	TraesCS2D01G601800	chrUn	83.014	1201	184	16	1044	2235	31412887	31414076	0.000000e+00	1070.0
16	TraesCS2D01G601800	chrUn	82.689	1138	158	26	1114	2243	31435697	31436803	0.000000e+00	974.0
17	TraesCS2D01G601800	chrUn	85.991	928	64	28	4095	4987	269891569	269892465	0.000000e+00	933.0
18	TraesCS2D01G601800	chrUn	82.974	881	136	10	1094	1968	31432892	31433764	0.000000e+00	784.0
19	TraesCS2D01G601800	chrUn	94.770	478	23	1	1466	1943	31380702	31381177	0.000000e+00	743.0
20	TraesCS2D01G601800	chrUn	95.312	384	16	2	2239	2622	31381849	31382230	4.730000e-170	608.0
21	TraesCS2D01G601800	chrUn	79.730	666	104	20	30	692	269890188	269890825	2.340000e-123	453.0
22	TraesCS2D01G601800	chrUn	95.261	211	9	1	1941	2151	31381345	31381554	3.190000e-87	333.0
23	TraesCS2D01G601800	chrUn	98.810	168	1	1	3932	4098	31424546	31424713	1.160000e-76	298.0
24	TraesCS2D01G601800	chrUn	95.210	167	8	0	3932	4098	31383612	31383778	1.180000e-66	265.0
25	TraesCS2D01G601800	chrUn	91.620	179	15	0	2239	2417	31436938	31437116	1.190000e-61	248.0
26	TraesCS2D01G601800	chrUn	91.061	179	16	0	2239	2417	31414208	31414386	5.520000e-60	243.0
27	TraesCS2D01G601800	chrUn	93.671	79	5	0	2165	2243	31381606	31381684	9.710000e-23	119.0
28	TraesCS2D01G601800	chr2B	90.369	1952	145	20	1	1943	781926685	781928602	0.000000e+00	2523.0
29	TraesCS2D01G601800	chr2B	94.440	1133	50	8	2808	3933	781929728	781930854	0.000000e+00	1731.0
30	TraesCS2D01G601800	chr2B	89.402	1104	62	27	4113	5169	781931432	781932527	0.000000e+00	1339.0
31	TraesCS2D01G601800	chr2B	84.375	704	98	8	1	697	781667126	781666428	0.000000e+00	680.0
32	TraesCS2D01G601800	chr2B	85.474	654	87	8	1	652	781693415	781692768	0.000000e+00	675.0
33	TraesCS2D01G601800	chr2B	84.661	678	79	12	38	698	781679782	781679113	0.000000e+00	652.0
34	TraesCS2D01G601800	chr2B	96.727	275	9	0	2239	2513	781929309	781929583	5.040000e-125	459.0
35	TraesCS2D01G601800	chr2B	91.469	211	15	1	1941	2151	781928771	781928978	2.520000e-73	287.0
36	TraesCS2D01G601800	chr2B	95.714	70	3	0	2703	2772	781929654	781929723	4.520000e-21	113.0
37	TraesCS2D01G601800	chr2B	94.737	57	2	1	2620	2675	781929597	781929653	2.740000e-13	87.9
38	TraesCS2D01G601800	chr2A	89.248	958	42	32	4095	5013	48433786	48432851	0.000000e+00	1142.0
39	TraesCS2D01G601800	chr5D	80.296	203	33	3	1343	1545	32416335	32416530	4.450000e-31	147.0
40	TraesCS2D01G601800	chr7D	76.316	190	32	7	1003	1180	44623617	44623429	7.610000e-14	89.8
41	TraesCS2D01G601800	chr5B	100.000	34	0	0	2198	2231	292746814	292746781	4.610000e-06	63.9

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	TraesCS2D01G601800	chr2D	651818675	651824192	5517	True	10190.000000	10190	100.000000	1	5518	1	chr2D.!!$R2	5517
1	TraesCS2D01G601800	chr2D	651777545	651785539	7994	True	615.250000	955	84.629000	2	2420	4	chr2D.!!$R4	2418
2	TraesCS2D01G601800	chr2D	651740464	651742734	2270	True	539.000000	562	82.712000	30	4987	2	chr2D.!!$R3	4957
