AutoCloner

Multiple sequence alignment - TraesCS6B01G042300

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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	TraesCS6B01G042300	chr6B	100.000	5679	0	0	1	5679	26000751	26006429	0.000000e+00	10488.0
1	TraesCS6B01G042300	chr6B	97.767	2150	31	3	3531	5679	26121340	26119207	0.000000e+00	3688.0
2	TraesCS6B01G042300	chr6B	94.553	2056	75	15	1289	3321	26123373	26121332	0.000000e+00	3142.0
3	TraesCS6B01G042300	chr6B	89.468	902	86	6	3876	4773	25972501	25971605	0.000000e+00	1131.0
4	TraesCS6B01G042300	chr6B	98.476	525	8	0	736	1260	26123895	26123371	0.000000e+00	926.0
5	TraesCS6B01G042300	chr6B	89.688	640	57	4	1066	1702	25976120	25975487	0.000000e+00	808.0
6	TraesCS6B01G042300	chr6B	90.909	209	18	1	3323	3530	720142270	720142062	4.330000e-71	279.0
7	TraesCS6B01G042300	chr6B	95.745	141	3	1	598	738	26125383	26125246	2.060000e-54	224.0
8	TraesCS6B01G042300	chr6B	81.961	255	31	7	2	254	26125756	26125515	9.650000e-48	202.0
9	TraesCS6B01G042300	chr6D	91.662	1775	109	13	2	1765	14238388	14240134	0.000000e+00	2422.0
10	TraesCS6B01G042300	chr6D	91.667	1476	99	21	3766	5227	14241166	14242631	0.000000e+00	2023.0
11	TraesCS6B01G042300	chr6D	90.461	912	81	2	3868	4773	14202030	14201119	0.000000e+00	1197.0
12	TraesCS6B01G042300	chr6D	85.413	1138	122	23	3757	4876	14231494	14230383	0.000000e+00	1142.0
13	TraesCS6B01G042300	chr6D	87.715	757	78	12	1028	1783	14232301	14231559	0.000000e+00	869.0
14	TraesCS6B01G042300	chr6D	88.193	703	69	9	1066	1764	14203504	14202812	0.000000e+00	826.0
15	TraesCS6B01G042300	chr6D	80.608	263	41	7	2771	3029	14202708	14202452	1.610000e-45	195.0
16	TraesCS6B01G042300	chr6D	86.857	175	22	1	1784	1957	389297215	389297389	1.610000e-45	195.0
17	TraesCS6B01G042300	chr6D	87.755	49	0	1	5432	5480	193225595	193225637	1.000000e-02	52.8
18	TraesCS6B01G042300	chr6A	91.503	1224	84	8	3757	4973	15542338	15543548	0.000000e+00	1666.0
19	TraesCS6B01G042300	chr6A	86.322	1199	134	15	2	1178	15504152	15505342	0.000000e+00	1279.0
20	TraesCS6B01G042300	chr6A	86.855	1027	116	8	3868	4876	15491621	15490596	0.000000e+00	1131.0
21	TraesCS6B01G042300	chr6A	88.765	899	84	10	3868	4757	15457469	15456579	0.000000e+00	1085.0
22	TraesCS6B01G042300	chr6A	92.725	756	48	3	929	1681	15540588	15541339	0.000000e+00	1085.0
23	TraesCS6B01G042300	chr6A	86.589	947	104	16	2	943	15539355	15540283	0.000000e+00	1024.0
24	TraesCS6B01G042300	chr6A	89.503	724	61	9	1028	1746	15492354	15491641	0.000000e+00	902.0
25	TraesCS6B01G042300	chr6A	88.423	691	64	8	1066	1753	15461668	15460991	0.000000e+00	819.0
26	TraesCS6B01G042300	chr6A	91.613	310	23	3	5224	5532	15549988	15550295	5.260000e-115	425.0
27	TraesCS6B01G042300	chr6A	85.833	120	15	2	4758	4876	15456527	15456409	5.970000e-25	126.0
28	TraesCS6B01G042300	chr6A	100.000	51	0	0	5051	5101	15548937	15548987	1.680000e-15	95.3
29	TraesCS6B01G042300	chr6A	85.075	67	3	3	4988	5054	15547053	15547112	1.710000e-05	62.1
30	TraesCS6B01G042300	chr6A	100.000	28	0	0	5432	5459	299299182	299299209	1.000000e-02	52.8
31	TraesCS6B01G042300	chr1B	86.483	799	95	8	3906	4701	465388665	465387877	0.000000e+00	865.0
32	TraesCS6B01G042300	chr1B	91.905	210	15	2	3323	3530	161317365	161317574	5.570000e-75	292.0
33	TraesCS6B01G042300	chr1B	84.530	181	18	5	3031	3203	675965674	675965496	2.720000e-38	171.0
34	TraesCS6B01G042300	chr1B	81.560	141	17	4	2475	2615	645469531	645469400	2.160000e-19	108.0
35	TraesCS6B01G042300	chr1B	96.970	33	0	1	3609	3641	430892102	430892133	3.000000e-03	54.7
36	TraesCS6B01G042300	chr1D	83.148	629	91	4	1066	1682	345375032	345375657	1.380000e-155	560.0
37	TraesCS6B01G042300	chr1D	84.659	176	22	4	1784	1957	319918482	319918310	2.720000e-38	171.0
38	TraesCS6B01G042300	chr5B	92.344	209	14	2	3323	3530	316603320	316603113	4.300000e-76	296.0
39	TraesCS6B01G042300	chr5B	91.388	209	16	2	3323	3530	667824509	667824302	9.310000e-73	285.0
40	TraesCS6B01G042300	chr5B	87.912	91	7	4	5432	5520	687391299	687391387	2.800000e-18	104.0
41	TraesCS6B01G042300	chr2B	91.943	211	15	2	3323	3531	658208287	658208497	1.550000e-75	294.0
42	TraesCS6B01G042300	chr2B	80.205	293	50	6	328	614	570064051	570063761	4.460000e-51	213.0
43	TraesCS6B01G042300	chr2B	79.208	303	57	5	327	624	162860825	162860524	7.460000e-49	206.0
44	TraesCS6B01G042300	chr2B	91.667	72	5	1	5222	5292	98451034	98450963	1.300000e-16	99.0
45	TraesCS6B01G042300	chr4B	91.080	213	16	3	3323	3533	328323717	328323928	9.310000e-73	285.0
46	TraesCS6B01G042300	chr4B	81.570	293	50	3	327	616	52934950	52934659	7.350000e-59	239.0
47	TraesCS6B01G042300	chr4B	88.764	178	14	3	3030	3201	544294491	544294668	4.460000e-51	213.0
