AutoCloner

Multiple sequence alignment - TraesCS1B01G055700

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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	TraesCS1B01G055700	chr1B	100.000	5060	0	0	1	5060	38594018	38588959	0.000000e+00	9345.0
1	TraesCS1B01G055700	chr1A	95.671	4158	139	17	914	5060	6072110	6067983	0.000000e+00	6643.0
2	TraesCS1B01G055700	chr1A	95.779	687	27	2	215	899	6072841	6072155	0.000000e+00	1107.0
3	TraesCS1B01G055700	chr1A	84.828	580	62	8	343	916	16478994	16478435	1.230000e-155	560.0
4	TraesCS1B01G055700	chr1A	82.353	425	47	16	914	1317	16478400	16477983	1.350000e-90	344.0
5	TraesCS1B01G055700	chr1A	93.220	118	8	0	215	332	20400700	20400817	1.870000e-39	174.0
6	TraesCS1B01G055700	chr3A	97.465	2919	65	6	969	3882	93565698	93568612	0.000000e+00	4972.0
7	TraesCS1B01G055700	chr3A	85.588	902	106	8	4181	5059	508450	509350	0.000000e+00	924.0
8	TraesCS1B01G055700	chr3A	95.446	549	23	1	370	916	93565122	93565670	0.000000e+00	874.0
9	TraesCS1B01G055700	chr3A	96.571	175	4	1	3883	4055	93568645	93568819	6.410000e-74	289.0
10	TraesCS1B01G055700	chr3A	72.621	515	92	35	4179	4666	538019767	538020259	1.910000e-24	124.0
11	TraesCS1B01G055700	chr3A	83.962	106	15	2	1851	1955	345577706	345577602	3.220000e-17	100.0
12	TraesCS1B01G055700	chr3A	100.000	31	0	0	3921	3951	93568621	93568651	1.970000e-04	58.4
13	TraesCS1B01G055700	chr7A	97.259	2919	71	6	969	3882	84693273	84696187	0.000000e+00	4939.0
14	TraesCS1B01G055700	chr7A	96.804	657	21	0	2951	3607	47816943	47817599	0.000000e+00	1098.0
15	TraesCS1B01G055700	chr7A	95.264	549	24	1	370	916	84692697	84693245	0.000000e+00	869.0
16	TraesCS1B01G055700	chr7A	80.509	903	134	21	4183	5059	674002958	674003844	0.000000e+00	654.0
17	TraesCS1B01G055700	chr7A	98.921	278	3	0	3605	3882	47819268	47819545	9.780000e-137	497.0
18	TraesCS1B01G055700	chr7A	97.143	175	3	1	3883	4055	47819578	47819752	1.380000e-75	294.0
19	TraesCS1B01G055700	chr7A	95.429	175	6	1	3883	4055	84696220	84696394	1.390000e-70	278.0
20	TraesCS1B01G055700	chr7A	72.452	893	197	30	4182	5059	8355118	8354260	1.820000e-59	241.0
21	TraesCS1B01G055700	chr7A	100.000	31	0	0	3921	3951	84696196	84696226	1.970000e-04	58.4
22	TraesCS1B01G055700	chr7A	100.000	29	0	0	3923	3951	47819556	47819584	3.000000e-03	54.7
23	TraesCS1B01G055700	chr4A	97.351	1699	42	2	2187	3882	636118429	636116731	0.000000e+00	2885.0
24	TraesCS1B01G055700	chr4A	96.832	1231	31	5	969	2193	636122051	636120823	0.000000e+00	2050.0
25	TraesCS1B01G055700	chr4A	95.281	551	21	3	371	916	636122629	636122079	0.000000e+00	869.0
26	TraesCS1B01G055700	chr4A	84.483	580	64	8	343	916	598523317	598522758	2.660000e-152	549.0
27	TraesCS1B01G055700	chr4A	82.353	425	47	16	914	1317	598522723	598522306	1.350000e-90	344.0
28	TraesCS1B01G055700	chr4A	96.571	175	4	1	3883	4055	636116698	636116524	6.410000e-74	289.0