3	TraesCS2D01G601800	chr2D	651768737	651769298	561	True	412.000000	412	80.138000	2	575	1	chr2D.!!$R1	573
4	TraesCS2D01G601800	chrUn	31420396	31426187	5791	False	1752.600000	2808	95.919600	1	5518	5	chrUn.!!$F3	5517
5	TraesCS2D01G601800	chrUn	31378869	31385254	6385	False	1041.875000	2290	94.449750	11	5518	8	chrUn.!!$F1	5507
6	TraesCS2D01G601800	chrUn	269890188	269892465	2277	False	693.000000	933	82.860500	30	4987	2	chrUn.!!$F5	4957
7	TraesCS2D01G601800	chrUn	31432892	31437116	4224	False	668.666667	974	85.761000	1094	2417	3	chrUn.!!$F4	1323
8	TraesCS2D01G601800	chrUn	31412887	31414386	1499	False	656.500000	1070	87.037500	1044	2417	2	chrUn.!!$F2	1373
9	TraesCS2D01G601800	chr2B	781926685	781932527	5842	False	934.271429	2523	93.265429	1	5169	7	chr2B.!!$F1	5168
10	TraesCS2D01G601800	chr2B	781666428	781667126	698	True	680.000000	680	84.375000	1	697	1	chr2B.!!$R1	696
11	TraesCS2D01G601800	chr2B	781692768	781693415	647	True	675.000000	675	85.474000	1	652	1	chr2B.!!$R3	651
12	TraesCS2D01G601800	chr2B	781679113	781679782	669	True	652.000000	652	84.661000	38	698	1	chr2B.!!$R2	660
13	TraesCS2D01G601800	chr2A	48432851	48433786	935	True	1142.000000	1142	89.248000	4095	5013	1	chr2A.!!$R1	918

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
97	1972	0.269173	ATCGATCCCTCCTTCCCCTT	59.731	55.000	0.0	0.0	0.00	3.95	F
821	2703	0.871057	TGTGTGTGTGTGTGTGTGTG	59.129	50.000	0.0	0.0	0.00	3.82	F
835	2717	0.871057	TGTGTGTGTGTGTGTGTGTG	59.129	50.000	0.0	0.0	0.00	3.82	F
843	2725	0.871057	TGTGTGTGTGTGTGTGTGTG	59.129	50.000	0.0	0.0	0.00	3.82	F
944	2826	1.004277	GTGGTGGTGCATCTTTAGGGA	59.996	52.381	0.0	0.0	0.00	4.20	F
2686	7041	0.806241	GTGTGAACCACGGTTGTGTT	59.194	50.000	6.1	0.0	44.92	3.32	F
2687	7042	1.088306	TGTGAACCACGGTTGTGTTC	58.912	50.000	6.1	7.6	44.92	3.18	F
4505	10519	0.105593	GCTCACATGCTAGGCTGCTA	59.894	55.000	0.0	0.0	0.00	3.49	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1334	3778	0.322546	GGGTTGTGATCACTGACCCC	60.323	60.000	36.33	28.59	44.86	4.95	R
2523	6820	0.613260	TTGACCTCCCCTTGATCACG	59.387	55.000	0.00	0.00	0.00	4.35	R
2686	7041	4.777896	AGTTGCCCTGAACATAGAAGTAGA	59.222	41.667	0.00	0.00	0.00	2.59	R
2687	7042	5.091261	AGTTGCCCTGAACATAGAAGTAG	57.909	43.478	0.00	0.00	0.00	2.57	R
2690	7045	5.698545	GCTATAGTTGCCCTGAACATAGAAG	59.301	44.000	0.84	0.00	0.00	2.85	R
4493	10507	1.690893	CAGATTCCTAGCAGCCTAGCA	59.309	52.381	0.00	0.00	39.81	3.49	R
4510	10524	3.434167	GGCCTTGATTGATTCCTAGCAGA	60.434	47.826	0.00	0.00	0.00	4.26	R
5340	11650	1.446792	CGGTGCTACAGGAGTGCAG	60.447	63.158	0.00	0.00	34.22	4.41	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
62	1937	1.227823	CCATCGCCGCCTCCAATTA	60.228	57.895	0.00	0.00	0.00	1.40
97	1972	0.269173	ATCGATCCCTCCTTCCCCTT	59.731	55.000	0.00	0.00	0.00	3.95
257	2135	2.594592	GTTGCACCCGCCACTCTT	60.595	61.111	0.00	0.00	37.32	2.85
340	2221	5.018149	TGATTTGTGATGGTGATGAATGGT	58.982	37.500	0.00	0.00	0.00	3.55
360	2241	4.386350	TGGTTTGTATGATTGTGACGTACG	59.614	41.667	15.01	15.01	33.88	3.67
