AutoCloner

Multiple sequence alignment - TraesCS5A01G077200

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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	TraesCS5A01G077200	chr5A	100.000	6921	0	0	1	6921	94082266	94089186	0.000000e+00	12781.0
1	TraesCS5A01G077200	chr5A	92.220	2712	180	20	917	3617	107392325	107389634	0.000000e+00	3810.0
2	TraesCS5A01G077200	chr5A	89.310	449	42	6	5691	6135	107388616	107388170	6.060000e-155	558.0
3	TraesCS5A01G077200	chr5A	81.716	536	76	13	4003	4535	112618405	112618921	1.780000e-115	427.0
4	TraesCS5A01G077200	chr5D	97.458	3777	78	7	4	3764	104158539	104154765	0.000000e+00	6427.0
5	TraesCS5A01G077200	chr5D	92.145	2699	185	17	930	3619	104473811	104471131	0.000000e+00	3784.0
6	TraesCS5A01G077200	chr5D	92.848	1580	67	19	5268	6815	104154239	104152674	0.000000e+00	2250.0
7	TraesCS5A01G077200	chr5D	87.939	456	49	6	5684	6135	104470115	104469662	3.670000e-147	532.0
8	TraesCS5A01G077200	chr5D	93.902	246	14	1	4960	5205	104154504	104154260	3.050000e-98	370.0
9	TraesCS5A01G077200	chr5D	94.017	234	13	1	3769	4002	104154729	104154497	3.070000e-93	353.0
10	TraesCS5A01G077200	chr5D	82.258	186	19	9	6198	6375	104469623	104469444	1.560000e-31	148.0
11	TraesCS5A01G077200	chr5D	93.814	97	6	0	6807	6903	104152117	104152021	5.590000e-31	147.0
12	TraesCS5A01G077200	chr5D	85.816	141	13	5	4812	4946	347018259	347018398	7.240000e-30	143.0
13	TraesCS5A01G077200	chr5B	97.940	3447	63	4	558	4002	113560331	113556891	0.000000e+00	5965.0
14	TraesCS5A01G077200	chr5B	92.885	2572	170	9	930	3499	113876628	113874068	0.000000e+00	3723.0
15	TraesCS5A01G077200	chr5B	95.166	1903	50	17	4960	6842	113556898	113555018	0.000000e+00	2966.0
16	TraesCS5A01G077200	chr5B	96.679	542	9	4	1	533	113560869	113560328	0.000000e+00	893.0
17	TraesCS5A01G077200	chr5B	88.210	458	45	7	5684	6135	113873152	113872698	7.900000e-149	538.0
18	TraesCS5A01G077200	chr5B	85.135	74	9	2	4004	4077	498543213	498543142	2.680000e-09	75.0
19	TraesCS5A01G077200	chr5B	91.667	48	1	3	4005	4052	416999560	416999604	5.800000e-06	63.9
20	TraesCS5A01G077200	chr5B	83.099	71	8	3	4007	4077	498544409	498544343	2.080000e-05	62.1
21	TraesCS5A01G077200	chr7A	93.481	951	36	12	4006	4934	670540450	670539504	0.000000e+00	1389.0
22	TraesCS5A01G077200	chr1A	92.739	964	47	11	4002	4946	509018892	509019851	0.000000e+00	1371.0
23	TraesCS5A01G077200	chr2D	92.324	964	50	10	4000	4944	15349670	15350628	0.000000e+00	1349.0
24	TraesCS5A01G077200	chr2D	86.429	140	12	7	4812	4946	547793350	547793487	5.590000e-31	147.0
25	TraesCS5A01G077200	chr2D	87.500	64	4	4	4003	4066	610411748	610411807	3.460000e-08	71.3
26	TraesCS5A01G077200	chr2A	90.487	862	54	11	5961	6802	592314530	592315383	0.000000e+00	1112.0
27	TraesCS5A01G077200	chr2A	77.503	769	109	33	4227	4946	73537605	73538358	3.010000e-108	403.0