48	TraesCS6B01G042300	chr4B	80.479	292	46	8	330	615	661882280	661881994	4.460000e-51	213.0
49	TraesCS6B01G042300	chr4B	96.970	33	1	0	3609	3641	500296009	500295977	7.950000e-04	56.5
50	TraesCS6B01G042300	chr5D	88.235	238	24	4	2103	2338	26821345	26821110	1.200000e-71	281.0
51	TraesCS6B01G042300	chr5D	88.235	136	14	2	2169	2303	26820839	26820973	1.640000e-35	161.0
52	TraesCS6B01G042300	chr3D	88.066	243	22	7	3305	3543	11456137	11456376	1.200000e-71	281.0
53	TraesCS6B01G042300	chr3D	84.659	176	23	3	1781	1955	98538124	98538296	7.560000e-39	172.0
54	TraesCS6B01G042300	chr3D	92.857	70	4	1	5226	5294	335220561	335220492	3.620000e-17	100.0
55	TraesCS6B01G042300	chr3D	91.549	71	5	1	5223	5292	582827206	582827276	4.680000e-16	97.1
56	TraesCS6B01G042300	chr3D	86.207	87	10	2	5432	5517	41726146	41726231	6.060000e-15	93.5
57	TraesCS6B01G042300	chr3D	81.416	113	17	3	2258	2367	574474038	574474149	7.840000e-14	89.8
58	TraesCS6B01G042300	chr5A	90.654	214	14	4	3323	3532	456461594	456461805	4.330000e-71	279.0
59	TraesCS6B01G042300	chr5A	86.286	175	22	2	1784	1956	631868322	631868148	7.510000e-44	189.0
60	TraesCS6B01G042300	chr5A	85.714	63	3	3	3597	3655	283299916	283299976	1.710000e-05	62.1
61	TraesCS6B01G042300	chrUn	90.278	216	16	4	3323	3535	138484938	138484725	1.560000e-70	278.0
62	TraesCS6B01G042300	chr1A	81.787	291	49	3	329	615	447639487	447639777	2.040000e-59	241.0
63	TraesCS6B01G042300	chr1A	83.626	171	26	2	2198	2367	369989225	369989394	5.890000e-35	159.0
64	TraesCS6B01G042300	chr4D	80.921	304	52	6	326	624	405720673	405720975	9.510000e-58	235.0
65	TraesCS6B01G042300	chr4D	87.079	178	18	5	1784	1957	51076108	51076284	4.490000e-46	196.0
66	TraesCS6B01G042300	chr4D	80.702	171	29	3	2198	2367	485357314	485357481	4.620000e-26	130.0
67	TraesCS6B01G042300	chr4D	91.549	71	4	2	5226	5294	334111540	334111610	4.680000e-16	97.1
68	TraesCS6B01G042300	chr7D	91.329	173	9	3	3033	3199	45146218	45146390	1.230000e-56	231.0
69	TraesCS6B01G042300	chr7D	81.641	256	36	4	2097	2344	154949374	154949122	9.650000e-48	202.0
70	TraesCS6B01G042300	chr7D	86.957	161	12	6	3033	3186	604913343	604913501	7.560000e-39	172.0
71	TraesCS6B01G042300	chr7D	83.237	173	26	3	1786	1957	617232622	617232452	7.620000e-34	156.0
72	TraesCS6B01G042300	chr7D	96.875	32	1	0	3609	3640	10068372	10068403	3.000000e-03	54.7
73	TraesCS6B01G042300	chr7A	84.932	219	31	2	2107	2324	637961500	637961283	2.660000e-53	220.0
74	TraesCS6B01G042300	chr7A	81.765	170	31	0	2198	2367	575948532	575948701	5.930000e-30	143.0
75	TraesCS6B01G042300	chr7B	88.889	180	14	3	3031	3204	692407584	692407405	3.450000e-52	217.0
76	TraesCS6B01G042300	chr7B	87.283	173	22	0	2198	2370	566015694	566015522	1.250000e-46	198.0
77	TraesCS6B01G042300	chr3A	85.068	221	24	7	3316	3531	730807452	730807668	3.450000e-52	217.0
78	TraesCS6B01G042300	chr3A	86.592	179	20	4	1781	1957	24786291	24786467	1.610000e-45	195.0
79	TraesCS6B01G042300	chr3A	86.441	177	21	2	1784	1957	63180767	63180591	2.090000e-44	191.0
80	TraesCS6B01G042300	chr3A	91.429	70	5	1	5226	5294	453313450	453313381	1.680000e-15	95.3
81	TraesCS6B01G042300	chr3B	88.439	173	12	4	3033	3199	487497388	487497558	9.650000e-48	202.0
82	TraesCS6B01G042300	chr3B	87.425	167	15	4	3039	3199	23917569	23917403	2.700000e-43	187.0
83	TraesCS6B01G042300	chr3B	94.286	70	3	1	5226	5294	685258348	685258279	7.780000e-19	106.0
84	TraesCS6B01G042300	chr2D	85.799	169	14	6	3031	3192	5442187	5442022	2.720000e-38	171.0
85	TraesCS6B01G042300	chr2D	74.359	273	59	11	1236	1501	637445458	637445190	7.780000e-19	106.0
86	TraesCS6B01G042300	chr2A	93.939	66	2	2	5230	5294	771620326	771620262	1.300000e-16	99.0
87	TraesCS6B01G042300	chr4A	87.097	62	3	3	3597	3655	716545378	716545319	1.320000e-06	65.8
88	TraesCS6B01G042300	chr4A	88.000	50	3	1	3609	3655	729615349	729615300	7.950000e-04	56.5

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	TraesCS6B01G042300	chr6B	26000751	26006429	5678	False	10488.000000	10488	100.000000	1	5679	1	chr6B.!!$F1	5678
1	TraesCS6B01G042300	chr6B	26119207	26125756	6549	True	1636.400000	3688	93.700400	2	5679	5	chr6B.!!$R3	5677
2	TraesCS6B01G042300	chr6B	25971605	25976120	4515	True	969.500000	1131	89.578000	1066	4773	2	chr6B.!!$R2	3707
3	TraesCS6B01G042300	chr6D	14238388	14242631	4243	False	2222.500000	2422	91.664500	2	5227	2	chr6D.!!$F3	5225
4	TraesCS6B01G042300	chr6D	14230383	14232301	1918	True	1005.500000	1142	86.564000	1028	4876	2	chr6D.!!$R2	3848
5	TraesCS6B01G042300	chr6D	14201119	14203504	2385	True	739.333333	1197	86.420667	1066	4773	3	chr6D.!!$R1	3707
