AutoCloner

Multiple sequence alignment - TraesCS5D01G489600

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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	TraesCS5D01G489600	chr5D	100.000	3161	0	0	1	3161	524576528	524579688	0.000000e+00	5838.0
1	TraesCS5D01G489600	chr5D	91.282	585	45	5	241	823	503522821	503522241	0.000000e+00	793.0
2	TraesCS5D01G489600	chr5A	96.011	2933	98	13	238	3161	650823791	650826713	0.000000e+00	4750.0
3	TraesCS5D01G489600	chr5A	83.806	494	39	10	238	692	456175009	456175500	6.260000e-117	431.0
4	TraesCS5D01G489600	chr5A	93.088	217	15	0	21	237	129619443	129619227	5.090000e-83	318.0
5	TraesCS5D01G489600	chr6D	88.365	1590	160	16	952	2522	7994326	7992743	0.000000e+00	1888.0
6	TraesCS5D01G489600	chr6D	87.825	1347	150	9	1182	2522	7715858	7717196	0.000000e+00	1567.0
7	TraesCS5D01G489600	chr6D	81.965	1486	240	23	988	2459	8967568	8969039	0.000000e+00	1234.0
8	TraesCS5D01G489600	chr6D	89.894	376	34	4	2523	2896	7717380	7717753	6.130000e-132	481.0
9	TraesCS5D01G489600	chr6D	88.360	378	34	7	2523	2899	7992561	7992193	2.240000e-121	446.0
10	TraesCS5D01G489600	chr6D	79.545	220	33	7	2925	3140	7997369	7997158	2.540000e-31	147.0
11	TraesCS5D01G489600	chr6D	82.812	128	21	1	2578	2705	9545017	9544891	2.580000e-21	113.0
12	TraesCS5D01G489600	chr6D	89.873	79	8	0	2908	2986	7992130	7992052	5.580000e-18	102.0
13	TraesCS5D01G489600	chr6A	86.328	1653	185	13	892	2522	7986674	7988307	0.000000e+00	1762.0
14	TraesCS5D01G489600	chr6A	85.681	1704	194	26	844	2522	8202482	8200804	0.000000e+00	1749.0
15	TraesCS5D01G489600	chr6A	88.859	377	33	4	2523	2898	8200626	8200258	3.720000e-124	455.0
16	TraesCS5D01G489600	chr6A	88.732	355	34	4	2523	2873	7988679	7989031	2.250000e-116	429.0
17	TraesCS5D01G489600	chr6A	93.897	213	13	0	21	233	315613832	315613620	3.930000e-84	322.0
18	TraesCS5D01G489600	chr6A	83.766	154	19	4	2990	3140	8210669	8210519	1.180000e-29	141.0
19	TraesCS5D01G489600	chr6A	85.088	114	17	0	2998	3111	8447246	8447133	1.990000e-22	117.0
20	TraesCS5D01G489600	chr6A	91.139	79	7	0	2908	2986	8200196	8200118	1.200000e-19	108.0
21	TraesCS5D01G489600	chr1B	85.594	1541	174	23	869	2390	27678244	27676733	0.000000e+00	1572.0
22	TraesCS5D01G489600	chr1B	85.188	1465	189	17	1078	2522	27752872	27751416	0.000000e+00	1478.0
23	TraesCS5D01G489600	chr1B	87.109	256	24	5	2907	3161	27675806	27675559	6.680000e-72	281.0
24	TraesCS5D01G489600	chr1B	92.683	164	12	0	2908	3071	27750844	27750681	1.470000e-58	237.0
25	TraesCS5D01G489600	chr1B	88.421	190	18	1	2650	2839	27751145	27750960	3.170000e-55	226.0
26	TraesCS5D01G489600	chr1B	91.753	97	6	2	2523	2619	27751238	27751144	1.980000e-27	134.0
27	TraesCS5D01G489600	chr6B	86.464	1448	168	16	953	2378	14330391	14331832	0.000000e+00	1563.0
28	TraesCS5D01G489600	chr6B	91.247	377	32	1	2523	2898	14548476	14548100	2.170000e-141	512.0
29	TraesCS5D01G489600	chr6B	88.594	377	33	7	2523	2898	14621054	14620687	1.730000e-122	449.0
30	TraesCS5D01G489600	chr6B	85.372	376	30	7	2523	2898	14332165	14332515	1.790000e-97	366.0
31	TraesCS5D01G489600	chr6B	93.925	214	13	0	21	234	8131745	8131958	1.090000e-84	324.0
32	TraesCS5D01G489600	chr6B	89.928	139	8	5	2387	2522	14548789	14548654	1.170000e-39	174.0
33	TraesCS5D01G489600	chr6B	79.397	199	37	4	2703	2899	16339922	16340118	1.530000e-28	137.0
34	TraesCS5D01G489600	chr6B	83.007	153	22	4	2990	3140	14627830	14627680	5.500000e-28	135.0
