AutoCloner

Multiple sequence alignment - TraesCS5D01G546200

Loading Multiple Alignment...

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	TraesCS5D01G546200	chr5D	100.000	6785	0	0	1	6785	554930626	554923842	0.000000e+00	12530.0
1	TraesCS5D01G546200	chr5D	82.288	1355	205	25	1182	2519	555024209	555022873	0.000000e+00	1140.0
2	TraesCS5D01G546200	chr5D	83.485	1211	157	35	3812	5007	555020063	555018881	0.000000e+00	1088.0
3	TraesCS5D01G546200	chr5D	83.903	994	129	19	3800	4787	554774161	554775129	0.000000e+00	920.0
4	TraesCS5D01G546200	chr5D	84.751	623	88	4	5178	5798	555018772	555018155	9.670000e-173	617.0
5	TraesCS5D01G546200	chr5D	77.946	925	173	25	1349	2251	554604921	554604006	3.580000e-152	549.0
6	TraesCS5D01G546200	chr5D	83.985	537	81	2	5263	5798	554816783	554817315	1.690000e-140	510.0
7	TraesCS5D01G546200	chr5D	86.618	411	55	0	180	590	370385957	370386367	8.020000e-124	455.0
8	TraesCS5D01G546200	chr5D	86.520	319	32	2	856	1174	555027830	555027523	2.340000e-89	340.0
9	TraesCS5D01G546200	chr5D	76.080	602	118	17	3980	4571	554601877	554601292	2.390000e-74	291.0
10	TraesCS5D01G546200	chr5D	82.069	290	41	6	6497	6785	205576772	205577051	3.160000e-58	237.0
11	TraesCS5D01G546200	chr5D	83.406	229	26	10	2957	3179	555020629	555020407	1.150000e-47	202.0
12	TraesCS5D01G546200	chr5D	85.227	176	22	4	1001	1174	554614719	554614546	1.940000e-40	178.0
13	TraesCS5D01G546200	chr5D	96.591	88	3	0	2871	2958	373214659	373214572	5.480000e-31	147.0
14	TraesCS5D01G546200	chr5D	80.952	189	25	7	996	1174	560035615	560035802	9.180000e-29	139.0
15	TraesCS5D01G546200	chr4A	93.892	3831	135	36	2995	6785	613858957	613862728	0.000000e+00	5686.0
16	TraesCS5D01G546200	chr4A	94.848	1650	63	8	1231	2875	613857302	613858934	0.000000e+00	2556.0
17	TraesCS5D01G546200	chr4A	95.161	1178	37	9	1	1174	613854303	613855464	0.000000e+00	1842.0
18	TraesCS5D01G546200	chr4A	82.555	1221	179	27	3808	5006	613810844	613812052	0.000000e+00	1044.0
19	TraesCS5D01G546200	chr4A	84.244	622	92	3	5178	5798	613812162	613812778	9.740000e-168	601.0
20	TraesCS5D01G546200	chr4A	82.006	628	102	5	5178	5798	613979817	613980440	2.170000e-144	523.0
21	TraesCS5D01G546200	chr4A	86.834	319	27	3	856	1174	613803989	613804292	6.520000e-90	342.0
22	TraesCS5D01G546200	chr4A	86.170	188	21	5	2957	3141	613810391	613810576	1.490000e-46	198.0
23	TraesCS5D01G546200	chr4A	84.153	183	27	2	993	1174	613697277	613697458	6.990000e-40	176.0
24	TraesCS5D01G546200	chr4A	94.444	36	2	0	2957	2992	613858933	613858968	1.000000e-03	56.5
25	TraesCS5D01G546200	chr5B	95.378	2899	105	16	3870	6760	696091439	696094316	0.000000e+00	4584.0
26	TraesCS5D01G546200	chr5B	95.990	1646	55	7	1231	2868	696088556	696090198	0.000000e+00	2663.0
27	TraesCS5D01G546200	chr5B	93.130	1179	45	12	1	1174	696085606	696086753	0.000000e+00	1696.0
28	TraesCS5D01G546200	chr5B	94.139	836	23	7	2958	3769	696090199	696091032	0.000000e+00	1249.0
29	TraesCS5D01G546200	chr5B	83.005	1218	172	28	3806	5006	696021175	696022374	0.000000e+00	1070.0
30	TraesCS5D01G546200	chr5B	84.084	622	93	3	5178	5798	696022484	696023100	4.530000e-166	595.0
31	TraesCS5D01G546200	chr5B	76.830	997	183	27	1388	2357	710478063	710479038	1.010000e-142	518.0
32	TraesCS5D01G546200	chr5B	76.906	918	157	37	1357	2251	696127665	696128550	2.860000e-128	470.0
33	TraesCS5D01G546200	chr5B	82.723	382	60	4	5393	5769	696130813	696131193	1.090000e-87	335.0
34	TraesCS5D01G546200	chr5B	83.801	321	36	7	856	1174	696015364	696015670	2.390000e-74	291.0
35	TraesCS5D01G546200	chr5B	86.036	222	28	3	6566	6785	206790203	206789983	1.140000e-57	235.0
36	TraesCS5D01G546200	chr5B	85.638	188	22	5	2957	3141	696020722	696020907	6.940000e-45	193.0
37	TraesCS5D01G546200	chr5B	85.083	181	23	4	996	1174	696120213	696120391	1.500000e-41	182.0
38	TraesCS5D01G546200	chr5B	96.552	87	3	0	2874	2960	296852578	296852664	1.970000e-30	145.0
39	TraesCS5D01G546200	chr5B	100.000	30	0	0	3839	3868	696091419	696091448	1.000000e-03	56.5
