AutoCloner

Multiple sequence alignment - TraesCS1D01G222000

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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	TraesCS1D01G222000	chr1D	100.000	6304	0	0	1	6304	309915877	309922180	0.000000e+00	11642.0
1	TraesCS1D01G222000	chr1D	85.382	1977	158	56	475	2400	309851743	309853639	0.000000e+00	1929.0
2	TraesCS1D01G222000	chr1D	91.756	558	46	0	3963	4520	309854454	309855011	0.000000e+00	776.0
3	TraesCS1D01G222000	chr1D	90.455	220	21	0	4729	4948	309855134	309855353	2.220000e-74	291.0
4	TraesCS1D01G222000	chr1D	83.030	330	38	5	3367	3681	309854081	309854407	3.720000e-72	283.0
5	TraesCS1D01G222000	chr1D	88.211	246	16	6	5119	5355	309901375	309901616	1.340000e-71	281.0
6	TraesCS1D01G222000	chr1D	78.737	475	59	19	5299	5761	309901505	309901949	4.810000e-71	279.0
7	TraesCS1D01G222000	chr1D	90.374	187	13	4	2481	2666	309853742	309853924	2.270000e-59	241.0
8	TraesCS1D01G222000	chr1D	90.141	142	12	1	4944	5085	309901242	309901381	3.880000e-42	183.0
9	TraesCS1D01G222000	chr1D	92.982	114	4	2	5299	5410	309921120	309921231	5.060000e-36	163.0
10	TraesCS1D01G222000	chr1D	92.683	82	6	0	4612	4693	309855046	309855127	1.110000e-22	119.0
11	TraesCS1D01G222000	chr1A	95.552	4317	137	28	1510	5806	389798938	389803219	0.000000e+00	6857.0
12	TraesCS1D01G222000	chr1A	86.804	1508	121	44	924	2400	389767544	389769004	0.000000e+00	1611.0
13	TraesCS1D01G222000	chr1A	92.945	567	26	5	862	1417	389798103	389798666	0.000000e+00	813.0
14	TraesCS1D01G222000	chr1A	91.935	558	44	1	3963	4520	389769788	389770344	0.000000e+00	780.0
15	TraesCS1D01G222000	chr1A	88.975	517	48	7	2	514	389794588	389795099	1.150000e-176	630.0
16	TraesCS1D01G222000	chr1A	90.476	357	32	1	4729	5085	389770466	389770820	2.660000e-128	470.0
17	TraesCS1D01G222000	chr1A	79.882	507	61	19	5299	5793	389770946	389771423	3.640000e-87	333.0
18	TraesCS1D01G222000	chr1A	95.408	196	8	1	6089	6283	389804351	389804546	1.710000e-80	311.0
19	TraesCS1D01G222000	chr1A	90.083	242	14	7	5865	6098	389803219	389803458	7.940000e-79	305.0
20	TraesCS1D01G222000	chr1A	84.098	327	36	4	3367	3681	389769412	389769734	1.030000e-77	302.0
21	TraesCS1D01G222000	chr1A	88.710	248	13	9	5119	5355	389770814	389771057	8.000000e-74	289.0
22	TraesCS1D01G222000	chr1A	81.928	332	45	5	5	336	389252567	389252883	3.750000e-67	267.0
23	TraesCS1D01G222000	chr1A	89.167	120	10	3	5865	5983	389771445	389771562	5.090000e-31	147.0
24	TraesCS1D01G222000	chr1A	92.593	81	6	0	4612	4692	389770378	389770458	3.990000e-22	117.0
25	TraesCS1D01G222000	chr3A	95.183	4318	143	32	1510	5806	128585631	128581358	0.000000e+00	6761.0
26	TraesCS1D01G222000	chr3A	86.605	1508	123	39	924	2400	128720287	128718828	0.000000e+00	1592.0
27	TraesCS1D01G222000	chr3A	91.408	710	39	10	723	1421	128586905	128586207	0.000000e+00	953.0
28	TraesCS1D01G222000	chr3A	91.979	561	44	1	3963	4523	128718043	128717484	0.000000e+00	785.0
29	TraesCS1D01G222000	chr3A	88.953	516	53	3	2	514	128587623	128587109	8.920000e-178	634.0
30	TraesCS1D01G222000	chr3A	90.196	357	33	1	4729	5085	128717365	128717011	1.240000e-126	464.0
31	TraesCS1D01G222000	chr3A	85.015	327	33	4	3367	3681	128718419	128718097	1.020000e-82	318.0
32	TraesCS1D01G222000	chr3A	90.909	242	11	8	5865	6098	128581358	128581120	1.320000e-81	315.0
33	TraesCS1D01G222000	chr3A	79.093	507	65	19	5299	5793	128716885	128716408	1.710000e-80	311.0
34	TraesCS1D01G222000	chr3A	94.898	196	9	1	6089	6283	128580226	128580031	7.940000e-79	305.0
35	TraesCS1D01G222000	chr3A	88.285	239	15	8	5119	5346	128717017	128716781	2.240000e-69	274.0
36	TraesCS1D01G222000	chr3A	98.837	86	1	0	4550	4635	741209482	741209567	3.040000e-33	154.0
37	TraesCS1D01G222000	chr3A	89.431	123	10	3	5865	5986	128716386	128716266	1.090000e-32	152.0
38	TraesCS1D01G222000	chr3A	92.593	81	6	0	4612	4692	128717453	128717373	3.990000e-22	117.0
39	TraesCS1D01G222000	chr1B	92.377	2676	116	25	715	3368	419940562	419943171	0.000000e+00	3731.0
40	TraesCS1D01G222000	chr1B	95.541	1951	66	15	3359	5297	419948442	419950383	0.000000e+00	3101.0
41	TraesCS1D01G222000	chr1B	85.835	1779	157	33	3367	5085	419770768	419772511	0.000000e+00	1801.0
