AutoCloner

Multiple sequence alignment - TraesCS3A01G072000

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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	TraesCS3A01G072000	chr3A	100.000	4589	0	0	1	4589	44549052	44553640	0.000000e+00	8475.0
1	TraesCS3A01G072000	chr3A	96.000	625	25	0	3963	4587	386214955	386214331	0.000000e+00	1016.0
2	TraesCS3A01G072000	chr3A	92.153	497	32	7	108	599	44521424	44521918	0.000000e+00	695.0
3	TraesCS3A01G072000	chr3A	85.632	174	21	4	1160	1331	696290023	696289852	3.650000e-41	180.0
4	TraesCS3A01G072000	chr3A	85.632	174	21	4	1160	1331	696637412	696637583	3.650000e-41	180.0
5	TraesCS3A01G072000	chr3A	90.385	52	4	1	1438	1489	149716650	149716600	2.960000e-07	67.6
6	TraesCS3A01G072000	chr3D	96.704	3398	32	20	607	3963	32146380	32149738	0.000000e+00	5581.0
7	TraesCS3A01G072000	chr3D	95.335	493	16	5	108	598	32135453	32135940	0.000000e+00	776.0
8	TraesCS3A01G072000	chr3D	92.958	497	29	6	108	599	32128584	32129079	0.000000e+00	719.0
9	TraesCS3A01G072000	chr3D	85.057	174	22	4	1160	1331	560827070	560827241	1.700000e-39	174.0
10	TraesCS3A01G072000	chr3D	84.358	179	21	7	1160	1335	560112501	560112327	7.900000e-38	169.0
11	TraesCS3A01G072000	chr3D	80.172	232	37	9	1103	1331	560198818	560198593	1.020000e-36	165.0
12	TraesCS3A01G072000	chr3D	87.500	56	7	0	1438	1493	134963996	134963941	1.070000e-06	65.8
13	TraesCS3A01G072000	chr4D	97.063	3337	33	19	607	3916	35656163	35652865	0.000000e+00	5559.0
14	TraesCS3A01G072000	chr4D	96.094	128	3	2	1	126	322577143	322577016	1.670000e-49	207.0
15	TraesCS3A01G072000	chr4D	86.667	165	21	1	1162	1326	93761213	93761050	1.010000e-41	182.0
16	TraesCS3A01G072000	chr4D	86.538	52	7	0	1438	1489	98015409	98015358	1.780000e-04	58.4
17	TraesCS3A01G072000	chr3B	96.542	1735	17	15	2118	3815	54739511	54741239	0.000000e+00	2832.0
18	TraesCS3A01G072000	chr3B	93.946	1404	29	17	714	2099	54738098	54739463	0.000000e+00	2071.0
19	TraesCS3A01G072000	chr3B	92.929	495	30	4	108	599	54702468	54702960	0.000000e+00	715.0
20	TraesCS3A01G072000	chr3B	91.348	497	37	6	108	599	54659234	54659729	0.000000e+00	675.0
21	TraesCS3A01G072000	chr3B	80.687	233	35	10	1103	1331	744340634	744340408	6.100000e-39	172.0
22	TraesCS3A01G072000	chr3B	84.393	173	25	2	1160	1331	745540319	745540490	7.900000e-38	169.0
23	TraesCS3A01G072000	chr5A	96.491	627	22	0	3963	4589	456823534	456822908	0.000000e+00	1037.0
24	TraesCS3A01G072000	chr5A	79.397	597	83	27	1	583	338468579	338468009	7.200000e-103	385.0