35	TraesCS5D01G489600	chr6B	90.625	64	2	2	2907	2966	14332593	14332656	7.270000e-12	82.4
36	TraesCS5D01G489600	chr2D	92.386	591	42	3	238	827	592108848	592109436	0.000000e+00	839.0
37	TraesCS5D01G489600	chr2D	90.365	301	24	4	238	535	585077094	585077392	1.060000e-104	390.0
38	TraesCS5D01G489600	chr2B	79.744	1170	201	29	980	2130	89494601	89495753	0.000000e+00	815.0
39	TraesCS5D01G489600	chr2B	91.540	591	41	8	238	824	362246317	362246902	0.000000e+00	806.0
40	TraesCS5D01G489600	chr2B	93.897	213	13	0	21	233	672040694	672040482	3.930000e-84	322.0
41	TraesCS5D01G489600	chr2B	87.500	160	14	4	538	692	707259801	707259959	2.500000e-41	180.0
42	TraesCS5D01G489600	chr7B	89.789	568	47	5	241	806	68745364	68744806	0.000000e+00	717.0
43	TraesCS5D01G489600	chr3D	90.554	307	25	3	241	544	449725749	449725444	1.370000e-108	403.0
44	TraesCS5D01G489600	chr3D	90.228	307	26	3	241	544	316545290	316544985	6.350000e-107	398.0
45	TraesCS5D01G489600	chr1D	94.393	214	12	0	21	234	378803594	378803807	2.350000e-86	329.0
46	TraesCS5D01G489600	chr5B	94.340	212	12	0	23	234	528889147	528889358	3.040000e-85	326.0
47	TraesCS5D01G489600	chr5B	93.458	214	14	0	21	234	658367723	658367936	5.090000e-83	318.0
48	TraesCS5D01G489600	chr3B	93.780	209	13	0	21	229	167964104	167963896	6.580000e-82	315.0
49	TraesCS5D01G489600	chr1A	91.667	228	17	1	12	237	532451620	532451393	6.580000e-82	315.0
50	TraesCS5D01G489600	chrUn	79.000	200	36	5	2703	2899	95438790	95438986	7.110000e-27	132.0
51	TraesCS5D01G489600	chr3A	100.000	33	0	0	788	820	210099570	210099602	9.470000e-06	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	TraesCS5D01G489600	chr5D	524576528	524579688	3160	False	5838.000000	5838	100.000000	1	3161	1	chr5D.!!$F1	3160
1	TraesCS5D01G489600	chr5D	503522241	503522821	580	True	793.000000	793	91.282000	241	823	1	chr5D.!!$R1	582
2	TraesCS5D01G489600	chr5A	650823791	650826713	2922	False	4750.000000	4750	96.011000	238	3161	1	chr5A.!!$F2	2923
3	TraesCS5D01G489600	chr6D	8967568	8969039	1471	False	1234.000000	1234	81.965000	988	2459	1	chr6D.!!$F1	1471
4	TraesCS5D01G489600	chr6D	7715858	7717753	1895	False	1024.000000	1567	88.859500	1182	2896	2	chr6D.!!$F2	1714
5	TraesCS5D01G489600	chr6D	7992052	7997369	5317	True	645.750000	1888	86.535750	952	3140	4	chr6D.!!$R2	2188
6	TraesCS5D01G489600	chr6A	7986674	7989031	2357	False	1095.500000	1762	87.530000	892	2873	2	chr6A.!!$F1	1981
7	TraesCS5D01G489600	chr6A	8200118	8202482	2364	True	770.666667	1749	88.559667	844	2986	3	chr6A.!!$R4	2142
8	TraesCS5D01G489600	chr1B	27675559	27678244	2685	True	926.500000	1572	86.351500	869	3161	2	chr1B.!!$R1	2292
9	TraesCS5D01G489600	chr1B	27750681	27752872	2191	True	518.750000	1478	89.511250	1078	3071	4	chr1B.!!$R2	1993
10	TraesCS5D01G489600	chr6B	14330391	14332656	2265	False	670.466667	1563	87.487000	953	2966	3	chr6B.!!$F3	2013
11	TraesCS5D01G489600	chr6B	14548100	14548789	689	True	343.000000	512	90.587500	2387	2898	2	chr6B.!!$R3	511
12	TraesCS5D01G489600	chr2D	592108848	592109436	588	False	839.000000	839	92.386000	238	827	1	chr2D.!!$F2	589
13	TraesCS5D01G489600	chr2B	89494601	89495753	1152	False	815.000000	815	79.744000	980	2130	1	chr2B.!!$F1	1150
14	TraesCS5D01G489600	chr2B	362246317	362246902	585	False	806.000000	806	91.540000	238	824	1	chr2B.!!$F2	586