42	TraesCS1D01G222000	chr1B	86.739	1561	120	41	878	2400	419768912	419770423	0.000000e+00	1655.0
43	TraesCS1D01G222000	chr1B	91.859	737	47	6	2	731	419939627	419940357	0.000000e+00	1016.0
44	TraesCS1D01G222000	chr1B	83.540	887	119	19	3	879	419767258	419768127	0.000000e+00	804.0
45	TraesCS1D01G222000	chr1B	88.333	240	14	7	5119	5346	419772505	419772742	6.230000e-70	276.0
46	TraesCS1D01G222000	chr1B	87.778	180	17	4	2481	2659	419770525	419770700	8.280000e-49	206.0
47	TraesCS1D01G222000	chr1B	90.909	143	13	0	5299	5441	419772638	419772780	6.450000e-45	193.0
48	TraesCS1D01G222000	chr1B	89.167	120	10	3	5865	5983	419780775	419780892	5.090000e-31	147.0
49	TraesCS1D01G222000	chr4A	83.209	536	68	11	2836	3365	406758913	406759432	7.400000e-129	472.0
50	TraesCS1D01G222000	chr6B	81.532	444	58	20	2753	3186	87325837	87326266	1.680000e-90	344.0
51	TraesCS1D01G222000	chr6B	87.940	199	22	1	3172	3368	87326289	87326487	3.800000e-57	233.0
52	TraesCS1D01G222000	chr6B	91.549	71	5	1	5805	5875	273665364	273665295	5.200000e-16	97.1
53	TraesCS1D01G222000	chr6B	88.732	71	7	1	5805	5875	668385916	668385985	1.130000e-12	86.1
54	TraesCS1D01G222000	chr2D	82.051	390	54	9	2756	3133	36119095	36119480	1.020000e-82	318.0
55	TraesCS1D01G222000	chr2D	83.562	219	32	3	2799	3015	3303622	3303838	1.070000e-47	202.0
56	TraesCS1D01G222000	chr4D	85.824	261	33	3	2757	3015	229900769	229901027	2.240000e-69	274.0
57	TraesCS1D01G222000	chr4D	78.832	137	8	6	1060	1196	509239605	509239490	8.770000e-09	73.1
58	TraesCS1D01G222000	chr7A	85.441	261	34	3	2757	3015	546012058	546012316	1.040000e-67	268.0
59	TraesCS1D01G222000	chr5D	89.231	195	21	0	3172	3366	9226937	9227131	1.760000e-60	244.0
60	TraesCS1D01G222000	chr2B	88.718	195	22	0	3172	3366	61334727	61334533	8.170000e-59	239.0
61	TraesCS1D01G222000	chr2B	90.141	71	6	1	5805	5875	605032340	605032409	2.420000e-14	91.6
62	TraesCS1D01G222000	chrUn	87.692	195	23	1	3172	3365	17288781	17288975	6.360000e-55	226.0
63	TraesCS1D01G222000	chr2A	88.298	188	20	2	3180	3366	18894767	18894581	2.290000e-54	224.0
64	TraesCS1D01G222000	chr2A	86.709	158	21	0	2760	2917	28790567	28790410	6.500000e-40	176.0
65	TraesCS1D01G222000	chr7B	91.549	71	5	1	5805	5875	355483054	355482985	5.200000e-16	97.1
66	TraesCS1D01G222000	chr7B	90.141	71	6	1	5805	5875	289577676	289577745	2.420000e-14	91.6
67	TraesCS1D01G222000	chr3B	90.141	71	6	1	5805	5875	391081821	391081890	2.420000e-14	91.6
68	TraesCS1D01G222000	chr3B	90.000	70	6	1	5806	5875	86727913	86727845	8.700000e-14	89.8
69	TraesCS1D01G222000	chr3B	94.872	39	2	0	5504	5542	749038033	749037995	1.900000e-05	62.1
70	TraesCS1D01G222000	chr6D	89.333	75	3	1	5805	5874	178857946	178858020	8.700000e-14	89.8
71	TraesCS1D01G222000	chr4B	88.732	71	7	1	5805	5875	167058364	167058433	1.130000e-12	86.1
72	TraesCS1D01G222000	chr5A	97.368	38	1	0	5505	5542	290689226	290689189	1.470000e-06	65.8
73	TraesCS1D01G222000	chr5A	92.105	38	3	0	5505	5542	703429639	703429676	3.000000e-03	54.7
74	TraesCS1D01G222000	chr6A	94.737	38	2	0	5505	5542	426636081	426636044	6.830000e-05	60.2

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	TraesCS1D01G222000	chr1D	309915877	309922180	6303	False	5902.500000	11642	96.491000	1	6304	2	chr1D.!!$F3	6303
1	TraesCS1D01G222000	chr1D	309851743	309855353	3610	False	606.500000	1929	88.946667	475	4948	6	chr1D.!!$F1	4473
2	TraesCS1D01G222000	chr1D	309901242	309901949	707	False	247.666667	281	85.696333	4944	5761	3	chr1D.!!$F2	817
3	TraesCS1D01G222000	chr1A	389794588	389804546	9958	False	1783.200000	6857	92.592600	2	6283	5	chr1A.!!$F3	6281
4	TraesCS1D01G222000	chr1A	389767544	389771562	4018	False	506.125000	1611	87.958125	924	5983	8	chr1A.!!$F2	5059
5	TraesCS1D01G222000	chr3A	128580031	128587623	7592	True	1793.600000	6761	92.270200	2	6283	5	chr3A.!!$R1	6281
6	TraesCS1D01G222000	chr3A	128716266	128720287	4021	True	501.625000	1592	87.899625	924	5986	8	chr3A.!!$R2	5062
7	TraesCS1D01G222000	chr1B	419948442	419950383	1941	False	3101.000000	3101	95.541000	3359	5297	1	chr1B.!!$F2	1938
8	TraesCS1D01G222000	chr1B	419939627	419943171	3544	False	2373.500000	3731	92.118000	2	3368	2	chr1B.!!$F4	3366