25	TraesCS3A01G072000	chr5A	96.032	126	4	1	1	126	704725466	704725590	2.160000e-48	204.0
26	TraesCS3A01G072000	chr5A	96.032	126	4	1	1	126	704765417	704765541	2.160000e-48	204.0
27	TraesCS3A01G072000	chr2A	96.320	625	23	0	3965	4589	677032402	677031778	0.000000e+00	1027.0
28	TraesCS3A01G072000	chr2A	96.013	627	25	0	3963	4589	612058174	612057548	0.000000e+00	1020.0
29	TraesCS3A01G072000	chr4A	96.172	627	24	0	3963	4589	36751226	36751852	0.000000e+00	1026.0
30	TraesCS3A01G072000	chr4A	95.853	627	26	0	3963	4589	390558516	390559142	0.000000e+00	1014.0
31	TraesCS3A01G072000	chr4A	96.970	33	1	0	3780	3812	649897871	649897903	6.410000e-04	56.5
32	TraesCS3A01G072000	chrUn	96.013	627	25	0	3963	4589	48375778	48376404	0.000000e+00	1020.0
33	TraesCS3A01G072000	chrUn	83.146	178	25	5	1160	1335	301717344	301717518	1.710000e-34	158.0
34	TraesCS3A01G072000	chr6A	96.013	627	25	0	3963	4589	77599707	77599081	0.000000e+00	1020.0
35	TraesCS3A01G072000	chr6A	97.521	121	1	2	1	121	516577810	516577928	6.020000e-49	206.0
36	TraesCS3A01G072000	chr6A	100.000	30	0	0	3783	3812	129336922	129336893	6.410000e-04	56.5
37	TraesCS3A01G072000	chr1A	95.853	627	26	0	3963	4589	413530135	413530761	0.000000e+00	1014.0
38	TraesCS3A01G072000	chr1A	92.308	39	2	1	3779	3816	107481943	107481981	2.000000e-03	54.7
39	TraesCS3A01G072000	chr2D	80.000	505	77	21	108	599	476412711	476412218	7.300000e-93	351.0
40	TraesCS3A01G072000	chr2D	78.529	503	83	21	108	599	579355793	579356281	1.600000e-79	307.0
41	TraesCS3A01G072000	chr2D	75.460	652	91	48	1	599	345567144	345566509	2.120000e-63	254.0
42	TraesCS3A01G072000	chr2D	100.000	28	0	0	3785	3812	558797762	558797789	8.000000e-03	52.8
43	TraesCS3A01G072000	chr1B	78.547	592	83	33	1	572	434467807	434468374	2.630000e-92	350.0
44	TraesCS3A01G072000	chr5D	80.294	477	69	23	110	572	484617105	484617570	2.050000e-88	337.0
45	TraesCS3A01G072000	chr6D	78.854	506	79	24	108	599	272881086	272881577	2.660000e-82	316.0
46	TraesCS3A01G072000	chr6D	87.500	56	7	0	1438	1493	61003321	61003376	1.070000e-06	65.8
47	TraesCS3A01G072000	chr2B	76.970	495	82	26	110	582	563023300	563023784	2.120000e-63	254.0
48	TraesCS3A01G072000	chr2B	92.308	39	1	1	3776	3812	182707636	182707674	2.000000e-03	54.7
49	TraesCS3A01G072000	chr2B	100.000	28	0	0	3860	3887	53464063	53464090	8.000000e-03	52.8
50	TraesCS3A01G072000	chr7D	98.333	120	1	1	1	120	133564247	133564365	4.650000e-50	209.0
51	TraesCS3A01G072000	chr7B	93.525	139	5	3	1	136	29931374	29931511	2.160000e-48	204.0
