AutoCloner

Multiple sequence alignment - TraesCS3B01G252500

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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	TraesCS3B01G252500	chr3B	100.000	5807	0	0	1	5807	405779382	405785188	0.000000e+00	10724.0
1	TraesCS3B01G252500	chr3B	99.173	967	6	2	4842	5807	754927488	754926523	0.000000e+00	1740.0
2	TraesCS3B01G252500	chr3D	96.383	2516	79	6	2373	4882	313818677	313816168	0.000000e+00	4132.0
3	TraesCS3B01G252500	chr3D	92.097	949	43	19	665	1592	313820752	313819815	0.000000e+00	1308.0
4	TraesCS3B01G252500	chr3D	88.139	489	38	11	1	482	313821752	313821277	1.090000e-156	564.0
5	TraesCS3B01G252500	chr3D	89.286	224	18	6	467	689	313820975	313820757	5.730000e-70	276.0
6	TraesCS3B01G252500	chr3A	93.787	2543	91	30	678	3156	416312928	416310389	0.000000e+00	3759.0
7	TraesCS3B01G252500	chr3A	96.312	1437	45	3	3419	4849	416307843	416306409	0.000000e+00	2353.0
8	TraesCS3B01G252500	chr3A	88.988	672	52	10	1	665	416313566	416312910	0.000000e+00	811.0
9	TraesCS3B01G252500	chr3A	95.745	282	11	1	3154	3434	416310082	416309801	2.470000e-123	453.0
10	TraesCS3B01G252500	chr3A	89.286	112	9	3	2233	2344	679924278	679924170	2.820000e-28	137.0
11	TraesCS3B01G252500	chr6A	86.183	1766	170	31	2360	4106	586837644	586835934	0.000000e+00	1842.0
12	TraesCS3B01G252500	chr6A	82.552	533	42	20	1722	2222	586838181	586837668	6.960000e-114	422.0
13	TraesCS3B01G252500	chr7A	99.478	958	5	0	4850	5807	124663551	124664508	0.000000e+00	1742.0
14	TraesCS3B01G252500	chr7A	99.172	966	7	1	4843	5807	2015438	2014473	0.000000e+00	1738.0
15	TraesCS3B01G252500	chr7A	92.126	127	7	2	2219	2342	400068824	400068950	5.980000e-40	176.0
16	TraesCS3B01G252500	chr7A	90.909	121	9	1	2222	2340	667232138	667232018	1.670000e-35	161.0
17	TraesCS3B01G252500	chr7B	99.174	968	5	3	4841	5807	220958904	220959869	0.000000e+00	1740.0
18	TraesCS3B01G252500	chr7B	99.068	966	7	2	4842	5807	6168656	6167693	0.000000e+00	1733.0
19	TraesCS3B01G252500	chr7B	86.777	121	10	6	4124	4243	48465500	48465615	4.720000e-26	130.0
20	TraesCS3B01G252500	chr7B	88.571	70	8	0	1345	1414	511463109	511463040	1.040000e-12	86.1
21	TraesCS3B01G252500	chr4A	99.478	958	4	1	4850	5807	658636041	658636997	0.000000e+00	1740.0
22	TraesCS3B01G252500	chr4A	92.126	127	8	2	2219	2344	617850698	617850573	1.660000e-40	178.0
23	TraesCS3B01G252500	chr4A	85.211	142	10	8	4114	4248	543368437	543368300	1.010000e-27	135.0
24	TraesCS3B01G252500	chr2A	99.070	968	8	1	4841	5807	277940339	277941306	0.000000e+00	1736.0
25	TraesCS3B01G252500	chr2A	91.339	127	9	1	2219	2343	88010248	88010122	7.740000e-39	172.0