9	TraesCS1D01G222000	chr1B	419767258	419772780	5522	False	822.500000	1801	87.189000	3	5441	6	chr1B.!!$F3	5438
10	TraesCS1D01G222000	chr4A	406758913	406759432	519	False	472.000000	472	83.209000	2836	3365	1	chr4A.!!$F1	529
11	TraesCS1D01G222000	chr6B	87325837	87326487	650	False	288.500000	344	84.736000	2753	3368	2	chr6B.!!$F2	615

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
570	737	0.040499	GGGGGCTTTACATTCACCCA	59.960	55.000	0.00	42.76	4.51	F
1864	6266	0.250858	TGTGCTGGACAAGGATGGTG	60.251	55.000	0.00	0.00	4.17	F
1866	6268	0.250858	TGCTGGACAAGGATGGTGTG	60.251	55.000	0.00	0.00	3.82	F
2969	7507	1.808411	AGCATTCCCGCGTATTATGG	58.192	50.000	4.92	36.85	2.74	F
3269	7856	1.003545	GTGCGTGCTATGGCTACAATG	60.004	52.381	1.68	39.59	2.82	F
4848	9520	1.942657	CATCAGTATCACGGGCCTTTG	59.057	52.381	0.84	0.00	2.77	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2041	6451	1.875009	TCTGACTTGCAACTGCTCAG	58.125	50.000	11.33	11.33	40.25	3.35	R
2969	7507	1.278238	CGGCTCATGTAAGACCGAAC	58.722	55.000	9.96	0.00	46.71	3.95	R
3000	7538	1.336980	GGAGGCGTATACAAGCTAGCC	60.337	57.143	12.13	8.65	44.45	3.93	R
4004	8655	1.160329	AACTGCACGGACTGAAGCAC	61.160	55.000	2.73	0.00	32.87	4.40	R
5058	9733	0.097674	CGGCCTTCGAAGCTTCATTG	59.902	55.000	25.47	13.62	42.43	2.82	R
5986	10741	0.248215	GGCTTGGCATCGTCAATTCG	60.248	55.000	0.00	0.00	0.00	3.34	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
24	25	3.275143	CGACTCACACTCTCCTCTATGT	58.725	50.000	0.00	0.00	0.00	2.29
38	39	3.823304	CCTCTATGTCATCGATGAGACCA	59.177	47.826	27.95	21.64	37.51	4.02
51	52	0.532573	GAGACCATCGCTGACAAGGA	59.467	55.000	0.00	0.00	0.00	3.36
63	64	2.757868	CTGACAAGGAGGATCGAGAGTT	59.242	50.000	0.00	0.00	34.37	3.01
223	226	4.945246	TCGTGCAACTAAAGATATCTCCC	58.055	43.478	5.51	0.00	31.75	4.30
257	261	5.362430	ACCACAAGTCAACACATACCAATTT	59.638	36.000	0.00	0.00	0.00	1.82
314	319	0.103390	TCAACGACGCTGGTTCAAGA	59.897	50.000	0.00	0.00	0.00	3.02
441	453	6.678547	AGAGATTACATCCTGTCCTAGACTT	58.321	40.000	0.00	0.00	33.15	3.01
465	479	3.915536	AGTTAGGTTGTCTCTTCTTCGC	58.084	45.455	0.00	0.00	0.00	4.70
570	737	0.040499	GGGGGCTTTACATTCACCCA	59.960	55.000	0.00	0.00	42.76	4.51
573	740	2.358195	GGGGCTTTACATTCACCCATCT	60.358	50.000	0.00	0.00	42.76	2.90
576	743	3.531538	GCTTTACATTCACCCATCTCGA	58.468	45.455	0.00	0.00	0.00	4.04
605	772	1.519898	GCATGCAAATGCGAAGGGG	60.520	57.895	14.21	0.00	45.83	4.79
677	853	1.808133	GCCCGCATAGAGTTCTCTTGG	60.808	57.143	7.66	5.64	0.00	3.61
678	854	1.202580	CCCGCATAGAGTTCTCTTGGG	60.203	57.143	7.66	12.43	0.00	4.12
762	1161	6.165577	GGCACAAATGATGGAATAAAGTGTT	58.834	36.000	0.00	0.00	0.00	3.32
784	1183	4.126208	TGCCCGACGAGATATAAAAACA	57.874	40.909	0.00	0.00	0.00	2.83
790	1189	7.466860	GCCCGACGAGATATAAAAACAGAAAAT	60.467	37.037	0.00	0.00	0.00	1.82
871	3943	5.648178	AAAGTGTCCTAAAACAAAACGGT	57.352	34.783	0.00	0.00	0.00	4.83
1234	5102	0.645868	GCGATCCTCGTTTTCTTCCG	59.354	55.000	0.00	0.00	42.81	4.30
1275	5143	1.892391	GTTCGGGGAATCGGGATGC	60.892	63.158	0.00	0.00	0.00	3.91
1462	5344	1.343506	CTTCTCGCCTTTGCATTTGC	58.656	50.000	0.00	0.00	42.50	3.68
1503	5880	2.101750	GCCTAGTTCTGCTACTTCCTCC	59.898	54.545	0.00	0.00	0.00	4.30
1504	5881	2.696187	CCTAGTTCTGCTACTTCCTCCC	59.304	54.545	0.00	0.00	0.00	4.30
1505	5882	1.187087	AGTTCTGCTACTTCCTCCCG	58.813	55.000	0.00	0.00	0.00	5.14
1506	5883	0.460459	GTTCTGCTACTTCCTCCCGC	60.460	60.000	0.00	0.00	0.00	6.13
1507	5884	0.902984	TTCTGCTACTTCCTCCCGCA	60.903	55.000	0.00	0.00	0.00	5.69
1508	5885	1.142748	CTGCTACTTCCTCCCGCAG	59.857	63.158	0.00	0.00	41.57	5.18
1509	5886	1.608717	CTGCTACTTCCTCCCGCAGT	61.609	60.000	0.00	0.00	42.19	4.40
1510	5887	1.142097	GCTACTTCCTCCCGCAGTC	59.858	63.158	0.00	0.00	0.00	3.51
1551	5928	5.008316	ACACCTTCAAAATTCGTGGTAGTTC	59.992	40.000	0.00	0.00	0.00	3.01
1553	5930	5.469084	ACCTTCAAAATTCGTGGTAGTTCTC	59.531	40.000	0.00	0.00	0.00	2.87
1696	6091	4.824289	AGATGTTTGTTTCCATGGCATTC	58.176	39.130	6.96	0.00	0.00	2.67
1863	6265	0.250901	GTGTGCTGGACAAGGATGGT	60.251	55.000	2.79	0.00	35.91	3.55
1864	6266	0.250858	TGTGCTGGACAAGGATGGTG	60.251	55.000	0.00	0.00	0.00	4.17
1865	6267	0.250901	GTGCTGGACAAGGATGGTGT	60.251	55.000	0.00	0.00	0.00	4.16