28	TraesCS5A01G077200	chr7D	85.190	763	90	14	4181	4921	630688425	630687664	0.000000e+00	761.0
29	TraesCS5A01G077200	chr6B	84.615	585	59	20	4383	4946	377964354	377963780	2.820000e-153	553.0
30	TraesCS5A01G077200	chr6B	87.468	391	42	5	4003	4392	377982019	377981635	1.770000e-120	444.0
31	TraesCS5A01G077200	chr6D	78.904	858	122	30	4003	4820	72224020	72223182	1.710000e-145	527.0
32	TraesCS5A01G077200	chr6D	85.507	138	14	4	4812	4946	72223156	72223022	9.360000e-29	139.0
33	TraesCS5A01G077200	chr3A	80.030	666	90	21	4003	4646	678885256	678885900	2.940000e-123	453.0
34	TraesCS5A01G077200	chr3A	82.276	536	72	11	4003	4535	678806064	678806579	6.370000e-120	442.0
35	TraesCS5A01G077200	chr4B	93.182	44	0	2	4011	4054	23824634	23824674	2.080000e-05	62.1

These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

	query	scaffold	start	end	length	rev.comp	avg.bitscore	max.bitscore	avg.percent.identical	query.start	query.end	num_hsp	groupid	homo_length
0	TraesCS5A01G077200	chr5A	94082266	94089186	6920	False	12781.000000	12781	100.000000	1	6921	1	chr5A.!!$F1	6920
1	TraesCS5A01G077200	chr5A	107388170	107392325	4155	True	2184.000000	3810	90.765000	917	6135	2	chr5A.!!$R1	5218
2	TraesCS5A01G077200	chr5A	112618405	112618921	516	False	427.000000	427	81.716000	4003	4535	1	chr5A.!!$F2	532
3	TraesCS5A01G077200	chr5D	104152021	104158539	6518	True	1909.400000	6427	94.407800	4	6903	5	chr5D.!!$R1	6899
4	TraesCS5A01G077200	chr5D	104469444	104473811	4367	True	1488.000000	3784	87.447333	930	6375	3	chr5D.!!$R2	5445
5	TraesCS5A01G077200	chr5B	113555018	113560869	5851	True	3274.666667	5965	96.595000	1	6842	3	chr5B.!!$R1	6841
6	TraesCS5A01G077200	chr5B	113872698	113876628	3930	True	2130.500000	3723	90.547500	930	6135	2	chr5B.!!$R2	5205
7	TraesCS5A01G077200	chr7A	670539504	670540450	946	True	1389.000000	1389	93.481000	4006	4934	1	chr7A.!!$R1	928
8	TraesCS5A01G077200	chr1A	509018892	509019851	959	False	1371.000000	1371	92.739000	4002	4946	1	chr1A.!!$F1	944
9	TraesCS5A01G077200	chr2D	15349670	15350628	958	False	1349.000000	1349	92.324000	4000	4944	1	chr2D.!!$F1	944
10	TraesCS5A01G077200	chr2A	592314530	592315383	853	False	1112.000000	1112	90.487000	5961	6802	1	chr2A.!!$F2	841
11	TraesCS5A01G077200	chr2A	73537605	73538358	753	False	403.000000	403	77.503000	4227	4946	1	chr2A.!!$F1	719
12	TraesCS5A01G077200	chr7D	630687664	630688425	761	True	761.000000	761	85.190000	4181	4921	1	chr7D.!!$R1	740
13	TraesCS5A01G077200	chr6B	377963780	377964354	574	True	553.000000	553	84.615000	4383	4946	1	chr6B.!!$R1	563
14	TraesCS5A01G077200	chr6D	72223022	72224020	998	True	333.000000	527	82.205500	4003	4946	2	chr6D.!!$R1	943
15	TraesCS5A01G077200	chr3A	678885256	678885900	644	False	453.000000	453	80.030000	4003	4646	1	chr3A.!!$F2	643