26	TraesCS3B01G252500	chr1B	99.068	966	8	1	4842	5807	467199199	467198235	0.000000e+00	1733.0
27	TraesCS3B01G252500	chr5B	98.671	978	9	4	4833	5807	32473902	32474878	0.000000e+00	1731.0
28	TraesCS3B01G252500	chr5B	91.603	131	8	2	2217	2344	693677507	693677637	1.660000e-40	178.0
29	TraesCS3B01G252500	chr6D	87.100	938	90	7	2360	3293	438308710	438307800	0.000000e+00	1033.0
30	TraesCS3B01G252500	chr6D	88.060	335	29	2	3499	3822	438305479	438305145	2.540000e-103	387.0
31	TraesCS3B01G252500	chr6D	90.530	264	23	2	3853	4116	438305145	438304884	1.200000e-91	348.0
32	TraesCS3B01G252500	chr6D	84.328	134	13	5	4124	4254	153810665	153810793	2.200000e-24	124.0
33	TraesCS3B01G252500	chr6B	85.926	945	93	21	2360	3296	663709882	663708970	0.000000e+00	972.0
34	TraesCS3B01G252500	chr6B	83.397	524	44	19	1722	2222	663710409	663709906	4.130000e-121	446.0
35	TraesCS3B01G252500	chr6B	91.257	183	16	0	3551	3733	663706416	663706234	3.470000e-62	250.0
36	TraesCS3B01G252500	chr6B	91.765	85	7	0	3722	3806	663698166	663698082	1.020000e-22	119.0
37	TraesCS3B01G252500	chr6B	91.935	62	5	0	2219	2280	713117910	713117971	2.880000e-13	87.9
38	TraesCS3B01G252500	chr5A	93.750	128	6	1	2219	2344	494231046	494231173	2.140000e-44	191.0
39	TraesCS3B01G252500	chr2D	93.798	129	5	2	2219	2344	87754317	87754189	2.140000e-44	191.0
40	TraesCS3B01G252500	chr2D	86.667	135	5	6	4125	4249	133769546	133769415	2.820000e-28	137.0
41	TraesCS3B01G252500	chr1D	92.000	125	8	1	2222	2344	324746968	324747092	2.150000e-39	174.0
42	TraesCS3B01G252500	chr1D	93.258	89	6	0	4016	4104	484391666	484391578	1.310000e-26	132.0
43	TraesCS3B01G252500	chr7D	86.777	121	10	6	4124	4243	94441114	94441229	4.720000e-26	130.0
44	TraesCS3B01G252500	chr7D	82.993	147	15	8	4114	4254	242791483	242791341	2.200000e-24	124.0
45	TraesCS3B01G252500	chr4D	84.507	142	11	8	4114	4248	53759994	53760131	4.720000e-26	130.0

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	TraesCS3B01G252500	chr3B	405779382	405785188	5806	False	10724.000000	10724	100.000000	1	5807	1	chr3B.!!$F1	5806
1	TraesCS3B01G252500	chr3B	754926523	754927488	965	True	1740.000000	1740	99.173000	4842	5807	1	chr3B.!!$R1	965
2	TraesCS3B01G252500	chr3D	313816168	313821752	5584	True	1570.000000	4132	91.476250	1	4882	4	chr3D.!!$R1	4881
3	TraesCS3B01G252500	chr3A	416306409	416313566	7157	True	1844.000000	3759	93.708000	1	4849	4	chr3A.!!$R2	4848
4	TraesCS3B01G252500	chr6A	586835934	586838181	2247	True	1132.000000	1842	84.367500	1722	4106	2	chr6A.!!$R1	2384