1866	6268	0.250858	TGCTGGACAAGGATGGTGTG	60.251	55.000	0.00	0.00	0.00	3.82
1887	6292	2.829120	GCATACACCTCCTATCCTCCTC	59.171	54.545	0.00	0.00	0.00	3.71
2053	6463	5.049474	CACATTAGTTTACTGAGCAGTTGCA	60.049	40.000	8.60	0.00	45.16	4.08
2128	6540	5.603596	TCAAACAGAGATGCTTTGCAAATT	58.396	33.333	13.23	0.48	43.62	1.82
2451	6866	8.974060	ACAGTCCAAATTGAGTACTTCTTAAA	57.026	30.769	0.00	0.00	0.00	1.52
2452	6867	9.403583	ACAGTCCAAATTGAGTACTTCTTAAAA	57.596	29.630	0.00	0.00	0.00	1.52
2512	6978	9.469807	TTGAAATGTTAATTGTTCACATACACC	57.530	29.630	0.00	0.00	30.74	4.16
2808	7344	2.021039	CCAAAACATTGGCGTGCCG	61.021	57.895	6.37	0.00	39.42	5.69
2934	7472	3.485216	GCGAGTTCGTCCACCAAAATATG	60.485	47.826	3.27	0.00	42.22	1.78
2969	7507	1.808411	AGCATTCCCGCGTATTATGG	58.192	50.000	4.92	0.00	36.85	2.74
2998	7536	6.255950	GTCTTACATGAGCCGGAAAATTAAC	58.744	40.000	5.05	0.00	0.00	2.01
3000	7538	4.701956	ACATGAGCCGGAAAATTAACTG	57.298	40.909	5.05	0.00	0.00	3.16
3149	7697	6.584185	TTGATCATCATGATTTATGGGCTG	57.416	37.500	5.16	0.00	37.20	4.85
3207	7792	5.221303	GCTGATATGTGGCATGTTAATTGGT	60.221	40.000	0.00	0.00	0.00	3.67
3269	7856	1.003545	GTGCGTGCTATGGCTACAATG	60.004	52.381	1.68	0.00	39.59	2.82
3287	7874	4.081972	ACAATGCAAACAACACTACCACAA	60.082	37.500	0.00	0.00	0.00	3.33
3288	7875	4.727507	ATGCAAACAACACTACCACAAA	57.272	36.364	0.00	0.00	0.00	2.83
3435	8022	3.115554	GCTCTTTGCAAAATCAACGTGT	58.884	40.909	13.84	0.00	42.31	4.49
3581	8183	6.943981	TGATCTGTTTGAAAGTTCTTGTACG	58.056	36.000	0.00	0.00	0.00	3.67
3720	8349	9.581289	TTTCTTGACTTTCATAGGTTGGATTTA	57.419	29.630	0.00	0.00	0.00	1.40
3721	8350	9.581289	TTCTTGACTTTCATAGGTTGGATTTAA	57.419	29.630	0.00	0.00	0.00	1.52
3722	8351	9.581289	TCTTGACTTTCATAGGTTGGATTTAAA	57.419	29.630	0.00	0.00	0.00	1.52
4004	8655	5.047188	GGGTTTGTGATGTTTGTACCTTTG	58.953	41.667	0.00	0.00	0.00	2.77
4034	8685	6.923508	TCAGTCCGTGCAGTTTTCATATATAG	59.076	38.462	0.00	0.00	0.00	1.31
4140	8791	5.450688	CCCTGTGTTTTGTTTGGACGAAATA	60.451	40.000	0.00	0.00	40.36	1.40
4383	9034	4.528987	AGGTACTTCTTTCTCTCTTCCACC	59.471	45.833	0.00	0.00	27.25	4.61
4639	9302	4.272991	TGTCATGAAATTTTTGCTTGGCAC	59.727	37.500	0.00	0.00	38.71	5.01
4755	9427	5.585390	ACCACCTTTTCACGTATAGTATCG	58.415	41.667	0.00	0.00	0.00	2.92
4848	9520	1.942657	CATCAGTATCACGGGCCTTTG	59.057	52.381	0.84	0.00	0.00	2.77
5058	9733	2.100631	CAACGCTCCCACATCCGAC	61.101	63.158	0.00	0.00	0.00	4.79
5323	10009	8.449625	AGACCATTACTACCTATGATAGAGTGT	58.550	37.037	0.00	0.00	0.00	3.55
5330	10016	2.408050	CTATGATAGAGTGTTGCCCGC	58.592	52.381	0.00	0.00	0.00	6.13
5473	10215	4.221262	ACATTATGCATTGCCTGTGTTCTT	59.779	37.500	3.54	0.00	0.00	2.52
5491	10233	5.234329	TGTTCTTGACTTCTCGTTCATGAAC	59.766	40.000	25.68	25.68	42.46	3.18
5503	10245	2.812011	GTTCATGAACGTTAAGGCCTGT	59.188	45.455	22.09	0.00	0.00	4.00
5532	10274	9.392506	TGGTTCAAAGGATAGGAATATCATAGA	57.607	33.333	0.00	0.00	0.00	1.98
5600	10343	5.094134	GGTGCTATTCGATTCGTAGGATAC	58.906	45.833	5.89	1.16	38.50	2.24
5601	10344	5.335426	GGTGCTATTCGATTCGTAGGATACA	60.335	44.000	5.89	0.00	43.24	2.29
5664	10418	6.046593	TGAAATGTGACGGATAATCCTACAC	58.953	40.000	0.00	0.00	39.14	2.90
5703	10457	6.029346	ACAAACCAAATAGCTCCAATGAAG	57.971	37.500	0.00	0.00	0.00	3.02
5798	10552	9.454859	CTATGTGAAGAGGTTTAGGAAAATCTT	57.545	33.333	0.00	0.00	36.14	2.40
5799	10553	8.712228	ATGTGAAGAGGTTTAGGAAAATCTTT	57.288	30.769	0.00	0.00	36.14	2.52
5800	10554	7.940850	TGTGAAGAGGTTTAGGAAAATCTTTG	58.059	34.615	0.00	0.00	36.14	2.77
5801	10555	7.777910	TGTGAAGAGGTTTAGGAAAATCTTTGA	59.222	33.333	0.00	0.00	36.14	2.69
5802	10556	8.797438	GTGAAGAGGTTTAGGAAAATCTTTGAT	58.203	33.333	0.00	0.00	36.14	2.57
5803	10557	8.796475	TGAAGAGGTTTAGGAAAATCTTTGATG	58.204	33.333	0.00	0.00	36.14	3.07
5804	10558	8.712228	AAGAGGTTTAGGAAAATCTTTGATGT	57.288	30.769	0.00	0.00	36.14	3.06
5805	10559	9.807921	AAGAGGTTTAGGAAAATCTTTGATGTA	57.192	29.630	0.00	0.00	36.14	2.29
5806	10560	9.232473	AGAGGTTTAGGAAAATCTTTGATGTAC	57.768	33.333	0.00	0.00	36.14	2.90
5807	10561	9.232473	GAGGTTTAGGAAAATCTTTGATGTACT	57.768	33.333	0.00	0.00	36.14	2.73
5808	10562	9.232473	AGGTTTAGGAAAATCTTTGATGTACTC	57.768	33.333	0.00	0.00	31.79	2.59