16	TraesCS5A01G077200	chr3A	678806064	678806579	515	False	442.000000	442	82.276000	4003	4535	1	chr3A.!!$F1	532

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
213	220	0.601576	TTTCTCGCCGTAGCTTGCAA	60.602	50.000	0.00	0.00	36.60	4.08	F
1890	1907	3.435671	AGGAAATCGACATTTTGGACGAC	59.564	43.478	0.00	0.00	34.56	4.34	F
2613	2630	3.498774	AATGAAGTTGTCAGGTGCTCT	57.501	42.857	0.00	0.00	40.43	4.09	F
2943	2960	1.196808	AACTTCGCAAAGTACATGGCG	59.803	47.619	13.56	13.56	45.07	5.69	F
3619	3644	4.222810	GGGCCAAAGTACTGGAAAATTGAT	59.777	41.667	4.39	0.00	38.96	2.57	F
4540	4691	0.038251	CAGGTAGCAGCACGACTTGA	60.038	55.000	0.00	0.00	33.58	3.02	F
4549	4700	0.109597	GCACGACTTGAATTGCTGGG	60.110	55.000	0.00	0.00	32.00	4.45	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1989	2006	1.625818	TCTTGGTCTTCCTCCTGCTTC	59.374	52.381	0.00	0.00	34.23	3.86	R
2943	2960	6.404734	CCATTTCCAAGTACTGGTAGAATTGC	60.405	42.308	0.00	0.00	46.51	3.56	R
3967	4112	0.324943	GCAGGAACACCTAGCCAGAA	59.675	55.000	0.00	0.00	32.14	3.02	R
3988	4133	0.327924	CCACTGATTGCAGGTACCCA	59.672	55.000	8.74	0.00	46.60	4.51	R
4952	5181	0.171903	CTTACATTGCAGGCAGTGGC	59.828	55.000	18.92	9.02	37.87	5.01	R
5562	5861	0.326713	AGGAGGCTTAAGGGGGAGAC	60.327	60.000	4.29	0.00	0.00	3.36	R
6497	6858	0.584876	CCGTCGAAGTTTTGACCACC	59.415	55.000	6.66	0.00	38.16	4.61	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
85	86	3.449018	ACTACCAGGCAGATCTGTTGTAG	59.551	47.826	23.38	24.43	36.49	2.74
112	113	2.625790	TGTGTGTTAAGGTGGATTTGGC	59.374	45.455	0.00	0.00	0.00	4.52
149	156	4.607239	TGTAACCCTAGATTCGGTTCTCT	58.393	43.478	4.60	0.00	41.50	3.10
213	220	0.601576	TTTCTCGCCGTAGCTTGCAA	60.602	50.000	0.00	0.00	36.60	4.08
469	479	7.639113	TTATACAGCTGTTTAGATTTTGGGG	57.361	36.000	27.06	0.00	0.00	4.96
481	491	3.578282	AGATTTTGGGGTTGATGTTCACC	59.422	43.478	0.00	0.00	0.00	4.02
537	547	5.165676	TCTGTGTAGTTGGTTACTTATGCG	58.834	41.667	0.00	0.00	38.33	4.73
557	567	6.141560	TGCGGATGTATTCATGCAATTTAA	57.858	33.333	4.79	0.00	41.45	1.52
608	618	7.147312	TGATTGCCTCATTTAAGAAACTTGTG	58.853	34.615	0.00	0.00	0.00	3.33
916	933	8.988934	GTGTCTTGTGTAATTTACATCTGAGAA	58.011	33.333	12.16	0.00	41.34	2.87
1503	1520	4.363991	AGTTTCTCCAGAAGCTGTTGAT	57.636	40.909	5.00	0.00	42.66	2.57
1542	1559	6.765989	ACAAGATACTTACAGCTGTTGTTCAA	59.234	34.615	27.06	11.83	41.29	2.69
1890	1907	3.435671	AGGAAATCGACATTTTGGACGAC	59.564	43.478	0.00	0.00	34.56	4.34
2251	2268	4.324402	CCTTGAATTTTATGTTGTCTGCGC	59.676	41.667	0.00	0.00	0.00	6.09
2613	2630	3.498774	AATGAAGTTGTCAGGTGCTCT	57.501	42.857	0.00	0.00	40.43	4.09
2943	2960	1.196808	AACTTCGCAAAGTACATGGCG	59.803	47.619	13.56	13.56	45.07	5.69
3438	3455	9.796180	AAGGATATGTAAGTCGTCTAGAATACT	57.204	33.333	0.00	0.00	0.00	2.12
