AutoCloner

Multiple sequence alignment - TraesCS2D01G298800

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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	TraesCS2D01G298800	chr2D	100.000	5009	0	0	1	5009	380922985	380927993	0.000000e+00	9250.0
1	TraesCS2D01G298800	chr2D	98.517	2966	16	3	1612	4549	381087855	381084890	0.000000e+00	5208.0
2	TraesCS2D01G298800	chr2D	94.822	927	14	16	1	897	381093798	381092876	0.000000e+00	1415.0
3	TraesCS2D01G298800	chr2D	86.717	1182	116	16	2685	3852	381196314	381195160	0.000000e+00	1275.0
4	TraesCS2D01G298800	chr2D	97.881	708	6	2	705	1406	380934670	380935374	0.000000e+00	1216.0
5	TraesCS2D01G298800	chr2D	82.600	1046	126	28	1673	2686	381197371	381196350	0.000000e+00	872.0
6	TraesCS2D01G298800	chr2D	91.590	654	12	17	3922	4549	637766834	637766198	0.000000e+00	863.0
7	TraesCS2D01G298800	chr2D	95.677	347	9	1	1246	1586	381088191	381087845	2.040000e-153	553.0
8	TraesCS2D01G298800	chr2D	97.189	249	7	0	949	1197	381092880	381092632	6.000000e-114	422.0
9	TraesCS2D01G298800	chr2D	90.476	168	14	2	3848	4014	381192650	381192484	2.350000e-53	220.0
10	TraesCS2D01G298800	chr2D	87.027	185	18	4	1400	1584	381202710	381202532	2.360000e-48	204.0
11	TraesCS2D01G298800	chr2D	85.455	165	8	2	1258	1406	381092626	381092462	1.870000e-34	158.0
12	TraesCS2D01G298800	chr2D	78.648	281	29	16	1673	1928	381202477	381202203	1.870000e-34	158.0
13	TraesCS2D01G298800	chr2D	72.857	420	73	34	80	476	244390986	244391387	6.860000e-19	106.0
14	TraesCS2D01G298800	chr2A	96.249	2559	50	8	1600	4147	762145154	762147677	0.000000e+00	4152.0
15	TraesCS2D01G298800	chr2A	85.820	1347	138	22	2685	4014	762089829	762091139	0.000000e+00	1380.0
16	TraesCS2D01G298800	chr2A	83.605	982	109	27	1736	2686	762088833	762089793	0.000000e+00	874.0
17	TraesCS2D01G298800	chr2A	79.041	959	146	36	1748	2682	762008108	762007181	1.540000e-169	606.0
18	TraesCS2D01G298800	chr2A	81.234	762	127	10	3271	4020	762006950	762006193	7.180000e-168	601.0
19	TraesCS2D01G298800	chr2A	91.081	370	7	5	4191	4560	762147675	762148018	1.260000e-130	477.0
20	TraesCS2D01G298800	chr2A	83.860	285	27	6	4681	4957	711635571	711635844	2.310000e-63	254.0
21	TraesCS2D01G298800	chr2A	82.114	246	22	6	3002	3245	762097261	762097486	1.840000e-44	191.0
22	TraesCS2D01G298800	chr2A	83.099	142	17	4	966	1106	762141170	762141305	6.810000e-24	122.0
23	TraesCS2D01G298800	chr2A	87.850	107	4	4	1284	1381	762141371	762141477	3.170000e-22	117.0
24	TraesCS2D01G298800	chr2A	86.458	96	13	0	1489	1584	762088635	762088730	6.860000e-19	106.0
25	TraesCS2D01G298800	chr2A	93.443	61	4	0	1196	1256	762141310	762141370	1.920000e-14	91.6
26	TraesCS2D01G298800	chr2A	89.231	65	7	0	1399	1463	762088566	762088630	1.160000e-11	82.4
27	TraesCS2D01G298800	chr2A	100.000	33	0	0	4977	5009	762148165	762148197	1.510000e-05	62.1
28	TraesCS2D01G298800	chr2A	100.000	29	0	0	4498	4526	762148015	762148043	3.000000e-03	54.7
29	TraesCS2D01G298800	chr2B	98.102	2002	31	2	2150	4147	795280498	795278500	0.000000e+00	3480.0
30	TraesCS2D01G298800	chr2B	87.063	1345	127	21	2685	4014	795306957	795305645	0.000000e+00	1476.0
31	TraesCS2D01G298800	chr2B	82.529	1036	123	30	1689	2686	795308008	795306993	0.000000e+00	857.0
32	TraesCS2D01G298800	chr2B	95.685	533	11	4	1600	2126	795281021	795280495	0.000000e+00	846.0
33	TraesCS2D01G298800	chr2B	78.168	1026	153	46	1681	2676	795440799	795441783	5.590000e-164	588.0
34	TraesCS2D01G298800	chr2B	91.081	370	7	5	4191	4560	795278502	795278159	1.260000e-130	477.0
35	TraesCS2D01G298800	chr2B	81.625	283	39	7	4685	4957	699105556	699105835	6.530000e-54	222.0
36	TraesCS2D01G298800	chr2B	82.258	248	31	4	4685	4925	734354120	734354361	8.500000e-48	202.0
37	TraesCS2D01G298800	chr2B	84.793	217	11	4	1196	1406	795283401	795283201	1.100000e-46	198.0
38	TraesCS2D01G298800	chr2B	79.861	288	42	10	4685	4958	156626692	156626407	3.960000e-46	196.0
39	TraesCS2D01G298800	chr2B	83.333	186	25	3	1399	1584	795308257	795308078	3.100000e-37	167.0
40	TraesCS2D01G298800	chr2B	83.060	183	24	4	925	1106	795283582	795283406	5.190000e-35	159.0
41	TraesCS2D01G298800	chr2B	100.000	29	0	0	4498	4526	795278162	795278134	3.000000e-03	54.7
42	TraesCS2D01G298800	chrUn	83.673	1372	144	38	1673	3003	22338884	22337552	0.000000e+00	1219.0
43	TraesCS2D01G298800	chrUn	87.071	1021	98	13	3002	4014	22336540	22335546	0.000000e+00	1123.0