15	TraesCS5D01G489600	chr7B	68744806	68745364	558	True	717.000000	717	89.789000	241	806	1	chr7B.!!$R1	565

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	Hairpin	End Stability	Orientation
194	195	0.037734	AAAAAGCTGGGTAGGGGTCG	59.962	55.0	0.00	0.00	4.79	F
202	203	0.468648	GGGTAGGGGTCGAATTCTGG	59.531	60.0	3.52	0.00	3.86	F
203	204	0.468648	GGTAGGGGTCGAATTCTGGG	59.531	60.0	3.52	0.00	4.45	F
523	526	0.829990	TCATTCGATGCCACCAGCTA	59.170	50.0	0.00	44.23	3.32	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1327	3445	2.414785	CGTTGGGGGCCAGTATTGC	61.415	63.158	4.39	0.0	33.81	3.56	R
1801	3922	3.851105	GCCTTAGAAATAGCAATGCGCAG	60.851	47.826	18.32	3.8	46.13	5.18	R
1973	4094	5.922544	CCATTTGCCTTAAGAAACTTCACAG	59.077	40.000	3.36	0.0	0.00	3.66	R
2422	4599	8.682936	AACACAAATATATTCATGGACTCTCC	57.317	34.615	0.00	0.0	36.96	3.71	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
21	22	4.510167	ACCTTTCATGGGAAGATAGTGG	57.490	45.455	10.23	0.00	33.82	4.00
22	23	3.217626	CCTTTCATGGGAAGATAGTGGC	58.782	50.000	10.23	0.00	33.82	5.01
24	25	1.140312	TCATGGGAAGATAGTGGCCC	58.860	55.000	0.00	0.00	41.08	5.80
27	28	0.253160	TGGGAAGATAGTGGCCCAGT	60.253	55.000	0.00	0.00	45.31	4.00
28	29	0.919710	GGGAAGATAGTGGCCCAGTT	59.080	55.000	0.00	0.00	40.39	3.16
29	30	1.134068	GGGAAGATAGTGGCCCAGTTC	60.134	57.143	0.00	0.00	40.39	3.01
30	31	1.840635	GGAAGATAGTGGCCCAGTTCT	59.159	52.381	0.00	0.00	0.00	3.01
34	35	3.690460	AGATAGTGGCCCAGTTCTTTTG	58.310	45.455	0.00	0.00	0.00	2.44
35	36	1.616159	TAGTGGCCCAGTTCTTTTGC	58.384	50.000	0.00	0.00	0.00	3.68
36	37	1.115326	AGTGGCCCAGTTCTTTTGCC	61.115	55.000	0.00	0.00	42.49	4.52
37	38	3.869481	GGCCCAGTTCTTTTGCCA	58.131	55.556	0.00	0.00	41.76	4.92
39	40	0.827507	GGCCCAGTTCTTTTGCCAGA	60.828	55.000	0.00	0.00	41.76	3.86
40	41	1.039856	GCCCAGTTCTTTTGCCAGAA	58.960	50.000	0.00	0.00	0.00	3.02
41	42	1.620323	GCCCAGTTCTTTTGCCAGAAT	59.380	47.619	0.00	0.00	35.23	2.40
42	43	2.353109	GCCCAGTTCTTTTGCCAGAATC	60.353	50.000	0.00	0.00	35.23	2.52
44	45	4.335416	CCCAGTTCTTTTGCCAGAATCTA	58.665	43.478	0.00	0.00	35.23	1.98
45	46	4.397417	CCCAGTTCTTTTGCCAGAATCTAG	59.603	45.833	0.00	0.00	35.23	2.43
46	47	4.397417	CCAGTTCTTTTGCCAGAATCTAGG	59.603	45.833	0.00	0.00	35.23	3.02
49	50	5.044550	AGTTCTTTTGCCAGAATCTAGGGAT	60.045	40.000	0.00	0.00	35.23	3.85
68	69	1.486211	TTCTCTCAGAATCCGACCCC	58.514	55.000	0.00	0.00	0.00	4.95
69	70	0.631753	TCTCTCAGAATCCGACCCCT	59.368	55.000	0.00	0.00	0.00	4.79
70	71	1.850998	TCTCTCAGAATCCGACCCCTA	59.149	52.381	0.00	0.00	0.00	3.53
72	73	1.569548	TCTCAGAATCCGACCCCTACT	59.430	52.381	0.00	0.00	0.00	2.57
73	74	1.957877	CTCAGAATCCGACCCCTACTC	59.042	57.143	0.00	0.00	0.00	2.59
74	75	1.286849	TCAGAATCCGACCCCTACTCA	59.713	52.381	0.00	0.00	0.00	3.41
76	77	2.108970	AGAATCCGACCCCTACTCAAC	58.891	52.381	0.00	0.00	0.00	3.18
77	78	2.108970	GAATCCGACCCCTACTCAACT	58.891	52.381	0.00	0.00	0.00	3.16
79	80	1.553706	TCCGACCCCTACTCAACTTC	58.446	55.000	0.00	0.00	0.00	3.01
80	81	1.076677	TCCGACCCCTACTCAACTTCT	59.923	52.381	0.00	0.00	0.00	2.85
82	83	1.477295	CGACCCCTACTCAACTTCTCC	59.523	57.143	0.00	0.00	0.00	3.71
83	84	1.832366	GACCCCTACTCAACTTCTCCC	59.168	57.143	0.00	0.00	0.00	4.30
85	86	1.834263	CCCCTACTCAACTTCTCCCAG	59.166	57.143	0.00	0.00	0.00	4.45
86	87	2.559931	CCCCTACTCAACTTCTCCCAGA	60.560	54.545	0.00	0.00	0.00	3.86
87	88	3.173965	CCCTACTCAACTTCTCCCAGAA	58.826	50.000	0.00	0.00	32.50	3.02