3527	3548	5.336690	GGAAACTGGTCATGCAAACACATAT	60.337	40.000	0.00	0.00	0.00	1.78
3528	3549	6.127758	GGAAACTGGTCATGCAAACACATATA	60.128	38.462	0.00	0.00	0.00	0.86
3619	3644	4.222810	GGGCCAAAGTACTGGAAAATTGAT	59.777	41.667	4.39	0.00	38.96	2.57
3701	3728	6.306987	TGCTATTCCCTCCTTCCAAAATATC	58.693	40.000	0.00	0.00	0.00	1.63
3797	3857	9.369672	CTTAGGGAAGGAGTACTGAATAACTAT	57.630	37.037	0.00	0.00	0.00	2.12
3798	3858	9.725206	TTAGGGAAGGAGTACTGAATAACTATT	57.275	33.333	0.00	0.00	0.00	1.73
3967	4112	4.858850	TGAGTCAACATGGATATGCCTTT	58.141	39.130	0.00	0.00	37.85	3.11
3988	4133	0.254178	CTGGCTAGGTGTTCCTGCAT	59.746	55.000	0.00	0.00	44.81	3.96
4009	4154	0.322456	GGTACCTGCAATCAGTGGCA	60.322	55.000	4.06	0.00	38.66	4.92
4163	4309	9.243105	TCTTACTTTTGCATAAGAAAAGCCTAT	57.757	29.630	21.69	0.83	41.98	2.57
4276	4422	7.225145	ACATTTTGTTCTTCAATGTGACAATGG	59.775	33.333	0.19	0.00	34.12	3.16
4466	4617	5.011635	TGGACAGAATTCAGCACAGTACTAA	59.988	40.000	8.44	0.00	0.00	2.24
4538	4689	0.898320	ATCAGGTAGCAGCACGACTT	59.102	50.000	0.00	0.00	0.00	3.01
4540	4691	0.038251	CAGGTAGCAGCACGACTTGA	60.038	55.000	0.00	0.00	33.58	3.02
4542	4693	1.276421	AGGTAGCAGCACGACTTGAAT	59.724	47.619	0.00	0.00	0.00	2.57
4546	4697	0.239347	GCAGCACGACTTGAATTGCT	59.761	50.000	0.00	0.00	46.27	3.91
4548	4699	0.877071	AGCACGACTTGAATTGCTGG	59.123	50.000	0.00	0.00	43.67	4.85
4549	4700	0.109597	GCACGACTTGAATTGCTGGG	60.110	55.000	0.00	0.00	32.00	4.45
4550	4701	0.109597	CACGACTTGAATTGCTGGGC	60.110	55.000	0.00	0.00	0.00	5.36
4568	4740	0.659957	GCGATGGGCAGAAATCTCAC	59.340	55.000	0.00	0.00	42.87	3.51
4756	4946	1.675641	GAACCAGGCGGCAAGTCAT	60.676	57.895	13.08	0.00	34.57	3.06
4949	5178	3.480133	GCGGCCCACCCTGTAGAT	61.480	66.667	0.00	0.00	0.00	1.98
4950	5179	2.822399	CGGCCCACCCTGTAGATC	59.178	66.667	0.00	0.00	0.00	2.75
4951	5180	2.808206	CGGCCCACCCTGTAGATCC	61.808	68.421	0.00	0.00	0.00	3.36
4952	5181	2.808206	GGCCCACCCTGTAGATCCG	61.808	68.421	0.00	0.00	0.00	4.18
4953	5182	2.822399	CCCACCCTGTAGATCCGC	59.178	66.667	0.00	0.00	0.00	5.54
4954	5183	2.808206	CCCACCCTGTAGATCCGCC	61.808	68.421	0.00	0.00	0.00	6.13
4955	5184	2.063979	CCACCCTGTAGATCCGCCA	61.064	63.158	0.00	0.00	0.00	5.69
4956	5185	1.144057	CACCCTGTAGATCCGCCAC	59.856	63.158	0.00	0.00	0.00	5.01
4957	5186	1.001760	ACCCTGTAGATCCGCCACT	59.998	57.895	0.00	0.00	0.00	4.00
4958	5187	1.330655	ACCCTGTAGATCCGCCACTG	61.331	60.000	0.00	0.00	0.00	3.66
4959	5188	1.227380	CCTGTAGATCCGCCACTGC	60.227	63.158	0.00	0.00	0.00	4.40
4960	5189	1.227380	CTGTAGATCCGCCACTGCC	60.227	63.158	0.00	0.00	0.00	4.85
4961	5190	1.680522	CTGTAGATCCGCCACTGCCT	61.681	60.000	0.00	0.00	0.00	4.75
4962	5191	1.227380	GTAGATCCGCCACTGCCTG	60.227	63.158	0.00	0.00	0.00	4.85
4963	5192	3.094062	TAGATCCGCCACTGCCTGC	62.094	63.158	0.00	0.00	0.00	4.85