5809	10563	8.459635	GGTTTAGGAAAATCTTTGATGTACTCC	58.540	37.037	0.00	0.00	0.00	3.85
5810	10564	8.459635	GTTTAGGAAAATCTTTGATGTACTCCC	58.540	37.037	0.00	0.00	0.00	4.30
5812	10566	6.418946	AGGAAAATCTTTGATGTACTCCCTC	58.581	40.000	0.00	0.00	0.00	4.30
5813	10567	5.590663	GGAAAATCTTTGATGTACTCCCTCC	59.409	44.000	0.00	0.00	0.00	4.30
5814	10568	4.408182	AATCTTTGATGTACTCCCTCCG	57.592	45.455	0.00	0.00	0.00	4.63
5815	10569	2.816411	TCTTTGATGTACTCCCTCCGT	58.184	47.619	0.00	0.00	0.00	4.69
5816	10570	2.758979	TCTTTGATGTACTCCCTCCGTC	59.241	50.000	0.00	0.00	0.00	4.79
5817	10571	1.481871	TTGATGTACTCCCTCCGTCC	58.518	55.000	0.00	0.00	0.00	4.79
5818	10572	0.396695	TGATGTACTCCCTCCGTCCC	60.397	60.000	0.00	0.00	0.00	4.46
5819	10573	0.396695	GATGTACTCCCTCCGTCCCA	60.397	60.000	0.00	0.00	0.00	4.37
5820	10574	0.264955	ATGTACTCCCTCCGTCCCAT	59.735	55.000	0.00	0.00	0.00	4.00
5821	10575	0.686441	TGTACTCCCTCCGTCCCATG	60.686	60.000	0.00	0.00	0.00	3.66
5822	10576	0.396695	GTACTCCCTCCGTCCCATGA	60.397	60.000	0.00	0.00	0.00	3.07
5823	10577	0.561184	TACTCCCTCCGTCCCATGAT	59.439	55.000	0.00	0.00	0.00	2.45
5824	10578	0.561184	ACTCCCTCCGTCCCATGATA	59.439	55.000	0.00	0.00	0.00	2.15
5825	10579	1.150135	ACTCCCTCCGTCCCATGATAT	59.850	52.381	0.00	0.00	0.00	1.63
5826	10580	2.382305	ACTCCCTCCGTCCCATGATATA	59.618	50.000	0.00	0.00	0.00	0.86
5827	10581	3.181410	ACTCCCTCCGTCCCATGATATAA	60.181	47.826	0.00	0.00	0.00	0.98
5828	10582	3.441101	TCCCTCCGTCCCATGATATAAG	58.559	50.000	0.00	0.00	0.00	1.73
5829	10583	3.076937	TCCCTCCGTCCCATGATATAAGA	59.923	47.826	0.00	0.00	0.00	2.10
5830	10584	3.449018	CCCTCCGTCCCATGATATAAGAG	59.551	52.174	0.00	0.00	0.00	2.85
5831	10585	3.118956	CCTCCGTCCCATGATATAAGAGC	60.119	52.174	0.00	0.00	0.00	4.09
5832	10586	2.492088	TCCGTCCCATGATATAAGAGCG	59.508	50.000	0.00	0.00	0.00	5.03
5833	10587	2.231478	CCGTCCCATGATATAAGAGCGT	59.769	50.000	0.00	0.00	0.00	5.07
5834	10588	3.306088	CCGTCCCATGATATAAGAGCGTT	60.306	47.826	0.00	0.00	0.00	4.84
5835	10589	4.307432	CGTCCCATGATATAAGAGCGTTT	58.693	43.478	0.00	0.00	0.00	3.60
5836	10590	4.750098	CGTCCCATGATATAAGAGCGTTTT	59.250	41.667	0.00	0.00	0.00	2.43
5837	10591	5.236478	CGTCCCATGATATAAGAGCGTTTTT	59.764	40.000	0.00	0.00	0.00	1.94
5858	10612	6.971527	TTTTACACTGTGTATTATGGGACG	57.028	37.500	20.31	0.00	32.20	4.79
5859	10613	3.536956	ACACTGTGTATTATGGGACGG	57.463	47.619	12.53	0.00	0.00	4.79
5860	10614	3.101437	ACACTGTGTATTATGGGACGGA	58.899	45.455	12.53	0.00	0.00	4.69
5861	10615	3.132289	ACACTGTGTATTATGGGACGGAG	59.868	47.826	12.53	0.00	0.00	4.63
5862	10616	2.698797	ACTGTGTATTATGGGACGGAGG	59.301	50.000	0.00	0.00	0.00	4.30
5863	10617	2.037251	CTGTGTATTATGGGACGGAGGG	59.963	54.545	0.00	0.00	0.00	4.30
5864	10618	2.322658	GTGTATTATGGGACGGAGGGA	58.677	52.381	0.00	0.00	0.00	4.20
5865	10619	2.299297	GTGTATTATGGGACGGAGGGAG	59.701	54.545	0.00	0.00	0.00	4.30
5866	10620	2.090943	TGTATTATGGGACGGAGGGAGT	60.091	50.000	0.00	0.00	0.00	3.85
5867	10621	3.140707	TGTATTATGGGACGGAGGGAGTA	59.859	47.826	0.00	0.00	0.00	2.59
6064	10826	2.840651	GTTGAAGAAGAGGATGGAGGGA	59.159	50.000	0.00	0.00	0.00	4.20
6071	10833	1.773391	AGGATGGAGGGATGGCCAG	60.773	63.158	13.05	0.00	37.64	4.85
6094	10856	4.767255	GCGGCAGACCAGTGGAGG	62.767	72.222	18.40	5.62	34.57	4.30
6114	11779	3.971702	GCAGCTTGGGGAGGGTGT	61.972	66.667	0.00	0.00	34.02	4.16
6128	11794	0.912486	GGGTGTGGTAGCAAGGAGAT	59.088	55.000	0.00	0.00	0.00	2.75
6130	11796	1.555075	GGTGTGGTAGCAAGGAGATCA	59.445	52.381	0.00	0.00	0.00	2.92
6173	11839	2.741228	CGCAGCAAGAGGAAGAAGCTAT	60.741	50.000	0.00	0.00	33.59	2.97
6229	11895	1.305623	CAGGGAATCCAGGCAGCTT	59.694	57.895	0.09	0.00	34.83	3.74
6284	11950	5.767816	ATGAAACTTTAGCGTTCCAAAGT	57.232	34.783	0.00	0.00	44.72	2.66
6285	11951	5.164606	TGAAACTTTAGCGTTCCAAAGTC	57.835	39.130	1.33	0.00	42.62	3.01
6286	11952	4.035909	TGAAACTTTAGCGTTCCAAAGTCC	59.964	41.667	1.33	0.00	42.62	3.85
6287	11953	3.202829	ACTTTAGCGTTCCAAAGTCCA	57.797	42.857	0.00	0.00	40.12	4.02
6288	11954	3.547746	ACTTTAGCGTTCCAAAGTCCAA	58.452	40.909	0.00	0.00	40.12	3.53
6289	11955	3.949113	ACTTTAGCGTTCCAAAGTCCAAA	59.051	39.130	0.00	0.00	40.12	3.28
6290	11956	3.974871	TTAGCGTTCCAAAGTCCAAAC	57.025	42.857	0.00	0.00	0.00	2.93