6	TraesCS6B01G042300	chr6A	15504152	15505342	1190	False	1279.000000	1279	86.322000	2	1178	1	chr6A.!!$F1	1176
7	TraesCS6B01G042300	chr6A	15490596	15492354	1758	True	1016.500000	1131	88.179000	1028	4876	2	chr6A.!!$R2	3848
8	TraesCS6B01G042300	chr6A	15539355	15550295	10940	False	726.233333	1666	91.250833	2	5532	6	chr6A.!!$F3	5530
9	TraesCS6B01G042300	chr6A	15456409	15461668	5259	True	676.666667	1085	87.673667	1066	4876	3	chr6A.!!$R1	3810
10	TraesCS6B01G042300	chr1B	465387877	465388665	788	True	865.000000	865	86.483000	3906	4701	1	chr1B.!!$R1	795
11	TraesCS6B01G042300	chr1D	345375032	345375657	625	False	560.000000	560	83.148000	1066	1682	1	chr1D.!!$F1	616

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	Hairpin	End Stability	Orientation
560	606	0.456995	CGCACCAAAACAACAACCGT	60.457	50.000	0.00	4.83	F
1851	3750	1.892474	TCATGGCAACTTTACTTGGGC	59.108	47.619	37.61	5.36	F
2626	4525	0.039074	CGGCTTCCCTATAGCTGACG	60.039	60.000	45.78	4.35	F
3424	7452	0.033503	CGGCCTCACCCCCTTAAAAT	60.034	55.000	33.26	1.82	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2042	3941	0.036388	CACCTGGCCGACTGTGTATT	60.036	55.0	0.00	0.00	0.00	1.89	R
3405	7433	0.033503	ATTTTAAGGGGGTGAGGCCG	60.034	55.0	0.00	0.00	38.44	6.13	R
3466	7494	0.108804	CCACTTCATCGTACGGCTGT	60.109	55.0	16.52	2.42	0.00	4.40	R
4891	10078	0.039798	TACTCAGCAACGACCGTGTC	60.040	55.0	0.00	0.00	0.00	3.67	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
177	180	5.458779	GGTTGTGTTCCAGAAATTTTTCTCG	59.541	40.000	2.59	0.00	45.23	4.04
215	220	4.021192	CCACTGCAACATTACCCATCTTTT	60.021	41.667	0.00	0.00	0.00	2.27
255	260	5.906113	TGCAAAAACCTTGAGACTTACAA	57.094	34.783	0.00	0.00	0.00	2.41
262	267	2.615493	CCTTGAGACTTACAATGGGCGT	60.615	50.000	0.00	0.00	0.00	5.68
271	316	0.618458	ACAATGGGCGTGGAGTGTAT	59.382	50.000	0.00	0.00	0.00	2.29
284	329	4.456911	GTGGAGTGTATAATCGTCCCGATA	59.543	45.833	0.00	0.00	46.30	2.92
360	405	8.183104	TCGATCTATTCATCATCTGTTAAGGT	57.817	34.615	0.00	0.00	0.00	3.50
410	455	6.921486	TTACATCTAGGTTTGTAGACCACA	57.079	37.500	0.00	0.00	42.35	4.17
411	456	5.818678	ACATCTAGGTTTGTAGACCACAA	57.181	39.130	0.00	0.00	45.49	3.33
447	492	0.976641	ATTGGAGTGAGTCGAAGGCA	59.023	50.000	0.00	0.00	0.00	4.75
505	550	7.010183	CCGGATAAACATTGTTGTAGTAGACAG	59.990	40.741	2.13	0.00	39.88	3.51
508	553	8.773404	ATAAACATTGTTGTAGTAGACAGTCC	57.227	34.615	2.13	0.00	39.88	3.85
512	557	4.761235	TGTTGTAGTAGACAGTCCGAAG	57.239	45.455	0.00	0.00	39.88	3.79
513	558	4.139786	TGTTGTAGTAGACAGTCCGAAGT	58.860	43.478	0.00	0.00	39.88	3.01
514	559	4.214971	TGTTGTAGTAGACAGTCCGAAGTC	59.785	45.833	0.00	0.00	39.88	3.01
515	560	4.011966	TGTAGTAGACAGTCCGAAGTCA	57.988	45.455	0.00	0.00	37.23	3.41
534	580	2.371841	TCATCGTGCTAAGCCCCAATAT	59.628	45.455	0.00	0.00	0.00	1.28
560	606	0.456995	CGCACCAAAACAACAACCGT	60.457	50.000	0.00	0.00	0.00	4.83
581	627	4.486090	GTCGCTGATGAAGAGAAGTGTAA	58.514	43.478	0.00	0.00	36.38	2.41
695	742	4.295119	GTCGCTGTGTGGGGACGT	62.295	66.667	0.00	0.00	38.87	4.34
744	2144	7.577303	ACCTTGCAACCCATATATCATATAGG	58.423	38.462	0.00	0.00	0.00	2.57
1398	3129	4.285790	TTGGGGGAGCTGGAGGGT	62.286	66.667	0.00	0.00	0.00	4.34
1529	3281	2.892425	CGATGGGAAGCAGGTCGC	60.892	66.667	0.00	0.00	42.91	5.19
1816	3715	8.219546	TGAATGTTCGGATTTTAAGCATATCA	57.780	30.769	0.00	0.00	0.00	2.15
1826	3725	5.478233	TTTAAGCATATCATCGCAAACGT	57.522	34.783	0.00	0.00	41.18	3.99
1851	3750	1.892474	TCATGGCAACTTTACTTGGGC	59.108	47.619	0.00	0.00	37.61	5.36
1960	3859	6.588719	AGTGAAATAAAGTTGCCATGCTTA	57.411	33.333	0.00	0.00	0.00	3.09
1961	3860	6.991938	AGTGAAATAAAGTTGCCATGCTTAA	58.008	32.000	0.00	0.00	0.00	1.85
1962	3861	7.441017	AGTGAAATAAAGTTGCCATGCTTAAA	58.559	30.769	0.00	0.00	0.00	1.52
1963	3862	7.930865	AGTGAAATAAAGTTGCCATGCTTAAAA	59.069	29.630	0.00	0.00	0.00	1.52
1965	3864	8.934825	TGAAATAAAGTTGCCATGCTTAAAATC	58.065	29.630	0.00	0.00	0.00	2.17
1966	3865	9.154847	GAAATAAAGTTGCCATGCTTAAAATCT	57.845	29.630	0.00	0.00	0.00	2.40
1967	3866	8.483307	AATAAAGTTGCCATGCTTAAAATCTG	57.517	30.769	0.00	0.00	0.00	2.90
1968	3867	4.460948	AGTTGCCATGCTTAAAATCTGG	57.539	40.909	0.00	0.00	0.00	3.86
1969	3868	3.834231	AGTTGCCATGCTTAAAATCTGGT	59.166	39.130	0.00	0.00	0.00	4.00
1970	3869	4.284234	AGTTGCCATGCTTAAAATCTGGTT	59.716	37.500	0.00	0.00	0.00	3.67
1971	3870	5.480073	AGTTGCCATGCTTAAAATCTGGTTA	59.520	36.000	0.00	0.00	0.00	2.85
2103	4002	3.881220	TGGCTTCCCTAAAACCGATTAG	58.119	45.455	0.00	0.00	33.54	1.73
2168	4067	3.328382	TCTCACCCTCAATGTTTACCG	57.672	47.619	0.00	0.00	0.00	4.02
2169	4068	1.737793	CTCACCCTCAATGTTTACCGC	59.262	52.381	0.00	0.00	0.00	5.68
2356	4255	1.000019	CGGAGACTCCACCACCCTA	60.000	63.158	21.49	0.00	35.91	3.53