89	90	4.141824	CCCTACTCAACTTCTCCCAGAATC	60.142	50.000	0.00	0.00	33.13	2.52
93	94	5.312079	ACTCAACTTCTCCCAGAATCTTTG	58.688	41.667	0.00	0.00	33.13	2.77
95	96	5.555017	TCAACTTCTCCCAGAATCTTTGAG	58.445	41.667	0.62	0.62	33.13	3.02
96	97	3.949132	ACTTCTCCCAGAATCTTTGAGC	58.051	45.455	1.93	0.00	33.13	4.26
98	99	1.561542	TCTCCCAGAATCTTTGAGCCC	59.438	52.381	1.93	0.00	0.00	5.19
101	102	1.063417	CCCAGAATCTTTGAGCCCCAT	60.063	52.381	0.00	0.00	0.00	4.00
102	103	2.625087	CCCAGAATCTTTGAGCCCCATT	60.625	50.000	0.00	0.00	0.00	3.16
103	104	3.102204	CCAGAATCTTTGAGCCCCATTT	58.898	45.455	0.00	0.00	0.00	2.32
104	105	3.118884	CCAGAATCTTTGAGCCCCATTTG	60.119	47.826	0.00	0.00	0.00	2.32
105	106	3.512724	CAGAATCTTTGAGCCCCATTTGT	59.487	43.478	0.00	0.00	0.00	2.83
106	107	4.020839	CAGAATCTTTGAGCCCCATTTGTT	60.021	41.667	0.00	0.00	0.00	2.83
108	109	4.980339	ATCTTTGAGCCCCATTTGTTTT	57.020	36.364	0.00	0.00	0.00	2.43
109	110	6.269769	AGAATCTTTGAGCCCCATTTGTTTTA	59.730	34.615	0.00	0.00	0.00	1.52
110	111	5.208463	TCTTTGAGCCCCATTTGTTTTAC	57.792	39.130	0.00	0.00	0.00	2.01
111	112	4.651503	TCTTTGAGCCCCATTTGTTTTACA	59.348	37.500	0.00	0.00	0.00	2.41
112	113	5.129485	TCTTTGAGCCCCATTTGTTTTACAA	59.871	36.000	0.00	0.00	36.11	2.41
113	114	5.559148	TTGAGCCCCATTTGTTTTACAAT	57.441	34.783	0.00	0.00	38.00	2.71
114	115	5.146010	TGAGCCCCATTTGTTTTACAATC	57.854	39.130	0.00	0.00	38.00	2.67
115	116	4.020662	TGAGCCCCATTTGTTTTACAATCC	60.021	41.667	0.00	0.00	38.00	3.01
117	118	5.337788	AGCCCCATTTGTTTTACAATCCTA	58.662	37.500	0.00	0.00	38.00	2.94
118	119	5.963865	AGCCCCATTTGTTTTACAATCCTAT	59.036	36.000	0.00	0.00	38.00	2.57
119	120	6.098266	AGCCCCATTTGTTTTACAATCCTATC	59.902	38.462	0.00	0.00	38.00	2.08
121	122	7.286775	GCCCCATTTGTTTTACAATCCTATCTA	59.713	37.037	0.00	0.00	38.00	1.98
122	123	9.196139	CCCCATTTGTTTTACAATCCTATCTAA	57.804	33.333	0.00	0.00	38.00	2.10
163	164	5.146010	TGATTGTAAAACAAATGGGGCTC	57.854	39.130	0.00	0.00	41.96	4.70
164	165	4.590647	TGATTGTAAAACAAATGGGGCTCA	59.409	37.500	0.00	0.00	41.96	4.26
166	167	5.359194	TTGTAAAACAAATGGGGCTCAAA	57.641	34.783	0.00	0.00	34.76	2.69
169	170	4.980339	AAAACAAATGGGGCTCAAAGAT	57.020	36.364	0.00	0.00	0.00	2.40
171	172	4.541973	AACAAATGGGGCTCAAAGATTC	57.458	40.909	0.00	0.00	0.00	2.52
173	174	3.512724	ACAAATGGGGCTCAAAGATTCTG	59.487	43.478	0.00	0.00	0.00	3.02
174	175	2.449137	ATGGGGCTCAAAGATTCTGG	57.551	50.000	0.00	0.00	0.00	3.86
175	176	1.371467	TGGGGCTCAAAGATTCTGGA	58.629	50.000	0.00	0.00	0.00	3.86
176	177	1.710244	TGGGGCTCAAAGATTCTGGAA	59.290	47.619	0.00	0.00	0.00	3.53
178	179	3.165071	GGGGCTCAAAGATTCTGGAAAA	58.835	45.455	0.00	0.00	0.00	2.29
179	180	3.578282	GGGGCTCAAAGATTCTGGAAAAA	59.422	43.478	0.00	0.00	0.00	1.94
180	181	4.322273	GGGGCTCAAAGATTCTGGAAAAAG	60.322	45.833	0.00	0.00	0.00	2.27
181	182	4.240888	GGCTCAAAGATTCTGGAAAAAGC	58.759	43.478	0.00	0.00	0.00	3.51
182	183	4.021632	GGCTCAAAGATTCTGGAAAAAGCT	60.022	41.667	0.00	0.00	0.00	3.74
183	184	4.922103	GCTCAAAGATTCTGGAAAAAGCTG	59.078	41.667	0.00	0.00	0.00	4.24
184	185	5.458041	TCAAAGATTCTGGAAAAAGCTGG	57.542	39.130	0.00	0.00	0.00	4.85
185	186	4.281688	TCAAAGATTCTGGAAAAAGCTGGG	59.718	41.667	0.00	0.00	0.00	4.45
186	187	3.532641	AGATTCTGGAAAAAGCTGGGT	57.467	42.857	0.00	0.00	0.00	4.51
187	188	4.657814	AGATTCTGGAAAAAGCTGGGTA	57.342	40.909	0.00	0.00	0.00	3.69
188	189	4.593956	AGATTCTGGAAAAAGCTGGGTAG	58.406	43.478	0.00	0.00	0.00	3.18