29	TraesCS1B01G055700	chr4A	87.879	99	9	3	3486	3581	673443981	673443883	4.140000e-21	113.0
30	TraesCS1B01G055700	chr4A	100.000	31	0	0	3921	3951	636116722	636116692	1.970000e-04	58.4
31	TraesCS1B01G055700	chr7D	85.126	1748	171	42	1938	3631	111372089	111373801	0.000000e+00	1705.0
32	TraesCS1B01G055700	chr7D	83.515	734	110	9	4334	5059	46454764	46455494	0.000000e+00	675.0
33	TraesCS1B01G055700	chr7D	85.714	329	32	12	3330	3643	111396041	111396369	2.920000e-87	333.0
34	TraesCS1B01G055700	chr7D	86.594	276	33	2	343	616	29885473	29885200	8.230000e-78	302.0
35	TraesCS1B01G055700	chr7D	87.879	99	9	3	3486	3581	56942229	56942131	4.140000e-21	113.0
36	TraesCS1B01G055700	chr5B	92.624	705	49	2	215	916	315245572	315244868	0.000000e+00	1011.0
37	TraesCS1B01G055700	chr5B	94.198	586	32	2	914	1499	315244833	315244250	0.000000e+00	893.0
38	TraesCS1B01G055700	chr5B	83.040	908	117	26	4181	5059	107922677	107923576	0.000000e+00	789.0
39	TraesCS1B01G055700	chr5B	89.600	125	7	4	215	339	641167527	641167645	2.440000e-33	154.0
40	TraesCS1B01G055700	chr5B	94.595	37	2	0	4181	4217	622614778	622614814	1.970000e-04	58.4
41	TraesCS1B01G055700	chr5D	84.564	907	109	17	4182	5059	500227884	500226980	0.000000e+00	870.0
42	TraesCS1B01G055700	chr2B	89.818	658	59	7	2427	3080	557344745	557345398	0.000000e+00	837.0
43	TraesCS1B01G055700	chr2B	89.600	125	7	4	215	339	178451019	178451137	2.440000e-33	154.0
44	TraesCS1B01G055700	chr2B	73.797	374	59	22	4181	4522	50356457	50356823	1.490000e-20	111.0
45	TraesCS1B01G055700	chr2B	95.238	42	2	0	2246	2287	557344702	557344743	3.270000e-07	67.6
46	TraesCS1B01G055700	chr3B	89.666	658	59	8	2427	3080	817429020	817429672	0.000000e+00	830.0
47	TraesCS1B01G055700	chr3B	85.547	685	94	5	4376	5058	616188309	616187628	0.000000e+00	712.0
48	TraesCS1B01G055700	chr3D	89.498	657	62	6	2427	3080	462274468	462273816	0.000000e+00	824.0
49	TraesCS1B01G055700	chr3D	86.778	537	44	8	391	916	528127648	528127128	1.580000e-159	573.0
50	TraesCS1B01G055700	chr3D	85.553	533	53	8	391	916	553220809	553220294	2.070000e-148	536.0
51	TraesCS1B01G055700	chr3D	83.182	440	45	14	914	1332	528127093	528126662	4.780000e-100	375.0
52	TraesCS1B01G055700	chr3D	84.275	407	38	13	914	1299	553220259	553219858	1.720000e-99	374.0
53	TraesCS1B01G055700	chr3D	95.556	45	2	0	2246	2290	462274511	462274467	7.030000e-09	73.1
54	TraesCS1B01G055700	chr2D	83.479	914	118	16	4179	5059	467998741	467999654	0.000000e+00	821.0
55	TraesCS1B01G055700	chr2D	93.220	118	8	0	215	332	401947394	401947511	1.870000e-39	174.0
56	TraesCS1B01G055700	chr1D	83.128	895	118	17	4181	5047	178234420	178235309	0.000000e+00	785.0
57	TraesCS1B01G055700	chr1D	73.841	906	177	46	4181	5045	9086368	9085482	6.360000e-79	305.0
58	TraesCS1B01G055700	chr6D	84.538	692	104	3	4370	5059	10687320	10688010	0.000000e+00	682.0