52	TraesCS3A01G072000	chr4B	86.667	165	21	1	1162	1326	132294956	132294793	1.010000e-41	182.0
53	TraesCS3A01G072000	chr4B	86.275	51	5	2	1441	1489	139593650	139593600	2.000000e-03	54.7
54	TraesCS3A01G072000	chr6B	87.500	56	7	0	1438	1493	134838679	134838734	1.070000e-06	65.8
55	TraesCS3A01G072000	chr5B	100.000	29	0	0	3784	3812	426991482	426991510	2.000000e-03	54.7

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	TraesCS3A01G072000	chr3A	44549052	44553640	4588	False	8475.0	8475	100.000	1	4589	1	chr3A.!!$F2	4588
1	TraesCS3A01G072000	chr3A	386214331	386214955	624	True	1016.0	1016	96.000	3963	4587	1	chr3A.!!$R2	624
2	TraesCS3A01G072000	chr3D	32146380	32149738	3358	False	5581.0	5581	96.704	607	3963	1	chr3D.!!$F3	3356
3	TraesCS3A01G072000	chr4D	35652865	35656163	3298	True	5559.0	5559	97.063	607	3916	1	chr4D.!!$R1	3309
4	TraesCS3A01G072000	chr3B	54738098	54741239	3141	False	2451.5	2832	95.244	714	3815	2	chr3B.!!$F4	3101
5	TraesCS3A01G072000	chr5A	456822908	456823534	626	True	1037.0	1037	96.491	3963	4589	1	chr5A.!!$R2	626
6	TraesCS3A01G072000	chr5A	338468009	338468579	570	True	385.0	385	79.397	1	583	1	chr5A.!!$R1	582
7	TraesCS3A01G072000	chr2A	677031778	677032402	624	True	1027.0	1027	96.320	3965	4589	1	chr2A.!!$R2	624
8	TraesCS3A01G072000	chr2A	612057548	612058174	626	True	1020.0	1020	96.013	3963	4589	1	chr2A.!!$R1	626
9	TraesCS3A01G072000	chr4A	36751226	36751852	626	False	1026.0	1026	96.172	3963	4589	1	chr4A.!!$F1	626
10	TraesCS3A01G072000	chr4A	390558516	390559142	626	False	1014.0	1014	95.853	3963	4589	1	chr4A.!!$F2	626
11	TraesCS3A01G072000	chrUn	48375778	48376404	626	False	1020.0	1020	96.013	3963	4589	1	chrUn.!!$F1	626
12	TraesCS3A01G072000	chr6A	77599081	77599707	626	True	1020.0	1020	96.013	3963	4589	1	chr6A.!!$R1	626
13	TraesCS3A01G072000	chr1A	413530135	413530761	626	False	1014.0	1014	95.853	3963	4589	1	chr1A.!!$F2	626
14	TraesCS3A01G072000	chr2D	345566509	345567144	635	True	254.0	254	75.460	1	599	1	chr2D.!!$R1	598
15	TraesCS3A01G072000	chr1B	434467807	434468374	567	False	350.0	350	78.547	1	572	1	chr1B.!!$F1	571

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
326	353	0.178831	CCCTCCCCCTTGCCCTATAT	60.179	60.000	0.00	0.00	0.00	0.86	F
393	427	0.178918	CCTCCCCCTCTCATACTCCC	60.179	65.000	0.00	0.00	0.00	4.30	F
601	653	0.535102	GGGTCGCGATTTGGATCCAT	60.535	55.000	17.06	0.06	33.48	3.41	F
602	654	0.588252	GGTCGCGATTTGGATCCATG	59.412	55.000	17.06	7.34	0.00	3.66	F