430	2311	6.448207	TGCATTTTCGGATGAAATGTGATA	57.552	33.333	13.71	1.03	43.32	2.15
494	2375	6.358974	AAAGGGAAGAGAGAAGAGAGAAAG	57.641	41.667	0.00	0.00	0.00	2.62
595	2476	4.754372	ACATCGTATGCCATTGCTAATG	57.246	40.909	0.00	0.00	38.71	1.90
794	2676	4.277423	GGCTAAAAACCACTGTGTGTGTAT	59.723	41.667	7.08	0.00	44.81	2.29
796	2678	6.150474	GGCTAAAAACCACTGTGTGTGTATAT	59.850	38.462	7.08	0.00	44.81	0.86
797	2679	7.334921	GGCTAAAAACCACTGTGTGTGTATATA	59.665	37.037	7.08	0.00	44.81	0.86
798	2680	8.889717	GCTAAAAACCACTGTGTGTGTATATAT	58.110	33.333	7.08	0.00	44.81	0.86
804	2686	9.899661	AACCACTGTGTGTGTATATATTTATGT	57.100	29.630	7.08	0.00	44.81	2.29
805	2687	9.325198	ACCACTGTGTGTGTATATATTTATGTG	57.675	33.333	7.08	0.00	44.81	3.21
806	2688	9.325198	CCACTGTGTGTGTATATATTTATGTGT	57.675	33.333	7.08	0.00	44.81	3.72
808	2690	9.884636	ACTGTGTGTGTATATATTTATGTGTGT	57.115	29.630	0.00	0.00	0.00	3.72
812	2694	9.660180	TGTGTGTATATATTTATGTGTGTGTGT	57.340	29.630	0.00	0.00	0.00	3.72
813	2695	9.914923	GTGTGTATATATTTATGTGTGTGTGTG	57.085	33.333	0.00	0.00	0.00	3.82
814	2696	9.660180	TGTGTATATATTTATGTGTGTGTGTGT	57.340	29.630	0.00	0.00	0.00	3.72
815	2697	9.914923	GTGTATATATTTATGTGTGTGTGTGTG	57.085	33.333	0.00	0.00	0.00	3.82
817	2699	9.914923	GTATATATTTATGTGTGTGTGTGTGTG	57.085	33.333	0.00	0.00	0.00	3.82
819	2701	4.348198	TTTATGTGTGTGTGTGTGTGTG	57.652	40.909	0.00	0.00	0.00	3.82
821	2703	0.871057	TGTGTGTGTGTGTGTGTGTG	59.129	50.000	0.00	0.00	0.00	3.82
822	2704	0.871722	GTGTGTGTGTGTGTGTGTGT	59.128	50.000	0.00	0.00	0.00	3.72
824	2706	0.871722	GTGTGTGTGTGTGTGTGTGT	59.128	50.000	0.00	0.00	0.00	3.72
825	2707	0.871057	TGTGTGTGTGTGTGTGTGTG	59.129	50.000	0.00	0.00	0.00	3.82
826	2708	0.871722	GTGTGTGTGTGTGTGTGTGT	59.128	50.000	0.00	0.00	0.00	3.72
827	2709	0.871057	TGTGTGTGTGTGTGTGTGTG	59.129	50.000	0.00	0.00	0.00	3.82
828	2710	0.871722	GTGTGTGTGTGTGTGTGTGT	59.128	50.000	0.00	0.00	0.00	3.72
829	2711	0.871057	TGTGTGTGTGTGTGTGTGTG	59.129	50.000	0.00	0.00	0.00	3.82
830	2712	0.871722	GTGTGTGTGTGTGTGTGTGT	59.128	50.000	0.00	0.00	0.00	3.72
831	2713	0.871057	TGTGTGTGTGTGTGTGTGTG	59.129	50.000	0.00	0.00	0.00	3.82
832	2714	0.871722	GTGTGTGTGTGTGTGTGTGT	59.128	50.000	0.00	0.00	0.00	3.72
834	2716	0.871722	GTGTGTGTGTGTGTGTGTGT	59.128	50.000	0.00	0.00	0.00	3.72
835	2717	0.871057	TGTGTGTGTGTGTGTGTGTG	59.129	50.000	0.00	0.00	0.00	3.82
836	2718	0.871722	GTGTGTGTGTGTGTGTGTGT	59.128	50.000	0.00	0.00	0.00	3.72
840	2722	0.871722	GTGTGTGTGTGTGTGTGTGT	59.128	50.000	0.00	0.00	0.00	3.72
841	2723	0.871057	TGTGTGTGTGTGTGTGTGTG	59.129	50.000	0.00	0.00	0.00	3.82
842	2724	0.871722	GTGTGTGTGTGTGTGTGTGT	59.128	50.000	0.00	0.00	0.00	3.72
843	2725	0.871057	TGTGTGTGTGTGTGTGTGTG	59.129	50.000	0.00	0.00	0.00	3.82
940	2822	2.890311	CCTTTGTGGTGGTGCATCTTTA	59.110	45.455	0.00	0.00	0.00	1.85
941	2823	3.057315	CCTTTGTGGTGGTGCATCTTTAG	60.057	47.826	0.00	0.00	0.00	1.85
942	2824	2.198827	TGTGGTGGTGCATCTTTAGG	57.801	50.000	0.00	0.00	0.00	2.69