2403	4302	2.414138	GGTTATTGAAGGTCACCGTTCG	59.586	50.000	0.00	0.00	38.10	3.95
2404	4303	3.319755	GTTATTGAAGGTCACCGTTCGA	58.680	45.455	0.00	0.00	38.10	3.71
2425	4324	4.091365	CGATATTGCTTCACACGTTTCAGA	59.909	41.667	0.00	0.00	0.00	3.27
2469	4368	2.587612	TTGTTATCGTTGCTTCGCAC	57.412	45.000	0.00	0.00	38.71	5.34
2474	4373	2.498761	ATCGTTGCTTCGCACGCTTG	62.499	55.000	0.00	0.00	38.71	4.01
2504	4403	0.243636	CGTTGGGGGTGAGAAAATGC	59.756	55.000	0.00	0.00	0.00	3.56
2505	4404	1.337118	GTTGGGGGTGAGAAAATGCA	58.663	50.000	0.00	0.00	0.00	3.96
2549	4448	6.387220	ACAGGGAAGCCAATTAGTACTAATCT	59.613	38.462	24.80	16.27	34.90	2.40
2557	4456	5.696724	CCAATTAGTACTAATCTGCTTCGGG	59.303	44.000	24.80	13.62	34.90	5.14
2626	4525	0.039074	CGGCTTCCCTATAGCTGACG	60.039	60.000	0.00	0.00	45.78	4.35
2768	4669	4.119862	CGTTCAGGATTTATCATGTCCGT	58.880	43.478	4.53	0.00	39.42	4.69
2875	4876	3.500680	GTGAAGGTCTCGTTGCCAAAATA	59.499	43.478	0.00	0.00	0.00	1.40
3058	5810	2.890945	GTGTTTGGTTGCAAGGGACTAT	59.109	45.455	0.00	0.00	38.49	2.12
3060	5812	4.521256	GTGTTTGGTTGCAAGGGACTATAA	59.479	41.667	0.00	0.00	38.49	0.98
3119	5873	5.935206	CCTTCAGAAGAGTCTTTTTAGTCCC	59.065	44.000	12.14	0.00	28.78	4.46
3120	5874	6.239743	CCTTCAGAAGAGTCTTTTTAGTCCCT	60.240	42.308	12.14	0.00	28.78	4.20
3121	5875	6.102897	TCAGAAGAGTCTTTTTAGTCCCTG	57.897	41.667	6.88	7.17	28.78	4.45
3143	5897	6.465321	CCTGTAGAAAAAGTCCCTCCTGTTTA	60.465	42.308	0.00	0.00	0.00	2.01
3144	5898	6.531021	TGTAGAAAAAGTCCCTCCTGTTTAG	58.469	40.000	0.00	0.00	0.00	1.85
3156	5913	4.463891	CCTCCTGTTTAGTTACGGGACTAA	59.536	45.833	8.32	8.32	46.25	2.24
3322	7350	2.515926	TGCTAGCCGCTAATCTTCAG	57.484	50.000	13.29	0.00	40.11	3.02
3323	7351	2.031870	TGCTAGCCGCTAATCTTCAGA	58.968	47.619	13.29	0.00	40.11	3.27
3324	7352	2.223829	TGCTAGCCGCTAATCTTCAGAC	60.224	50.000	13.29	0.00	40.11	3.51
3326	7354	1.103803	AGCCGCTAATCTTCAGACGA	58.896	50.000	0.00	0.00	0.00	4.20
3327	7355	1.066303	AGCCGCTAATCTTCAGACGAG	59.934	52.381	0.00	0.00	0.00	4.18
3328	7356	1.065701	GCCGCTAATCTTCAGACGAGA	59.934	52.381	0.00	0.00	0.00	4.04
3329	7357	2.722071	CCGCTAATCTTCAGACGAGAC	58.278	52.381	0.00	0.00	0.00	3.36
3330	7358	2.356382	CCGCTAATCTTCAGACGAGACT	59.644	50.000	0.00	0.00	0.00	3.24
3332	7360	3.788694	CGCTAATCTTCAGACGAGACTTG	59.211	47.826	0.00	0.00	0.00	3.16
3333	7361	3.549873	GCTAATCTTCAGACGAGACTTGC	59.450	47.826	0.00	0.00	0.00	4.01
3334	7362	2.663826	ATCTTCAGACGAGACTTGCC	57.336	50.000	0.00	0.00	0.00	4.52
3335	7363	1.621992	TCTTCAGACGAGACTTGCCT	58.378	50.000	0.00	0.00	0.00	4.75
3336	7364	1.270826	TCTTCAGACGAGACTTGCCTG	59.729	52.381	0.00	0.00	0.00	4.85
3337	7365	0.319900	TTCAGACGAGACTTGCCTGC	60.320	55.000	1.20	0.00	0.00	4.85
3338	7366	1.181741	TCAGACGAGACTTGCCTGCT	61.182	55.000	1.20	0.00	0.00	4.24
3339	7367	0.735632	CAGACGAGACTTGCCTGCTC	60.736	60.000	0.00	0.00	0.00	4.26
3340	7368	1.446966	GACGAGACTTGCCTGCTCC	60.447	63.158	0.00	0.00	0.00	4.70
3341	7369	1.882989	GACGAGACTTGCCTGCTCCT	61.883	60.000	0.00	0.00	0.00	3.69
3342	7370	1.153667	CGAGACTTGCCTGCTCCTC	60.154	63.158	0.00	0.00	0.00	3.71
3343	7371	1.220477	GAGACTTGCCTGCTCCTCC	59.780	63.158	0.00	0.00	0.00	4.30
3346	7374	2.125350	CTTGCCTGCTCCTCCGAC	60.125	66.667	0.00	0.00	0.00	4.79
3347	7375	3.997064	CTTGCCTGCTCCTCCGACG	62.997	68.421	0.00	0.00	0.00	5.12
3349	7377	4.803426	GCCTGCTCCTCCGACGTG	62.803	72.222	0.00	0.00	0.00	4.49
3351	7379	2.126307	CTGCTCCTCCGACGTGTG	60.126	66.667	0.00	0.00	0.00	3.82
3352	7380	4.357947	TGCTCCTCCGACGTGTGC	62.358	66.667	0.00	0.00	0.00	4.57
3354	7382	4.436998	CTCCTCCGACGTGTGCCC	62.437	72.222	0.00	0.00	0.00	5.36
3356	7384	4.082523	CCTCCGACGTGTGCCCAT	62.083	66.667	0.00	0.00	0.00	4.00
3357	7385	2.509336	CTCCGACGTGTGCCCATC	60.509	66.667	0.00	0.00	0.00	3.51
3358	7386	4.077184	TCCGACGTGTGCCCATCC	62.077	66.667	0.00	0.00	0.00	3.51
3361	7389	3.118454	GACGTGTGCCCATCCGTG	61.118	66.667	0.00	0.00	33.03	4.94
3364	7392	3.127533	GTGTGCCCATCCGTGCTC	61.128	66.667	0.00	0.00	0.00	4.26
3365	7393	4.408821	TGTGCCCATCCGTGCTCC	62.409	66.667	0.00	0.00	0.00	4.70
3371	7399	4.201679	CATCCGTGCTCCCGCGTA	62.202	66.667	4.92	0.00	43.11	4.42
3372	7400	4.203076	ATCCGTGCTCCCGCGTAC	62.203	66.667	4.92	0.00	43.11	3.67
3376	7404	4.409218	GTGCTCCCGCGTACGTGA	62.409	66.667	29.24	15.77	39.65	4.35
3377	7405	4.409218	TGCTCCCGCGTACGTGAC	62.409	66.667	29.24	15.52	39.65	3.67
3378	7406	4.112341	GCTCCCGCGTACGTGACT	62.112	66.667	29.24	0.00	37.70	3.41
3379	7407	2.564975	CTCCCGCGTACGTGACTT	59.435	61.111	29.24	0.00	37.70	3.01
3380	7408	1.800315	CTCCCGCGTACGTGACTTG	60.800	63.158	29.24	12.62	37.70	3.16
3381	7409	3.475774	CCCGCGTACGTGACTTGC	61.476	66.667	29.24	3.39	37.70	4.01