6291	11957	1.757682	AGCGTTCCAAAGTCCAAACA	58.242	45.000	0.00	0.00	0.00	2.83
6292	11958	2.096248	AGCGTTCCAAAGTCCAAACAA	58.904	42.857	0.00	0.00	0.00	2.83
6293	11959	2.494073	AGCGTTCCAAAGTCCAAACAAA	59.506	40.909	0.00	0.00	0.00	2.83
6294	11960	2.601314	GCGTTCCAAAGTCCAAACAAAC	59.399	45.455	0.00	0.00	0.00	2.93
6295	11961	3.183754	CGTTCCAAAGTCCAAACAAACC	58.816	45.455	0.00	0.00	0.00	3.27
6296	11962	3.527533	GTTCCAAAGTCCAAACAAACCC	58.472	45.455	0.00	0.00	0.00	4.11
6297	11963	2.821437	TCCAAAGTCCAAACAAACCCA	58.179	42.857	0.00	0.00	0.00	4.51
6298	11964	2.763448	TCCAAAGTCCAAACAAACCCAG	59.237	45.455	0.00	0.00	0.00	4.45
6299	11965	2.499693	CCAAAGTCCAAACAAACCCAGT	59.500	45.455	0.00	0.00	0.00	4.00
6300	11966	3.055458	CCAAAGTCCAAACAAACCCAGTT	60.055	43.478	0.00	0.00	0.00	3.16
6301	11967	4.180817	CAAAGTCCAAACAAACCCAGTTC	58.819	43.478	0.00	0.00	0.00	3.01
6302	11968	3.094484	AGTCCAAACAAACCCAGTTCA	57.906	42.857	0.00	0.00	0.00	3.18
6303	11969	3.642141	AGTCCAAACAAACCCAGTTCAT	58.358	40.909	0.00	0.00	0.00	2.57

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	0.806241	GAGGAGAGTGTGAGTCGTCC	59.194	60.000	0.00	0.00	0.00	4.79
38	39	0.387202	CGATCCTCCTTGTCAGCGAT	59.613	55.000	0.00	0.00	0.00	4.58
51	52	4.382852	CCCCCAACTCTCGATCCT	57.617	61.111	0.00	0.00	0.00	3.24
223	226	1.845809	GACTTGTGGTCGGCAGCTTG	61.846	60.000	0.00	0.00	35.07	4.01
257	261	5.822519	GGTGCATCCTCACATTTGATAACTA	59.177	40.000	0.00	0.00	38.66	2.24
370	379	5.921976	CGGTTGTTAGTGTAGTGATGTACAA	59.078	40.000	0.00	0.00	34.69	2.41
441	453	5.564259	GCGAAGAAGAGACAACCTAACTACA	60.564	44.000	0.00	0.00	0.00	2.74
465	479	3.733988	CGAATGGTGGATCGGGATATACG	60.734	52.174	0.00	0.00	35.49	3.06
570	737	0.108186	TGCCGCTTTGATGTCGAGAT	60.108	50.000	0.00	0.00	0.00	2.75
573	740	1.980951	GCATGCCGCTTTGATGTCGA	61.981	55.000	6.36	0.00	37.77	4.20
576	743	0.317799	TTTGCATGCCGCTTTGATGT	59.682	45.000	16.68	0.00	43.06	3.06
605	772	2.893398	CAGGTCAGGCTACGGGTC	59.107	66.667	0.00	0.00	0.00	4.46
684	860	9.944376	ATGTTAAACTGAGAGAACTTGCTATAA	57.056	29.630	0.00	0.00	0.00	0.98
685	861	9.944376	AATGTTAAACTGAGAGAACTTGCTATA	57.056	29.630	0.00	0.00	0.00	1.31
686	862	8.725148	CAATGTTAAACTGAGAGAACTTGCTAT	58.275	33.333	0.00	0.00	0.00	2.97
687	863	7.307989	GCAATGTTAAACTGAGAGAACTTGCTA	60.308	37.037	15.75	0.00	35.47	3.49
747	1144	3.442273	TCGGGCAAACACTTTATTCCATC	59.558	43.478	0.00	0.00	0.00	3.51
762	1161	4.505808	TGTTTTTATATCTCGTCGGGCAA	58.494	39.130	0.00	0.00	0.00	4.52
847	1249	6.457355	ACCGTTTTGTTTTAGGACACTTTTT	58.543	32.000	0.00	0.00	0.00	1.94
848	1250	6.028146	ACCGTTTTGTTTTAGGACACTTTT	57.972	33.333	0.00	0.00	0.00	2.27
849	1251	5.648178	ACCGTTTTGTTTTAGGACACTTT	57.352	34.783	0.00	0.00	0.00	2.66
871	3943	1.937278	TCACGCAAAGGTCACGTTTA	58.063	45.000	0.00	0.00	38.09	2.01
901	4761	2.699954	GTCAGGTCAATGACGGTTCAT	58.300	47.619	7.35	0.00	44.98	2.57
1010	4877	1.175983	TTTTGGGCTGCCGACGAAAT	61.176	50.000	13.40	0.00	0.00	2.17
1011	4878	1.384989	TTTTTGGGCTGCCGACGAAA	61.385	50.000	13.40	9.23	0.00	3.46
1234	5102	2.986306	AATCGCAGCAGCAGCAACC	61.986	57.895	10.77	0.00	45.49	3.77
1275	5143	0.940126	CGCCCAAAATCAGATCGGAG	59.060	55.000	1.20	0.00	0.00	4.63
1503	5880	2.829003	TCTAGAGCGGGACTGCGG	60.829	66.667	0.00	0.00	40.67	5.69
1504	5881	2.409651	GTCTAGAGCGGGACTGCG	59.590	66.667	0.00	0.00	40.67	5.18
1505	5882	2.409651	CGTCTAGAGCGGGACTGC	59.590	66.667	0.00	0.00	0.00	4.40
1506	5883	3.111939	CCGTCTAGAGCGGGACTG	58.888	66.667	19.82	1.57	44.98	3.51
1551	5928	3.067833	CTCTGGCATATCAGCACATGAG	58.932	50.000	0.00	0.00	42.53	2.90
1553	5930	2.847441	ACTCTGGCATATCAGCACATG	58.153	47.619	0.00	0.00	34.91	3.21
1696	6091	3.245284	CGGTGACACTTCAGTAACACTTG	59.755	47.826	5.39	5.54	35.34	3.16
1863	6265	2.965831	GAGGATAGGAGGTGTATGCACA	59.034	50.000	16.11	0.00	46.95	4.57
1864	6266	2.300437	GGAGGATAGGAGGTGTATGCAC	59.700	54.545	5.22	5.22	44.53	4.57
1865	6267	2.180086	AGGAGGATAGGAGGTGTATGCA	59.820	50.000	0.00	0.00	0.00	3.96
1866	6268	2.829120	GAGGAGGATAGGAGGTGTATGC	59.171	54.545	0.00	0.00	0.00	3.14
2041	6451	1.875009	TCTGACTTGCAACTGCTCAG	58.125	50.000	11.33	11.33	40.25	3.35
2053	6463	4.141158	AGGAGGTCACCAAATTTCTGACTT	60.141	41.667	18.57	14.09	35.60	3.01