937	1017	1.379044	CCATTCCCACCAGCTCCAC	60.379	63.158	0.00	0.00	0.00	4.02	F
1693	1782	2.040544	CCGGACACAAGCACATCCC	61.041	63.158	0.00	0.00	0.00	3.85	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1777	1866	2.124403	GGGGCATCTGTCCAGCAG	60.124	66.667	2.81	0.0	42.93	4.24	R
2237	2367	2.270352	TGGACTTGCCTTGGTGTTAG	57.730	50.000	0.00	0.0	37.63	2.34	R
2870	3021	0.587242	CGCGGCATTTTGAGACATCG	60.587	55.000	0.00	0.0	0.00	3.84	R
3032	3187	7.607607	TCTGCAAGAGAAATGATAGTGCTAAAA	59.392	33.333	0.00	0.0	38.67	1.52	R
3222	3377	5.928264	AGCACCATAGAGAATTTGCAAAAAC	59.072	36.000	17.19	12.8	32.24	2.43	R
4047	4219	0.108567	GGGCGTGAGGAAGAGAAGAC	60.109	60.000	0.00	0.0	0.00	3.01	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
145	146	1.751927	CACATGGGCTGAGAAGGGC	60.752	63.158	0.00	0.00	0.00	5.19
209	211	4.738998	CATGCGCCAAGGGTGGGA	62.739	66.667	4.18	0.00	46.09	4.37
211	213	3.944250	ATGCGCCAAGGGTGGGAAG	62.944	63.158	4.18	0.00	46.09	3.46
253	270	3.818787	CATGCTTGGCGGGCACTC	61.819	66.667	2.73	0.00	42.69	3.51
285	302	2.066999	GCCTCCGATCCCTCCTTGT	61.067	63.158	0.00	0.00	0.00	3.16
326	353	0.178831	CCCTCCCCCTTGCCCTATAT	60.179	60.000	0.00	0.00	0.00	0.86
361	389	2.903855	GGGCAGTCGCATCCCATG	60.904	66.667	0.00	0.00	41.24	3.66
386	420	2.610859	GCAACCCTCCCCCTCTCA	60.611	66.667	0.00	0.00	0.00	3.27
387	421	2.003548	GCAACCCTCCCCCTCTCAT	61.004	63.158	0.00	0.00	0.00	2.90
390	424	1.027815	AACCCTCCCCCTCTCATACT	58.972	55.000	0.00	0.00	0.00	2.12
393	427	0.178918	CCTCCCCCTCTCATACTCCC	60.179	65.000	0.00	0.00	0.00	4.30
402	436	0.178918	CTCATACTCCCCCTCCTCCC	60.179	65.000	0.00	0.00	0.00	4.30
403	437	1.534235	CATACTCCCCCTCCTCCCG	60.534	68.421	0.00	0.00	0.00	5.14
435	484	3.335356	AAGCCCTGCTGGATCACCG	62.335	63.158	11.88	0.00	39.62	4.94
436	485	3.785859	GCCCTGCTGGATCACCGA	61.786	66.667	11.88	0.00	39.42	4.69
438	487	2.362369	CCCTGCTGGATCACCGAGT	61.362	63.158	11.88	0.00	39.42	4.18
448	497	0.904649	ATCACCGAGTGCTCCATCAA	59.095	50.000	0.00	0.00	32.98	2.57
449	498	0.904649	TCACCGAGTGCTCCATCAAT	59.095	50.000	0.00	0.00	32.98	2.57
457	506	0.541392	TGCTCCATCAATACCACGCT	59.459	50.000	0.00	0.00	0.00	5.07
476	525	3.838271	TCGTGCTGCCGGAGATCC	61.838	66.667	5.05	0.00	0.00	3.36
478	527	3.785859	GTGCTGCCGGAGATCCCA	61.786	66.667	5.05	0.00	34.14	4.37
479	528	2.769621	TGCTGCCGGAGATCCCAT	60.770	61.111	5.05	0.00	34.14	4.00
492	542	4.086457	GAGATCCCATCTACTTCTCCTCC	58.914	52.174	0.00	0.00	40.38	4.30
573	625	3.455685	CCGTACGTTCGGTGCTTC	58.544	61.111	23.71	0.00	44.77	3.86