4999	5228	6.069905	TGCTTCTCTGTAAAATACCCATGGTA	60.070	38.462	11.73	3.74	42.80	3.25
5206	5467	3.389983	TCTCCCAAAATGAGGGTATACCG	59.610	47.826	15.80	0.00	46.82	4.02
5207	5468	3.116959	TCCCAAAATGAGGGTATACCGT	58.883	45.455	16.89	16.89	46.82	4.83
5208	5469	3.524380	TCCCAAAATGAGGGTATACCGTT	59.476	43.478	17.86	7.85	46.82	4.44
5209	5470	4.720773	TCCCAAAATGAGGGTATACCGTTA	59.279	41.667	17.86	14.38	46.82	3.18
5210	5471	5.061179	CCCAAAATGAGGGTATACCGTTAG	58.939	45.833	17.86	3.02	46.96	2.34
5211	5472	5.397109	CCCAAAATGAGGGTATACCGTTAGT	60.397	44.000	17.86	10.73	46.96	2.24
5212	5473	5.756833	CCAAAATGAGGGTATACCGTTAGTC	59.243	44.000	17.86	6.35	46.96	2.59
5213	5474	5.541953	AAATGAGGGTATACCGTTAGTCC	57.458	43.478	17.86	6.01	46.96	3.85
5214	5475	2.575532	TGAGGGTATACCGTTAGTCCG	58.424	52.381	17.86	0.00	46.96	4.79
5215	5476	2.092429	TGAGGGTATACCGTTAGTCCGT	60.092	50.000	17.86	0.00	46.96	4.69
5216	5477	2.952310	GAGGGTATACCGTTAGTCCGTT	59.048	50.000	17.86	0.00	46.96	4.44
5217	5478	4.134563	GAGGGTATACCGTTAGTCCGTTA	58.865	47.826	17.86	0.00	46.96	3.18
5218	5479	3.883489	AGGGTATACCGTTAGTCCGTTAC	59.117	47.826	15.80	0.00	46.96	2.50
5219	5480	3.630312	GGGTATACCGTTAGTCCGTTACA	59.370	47.826	15.80	0.00	36.71	2.41
5220	5481	4.261197	GGGTATACCGTTAGTCCGTTACAG	60.261	50.000	15.80	0.00	36.71	2.74
5221	5482	4.335594	GGTATACCGTTAGTCCGTTACAGT	59.664	45.833	6.06	0.00	0.00	3.55
5222	5483	2.712057	ACCGTTAGTCCGTTACAGTG	57.288	50.000	0.00	0.00	0.00	3.66
5223	5484	1.336240	ACCGTTAGTCCGTTACAGTGC	60.336	52.381	0.00	0.00	0.00	4.40
5224	5485	1.336148	CCGTTAGTCCGTTACAGTGCA	60.336	52.381	0.00	0.00	0.00	4.57
5225	5486	2.396601	CGTTAGTCCGTTACAGTGCAA	58.603	47.619	0.00	0.00	0.00	4.08
5226	5487	2.796031	CGTTAGTCCGTTACAGTGCAAA	59.204	45.455	0.00	0.00	0.00	3.68
5227	5488	3.245754	CGTTAGTCCGTTACAGTGCAAAA	59.754	43.478	0.00	0.00	0.00	2.44
5228	5489	4.084223	CGTTAGTCCGTTACAGTGCAAAAT	60.084	41.667	0.00	0.00	0.00	1.82
5229	5490	5.118971	CGTTAGTCCGTTACAGTGCAAAATA	59.881	40.000	0.00	0.00	0.00	1.40
5230	5491	6.531439	GTTAGTCCGTTACAGTGCAAAATAG	58.469	40.000	0.00	0.00	0.00	1.73
5274	5537	4.454504	CGTTACAGGCCTGTTCTAACAATT	59.545	41.667	41.69	16.70	41.83	2.32
5340	5618	3.693654	CCTTGCAAATTTTTGTGTTGGC	58.306	40.909	0.00	0.00	40.24	4.52
5505	5804	2.091610	TGATGGAAAAGACCACACCCAA	60.092	45.455	0.00	0.00	43.03	4.12
5562	5861	6.293081	CCTTACACTATTGCCAGAATCGAATG	60.293	42.308	0.00	0.00	0.00	2.67
5740	6062	5.440207	TCAGGGATGATTCTGTGATGAAA	57.560	39.130	0.00	0.00	33.13	2.69
6073	6407	3.683365	TGCATCAGTACATGTGTCAGT	57.317	42.857	9.11	0.00	0.00	3.41
6240	6574	2.064581	ATGCCCTACGGTCTGGGTC	61.065	63.158	17.03	11.45	45.06	4.46
6416	6777	9.104126	GCTTGTTTATTTCTTTTTCGAGAGTAC	57.896	33.333	0.00	0.00	0.00	2.73
6470	6831	2.570365	TGCATTGTCCTGCATCCAC	58.430	52.632	0.00	0.00	46.76	4.02