943	2825	1.271871	TGTGGTGGTGCATCTTTAGGG	60.272	52.381	0.00	0.00	0.00	3.53
944	2826	1.004277	GTGGTGGTGCATCTTTAGGGA	59.996	52.381	0.00	0.00	0.00	4.20
947	2829	2.689983	GGTGGTGCATCTTTAGGGATTG	59.310	50.000	0.00	0.00	0.00	2.67
949	2831	4.210331	GTGGTGCATCTTTAGGGATTGAT	58.790	43.478	0.00	0.00	0.00	2.57
950	2832	4.276926	GTGGTGCATCTTTAGGGATTGATC	59.723	45.833	0.00	0.00	0.00	2.92
951	2833	3.499918	GGTGCATCTTTAGGGATTGATCG	59.500	47.826	0.00	0.00	0.00	3.69
952	2834	4.130118	GTGCATCTTTAGGGATTGATCGT	58.870	43.478	0.00	0.00	0.00	3.73
953	2835	4.576463	GTGCATCTTTAGGGATTGATCGTT	59.424	41.667	0.00	0.00	0.00	3.85
955	2837	5.059833	GCATCTTTAGGGATTGATCGTTCT	58.940	41.667	0.00	0.00	0.00	3.01
957	2839	6.512415	GCATCTTTAGGGATTGATCGTTCTTG	60.512	42.308	0.00	0.00	0.00	3.02
958	2840	4.876107	TCTTTAGGGATTGATCGTTCTTGC	59.124	41.667	0.00	0.00	0.00	4.01
1081	2963	6.982852	AGTCAAGTAACATAGACATATCCCG	58.017	40.000	0.00	0.00	33.56	5.14
1083	2965	7.069578	AGTCAAGTAACATAGACATATCCCGTT	59.930	37.037	0.00	0.00	33.56	4.44
1085	2967	8.262227	TCAAGTAACATAGACATATCCCGTTTT	58.738	33.333	0.00	0.00	0.00	2.43
1087	2969	8.433421	AGTAACATAGACATATCCCGTTTTTG	57.567	34.615	0.00	0.00	0.00	2.44
1210	3652	3.245371	TGTTTCCATGCTCTCCTCCATTT	60.245	43.478	0.00	0.00	0.00	2.32
1229	3671	6.262049	TCCATTTCGAGACAAAGTTTCAATCA	59.738	34.615	0.00	0.00	0.00	2.57
1235	3679	3.636764	AGACAAAGTTTCAATCACACCCC	59.363	43.478	0.00	0.00	0.00	4.95
1236	3680	3.370104	ACAAAGTTTCAATCACACCCCA	58.630	40.909	0.00	0.00	0.00	4.96
1246	3690	2.335316	TCACACCCCACTGTTGTTAC	57.665	50.000	0.00	0.00	0.00	2.50
1290	3734	5.733226	TTGTTGTCAAGATGTGTACACTG	57.267	39.130	25.60	15.78	0.00	3.66
1334	3778	4.353737	CAAATGGTTATTCAGTGCATCCG	58.646	43.478	0.00	0.00	0.00	4.18
1372	3816	2.998279	GCATCACTGGCCAGCCAAC	61.998	63.158	33.06	14.77	46.63	3.77
1487	4339	6.992715	CCGGTCAGTGATATCTTTAGGAAAAT	59.007	38.462	3.98	0.00	0.00	1.82
1510	4363	4.281657	ACCCCAAAAATAGCAGAATCTCC	58.718	43.478	0.00	0.00	0.00	3.71
1575	4434	9.733556	TGTGTAATCAAACATACAACTAGGAAT	57.266	29.630	0.00	0.00	34.08	3.01
1603	4462	4.979943	TGAAGCACAACAAGAACATCAA	57.020	36.364	0.00	0.00	0.00	2.57
1694	4553	1.374343	CCAATGTGCTCTGCATCGCT	61.374	55.000	8.56	0.00	41.91	4.93
1774	4634	7.630242	ACAACCATGTAAACCTCTAATCATG	57.370	36.000	0.00	0.00	38.24	3.07
1879	4739	2.686915	TGTGTGCACATGTTGACATTGA	59.313	40.909	24.69	0.00	36.21	2.57
2074	5185	3.695816	GAAGTTGTTCAACTTGGTGAGC	58.304	45.455	27.99	13.54	42.57	4.26
2116	5227	8.108551	TGGGCAATTTTTCTTTTAAATCCATG	57.891	30.769	0.00	0.00	0.00	3.66
2173	5322	4.326278	CACGTATCACACAGTGTATGGAAC	59.674	45.833	5.69	0.00	34.79	3.62
2442	5993	4.083324	CCTCTTCGTTCTTGCATGCTTTTA	60.083	41.667	20.33	0.00	0.00	1.52
2523	6820	3.843240	CGCAGGTTCGAGAAGCGC	61.843	66.667	0.00	0.00	43.06	5.92
2624	6978	6.446318	ACATAAATGTTGTTGATGGTGTGTC	58.554	36.000	0.00	0.00	37.90	3.67
2685	7040	1.027792	GGTGTGAACCACGGTTGTGT	61.028	55.000	6.10	0.00	45.52	3.72