574	626	2.430942	CCGTACGTTCGGTGCTTCG	61.431	63.158	23.71	0.00	44.77	3.79
581	633	1.153901	TTCGGTGCTTCGTCGGATC	60.154	57.895	0.00	0.00	0.00	3.36
584	636	2.582498	GTGCTTCGTCGGATCGGG	60.582	66.667	0.00	0.00	0.00	5.14
588	640	4.183686	TTCGTCGGATCGGGTCGC	62.184	66.667	0.00	0.00	0.00	5.19
593	645	2.279252	CGGATCGGGTCGCGATTT	60.279	61.111	23.63	5.69	0.00	2.17
595	647	2.244651	GGATCGGGTCGCGATTTGG	61.245	63.158	23.63	2.23	0.00	3.28
596	648	1.227147	GATCGGGTCGCGATTTGGA	60.227	57.895	23.63	8.38	0.00	3.53
597	649	0.600255	GATCGGGTCGCGATTTGGAT	60.600	55.000	23.63	13.11	0.00	3.41
598	650	0.600255	ATCGGGTCGCGATTTGGATC	60.600	55.000	18.16	0.00	0.00	3.36
599	651	2.244651	CGGGTCGCGATTTGGATCC	61.245	63.158	14.06	4.20	0.00	3.36
600	652	1.153249	GGGTCGCGATTTGGATCCA	60.153	57.895	14.06	11.44	33.48	3.41
601	653	0.535102	GGGTCGCGATTTGGATCCAT	60.535	55.000	17.06	0.06	33.48	3.41
602	654	0.588252	GGTCGCGATTTGGATCCATG	59.412	55.000	17.06	7.34	0.00	3.66
603	655	1.581934	GTCGCGATTTGGATCCATGA	58.418	50.000	17.06	8.10	0.00	3.07
604	656	2.146342	GTCGCGATTTGGATCCATGAT	58.854	47.619	17.06	12.94	0.00	2.45
605	657	3.325870	GTCGCGATTTGGATCCATGATA	58.674	45.455	17.06	0.00	0.00	2.15
646	698	8.903820	AGGTTTAAGCTAAAACATCCATGATAC	58.096	33.333	0.00	0.00	40.42	2.24
672	724	5.982890	AAAAATGATCTCGAACCCACAAT	57.017	34.783	0.00	0.00	0.00	2.71
707	759	4.985538	AACTCGGTAACAGATGGAGTAG	57.014	45.455	0.00	0.00	36.99	2.57
745	797	5.376625	TGACAAACTAAAGAGGCATTGAGT	58.623	37.500	0.00	0.00	0.00	3.41
746	798	5.827797	TGACAAACTAAAGAGGCATTGAGTT	59.172	36.000	0.60	0.60	0.00	3.01
747	799	6.076981	ACAAACTAAAGAGGCATTGAGTTG	57.923	37.500	6.11	4.37	0.00	3.16
748	800	5.827797	ACAAACTAAAGAGGCATTGAGTTGA	59.172	36.000	6.11	0.00	0.00	3.18
749	801	6.016777	ACAAACTAAAGAGGCATTGAGTTGAG	60.017	38.462	6.11	5.45	0.00	3.02
774	826	8.508875	AGCTTGCCTTCAATTTCAAATTAAATG	58.491	29.630	0.00	0.00	0.00	2.32
775	827	7.751793	GCTTGCCTTCAATTTCAAATTAAATGG	59.248	33.333	0.00	0.94	0.00	3.16
776	828	8.915057	TTGCCTTCAATTTCAAATTAAATGGA	57.085	26.923	11.02	0.00	28.84	3.41
777	829	8.550710	TGCCTTCAATTTCAAATTAAATGGAG	57.449	30.769	11.02	0.00	31.88	3.86
937	1017	1.379044	CCATTCCCACCAGCTCCAC	60.379	63.158	0.00	0.00	0.00	4.02
938	1018	1.379044	CATTCCCACCAGCTCCACC	60.379	63.158	0.00	0.00	0.00	4.61
939	1019	2.971598	ATTCCCACCAGCTCCACCG	61.972	63.158	0.00	0.00	0.00	4.94
1693	1782	2.040544	CCGGACACAAGCACATCCC	61.041	63.158	0.00	0.00	0.00	3.85
1710	1799	4.162690	CACCTCCCGCCTACTGCC	62.163	72.222	0.00	0.00	36.24	4.85