40	TraesCS5D01G546200	chr4B	86.650	412	55	0	179	590	626467495	626467084	2.230000e-124	457.0
41	TraesCS5D01G546200	chr4B	92.157	102	6	2	2871	2971	99437505	99437405	7.090000e-30	143.0
42	TraesCS5D01G546200	chr1B	86.275	408	56	0	183	590	288040779	288040372	1.740000e-120	444.0
43	TraesCS5D01G546200	chr1B	75.367	341	72	12	249	583	48802068	48802402	3.280000e-33	154.0
44	TraesCS5D01G546200	chr2A	85.819	409	57	1	180	588	332065336	332065743	3.760000e-117	433.0
45	TraesCS5D01G546200	chr2A	97.674	86	2	0	2874	2959	16150380	16150295	1.520000e-31	148.0
46	TraesCS5D01G546200	chr2A	90.196	102	10	0	2873	2974	5636525	5636626	4.270000e-27	134.0
47	TraesCS5D01G546200	chr7B	88.070	285	31	2	6502	6784	15336615	15336898	1.090000e-87	335.0
48	TraesCS5D01G546200	chr7B	100.000	28	0	0	75	102	220355031	220355004	1.200000e-02	52.8
49	TraesCS5D01G546200	chr3B	80.645	403	76	2	187	589	736540975	736540575	1.840000e-80	311.0
50	TraesCS5D01G546200	chr3B	94.444	90	5	0	2871	2960	125879683	125879594	9.180000e-29	139.0
51	TraesCS5D01G546200	chr3B	94.444	90	5	0	2871	2960	125897374	125897285	9.180000e-29	139.0
52	TraesCS5D01G546200	chr6A	86.022	186	26	0	1	186	114476766	114476581	4.150000e-47	200.0
53	TraesCS5D01G546200	chr6A	90.244	41	4	0	75	115	521994372	521994332	3.000000e-03	54.7
54	TraesCS5D01G546200	chr2B	85.366	164	22	1	6509	6670	662348829	662348666	1.170000e-37	169.0
55	TraesCS5D01G546200	chr2B	82.609	69	8	4	34	100	254363307	254363373	2.640000e-04	58.4
56	TraesCS5D01G546200	chr2D	88.235	136	11	4	6548	6680	555568551	555568418	2.530000e-34	158.0
57	TraesCS5D01G546200	chr2D	88.430	121	14	0	469	589	597826860	597826980	5.480000e-31	147.0
58	TraesCS5D01G546200	chr2D	95.506	89	4	0	2872	2960	378043180	378043092	7.090000e-30	143.0
59	TraesCS5D01G546200	chr2D	80.435	92	17	1	30	121	565864656	565864566	1.220000e-07	69.4
60	TraesCS5D01G546200	chr1D	93.684	95	6	0	2860	2954	35756854	35756948	7.090000e-30	143.0
61	TraesCS5D01G546200	chr1D	80.682	88	16	1	30	117	254641582	254641496	4.390000e-07	67.6
62	TraesCS5D01G546200	chr5A	84.615	65	10	0	53	117	351490589	351490653	1.580000e-06	65.8

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	TraesCS5D01G546200	chr5D	554923842	554930626	6784	True	12530.000000	12530	100.000000	1	6785	1	chr5D.!!$R3	6784
1	TraesCS5D01G546200	chr5D	554774161	554775129	968	False	920.000000	920	83.903000	3800	4787	1	chr5D.!!$F3	987
2	TraesCS5D01G546200	chr5D	555018155	555027830	9675	True	677.400000	1140	84.090000	856	5798	5	chr5D.!!$R5	4942
3	TraesCS5D01G546200	chr5D	554816783	554817315	532	False	510.000000	510	83.985000	5263	5798	1	chr5D.!!$F4	535
4	TraesCS5D01G546200	chr5D	554601292	554604921	3629	True	420.000000	549	77.013000	1349	4571	2	chr5D.!!$R4	3222
5	TraesCS5D01G546200	chr4A	613854303	613862728	8425	False	2535.125000	5686	94.586250	1	6785	4	chr4A.!!$F5	6784
6	TraesCS5D01G546200	chr4A	613810391	613812778	2387	False	614.333333	1044	84.323000	2957	5798	3	chr4A.!!$F4	2841
7	TraesCS5D01G546200	chr4A	613979817	613980440	623	False	523.000000	523	82.006000	5178	5798	1	chr4A.!!$F3	620
8	TraesCS5D01G546200	chr5B	696085606	696094316	8710	False	2049.700000	4584	95.727400	1	6760	5	chr5B.!!$F6	6759
9	TraesCS5D01G546200	chr5B	696020722	696023100	2378	False	619.333333	1070	84.242333	2957	5798	3	chr5B.!!$F5	2841
10	TraesCS5D01G546200	chr5B	710478063	710479038	975	False	518.000000	518	76.830000	1388	2357	1	chr5B.!!$F4	969
11	TraesCS5D01G546200	chr5B	696127665	696131193	3528	False	402.500000	470	79.814500	1357	5769	2	chr5B.!!$F7	4412

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
447	448	0.976641	TCCTCCAAGCGAGAACACAT	59.023	50.000	0.00	0.00	41.63	3.21	F
1531	5892	0.463295	CAGCCTGCATTCGACCATCT	60.463	55.000	0.00	0.00	0.00	2.90	F
1633	5996	3.149196	CAGTGCCCCATAATATCACACC	58.851	50.000	0.00	0.00	0.00	4.16	F
2190	6573	3.737559	ACCATTGAAGTAGGATGGCAA	57.262	42.857	0.00	0.00	43.25	4.52	F
2892	10284	0.042131	TACTCCCTCCGTCCCACAAT	59.958	55.000	0.00	0.00	0.00	2.71	F
3621	11046	1.207791	AAGAGCGAGATTCCATGGGT	58.792	50.000	13.02	0.24	0.00	4.51	F