2128	6540	8.469309	AAATGACAGAGAGGAAGAAAATTCAA	57.531	30.769	0.00	0.00	0.00	2.69
2243	6655	6.757947	GTGCAATGTAAAATATCAACCATGCT	59.242	34.615	0.00	0.00	0.00	3.79
2451	6866	9.907229	AGTACTCCTAAGCAAGCTATAAATTTT	57.093	29.630	0.00	0.00	0.00	1.82
2452	6867	9.907229	AAGTACTCCTAAGCAAGCTATAAATTT	57.093	29.630	0.00	0.00	0.00	1.82
2453	6868	9.549078	GAAGTACTCCTAAGCAAGCTATAAATT	57.451	33.333	0.00	0.00	0.00	1.82
2454	6869	8.929487	AGAAGTACTCCTAAGCAAGCTATAAAT	58.071	33.333	0.00	0.00	0.00	1.40
2493	6958	9.308318	ACAAAAAGGTGTATGTGAACAATTAAC	57.692	29.630	0.00	0.00	0.00	2.01
2808	7344	3.803778	CCAAACAACAGCCAAAACTCATC	59.196	43.478	0.00	0.00	0.00	2.92
2906	7442	3.998672	GGACGAACTCGCCCCACA	61.999	66.667	0.00	0.00	44.43	4.17
2916	7454	2.159296	GCCCATATTTTGGTGGACGAAC	60.159	50.000	0.00	0.00	44.83	3.95
2969	7507	1.278238	CGGCTCATGTAAGACCGAAC	58.722	55.000	9.96	0.00	46.71	3.95
2998	7536	1.341531	AGGCGTATACAAGCTAGCCAG	59.658	52.381	12.13	6.80	46.34	4.85
3000	7538	1.336980	GGAGGCGTATACAAGCTAGCC	60.337	57.143	12.13	8.65	44.45	3.93
3207	7792	5.480205	GTTGGGTTTCAGTTTGGTTTGTAA	58.520	37.500	0.00	0.00	0.00	2.41
3223	7808	3.372440	TTTTGGCAAAATGGTTGGGTT	57.628	38.095	20.81	0.00	0.00	4.11
3293	7880	3.404899	CAAAGCAAGGGCATGAACAATT	58.595	40.909	0.00	0.00	44.61	2.32
3294	7881	2.289819	CCAAAGCAAGGGCATGAACAAT	60.290	45.455	0.00	0.00	44.61	2.71
3390	7977	7.834181	AGCCTAAAAGAGCTAAAATGATAACCA	59.166	33.333	0.00	0.00	37.64	3.67
3435	8022	7.451501	TTTCAATATGAGCACATTCTCACAA	57.548	32.000	0.83	0.00	44.88	3.33
3581	8183	6.963049	CACTTATAGTGGGAAAGTGTACAC	57.037	41.667	18.56	18.56	43.20	2.90
3813	8446	3.054065	GGAGATGGTCCCTCTTGTGATTT	60.054	47.826	0.00	0.00	39.88	2.17
3878	8525	1.883275	CCGCAAACTTTATGGTGGTCA	59.117	47.619	0.00	0.00	0.00	4.02
4004	8655	1.160329	AACTGCACGGACTGAAGCAC	61.160	55.000	2.73	0.00	32.87	4.40
4140	8791	5.487131	GGATATCTTCTCTAAGGGCCTGAAT	59.513	44.000	6.92	0.00	33.22	2.57
4383	9034	9.605955	TTTATCATGACACATACAAAGAAAACG	57.394	29.630	0.00	0.00	0.00	3.60
4639	9302	2.125512	GCTACCGCCAGTGGACAG	60.126	66.667	15.20	2.30	0.00	3.51
4755	9427	8.784043	ACTGATTAGAATTAGTGACCACAAAAC	58.216	33.333	2.78	0.00	34.40	2.43
4848	9520	5.506317	GCAGAACAATATGTGATGGTTAGCC	60.506	44.000	0.00	0.00	0.00	3.93
5058	9733	0.097674	CGGCCTTCGAAGCTTCATTG	59.902	55.000	25.47	13.62	42.43	2.82
5117	9792	4.454678	TGTCAGTTTCAGTTCTCATGCTT	58.545	39.130	0.00	0.00	0.00	3.91
5198	9883	3.625764	CCAATGTTTCATACGGTACCTGG	59.374	47.826	10.90	2.06	0.00	4.45
5265	9951	3.351794	TTATATGCCCACGGTCAACAA	57.648	42.857	0.00	0.00	0.00	2.83
5330	10016	8.585018	TCTCCACACATATATATTATATGCCCG	58.415	37.037	12.33	6.23	35.88	6.13
5342	10028	7.956315	AGGTAGTAATGGTCTCCACACATATAT	59.044	37.037	0.00	0.00	35.80	0.86
5343	10029	7.302948	AGGTAGTAATGGTCTCCACACATATA	58.697	38.462	0.00	0.00	35.80	0.86
5418	10160	9.337396	GAACATAGGACATACCAATCACAAATA	57.663	33.333	0.00	0.00	42.04	1.40
5427	10169	6.613679	TGTGGATAGAACATAGGACATACCAA	59.386	38.462	0.00	0.00	42.04	3.67
5491	10233	2.359531	TGAACCAAAACAGGCCTTAACG	59.640	45.455	0.00	0.00	0.00	3.18
5503	10245	9.713684	ATGATATTCCTATCCTTTGAACCAAAA	57.286	29.630	0.00	0.00	34.03	2.44
5564	10307	4.215399	CGAATAGCACCTCTTTTCCAACAA	59.785	41.667	0.00	0.00	31.59	2.83
5566	10309	4.000988	TCGAATAGCACCTCTTTTCCAAC	58.999	43.478	0.00	0.00	31.59	3.77
5568	10311	3.973206	TCGAATAGCACCTCTTTTCCA	57.027	42.857	0.00	0.00	31.59	3.53
5600	10343	7.495135	AGCACAAACCTTATGGAAAATTTTG	57.505	32.000	8.47	4.25	37.04	2.44
5601	10344	9.791801	ATTAGCACAAACCTTATGGAAAATTTT	57.208	25.926	2.28	2.28	37.04	1.82
5664	10418	4.517453	TGGTTTGTAAGAACGGATTTCCTG	59.483	41.667	0.00	0.00	34.32	3.86
5776	10530	8.166422	TCAAAGATTTTCCTAAACCTCTTCAC	57.834	34.615	0.00	0.00	0.00	3.18
5798	10552	1.481871	GGACGGAGGGAGTACATCAA	58.518	55.000	0.00	0.00	0.00	2.57
5799	10553	0.396695	GGGACGGAGGGAGTACATCA	60.397	60.000	0.00	0.00	0.00	3.07
5800	10554	0.396695	TGGGACGGAGGGAGTACATC	60.397	60.000	0.00	0.00	0.00	3.06
5801	10555	0.264955	ATGGGACGGAGGGAGTACAT	59.735	55.000	0.00	0.00	0.00	2.29
5802	10556	0.686441	CATGGGACGGAGGGAGTACA	60.686	60.000	0.00	0.00	0.00	2.90
5803	10557	0.396695	TCATGGGACGGAGGGAGTAC	60.397	60.000	0.00	0.00	0.00	2.73