1823	1912	3.640231	GCTCATGATCGCCAGAGC	58.360	61.111	11.13	11.13	45.50	4.09
2097	2186	4.133820	CCATCATGGTCCGTGCTTTAATA	58.866	43.478	6.17	0.00	31.35	0.98
2098	2187	4.024048	CCATCATGGTCCGTGCTTTAATAC	60.024	45.833	6.17	0.00	31.35	1.89
2100	2189	4.439057	TCATGGTCCGTGCTTTAATACTC	58.561	43.478	6.17	0.00	0.00	2.59
2102	2191	4.546829	TGGTCCGTGCTTTAATACTCTT	57.453	40.909	0.00	0.00	0.00	2.85
2103	2192	4.501071	TGGTCCGTGCTTTAATACTCTTC	58.499	43.478	0.00	0.00	0.00	2.87
2105	2194	5.176592	GGTCCGTGCTTTAATACTCTTCTT	58.823	41.667	0.00	0.00	0.00	2.52
2106	2195	6.071221	TGGTCCGTGCTTTAATACTCTTCTTA	60.071	38.462	0.00	0.00	0.00	2.10
2107	2196	6.815142	GGTCCGTGCTTTAATACTCTTCTTAA	59.185	38.462	0.00	0.00	0.00	1.85
2109	2198	9.525409	GTCCGTGCTTTAATACTCTTCTTAATA	57.475	33.333	0.00	0.00	0.00	0.98
2148	2269	5.499139	TCTTTAATTCCGAATCACCATGC	57.501	39.130	0.00	0.00	0.00	4.06
2149	2270	4.946772	TCTTTAATTCCGAATCACCATGCA	59.053	37.500	0.00	0.00	0.00	3.96
2151	2272	3.720949	AATTCCGAATCACCATGCATG	57.279	42.857	20.19	20.19	0.00	4.06
2152	2273	2.127271	TTCCGAATCACCATGCATGT	57.873	45.000	24.58	10.59	0.00	3.21
2153	2274	2.127271	TCCGAATCACCATGCATGTT	57.873	45.000	24.58	12.61	0.00	2.71
2155	2276	2.824936	TCCGAATCACCATGCATGTTTT	59.175	40.909	24.58	12.18	0.00	2.43
2156	2277	4.013050	TCCGAATCACCATGCATGTTTTA	58.987	39.130	24.58	8.18	0.00	1.52
2157	2278	4.460731	TCCGAATCACCATGCATGTTTTAA	59.539	37.500	24.58	6.46	0.00	1.52
2222	2347	6.757947	GCAGTATTACCACAAAATGCATCATT	59.242	34.615	0.00	0.00	35.39	2.57
2237	2367	6.847956	TGCATCATTAATTAATTTGCAGGC	57.152	33.333	26.70	17.00	37.34	4.85
3032	3187	5.473504	CAGTGACTATTAAGTGCCCAAGTTT	59.526	40.000	0.00	0.00	35.56	2.66
3079	3234	9.719355	TGCAGAAGACTATTGTTAGTTAAATGA	57.281	29.630	0.00	0.00	38.81	2.57
3141	3296	5.066505	GGAGTTTGTCTAAATGTATGGCTGG	59.933	44.000	0.00	0.00	0.00	4.85
3222	3377	1.401931	CCTTTTGGCATCGTGCTTCAG	60.402	52.381	9.31	2.65	44.28	3.02
3408	3563	6.655930	GGGTCTGGGTGACACTTATTTATAA	58.344	40.000	5.39	0.00	45.31	0.98
3462	3617	8.957466	GTCTAGGCTTCATTTTACCTTAAACAT	58.043	33.333	0.00	0.00	33.60	2.71
3718	3876	1.702182	TTCTTGGTGCCATGCTTTCA	58.298	45.000	0.00	0.00	0.00	2.69
3929	4101	5.299531	GGGAATTTGGGTTAGAGAGCAATAC	59.700	44.000	0.00	0.00	0.00	1.89
4047	4219	2.222886	CCGAACAGTGCATCTCATTTCG	60.223	50.000	0.00	3.93	35.68	3.46
4069	4241	0.040646	TTCTCTTCCTCACGCCCCTA	59.959	55.000	0.00	0.00	0.00	3.53
4174	4346	2.040544	CGGGCAAAGAAGGCGACAT	61.041	57.895	0.00	0.00	34.40	3.06