4666	12477	1.073964	CGGCATAGAGAATCCATGCG	58.926	55.000	4.51	0.00	44.77	4.73	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
2190	6573	2.294791	CGTTTCACTCTGAGGTCTCACT	59.705	50.000	9.85	35.46	3.41	R
2873	10265	0.042131	ATTGTGGGACGGAGGGAGTA	59.958	55.000	0.00	0.00	2.59	R
2874	10266	0.042131	TATTGTGGGACGGAGGGAGT	59.958	55.000	0.00	0.00	3.85	R
3154	10549	0.902048	TCCAATTTGCATTCCGGCCA	60.902	50.000	2.24	0.00	5.36	R
3773	11208	2.370189	GGGAGAGAGAGAGAGAGAGAGG	59.630	59.091	0.00	0.00	3.69	R
4940	12773	0.405198	AGGATCATGTGGTGGTGCAA	59.595	50.000	0.00	30.50	4.08	R
6130	13976	0.032267	TACGTGAACATGGTGTGCGA	59.968	50.000	0.00	0.00	5.10	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
46	47	2.292126	TGCTGGTCTCTTCCTCTCTCAT	60.292	50.000	0.00	0.00	0.00	2.90
79	80	2.541762	GCTTGAGATTTTAGATCGCGCT	59.458	45.455	5.56	0.00	0.00	5.92
159	160	3.161450	TCATGGGGCGCCCTACTC	61.161	66.667	42.70	27.49	45.70	2.59
166	167	3.224324	GCGCCCTACTCCGATCCA	61.224	66.667	0.00	0.00	0.00	3.41
191	192	1.609555	ACTATCGCCGTCCTGATCTTC	59.390	52.381	0.00	0.00	0.00	2.87
336	337	1.410517	GTCCTCGCATGATCTCCTTGA	59.589	52.381	0.00	0.00	0.00	3.02
375	376	1.762460	CCGGCTATCCTGACACCCT	60.762	63.158	0.00	0.00	0.00	4.34
406	407	2.980233	GGCTGCTGCGTGTTCCTT	60.980	61.111	9.65	0.00	40.82	3.36
424	425	2.154798	TTGGCTCCAACCTCGTCTCG	62.155	60.000	0.00	0.00	0.00	4.04
447	448	0.976641	TCCTCCAAGCGAGAACACAT	59.023	50.000	0.00	0.00	41.63	3.21
652	653	3.556775	GCCGCAACTAAAATATACGGTGA	59.443	43.478	0.00	0.00	41.15	4.02
722	723	1.383799	CCTTGGGATCACCTTGCCA	59.616	57.895	0.00	0.00	41.11	4.92
930	934	3.894947	GCTCCGCCTCCTCTCGAC	61.895	72.222	0.00	0.00	0.00	4.20
972	976	2.030981	GCCGAATCTAGGAGAACCTACG	60.031	54.545	0.00	0.00	45.83	3.51
1174	1181	2.076100	CTGTCGCAAGCATTCAGGTAA	58.924	47.619	0.00	0.00	37.18	2.85
1175	1182	2.679837	CTGTCGCAAGCATTCAGGTAAT	59.320	45.455	0.00	0.00	37.18	1.89
1176	1183	2.677836	TGTCGCAAGCATTCAGGTAATC	59.322	45.455	0.00	0.00	37.18	1.75
1177	1184	2.032178	GTCGCAAGCATTCAGGTAATCC	59.968	50.000	0.00	0.00	37.18	3.01
1179	1186	3.133901	TCGCAAGCATTCAGGTAATCCTA	59.866	43.478	0.00	0.00	38.83	2.94
1182	1189	5.877012	CGCAAGCATTCAGGTAATCCTATAT	59.123	40.000	0.00	0.00	43.07	0.86
1186	1193	6.183347	AGCATTCAGGTAATCCTATATTGGC	58.817	40.000	0.00	0.00	43.07	4.52
1187	1194	5.945784	GCATTCAGGTAATCCTATATTGGCA	59.054	40.000	0.00	0.00	43.07	4.92
1188	1195	6.434028	GCATTCAGGTAATCCTATATTGGCAA	59.566	38.462	0.68	0.68	43.07	4.52
1189	1196	7.039784	GCATTCAGGTAATCCTATATTGGCAAA	60.040	37.037	3.01	0.00	43.07	3.68
1192	1199	6.006449	CAGGTAATCCTATATTGGCAAAGCT	58.994	40.000	3.01	0.00	43.07	3.74
1199	5560	5.068636	CCTATATTGGCAAAGCTCATGAGT	58.931	41.667	23.38	8.16	0.00	3.41
1201	5562	0.599558	TTGGCAAAGCTCATGAGTGC	59.400	50.000	23.38	22.79	34.56	4.40
1204	5565	1.162698	GCAAAGCTCATGAGTGCTCA	58.837	50.000	23.38	4.23	43.29	4.26
1507	5868	8.979534	AGATATCATAGACTGTGTGCATATCAT	58.020	33.333	15.60	5.01	29.31	2.45
1531	5892	0.463295	CAGCCTGCATTCGACCATCT	60.463	55.000	0.00	0.00	0.00	2.90
1567	5928	9.420551	GAACCATACTATACAGGTAATACTTGC	57.579	37.037	2.25	0.00	33.15	4.01
1633	5996	3.149196	CAGTGCCCCATAATATCACACC	58.851	50.000	0.00	0.00	0.00	4.16
2190	6573	3.737559	ACCATTGAAGTAGGATGGCAA	57.262	42.857	0.00	0.00	43.25	4.52
2518	8064	6.817765	ACGACACAACTAAATCAATTGGAT	57.182	33.333	5.42	0.00	38.05	3.41
2807	10199	9.569122	TTTTAATATGCCACTTACTATTCTCCC	57.431	33.333	0.00	0.00	0.00	4.30
2875	10267	9.893305	AAATGTTTGCTCATAACACTTTACTAC	57.107	29.630	0.00	0.00	38.23	2.73
2876	10268	8.848474	ATGTTTGCTCATAACACTTTACTACT	57.152	30.769	0.00	0.00	38.23	2.57
2877	10269	8.306680	TGTTTGCTCATAACACTTTACTACTC	57.693	34.615	0.00	0.00	30.96	2.59
2878	10270	7.386848	TGTTTGCTCATAACACTTTACTACTCC	59.613	37.037	0.00	0.00	30.96	3.85
2879	10271	5.974108	TGCTCATAACACTTTACTACTCCC	58.026	41.667	0.00	0.00	0.00	4.30
2880	10272	5.720041	TGCTCATAACACTTTACTACTCCCT	59.280	40.000	0.00	0.00	0.00	4.20
2881	10273	6.127423	TGCTCATAACACTTTACTACTCCCTC	60.127	42.308	0.00	0.00	0.00	4.30