5	TraesCS3B01G252500	chr7A	124663551	124664508	957	False	1742.000000	1742	99.478000	4850	5807	1	chr7A.!!$F1	957
6	TraesCS3B01G252500	chr7A	2014473	2015438	965	True	1738.000000	1738	99.172000	4843	5807	1	chr7A.!!$R1	964
7	TraesCS3B01G252500	chr7B	220958904	220959869	965	False	1740.000000	1740	99.174000	4841	5807	1	chr7B.!!$F2	966
8	TraesCS3B01G252500	chr7B	6167693	6168656	963	True	1733.000000	1733	99.068000	4842	5807	1	chr7B.!!$R1	965
9	TraesCS3B01G252500	chr4A	658636041	658636997	956	False	1740.000000	1740	99.478000	4850	5807	1	chr4A.!!$F1	957
10	TraesCS3B01G252500	chr2A	277940339	277941306	967	False	1736.000000	1736	99.070000	4841	5807	1	chr2A.!!$F1	966
11	TraesCS3B01G252500	chr1B	467198235	467199199	964	True	1733.000000	1733	99.068000	4842	5807	1	chr1B.!!$R1	965
12	TraesCS3B01G252500	chr5B	32473902	32474878	976	False	1731.000000	1731	98.671000	4833	5807	1	chr5B.!!$F1	974
13	TraesCS3B01G252500	chr6D	438304884	438308710	3826	True	589.333333	1033	88.563333	2360	4116	3	chr6D.!!$R1	1756
14	TraesCS3B01G252500	chr6B	663706234	663710409	4175	True	556.000000	972	86.860000	1722	3733	3	chr6B.!!$R2	2011

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
734	1124	0.108138	CCTTCGAACCGAATGAGCCT	60.108	55.000	0.00	0.0	44.85	4.58	F
1110	1526	1.003696	AGGCCAGTGAGCTTTAAGACC	59.996	52.381	5.01	0.0	0.00	3.85	F
1490	1915	1.271379	TCACTCGTTATCGCTGGTTGT	59.729	47.619	0.00	0.0	36.96	3.32	F
2246	2925	0.539438	TGCTACCCTTTGGCTGTTGG	60.539	55.000	0.00	0.0	33.59	3.77	F
3294	4506	0.769247	GGGTGGAAACTGGTAGTGGT	59.231	55.000	0.00	0.0	0.00	4.16	F
3984	11629	1.004628	TCATGTATGCACTTGGCCACT	59.995	47.619	3.88	0.0	43.89	4.00	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1689	2145	3.055530	GTGATTGTGTCTCCTCATCACCT	60.056	47.826	0.00	0.00	33.04	4.00	R
2146	2816	5.047847	TCGTTTATAGGTGCTTGATAGTGC	58.952	41.667	0.00	0.00	0.00	4.40	R
3453	8775	2.929161	GCCAACCCCGAAATTTAAGCAC	60.929	50.000	0.00	0.00	0.00	4.40	R
3984	11629	5.244851	TGCAAATACTCAAGTAAATTGCCCA	59.755	36.000	25.31	14.64	45.96	5.36	R
4680	12331	1.047002	CCCCCTTCACAAATGCAACA	58.953	50.000	0.00	0.00	0.00	3.33	R
4846	12497	2.709397	ACGGGCCCTTTTGCTAGTATAT	59.291	45.455	22.43	0.00	0.00	0.86	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
78	84	6.722328	AGTTTAAAAATAGAGTAGCTGGGCT	58.278	36.000	0.00	0.00	43.41	5.19
79	85	7.858498	AGTTTAAAAATAGAGTAGCTGGGCTA	58.142	34.615	0.00	0.00	40.44	3.93
84	90	5.693769	AATAGAGTAGCTGGGCTAAAACA	57.306	39.130	0.00	0.00	43.07	2.83
173	179	2.748461	TGCACGAAAAAGGAAGAACG	57.252	45.000	0.00	0.00	0.00	3.95