4284	4456	3.230134	CTCGAGGATCTCCCAAGAAGAT	58.770	50.000	3.91	0.00	37.41	2.40
4290	4462	3.831911	GGATCTCCCAAGAAGATCTCGAT	59.168	47.826	11.66	0.00	38.66	3.59
4398	4570	1.528309	CCTTCTTGCCACCCACGTT	60.528	57.895	0.00	0.00	0.00	3.99
4401	4573	0.179004	TTCTTGCCACCCACGTTGAT	60.179	50.000	0.00	0.00	0.00	2.57
4510	4682	1.392168	TCGTTTATCTTGCCGCTTTCG	59.608	47.619	0.00	0.00	0.00	3.46
4551	4723	1.150536	GGGTTGTTGGCCTCACTGA	59.849	57.895	3.32	0.00	0.00	3.41

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
148	149	4.473520	CCACTAGGGGCTGGTGCG	62.474	72.222	0.00	0.00	40.77	5.34
171	173	4.176752	CCTAGGGGGTTGAGGCGC	62.177	72.222	0.00	0.00	0.00	6.53
200	202	1.736491	GGGTTTCCCTTCCCACCCTT	61.736	60.000	0.00	0.00	45.04	3.95
262	279	3.117648	AGGGATCGGAGGCCCCTA	61.118	66.667	13.43	0.00	45.20	3.53
265	282	4.565850	AGGAGGGATCGGAGGCCC	62.566	72.222	0.00	10.00	41.68	5.80
270	287	0.931468	TCCTACAAGGAGGGATCGGA	59.069	55.000	0.00	0.00	40.06	4.55
386	420	2.944271	CGGGAGGAGGGGGAGTAT	59.056	66.667	0.00	0.00	0.00	2.12
430	479	0.904649	ATTGATGGAGCACTCGGTGA	59.095	50.000	8.04	0.00	35.23	4.02
431	480	2.205074	GTATTGATGGAGCACTCGGTG	58.795	52.381	0.25	0.25	36.51	4.94
435	484	2.205074	CGTGGTATTGATGGAGCACTC	58.795	52.381	3.13	0.00	40.96	3.51
436	485	1.743772	GCGTGGTATTGATGGAGCACT	60.744	52.381	3.13	0.00	40.96	4.40
438	487	0.541392	AGCGTGGTATTGATGGAGCA	59.459	50.000	0.00	0.00	0.00	4.26
457	506	3.356639	GATCTCCGGCAGCACGACA	62.357	63.158	0.00	0.00	35.47	4.35
476	525	1.723288	GGGGGAGGAGAAGTAGATGG	58.277	60.000	0.00	0.00	0.00	3.51
492	542	0.332632	TTCTTGATCCAGCAAGGGGG	59.667	55.000	4.79	0.00	44.14	5.40
560	611	2.728383	CGACGAAGCACCGAACGT	60.728	61.111	4.78	0.00	41.57	3.99
581	633	2.244651	GGATCCAAATCGCGACCCG	61.245	63.158	12.93	1.50	38.61	5.28
584	636	1.581934	TCATGGATCCAAATCGCGAC	58.418	50.000	20.67	0.00	32.24	5.19
588	640	6.294176	GGGACTTTTATCATGGATCCAAATCG	60.294	42.308	20.67	7.99	32.24	3.34
593	645	5.464588	TTGGGACTTTTATCATGGATCCA	57.535	39.130	18.88	18.88	0.00	3.41
595	647	7.000472	TGAGATTGGGACTTTTATCATGGATC	59.000	38.462	0.00	0.00	0.00	3.36
596	648	6.914665	TGAGATTGGGACTTTTATCATGGAT	58.085	36.000	0.00	0.00	0.00	3.41
597	649	6.325993	TGAGATTGGGACTTTTATCATGGA	57.674	37.500	0.00	0.00	0.00	3.41
598	650	5.533903	CCTGAGATTGGGACTTTTATCATGG	59.466	44.000	0.00	0.00	0.00	3.66
599	651	6.125029	ACCTGAGATTGGGACTTTTATCATG	58.875	40.000	0.00	0.00	0.00	3.07
600	652	6.332976	ACCTGAGATTGGGACTTTTATCAT	57.667	37.500	0.00	0.00	0.00	2.45