44	TraesCS2D01G298800	chrUn	83.417	199	21	4	4685	4871	3241651	3241849	1.850000e-39	174.0
45	TraesCS2D01G298800	chrUn	85.143	175	20	3	1410	1584	22339107	22338939	1.850000e-39	174.0
46	TraesCS2D01G298800	chr6A	83.408	1338	143	32	1697	3003	18601746	18600457	0.000000e+00	1168.0
47	TraesCS2D01G298800	chr6A	85.673	1026	120	12	3005	4020	18599441	18598433	0.000000e+00	1055.0
48	TraesCS2D01G298800	chr6A	83.889	180	22	4	1406	1584	18601996	18601823	1.120000e-36	165.0
49	TraesCS2D01G298800	chr6B	83.505	291	35	5	4681	4958	563500120	563500410	4.970000e-65	259.0
50	TraesCS2D01G298800	chr6B	82.119	151	17	7	4833	4975	702839331	702839479	2.450000e-23	121.0
51	TraesCS2D01G298800	chr1A	83.803	284	30	8	4681	4958	555645061	555644788	6.440000e-64	255.0
52	TraesCS2D01G298800	chr7A	82.143	280	33	8	4685	4958	652304849	652305117	1.810000e-54	224.0
53	TraesCS2D01G298800	chr7A	87.975	158	18	1	4801	4957	581043128	581043285	8.560000e-43	185.0
54	TraesCS2D01G298800	chr7A	100.000	29	0	0	357	385	389009924	389009896	3.000000e-03	54.7
55	TraesCS2D01G298800	chr5B	80.887	293	39	10	4681	4958	379154649	379154939	1.090000e-51	215.0
56	TraesCS2D01G298800	chr5B	92.308	39	2	1	358	396	508452593	508452630	3.000000e-03	54.7
57	TraesCS2D01G298800	chr5A	81.295	278	39	7	4694	4958	568291185	568291462	3.930000e-51	213.0
58	TraesCS2D01G298800	chr5A	94.937	79	4	0	599	677	548462532	548462610	1.890000e-24	124.0
59	TraesCS2D01G298800	chr5A	94.937	79	4	0	601	679	548481480	548481558	1.890000e-24	124.0
60	TraesCS2D01G298800	chr5A	86.667	75	8	2	4905	4978	643342404	643342331	1.160000e-11	82.4
61	TraesCS2D01G298800	chr3B	80.702	285	37	8	4685	4956	749859424	749859703	6.570000e-49	206.0
62	TraesCS2D01G298800	chr3B	96.104	77	3	0	600	676	544181797	544181721	5.260000e-25	126.0
63	TraesCS2D01G298800	chr3A	97.500	80	2	0	599	678	387280706	387280785	2.430000e-28	137.0
64	TraesCS2D01G298800	chr3A	84.071	113	10	4	4853	4958	565454670	565454559	8.870000e-18	102.0
65	TraesCS2D01G298800	chr3D	96.203	79	3	0	599	677	292039954	292039876	4.070000e-26	130.0
66	TraesCS2D01G298800	chr3D	95.000	80	3	1	599	677	417746491	417746412	1.890000e-24	124.0
67	TraesCS2D01G298800	chr5D	96.053	76	3	0	598	673	88464077	88464002	1.890000e-24	124.0
68	TraesCS2D01G298800	chr4D	92.683	82	5	1	599	679	264060871	264060790	3.170000e-22	117.0
69	TraesCS2D01G298800	chr7B	82.258	124	16	3	4685	4802	483344131	483344008	8.870000e-18	102.0
70	TraesCS2D01G298800	chr6D	100.000	29	0	0	357	385	248929324	248929296	3.000000e-03	54.7
71	TraesCS2D01G298800	chr4B	96.875	32	1	0	354	385	333327260	333327291	3.000000e-03	54.7

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	TraesCS2D01G298800	chr2D	380922985	380927993	5008	False	9250.000000	9250	100.000000	1	5009	1	chr2D.!!$F2	5008
1	TraesCS2D01G298800	chr2D	381084890	381088191	3301	True	2880.500000	5208	97.097000	1246	4549	2	chr2D.!!$R2	3303
2	TraesCS2D01G298800	chr2D	380934670	380935374	704	False	1216.000000	1216	97.881000	705	1406	1	chr2D.!!$F3	701
3	TraesCS2D01G298800	chr2D	637766198	637766834	636	True	863.000000	863	91.590000	3922	4549	1	chr2D.!!$R1	627
4	TraesCS2D01G298800	chr2D	381192484	381197371	4887	True	789.000000	1275	86.597667	1673	4014	3	chr2D.!!$R4	2341
5	TraesCS2D01G298800	chr2D	381092462	381093798	1336	True	665.000000	1415	92.488667	1	1406	3	chr2D.!!$R3	1405
6	TraesCS2D01G298800	chr2A	762141170	762148197	7027	False	725.200000	4152	93.103143	966	5009	7	chr2A.!!$F4	4043
7	TraesCS2D01G298800	chr2A	762088566	762091139	2573	False	610.600000	1380	86.278500	1399	4014	4	chr2A.!!$F3	2615
8	TraesCS2D01G298800	chr2A	762006193	762008108	1915	True	603.500000	606	80.137500	1748	4020	2	chr2A.!!$R1	2272
9	TraesCS2D01G298800	chr2B	795278134	795283582	5448	True	869.116667	3480	92.120167	925	4560	6	chr2B.!!$R2	3635
10	TraesCS2D01G298800	chr2B	795305645	795308257	2612	True	833.333333	1476	84.308333	1399	4014	3	chr2B.!!$R3	2615
11	TraesCS2D01G298800	chr2B	795440799	795441783	984	False	588.000000	588	78.168000	1681	2676	1	chr2B.!!$F3	995
12	TraesCS2D01G298800	chrUn	22335546	22339107	3561	True	838.666667	1219	85.295667	1410	4014	3	chrUn.!!$R1	2604
13	TraesCS2D01G298800	chr6A	18598433	18601996	3563	True	796.000000	1168	84.323333	1406	4020	3	chr6A.!!$R1	2614

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
899	930	0.325390	ACCCTAGTAGGACACCAGGC	60.325	60.0	18.43	37.67	4.85	F