190	191	1.354368	TCTGGAAAAAGCTGGGTAGGG	59.646	52.381	0.00	0.00	0.00	3.53
191	192	0.407918	TGGAAAAAGCTGGGTAGGGG	59.592	55.000	0.00	0.00	0.00	4.79
192	193	0.408309	GGAAAAAGCTGGGTAGGGGT	59.592	55.000	0.00	0.00	0.00	4.95
194	195	0.037734	AAAAAGCTGGGTAGGGGTCG	59.962	55.000	0.00	0.00	0.00	4.79
195	196	0.838987	AAAAGCTGGGTAGGGGTCGA	60.839	55.000	0.00	0.00	0.00	4.20
196	197	0.838987	AAAGCTGGGTAGGGGTCGAA	60.839	55.000	0.00	0.00	0.00	3.71
197	198	0.620700	AAGCTGGGTAGGGGTCGAAT	60.621	55.000	0.00	0.00	0.00	3.34
200	201	1.497161	CTGGGTAGGGGTCGAATTCT	58.503	55.000	3.52	0.00	0.00	2.40
201	202	1.139058	CTGGGTAGGGGTCGAATTCTG	59.861	57.143	3.52	0.00	0.00	3.02
202	203	0.468648	GGGTAGGGGTCGAATTCTGG	59.531	60.000	3.52	0.00	0.00	3.86
203	204	0.468648	GGTAGGGGTCGAATTCTGGG	59.531	60.000	3.52	0.00	0.00	4.45
204	205	1.492764	GTAGGGGTCGAATTCTGGGA	58.507	55.000	3.52	0.00	0.00	4.37
205	206	1.413077	GTAGGGGTCGAATTCTGGGAG	59.587	57.143	3.52	0.00	0.00	4.30
207	208	0.909623	GGGGTCGAATTCTGGGAGAA	59.090	55.000	3.52	0.00	38.78	2.87
208	209	1.490910	GGGGTCGAATTCTGGGAGAAT	59.509	52.381	3.52	0.00	46.22	2.40
210	211	2.170607	GGGTCGAATTCTGGGAGAATCA	59.829	50.000	3.52	0.00	43.67	2.57
211	212	3.198872	GGTCGAATTCTGGGAGAATCAC	58.801	50.000	3.52	0.00	43.67	3.06
214	215	3.118629	TCGAATTCTGGGAGAATCACCAG	60.119	47.826	15.14	15.14	43.67	4.00
233	234	4.501071	CCAGATTCTGGCAAAAGAATTGG	58.499	43.478	19.49	12.61	45.13	3.16
234	235	4.221262	CCAGATTCTGGCAAAAGAATTGGA	59.779	41.667	19.49	0.00	45.13	3.53
235	236	5.166398	CAGATTCTGGCAAAAGAATTGGAC	58.834	41.667	5.73	0.00	44.96	4.02
239	240	1.344114	TGGCAAAAGAATTGGACCAGC	59.656	47.619	0.00	0.00	0.00	4.85
300	302	4.938226	TGCGTTGTATTATTGACATGGTCA	59.062	37.500	0.00	0.00	41.09	4.02
310	312	5.571784	ATTGACATGGTCATAACAAGCAG	57.428	39.130	0.00	0.00	42.40	4.24
346	349	6.099557	TGTTTTTGATTTCCTTGGGATGAAGT	59.900	34.615	0.00	0.00	0.00	3.01
395	398	9.452287	GTTTACTAATACATAGTGGGGTTTTGA	57.548	33.333	0.00	0.00	44.64	2.69
414	417	7.818446	GGTTTTGAAAACTGGTGGTTACTTTTA	59.182	33.333	18.95	0.00	37.12	1.52
523	526	0.829990	TCATTCGATGCCACCAGCTA	59.170	50.000	0.00	0.00	44.23	3.32
592	596	4.404394	TCCTTTTGTGCTCGATATCTACCA	59.596	41.667	0.34	0.00	0.00	3.25
766	775	9.630098	CGTTCTACTAACTTTGACCATTACTTA	57.370	33.333	0.00	0.00	0.00	2.24
820	829	1.878088	CCAAGGCATGATTCCGATCTG	59.122	52.381	0.00	0.00	33.28	2.90
853	862	2.124983	GGCCAGCGAGCATGAGAA	60.125	61.111	0.00	0.00	0.00	2.87
889	898	3.466881	CCACTCCACTTGGGTCGA	58.533	61.111	0.00	0.00	38.11	4.20
1647	3768	2.591429	TGCAACCCAGAGCGTGTG	60.591	61.111	0.00	0.00	0.00	3.82
1801	3922	2.512515	GGTGGTCGGATGCTGAGC	60.513	66.667	0.00	0.00	37.71	4.26
2422	4599	4.261489	GCATTGCCTACAATCTCTGGAATG	60.261	45.833	0.00	0.00	44.83	2.67
2608	5177	4.093556	CCTGATTTTACTTCCGCTGAGAAC	59.906	45.833	0.00	0.00	0.00	3.01
2845	5653	7.771927	AAATTTCATATGCCCTCATAAGGAG	57.228	36.000	0.00	0.00	46.67	3.69
2876	5685	2.096713	CACCGCGCTAAAGAATATGCTC	60.097	50.000	5.56	0.00	0.00	4.26
2947	5832	7.007725	CGCTAGCTGTTTCTGTTATGAAAAATG	59.992	37.037	13.93	0.00	37.63	2.32
2960	5845	2.061028	GAAAAATGCTTGGCTGTTCCG	58.939	47.619	0.00	0.00	37.80	4.30
3009	5894	7.231519	CCTCCCCTTTTGAAAGCCTTATATTAG	59.768	40.741	0.00	0.00	34.69	1.73

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	3.372025	GCCACTATCTTCCCATGAAAGGT	60.372	47.826	0.00	0.00	0.00	3.50