180	186	4.820173	ACGAAAAAGGAAGAACGAGGATTT	59.180	37.500	0.00	0.00	0.00	2.17
199	205	4.532314	TTTAAACTCGGGTCTCCTCTTC	57.468	45.455	0.00	0.00	0.00	2.87
200	206	0.889306	AAACTCGGGTCTCCTCTTCG	59.111	55.000	0.00	0.00	0.00	3.79
201	207	0.966370	AACTCGGGTCTCCTCTTCGG	60.966	60.000	0.00	0.00	0.00	4.30
202	208	1.077644	CTCGGGTCTCCTCTTCGGA	60.078	63.158	0.00	0.00	40.30	4.55
269	275	0.831711	AAACATTTGGGGCCTCGCTT	60.832	50.000	0.84	0.00	0.00	4.68
312	318	3.435671	CGGCGACTTAGAAGGAAAAACAT	59.564	43.478	0.00	0.00	0.00	2.71
338	348	3.586470	TTCCATTTACCGGTGGCATAT	57.414	42.857	19.93	0.00	35.43	1.78
348	358	1.885887	CGGTGGCATATGGGGTAATTG	59.114	52.381	4.56	0.00	0.00	2.32
359	369	7.255942	GCATATGGGGTAATTGCTGATAACTTT	60.256	37.037	4.56	0.00	0.00	2.66
374	385	7.939588	GCTGATAACTTTAGGGGTAAATCTGAT	59.060	37.037	0.00	0.00	0.00	2.90
394	405	1.569479	GACGGGCAGACAGAAGCAAC	61.569	60.000	0.00	0.00	0.00	4.17
396	407	1.165907	CGGGCAGACAGAAGCAACAA	61.166	55.000	0.00	0.00	0.00	2.83
400	411	1.299541	CAGACAGAAGCAACAACCGT	58.700	50.000	0.00	0.00	0.00	4.83
482	812	9.801873	TTTTAATAATAAAAGTGCCATGCTCTC	57.198	29.630	0.00	0.00	36.36	3.20
574	904	1.134965	CCCAAAAGCAAACCGACAACA	60.135	47.619	0.00	0.00	0.00	3.33
588	918	1.597663	GACAACAGAACCGGTGAACTG	59.402	52.381	25.00	25.00	36.58	3.16
607	938	1.020861	GGCGGTCCGACGGTAAAAAT	61.021	55.000	17.49	0.00	0.00	1.82
615	946	3.055675	TCCGACGGTAAAAATCTGACCAT	60.056	43.478	14.79	0.00	32.39	3.55
650	1040	5.390145	CGATTCGATTACCTGTTCGGTTTTT	60.390	40.000	0.00	0.00	46.37	1.94
651	1041	4.996062	TCGATTACCTGTTCGGTTTTTC	57.004	40.909	0.00	0.00	46.37	2.29
652	1042	4.378774	TCGATTACCTGTTCGGTTTTTCA	58.621	39.130	0.00	0.00	46.37	2.69
653	1043	4.815308	TCGATTACCTGTTCGGTTTTTCAA	59.185	37.500	0.00	0.00	46.37	2.69
654	1044	5.296283	TCGATTACCTGTTCGGTTTTTCAAA	59.704	36.000	0.00	0.00	46.37	2.69
655	1045	5.397240	CGATTACCTGTTCGGTTTTTCAAAC	59.603	40.000	0.00	0.00	46.37	2.93
656	1046	5.900865	TTACCTGTTCGGTTTTTCAAACT	57.099	34.783	0.00	0.00	46.37	2.66
657	1047	4.365899	ACCTGTTCGGTTTTTCAAACTC	57.634	40.909	0.00	0.00	46.37	3.01
658	1048	4.014406	ACCTGTTCGGTTTTTCAAACTCT	58.986	39.130	0.00	0.00	46.37	3.24
659	1049	4.142469	ACCTGTTCGGTTTTTCAAACTCTG	60.142	41.667	0.00	0.00	46.37	3.35
660	1050	3.765026	TGTTCGGTTTTTCAAACTCTGC	58.235	40.909	0.00	0.00	0.00	4.26
661	1051	3.442273	TGTTCGGTTTTTCAAACTCTGCT	59.558	39.130	0.00	0.00	0.00	4.24
662	1052	4.636648	TGTTCGGTTTTTCAAACTCTGCTA	59.363	37.500	0.00	0.00	0.00	3.49
663	1053	4.806342	TCGGTTTTTCAAACTCTGCTAC	57.194	40.909	0.00	0.00	0.00	3.58
664	1054	4.448210	TCGGTTTTTCAAACTCTGCTACT	58.552	39.130	0.00	0.00	0.00	2.57