901	932	0.395311	CCTAGTAGGACACCAGGCGA	60.395	60.0	11.09	37.67	5.54	F
2452	6196	0.179043	TGCAGTTTACGGCTTCCACA	60.179	50.0	6.56	37.92	4.17	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1876	5583	1.216990	AGATTTTCATCGAGGGGCCT	58.783	50.000	0.84	34.17	5.19	R
2488	6232	3.068732	TGATTGAGTAGATCTCCAAGGCG	59.931	47.826	0.00	42.12	5.52	R
4531	12052	3.419793	CCTGGTGAGGCAAGAACAA	57.580	52.632	0.00	30.52	2.83	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
195	196	3.983044	ATGTGACTTTACTGGACCCTC	57.017	47.619	0.00	0.00	0.00	4.30
227	228	9.362539	GCTGCATAATATATTTCAGGGATTTTG	57.637	33.333	2.68	0.00	0.00	2.44
370	371	9.991906	CAATTCTCAAATATTAATGAAGGGCAT	57.008	29.630	0.00	0.00	39.43	4.40
389	390	4.220602	GGCATTTTGGGTTCATTGAGTACT	59.779	41.667	0.00	0.00	0.00	2.73
775	805	5.695851	AAGAGTCGTTCTCCGTTTTAGTA	57.304	39.130	6.73	0.00	43.71	1.82
776	806	5.893897	AGAGTCGTTCTCCGTTTTAGTAT	57.106	39.130	6.73	0.00	43.71	2.12
777	807	6.992063	AGAGTCGTTCTCCGTTTTAGTATA	57.008	37.500	6.73	0.00	43.71	1.47
861	892	2.085343	ATGAAACCAGCACTGCCCCT	62.085	55.000	0.00	0.00	0.00	4.79
894	925	3.935315	GGTTGAAACCCTAGTAGGACAC	58.065	50.000	18.43	6.72	43.43	3.67
895	926	3.307269	GGTTGAAACCCTAGTAGGACACC	60.307	52.174	18.43	9.60	43.43	4.16
896	927	3.263369	TGAAACCCTAGTAGGACACCA	57.737	47.619	18.43	7.40	37.67	4.17
897	928	3.170717	TGAAACCCTAGTAGGACACCAG	58.829	50.000	18.43	2.05	37.67	4.00
898	929	2.249309	AACCCTAGTAGGACACCAGG	57.751	55.000	18.43	1.30	37.67	4.45
899	930	0.325390	ACCCTAGTAGGACACCAGGC	60.325	60.000	18.43	0.00	37.67	4.85
900	931	1.392710	CCCTAGTAGGACACCAGGCG	61.393	65.000	18.43	0.00	37.67	5.52
901	932	0.395311	CCTAGTAGGACACCAGGCGA	60.395	60.000	11.09	0.00	37.67	5.54
902	933	1.025812	CTAGTAGGACACCAGGCGAG	58.974	60.000	0.00	0.00	0.00	5.03
903	934	1.035932	TAGTAGGACACCAGGCGAGC	61.036	60.000	0.00	0.00	0.00	5.03
904	935	3.449227	TAGGACACCAGGCGAGCG	61.449	66.667	0.00	0.00	0.00	5.03
943	974	4.081420	TGGTTAGCCATGTCTTCTCTTCTC	60.081	45.833	0.00	0.00	40.46	2.87
1577	5260	1.383109	TGATGAGGCAGTCCGGGAT	60.383	57.895	0.00	0.00	37.47	3.85
1578	5261	1.070445	GATGAGGCAGTCCGGGATG	59.930	63.158	0.00	1.32	37.47	3.51
1579	5262	2.388890	GATGAGGCAGTCCGGGATGG	62.389	65.000	0.00	0.00	37.47	3.51
1580	5263	3.866582	GAGGCAGTCCGGGATGGG	61.867	72.222	0.00	0.00	38.76	4.00
1583	5266	3.171388	GCAGTCCGGGATGGGGAT	61.171	66.667	0.00	0.00	38.76	3.85
1584	5267	2.831770	CAGTCCGGGATGGGGATG	59.168	66.667	0.00	0.00	38.76	3.51
1585	5268	2.448542	AGTCCGGGATGGGGATGG	60.449	66.667	0.00	0.00	38.76	3.51
1586	5269	3.570212	GTCCGGGATGGGGATGGG	61.570	72.222	0.00	0.00	38.76	4.00
1587	5270	4.918360	TCCGGGATGGGGATGGGG	62.918	72.222	0.00	0.00	38.76	4.96
1588	5271	4.918360	CCGGGATGGGGATGGGGA	62.918	72.222	0.00	0.00	0.00	4.81
1589	5272	2.532715	CGGGATGGGGATGGGGAT	60.533	66.667	0.00	0.00	0.00	3.85
1590	5273	2.910737	CGGGATGGGGATGGGGATG	61.911	68.421	0.00	0.00	0.00	3.51
1591	5274	2.551413	GGGATGGGGATGGGGATGG	61.551	68.421	0.00	0.00	0.00	3.51
1592	5275	2.551413	GGATGGGGATGGGGATGGG	61.551	68.421	0.00	0.00	0.00	4.00
1593	5276	2.455122	ATGGGGATGGGGATGGGG	60.455	66.667	0.00	0.00	0.00	4.96
1594	5277	3.078909	ATGGGGATGGGGATGGGGA	62.079	63.158	0.00	0.00	0.00	4.81
1595	5278	2.120854	GGGGATGGGGATGGGGAT	60.121	66.667	0.00	0.00	0.00	3.85
1596	5279	2.551413	GGGGATGGGGATGGGGATG	61.551	68.421	0.00	0.00	0.00	3.51
1597	5280	2.551413	GGGATGGGGATGGGGATGG	61.551	68.421	0.00	0.00	0.00	3.51
1598	5281	1.465986	GGATGGGGATGGGGATGGA	60.466	63.158	0.00	0.00	0.00	3.41
1599	5282	1.504275	GGATGGGGATGGGGATGGAG	61.504	65.000	0.00	0.00	0.00	3.86
1600	5283	0.476415	GATGGGGATGGGGATGGAGA	60.476	60.000	0.00	0.00	0.00	3.71
1876	5583	6.381133	TCAAGAGCAGATCATGTCTAACCTAA	59.619	38.462	0.00	0.00	34.69	2.69
2017	5745	5.351465	TCTCTCGCATCCATTCTACAAAAAC	59.649	40.000	0.00	0.00	0.00	2.43
2452	6196	0.179043	TGCAGTTTACGGCTTCCACA	60.179	50.000	6.56	0.00	37.92	4.17
2797	6580	7.148137	GGTTACCTACATACCTTGGAATTGTTG	60.148	40.741	0.00	0.00	0.00	3.33
4592	12146	4.123497	GGCCTGGTGGACATTAATTTTC	57.877	45.455	0.00	0.00	42.34	2.29
4593	12147	3.118775	GGCCTGGTGGACATTAATTTTCC	60.119	47.826	0.00	6.06	42.34	3.13
4594	12148	3.513515	GCCTGGTGGACATTAATTTTCCA	59.486	43.478	10.41	10.41	37.07	3.53
4601	12155	6.773976	TGGACATTAATTTTCCACATCCTC	57.226	37.500	10.41	0.00	34.35	3.71
4602	12156	5.656416	TGGACATTAATTTTCCACATCCTCC	59.344	40.000	10.41	0.00	34.35	4.30