5	6	1.140312	GGGCCACTATCTTCCCATGA	58.860	55.000	4.39	0.00	38.62	3.07
7	8	1.143813	CTGGGCCACTATCTTCCCAT	58.856	55.000	0.00	0.00	46.71	4.00
8	9	0.253160	ACTGGGCCACTATCTTCCCA	60.253	55.000	0.00	0.00	45.87	4.37
9	10	0.919710	AACTGGGCCACTATCTTCCC	59.080	55.000	0.00	0.00	39.22	3.97
10	11	1.840635	AGAACTGGGCCACTATCTTCC	59.159	52.381	0.00	0.00	0.00	3.46
12	13	4.082125	CAAAAGAACTGGGCCACTATCTT	58.918	43.478	0.00	9.98	0.00	2.40
13	14	3.690460	CAAAAGAACTGGGCCACTATCT	58.310	45.455	0.00	3.36	0.00	1.98
14	15	2.164422	GCAAAAGAACTGGGCCACTATC	59.836	50.000	0.00	0.60	0.00	2.08
15	16	2.171003	GCAAAAGAACTGGGCCACTAT	58.829	47.619	0.00	0.00	0.00	2.12
16	17	1.616159	GCAAAAGAACTGGGCCACTA	58.384	50.000	0.00	0.00	0.00	2.74
18	19	1.367471	GGCAAAAGAACTGGGCCAC	59.633	57.895	0.00	0.00	44.01	5.01
19	20	3.869481	GGCAAAAGAACTGGGCCA	58.131	55.556	5.85	5.85	44.01	5.36
21	22	1.039856	TTCTGGCAAAAGAACTGGGC	58.960	50.000	0.00	0.00	31.19	5.36
22	23	3.160269	AGATTCTGGCAAAAGAACTGGG	58.840	45.455	0.00	0.00	38.95	4.45
24	25	4.397417	CCCTAGATTCTGGCAAAAGAACTG	59.603	45.833	0.00	0.00	38.95	3.16
25	26	4.289672	TCCCTAGATTCTGGCAAAAGAACT	59.710	41.667	0.00	2.31	38.95	3.01
27	28	4.927267	TCCCTAGATTCTGGCAAAAGAA	57.073	40.909	0.00	0.00	40.36	2.52
28	29	5.456921	AATCCCTAGATTCTGGCAAAAGA	57.543	39.130	0.00	0.00	38.36	2.52
49	50	1.007238	AGGGGTCGGATTCTGAGAGAA	59.993	52.381	0.00	0.00	38.78	2.87
51	52	1.957877	GTAGGGGTCGGATTCTGAGAG	59.042	57.143	0.00	0.00	0.00	3.20
53	54	1.957877	GAGTAGGGGTCGGATTCTGAG	59.042	57.143	0.00	0.00	0.00	3.35
54	55	1.286849	TGAGTAGGGGTCGGATTCTGA	59.713	52.381	0.00	0.00	0.00	3.27
55	56	1.776662	TGAGTAGGGGTCGGATTCTG	58.223	55.000	0.00	0.00	0.00	3.02
56	57	2.108970	GTTGAGTAGGGGTCGGATTCT	58.891	52.381	0.00	0.00	0.00	2.40
57	58	2.108970	AGTTGAGTAGGGGTCGGATTC	58.891	52.381	0.00	0.00	0.00	2.52
58	59	2.249309	AGTTGAGTAGGGGTCGGATT	57.751	50.000	0.00	0.00	0.00	3.01
60	61	1.076677	AGAAGTTGAGTAGGGGTCGGA	59.923	52.381	0.00	0.00	0.00	4.55
62	63	1.477295	GGAGAAGTTGAGTAGGGGTCG	59.523	57.143	0.00	0.00	0.00	4.79
63	64	1.832366	GGGAGAAGTTGAGTAGGGGTC	59.168	57.143	0.00	0.00	0.00	4.46
64	65	1.151413	TGGGAGAAGTTGAGTAGGGGT	59.849	52.381	0.00	0.00	0.00	4.95
65	66	1.834263	CTGGGAGAAGTTGAGTAGGGG	59.166	57.143	0.00	0.00	0.00	4.79
66	67	2.821437	TCTGGGAGAAGTTGAGTAGGG	58.179	52.381	0.00	0.00	0.00	3.53
67	68	4.714308	AGATTCTGGGAGAAGTTGAGTAGG	59.286	45.833	0.00	0.00	37.69	3.18
68	69	5.930837	AGATTCTGGGAGAAGTTGAGTAG	57.069	43.478	0.00	0.00	37.69	2.57
69	70	6.270000	TCAAAGATTCTGGGAGAAGTTGAGTA	59.730	38.462	0.00	0.00	37.69	2.59
70	71	5.072329	TCAAAGATTCTGGGAGAAGTTGAGT	59.928	40.000	0.00	0.00	37.69	3.41
72	73	5.555017	CTCAAAGATTCTGGGAGAAGTTGA	58.445	41.667	8.46	0.00	37.69	3.18
73	74	4.155644	GCTCAAAGATTCTGGGAGAAGTTG	59.844	45.833	15.41	2.65	37.69	3.16
74	75	4.331108	GCTCAAAGATTCTGGGAGAAGTT	58.669	43.478	15.41	0.00	37.69	2.66
76	77	3.277715	GGCTCAAAGATTCTGGGAGAAG	58.722	50.000	15.41	0.00	37.69	2.85
77	78	2.025887	GGGCTCAAAGATTCTGGGAGAA	60.026	50.000	15.41	0.00	38.78	2.87
79	80	1.409381	GGGGCTCAAAGATTCTGGGAG	60.409	57.143	9.42	9.42	0.00	4.30
80	81	0.625849	GGGGCTCAAAGATTCTGGGA	59.374	55.000	0.00	0.00	0.00	4.37
82	83	2.449137	ATGGGGCTCAAAGATTCTGG	57.551	50.000	0.00	0.00	0.00	3.86
83	84	3.512724	ACAAATGGGGCTCAAAGATTCTG	59.487	43.478	0.00	0.00	0.00	3.02
85	86	4.541973	AACAAATGGGGCTCAAAGATTC	57.458	40.909	0.00	0.00	0.00	2.52