3382	7410	2.430244	CCGCGTACGTGACTTGCT	60.430	61.111	29.24	0.00	37.70	3.91
3383	7411	2.019951	CCGCGTACGTGACTTGCTT	61.020	57.895	29.24	0.00	37.70	3.91
3384	7412	1.554042	CCGCGTACGTGACTTGCTTT	61.554	55.000	29.24	0.00	37.70	3.51
3385	7413	0.448861	CGCGTACGTGACTTGCTTTG	60.449	55.000	23.95	0.00	33.53	2.77
3386	7414	0.856641	GCGTACGTGACTTGCTTTGA	59.143	50.000	17.90	0.00	0.00	2.69
3387	7415	1.459592	GCGTACGTGACTTGCTTTGAT	59.540	47.619	17.90	0.00	0.00	2.57
3388	7416	2.096417	GCGTACGTGACTTGCTTTGATT	60.096	45.455	17.90	0.00	0.00	2.57
3389	7417	3.469629	CGTACGTGACTTGCTTTGATTG	58.530	45.455	7.22	0.00	0.00	2.67
3390	7418	3.664276	CGTACGTGACTTGCTTTGATTGG	60.664	47.826	7.22	0.00	0.00	3.16
3391	7419	2.571212	ACGTGACTTGCTTTGATTGGA	58.429	42.857	0.00	0.00	0.00	3.53
3392	7420	2.948979	ACGTGACTTGCTTTGATTGGAA	59.051	40.909	0.00	0.00	0.00	3.53
3393	7421	3.243068	ACGTGACTTGCTTTGATTGGAAC	60.243	43.478	0.00	0.00	0.00	3.62
3394	7422	3.243035	CGTGACTTGCTTTGATTGGAACA	60.243	43.478	0.00	0.00	0.00	3.18
3407	7435	1.551452	TGGAACAAAATAAGGCCCGG	58.449	50.000	0.00	0.00	31.92	5.73
3408	7436	0.174845	GGAACAAAATAAGGCCCGGC	59.825	55.000	0.00	0.00	0.00	6.13
3421	7449	3.012722	CCGGCCTCACCCCCTTAA	61.013	66.667	0.00	0.00	33.26	1.85
3422	7450	2.608550	CCGGCCTCACCCCCTTAAA	61.609	63.158	0.00	0.00	33.26	1.52
3423	7451	1.381076	CGGCCTCACCCCCTTAAAA	59.619	57.895	0.00	0.00	33.26	1.52
3424	7452	0.033503	CGGCCTCACCCCCTTAAAAT	60.034	55.000	0.00	0.00	33.26	1.82
3425	7453	1.776662	GGCCTCACCCCCTTAAAATC	58.223	55.000	0.00	0.00	0.00	2.17
3426	7454	1.006639	GGCCTCACCCCCTTAAAATCA	59.993	52.381	0.00	0.00	0.00	2.57
3427	7455	2.379005	GCCTCACCCCCTTAAAATCAG	58.621	52.381	0.00	0.00	0.00	2.90
3428	7456	2.950418	GCCTCACCCCCTTAAAATCAGG	60.950	54.545	0.00	0.00	0.00	3.86
3437	7465	4.723309	CCCTTAAAATCAGGGGAGAGATG	58.277	47.826	0.00	0.00	46.90	2.90
3438	7466	4.413520	CCCTTAAAATCAGGGGAGAGATGA	59.586	45.833	0.00	0.00	46.90	2.92
3439	7467	5.074239	CCCTTAAAATCAGGGGAGAGATGAT	59.926	44.000	0.00	0.00	46.90	2.45
3442	7470	7.882271	CCTTAAAATCAGGGGAGAGATGATTAG	59.118	40.741	0.49	0.00	41.56	1.73
3445	7473	7.645132	AAATCAGGGGAGAGATGATTAGATT	57.355	36.000	0.49	0.00	41.56	2.40
3448	7476	8.748179	ATCAGGGGAGAGATGATTAGATTAAA	57.252	34.615	0.00	0.00	29.42	1.52
3482	7510	3.806316	AAAAACAGCCGTACGATGAAG	57.194	42.857	18.76	0.00	0.00	3.02
3483	7511	2.450609	AAACAGCCGTACGATGAAGT	57.549	45.000	18.76	4.94	0.00	3.01
3484	7512	1.710013	AACAGCCGTACGATGAAGTG	58.290	50.000	18.76	6.86	0.00	3.16
3486	7514	0.806102	CAGCCGTACGATGAAGTGGG	60.806	60.000	18.76	0.00	0.00	4.61
3487	7515	0.968901	AGCCGTACGATGAAGTGGGA	60.969	55.000	18.76	0.00	0.00	4.37
3494	7522	0.178767	CGATGAAGTGGGAGCATGGA	59.821	55.000	0.00	0.00	0.00	3.41
3495	7523	1.202734	CGATGAAGTGGGAGCATGGAT	60.203	52.381	0.00	0.00	0.00	3.41
3496	7524	2.228059	GATGAAGTGGGAGCATGGATG	58.772	52.381	0.00	0.00	0.00	3.51
3497	7525	0.256752	TGAAGTGGGAGCATGGATGG	59.743	55.000	0.00	0.00	0.00	3.51
3499	7527	1.002069	AAGTGGGAGCATGGATGGAA	58.998	50.000	0.00	0.00	0.00	3.53
3500	7528	0.549950	AGTGGGAGCATGGATGGAAG	59.450	55.000	0.00	0.00	0.00	3.46
3501	7529	1.105759	GTGGGAGCATGGATGGAAGC	61.106	60.000	0.00	0.00	0.00	3.86
3502	7530	1.228228	GGGAGCATGGATGGAAGCA	59.772	57.895	0.00	0.00	0.00	3.91
3506	7534	2.484062	GCATGGATGGAAGCACGGG	61.484	63.158	0.00	0.00	0.00	5.28
3507	7535	1.224315	CATGGATGGAAGCACGGGA	59.776	57.895	0.00	0.00	0.00	5.14
3508	7536	0.394216	CATGGATGGAAGCACGGGAA	60.394	55.000	0.00	0.00	0.00	3.97
3509	7537	0.107017	ATGGATGGAAGCACGGGAAG	60.107	55.000	0.00	0.00	0.00	3.46
3511	7539	1.452108	GATGGAAGCACGGGAAGGG	60.452	63.158	0.00	0.00	0.00	3.95
3512	7540	1.910580	GATGGAAGCACGGGAAGGGA	61.911	60.000	0.00	0.00	0.00	4.20
3517	7545	4.785453	GCACGGGAAGGGAGCAGG	62.785	72.222	0.00	0.00	0.00	4.85
3518	7546	4.785453	CACGGGAAGGGAGCAGGC	62.785	72.222	0.00	0.00	0.00	4.85
3520	7548	4.033776	CGGGAAGGGAGCAGGCAA	62.034	66.667	0.00	0.00	0.00	4.52
3521	7549	2.685999	GGGAAGGGAGCAGGCAAT	59.314	61.111	0.00	0.00	0.00	3.56
3523	7551	1.454663	GGAAGGGAGCAGGCAATCC	60.455	63.158	0.00	0.00	34.64	3.01
3524	7552	1.821332	GAAGGGAGCAGGCAATCCG	60.821	63.158	0.00	0.00	36.38	4.18
3526	7554	3.797353	GGGAGCAGGCAATCCGGA	61.797	66.667	6.61	6.61	36.38	5.14
3527	7555	2.512896	GGAGCAGGCAATCCGGAT	59.487	61.111	12.38	12.38	37.47	4.18
3528	7556	1.599240	GGAGCAGGCAATCCGGATC	60.599	63.158	19.43	5.94	41.33	3.36
3530	7558	2.595754	GCAGGCAATCCGGATCCC	60.596	66.667	19.43	20.37	37.47	3.85
3534	7562	1.352352	CAGGCAATCCGGATCCCTAAT	59.648	52.381	27.20	7.20	37.47	1.73
3535	7563	1.630878	AGGCAATCCGGATCCCTAATC	59.369	52.381	26.79	10.84	37.47	1.75