4603	12157	5.893824	GGACATTAATTTTCCACATCCTCCT	59.106	40.000	7.69	0.00	0.00	3.69
4604	12158	6.039829	GGACATTAATTTTCCACATCCTCCTC	59.960	42.308	7.69	0.00	0.00	3.71
4612	12181	4.837093	TCCACATCCTCCTCGTTTTATT	57.163	40.909	0.00	0.00	0.00	1.40
4644	12213	1.606313	ACCAGGCGTCCAAAATGGG	60.606	57.895	0.00	0.00	38.32	4.00
4645	12214	1.606313	CCAGGCGTCCAAAATGGGT	60.606	57.895	0.00	0.00	38.32	4.51
4646	12215	1.586028	CAGGCGTCCAAAATGGGTG	59.414	57.895	0.00	0.00	38.32	4.61
4647	12216	1.606313	AGGCGTCCAAAATGGGTGG	60.606	57.895	0.00	0.00	38.32	4.61
4648	12217	2.261361	GCGTCCAAAATGGGTGGC	59.739	61.111	0.00	0.00	38.32	5.01
4649	12218	2.969827	CGTCCAAAATGGGTGGCC	59.030	61.111	0.00	0.00	38.32	5.36
4650	12219	1.606313	CGTCCAAAATGGGTGGCCT	60.606	57.895	3.32	0.00	38.32	5.19
4651	12220	1.876497	CGTCCAAAATGGGTGGCCTG	61.876	60.000	3.32	0.00	38.32	4.85
4652	12221	1.229145	TCCAAAATGGGTGGCCTGG	60.229	57.895	3.32	0.00	38.32	4.45
4653	12222	1.229145	CCAAAATGGGTGGCCTGGA	60.229	57.895	3.32	0.00	32.67	3.86
4654	12223	1.543944	CCAAAATGGGTGGCCTGGAC	61.544	60.000	3.32	0.00	32.67	4.02
4655	12224	1.229177	AAAATGGGTGGCCTGGACC	60.229	57.895	3.32	2.54	0.00	4.46
4656	12225	2.029892	AAAATGGGTGGCCTGGACCA	62.030	55.000	12.53	11.19	37.38	4.02
4657	12226	2.445492	AAATGGGTGGCCTGGACCAG	62.445	60.000	15.15	15.15	41.46	4.00
4675	12244	2.047274	GCTAACCGTGCTGCCTCA	60.047	61.111	0.00	0.00	0.00	3.86
4676	12245	1.450312	GCTAACCGTGCTGCCTCAT	60.450	57.895	0.00	0.00	0.00	2.90
4677	12246	1.709147	GCTAACCGTGCTGCCTCATG	61.709	60.000	0.00	0.00	0.00	3.07
4678	12247	1.709147	CTAACCGTGCTGCCTCATGC	61.709	60.000	0.00	0.00	41.77	4.06
4679	12248	2.184020	TAACCGTGCTGCCTCATGCT	62.184	55.000	0.00	0.00	42.00	3.79
4680	12249	2.749044	CCGTGCTGCCTCATGCTT	60.749	61.111	0.00	0.00	42.00	3.91
4681	12250	1.450134	CCGTGCTGCCTCATGCTTA	60.450	57.895	0.00	0.00	42.00	3.09
4682	12251	1.434622	CCGTGCTGCCTCATGCTTAG	61.435	60.000	0.00	0.00	42.00	2.18
4683	12252	0.742281	CGTGCTGCCTCATGCTTAGT	60.742	55.000	0.00	0.00	42.00	2.24
4684	12253	1.012841	GTGCTGCCTCATGCTTAGTC	58.987	55.000	0.00	0.00	42.00	2.59
4685	12254	0.107508	TGCTGCCTCATGCTTAGTCC	60.108	55.000	0.00	0.00	42.00	3.85
4686	12255	0.179936	GCTGCCTCATGCTTAGTCCT	59.820	55.000	0.00	0.00	42.00	3.85
4687	12256	1.950828	CTGCCTCATGCTTAGTCCTG	58.049	55.000	0.00	0.00	42.00	3.86
4688	12257	0.543277	TGCCTCATGCTTAGTCCTGG	59.457	55.000	0.00	0.00	42.00	4.45
4689	12258	0.817229	GCCTCATGCTTAGTCCTGGC	60.817	60.000	0.00	0.00	36.87	4.85
4690	12259	0.179034	CCTCATGCTTAGTCCTGGCC	60.179	60.000	0.00	0.00	0.00	5.36
4691	12260	0.543277	CTCATGCTTAGTCCTGGCCA	59.457	55.000	4.71	4.71	0.00	5.36
4692	12261	1.142465	CTCATGCTTAGTCCTGGCCAT	59.858	52.381	5.51	0.00	0.00	4.40
4693	12262	1.134007	TCATGCTTAGTCCTGGCCATG	60.134	52.381	5.51	2.84	0.00	3.66
4694	12263	0.184451	ATGCTTAGTCCTGGCCATGG	59.816	55.000	5.51	7.63	0.00	3.66
4695	12264	1.152881	GCTTAGTCCTGGCCATGGG	60.153	63.158	15.13	4.96	0.00	4.00
4696	12265	1.635817	GCTTAGTCCTGGCCATGGGA	61.636	60.000	15.13	8.01	0.00	4.37
4697	12266	0.918983	CTTAGTCCTGGCCATGGGAA	59.081	55.000	15.05	8.86	33.01	3.97
4698	12267	0.918983	TTAGTCCTGGCCATGGGAAG	59.081	55.000	15.05	0.00	33.01	3.46
4699	12268	1.635817	TAGTCCTGGCCATGGGAAGC	61.636	60.000	15.05	4.61	33.01	3.86
4719	12288	4.116328	GGCTCGGCCCGAAAAAGC	62.116	66.667	7.50	6.95	44.06	3.51
4720	12289	4.116328	GCTCGGCCCGAAAAAGCC	62.116	66.667	7.50	0.00	46.17	4.35
4724	12293	3.744719	GGCCCGAAAAAGCCCGAC	61.745	66.667	0.00	0.00	43.76	4.79
4725	12294	3.744719	GCCCGAAAAAGCCCGACC	61.745	66.667	0.00	0.00	0.00	4.79
4726	12295	3.428282	CCCGAAAAAGCCCGACCG	61.428	66.667	0.00	0.00	0.00	4.79
4727	12296	3.428282	CCGAAAAAGCCCGACCGG	61.428	66.667	0.00	0.00	0.00	5.28
4745	12314	4.816984	GCCTGGCCTGATGCTGCT	62.817	66.667	11.88	0.00	40.92	4.24
4746	12315	2.516460	CCTGGCCTGATGCTGCTC	60.516	66.667	11.88	0.00	40.92	4.26
4747	12316	2.516460	CTGGCCTGATGCTGCTCC	60.516	66.667	3.32	0.00	40.92	4.70
4748	12317	4.119363	TGGCCTGATGCTGCTCCC	62.119	66.667	3.32	0.00	40.92	4.30
4751	12320	4.559063	CCTGATGCTGCTCCCGGG	62.559	72.222	16.85	16.85	0.00	5.73
4776	12345	1.406898	GCTTGGGCCTAGATTTTGAGC	59.593	52.381	19.48	0.00	0.00	4.26
4777	12346	2.027385	CTTGGGCCTAGATTTTGAGCC	58.973	52.381	9.57	0.00	43.09	4.70
4778	12347	1.298953	TGGGCCTAGATTTTGAGCCT	58.701	50.000	4.53	0.00	43.36	4.58
4779	12348	1.064463	TGGGCCTAGATTTTGAGCCTG	60.064	52.381	4.53	0.00	43.36	4.85