5804	10558	0.561184	ATCATGGGACGGAGGGAGTA	59.439	55.000	0.00	0.00	0.00	2.59
5805	10559	0.561184	TATCATGGGACGGAGGGAGT	59.439	55.000	0.00	0.00	0.00	3.85
5806	10560	1.944177	ATATCATGGGACGGAGGGAG	58.056	55.000	0.00	0.00	0.00	4.30
5807	10561	3.076937	TCTTATATCATGGGACGGAGGGA	59.923	47.826	0.00	0.00	0.00	4.20
5808	10562	3.441101	TCTTATATCATGGGACGGAGGG	58.559	50.000	0.00	0.00	0.00	4.30
5809	10563	3.118956	GCTCTTATATCATGGGACGGAGG	60.119	52.174	0.00	0.00	0.00	4.30
5810	10564	3.428180	CGCTCTTATATCATGGGACGGAG	60.428	52.174	0.00	0.00	0.00	4.63
5812	10566	2.231478	ACGCTCTTATATCATGGGACGG	59.769	50.000	0.00	0.00	0.00	4.79
5813	10567	3.577649	ACGCTCTTATATCATGGGACG	57.422	47.619	0.00	0.00	0.00	4.79
5814	10568	6.619801	AAAAACGCTCTTATATCATGGGAC	57.380	37.500	0.00	0.00	0.00	4.46
5834	10588	6.372103	CCGTCCCATAATACACAGTGTAAAAA	59.628	38.462	17.43	6.50	36.31	1.94
5835	10589	5.875910	CCGTCCCATAATACACAGTGTAAAA	59.124	40.000	17.43	8.90	36.31	1.52
5836	10590	5.187381	TCCGTCCCATAATACACAGTGTAAA	59.813	40.000	17.43	9.25	36.31	2.01
5837	10591	4.710865	TCCGTCCCATAATACACAGTGTAA	59.289	41.667	17.43	2.47	36.31	2.41
5838	10592	4.279982	TCCGTCCCATAATACACAGTGTA	58.720	43.478	15.90	15.90	37.24	2.90
5839	10593	3.101437	TCCGTCCCATAATACACAGTGT	58.899	45.455	11.87	11.87	0.00	3.55
5840	10594	3.492656	CCTCCGTCCCATAATACACAGTG	60.493	52.174	0.00	0.00	0.00	3.66
5841	10595	2.698797	CCTCCGTCCCATAATACACAGT	59.301	50.000	0.00	0.00	0.00	3.55
5842	10596	2.037251	CCCTCCGTCCCATAATACACAG	59.963	54.545	0.00	0.00	0.00	3.66
5843	10597	2.043992	CCCTCCGTCCCATAATACACA	58.956	52.381	0.00	0.00	0.00	3.72
5844	10598	2.299297	CTCCCTCCGTCCCATAATACAC	59.701	54.545	0.00	0.00	0.00	2.90
5845	10599	2.090943	ACTCCCTCCGTCCCATAATACA	60.091	50.000	0.00	0.00	0.00	2.29
5846	10600	2.606378	ACTCCCTCCGTCCCATAATAC	58.394	52.381	0.00	0.00	0.00	1.89
5847	10601	3.400322	ACTACTCCCTCCGTCCCATAATA	59.600	47.826	0.00	0.00	0.00	0.98
5848	10602	2.179424	ACTACTCCCTCCGTCCCATAAT	59.821	50.000	0.00	0.00	0.00	1.28
5849	10603	1.572415	ACTACTCCCTCCGTCCCATAA	59.428	52.381	0.00	0.00	0.00	1.90
5850	10604	1.229131	ACTACTCCCTCCGTCCCATA	58.771	55.000	0.00	0.00	0.00	2.74
5851	10605	1.145325	CTACTACTCCCTCCGTCCCAT	59.855	57.143	0.00	0.00	0.00	4.00
5852	10606	0.549950	CTACTACTCCCTCCGTCCCA	59.450	60.000	0.00	0.00	0.00	4.37
5853	10607	0.842635	TCTACTACTCCCTCCGTCCC	59.157	60.000	0.00	0.00	0.00	4.46
5854	10608	2.955342	ATCTACTACTCCCTCCGTCC	57.045	55.000	0.00	0.00	0.00	4.79
5855	10609	3.752747	GCTAATCTACTACTCCCTCCGTC	59.247	52.174	0.00	0.00	0.00	4.79
5856	10610	3.137913	TGCTAATCTACTACTCCCTCCGT	59.862	47.826	0.00	0.00	0.00	4.69
5857	10611	3.752665	TGCTAATCTACTACTCCCTCCG	58.247	50.000	0.00	0.00	0.00	4.63
5858	10612	6.673839	AAATGCTAATCTACTACTCCCTCC	57.326	41.667	0.00	0.00	0.00	4.30
5859	10613	7.040548	ACGTAAATGCTAATCTACTACTCCCTC	60.041	40.741	0.00	0.00	0.00	4.30
5860	10614	6.776603	ACGTAAATGCTAATCTACTACTCCCT	59.223	38.462	0.00	0.00	0.00	4.20
5861	10615	6.862090	CACGTAAATGCTAATCTACTACTCCC	59.138	42.308	0.00	0.00	0.00	4.30
5862	10616	7.646314	TCACGTAAATGCTAATCTACTACTCC	58.354	38.462	0.00	0.00	0.00	3.85
5863	10617	9.512435	TTTCACGTAAATGCTAATCTACTACTC	57.488	33.333	0.00	0.00	0.00	2.59
5867	10621	9.601217	AGAATTTCACGTAAATGCTAATCTACT	57.399	29.630	8.41	0.00	41.06	2.57
5986	10741	0.248215	GGCTTGGCATCGTCAATTCG	60.248	55.000	0.00	0.00	0.00	3.34
6043	10799	2.840651	TCCCTCCATCCTCTTCTTCAAC	59.159	50.000	0.00	0.00	0.00	3.18
6044	10800	3.205519	TCCCTCCATCCTCTTCTTCAA	57.794	47.619	0.00	0.00	0.00	2.69
6045	10801	2.948889	TCCCTCCATCCTCTTCTTCA	57.051	50.000	0.00	0.00	0.00	3.02
6047	10803	2.416638	CCATCCCTCCATCCTCTTCTT	58.583	52.381	0.00	0.00	0.00	2.52
6094	10856	4.748144	CCCTCCCCAAGCTGCCAC	62.748	72.222	0.00	0.00	0.00	5.01
6114	11779	1.571955	TGCTGATCTCCTTGCTACCA	58.428	50.000	0.00	0.00	0.00	3.25
6128	11794	2.125147	CTCCGGCCGAATTGCTGA	60.125	61.111	30.73	12.64	40.15	4.26
6130	11796	2.125106	GACTCCGGCCGAATTGCT	60.125	61.111	30.73	1.48	0.00	3.91
6155	11821	3.954904	TCGTATAGCTTCTTCCTCTTGCT	59.045	43.478	0.00	0.00	37.72	3.91
6173	11839	5.100259	CGCTAGTCAAATTTCTCCTTCGTA	58.900	41.667	0.00	0.00	0.00	3.43

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.