6474	6835	2.954318	GCATTGTCCTGCATCCACTATT	59.046	45.455	0.00	0.00	41.87	1.73
6497	6858	3.568430	GGACTGTTTTGTAAGGGTTCCTG	59.432	47.826	0.00	0.00	32.13	3.86
6562	6927	2.028294	TGCGTCGGTTTATTTCCAGGTA	60.028	45.455	0.00	0.00	0.00	3.08
6706	7073	3.411446	CAGCTGTGGAGTTGGATTTGTA	58.589	45.455	5.25	0.00	0.00	2.41
6717	7084	6.206048	GGAGTTGGATTTGTATATTTACGGGG	59.794	42.308	0.00	0.00	0.00	5.73
6796	7163	5.513141	CGCTGTGTATACAAGGATATGATCG	59.487	44.000	7.25	1.41	36.14	3.69
6820	7752	1.209504	ACGGGTTCAGTGATATGGGTG	59.790	52.381	0.00	0.00	0.00	4.61
6877	7809	0.110509	GCATGCGCGTGAATCATAGG	60.111	55.000	32.94	3.44	0.00	2.57
6895	7827	2.272923	GGCGTATTTGGGCCTGTTT	58.727	52.632	4.53	0.00	45.93	2.83
6897	7829	0.601057	GCGTATTTGGGCCTGTTTGT	59.399	50.000	4.53	0.00	0.00	2.83
6913	7845	3.885814	GTCACAGGGACACAGGGA	58.114	61.111	0.00	0.00	46.19	4.20
6914	7846	2.377136	GTCACAGGGACACAGGGAT	58.623	57.895	0.00	0.00	46.19	3.85
6915	7847	0.250513	GTCACAGGGACACAGGGATC	59.749	60.000	0.00	0.00	46.19	3.36
6916	7848	0.178906	TCACAGGGACACAGGGATCA	60.179	55.000	0.00	0.00	0.00	2.92
6917	7849	0.251354	CACAGGGACACAGGGATCAG	59.749	60.000	0.00	0.00	0.00	2.90
6918	7850	1.222936	CAGGGACACAGGGATCAGC	59.777	63.158	0.00	0.00	0.00	4.26
6919	7851	1.081833	AGGGACACAGGGATCAGCT	59.918	57.895	0.00	0.00	0.00	4.24
6920	7852	0.548682	AGGGACACAGGGATCAGCTT	60.549	55.000	0.00	0.00	0.00	3.74

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
13	14	0.754957	AGAGATGTGGAGAGAGGCGG	60.755	60.000	0.00	0.00	0.00	6.13
85	86	2.685897	TCCACCTTAACACACAGCAAAC	59.314	45.455	0.00	0.00	0.00	2.93
112	113	5.841810	AGGGTTACAAATTCAACATGTGTG	58.158	37.500	0.00	0.09	0.00	3.82
213	220	5.340803	CGCTTATGCATAGTACGTGGATAT	58.659	41.667	6.50	0.00	39.64	1.63
469	479	7.201350	GCAAGAAAATAATCGGTGAACATCAAC	60.201	37.037	0.00	0.00	0.00	3.18
557	567	8.649973	TTAATTGCACGGAATTTTGTAAAAGT	57.350	26.923	1.72	0.00	0.00	2.66
632	642	9.950496	ATCAAGAAACTATCAACTACAATGAGT	57.050	29.630	0.00	0.00	0.00	3.41
802	812	4.199310	CGGTCCACATACAAGGAAATCAT	58.801	43.478	0.00	0.00	35.29	2.45
809	819	1.270625	ACACACGGTCCACATACAAGG	60.271	52.381	0.00	0.00	0.00	3.61
916	933	5.163332	TGCATCATCAAAGAGATACAGCTCT	60.163	40.000	0.00	0.00	46.81	4.09
1503	1520	6.174720	AGTATCTTGTTGACTTGGTCTTGA	57.825	37.500	0.00	0.00	33.15	3.02
1890	1907	6.255596	TCAGCTGTAAACTCACTACTGTAG	57.744	41.667	14.67	13.13	0.00	2.74
1989	2006	1.625818	TCTTGGTCTTCCTCCTGCTTC	59.374	52.381	0.00	0.00	34.23	3.86
2251	2268	4.148838	TGGTTATTTGGGTCCTTCAACAG	58.851	43.478	0.00	0.00	0.00	3.16
2943	2960	6.404734	CCATTTCCAAGTACTGGTAGAATTGC	60.405	42.308	0.00	0.00	46.51	3.56
3797	3857	6.745159	TTAGCGGCATATGACAAAACTTAA	57.255	33.333	9.77	0.00	0.00	1.85
3798	3858	6.745159	TTTAGCGGCATATGACAAAACTTA	57.255	33.333	9.77	0.00	0.00	2.24