86	87	4.980339	AAACAAATGGGGCTCAAAGATT	57.020	36.364	0.00	0.00	0.00	2.40
87	88	4.980339	AAAACAAATGGGGCTCAAAGAT	57.020	36.364	0.00	0.00	0.00	2.40
89	90	4.954875	TGTAAAACAAATGGGGCTCAAAG	58.045	39.130	0.00	0.00	0.00	2.77
93	94	4.222810	AGGATTGTAAAACAAATGGGGCTC	59.777	41.667	0.00	0.00	41.96	4.70
95	96	4.551702	AGGATTGTAAAACAAATGGGGC	57.448	40.909	0.00	0.00	41.96	5.80
96	97	7.660030	AGATAGGATTGTAAAACAAATGGGG	57.340	36.000	0.00	0.00	41.96	4.96
109	110	9.900112	AGTTAGGGTCTAATTAGATAGGATTGT	57.100	33.333	17.95	0.00	34.39	2.71
137	138	7.500141	AGCCCCATTTGTTTTACAATCATATC	58.500	34.615	0.00	0.00	38.00	1.63
138	139	7.125507	TGAGCCCCATTTGTTTTACAATCATAT	59.874	33.333	0.00	0.00	38.00	1.78
139	140	6.438741	TGAGCCCCATTTGTTTTACAATCATA	59.561	34.615	0.00	0.00	38.00	2.15
140	141	5.248020	TGAGCCCCATTTGTTTTACAATCAT	59.752	36.000	0.00	0.00	38.00	2.45
141	142	4.590647	TGAGCCCCATTTGTTTTACAATCA	59.409	37.500	0.00	0.00	38.00	2.57
142	143	5.146010	TGAGCCCCATTTGTTTTACAATC	57.854	39.130	0.00	0.00	38.00	2.67
143	144	5.559148	TTGAGCCCCATTTGTTTTACAAT	57.441	34.783	0.00	0.00	38.00	2.71
144	145	5.129485	TCTTTGAGCCCCATTTGTTTTACAA	59.871	36.000	0.00	0.00	36.11	2.41
146	147	5.208463	TCTTTGAGCCCCATTTGTTTTAC	57.792	39.130	0.00	0.00	0.00	2.01
147	148	6.269769	AGAATCTTTGAGCCCCATTTGTTTTA	59.730	34.615	0.00	0.00	0.00	1.52
149	150	4.594491	AGAATCTTTGAGCCCCATTTGTTT	59.406	37.500	0.00	0.00	0.00	2.83
150	151	4.020839	CAGAATCTTTGAGCCCCATTTGTT	60.021	41.667	0.00	0.00	0.00	2.83
151	152	3.512724	CAGAATCTTTGAGCCCCATTTGT	59.487	43.478	0.00	0.00	0.00	2.83
152	153	3.118884	CCAGAATCTTTGAGCCCCATTTG	60.119	47.826	0.00	0.00	0.00	2.32
153	154	3.102204	CCAGAATCTTTGAGCCCCATTT	58.898	45.455	0.00	0.00	0.00	2.32
154	155	2.312741	TCCAGAATCTTTGAGCCCCATT	59.687	45.455	0.00	0.00	0.00	3.16
158	159	4.814147	CTTTTTCCAGAATCTTTGAGCCC	58.186	43.478	0.00	0.00	0.00	5.19
159	160	4.021632	AGCTTTTTCCAGAATCTTTGAGCC	60.022	41.667	0.00	0.00	0.00	4.70
160	161	4.922103	CAGCTTTTTCCAGAATCTTTGAGC	59.078	41.667	0.00	0.00	0.00	4.26
163	164	4.039609	ACCCAGCTTTTTCCAGAATCTTTG	59.960	41.667	0.00	0.00	0.00	2.77
164	165	4.226384	ACCCAGCTTTTTCCAGAATCTTT	58.774	39.130	0.00	0.00	0.00	2.52
166	167	3.532641	ACCCAGCTTTTTCCAGAATCT	57.467	42.857	0.00	0.00	0.00	2.40
169	170	2.225017	CCCTACCCAGCTTTTTCCAGAA	60.225	50.000	0.00	0.00	0.00	3.02
171	172	1.616994	CCCCTACCCAGCTTTTTCCAG	60.617	57.143	0.00	0.00	0.00	3.86
173	174	0.408309	ACCCCTACCCAGCTTTTTCC	59.592	55.000	0.00	0.00	0.00	3.13
174	175	1.835494	GACCCCTACCCAGCTTTTTC	58.165	55.000	0.00	0.00	0.00	2.29
175	176	0.037734	CGACCCCTACCCAGCTTTTT	59.962	55.000	0.00	0.00	0.00	1.94
176	177	0.838987	TCGACCCCTACCCAGCTTTT	60.839	55.000	0.00	0.00	0.00	2.27
178	179	0.620700	ATTCGACCCCTACCCAGCTT	60.621	55.000	0.00	0.00	0.00	3.74
179	180	0.620700	AATTCGACCCCTACCCAGCT	60.621	55.000	0.00	0.00	0.00	4.24
180	181	0.179054	GAATTCGACCCCTACCCAGC	60.179	60.000	0.00	0.00	0.00	4.85
181	182	1.139058	CAGAATTCGACCCCTACCCAG	59.861	57.143	0.00	0.00	0.00	4.45
182	183	1.200519	CAGAATTCGACCCCTACCCA	58.799	55.000	0.00	0.00	0.00	4.51
183	184	0.468648	CCAGAATTCGACCCCTACCC	59.531	60.000	0.00	0.00	0.00	3.69
184	185	0.468648	CCCAGAATTCGACCCCTACC	59.531	60.000	0.00	0.00	0.00	3.18
185	186	1.413077	CTCCCAGAATTCGACCCCTAC	59.587	57.143	0.00	0.00	0.00	3.18
186	187	1.289830	TCTCCCAGAATTCGACCCCTA	59.710	52.381	0.00	0.00	0.00	3.53