2686	7041	0.806241	GTGTGAACCACGGTTGTGTT	59.194	50.000	6.10	0.00	44.92	3.32
2687	7042	1.088306	TGTGAACCACGGTTGTGTTC	58.912	50.000	6.10	7.60	44.92	3.18
2688	7043	1.339247	TGTGAACCACGGTTGTGTTCT	60.339	47.619	6.10	0.00	44.92	3.01
2689	7044	2.093606	TGTGAACCACGGTTGTGTTCTA	60.094	45.455	6.10	3.91	44.92	2.10
2690	7045	2.286025	GTGAACCACGGTTGTGTTCTAC	59.714	50.000	6.10	8.13	44.92	2.59
3016	7758	8.836413	CACACATACACCTCTTTTCTTTTTCTA	58.164	33.333	0.00	0.00	0.00	2.10
3017	7759	9.403583	ACACATACACCTCTTTTCTTTTTCTAA	57.596	29.630	0.00	0.00	0.00	2.10
3188	7975	6.231211	ACTCACTAAACTTGAACATACCCTG	58.769	40.000	0.00	0.00	0.00	4.45
3243	8030	6.586082	GGTGCGATTTACAAACAAAGATGATT	59.414	34.615	0.00	0.00	0.00	2.57
3279	8066	5.622770	AAAAATAGTACGAGTGCCAAAGG	57.377	39.130	0.00	0.00	0.00	3.11
3327	8114	7.284074	TGGGTCTAAACAAGATGTGTCTAAAA	58.716	34.615	0.00	0.00	40.60	1.52
3606	8393	2.907042	AGGAAACCTACTTCAGACCAGG	59.093	50.000	0.00	0.00	28.47	4.45
3922	9065	4.832266	ACTTGATTGGTAATTGTTGCTCCA	59.168	37.500	0.00	0.00	0.00	3.86
4132	10139	4.580580	ACCATGTCTCAAGGTTGTCTTTTC	59.419	41.667	0.00	0.00	30.86	2.29
4493	10507	0.330604	AGGCAATGACCTGCTCACAT	59.669	50.000	0.00	0.00	42.25	3.21
4500	10514	0.813210	GACCTGCTCACATGCTAGGC	60.813	60.000	0.00	0.00	35.87	3.93
4501	10515	1.270414	ACCTGCTCACATGCTAGGCT	61.270	55.000	0.00	0.00	35.87	4.58
4502	10516	0.814410	CCTGCTCACATGCTAGGCTG	60.814	60.000	0.00	0.00	0.00	4.85
4503	10517	1.437772	CTGCTCACATGCTAGGCTGC	61.438	60.000	0.00	0.00	0.00	5.25
4504	10518	1.153208	GCTCACATGCTAGGCTGCT	60.153	57.895	0.00	0.00	0.00	4.24
4505	10519	0.105593	GCTCACATGCTAGGCTGCTA	59.894	55.000	0.00	0.00	0.00	3.49
4506	10520	1.873069	GCTCACATGCTAGGCTGCTAG	60.873	57.143	0.00	0.84	0.00	3.42
4507	10521	0.755079	TCACATGCTAGGCTGCTAGG	59.245	55.000	0.00	0.00	0.00	3.02
4508	10522	0.755079	CACATGCTAGGCTGCTAGGA	59.245	55.000	0.00	1.33	0.00	2.94
4509	10523	1.139654	CACATGCTAGGCTGCTAGGAA	59.860	52.381	0.00	0.00	31.29	3.36
4510	10524	2.053244	ACATGCTAGGCTGCTAGGAAT	58.947	47.619	0.00	0.00	31.29	3.01
4580	10607	3.305094	GTGATCAATGGCAGCATTTTTCG	59.695	43.478	0.00	0.00	0.00	3.46
4582	10609	0.722848	CAATGGCAGCATTTTTCGGC	59.277	50.000	0.00	0.00	0.00	5.54
4583	10610	0.609662	AATGGCAGCATTTTTCGGCT	59.390	45.000	0.00	0.00	42.06	5.52
4637	10669	4.980573	AGCTATTTCCACCTTGTGTTGTA	58.019	39.130	0.00	0.00	0.00	2.41
4955	11041	8.577939	CAACAACGAAACATCATAAGCATTTAG	58.422	33.333	0.00	0.00	0.00	1.85
5054	11360	3.046390	GCGTATGAGTGTCTATGTCTGC	58.954	50.000	0.00	0.00	0.00	4.26
5068	11378	2.135139	TGTCTGCACTGCGTTTAAGAG	58.865	47.619	0.00	0.00	0.00	2.85
5078	11388	6.511282	GCACTGCGTTTAAGAGAAAGTAGTTT	60.511	38.462	0.00	0.00	33.38	2.66
5121	11431	0.443869	GACATACAACACGCCAGCAG	59.556	55.000	0.00	0.00	0.00	4.24
5209	11519	2.668550	GTTTTCCTGCCGACCGCT	60.669	61.111	0.00	0.00	38.78	5.52
5215	11525	2.495409	CCTGCCGACCGCTACCATA	61.495	63.158	0.00	0.00	38.78	2.74
5297	11607	1.431488	GCGCGATCTTGATCTTGCCA	61.431	55.000	12.10	0.00	0.00	4.92