601	653	5.779241	ACCTGAGATTGGGACTTTTATCA	57.221	39.130	0.00	0.00	0.00	2.15
602	654	8.575649	TTAAACCTGAGATTGGGACTTTTATC	57.424	34.615	0.00	0.00	0.00	1.75
603	655	7.122799	GCTTAAACCTGAGATTGGGACTTTTAT	59.877	37.037	0.00	0.00	0.00	1.40
604	656	6.433093	GCTTAAACCTGAGATTGGGACTTTTA	59.567	38.462	0.00	0.00	0.00	1.52
605	657	5.243954	GCTTAAACCTGAGATTGGGACTTTT	59.756	40.000	0.00	0.00	0.00	2.27
672	724	9.672086	CTGTTACCGAGTTTAATGAAAATGAAA	57.328	29.630	0.00	0.00	0.00	2.69
707	759	1.909700	TGTCAAATGAGGGAAGCACC	58.090	50.000	0.00	0.00	38.08	5.01
745	797	4.669206	TTGAAATTGAAGGCAAGCTCAA	57.331	36.364	0.00	0.16	37.45	3.02
746	798	4.669206	TTTGAAATTGAAGGCAAGCTCA	57.331	36.364	0.00	0.00	37.45	4.26
747	799	7.656707	TTAATTTGAAATTGAAGGCAAGCTC	57.343	32.000	13.08	0.00	37.45	4.09
748	800	8.508875	CATTTAATTTGAAATTGAAGGCAAGCT	58.491	29.630	13.08	0.00	37.45	3.74
749	801	7.751793	CCATTTAATTTGAAATTGAAGGCAAGC	59.248	33.333	13.08	0.00	37.45	4.01
774	826	1.222113	GCTCCTACTTGGTGCCTCC	59.778	63.158	0.00	0.00	46.47	4.30
775	827	4.943822	GCTCCTACTTGGTGCCTC	57.056	61.111	0.00	0.00	46.47	4.70
1350	1436	3.649277	CTCGCGGAACTGGGTGGAG	62.649	68.421	6.13	0.00	0.00	3.86
1693	1782	4.162690	GGCAGTAGGCGGGAGGTG	62.163	72.222	0.00	0.00	46.16	4.00
1777	1866	2.124403	GGGGCATCTGTCCAGCAG	60.124	66.667	2.81	0.00	42.93	4.24
2131	2252	3.025978	ACATGCATGGTGATTCGGAATT	58.974	40.909	29.41	1.63	0.00	2.17
2222	2347	6.842437	TGGTGTTAGCCTGCAAATTAATTA	57.158	33.333	0.01	0.00	0.00	1.40
2237	2367	2.270352	TGGACTTGCCTTGGTGTTAG	57.730	50.000	0.00	0.00	37.63	2.34
2870	3021	0.587242	CGCGGCATTTTGAGACATCG	60.587	55.000	0.00	0.00	0.00	3.84
3032	3187	7.607607	TCTGCAAGAGAAATGATAGTGCTAAAA	59.392	33.333	0.00	0.00	38.67	1.52
3222	3377	5.928264	AGCACCATAGAGAATTTGCAAAAAC	59.072	36.000	17.19	12.80	32.24	2.43
3423	3578	6.143915	TGAAGCCTAGACTTATGTCCCTATT	58.856	40.000	5.19	0.00	43.91	1.73
4047	4219	0.108567	GGGCGTGAGGAAGAGAAGAC	60.109	60.000	0.00	0.00	0.00	3.01
4284	4456	1.205655	CCTTCAGCCAAGTCATCGAGA	59.794	52.381	0.00	0.00	0.00	4.04
4290	4462	3.170362	CCCCCTTCAGCCAAGTCA	58.830	61.111	0.00	0.00	0.00	3.41
4398	4570	2.091541	GGCAAGGAAAATCCACGATCA	58.908	47.619	0.00	0.00	39.61	2.92
4401	4573	0.610785	GGGGCAAGGAAAATCCACGA	60.611	55.000	0.00	0.00	39.61	4.35
4510	4682	5.449177	CCAGGAAGTTCTCACACAAAGAAAC	60.449	44.000	2.25	0.00	34.68	2.78
4551	4723	6.479884	AGTGAAAATATGCTTGAAGAGACCT	58.520	36.000	0.00	0.00	0.00	3.85

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.