4780	12349	1.212935	GGGCCTAGATTTTGAGCCTGA	59.787	52.381	0.84	0.00	43.36	3.86
4781	12350	2.357154	GGGCCTAGATTTTGAGCCTGAA	60.357	50.000	0.84	0.00	43.36	3.02
4782	12351	2.948315	GGCCTAGATTTTGAGCCTGAAG	59.052	50.000	0.00	0.00	40.57	3.02
4783	12352	2.948315	GCCTAGATTTTGAGCCTGAAGG	59.052	50.000	0.00	0.00	38.53	3.46
4816	12385	2.596338	CCCGGGCCTGTCGTTTTT	60.596	61.111	8.08	0.00	0.00	1.94
4817	12386	2.642700	CCGGGCCTGTCGTTTTTG	59.357	61.111	11.58	0.00	0.00	2.44
4818	12387	2.050442	CGGGCCTGTCGTTTTTGC	60.050	61.111	2.29	0.00	0.00	3.68
4819	12388	2.840066	CGGGCCTGTCGTTTTTGCA	61.840	57.895	2.29	0.00	0.00	4.08
4820	12389	1.439644	GGGCCTGTCGTTTTTGCAA	59.560	52.632	0.84	0.00	0.00	4.08
4821	12390	0.033366	GGGCCTGTCGTTTTTGCAAT	59.967	50.000	0.84	0.00	0.00	3.56
4822	12391	1.540146	GGGCCTGTCGTTTTTGCAATT	60.540	47.619	0.84	0.00	0.00	2.32
4823	12392	2.209273	GGCCTGTCGTTTTTGCAATTT	58.791	42.857	0.00	0.00	0.00	1.82
4824	12393	2.220824	GGCCTGTCGTTTTTGCAATTTC	59.779	45.455	0.00	0.00	0.00	2.17
4825	12394	2.220824	GCCTGTCGTTTTTGCAATTTCC	59.779	45.455	0.00	0.00	0.00	3.13
4826	12395	2.799978	CCTGTCGTTTTTGCAATTTCCC	59.200	45.455	0.00	0.00	0.00	3.97
4827	12396	2.464865	TGTCGTTTTTGCAATTTCCCG	58.535	42.857	0.00	0.00	0.00	5.14
4828	12397	2.099263	TGTCGTTTTTGCAATTTCCCGA	59.901	40.909	0.00	1.52	0.00	5.14
4829	12398	3.117046	GTCGTTTTTGCAATTTCCCGAA	58.883	40.909	0.00	0.00	0.00	4.30
4830	12399	3.181575	GTCGTTTTTGCAATTTCCCGAAG	59.818	43.478	0.00	0.00	0.00	3.79
4831	12400	3.066900	TCGTTTTTGCAATTTCCCGAAGA	59.933	39.130	0.00	0.00	0.00	2.87
4832	12401	3.425193	CGTTTTTGCAATTTCCCGAAGAG	59.575	43.478	0.00	0.00	0.00	2.85
4833	12402	3.658757	TTTTGCAATTTCCCGAAGAGG	57.341	42.857	0.00	0.00	40.63	3.69
4834	12403	0.887933	TTGCAATTTCCCGAAGAGGC	59.112	50.000	0.00	0.00	39.21	4.70
4835	12404	0.965363	TGCAATTTCCCGAAGAGGCC	60.965	55.000	0.00	0.00	39.21	5.19
4836	12405	0.681243	GCAATTTCCCGAAGAGGCCT	60.681	55.000	3.86	3.86	39.21	5.19
4837	12406	1.098050	CAATTTCCCGAAGAGGCCTG	58.902	55.000	12.00	0.00	39.21	4.85
4838	12407	0.034089	AATTTCCCGAAGAGGCCTGG	60.034	55.000	12.00	4.39	39.21	4.45
4839	12408	2.558380	ATTTCCCGAAGAGGCCTGGC	62.558	60.000	12.00	11.05	39.21	4.85
4867	12436	3.913089	CCTGTTGGGCTTTTATGTGTTC	58.087	45.455	0.00	0.00	0.00	3.18
4868	12437	3.564511	CTGTTGGGCTTTTATGTGTTCG	58.435	45.455	0.00	0.00	0.00	3.95
4869	12438	2.294791	TGTTGGGCTTTTATGTGTTCGG	59.705	45.455	0.00	0.00	0.00	4.30
4870	12439	1.540267	TGGGCTTTTATGTGTTCGGG	58.460	50.000	0.00	0.00	0.00	5.14
4871	12440	0.172578	GGGCTTTTATGTGTTCGGGC	59.827	55.000	0.00	0.00	0.00	6.13
4872	12441	1.173913	GGCTTTTATGTGTTCGGGCT	58.826	50.000	0.00	0.00	0.00	5.19
4873	12442	1.135402	GGCTTTTATGTGTTCGGGCTG	60.135	52.381	0.00	0.00	0.00	4.85
4874	12443	1.135402	GCTTTTATGTGTTCGGGCTGG	60.135	52.381	0.00	0.00	0.00	4.85
4875	12444	1.472480	CTTTTATGTGTTCGGGCTGGG	59.528	52.381	0.00	0.00	0.00	4.45
4876	12445	0.963355	TTTATGTGTTCGGGCTGGGC	60.963	55.000	0.00	0.00	0.00	5.36
4877	12446	1.847798	TTATGTGTTCGGGCTGGGCT	61.848	55.000	0.00	0.00	0.00	5.19
4878	12447	1.847798	TATGTGTTCGGGCTGGGCTT	61.848	55.000	0.00	0.00	0.00	4.35
4879	12448	3.365265	GTGTTCGGGCTGGGCTTG	61.365	66.667	0.00	0.00	0.00	4.01
4880	12449	4.659172	TGTTCGGGCTGGGCTTGG	62.659	66.667	0.00	0.00	0.00	3.61
4894	12463	0.608130	GCTTGGGCCTAAAAACCAGG	59.392	55.000	4.53	0.00	35.37	4.45
4902	12471	2.102578	CCTAAAAACCAGGCCTGATGG	58.897	52.381	34.91	21.25	43.87	3.51
4926	12495	2.437897	CAGGCTCAGGCTTGGGTT	59.562	61.111	0.00	0.00	41.09	4.11
4927	12496	1.228675	CAGGCTCAGGCTTGGGTTT	60.229	57.895	0.00	0.00	41.09	3.27
4928	12497	0.829182	CAGGCTCAGGCTTGGGTTTT	60.829	55.000	0.00	0.00	41.09	2.43
4929	12498	0.105504	AGGCTCAGGCTTGGGTTTTT	60.106	50.000	0.00	0.00	33.67	1.94
4947	12516	2.507407	TTTACTTGGGCTTGGCTAGG	57.493	50.000	0.00	0.00	0.00	3.02

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
177	178	1.278413	GGGAGGGTCCAGTAAAGTCAC	59.722	57.143	0.00	0.00	38.64	3.67
195	196	6.252967	TGAAATATATTATGCAGCGTTGGG	57.747	37.500	0.16	0.00	0.00	4.12
357	358	4.594920	TGAACCCAAAATGCCCTTCATTAA	59.405	37.500	0.00	0.00	44.23	1.40
518	519	9.838975	CAGACAATAGTGTAAATTGTTGCATTA	57.161	29.630	0.00	0.00	45.24	1.90
567	569	1.476891	TCGTGTCACAGCCCTAGAATC	59.523	52.381	3.42	0.00	0.00	2.52
775	805	6.263168	CCACTGGATCGCCTTTTCTTTATTAT	59.737	38.462	0.00	0.00	34.31	1.28
776	806	5.588648	CCACTGGATCGCCTTTTCTTTATTA	59.411	40.000	0.00	0.00	34.31	0.98