5376	11686	1.039785	CGTCTCCAGAGGGATGCTCA	61.040	60.000	0.00	0.00	43.91	4.26
5460	11770	3.817647	GACACTTCTGGCATCTTGTTCTT	59.182	43.478	0.00	0.00	0.00	2.52
5514	11824	1.997669	ACTGAAGAAATCGGAGTCGC	58.002	50.000	0.00	0.00	37.88	5.19

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
35	1909	1.143183	GCGGCGATGGAAGGTAAGA	59.857	57.895	12.98	0.00	0.00	2.10
62	1937	2.193127	TCGATGGTTGGTAGGGTTGAT	58.807	47.619	0.00	0.00	0.00	2.57
340	2221	4.321480	CGACGTACGTCACAATCATACAAA	59.679	41.667	38.60	0.00	44.77	2.83
360	2241	2.034001	GCAACCACTTCGCATATACGAC	60.034	50.000	0.00	0.00	42.78	4.34
430	2311	7.733955	TCCCTCATCTCTCTTCTCATTTATGAT	59.266	37.037	0.00	0.00	36.02	2.45
494	2375	0.692756	CTCCCTCTTCCCTCTTCCCC	60.693	65.000	0.00	0.00	0.00	4.81
727	2608	6.052360	ACTCACACATACACACATAAACACA	58.948	36.000	0.00	0.00	0.00	3.72
794	2676	7.442666	ACACACACACACACACACATAAATATA	59.557	33.333	0.00	0.00	0.00	0.86
796	2678	5.586643	ACACACACACACACACACATAAATA	59.413	36.000	0.00	0.00	0.00	1.40
797	2679	4.397730	ACACACACACACACACACATAAAT	59.602	37.500	0.00	0.00	0.00	1.40
798	2680	3.753797	ACACACACACACACACACATAAA	59.246	39.130	0.00	0.00	0.00	1.40
799	2681	3.126000	CACACACACACACACACACATAA	59.874	43.478	0.00	0.00	0.00	1.90
801	2683	1.468127	CACACACACACACACACACAT	59.532	47.619	0.00	0.00	0.00	3.21
802	2684	0.871057	CACACACACACACACACACA	59.129	50.000	0.00	0.00	0.00	3.72
804	2686	0.871057	CACACACACACACACACACA	59.129	50.000	0.00	0.00	0.00	3.72
805	2687	0.871722	ACACACACACACACACACAC	59.128	50.000	0.00	0.00	0.00	3.82
806	2688	0.871057	CACACACACACACACACACA	59.129	50.000	0.00	0.00	0.00	3.72
807	2689	0.871722	ACACACACACACACACACAC	59.128	50.000	0.00	0.00	0.00	3.82
808	2690	0.871057	CACACACACACACACACACA	59.129	50.000	0.00	0.00	0.00	3.72
809	2691	0.871722	ACACACACACACACACACAC	59.128	50.000	0.00	0.00	0.00	3.82
812	2694	0.871057	CACACACACACACACACACA	59.129	50.000	0.00	0.00	0.00	3.72
813	2695	0.871722	ACACACACACACACACACAC	59.128	50.000	0.00	0.00	0.00	3.82
814	2696	0.871057	CACACACACACACACACACA	59.129	50.000	0.00	0.00	0.00	3.72
815	2697	0.871722	ACACACACACACACACACAC	59.128	50.000	0.00	0.00	0.00	3.82
817	2699	0.871722	ACACACACACACACACACAC	59.128	50.000	0.00	0.00	0.00	3.82
819	2701	0.871722	ACACACACACACACACACAC	59.128	50.000	0.00	0.00	0.00	3.82
821	2703	0.871722	ACACACACACACACACACAC	59.128	50.000	0.00	0.00	0.00	3.82
822	2704	0.871057	CACACACACACACACACACA	59.129	50.000	0.00	0.00	0.00	3.72
824	2706	0.871057	CACACACACACACACACACA	59.129	50.000	0.00	0.00	0.00	3.72
825	2707	0.871722	ACACACACACACACACACAC	59.128	50.000	0.00	0.00	0.00	3.82
826	2708	1.152510	GACACACACACACACACACA	58.847	50.000	0.00	0.00	0.00	3.72
827	2709	1.152510	TGACACACACACACACACAC	58.847	50.000	0.00	0.00	0.00	3.82
828	2710	2.106477	ATGACACACACACACACACA	57.894	45.000	0.00	0.00	0.00	3.72
829	2711	2.418280	TGAATGACACACACACACACAC	59.582	45.455	0.00	0.00	0.00	3.82
830	2712	2.704572	TGAATGACACACACACACACA	58.295	42.857	0.00	0.00	0.00	3.72