187	188	0.042731	TCTCCCAGAATTCGACCCCT	59.957	55.000	0.00	0.00	0.00	4.79
188	189	0.909623	TTCTCCCAGAATTCGACCCC	59.090	55.000	0.00	0.00	0.00	4.95
190	191	3.198872	GTGATTCTCCCAGAATTCGACC	58.801	50.000	0.00	0.00	44.41	4.79
191	192	3.198872	GGTGATTCTCCCAGAATTCGAC	58.801	50.000	0.00	0.00	44.41	4.20
192	193	2.837591	TGGTGATTCTCCCAGAATTCGA	59.162	45.455	0.00	0.00	44.41	3.71
214	215	4.021192	TGGTCCAATTCTTTTGCCAGAATC	60.021	41.667	0.00	0.00	41.78	2.52
215	216	3.903090	TGGTCCAATTCTTTTGCCAGAAT	59.097	39.130	0.00	0.00	44.05	2.40
216	217	3.303938	TGGTCCAATTCTTTTGCCAGAA	58.696	40.909	0.00	0.00	37.20	3.02
217	218	2.892852	CTGGTCCAATTCTTTTGCCAGA	59.107	45.455	0.00	0.00	43.22	3.86
218	219	2.611224	GCTGGTCCAATTCTTTTGCCAG	60.611	50.000	0.00	0.00	43.35	4.85
220	221	1.669795	CGCTGGTCCAATTCTTTTGCC	60.670	52.381	0.00	0.00	0.00	4.52
221	222	1.000274	ACGCTGGTCCAATTCTTTTGC	60.000	47.619	0.00	0.00	0.00	3.68
222	223	2.034558	ACACGCTGGTCCAATTCTTTTG	59.965	45.455	0.00	0.00	0.00	2.44
223	224	2.293399	GACACGCTGGTCCAATTCTTTT	59.707	45.455	0.00	0.00	0.00	2.27
224	225	1.880027	GACACGCTGGTCCAATTCTTT	59.120	47.619	0.00	0.00	0.00	2.52
225	226	1.202758	TGACACGCTGGTCCAATTCTT	60.203	47.619	0.00	0.00	36.97	2.52
226	227	0.396435	TGACACGCTGGTCCAATTCT	59.604	50.000	0.00	0.00	36.97	2.40
227	228	1.453155	ATGACACGCTGGTCCAATTC	58.547	50.000	0.00	0.00	36.97	2.17
228	229	1.909700	AATGACACGCTGGTCCAATT	58.090	45.000	0.00	0.00	36.97	2.32
229	230	1.812571	GAAATGACACGCTGGTCCAAT	59.187	47.619	0.00	0.00	36.97	3.16
231	232	0.605319	GGAAATGACACGCTGGTCCA	60.605	55.000	0.00	0.00	36.97	4.02
232	233	1.305930	GGGAAATGACACGCTGGTCC	61.306	60.000	2.66	0.00	36.97	4.46
233	234	1.305930	GGGGAAATGACACGCTGGTC	61.306	60.000	0.00	0.00	38.29	4.02
234	235	1.303317	GGGGAAATGACACGCTGGT	60.303	57.895	0.00	0.00	0.00	4.00
235	236	0.680921	ATGGGGAAATGACACGCTGG	60.681	55.000	0.00	0.00	0.00	4.85
300	302	9.889128	AAAACAATATTTATGGCTGCTTGTTAT	57.111	25.926	11.18	2.66	35.09	1.89
346	349	7.994425	ACATATGGTTGTCACATAAAAGTGA	57.006	32.000	7.80	0.00	45.64	3.41
523	526	1.881973	GTTCACATGGTGCATCACAGT	59.118	47.619	0.00	0.41	35.86	3.55
717	724	5.525378	CGCCAGGCTTTATGAGGATATAATC	59.475	44.000	10.54	0.00	0.00	1.75
718	725	5.045578	ACGCCAGGCTTTATGAGGATATAAT	60.046	40.000	10.54	0.00	0.00	1.28
728	737	2.906354	AGTAGAACGCCAGGCTTTATG	58.094	47.619	10.54	0.00	0.00	1.90
766	775	1.178534	CCCCAACGATGTGGCAAAGT	61.179	55.000	0.00	0.00	37.34	2.66
820	829	0.745486	GGCCCGTACCATGTACAACC	60.745	60.000	0.00	0.00	0.00	3.77
853	862	2.574955	GCCCCACACGTCAGTCTCT	61.575	63.158	0.00	0.00	0.00	3.10
887	896	2.738521	CGTGGGTGCTCTGGTTCG	60.739	66.667	0.00	0.00	0.00	3.95
888	897	2.358737	CCGTGGGTGCTCTGGTTC	60.359	66.667	0.00	0.00	0.00	3.62
889	898	1.990160	TTTCCGTGGGTGCTCTGGTT	61.990	55.000	0.00	0.00	0.00	3.67
1327	3445	2.414785	CGTTGGGGGCCAGTATTGC	61.415	63.158	4.39	0.00	33.81	3.56
1801	3922	3.851105	GCCTTAGAAATAGCAATGCGCAG	60.851	47.826	18.32	3.80	46.13	5.18
1973	4094	5.922544	CCATTTGCCTTAAGAAACTTCACAG	59.077	40.000	3.36	0.00	0.00	3.66
2422	4599	8.682936	AACACAAATATATTCATGGACTCTCC	57.317	34.615	0.00	0.00	36.96	3.71
2902	5711	1.066002	CGCCAATGGAAATGCTAGGTG	59.934	52.381	2.05	0.00	0.00	4.00
2960	5845	4.965119	AACCAAAATTCTGAGTATCCGC	57.035	40.909	0.00	0.00	0.00	5.54
3009	5894	6.751888	TCTTTCTGTGCTTGAAAAAGCTTAAC	59.248	34.615	0.00	2.90	45.66	2.01

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.