2882	10274	6.683360	GCTCATAACACTTTACTACTCCCTCC	60.683	46.154	0.00	0.00	0.00	4.30
2883	10275	5.359009	TCATAACACTTTACTACTCCCTCCG	59.641	44.000	0.00	0.00	0.00	4.63
2884	10276	3.166560	ACACTTTACTACTCCCTCCGT	57.833	47.619	0.00	0.00	0.00	4.69
2885	10277	3.087781	ACACTTTACTACTCCCTCCGTC	58.912	50.000	0.00	0.00	0.00	4.79
2886	10278	2.426381	CACTTTACTACTCCCTCCGTCC	59.574	54.545	0.00	0.00	0.00	4.79
2887	10279	2.030371	CTTTACTACTCCCTCCGTCCC	58.970	57.143	0.00	0.00	0.00	4.46
2888	10280	1.002069	TTACTACTCCCTCCGTCCCA	58.998	55.000	0.00	0.00	0.00	4.37
2889	10281	0.257039	TACTACTCCCTCCGTCCCAC	59.743	60.000	0.00	0.00	0.00	4.61
2890	10282	1.000019	CTACTCCCTCCGTCCCACA	60.000	63.158	0.00	0.00	0.00	4.17
2891	10283	0.613853	CTACTCCCTCCGTCCCACAA	60.614	60.000	0.00	0.00	0.00	3.33
2892	10284	0.042131	TACTCCCTCCGTCCCACAAT	59.958	55.000	0.00	0.00	0.00	2.71
2893	10285	0.042131	ACTCCCTCCGTCCCACAATA	59.958	55.000	0.00	0.00	0.00	1.90
2894	10286	1.344087	ACTCCCTCCGTCCCACAATAT	60.344	52.381	0.00	0.00	0.00	1.28
2895	10287	2.090943	ACTCCCTCCGTCCCACAATATA	60.091	50.000	0.00	0.00	0.00	0.86
2896	10288	2.969950	CTCCCTCCGTCCCACAATATAA	59.030	50.000	0.00	0.00	0.00	0.98
2897	10289	2.969950	TCCCTCCGTCCCACAATATAAG	59.030	50.000	0.00	0.00	0.00	1.73
2898	10290	2.969950	CCCTCCGTCCCACAATATAAGA	59.030	50.000	0.00	0.00	0.00	2.10
2899	10291	3.389983	CCCTCCGTCCCACAATATAAGAA	59.610	47.826	0.00	0.00	0.00	2.52
2900	10292	4.041691	CCCTCCGTCCCACAATATAAGAAT	59.958	45.833	0.00	0.00	0.00	2.40
2901	10293	4.997395	CCTCCGTCCCACAATATAAGAATG	59.003	45.833	0.00	0.00	0.00	2.67
2902	10294	5.454755	CCTCCGTCCCACAATATAAGAATGT	60.455	44.000	0.00	0.00	0.00	2.71
2903	10295	5.996644	TCCGTCCCACAATATAAGAATGTT	58.003	37.500	0.00	0.00	0.00	2.71
2904	10296	6.419791	TCCGTCCCACAATATAAGAATGTTT	58.580	36.000	0.00	0.00	0.00	2.83
2905	10297	6.887545	TCCGTCCCACAATATAAGAATGTTTT	59.112	34.615	0.00	0.00	0.00	2.43
2906	10298	7.394923	TCCGTCCCACAATATAAGAATGTTTTT	59.605	33.333	0.00	0.00	0.00	1.94
2931	10323	6.701432	ATACTAGTGTAGTGTCAAAAACGC	57.299	37.500	5.39	0.00	39.81	4.84
2933	10325	4.743644	ACTAGTGTAGTGTCAAAAACGCTC	59.256	41.667	0.00	0.00	45.69	5.03
2934	10326	3.793559	AGTGTAGTGTCAAAAACGCTCT	58.206	40.909	0.00	0.00	45.69	4.09
2935	10327	4.189231	AGTGTAGTGTCAAAAACGCTCTT	58.811	39.130	0.00	0.00	45.69	2.85
2936	10328	5.353938	AGTGTAGTGTCAAAAACGCTCTTA	58.646	37.500	0.00	0.00	45.69	2.10
2937	10329	5.989777	AGTGTAGTGTCAAAAACGCTCTTAT	59.010	36.000	0.00	0.00	45.69	1.73
2938	10330	7.149973	AGTGTAGTGTCAAAAACGCTCTTATA	58.850	34.615	0.00	0.00	45.69	0.98
2939	10331	7.817962	AGTGTAGTGTCAAAAACGCTCTTATAT	59.182	33.333	0.00	0.00	45.69	0.86
2940	10332	8.440833	GTGTAGTGTCAAAAACGCTCTTATATT	58.559	33.333	0.00	0.00	45.69	1.28
2941	10333	9.642327	TGTAGTGTCAAAAACGCTCTTATATTA	57.358	29.630	0.00	0.00	45.69	0.98
2944	10336	8.612619	AGTGTCAAAAACGCTCTTATATTATGG	58.387	33.333	0.00	0.00	45.69	2.74
2945	10337	7.855904	GTGTCAAAAACGCTCTTATATTATGGG	59.144	37.037	0.00	0.00	35.42	4.00
2946	10338	7.771361	TGTCAAAAACGCTCTTATATTATGGGA	59.229	33.333	0.00	0.00	0.00	4.37
2947	10339	8.068380	GTCAAAAACGCTCTTATATTATGGGAC	58.932	37.037	0.00	0.00	0.00	4.46
2948	10340	6.780706	AAAACGCTCTTATATTATGGGACG	57.219	37.500	0.00	0.00	0.00	4.79
2949	10341	4.451629	ACGCTCTTATATTATGGGACGG	57.548	45.455	0.00	0.00	0.00	4.79
2950	10342	4.084287	ACGCTCTTATATTATGGGACGGA	58.916	43.478	0.00	0.00	0.00	4.69
2951	10343	4.158025	ACGCTCTTATATTATGGGACGGAG	59.842	45.833	0.00	0.00	0.00	4.63
2952	10344	4.440250	CGCTCTTATATTATGGGACGGAGG	60.440	50.000	0.00	0.00	0.00	4.30
2953	10345	4.141914	GCTCTTATATTATGGGACGGAGGG	60.142	50.000	0.00	0.00	0.00	4.30
2954	10346	5.269991	CTCTTATATTATGGGACGGAGGGA	58.730	45.833	0.00	0.00	0.00	4.20
2955	10347	5.269991	TCTTATATTATGGGACGGAGGGAG	58.730	45.833	0.00	0.00	0.00	4.30
3150	10545	8.948631	TTCAAATTAGCACCAATAAAACACAA	57.051	26.923	0.00	0.00	0.00	3.33
3178	10573	3.439825	GCCGGAATGCAAATTGGAAAAAT	59.560	39.130	5.05	0.00	0.00	1.82