3967	4112	0.324943	GCAGGAACACCTAGCCAGAA	59.675	55.000	0.00	0.00	32.14	3.02
3975	4120	0.328258	GTACCCATGCAGGAACACCT	59.672	55.000	0.00	0.00	41.22	4.00
3988	4133	0.327924	CCACTGATTGCAGGTACCCA	59.672	55.000	8.74	0.00	46.60	4.51
3999	4144	5.643421	AAATCCTAGATCTGCCACTGATT	57.357	39.130	5.18	2.04	0.00	2.57
4000	4145	5.131642	TCAAAATCCTAGATCTGCCACTGAT	59.868	40.000	5.18	0.00	0.00	2.90
4009	4154	4.476479	ACCCTGCTTCAAAATCCTAGATCT	59.524	41.667	0.00	0.00	0.00	2.75
4142	4288	7.702348	GGTACATAGGCTTTTCTTATGCAAAAG	59.298	37.037	0.00	3.87	41.79	2.27
4216	4362	9.148104	CATCACAGGATTACATACATGTATCAG	57.852	37.037	15.60	8.37	42.32	2.90
4351	4499	8.593945	TGAGCTGTAATTTCCAGGAATTTTAT	57.406	30.769	13.40	0.00	31.96	1.40
4466	4617	8.200792	TGTTGTGCTCCTTTGTAAATTGTAATT	58.799	29.630	0.00	0.00	0.00	1.40
4538	4689	1.753848	CCCATCGCCCAGCAATTCA	60.754	57.895	0.00	0.00	0.00	2.57
4540	4691	3.149648	GCCCATCGCCCAGCAATT	61.150	61.111	0.00	0.00	0.00	2.32
4546	4697	1.453745	GATTTCTGCCCATCGCCCA	60.454	57.895	0.00	0.00	36.24	5.36
4547	4698	1.152881	AGATTTCTGCCCATCGCCC	60.153	57.895	0.00	0.00	36.24	6.13
4548	4699	0.464373	TGAGATTTCTGCCCATCGCC	60.464	55.000	0.00	0.00	36.24	5.54
4549	4700	0.659957	GTGAGATTTCTGCCCATCGC	59.340	55.000	0.00	0.00	38.31	4.58
4550	4701	1.303309	GGTGAGATTTCTGCCCATCG	58.697	55.000	0.00	0.00	0.00	3.84
4568	4740	4.082125	AGCAATTCTTGAGGTACCTTTGG	58.918	43.478	17.53	9.08	0.00	3.28
4786	4976	2.510906	CCCAATTCCCCTCGCGAT	59.489	61.111	10.36	0.00	0.00	4.58
4946	5175	4.479993	GCAGGCAGTGGCGGATCT	62.480	66.667	20.72	0.00	42.47	2.75
4947	5176	4.783621	TGCAGGCAGTGGCGGATC	62.784	66.667	20.72	4.36	42.47	3.36
4948	5177	3.650298	ATTGCAGGCAGTGGCGGAT	62.650	57.895	20.72	3.17	42.47	4.18
4949	5178	4.349503	ATTGCAGGCAGTGGCGGA	62.350	61.111	20.72	9.60	42.47	5.54
4950	5179	4.124351	CATTGCAGGCAGTGGCGG	62.124	66.667	12.54	12.54	42.47	6.13
4951	5180	1.585267	TTACATTGCAGGCAGTGGCG	61.585	55.000	18.92	7.56	42.47	5.69
4952	5181	0.171903	CTTACATTGCAGGCAGTGGC	59.828	55.000	18.92	9.02	37.87	5.01
4953	5182	0.813184	CCTTACATTGCAGGCAGTGG	59.187	55.000	18.92	4.86	37.87	4.00
4959	5188	1.133790	GAAGCAGCCTTACATTGCAGG	59.866	52.381	0.00	0.00	40.22	4.85
4960	5189	2.089980	AGAAGCAGCCTTACATTGCAG	58.910	47.619	0.00	0.00	40.22	4.41
4961	5190	2.086869	GAGAAGCAGCCTTACATTGCA	58.913	47.619	0.00	0.00	40.22	4.08
4962	5191	2.097142	CAGAGAAGCAGCCTTACATTGC	59.903	50.000	0.00	0.00	38.09	3.56
4963	5192	3.341823	ACAGAGAAGCAGCCTTACATTG	58.658	45.455	0.00	0.00	0.00	2.82
5206	5467	4.799419	TTTTGCACTGTAACGGACTAAC	57.201	40.909	0.00	0.00	0.00	2.34
5207	5468	6.457355	TCTATTTTGCACTGTAACGGACTAA	58.543	36.000	0.00	0.00	0.00	2.24
5208	5469	6.028146	TCTATTTTGCACTGTAACGGACTA	57.972	37.500	0.00	0.00	0.00	2.59
5209	5470	4.890088	TCTATTTTGCACTGTAACGGACT	58.110	39.130	0.00	0.00	0.00	3.85