3536	7564	1.630878	GGCAATCCGGATCCCTAATCT	59.369	52.381	19.43	0.00	34.56	2.40
3538	7566	3.339141	GCAATCCGGATCCCTAATCTTC	58.661	50.000	19.43	0.00	34.56	2.87
3563	7591	2.544267	CCGTGTGGTCAGTTTTCTCTTC	59.456	50.000	0.00	0.00	0.00	2.87
3658	7859	0.312416	TTCCAACCAAAACGCATCCG	59.688	50.000	0.00	0.00	41.14	4.18
3678	7879	2.162809	CGCCTACCAAACAAATACCACC	59.837	50.000	0.00	0.00	0.00	4.61
3751	7970	9.577110	CTACAGATATTAACTTGGTGTAAACGA	57.423	33.333	0.00	0.00	0.00	3.85
3752	7971	8.248117	ACAGATATTAACTTGGTGTAAACGAC	57.752	34.615	0.00	0.00	0.00	4.34
3753	7972	8.092687	ACAGATATTAACTTGGTGTAAACGACT	58.907	33.333	0.00	0.00	0.00	4.18
3754	7973	8.932791	CAGATATTAACTTGGTGTAAACGACTT	58.067	33.333	0.00	0.00	0.00	3.01
3755	7974	8.932791	AGATATTAACTTGGTGTAAACGACTTG	58.067	33.333	0.00	0.00	0.00	3.16
4741	9844	3.272581	TCGATCTTGCTGCATGAATTCA	58.727	40.909	20.10	11.26	0.00	2.57
4923	10110	1.539827	GCTGAGTATTTGGGCGTGTTT	59.460	47.619	0.00	0.00	0.00	2.83
4958	10145	2.334977	ACGCCCTATGACCAATGGATA	58.665	47.619	6.16	0.00	0.00	2.59
4960	10147	3.137544	ACGCCCTATGACCAATGGATAAA	59.862	43.478	6.16	0.00	0.00	1.40
5120	16092	3.749981	CACACAGTGGAAGTGGCC	58.250	61.111	5.31	0.00	43.12	5.36
5153	16125	1.066430	ACGTTATTGACCGGCTGATGT	60.066	47.619	0.00	0.00	0.00	3.06
5571	16955	0.885196	TGTGCCGGGAATAAAACAGC	59.115	50.000	2.18	0.00	0.00	4.40
5577	16961	1.268539	CGGGAATAAAACAGCGATGCC	60.269	52.381	0.00	0.00	0.00	4.40
5603	16987	2.158415	AGGCAATCATTATGGAGGGTGG	60.158	50.000	0.00	0.00	0.00	4.61

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
157	160	3.981416	GCCGAGAAAAATTTCTGGAACAC	59.019	43.478	16.48	1.11	46.84	3.32
255	260	2.288825	CGATTATACACTCCACGCCCAT	60.289	50.000	0.00	0.00	0.00	4.00
410	455	3.127548	CCAATGCTTGTAGTCATCGCTTT	59.872	43.478	0.00	0.00	0.00	3.51
411	456	2.679837	CCAATGCTTGTAGTCATCGCTT	59.320	45.455	0.00	0.00	0.00	4.68
512	557	0.392461	TTGGGGCTTAGCACGATGAC	60.392	55.000	6.53	0.00	29.41	3.06
513	558	0.546122	ATTGGGGCTTAGCACGATGA	59.454	50.000	6.53	0.00	29.41	2.92
514	559	2.254546	TATTGGGGCTTAGCACGATG	57.745	50.000	6.53	0.00	29.41	3.84
515	560	2.371841	TCATATTGGGGCTTAGCACGAT	59.628	45.455	6.53	6.35	29.41	3.73
534	580	1.315981	TTGTTTTGGTGCGCTGGTCA	61.316	50.000	9.73	0.00	0.00	4.02
560	606	4.783764	TTACACTTCTCTTCATCAGCGA	57.216	40.909	0.00	0.00	0.00	4.93
581	627	0.035056	CAGGTTGGATCCTTCCGCTT	60.035	55.000	14.23	0.00	45.89	4.68
695	742	2.356382	ACGCGGAAATGTTCTTTCAACA	59.644	40.909	12.47	0.00	34.31	3.33
767	2168	6.918892	AAATCGCATGCAGTTTAGTACATA	57.081	33.333	19.57	0.00	0.00	2.29
1398	3129	1.509463	GTCGAGGTCCATGTACGCA	59.491	57.895	0.00	0.00	0.00	5.24
1651	3403	3.416156	GCTTTCCACTCTCAACCTCAAT	58.584	45.455	0.00	0.00	0.00	2.57
1849	3748	0.605589	ACTAAAGTTGCCACCTCGCC	60.606	55.000	0.00	0.00	0.00	5.54
1909	3808	7.378181	AGGTTGGTAAACATAGCAATTTTCTG	58.622	34.615	4.08	0.00	39.27	3.02
2040	3939	2.116238	ACCTGGCCGACTGTGTATTAT	58.884	47.619	0.00	0.00	0.00	1.28
2041	3940	1.206132	CACCTGGCCGACTGTGTATTA	59.794	52.381	0.00	0.00	0.00	0.98
2042	3941	0.036388	CACCTGGCCGACTGTGTATT	60.036	55.000	0.00	0.00	0.00	1.89
2168	4067	4.816925	AGATATAAGCCGAAACCAAGAAGC	59.183	41.667	0.00	0.00	0.00	3.86
2169	4068	5.175856	CGAGATATAAGCCGAAACCAAGAAG	59.824	44.000	0.00	0.00	0.00	2.85
2238	4137	1.712977	CGTCCGAGTTCCTCCGGTAG	61.713	65.000	0.00	0.00	45.48	3.18
2320	4219	3.827898	GCTCCGGCTACTGCGAGT	61.828	66.667	0.00	0.00	40.82	4.18
2321	4220	4.577246	GGCTCCGGCTACTGCGAG	62.577	72.222	0.00	0.00	40.82	5.03
2403	4302	5.446473	CCTCTGAAACGTGTGAAGCAATATC	60.446	44.000	0.00	0.00	0.00	1.63
2404	4303	4.393062	CCTCTGAAACGTGTGAAGCAATAT	59.607	41.667	0.00	0.00	0.00	1.28
2474	4373	2.622962	CCCCAACGTTTCCCGCTTC	61.623	63.158	0.00	0.00	41.42	3.86
2504	4403	0.887836	AGCGGATAGGTGCATGCATG	60.888	55.000	25.64	22.70	0.00	4.06
2505	4404	0.686789	TAGCGGATAGGTGCATGCAT	59.313	50.000	25.64	11.73	0.00	3.96
2557	4456	2.618709	CGAATGGGACTAATTGGCTTCC	59.381	50.000	0.00	0.00	0.00	3.46
2875	4876	7.174946	CCGTGTGCCCTCTTTTATATATTTGAT	59.825	37.037	0.00	0.00	0.00	2.57
2992	5533	0.243095	GGTGAACTACGTCGCCTCTT	59.757	55.000	0.00	0.00	43.62	2.85
3101	5853	7.229581	TCTACAGGGACTAAAAAGACTCTTC	57.770	40.000	0.00	0.00	36.02	2.87
3112	5864	5.160386	AGGGACTTTTTCTACAGGGACTAA	58.840	41.667	0.00	0.00	28.08	2.24
3119	5873	4.625607	ACAGGAGGGACTTTTTCTACAG	57.374	45.455	0.00	0.00	41.55	2.74
3120	5874	5.382664	AAACAGGAGGGACTTTTTCTACA	57.617	39.130	0.00	0.00	41.55	2.74
3121	5875	6.531923	ACTAAACAGGAGGGACTTTTTCTAC	58.468	40.000	0.00	0.00	41.55	2.59
3143	5897	3.514539	AGTCCCTTTTAGTCCCGTAACT	58.485	45.455	0.00	0.00	0.00	2.24