3298	10716	6.659242	ACCTCAAATTTTATCCACGAACATCT	59.341	34.615	0.00	0.00	0.00	2.90
3581	11006	5.906772	ACTACCGAGGGATTGGAATAAAT	57.093	39.130	0.00	0.00	0.00	1.40
3621	11046	1.207791	AAGAGCGAGATTCCATGGGT	58.792	50.000	13.02	0.24	0.00	4.51
3768	11203	4.983671	ACAAACAACCTCAAAACCTCTC	57.016	40.909	0.00	0.00	0.00	3.20
3769	11204	3.699538	ACAAACAACCTCAAAACCTCTCC	59.300	43.478	0.00	0.00	0.00	3.71
3770	11205	2.658807	ACAACCTCAAAACCTCTCCC	57.341	50.000	0.00	0.00	0.00	4.30
3771	11206	1.850345	ACAACCTCAAAACCTCTCCCA	59.150	47.619	0.00	0.00	0.00	4.37
3772	11207	2.447047	ACAACCTCAAAACCTCTCCCAT	59.553	45.455	0.00	0.00	0.00	4.00
3773	11208	3.084786	CAACCTCAAAACCTCTCCCATC	58.915	50.000	0.00	0.00	0.00	3.51
3774	11209	1.636003	ACCTCAAAACCTCTCCCATCC	59.364	52.381	0.00	0.00	0.00	3.51
3775	11210	1.918957	CCTCAAAACCTCTCCCATCCT	59.081	52.381	0.00	0.00	0.00	3.24
3776	11211	2.092699	CCTCAAAACCTCTCCCATCCTC	60.093	54.545	0.00	0.00	0.00	3.71
3777	11212	2.843113	CTCAAAACCTCTCCCATCCTCT	59.157	50.000	0.00	0.00	0.00	3.69
3778	11213	2.840651	TCAAAACCTCTCCCATCCTCTC	59.159	50.000	0.00	0.00	0.00	3.20
3779	11214	2.843113	CAAAACCTCTCCCATCCTCTCT	59.157	50.000	0.00	0.00	0.00	3.10
3780	11215	2.470057	AACCTCTCCCATCCTCTCTC	57.530	55.000	0.00	0.00	0.00	3.20
3781	11216	1.619298	ACCTCTCCCATCCTCTCTCT	58.381	55.000	0.00	0.00	0.00	3.10
3782	11217	1.499007	ACCTCTCCCATCCTCTCTCTC	59.501	57.143	0.00	0.00	0.00	3.20
3783	11218	1.782752	CCTCTCCCATCCTCTCTCTCT	59.217	57.143	0.00	0.00	0.00	3.10
3784	11219	2.224867	CCTCTCCCATCCTCTCTCTCTC	60.225	59.091	0.00	0.00	0.00	3.20
3785	11220	2.713167	CTCTCCCATCCTCTCTCTCTCT	59.287	54.545	0.00	0.00	0.00	3.10
3786	11221	2.711009	TCTCCCATCCTCTCTCTCTCTC	59.289	54.545	0.00	0.00	0.00	3.20
3787	11222	2.713167	CTCCCATCCTCTCTCTCTCTCT	59.287	54.545	0.00	0.00	0.00	3.10
3788	11223	2.711009	TCCCATCCTCTCTCTCTCTCTC	59.289	54.545	0.00	0.00	0.00	3.20
3789	11224	2.713167	CCCATCCTCTCTCTCTCTCTCT	59.287	54.545	0.00	0.00	0.00	3.10
3790	11225	3.244700	CCCATCCTCTCTCTCTCTCTCTC	60.245	56.522	0.00	0.00	0.00	3.20
3791	11226	3.649981	CCATCCTCTCTCTCTCTCTCTCT	59.350	52.174	0.00	0.00	0.00	3.10
3792	11227	4.262808	CCATCCTCTCTCTCTCTCTCTCTC	60.263	54.167	0.00	0.00	0.00	3.20
3793	11228	3.309296	TCCTCTCTCTCTCTCTCTCTCC	58.691	54.545	0.00	0.00	0.00	3.71
3932	11711	6.146837	GTGGTCATGCTTAGACATAGCTATTG	59.853	42.308	2.64	2.70	39.38	1.90
4098	11878	8.148999	GGACCGTAAGATAAACTTCATATTCCT	58.851	37.037	0.00	0.00	39.72	3.36
4212	11997	3.444916	CGATGCGTATCAAACTACAGGT	58.555	45.455	14.06	0.00	32.67	4.00
4236	12021	6.308015	TGTTACAACCTATTATGCTCAGGT	57.692	37.500	0.00	0.00	44.66	4.00
4504	12290	7.333423	CACCGAAATGTTCAAATAGGAGTCTAA	59.667	37.037	0.00	0.00	0.00	2.10
4566	12356	4.156455	TGAGACCTCTTGCTTTGAGTTT	57.844	40.909	0.00	0.00	0.00	2.66
4588	12378	1.290009	GCACCGGCAATTTCAAGCT	59.710	52.632	0.00	0.00	40.72	3.74
4666	12477	1.073964	CGGCATAGAGAATCCATGCG	58.926	55.000	4.51	0.00	44.77	4.73
4788	12612	8.797350	ATGCAATAATGTCATGCTAGCTATTA	57.203	30.769	17.23	12.32	40.66	0.98
4940	12773	8.137745	ACATCTTGTGAATTTTATGGGATGTT	57.862	30.769	0.00	0.00	38.28	2.71
5451	13290	2.675658	ATTGGTGGCTACAAGTTGGT	57.324	45.000	7.96	0.00	0.00	3.67
5457	13296	1.271163	TGGCTACAAGTTGGTGGCTAC	60.271	52.381	19.08	0.00	43.84	3.58
5462	13301	3.222173	ACAAGTTGGTGGCTACAATGA	57.778	42.857	7.96	0.00	0.00	2.57
5690	13530	1.009829	GTGGGCTTGATAACTGAGCG	58.990	55.000	0.00	0.00	37.29	5.03
5882	13727	7.933033	TCCGTTAAATCTGTGTTAACCTTAAGT	59.067	33.333	2.48	0.00	37.91	2.24
5907	13752	3.404899	ACGGCCGAGATTAAAAGAAACA	58.595	40.909	35.90	0.00	0.00	2.83
5935	13780	4.150980	CAGCAATGTTTACGACCGTTTCTA	59.849	41.667	0.00	0.00	0.00	2.10
6101	13947	3.469899	CACGTGGTGTGGTTCATATTG	57.530	47.619	7.95	0.00	45.21	1.90
6139	13985	0.108662	CTCATAGCTGTCGCACACCA	60.109	55.000	0.00	0.00	39.10	4.17
6158	14004	3.475774	GTTCACGTACGCGGCCAG	61.476	66.667	16.72	0.00	43.45	4.85
6229	14075	0.036952	CATTCTGCACGAGGACCAGT	60.037	55.000	0.00	0.00	0.00	4.00
6335	14181	0.308993	GCAATAAGCCATCTCCGTGC	59.691	55.000	0.00	0.00	37.23	5.34