59	TraesCS1B01G055700	chr6D	86.643	277	32	3	343	616	454645126	454644852	8.230000e-78	302.0
60	TraesCS1B01G055700	chr6D	88.889	90	9	1	1866	1955	86946036	86946124	5.360000e-20	110.0
61	TraesCS1B01G055700	chrUn	84.071	226	27	5	3427	3643	30148632	30148407	5.130000e-50	209.0
62	TraesCS1B01G055700	chr6A	94.309	123	6	1	215	337	60564694	60564815	2.410000e-43	187.0
63	TraesCS1B01G055700	chr2A	92.683	123	8	1	215	337	560736842	560736721	5.210000e-40	176.0
64	TraesCS1B01G055700	chr2A	89.076	119	13	0	221	339	314855271	314855389	1.140000e-31	148.0
65	TraesCS1B01G055700	chr4B	81.022	137	20	5	4182	4312	17826290	17826426	2.490000e-18	104.0
66	TraesCS1B01G055700	chr4B	77.869	122	19	7	4182	4299	2505489	2505372	9.090000e-08	69.4
67	TraesCS1B01G055700	chr6B	88.462	78	8	1	1878	1955	164861486	164861562	5.390000e-15	93.5
68	TraesCS1B01G055700	chr6B	79.167	144	17	13	4182	4317	23550446	23550308	2.510000e-13	87.9

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	TraesCS1B01G055700	chr1B	38588959	38594018	5059	True	9345.000	9345	100.0000	1	5060	1	chr1B.!!$R1	5059
1	TraesCS1B01G055700	chr1A	6067983	6072841	4858	True	3875.000	6643	95.7250	215	5060	2	chr1A.!!$R1	4845
2	TraesCS1B01G055700	chr1A	16477983	16478994	1011	True	452.000	560	83.5905	343	1317	2	chr1A.!!$R2	974
3	TraesCS1B01G055700	chr3A	93565122	93568819	3697	False	1548.350	4972	97.3705	370	4055	4	chr3A.!!$F3	3685
4	TraesCS1B01G055700	chr3A	508450	509350	900	False	924.000	924	85.5880	4181	5059	1	chr3A.!!$F1	878
5	TraesCS1B01G055700	chr7A	84692697	84696394	3697	False	1536.100	4939	96.9880	370	4055	4	chr7A.!!$F3	3685
6	TraesCS1B01G055700	chr7A	674002958	674003844	886	False	654.000	654	80.5090	4183	5059	1	chr7A.!!$F1	876
7	TraesCS1B01G055700	chr7A	47816943	47819752	2809	False	485.925	1098	98.2170	2951	4055	4	chr7A.!!$F2	1104
8	TraesCS1B01G055700	chr7A	8354260	8355118	858	True	241.000	241	72.4520	4182	5059	1	chr7A.!!$R1	877
9	TraesCS1B01G055700	chr4A	636116524	636122629	6105	True	1230.280	2885	97.2070	371	4055	5	chr4A.!!$R3	3684
10	TraesCS1B01G055700	chr4A	598522306	598523317	1011	True	446.500	549	83.4180	343	1317	2	chr4A.!!$R2	974
11	TraesCS1B01G055700	chr7D	111372089	111373801	1712	False	1705.000	1705	85.1260	1938	3631	1	chr7D.!!$F2	1693
12	TraesCS1B01G055700	chr7D	46454764	46455494	730	False	675.000	675	83.5150	4334	5059	1	chr7D.!!$F1	725
13	TraesCS1B01G055700	chr5B	315244250	315245572	1322	True	952.000	1011	93.4110	215	1499	2	chr5B.!!$R1	1284
14	TraesCS1B01G055700	chr5B	107922677	107923576	899	False	789.000	789	83.0400	4181	5059	1	chr5B.!!$F1	878
15	TraesCS1B01G055700	chr5D	500226980	500227884	904	True	870.000	870	84.5640	4182	5059	1	chr5D.!!$R1	877
16	TraesCS1B01G055700	chr2B	557344702	557345398	696	False	452.300	837	92.5280	2246	3080	2	chr2B.!!$F3	834
17	TraesCS1B01G055700	chr3B	817429020	817429672	652	False	830.000	830	89.6660	2427	3080	1	chr3B.!!$F1	653