3144	5898	3.969287	AGTCCCTTTTAGTCCCGTAAC	57.031	47.619	0.00	0.00	0.00	2.50
3189	5947	5.133153	TGGGAATTAATACTAAGGGGGTGTC	59.867	44.000	0.00	0.00	0.00	3.67
3282	7310	1.000396	AGAAGCAAGGTGGCATCCC	60.000	57.895	0.00	0.00	32.18	3.85
3322	7350	1.446966	GGAGCAGGCAAGTCTCGTC	60.447	63.158	0.00	0.00	0.00	4.20
3323	7351	1.882989	GAGGAGCAGGCAAGTCTCGT	61.883	60.000	0.00	0.00	0.00	4.18
3324	7352	1.153667	GAGGAGCAGGCAAGTCTCG	60.154	63.158	0.00	0.00	0.00	4.04
3326	7354	2.654079	CGGAGGAGCAGGCAAGTCT	61.654	63.158	0.00	0.00	0.00	3.24
3327	7355	2.125350	CGGAGGAGCAGGCAAGTC	60.125	66.667	0.00	0.00	0.00	3.01
3328	7356	2.604686	TCGGAGGAGCAGGCAAGT	60.605	61.111	0.00	0.00	0.00	3.16
3329	7357	2.125350	GTCGGAGGAGCAGGCAAG	60.125	66.667	0.00	0.00	0.00	4.01
3330	7358	4.069232	CGTCGGAGGAGCAGGCAA	62.069	66.667	0.00	0.00	0.00	4.52
3332	7360	4.803426	CACGTCGGAGGAGCAGGC	62.803	72.222	4.48	0.00	0.00	4.85
3333	7361	3.374402	ACACGTCGGAGGAGCAGG	61.374	66.667	4.48	0.00	0.00	4.85
3334	7362	2.126307	CACACGTCGGAGGAGCAG	60.126	66.667	4.48	0.00	0.00	4.24
3335	7363	4.357947	GCACACGTCGGAGGAGCA	62.358	66.667	4.48	0.00	0.00	4.26
3337	7365	4.436998	GGGCACACGTCGGAGGAG	62.437	72.222	4.48	0.00	0.00	3.69
3339	7367	4.082523	ATGGGCACACGTCGGAGG	62.083	66.667	0.00	0.00	0.00	4.30
3340	7368	2.509336	GATGGGCACACGTCGGAG	60.509	66.667	0.00	0.00	0.00	4.63
3341	7369	4.077184	GGATGGGCACACGTCGGA	62.077	66.667	0.00	0.00	0.00	4.55
3343	7371	4.735132	ACGGATGGGCACACGTCG	62.735	66.667	0.00	2.39	33.92	5.12
3347	7375	3.127533	GAGCACGGATGGGCACAC	61.128	66.667	0.00	0.00	0.00	3.82
3364	7392	3.475774	GCAAGTCACGTACGCGGG	61.476	66.667	16.72	5.46	44.11	6.13
3365	7393	1.554042	AAAGCAAGTCACGTACGCGG	61.554	55.000	16.72	8.28	43.45	6.46
3366	7394	0.448861	CAAAGCAAGTCACGTACGCG	60.449	55.000	16.72	3.53	44.93	6.01
3367	7395	0.856641	TCAAAGCAAGTCACGTACGC	59.143	50.000	16.72	0.00	0.00	4.42
3368	7396	3.469629	CAATCAAAGCAAGTCACGTACG	58.530	45.455	15.01	15.01	0.00	3.67
3370	7398	3.734463	TCCAATCAAAGCAAGTCACGTA	58.266	40.909	0.00	0.00	0.00	3.57
3371	7399	2.571212	TCCAATCAAAGCAAGTCACGT	58.429	42.857	0.00	0.00	0.00	4.49
3372	7400	3.243035	TGTTCCAATCAAAGCAAGTCACG	60.243	43.478	0.00	0.00	0.00	4.35
3373	7401	4.305989	TGTTCCAATCAAAGCAAGTCAC	57.694	40.909	0.00	0.00	0.00	3.67
3374	7402	4.998671	TTGTTCCAATCAAAGCAAGTCA	57.001	36.364	0.00	0.00	0.00	3.41
3375	7403	6.849588	ATTTTGTTCCAATCAAAGCAAGTC	57.150	33.333	0.00	0.00	36.40	3.01
3376	7404	7.442062	CCTTATTTTGTTCCAATCAAAGCAAGT	59.558	33.333	0.00	0.00	36.40	3.16
3377	7405	7.571798	GCCTTATTTTGTTCCAATCAAAGCAAG	60.572	37.037	0.00	0.00	36.40	4.01
3378	7406	6.204495	GCCTTATTTTGTTCCAATCAAAGCAA	59.796	34.615	0.00	0.00	36.40	3.91
3379	7407	5.700373	GCCTTATTTTGTTCCAATCAAAGCA	59.300	36.000	0.00	0.00	36.40	3.91
3380	7408	5.122239	GGCCTTATTTTGTTCCAATCAAAGC	59.878	40.000	0.00	0.00	36.40	3.51
3381	7409	5.643348	GGGCCTTATTTTGTTCCAATCAAAG	59.357	40.000	0.84	0.00	36.40	2.77
3382	7410	5.555966	GGGCCTTATTTTGTTCCAATCAAA	58.444	37.500	0.84	0.00	33.76	2.69
3383	7411	4.322349	CGGGCCTTATTTTGTTCCAATCAA	60.322	41.667	0.84	0.00	0.00	2.57
3384	7412	3.194542	CGGGCCTTATTTTGTTCCAATCA	59.805	43.478	0.84	0.00	0.00	2.57
3385	7413	3.430236	CCGGGCCTTATTTTGTTCCAATC	60.430	47.826	0.84	0.00	0.00	2.67
3386	7414	2.499693	CCGGGCCTTATTTTGTTCCAAT	59.500	45.455	0.84	0.00	0.00	3.16
3387	7415	1.896465	CCGGGCCTTATTTTGTTCCAA	59.104	47.619	0.84	0.00	0.00	3.53
3388	7416	1.551452	CCGGGCCTTATTTTGTTCCA	58.449	50.000	0.84	0.00	0.00	3.53
3389	7417	0.174845	GCCGGGCCTTATTTTGTTCC	59.825	55.000	8.12	0.00	0.00	3.62
3390	7418	0.174845	GGCCGGGCCTTATTTTGTTC	59.825	55.000	30.86	0.00	46.69	3.18
3391	7419	2.282827	GGCCGGGCCTTATTTTGTT	58.717	52.632	30.86	0.00	46.69	2.83
3392	7420	4.027884	GGCCGGGCCTTATTTTGT	57.972	55.556	30.86	0.00	46.69	2.83
3404	7432	2.144859	TTTTAAGGGGGTGAGGCCGG	62.145	60.000	0.00	0.00	38.44	6.13
3405	7433	0.033503	ATTTTAAGGGGGTGAGGCCG	60.034	55.000	0.00	0.00	38.44	6.13
3406	7434	1.006639	TGATTTTAAGGGGGTGAGGCC	59.993	52.381	0.00	0.00	0.00	5.19
3407	7435	2.379005	CTGATTTTAAGGGGGTGAGGC	58.621	52.381	0.00	0.00	0.00	4.70
3408	7436	3.018423	CCTGATTTTAAGGGGGTGAGG	57.982	52.381	0.00	0.00	0.00	3.86
3416	7444	5.636903	TCATCTCTCCCCTGATTTTAAGG	57.363	43.478	0.00	0.00	34.31	2.69
3417	7445	8.654997	TCTAATCATCTCTCCCCTGATTTTAAG	58.345	37.037	2.71	0.00	39.60	1.85
3418	7446	8.567198	TCTAATCATCTCTCCCCTGATTTTAA	57.433	34.615	2.71	0.00	39.60	1.52
3419	7447	8.748179	ATCTAATCATCTCTCCCCTGATTTTA	57.252	34.615	2.71	0.00	39.60	1.52
3420	7448	7.645132	ATCTAATCATCTCTCCCCTGATTTT	57.355	36.000	2.71	0.00	39.60	1.82
3421	7449	7.645132	AATCTAATCATCTCTCCCCTGATTT	57.355	36.000	2.71	0.00	39.60	2.17