6587	14438	0.893727	GGAACAACACCCAGCCGATT	60.894	55.000	0.00	0.00	0.00	3.34
6772	14623	7.675170	GCGTGTCCTTGAGAAATAAGATTCTTC	60.675	40.741	1.27	0.00	39.70	2.87

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
46	47	0.532115	TCTCAAGCGCATACTGCTCA	59.468	50.000	11.47	0.00	43.14	4.26
150	151	1.067582	GTTGGATCGGAGTAGGGCG	59.932	63.158	0.00	0.00	0.00	6.13
159	160	1.209128	GCGATAGTGTGTTGGATCGG	58.791	55.000	5.40	0.00	41.11	4.18
166	167	0.108804	CAGGACGGCGATAGTGTGTT	60.109	55.000	16.62	0.00	39.35	3.32
191	192	3.028130	CTGCTGCATGGCATACGG	58.972	61.111	1.31	0.00	41.63	4.02
336	337	2.739932	GCTCAGTCGGCATCACTGTAAT	60.740	50.000	8.34	0.00	41.82	1.89
406	407	2.636412	CGAGACGAGGTTGGAGCCA	61.636	63.158	0.00	0.00	0.00	4.75
424	425	0.670854	GTTCTCGCTTGGAGGACCAC	60.671	60.000	0.00	0.00	44.37	4.16
447	448	0.974010	GGTACTGGATCGGGACACCA	60.974	60.000	0.00	0.00	36.13	4.17
487	488	0.758734	ACTCAGCCACACAGTTAGCA	59.241	50.000	0.00	0.00	0.00	3.49
754	756	4.483311	GTCCGTTCTGTAAACGATCTCTT	58.517	43.478	11.53	0.00	45.64	2.85
930	934	3.515630	CTGCCGTGCTATATATGAGTGG	58.484	50.000	0.00	0.00	0.00	4.00
986	990	1.151668	CGCCATTGTGCTAGCTATCC	58.848	55.000	17.23	1.90	0.00	2.59
1029	1033	0.672342	ACGTAAGAGCCACAACGAGT	59.328	50.000	6.31	0.00	43.62	4.18
1174	1181	5.884322	TCATGAGCTTTGCCAATATAGGAT	58.116	37.500	0.00	0.00	0.00	3.24
1175	1182	5.163163	ACTCATGAGCTTTGCCAATATAGGA	60.163	40.000	22.83	0.00	0.00	2.94
1176	1183	5.048921	CACTCATGAGCTTTGCCAATATAGG	60.049	44.000	22.83	0.00	0.00	2.57
1177	1184	5.562307	GCACTCATGAGCTTTGCCAATATAG	60.562	44.000	22.83	0.00	0.00	1.31
1179	1186	3.067742	GCACTCATGAGCTTTGCCAATAT	59.932	43.478	22.83	0.00	0.00	1.28
1182	1189	0.599558	GCACTCATGAGCTTTGCCAA	59.400	50.000	22.83	0.00	0.00	4.52
1201	5562	4.338964	ACATCTCTAGACACTGCTCATGAG	59.661	45.833	18.84	18.84	0.00	2.90
1204	5565	6.015519	GGATTACATCTCTAGACACTGCTCAT	60.016	42.308	0.00	0.00	0.00	2.90
1453	5814	4.202367	CCGGGCTCTGTTAATTTCTAGGAT	60.202	45.833	0.00	0.00	0.00	3.24
1507	5868	3.874873	CGAATGCAGGCTGTTCGA	58.125	55.556	26.77	7.16	45.40	3.71
1531	5892	7.287927	CCTGTATAGTATGGTTCTTGAGGAGAA	59.712	40.741	0.00	0.00	42.03	2.87
1633	5996	7.386025	ACAATTGAGTGATATCATGATACGTGG	59.614	37.037	17.60	2.87	0.00	4.94
1957	6335	9.237187	TGACAATAACAATAGCACCAATCTAAA	57.763	29.630	0.00	0.00	0.00	1.85
2005	6387	4.314121	GCATACTGCTTAATGGGAGAGAG	58.686	47.826	0.00	0.00	40.96	3.20
2190	6573	2.294791	CGTTTCACTCTGAGGTCTCACT	59.705	50.000	9.85	0.00	35.46	3.41
2367	6783	9.483489	TGTCTACATGTCCTTAGGTATTAGAAA	57.517	33.333	0.00	0.00	0.00	2.52
2487	8033	6.518493	TGATTTAGTTGTGTCGTAAACTCCT	58.482	36.000	0.00	0.00	37.74	3.69
2799	10191	3.452990	TGTGTTTCCGCTATGGGAGAATA	59.547	43.478	0.00	0.00	37.40	1.75
2805	10197	1.821216	AGTTGTGTTTCCGCTATGGG	58.179	50.000	0.00	0.00	38.76	4.00
2806	10198	3.074412	AGAAGTTGTGTTTCCGCTATGG	58.926	45.455	0.00	0.00	40.09	2.74
2807	10199	3.125316	GGAGAAGTTGTGTTTCCGCTATG	59.875	47.826	0.00	0.00	0.00	2.23
2873	10265	0.042131	ATTGTGGGACGGAGGGAGTA	59.958	55.000	0.00	0.00	0.00	2.59
2874	10266	0.042131	TATTGTGGGACGGAGGGAGT	59.958	55.000	0.00	0.00	0.00	3.85
2875	10267	1.424638	ATATTGTGGGACGGAGGGAG	58.575	55.000	0.00	0.00	0.00	4.30
2876	10268	2.779429	TATATTGTGGGACGGAGGGA	57.221	50.000	0.00	0.00	0.00	4.20
2877	10269	2.969950	TCTTATATTGTGGGACGGAGGG	59.030	50.000	0.00	0.00	0.00	4.30
2878	10270	4.682778	TTCTTATATTGTGGGACGGAGG	57.317	45.455	0.00	0.00	0.00	4.30
2879	10271	5.611374	ACATTCTTATATTGTGGGACGGAG	58.389	41.667	0.00	0.00	0.00	4.63
2880	10272	5.623956	ACATTCTTATATTGTGGGACGGA	57.376	39.130	0.00	0.00	0.00	4.69
2881	10273	6.693315	AAACATTCTTATATTGTGGGACGG	57.307	37.500	0.00	0.00	0.00	4.79
2905	10297	8.702438	GCGTTTTTGACACTACACTAGTATAAA	58.298	33.333	0.00	0.00	37.23	1.40
2906	10298	8.084073	AGCGTTTTTGACACTACACTAGTATAA	58.916	33.333	0.00	0.00	37.23	0.98
2907	10299	7.596494	AGCGTTTTTGACACTACACTAGTATA	58.404	34.615	0.00	0.00	37.23	1.47
2908	10300	6.453092	AGCGTTTTTGACACTACACTAGTAT	58.547	36.000	0.00	0.00	37.23	2.12