5210	5471	4.689345	ACTCTATTTTGCACTGTAACGGAC	59.311	41.667	0.00	0.00	0.00	4.79
5211	5472	4.688879	CACTCTATTTTGCACTGTAACGGA	59.311	41.667	0.00	0.00	0.00	4.69
5212	5473	4.451096	ACACTCTATTTTGCACTGTAACGG	59.549	41.667	0.00	0.00	0.00	4.44
5213	5474	5.591643	ACACTCTATTTTGCACTGTAACG	57.408	39.130	0.00	0.00	0.00	3.18
5215	5476	8.879759	GCTATAACACTCTATTTTGCACTGTAA	58.120	33.333	0.00	0.00	0.00	2.41
5216	5477	7.494625	GGCTATAACACTCTATTTTGCACTGTA	59.505	37.037	0.00	0.00	0.00	2.74
5217	5478	6.316390	GGCTATAACACTCTATTTTGCACTGT	59.684	38.462	0.00	0.00	0.00	3.55
5218	5479	6.316140	TGGCTATAACACTCTATTTTGCACTG	59.684	38.462	0.00	0.00	0.00	3.66
5219	5480	6.414732	TGGCTATAACACTCTATTTTGCACT	58.585	36.000	0.00	0.00	0.00	4.40
5220	5481	6.677781	TGGCTATAACACTCTATTTTGCAC	57.322	37.500	0.00	0.00	0.00	4.57
5226	5487	8.904834	CGGACTATATGGCTATAACACTCTATT	58.095	37.037	0.00	0.00	0.00	1.73
5227	5488	8.053963	ACGGACTATATGGCTATAACACTCTAT	58.946	37.037	0.00	0.00	0.00	1.98
5228	5489	7.400439	ACGGACTATATGGCTATAACACTCTA	58.600	38.462	0.00	0.00	0.00	2.43
5229	5490	6.246919	ACGGACTATATGGCTATAACACTCT	58.753	40.000	0.00	0.00	0.00	3.24
5230	5491	6.512342	ACGGACTATATGGCTATAACACTC	57.488	41.667	0.00	0.00	0.00	3.51
5340	5618	7.144661	AGTAGCAGATCATAATCAGAAGTTCG	58.855	38.462	0.00	0.00	34.07	3.95
5528	5827	3.306166	GCAATAGTGTAAGGTGTGCGTAG	59.694	47.826	0.00	0.00	0.00	3.51
5562	5861	0.326713	AGGAGGCTTAAGGGGGAGAC	60.327	60.000	4.29	0.00	0.00	3.36
5611	5910	0.602638	TCACTGTCCGTGTTCATGGC	60.603	55.000	6.21	3.16	44.16	4.40
5740	6062	2.375174	TCCCAAGACACCTATTGCAGTT	59.625	45.455	0.00	0.00	0.00	3.16
5959	6281	0.959553	GAAGACCCAGACTCGACACA	59.040	55.000	0.00	0.00	0.00	3.72
6073	6407	2.733956	ACACAAGTGAAAAAGGCTGGA	58.266	42.857	7.28	0.00	0.00	3.86
6142	6476	5.104941	CCCCCAATAAGAAATTGAAGGTTCC	60.105	44.000	0.00	0.00	0.00	3.62
6416	6777	7.305474	AGGAAACATGAAATAAACAAGCTACG	58.695	34.615	0.00	0.00	0.00	3.51
6470	6831	6.072119	GGAACCCTTACAAAACAGTCCAATAG	60.072	42.308	0.00	0.00	0.00	1.73
6474	6835	3.203487	AGGAACCCTTACAAAACAGTCCA	59.797	43.478	0.00	0.00	0.00	4.02
6497	6858	0.584876	CCGTCGAAGTTTTGACCACC	59.415	55.000	6.66	0.00	38.16	4.61
6706	7073	7.392393	GCCAAATTATACAGTCCCCGTAAATAT	59.608	37.037	0.00	0.00	0.00	1.28
6717	7084	5.006746	CAGAGTTCCGCCAAATTATACAGTC	59.993	44.000	0.00	0.00	0.00	3.51
6745	7112	6.368805	TGATACTGACACATGAGATAGGAGT	58.631	40.000	0.00	0.00	0.00	3.85
6796	7163	2.936498	CCATATCACTGAACCCGTTCAC	59.064	50.000	6.17	0.00	43.90	3.18
6820	7752	9.548208	GCAGTATGAAGAAAATAAGAGACAAAC	57.452	33.333	0.00	0.00	39.69	2.93
6877	7809	0.108851	CAAACAGGCCCAAATACGCC	60.109	55.000	0.00	0.00	46.09	5.68
6897	7829	0.178906	TGATCCCTGTGTCCCTGTGA	60.179	55.000	0.00	0.00	0.00	3.58

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.