18	TraesCS1B01G055700	chr3B	616187628	616188309	681	True	712.000	712	85.5470	4376	5058	1	chr3B.!!$R1	682
19	TraesCS1B01G055700	chr3D	528126662	528127648	986	True	474.000	573	84.9800	391	1332	2	chr3D.!!$R2	941
20	TraesCS1B01G055700	chr3D	553219858	553220809	951	True	455.000	536	84.9140	391	1299	2	chr3D.!!$R3	908
21	TraesCS1B01G055700	chr3D	462273816	462274511	695	True	448.550	824	92.5270	2246	3080	2	chr3D.!!$R1	834
22	TraesCS1B01G055700	chr2D	467998741	467999654	913	False	821.000	821	83.4790	4179	5059	1	chr2D.!!$F2	880
23	TraesCS1B01G055700	chr1D	178234420	178235309	889	False	785.000	785	83.1280	4181	5047	1	chr1D.!!$F1	866
24	TraesCS1B01G055700	chr1D	9085482	9086368	886	True	305.000	305	73.8410	4181	5045	1	chr1D.!!$R1	864
25	TraesCS1B01G055700	chr6D	10687320	10688010	690	False	682.000	682	84.5380	4370	5059	1	chr6D.!!$F1	689

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
190	191	0.033781	TTGTAAGCGTACGGGCAAGT	59.966	50.000	18.39	32.40	3.16	F
210	211	0.035630	GCCCTGACTTGCATCTGACT	60.036	55.000	0.00	0.00	3.41	F
1704	1829	1.003580	TGCTTTAGGCTCACTCCTTGG	59.996	52.381	0.00	42.39	3.61	F
2763	5319	2.095461	GGTGATTTCTCTTGCCCCTTC	58.905	52.381	0.00	0.00	3.46	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1689	1814	0.324943	GTTGCCAAGGAGTGAGCCTA	59.675	55.000	0.00	0.00	37.26	3.93	R
1864	1989	2.224719	ACTCTTTCAGGCTGAGTTGCAT	60.225	45.455	17.91	0.47	37.76	3.96	R
2905	5461	0.178932	CATGGTATCCCCCTCCTCGA	60.179	60.000	0.00	0.00	0.00	4.04	R
4522	8863	1.077357	AGAGATCGAGACAGGGCGT	60.077	57.895	0.00	0.00	0.00	5.68	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
70	71	3.217743	GGGCCGGTCGAGGAGTAG	61.218	72.222	1.90	0.00	0.00	2.57
71	72	2.124403	GGCCGGTCGAGGAGTAGA	60.124	66.667	1.90	0.00	0.00	2.59
72	73	2.479750	GGCCGGTCGAGGAGTAGAC	61.480	68.421	1.90	0.00	36.70	2.59
73	74	2.821688	GCCGGTCGAGGAGTAGACG	61.822	68.421	1.90	0.00	38.20	4.18
74	75	2.708255	CGGTCGAGGAGTAGACGC	59.292	66.667	0.00	0.00	38.20	5.19
75	76	1.814586	CGGTCGAGGAGTAGACGCT	60.815	63.158	0.00	0.00	38.20	5.07
76	77	1.764180	CGGTCGAGGAGTAGACGCTC	61.764	65.000	0.00	0.00	38.20	5.03
77	78	0.743701	GGTCGAGGAGTAGACGCTCA	60.744	60.000	0.00	0.00	38.20	4.26
78	79	0.653636	GTCGAGGAGTAGACGCTCAG	59.346	60.000	0.00	0.00	37.24	3.35
79	80	1.090625	TCGAGGAGTAGACGCTCAGC	61.091	60.000	0.00	0.00	37.24	4.26
80	81	1.731093	GAGGAGTAGACGCTCAGCC	59.269	63.158	0.00	0.00	37.24	4.85
81	82	1.000771	AGGAGTAGACGCTCAGCCA	60.001	57.895	0.00	0.00	37.24	4.75
82	83	1.139947	GGAGTAGACGCTCAGCCAC	59.860	63.158	0.00	0.00	37.24	5.01
83	84	1.316706	GGAGTAGACGCTCAGCCACT	61.317	60.000	0.00	0.00	37.24	4.00
84	85	0.179150	GAGTAGACGCTCAGCCACTG	60.179	60.000	0.00	0.00	35.67	3.66
85	86	1.807573	GTAGACGCTCAGCCACTGC	60.808	63.158	0.00	0.00	37.95	4.40
95	96	3.499050	GCCACTGCTGATGCTCAG	58.501	61.111	8.34	8.34	46.90	3.35