2909	10301	5.835257	AGCGTTTTTGACACTACACTAGTA	58.165	37.500	0.00	0.00	37.23	1.82
2910	10302	4.690122	AGCGTTTTTGACACTACACTAGT	58.310	39.130	0.00	0.00	40.28	2.57
2911	10303	4.982916	AGAGCGTTTTTGACACTACACTAG	59.017	41.667	0.00	0.00	0.00	2.57
2912	10304	4.940463	AGAGCGTTTTTGACACTACACTA	58.060	39.130	0.00	0.00	0.00	2.74
2913	10305	3.793559	AGAGCGTTTTTGACACTACACT	58.206	40.909	0.00	0.00	0.00	3.55
2914	10306	4.531659	AAGAGCGTTTTTGACACTACAC	57.468	40.909	0.00	0.00	0.00	2.90
2915	10307	8.542497	AATATAAGAGCGTTTTTGACACTACA	57.458	30.769	0.00	0.00	0.00	2.74
2918	10310	8.612619	CCATAATATAAGAGCGTTTTTGACACT	58.387	33.333	0.00	0.00	0.00	3.55
2919	10311	7.855904	CCCATAATATAAGAGCGTTTTTGACAC	59.144	37.037	0.00	0.00	0.00	3.67
2920	10312	7.771361	TCCCATAATATAAGAGCGTTTTTGACA	59.229	33.333	0.00	0.00	0.00	3.58
2921	10313	8.068380	GTCCCATAATATAAGAGCGTTTTTGAC	58.932	37.037	0.00	0.00	0.00	3.18
2922	10314	7.042321	CGTCCCATAATATAAGAGCGTTTTTGA	60.042	37.037	0.00	0.00	0.00	2.69
2923	10315	7.069569	CGTCCCATAATATAAGAGCGTTTTTG	58.930	38.462	0.00	0.00	0.00	2.44
2924	10316	6.204108	CCGTCCCATAATATAAGAGCGTTTTT	59.796	38.462	0.00	0.00	0.00	1.94
2925	10317	5.699458	CCGTCCCATAATATAAGAGCGTTTT	59.301	40.000	0.00	0.00	0.00	2.43
2926	10318	5.011329	TCCGTCCCATAATATAAGAGCGTTT	59.989	40.000	0.00	0.00	0.00	3.60
2927	10319	4.525487	TCCGTCCCATAATATAAGAGCGTT	59.475	41.667	0.00	0.00	0.00	4.84
2928	10320	4.084287	TCCGTCCCATAATATAAGAGCGT	58.916	43.478	0.00	0.00	0.00	5.07
2929	10321	4.440250	CCTCCGTCCCATAATATAAGAGCG	60.440	50.000	0.00	0.00	0.00	5.03
2930	10322	4.141914	CCCTCCGTCCCATAATATAAGAGC	60.142	50.000	0.00	0.00	0.00	4.09
2931	10323	5.269991	TCCCTCCGTCCCATAATATAAGAG	58.730	45.833	0.00	0.00	0.00	2.85
2932	10324	5.222484	ACTCCCTCCGTCCCATAATATAAGA	60.222	44.000	0.00	0.00	0.00	2.10
2933	10325	5.024118	ACTCCCTCCGTCCCATAATATAAG	58.976	45.833	0.00	0.00	0.00	1.73
2934	10326	5.019657	ACTCCCTCCGTCCCATAATATAA	57.980	43.478	0.00	0.00	0.00	0.98
2935	10327	4.687262	ACTCCCTCCGTCCCATAATATA	57.313	45.455	0.00	0.00	0.00	0.86
2936	10328	3.562108	ACTCCCTCCGTCCCATAATAT	57.438	47.619	0.00	0.00	0.00	1.28
2937	10329	4.474303	TTACTCCCTCCGTCCCATAATA	57.526	45.455	0.00	0.00	0.00	0.98
2938	10330	3.339713	TTACTCCCTCCGTCCCATAAT	57.660	47.619	0.00	0.00	0.00	1.28
2939	10331	2.852714	TTACTCCCTCCGTCCCATAA	57.147	50.000	0.00	0.00	0.00	1.90
2940	10332	2.178325	TGATTACTCCCTCCGTCCCATA	59.822	50.000	0.00	0.00	0.00	2.74
2941	10333	1.062428	TGATTACTCCCTCCGTCCCAT	60.062	52.381	0.00	0.00	0.00	4.00
2942	10334	0.337082	TGATTACTCCCTCCGTCCCA	59.663	55.000	0.00	0.00	0.00	4.37
2943	10335	1.492764	TTGATTACTCCCTCCGTCCC	58.507	55.000	0.00	0.00	0.00	4.46
2944	10336	3.896272	ACTATTGATTACTCCCTCCGTCC	59.104	47.826	0.00	0.00	0.00	4.79
2945	10337	4.262079	CCACTATTGATTACTCCCTCCGTC	60.262	50.000	0.00	0.00	0.00	4.79
2946	10338	3.641906	CCACTATTGATTACTCCCTCCGT	59.358	47.826	0.00	0.00	0.00	4.69
2947	10339	3.895656	TCCACTATTGATTACTCCCTCCG	59.104	47.826	0.00	0.00	0.00	4.63
2948	10340	4.902448	ACTCCACTATTGATTACTCCCTCC	59.098	45.833	0.00	0.00	0.00	4.30
2949	10341	5.740513	GCACTCCACTATTGATTACTCCCTC	60.741	48.000	0.00	0.00	0.00	4.30
2950	10342	4.101741	GCACTCCACTATTGATTACTCCCT	59.898	45.833	0.00	0.00	0.00	4.20
2951	10343	4.141711	TGCACTCCACTATTGATTACTCCC	60.142	45.833	0.00	0.00	0.00	4.30
2952	10344	5.023533	TGCACTCCACTATTGATTACTCC	57.976	43.478	0.00	0.00	0.00	3.85
2953	10345	8.839310	ATTATGCACTCCACTATTGATTACTC	57.161	34.615	0.00	0.00	0.00	2.59
3139	10532	4.962155	TCCGGCCATTTTTGTGTTTTATT	58.038	34.783	2.24	0.00	0.00	1.40
3150	10545	2.748532	CAATTTGCATTCCGGCCATTTT	59.251	40.909	2.24	0.00	0.00	1.82
3154	10549	0.902048	TCCAATTTGCATTCCGGCCA	60.902	50.000	2.24	0.00	0.00	5.36
3246	10664	8.645110	CCATGGCTAATCAAATTTCTTATCCTT	58.355	33.333	0.00	3.71	0.00	3.36
3768	11203	2.713167	AGAGAGAGAGAGAGAGGATGGG	59.287	54.545	0.00	0.00	0.00	4.00
3769	11204	3.649981	AGAGAGAGAGAGAGAGAGGATGG	59.350	52.174	0.00	0.00	0.00	3.51
3770	11205	4.262808	GGAGAGAGAGAGAGAGAGAGGATG	60.263	54.167	0.00	0.00	0.00	3.51