665	1055	4.879545	TCGGTTTTTCAAACTCTGCTACTT	59.120	37.500	0.00	0.00	0.00	2.24
666	1056	5.355910	TCGGTTTTTCAAACTCTGCTACTTT	59.644	36.000	0.00	0.00	0.00	2.66
667	1057	6.033966	CGGTTTTTCAAACTCTGCTACTTTT	58.966	36.000	0.00	0.00	0.00	2.27
668	1058	6.530181	CGGTTTTTCAAACTCTGCTACTTTTT	59.470	34.615	0.00	0.00	0.00	1.94
734	1124	0.108138	CCTTCGAACCGAATGAGCCT	60.108	55.000	0.00	0.00	44.85	4.58
748	1138	3.608432	GCCTTTAGCTGGGCCTTG	58.392	61.111	4.53	0.00	42.30	3.61
810	1207	2.048222	TCGTCAAAGCCAGCTCGG	60.048	61.111	0.00	0.00	38.11	4.63
848	1245	4.367023	CCGCAGAACCGAACGGGA	62.367	66.667	17.44	0.00	41.95	5.14
911	1308	2.515996	GAATTCACGCCCGGACTCCA	62.516	60.000	0.73	0.00	0.00	3.86
1110	1526	1.003696	AGGCCAGTGAGCTTTAAGACC	59.996	52.381	5.01	0.00	0.00	3.85
1121	1537	2.609916	GCTTTAAGACCAAGAGGATCGC	59.390	50.000	0.00	0.00	42.67	4.58
1174	1590	2.351276	GGGCCACCAAGACGATGT	59.649	61.111	4.39	0.00	36.50	3.06
1198	1621	4.933064	CCTCATCGTCCGCTCGGC	62.933	72.222	2.96	0.00	34.68	5.54
1199	1622	3.893763	CTCATCGTCCGCTCGGCT	61.894	66.667	2.96	0.00	34.68	5.52
1230	1653	3.288381	AGAGAGGTGGGGGAGGCT	61.288	66.667	0.00	0.00	0.00	4.58
1339	1762	2.736347	TGACCCTACTGTTCTCTAGGC	58.264	52.381	0.00	0.00	0.00	3.93
1341	1764	1.361543	ACCCTACTGTTCTCTAGGCCA	59.638	52.381	5.01	0.00	0.00	5.36
1442	1867	2.047830	GGGGTAAGATGGTCACTAGGG	58.952	57.143	0.00	0.00	0.00	3.53
1446	1871	4.226620	GGGTAAGATGGTCACTAGGGAAAA	59.773	45.833	0.00	0.00	0.00	2.29
1447	1872	5.280830	GGGTAAGATGGTCACTAGGGAAAAA	60.281	44.000	0.00	0.00	0.00	1.94
1490	1915	1.271379	TCACTCGTTATCGCTGGTTGT	59.729	47.619	0.00	0.00	36.96	3.32
1504	1958	3.119849	GCTGGTTGTCGCATTTGTAGATT	60.120	43.478	0.00	0.00	0.00	2.40
1505	1959	4.094294	GCTGGTTGTCGCATTTGTAGATTA	59.906	41.667	0.00	0.00	0.00	1.75
1664	2120	2.336945	TTCCTAGTCCGCGTAGATGA	57.663	50.000	4.92	0.00	0.00	2.92
1694	2150	6.822442	TGTCAAGTACATACTTCAAAGGTGA	58.178	36.000	1.18	0.00	44.19	4.02
1867	2330	6.795114	GCTGAAAATTGCAAAAATGTCTCATG	59.205	34.615	1.71	0.00	0.00	3.07
1901	2364	7.338703	ACAGATTCTGTAATTAGTACTCGGTGA	59.661	37.037	17.63	0.00	43.46	4.02
1978	2441	1.400242	GGCGTCAATTGCTTGTGTCTC	60.400	52.381	0.00	0.00	33.87	3.36
2146	2816	1.071542	TGGTGATGTGTGGTACTGTGG	59.928	52.381	0.00	0.00	0.00	4.17
2246	2925	0.539438	TGCTACCCTTTGGCTGTTGG	60.539	55.000	0.00	0.00	33.59	3.77
2324	3216	7.929245	TGACTAAATATATGCTAAACGGCTTGA	59.071	33.333	0.00	0.00	0.00	3.02
2362	3254	6.711277	ACATATCCATATCGGTGCAAAGTAT	58.289	36.000	0.00	0.00	35.57	2.12
2646	3538	4.101790	GGTGGTTCATGTGCCGCG	62.102	66.667	0.00	0.00	36.21	6.46