777	807	4.399303	CCACTGGATCGCCTTTTCTTTATT	59.601	41.667	0.00	0.00	34.31	1.40
861	892	0.179234	TTTCAACCAGACAGACGCCA	59.821	50.000	0.00	0.00	0.00	5.69
921	952	4.081420	TGAGAAGAGAAGACATGGCTAACC	60.081	45.833	0.00	0.00	0.00	2.85
922	953	5.078411	TGAGAAGAGAAGACATGGCTAAC	57.922	43.478	0.00	0.00	0.00	2.34
923	954	4.382470	GCTGAGAAGAGAAGACATGGCTAA	60.382	45.833	0.00	0.00	0.00	3.09
927	958	2.419851	GGGCTGAGAAGAGAAGACATGG	60.420	54.545	0.00	0.00	0.00	3.66
931	962	1.066502	GGTGGGCTGAGAAGAGAAGAC	60.067	57.143	0.00	0.00	0.00	3.01
936	967	1.818642	CTTTGGTGGGCTGAGAAGAG	58.181	55.000	0.00	0.00	0.00	2.85
943	974	1.114722	TTTCTGGCTTTGGTGGGCTG	61.115	55.000	0.00	0.00	0.00	4.85
1016	1103	2.526873	CCCCCTCCGTCCCCATAG	60.527	72.222	0.00	0.00	0.00	2.23
1067	1161	2.240162	CTTCCCGAGTTTCCTCCCCG	62.240	65.000	0.00	0.00	33.93	5.73
1577	5260	3.078909	ATCCCCATCCCCATCCCCA	62.079	63.158	0.00	0.00	0.00	4.96
1578	5261	2.120854	ATCCCCATCCCCATCCCC	60.121	66.667	0.00	0.00	0.00	4.81
1579	5262	2.551413	CCATCCCCATCCCCATCCC	61.551	68.421	0.00	0.00	0.00	3.85
1580	5263	1.465986	TCCATCCCCATCCCCATCC	60.466	63.158	0.00	0.00	0.00	3.51
1581	5264	0.476415	TCTCCATCCCCATCCCCATC	60.476	60.000	0.00	0.00	0.00	3.51
1582	5265	0.200522	ATCTCCATCCCCATCCCCAT	59.799	55.000	0.00	0.00	0.00	4.00
1583	5266	0.773305	CATCTCCATCCCCATCCCCA	60.773	60.000	0.00	0.00	0.00	4.96
1584	5267	1.504275	CCATCTCCATCCCCATCCCC	61.504	65.000	0.00	0.00	0.00	4.81
1585	5268	0.476415	TCCATCTCCATCCCCATCCC	60.476	60.000	0.00	0.00	0.00	3.85
1586	5269	0.990374	CTCCATCTCCATCCCCATCC	59.010	60.000	0.00	0.00	0.00	3.51
1587	5270	2.035910	TCTCCATCTCCATCCCCATC	57.964	55.000	0.00	0.00	0.00	3.51
1588	5271	2.276391	CATCTCCATCTCCATCCCCAT	58.724	52.381	0.00	0.00	0.00	4.00
1589	5272	1.738474	CATCTCCATCTCCATCCCCA	58.262	55.000	0.00	0.00	0.00	4.96
1590	5273	0.990374	CCATCTCCATCTCCATCCCC	59.010	60.000	0.00	0.00	0.00	4.81
1591	5274	1.907936	CTCCATCTCCATCTCCATCCC	59.092	57.143	0.00	0.00	0.00	3.85
1592	5275	2.899975	TCTCCATCTCCATCTCCATCC	58.100	52.381	0.00	0.00	0.00	3.51
1593	5276	3.198200	CCATCTCCATCTCCATCTCCATC	59.802	52.174	0.00	0.00	0.00	3.51
1594	5277	3.181398	TCCATCTCCATCTCCATCTCCAT	60.181	47.826	0.00	0.00	0.00	3.41
1595	5278	2.180751	TCCATCTCCATCTCCATCTCCA	59.819	50.000	0.00	0.00	0.00	3.86
1596	5279	2.833338	CTCCATCTCCATCTCCATCTCC	59.167	54.545	0.00	0.00	0.00	3.71
1597	5280	3.777087	TCTCCATCTCCATCTCCATCTC	58.223	50.000	0.00	0.00	0.00	2.75
1598	5281	3.919304	TCTCCATCTCCATCTCCATCT	57.081	47.619	0.00	0.00	0.00	2.90
1599	5282	3.198200	CCATCTCCATCTCCATCTCCATC	59.802	52.174	0.00	0.00	0.00	3.51
1600	5283	3.181398	TCCATCTCCATCTCCATCTCCAT	60.181	47.826	0.00	0.00	0.00	3.41
1876	5583	1.216990	AGATTTTCATCGAGGGGCCT	58.783	50.000	0.84	0.00	34.17	5.19
2017	5745	3.834813	TCGGAAGATATGGGGATTCTGAG	59.165	47.826	0.00	0.00	33.31	3.35
2234	5965	6.206634	AGAGAGGAAAAGATAGCTAGATGACG	59.793	42.308	0.00	0.00	0.00	4.35
2488	6232	3.068732	TGATTGAGTAGATCTCCAAGGCG	59.931	47.826	0.00	0.00	42.12	5.52
2797	6580	7.360575	ACCTTAAACGAATCTGATTACACAC	57.639	36.000	2.28	0.00	0.00	3.82
4531	12052	3.419793	CCTGGTGAGGCAAGAACAA	57.580	52.632	0.00	0.00	30.52	2.83
4560	12081	1.920835	ACCAGGCCAGACCCTCTTC	60.921	63.158	5.01	0.00	40.58	2.87
4561	12082	2.208349	ACCAGGCCAGACCCTCTT	59.792	61.111	5.01	0.00	40.58	2.85
4562	12083	2.608988	CACCAGGCCAGACCCTCT	60.609	66.667	5.01	0.00	40.58	3.69
4564	12085	4.270153	TCCACCAGGCCAGACCCT	62.270	66.667	5.01	0.00	40.58	4.34
4583	12137	5.755849	ACGAGGAGGATGTGGAAAATTAAT	58.244	37.500	0.00	0.00	0.00	1.40
4584	12138	5.174037	ACGAGGAGGATGTGGAAAATTAA	57.826	39.130	0.00	0.00	0.00	1.40
4588	12142	3.502123	AAACGAGGAGGATGTGGAAAA	57.498	42.857	0.00	0.00	0.00	2.29
4589	12143	3.502123	AAAACGAGGAGGATGTGGAAA	57.498	42.857	0.00	0.00	0.00	3.13
4592	12146	5.414454	TGAAAATAAAACGAGGAGGATGTGG	59.586	40.000	0.00	0.00	0.00	4.17
4593	12147	6.403636	CCTGAAAATAAAACGAGGAGGATGTG	60.404	42.308	0.00	0.00	0.00	3.21
4594	12148	5.648092	CCTGAAAATAAAACGAGGAGGATGT	59.352	40.000	0.00	0.00	0.00	3.06
4595	12149	5.449177	GCCTGAAAATAAAACGAGGAGGATG	60.449	44.000	0.00	0.00	0.00	3.51
4596	12150	4.640647	GCCTGAAAATAAAACGAGGAGGAT	59.359	41.667	0.00	0.00	0.00	3.24
4598	12152	4.010349	AGCCTGAAAATAAAACGAGGAGG	58.990	43.478	0.00	0.00	0.00	4.30
4599	12153	4.695455	TCAGCCTGAAAATAAAACGAGGAG	59.305	41.667	0.00	0.00	0.00	3.69
4601	12155	5.335127	CATCAGCCTGAAAATAAAACGAGG	58.665	41.667	0.00	0.00	0.00	4.63