831	2713	3.755965	TTGAATGACACACACACACAC	57.244	42.857	0.00	0.00	0.00	3.82
832	2714	4.022849	TGTTTTGAATGACACACACACACA	60.023	37.500	0.00	0.00	0.00	3.72
834	2716	4.773323	TGTTTTGAATGACACACACACA	57.227	36.364	0.00	0.00	0.00	3.72
835	2717	6.645700	AATTGTTTTGAATGACACACACAC	57.354	33.333	0.00	0.00	0.00	3.82
836	2718	7.095910	AGAAATTGTTTTGAATGACACACACA	58.904	30.769	0.00	0.00	0.00	3.72
940	2822	2.636830	CTGCAAGAACGATCAATCCCT	58.363	47.619	0.00	0.00	34.07	4.20
941	2823	1.672881	CCTGCAAGAACGATCAATCCC	59.327	52.381	0.00	0.00	34.07	3.85
942	2824	1.064654	GCCTGCAAGAACGATCAATCC	59.935	52.381	0.00	0.00	34.07	3.01
943	2825	1.064654	GGCCTGCAAGAACGATCAATC	59.935	52.381	0.00	0.00	34.07	2.67
944	2826	1.098050	GGCCTGCAAGAACGATCAAT	58.902	50.000	0.00	0.00	34.07	2.57
947	2829	1.131315	GAAAGGCCTGCAAGAACGATC	59.869	52.381	5.69	0.00	34.07	3.69
949	2831	0.108585	AGAAAGGCCTGCAAGAACGA	59.891	50.000	5.69	0.00	34.07	3.85
950	2832	1.464997	GTAGAAAGGCCTGCAAGAACG	59.535	52.381	5.69	0.00	34.07	3.95
951	2833	2.485814	CTGTAGAAAGGCCTGCAAGAAC	59.514	50.000	5.69	0.69	34.07	3.01
952	2834	2.553028	CCTGTAGAAAGGCCTGCAAGAA	60.553	50.000	5.69	0.00	34.07	2.52
953	2835	1.003580	CCTGTAGAAAGGCCTGCAAGA	59.996	52.381	5.69	0.00	34.07	3.02
955	2837	1.003580	CTCCTGTAGAAAGGCCTGCAA	59.996	52.381	5.69	0.00	37.24	4.08
957	2839	0.905357	TCTCCTGTAGAAAGGCCTGC	59.095	55.000	5.69	0.73	37.24	4.85
958	2840	2.167487	GTCTCTCCTGTAGAAAGGCCTG	59.833	54.545	5.69	0.00	37.24	4.85
1210	3652	4.272504	GGTGTGATTGAAACTTTGTCTCGA	59.727	41.667	0.00	0.00	0.00	4.04
1229	3671	3.813080	GGTAACAACAGTGGGGTGT	57.187	52.632	0.00	0.00	0.00	4.16
1290	3734	2.603173	GCCGATTTAGCAGCATTGTAGC	60.603	50.000	0.00	0.00	0.00	3.58
1334	3778	0.322546	GGGTTGTGATCACTGACCCC	60.323	60.000	36.33	28.59	44.86	4.95
1372	3816	3.391506	TGAGTCATCACAGACCAGTTG	57.608	47.619	0.00	0.00	39.34	3.16
1487	4339	5.044476	TGGAGATTCTGCTATTTTTGGGGTA	60.044	40.000	6.74	0.00	0.00	3.69
1510	4363	6.907212	GTGGCTCAACTATTCGTATTTGAATG	59.093	38.462	0.00	0.00	38.92	2.67
1575	4434	9.098355	GATGTTCTTGTTGTGCTTCATATAGTA	57.902	33.333	0.00	0.00	0.00	1.82
1694	4553	1.725641	GATGGTCACAAGCATCGACA	58.274	50.000	2.26	0.00	46.91	4.35
1703	4562	3.684908	CATGGGTAACTGATGGTCACAA	58.315	45.455	0.00	0.00	0.00	3.33
1774	4634	8.530269	AGCTCATCATTTCAATTTTGAAGTTC	57.470	30.769	5.92	0.00	46.68	3.01
1879	4739	8.908903	TCACTTGTATGTTCATTTGGTTTTACT	58.091	29.630	0.00	0.00	0.00	2.24
1936	4796	8.721478	ACTAAACAATCATGTCACTTGTATGTC	58.279	33.333	0.00	0.00	39.40	3.06
2074	5185	3.119173	TGCCCAACAAGAAACTTGTTCTG	60.119	43.478	21.67	17.11	40.30	3.02
2173	5322	5.594317	CCAAAGTTAGAATACAATCCCCTGG	59.406	44.000	0.00	0.00	0.00	4.45
2442	5993	9.217278	CTCGTAATAGGACATGTGTAGTACTAT	57.783	37.037	1.15	0.00	43.32	2.12
2523	6820	0.613260	TTGACCTCCCCTTGATCACG	59.387	55.000	0.00	0.00	0.00	4.35
2635	6989	7.369607	TCTCAACACCATCAACAACATTTATG	58.630	34.615	0.00	0.00	0.00	1.90
2636	6990	7.523293	TCTCAACACCATCAACAACATTTAT	57.477	32.000	0.00	0.00	0.00	1.40