2750	3642	5.805486	TGATGTTTACTCATGAGCGTTACTC	59.195	40.000	22.83	13.00	46.45	2.59
2757	3649	5.003804	ACTCATGAGCGTTACTCCAAAATT	58.996	37.500	22.83	0.00	45.61	1.82
2777	3673	9.330063	CAAAATTATTCAGTGCATCTAGTAGGA	57.670	33.333	0.00	0.00	0.00	2.94
3131	4034	8.984891	TTTAAATTTGCGATGAATCTCATTGT	57.015	26.923	0.00	0.00	39.82	2.71
3136	4039	2.604914	GCGATGAATCTCATTGTGACGT	59.395	45.455	0.00	0.00	39.82	4.34
3138	4041	4.267690	GCGATGAATCTCATTGTGACGTAA	59.732	41.667	5.90	0.00	39.82	3.18
3242	4454	9.434420	ACATTCACTTTTCTTTGTCAAATGAAA	57.566	25.926	11.71	12.94	37.55	2.69
3294	4506	0.769247	GGGTGGAAACTGGTAGTGGT	59.231	55.000	0.00	0.00	0.00	4.16
3376	4593	5.245751	ACTGAAAATGCATATGGGAAACACA	59.754	36.000	0.00	0.00	0.00	3.72
3453	8775	7.041440	TGTTGGATAATGCATTTATGTCGTAGG	60.041	37.037	18.75	0.00	30.44	3.18
3698	11343	1.550976	AGTGGTAAGCCTGACACTAGC	59.449	52.381	0.00	0.00	41.95	3.42
3916	11561	8.397575	TCATTAACTTGCTGTTGTTTATACCA	57.602	30.769	6.04	0.00	39.55	3.25
3984	11629	1.004628	TCATGTATGCACTTGGCCACT	59.995	47.619	3.88	0.00	43.89	4.00
4122	11767	9.393786	AGGTCAGTATACCATAATACTCCATTT	57.606	33.333	0.00	0.00	40.02	2.32
4183	11830	4.889241	ACGTTTTAGTGTTTGTTCACTCG	58.111	39.130	2.59	3.92	45.79	4.18
4187	11834	6.303733	CGTTTTAGTGTTTGTTCACTCGTTTT	59.696	34.615	2.59	0.00	45.79	2.43
4249	11896	2.781681	AGTATTTGTGAACGGAGGGG	57.218	50.000	0.00	0.00	0.00	4.79
4304	11951	5.508124	TTTATTTTCCATTTCTTTGCGCG	57.492	34.783	0.00	0.00	0.00	6.86
4386	12037	3.681593	TGTGGCAAATAGGGACTTGTAC	58.318	45.455	0.00	0.00	41.75	2.90
4412	12063	5.754543	TCGTACCGACATGTGATGTATTA	57.245	39.130	1.15	0.00	45.03	0.98
4545	12196	3.694734	ACAATTCGTTGACTTGTGCAAG	58.305	40.909	10.09	10.09	43.79	4.01
4680	12331	2.412937	GTGGTTTTGCAGCACGCT	59.587	55.556	0.00	0.00	43.81	5.07
4697	12348	1.787012	GCTGTTGCATTTGTGAAGGG	58.213	50.000	0.00	0.00	39.41	3.95
4707	12358	2.531942	GTGAAGGGGGAGGTGGGT	60.532	66.667	0.00	0.00	0.00	4.51
4740	12391	1.677217	GCCCGAAAGCTGACAGAGATT	60.677	52.381	6.65	0.00	0.00	2.40
4812	12463	1.136085	CACCGTGCCAAATAAGTGACG	60.136	52.381	0.00	0.00	0.00	4.35

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
78	84	5.900425	TCTTTGCACAATCTTGCTGTTTTA	58.100	33.333	0.00	0.00	43.41	1.52
79	85	4.757594	TCTTTGCACAATCTTGCTGTTTT	58.242	34.783	0.00	0.00	43.41	2.43
84	90	2.232941	CCCATCTTTGCACAATCTTGCT	59.767	45.455	0.00	0.00	43.41	3.91
98	104	0.767998	GCCTAGCCTAAGCCCATCTT	59.232	55.000	0.00	0.00	41.25	2.40
173	179	3.451540	AGGAGACCCGAGTTTAAATCCTC	59.548	47.826	0.00	0.00	37.58	3.71
180	186	2.089980	CGAAGAGGAGACCCGAGTTTA	58.910	52.381	0.00	0.00	37.58	2.01