4602	12156	4.795278	GCATCAGCCTGAAAATAAAACGAG	59.205	41.667	0.00	0.00	33.58	4.18
4603	12157	4.217334	TGCATCAGCCTGAAAATAAAACGA	59.783	37.500	0.00	0.00	41.13	3.85
4604	12158	4.324402	GTGCATCAGCCTGAAAATAAAACG	59.676	41.667	0.00	0.00	41.13	3.60
4612	12181	0.609957	CCTGGTGCATCAGCCTGAAA	60.610	55.000	22.09	0.00	41.13	2.69
4632	12201	2.969827	GGCCACCCATTTTGGACG	59.030	61.111	0.00	0.00	40.96	4.79
4649	12218	1.079127	CACGGTTAGCCTGGTCCAG	60.079	63.158	12.40	12.40	0.00	3.86
4650	12219	3.065306	CACGGTTAGCCTGGTCCA	58.935	61.111	0.00	0.00	0.00	4.02
4651	12220	2.436115	GCACGGTTAGCCTGGTCC	60.436	66.667	0.00	0.00	0.00	4.46
4652	12221	1.741770	CAGCACGGTTAGCCTGGTC	60.742	63.158	0.00	0.00	0.00	4.02
4653	12222	2.347490	CAGCACGGTTAGCCTGGT	59.653	61.111	0.00	0.00	0.00	4.00
4654	12223	3.127533	GCAGCACGGTTAGCCTGG	61.128	66.667	0.00	0.00	0.00	4.45
4655	12224	3.127533	GGCAGCACGGTTAGCCTG	61.128	66.667	7.73	0.69	43.70	4.85
4658	12227	1.450312	ATGAGGCAGCACGGTTAGC	60.450	57.895	0.00	0.00	0.00	3.09
4659	12228	1.709147	GCATGAGGCAGCACGGTTAG	61.709	60.000	0.00	0.00	43.97	2.34
4675	12244	0.184451	CCATGGCCAGGACTAAGCAT	59.816	55.000	21.32	0.00	0.00	3.79
4676	12245	1.609239	CCATGGCCAGGACTAAGCA	59.391	57.895	21.32	0.00	0.00	3.91
4677	12246	1.152881	CCCATGGCCAGGACTAAGC	60.153	63.158	21.32	0.00	0.00	3.09
4678	12247	0.918983	TTCCCATGGCCAGGACTAAG	59.081	55.000	21.32	0.51	0.00	2.18
4679	12248	0.918983	CTTCCCATGGCCAGGACTAA	59.081	55.000	21.32	8.83	0.00	2.24
4680	12249	1.635817	GCTTCCCATGGCCAGGACTA	61.636	60.000	21.32	1.89	0.00	2.59
4681	12250	2.988839	GCTTCCCATGGCCAGGACT	61.989	63.158	21.32	0.00	0.00	3.85
4682	12251	2.440980	GCTTCCCATGGCCAGGAC	60.441	66.667	21.32	2.25	0.00	3.85
4683	12252	3.743017	GGCTTCCCATGGCCAGGA	61.743	66.667	21.32	15.01	46.84	3.86
4689	12258	4.883354	GAGCCGGGCTTCCCATGG	62.883	72.222	24.71	4.14	45.83	3.66
4703	12272	4.116328	GGCTTTTTCGGGCCGAGC	62.116	66.667	29.30	26.70	38.91	5.03
4707	12276	3.744719	GTCGGGCTTTTTCGGGCC	61.745	66.667	0.00	0.00	46.89	5.80
4708	12277	3.744719	GGTCGGGCTTTTTCGGGC	61.745	66.667	0.00	0.00	0.00	6.13
4709	12278	3.428282	CGGTCGGGCTTTTTCGGG	61.428	66.667	0.00	0.00	0.00	5.14
4710	12279	3.428282	CCGGTCGGGCTTTTTCGG	61.428	66.667	0.74	0.00	0.00	4.30
4728	12297	4.816984	AGCAGCATCAGGCCAGGC	62.817	66.667	5.01	1.26	46.50	4.85
4729	12298	2.516460	GAGCAGCATCAGGCCAGG	60.516	66.667	5.01	0.00	46.50	4.45
4730	12299	2.516460	GGAGCAGCATCAGGCCAG	60.516	66.667	5.01	0.00	46.50	4.85
4731	12300	4.119363	GGGAGCAGCATCAGGCCA	62.119	66.667	5.01	0.00	46.50	5.36
4734	12303	4.559063	CCCGGGAGCAGCATCAGG	62.559	72.222	18.48	0.00	0.00	3.86
4756	12325	1.406898	GCTCAAAATCTAGGCCCAAGC	59.593	52.381	0.00	0.00	38.76	4.01
4757	12326	2.027385	GGCTCAAAATCTAGGCCCAAG	58.973	52.381	0.00	0.00	37.12	3.61
4758	12327	1.640670	AGGCTCAAAATCTAGGCCCAA	59.359	47.619	0.00	0.00	43.36	4.12
4759	12328	1.064463	CAGGCTCAAAATCTAGGCCCA	60.064	52.381	0.00	0.00	43.36	5.36
4760	12329	1.212935	TCAGGCTCAAAATCTAGGCCC	59.787	52.381	0.00	0.00	43.36	5.80
4761	12330	2.717639	TCAGGCTCAAAATCTAGGCC	57.282	50.000	0.00	0.00	42.74	5.19
4762	12331	2.948315	CCTTCAGGCTCAAAATCTAGGC	59.052	50.000	0.00	0.00	38.50	3.93
4799	12368	2.596338	AAAAACGACAGGCCCGGG	60.596	61.111	19.09	19.09	0.00	5.73
4800	12369	2.642700	CAAAAACGACAGGCCCGG	59.357	61.111	0.00	0.00	0.00	5.73
4801	12370	2.050442	GCAAAAACGACAGGCCCG	60.050	61.111	0.00	0.00	0.00	6.13
4802	12371	0.033366	ATTGCAAAAACGACAGGCCC	59.967	50.000	1.71	0.00	0.00	5.80
4803	12372	1.864565	AATTGCAAAAACGACAGGCC	58.135	45.000	1.71	0.00	0.00	5.19
4804	12373	2.220824	GGAAATTGCAAAAACGACAGGC	59.779	45.455	1.71	0.00	0.00	4.85
4805	12374	2.799978	GGGAAATTGCAAAAACGACAGG	59.200	45.455	1.71	0.00	0.00	4.00
4806	12375	2.470999	CGGGAAATTGCAAAAACGACAG	59.529	45.455	1.71	0.00	0.00	3.51
4807	12376	2.099263	TCGGGAAATTGCAAAAACGACA	59.901	40.909	1.71	0.00	0.00	4.35
4808	12377	2.733517	TCGGGAAATTGCAAAAACGAC	58.266	42.857	1.71	0.00	0.00	4.34
4809	12378	3.066900	TCTTCGGGAAATTGCAAAAACGA	59.933	39.130	1.71	7.09	0.00	3.85
4810	12379	3.376540	TCTTCGGGAAATTGCAAAAACG	58.623	40.909	1.71	4.64	0.00	3.60
4811	12380	3.740832	CCTCTTCGGGAAATTGCAAAAAC	59.259	43.478	1.71	0.00	0.00	2.43
4812	12381	3.801983	GCCTCTTCGGGAAATTGCAAAAA	60.802	43.478	1.71	0.00	0.00	1.94
4813	12382	2.288763	GCCTCTTCGGGAAATTGCAAAA	60.289	45.455	1.71	0.00	0.00	2.44