2637	6991	6.951062	TCTCAACACCATCAACAACATTTA	57.049	33.333	0.00	0.00	0.00	1.40
2685	7040	5.248477	AGTTGCCCTGAACATAGAAGTAGAA	59.752	40.000	0.00	0.00	0.00	2.10
2686	7041	4.777896	AGTTGCCCTGAACATAGAAGTAGA	59.222	41.667	0.00	0.00	0.00	2.59
2687	7042	5.091261	AGTTGCCCTGAACATAGAAGTAG	57.909	43.478	0.00	0.00	0.00	2.57
2688	7043	6.808321	ATAGTTGCCCTGAACATAGAAGTA	57.192	37.500	0.00	0.00	0.00	2.24
2689	7044	5.700402	ATAGTTGCCCTGAACATAGAAGT	57.300	39.130	0.00	0.00	0.00	3.01
2690	7045	5.698545	GCTATAGTTGCCCTGAACATAGAAG	59.301	44.000	0.84	0.00	0.00	2.85
3117	7904	4.582869	CTTGGTTCTCATCTGACCAATGA	58.417	43.478	7.55	0.00	39.39	2.57
3188	7975	4.184629	ACTTATGGACGAAGAACTGCATC	58.815	43.478	0.00	0.00	0.00	3.91
3279	8066	0.895100	TCTTTGGATGGCAGTGGCAC	60.895	55.000	23.12	10.29	41.84	5.01
3327	8114	1.953559	TCAAAGAGCAGCACGTCTTT	58.046	45.000	2.92	2.92	42.51	2.52
3410	8197	2.915349	ACGTTATCCTGAGAGCTCGTA	58.085	47.619	8.37	0.00	0.00	3.43
3489	8276	4.756642	TGTTAGCCAGTTCTTGAGAATGTG	59.243	41.667	0.00	0.00	36.33	3.21
3606	8393	6.206498	ACCGTGTCTTTCTTATTTTTCTTGC	58.794	36.000	0.00	0.00	0.00	4.01
4493	10507	1.690893	CAGATTCCTAGCAGCCTAGCA	59.309	52.381	0.00	0.00	39.81	3.49
4500	10514	4.282957	TGATTCCTAGCAGATTCCTAGCAG	59.717	45.833	0.00	0.00	32.74	4.24
4501	10515	4.226384	TGATTCCTAGCAGATTCCTAGCA	58.774	43.478	0.00	0.00	32.74	3.49
4502	10516	4.881019	TGATTCCTAGCAGATTCCTAGC	57.119	45.455	0.00	0.00	32.74	3.42
4503	10517	7.002250	TGATTGATTCCTAGCAGATTCCTAG	57.998	40.000	0.00	0.00	33.64	3.02
4504	10518	7.379059	TTGATTGATTCCTAGCAGATTCCTA	57.621	36.000	0.00	0.00	0.00	2.94
4505	10519	5.901413	TGATTGATTCCTAGCAGATTCCT	57.099	39.130	0.00	0.00	0.00	3.36
4506	10520	5.472820	CCTTGATTGATTCCTAGCAGATTCC	59.527	44.000	0.00	0.00	0.00	3.01
4507	10521	5.048852	GCCTTGATTGATTCCTAGCAGATTC	60.049	44.000	0.00	0.00	0.00	2.52
4508	10522	4.826183	GCCTTGATTGATTCCTAGCAGATT	59.174	41.667	0.00	0.00	0.00	2.40
4509	10523	4.396522	GCCTTGATTGATTCCTAGCAGAT	58.603	43.478	0.00	0.00	0.00	2.90
4510	10524	3.434167	GGCCTTGATTGATTCCTAGCAGA	60.434	47.826	0.00	0.00	0.00	4.26
4637	10669	8.463607	CGACAAACCCACCATATAATTAAGTTT	58.536	33.333	0.00	0.00	0.00	2.66
5054	11360	6.526566	AACTACTTTCTCTTAAACGCAGTG	57.473	37.500	0.00	0.00	45.00	3.66
5068	11378	5.918576	CCCGACAAAATGGAAAACTACTTTC	59.081	40.000	0.00	0.00	42.45	2.62
5078	11388	2.350057	TCACACCCGACAAAATGGAA	57.650	45.000	0.00	0.00	0.00	3.53
5121	11431	1.064060	GCGCATCCACAACCAAGATAC	59.936	52.381	0.30	0.00	0.00	2.24
5209	11519	1.135717	CGTGTGGTCGTCGTTATGGTA	60.136	52.381	0.00	0.00	0.00	3.25
5297	11607	2.161030	GTCGTCAAGGAGGAGTACTGT	58.839	52.381	0.00	0.00	0.00	3.55
5340	11650	1.446792	CGGTGCTACAGGAGTGCAG	60.447	63.158	0.00	0.00	34.22	4.41
5376	11686	6.594788	ATGTAATGCACTGAACATTTTCCT	57.405	33.333	0.00	0.00	38.62	3.36
5460	11770	4.158579	CACACACAAGCCTCTACTCTCATA	59.841	45.833	0.00	0.00	0.00	2.15

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.