200	206	2.756207	GAGCCTAATATCTCCGGTCTCC	59.244	54.545	0.00	0.00	0.00	3.71
201	207	3.422796	TGAGCCTAATATCTCCGGTCTC	58.577	50.000	0.00	0.00	0.00	3.36
202	208	3.527507	TGAGCCTAATATCTCCGGTCT	57.472	47.619	0.00	0.00	0.00	3.85
203	209	4.382147	GGATTGAGCCTAATATCTCCGGTC	60.382	50.000	0.00	0.00	0.00	4.79
204	210	3.515901	GGATTGAGCCTAATATCTCCGGT	59.484	47.826	0.00	0.00	0.00	5.28
205	211	3.515502	TGGATTGAGCCTAATATCTCCGG	59.484	47.826	0.00	0.00	0.00	5.14
206	212	4.499183	GTGGATTGAGCCTAATATCTCCG	58.501	47.826	0.00	0.00	0.00	4.63
269	275	7.583860	GCCGTTGGCTTTATTGTTTATTTAA	57.416	32.000	0.00	0.00	46.69	1.52
289	295	2.804527	GTTTTTCCTTCTAAGTCGCCGT	59.195	45.455	0.00	0.00	0.00	5.68
320	330	1.885887	CCATATGCCACCGGTAAATGG	59.114	52.381	6.87	12.24	39.16	3.16
323	333	0.183971	CCCCATATGCCACCGGTAAA	59.816	55.000	6.87	0.00	0.00	2.01
338	348	6.126409	CCTAAAGTTATCAGCAATTACCCCA	58.874	40.000	0.00	0.00	0.00	4.96
348	358	7.280356	TCAGATTTACCCCTAAAGTTATCAGC	58.720	38.462	0.00	0.00	0.00	4.26
359	369	2.969950	CCCGTCATCAGATTTACCCCTA	59.030	50.000	0.00	0.00	0.00	3.53
374	385	2.038814	TTGCTTCTGTCTGCCCGTCA	62.039	55.000	0.00	0.00	0.00	4.35
527	857	9.729281	AAATTTTATCACTTCTTCATGGCAATT	57.271	25.926	0.00	0.00	0.00	2.32
574	904	2.030562	CGCCAGTTCACCGGTTCT	59.969	61.111	2.97	0.22	0.00	3.01
588	918	1.020861	ATTTTTACCGTCGGACCGCC	61.021	55.000	20.51	0.00	0.00	6.13
607	938	1.754803	CGGTAAGGCTGTATGGTCAGA	59.245	52.381	0.00	0.00	37.61	3.27
615	946	4.261741	GGTAATCGAATCGGTAAGGCTGTA	60.262	45.833	1.76	0.00	0.00	2.74
748	1138	2.817423	CGCTGCGAAATGAGGCCTC	61.817	63.158	26.78	26.78	0.00	4.70
791	1188	1.664649	CGAGCTGGCTTTGACGACA	60.665	57.895	0.00	0.00	0.00	4.35
848	1245	1.280457	AGAAATCGAGCCCCTGTTCT	58.720	50.000	0.00	0.00	0.00	3.01
1015	1431	2.266055	CTCCTGGTCCTTGACGCC	59.734	66.667	0.00	0.00	32.65	5.68
1110	1526	2.125552	TGCCACGCGATCCTCTTG	60.126	61.111	15.93	0.00	0.00	3.02
1199	1622	0.325671	CTCTCTGGCTCCCCTTACCA	60.326	60.000	0.00	0.00	0.00	3.25
1291	1714	3.683847	GCATGATGTTACCTCTTCCAGCT	60.684	47.826	0.00	0.00	0.00	4.24
1381	1806	1.289231	TGGCCTAGATCCTCTCACTGT	59.711	52.381	3.32	0.00	0.00	3.55
1446	1871	5.944007	ACGAGGAACCAAGCTATGTATTTTT	59.056	36.000	0.00	0.00	0.00	1.94
1447	1872	5.497474	ACGAGGAACCAAGCTATGTATTTT	58.503	37.500	0.00	0.00	0.00	1.82
1527	1981	3.421844	ACTAAACACATGAGGGCTTTCC	58.578	45.455	0.00	0.00	0.00	3.13
1532	1986	3.610911	AGCTAACTAAACACATGAGGGC	58.389	45.455	0.00	0.00	0.00	5.19
1689	2145	3.055530	GTGATTGTGTCTCCTCATCACCT	60.056	47.826	0.00	0.00	33.04	4.00