3422	7450	8.748179	TTAATCTAATCATCTCTCCCCTGATT	57.252	34.615	0.00	0.00	41.28	2.57
3423	7451	8.748179	TTTAATCTAATCATCTCTCCCCTGAT	57.252	34.615	0.00	0.00	0.00	2.90
3424	7452	8.567198	TTTTAATCTAATCATCTCTCCCCTGA	57.433	34.615	0.00	0.00	0.00	3.86
3464	7492	2.066262	CACTTCATCGTACGGCTGTTT	58.934	47.619	16.52	0.58	0.00	2.83
3465	7493	1.671850	CCACTTCATCGTACGGCTGTT	60.672	52.381	16.52	0.90	0.00	3.16
3466	7494	0.108804	CCACTTCATCGTACGGCTGT	60.109	55.000	16.52	2.42	0.00	4.40
3467	7495	0.806102	CCCACTTCATCGTACGGCTG	60.806	60.000	16.52	13.35	0.00	4.85
3468	7496	0.968901	TCCCACTTCATCGTACGGCT	60.969	55.000	16.52	0.00	0.00	5.52
3470	7498	0.527817	GCTCCCACTTCATCGTACGG	60.528	60.000	16.52	0.00	0.00	4.02
3471	7499	0.172578	TGCTCCCACTTCATCGTACG	59.827	55.000	9.53	9.53	0.00	3.67
3472	7500	2.205074	CATGCTCCCACTTCATCGTAC	58.795	52.381	0.00	0.00	0.00	3.67
3473	7501	1.138859	CCATGCTCCCACTTCATCGTA	59.861	52.381	0.00	0.00	0.00	3.43
3475	7503	0.178767	TCCATGCTCCCACTTCATCG	59.821	55.000	0.00	0.00	0.00	3.84
3476	7504	2.228059	CATCCATGCTCCCACTTCATC	58.772	52.381	0.00	0.00	0.00	2.92
3478	7506	0.256752	CCATCCATGCTCCCACTTCA	59.743	55.000	0.00	0.00	0.00	3.02
3480	7508	1.002069	TTCCATCCATGCTCCCACTT	58.998	50.000	0.00	0.00	0.00	3.16
3482	7510	1.105759	GCTTCCATCCATGCTCCCAC	61.106	60.000	0.00	0.00	0.00	4.61
3483	7511	1.228228	GCTTCCATCCATGCTCCCA	59.772	57.895	0.00	0.00	0.00	4.37
3484	7512	1.105759	GTGCTTCCATCCATGCTCCC	61.106	60.000	0.00	0.00	0.00	4.30
3486	7514	1.442526	CCGTGCTTCCATCCATGCTC	61.443	60.000	0.00	0.00	0.00	4.26
3487	7515	1.452651	CCGTGCTTCCATCCATGCT	60.453	57.895	0.00	0.00	0.00	3.79
3494	7522	1.915078	CTCCCTTCCCGTGCTTCCAT	61.915	60.000	0.00	0.00	0.00	3.41
3495	7523	2.528127	TCCCTTCCCGTGCTTCCA	60.528	61.111	0.00	0.00	0.00	3.53
3496	7524	2.269241	CTCCCTTCCCGTGCTTCC	59.731	66.667	0.00	0.00	0.00	3.46
3497	7525	2.436824	GCTCCCTTCCCGTGCTTC	60.437	66.667	0.00	0.00	0.00	3.86
3499	7527	3.710722	CTGCTCCCTTCCCGTGCT	61.711	66.667	0.00	0.00	0.00	4.40
3500	7528	4.785453	CCTGCTCCCTTCCCGTGC	62.785	72.222	0.00	0.00	0.00	5.34
3501	7529	4.785453	GCCTGCTCCCTTCCCGTG	62.785	72.222	0.00	0.00	0.00	4.94
3506	7534	1.821332	CGGATTGCCTGCTCCCTTC	60.821	63.158	0.00	0.00	0.00	3.46
3507	7535	2.273449	CGGATTGCCTGCTCCCTT	59.727	61.111	0.00	0.00	0.00	3.95
3508	7536	3.801997	CCGGATTGCCTGCTCCCT	61.802	66.667	0.00	0.00	0.00	4.20
3509	7537	3.125376	ATCCGGATTGCCTGCTCCC	62.125	63.158	12.38	0.00	0.00	4.30
3511	7539	1.599240	GGATCCGGATTGCCTGCTC	60.599	63.158	20.22	3.33	0.00	4.26
3512	7540	2.512896	GGATCCGGATTGCCTGCT	59.487	61.111	20.22	0.00	0.00	4.24
3517	7545	3.339141	GAAGATTAGGGATCCGGATTGC	58.661	50.000	20.22	6.49	35.21	3.56
3518	7546	3.327757	TGGAAGATTAGGGATCCGGATTG	59.672	47.826	20.22	0.00	35.21	2.67
3520	7548	2.907042	GTGGAAGATTAGGGATCCGGAT	59.093	50.000	19.21	19.21	35.21	4.18
3521	7549	2.326428	GTGGAAGATTAGGGATCCGGA	58.674	52.381	6.61	6.61	35.21	5.14
3523	7551	1.348036	GGGTGGAAGATTAGGGATCCG	59.652	57.143	5.45	0.00	35.21	4.18
3524	7552	1.348036	CGGGTGGAAGATTAGGGATCC	59.652	57.143	1.92	1.92	35.21	3.36
3526	7554	1.768870	CACGGGTGGAAGATTAGGGAT	59.231	52.381	0.00	0.00	0.00	3.85
3527	7555	1.200519	CACGGGTGGAAGATTAGGGA	58.799	55.000	0.00	0.00	0.00	4.20
3528	7556	0.909623	ACACGGGTGGAAGATTAGGG	59.090	55.000	0.00	0.00	34.19	3.53
3658	7859	3.158676	TGGTGGTATTTGTTTGGTAGGC	58.841	45.455	0.00	0.00	0.00	3.93
3678	7879	4.213564	AGGTCCTTAGTGCTCAGATTTG	57.786	45.455	0.00	0.00	0.00	2.32
3749	7968	3.002965	GGGGTAACAAGACAAACAAGTCG	59.997	47.826	0.00	0.00	40.50	4.18
3751	7970	3.970842	TGGGGTAACAAGACAAACAAGT	58.029	40.909	0.00	0.00	39.74	3.16
3752	7971	4.158764	TGTTGGGGTAACAAGACAAACAAG	59.841	41.667	0.00	0.00	45.86	3.16
3753	7972	4.087182	TGTTGGGGTAACAAGACAAACAA	58.913	39.130	0.00	0.00	45.86	2.83
3754	7973	3.698289	TGTTGGGGTAACAAGACAAACA	58.302	40.909	0.00	0.00	45.86	2.83
4741	9844	8.389779	ACAAAACCTCAAACAGAAAACAAAAT	57.610	26.923	0.00	0.00	0.00	1.82
4891	10078	0.039798	TACTCAGCAACGACCGTGTC	60.040	55.000	0.00	0.00	0.00	3.67
4923	10110	2.231964	AGGGCGTAACATTTACACTCGA	59.768	45.455	0.00	0.00	0.00	4.04
4958	10145	5.584551	ATTTAATCGCTAGGGGAGGATTT	57.415	39.130	6.99	0.00	31.46	2.17
4960	10147	4.322801	CGAATTTAATCGCTAGGGGAGGAT	60.323	45.833	6.99	0.00	35.85	3.24
5120	16092	4.150627	GTCAATAACGTCCCATGATCATCG	59.849	45.833	4.86	9.05	0.00	3.84
5153	16125	5.172934	CGGTCTTATTAGCCAACACTACAA	58.827	41.667	0.00	0.00	0.00	2.41
5483	16867	1.270839	CCTCGACAAAGGCAGAAAGGA	60.271	52.381	0.00	0.00	0.00	3.36
5577	16961	3.688185	CCTCCATAATGATTGCCTCGATG	59.312	47.826	0.00	0.00	0.00	3.84

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.