4814	12383	1.272212	GCCTCTTCGGGAAATTGCAAA	59.728	47.619	1.71	0.00	0.00	3.68
4815	12384	0.887933	GCCTCTTCGGGAAATTGCAA	59.112	50.000	0.00	0.00	0.00	4.08
4816	12385	0.965363	GGCCTCTTCGGGAAATTGCA	60.965	55.000	0.00	0.00	0.00	4.08
4817	12386	0.681243	AGGCCTCTTCGGGAAATTGC	60.681	55.000	0.00	0.00	0.00	3.56
4818	12387	1.098050	CAGGCCTCTTCGGGAAATTG	58.902	55.000	0.00	0.00	0.00	2.32
4819	12388	0.034089	CCAGGCCTCTTCGGGAAATT	60.034	55.000	0.00	0.00	0.00	1.82
4820	12389	1.609783	CCAGGCCTCTTCGGGAAAT	59.390	57.895	0.00	0.00	0.00	2.17
4821	12390	3.077907	CCAGGCCTCTTCGGGAAA	58.922	61.111	0.00	0.00	0.00	3.13
4822	12391	3.717294	GCCAGGCCTCTTCGGGAA	61.717	66.667	0.00	0.00	0.00	3.97
4846	12415	3.611530	CGAACACATAAAAGCCCAACAGG	60.612	47.826	0.00	0.00	39.47	4.00
4847	12416	3.564511	CGAACACATAAAAGCCCAACAG	58.435	45.455	0.00	0.00	0.00	3.16
4848	12417	2.294791	CCGAACACATAAAAGCCCAACA	59.705	45.455	0.00	0.00	0.00	3.33
4849	12418	2.352323	CCCGAACACATAAAAGCCCAAC	60.352	50.000	0.00	0.00	0.00	3.77
4850	12419	1.889829	CCCGAACACATAAAAGCCCAA	59.110	47.619	0.00	0.00	0.00	4.12
4851	12420	1.540267	CCCGAACACATAAAAGCCCA	58.460	50.000	0.00	0.00	0.00	5.36
4852	12421	0.172578	GCCCGAACACATAAAAGCCC	59.827	55.000	0.00	0.00	0.00	5.19
4853	12422	1.135402	CAGCCCGAACACATAAAAGCC	60.135	52.381	0.00	0.00	0.00	4.35
4854	12423	1.135402	CCAGCCCGAACACATAAAAGC	60.135	52.381	0.00	0.00	0.00	3.51
4855	12424	1.472480	CCCAGCCCGAACACATAAAAG	59.528	52.381	0.00	0.00	0.00	2.27
4856	12425	1.540267	CCCAGCCCGAACACATAAAA	58.460	50.000	0.00	0.00	0.00	1.52
4857	12426	0.963355	GCCCAGCCCGAACACATAAA	60.963	55.000	0.00	0.00	0.00	1.40
4858	12427	1.377987	GCCCAGCCCGAACACATAA	60.378	57.895	0.00	0.00	0.00	1.90
4859	12428	1.847798	AAGCCCAGCCCGAACACATA	61.848	55.000	0.00	0.00	0.00	2.29
4860	12429	3.210012	AAGCCCAGCCCGAACACAT	62.210	57.895	0.00	0.00	0.00	3.21
4861	12430	3.884774	AAGCCCAGCCCGAACACA	61.885	61.111	0.00	0.00	0.00	3.72
4862	12431	3.365265	CAAGCCCAGCCCGAACAC	61.365	66.667	0.00	0.00	0.00	3.32
4863	12432	4.659172	CCAAGCCCAGCCCGAACA	62.659	66.667	0.00	0.00	0.00	3.18
4875	12444	0.608130	CCTGGTTTTTAGGCCCAAGC	59.392	55.000	0.00	0.00	38.76	4.01
4882	12451	2.102578	CCATCAGGCCTGGTTTTTAGG	58.897	52.381	32.23	18.53	38.39	2.69
4909	12478	0.829182	AAAACCCAAGCCTGAGCCTG	60.829	55.000	0.00	0.00	41.25	4.85
4910	12479	0.105504	AAAAACCCAAGCCTGAGCCT	60.106	50.000	0.00	0.00	41.25	4.58
4911	12480	2.440946	AAAAACCCAAGCCTGAGCC	58.559	52.632	0.00	0.00	41.25	4.70
4926	12495	3.161866	CCTAGCCAAGCCCAAGTAAAAA	58.838	45.455	0.00	0.00	0.00	1.94
4927	12496	2.802719	CCTAGCCAAGCCCAAGTAAAA	58.197	47.619	0.00	0.00	0.00	1.52
4928	12497	1.615919	GCCTAGCCAAGCCCAAGTAAA	60.616	52.381	0.00	0.00	0.00	2.01
4929	12498	0.034477	GCCTAGCCAAGCCCAAGTAA	60.034	55.000	0.00	0.00	0.00	2.24
4930	12499	1.607612	GCCTAGCCAAGCCCAAGTA	59.392	57.895	0.00	0.00	0.00	2.24
4931	12500	2.356667	GCCTAGCCAAGCCCAAGT	59.643	61.111	0.00	0.00	0.00	3.16
4960	12529	4.599041	AGCATGACTATACCTGGCAAAAA	58.401	39.130	0.00	0.00	0.00	1.94
4961	12530	4.199310	GAGCATGACTATACCTGGCAAAA	58.801	43.478	0.00	0.00	0.00	2.44
4962	12531	3.433598	GGAGCATGACTATACCTGGCAAA	60.434	47.826	0.00	0.00	0.00	3.68
4963	12532	2.104792	GGAGCATGACTATACCTGGCAA	59.895	50.000	0.00	0.00	0.00	4.52
4964	12533	1.694150	GGAGCATGACTATACCTGGCA	59.306	52.381	0.00	0.00	0.00	4.92
4965	12534	1.694150	TGGAGCATGACTATACCTGGC	59.306	52.381	0.00	0.00	0.00	4.85
4966	12535	3.055530	GGATGGAGCATGACTATACCTGG	60.056	52.174	0.00	0.00	0.00	4.45
4967	12536	3.580022	TGGATGGAGCATGACTATACCTG	59.420	47.826	0.00	0.00	0.00	4.00
4968	12537	3.837146	CTGGATGGAGCATGACTATACCT	59.163	47.826	0.00	0.00	0.00	3.08
4969	12538	3.055530	CCTGGATGGAGCATGACTATACC	60.056	52.174	0.00	0.00	38.35	2.73
4970	12539	3.618507	GCCTGGATGGAGCATGACTATAC	60.619	52.174	0.00	0.00	38.35	1.47
4971	12540	2.568956	GCCTGGATGGAGCATGACTATA	59.431	50.000	0.00	0.00	38.35	1.31
4972	12541	1.350351	GCCTGGATGGAGCATGACTAT	59.650	52.381	0.00	0.00	38.35	2.12
4973	12542	0.761187	GCCTGGATGGAGCATGACTA	59.239	55.000	0.00	0.00	38.35	2.59
4974	12543	0.987081	AGCCTGGATGGAGCATGACT	60.987	55.000	0.00	0.00	38.35	3.41
4975	12544	0.761187	TAGCCTGGATGGAGCATGAC	59.239	55.000	0.00	0.00	38.35	3.06
4976	12545	1.141657	GTTAGCCTGGATGGAGCATGA	59.858	52.381	0.00	0.00	38.35	3.07
4977	12546	1.142465	AGTTAGCCTGGATGGAGCATG	59.858	52.381	0.00	0.00	38.35	4.06

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.