3771	11206	3.906846	GGAGAGAGAGAGAGAGAGAGGAT	59.093	52.174	0.00	0.00	0.00	3.24
3772	11207	3.309296	GGAGAGAGAGAGAGAGAGAGGA	58.691	54.545	0.00	0.00	0.00	3.71
3773	11208	2.370189	GGGAGAGAGAGAGAGAGAGAGG	59.630	59.091	0.00	0.00	0.00	3.69
3774	11209	3.312890	AGGGAGAGAGAGAGAGAGAGAG	58.687	54.545	0.00	0.00	0.00	3.20
3775	11210	3.051803	AGAGGGAGAGAGAGAGAGAGAGA	60.052	52.174	0.00	0.00	0.00	3.10
3776	11211	3.312890	AGAGGGAGAGAGAGAGAGAGAG	58.687	54.545	0.00	0.00	0.00	3.20
3777	11212	3.051803	AGAGAGGGAGAGAGAGAGAGAGA	60.052	52.174	0.00	0.00	0.00	3.10
3778	11213	3.312890	AGAGAGGGAGAGAGAGAGAGAG	58.687	54.545	0.00	0.00	0.00	3.20
3779	11214	3.051803	AGAGAGAGGGAGAGAGAGAGAGA	60.052	52.174	0.00	0.00	0.00	3.10
3780	11215	3.312890	AGAGAGAGGGAGAGAGAGAGAG	58.687	54.545	0.00	0.00	0.00	3.20
3781	11216	3.051803	AGAGAGAGAGGGAGAGAGAGAGA	60.052	52.174	0.00	0.00	0.00	3.10
3782	11217	3.312890	AGAGAGAGAGGGAGAGAGAGAG	58.687	54.545	0.00	0.00	0.00	3.20
3783	11218	3.051803	AGAGAGAGAGAGGGAGAGAGAGA	60.052	52.174	0.00	0.00	0.00	3.10
3784	11219	3.312890	AGAGAGAGAGAGGGAGAGAGAG	58.687	54.545	0.00	0.00	0.00	3.20
3785	11220	3.051803	AGAGAGAGAGAGAGGGAGAGAGA	60.052	52.174	0.00	0.00	0.00	3.10
3786	11221	3.312890	AGAGAGAGAGAGAGGGAGAGAG	58.687	54.545	0.00	0.00	0.00	3.20
3787	11222	3.051803	AGAGAGAGAGAGAGAGGGAGAGA	60.052	52.174	0.00	0.00	0.00	3.10
3788	11223	3.312890	AGAGAGAGAGAGAGAGGGAGAG	58.687	54.545	0.00	0.00	0.00	3.20
3789	11224	3.051803	AGAGAGAGAGAGAGAGAGGGAGA	60.052	52.174	0.00	0.00	0.00	3.71
3790	11225	3.312890	AGAGAGAGAGAGAGAGAGGGAG	58.687	54.545	0.00	0.00	0.00	4.30
3791	11226	3.051803	AGAGAGAGAGAGAGAGAGAGGGA	60.052	52.174	0.00	0.00	0.00	4.20
3792	11227	3.312890	AGAGAGAGAGAGAGAGAGAGGG	58.687	54.545	0.00	0.00	0.00	4.30
3793	11228	4.222336	AGAGAGAGAGAGAGAGAGAGAGG	58.778	52.174	0.00	0.00	0.00	3.69
3884	11663	7.039082	CCACATGGGATTTATTAATTAGGTGGG	60.039	40.741	0.00	0.00	40.01	4.61
3956	11736	7.483580	AAGATAAGGCACAACTAACTAGACT	57.516	36.000	0.00	0.00	0.00	3.24
4212	11997	6.717289	ACCTGAGCATAATAGGTTGTAACAA	58.283	36.000	0.00	0.00	0.00	2.83
4236	12021	6.990939	TGATTTGATTGCTTGTTTGGATGAAA	59.009	30.769	0.00	0.00	0.00	2.69
4540	12330	4.130118	TCAAAGCAAGAGGTCTCAAGTTC	58.870	43.478	0.55	0.00	0.00	3.01
4588	12378	7.171337	GGAGTGTAAGTGAACATACGGTTTTTA	59.829	37.037	0.00	0.00	40.63	1.52
4788	12612	6.128138	AGTAACTTGATAGAGCCCTTGTTT	57.872	37.500	0.00	0.00	0.00	2.83
4940	12773	0.405198	AGGATCATGTGGTGGTGCAA	59.595	50.000	0.00	0.00	30.50	4.08
5195	13028	5.178623	TCAATTCGCGATTTAGAACACTTGT	59.821	36.000	10.88	0.00	0.00	3.16
5201	13034	8.822105	AGTTTAATCAATTCGCGATTTAGAAC	57.178	30.769	10.88	12.52	34.89	3.01
5250	13083	6.124088	AGTGTTTTTGTTAGTGAGCTGAAG	57.876	37.500	0.00	0.00	0.00	3.02
5253	13086	5.484173	TGAGTGTTTTTGTTAGTGAGCTG	57.516	39.130	0.00	0.00	0.00	4.24
5451	13290	3.831323	CCAATACCCATCATTGTAGCCA	58.169	45.455	0.00	0.00	32.55	4.75
5462	13301	4.293102	AGATGTATGATGGCCAATACCCAT	59.707	41.667	20.19	15.07	45.47	4.00
5512	13351	2.325082	CGCCGCCCCACATAATAGC	61.325	63.158	0.00	0.00	0.00	2.97
5714	13554	1.091771	CCAGTCGCCATAGTTGCCAG	61.092	60.000	0.00	0.00	0.00	4.85
5820	13663	5.195940	ACGGATGAGAACCATGAAATCATT	58.804	37.500	0.00	0.00	35.17	2.57
5882	13727	6.017275	TGTTTCTTTTAATCTCGGCCGTTAAA	60.017	34.615	27.15	23.72	0.00	1.52
5907	13752	2.289547	GGTCGTAAACATTGCTGTGTGT	59.710	45.455	0.00	0.00	35.22	3.72
6100	13946	1.199789	GCAGTGCGAAAATGGATGACA	59.800	47.619	0.00	0.00	0.00	3.58
6101	13947	1.470098	AGCAGTGCGAAAATGGATGAC	59.530	47.619	10.00	0.00	0.00	3.06
6130	13976	0.032267	TACGTGAACATGGTGTGCGA	59.968	50.000	0.00	0.00	0.00	5.10
6139	13985	2.812178	GGCCGCGTACGTGAACAT	60.812	61.111	29.24	0.00	37.70	2.71
6520	14369	8.240682	TCCATTGATTGAGTAATAAAAACACCG	58.759	33.333	0.00	0.00	0.00	4.94
6587	14438	0.671472	CGCACTGCTCTGTGGATTCA	60.671	55.000	8.59	0.00	38.31	2.57
6677	14528	1.979693	ACGAGGGCAGAGAGGTGAC	60.980	63.158	0.00	0.00	0.00	3.67

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.