1694	2150	4.019051	TCAATGGTGATTGTGTCTCCTCAT	60.019	41.667	0.00	0.00	40.43	2.90
1978	2441	8.502387	CAAAAAGGTTCAGTGAGAGAGAAATAG	58.498	37.037	0.00	0.00	0.00	1.73
2146	2816	5.047847	TCGTTTATAGGTGCTTGATAGTGC	58.952	41.667	0.00	0.00	0.00	4.40
2246	2925	9.860898	ATCCATAATTCTAACAAAAGCAAGAAC	57.139	29.630	0.00	0.00	31.20	3.01
2362	3254	9.256228	AGGAATATAATAGAAGACGAATAGGCA	57.744	33.333	0.00	0.00	0.00	4.75
2530	3422	7.004086	TCTCACCATCAAATACTCCAAAAAGT	58.996	34.615	0.00	0.00	0.00	2.66
2646	3538	5.799827	ATAAGTGCTCCTTGAGATACTCC	57.200	43.478	0.00	0.00	34.46	3.85
2750	3642	8.562892	CCTACTAGATGCACTGAATAATTTTGG	58.437	37.037	0.00	0.00	0.00	3.28
2757	3649	8.678199	CGATTATCCTACTAGATGCACTGAATA	58.322	37.037	0.00	0.00	0.00	1.75
3176	4388	6.183360	TGCATTACTGACATGATACGACAAAC	60.183	38.462	0.00	0.00	0.00	2.93
3242	4454	4.801330	TGAAACACGATCTGTCCAGTAT	57.199	40.909	0.00	0.00	30.29	2.12
3294	4506	7.455641	ACAAACACCGGATATTTCACATTAA	57.544	32.000	9.46	0.00	0.00	1.40
3376	4593	7.051000	GGAAACATAGCTCCTATTCAGTCTTT	58.949	38.462	0.00	0.00	0.00	2.52
3453	8775	2.929161	GCCAACCCCGAAATTTAAGCAC	60.929	50.000	0.00	0.00	0.00	4.40
3725	11370	7.870826	AGATATTTCAACAAACACGTGATTGA	58.129	30.769	35.83	26.38	32.92	2.57
3756	11401	7.137426	GCAAAACAAACATTTGGCATTATCAA	58.863	30.769	9.09	0.00	42.34	2.57
3916	11561	6.892658	TTGTGTAATGGTATCTTTGCAGTT	57.107	33.333	0.00	0.00	0.00	3.16
3984	11629	5.244851	TGCAAATACTCAAGTAAATTGCCCA	59.755	36.000	25.31	14.64	45.96	5.36
4183	11830	8.975439	CAATATGGACTACATACGGACTAAAAC	58.025	37.037	0.00	0.00	44.41	2.43
4187	11834	8.467963	TTTCAATATGGACTACATACGGACTA	57.532	34.615	0.00	0.00	44.41	2.59
4249	11896	3.056607	AGCTGTGCATGAAATTTGGTACC	60.057	43.478	4.43	4.43	0.00	3.34
4278	11925	6.249050	GCGCAAAGAAATGGAAAATAAAATGC	59.751	34.615	0.30	0.00	0.00	3.56
4304	11951	4.767928	ACCGGAGATCTATTGGTAGTCATC	59.232	45.833	9.46	0.00	0.00	2.92
4412	12063	3.815401	GGTGCACTAGACATGTCAAGTTT	59.185	43.478	27.02	9.10	0.00	2.66
4545	12196	7.213678	CCTGAAGAGAATAAGAGATGGTAACC	58.786	42.308	0.00	0.00	0.00	2.85
4680	12331	1.047002	CCCCCTTCACAAATGCAACA	58.953	50.000	0.00	0.00	0.00	3.33
4740	12391	3.659092	CTCCCACGCGCAAAAGCA	61.659	61.111	5.73	0.00	36.85	3.91
4761	12412	9.489084	TCTACAACTATGCATGTTATATTGTCC	57.511	33.333	10.16	0.00	31.81	4.02
4844	12495	4.348754	ACGGGCCCTTTTGCTAGTATATAA	59.651	41.667	22.43	0.00	0.00	0.98
4845	12496	3.905591	ACGGGCCCTTTTGCTAGTATATA	59.094	43.478	22.43	0.00	0.00	0.86
4846	12497	2.709397	ACGGGCCCTTTTGCTAGTATAT	59.291	45.455	22.43	0.00	0.00	0.86

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.