96	97	2.113433	GCCACTGCTGATGCTCAGG	61.113	63.158	12.98	2.96	44.43	3.86
97	98	1.451567	CCACTGCTGATGCTCAGGG	60.452	63.158	12.98	4.41	44.43	4.45
98	99	1.298993	CACTGCTGATGCTCAGGGT	59.701	57.895	12.98	0.00	44.43	4.34
99	100	1.025113	CACTGCTGATGCTCAGGGTG	61.025	60.000	12.98	0.00	44.43	4.61
100	101	1.451567	CTGCTGATGCTCAGGGTGG	60.452	63.158	12.98	0.00	44.43	4.61
101	102	1.907222	CTGCTGATGCTCAGGGTGGA	61.907	60.000	12.98	0.00	44.43	4.02
102	103	1.153208	GCTGATGCTCAGGGTGGAG	60.153	63.158	12.98	0.00	44.43	3.86
103	104	1.525923	CTGATGCTCAGGGTGGAGG	59.474	63.158	5.54	0.00	40.71	4.30
104	105	2.191641	GATGCTCAGGGTGGAGGC	59.808	66.667	0.00	0.00	35.41	4.70
105	106	3.746949	GATGCTCAGGGTGGAGGCG	62.747	68.421	0.00	0.00	35.41	5.52
111	112	4.815973	AGGGTGGAGGCGGGCATA	62.816	66.667	3.78	0.00	0.00	3.14
112	113	3.570212	GGGTGGAGGCGGGCATAT	61.570	66.667	3.78	0.00	0.00	1.78
113	114	2.032681	GGTGGAGGCGGGCATATC	59.967	66.667	3.78	0.00	0.00	1.63
114	115	2.818169	GGTGGAGGCGGGCATATCA	61.818	63.158	3.78	0.00	0.00	2.15
115	116	1.302033	GTGGAGGCGGGCATATCAG	60.302	63.158	3.78	0.00	0.00	2.90
116	117	2.359230	GGAGGCGGGCATATCAGC	60.359	66.667	3.78	0.00	0.00	4.26
117	118	2.746359	GAGGCGGGCATATCAGCT	59.254	61.111	3.78	0.00	34.17	4.24
118	119	1.375268	GAGGCGGGCATATCAGCTC	60.375	63.158	3.78	0.00	34.17	4.09
123	124	3.223661	GGGCATATCAGCTCGAAGG	57.776	57.895	0.00	0.00	34.17	3.46
124	125	0.952984	GGGCATATCAGCTCGAAGGC	60.953	60.000	0.00	0.00	34.17	4.35
125	126	1.287730	GGCATATCAGCTCGAAGGCG	61.288	60.000	0.00	0.00	37.29	5.52
126	127	1.895280	GCATATCAGCTCGAAGGCGC	61.895	60.000	0.00	0.00	37.46	6.53
127	128	0.598419	CATATCAGCTCGAAGGCGCA	60.598	55.000	10.83	0.00	37.46	6.09
128	129	0.319383	ATATCAGCTCGAAGGCGCAG	60.319	55.000	10.83	0.00	37.46	5.18
129	130	1.384222	TATCAGCTCGAAGGCGCAGA	61.384	55.000	10.83	1.44	37.46	4.26
130	131	2.230994	ATCAGCTCGAAGGCGCAGAA	62.231	55.000	10.83	0.00	37.46	3.02
131	132	2.125753	AGCTCGAAGGCGCAGAAG	60.126	61.111	10.83	0.00	37.46	2.85
132	133	3.191539	GCTCGAAGGCGCAGAAGG	61.192	66.667	10.83	0.00	37.46	3.46
133	134	2.573869	CTCGAAGGCGCAGAAGGA	59.426	61.111	10.83	0.00	37.46	3.36
134	135	1.518133	CTCGAAGGCGCAGAAGGAG	60.518	63.158	10.83	4.98	37.46	3.69
135	136	3.191539	CGAAGGCGCAGAAGGAGC	61.192	66.667	10.83	0.00	42.17	4.70
136	137	2.046892	GAAGGCGCAGAAGGAGCA	60.047	61.111	10.83	0.00	45.03	4.26
137	138	2.046507	AAGGCGCAGAAGGAGCAG	60.047	61.111	10.83	0.00	45.03	4.24
138	139	4.774503	AGGCGCAGAAGGAGCAGC	62.775	66.667	10.83	0.00	45.03	5.25
139	140	4.774503	GGCGCAGAAGGAGCAGCT	62.775	66.667	10.83	0.00	45.03	4.24
140	141	2.185350	GCGCAGAAGGAGCAGCTA	59.815	61.111	0.30	0.00	42.48	3.32
141	142	2.170434	GCGCAGAAGGAGCAGCTAC	61.170	63.158	0.30	0.00	42.48	3.58
142	143	1.216444	CGCAGAAGGAGCAGCTACA	59.784	57.895	7.59	0.00	0.00	2.74
143	144	0.179089	CGCAGAAGGAGCAGCTACAT	60.179	55.000	7.59	0.00	0.00	2.29
144	145	1.741732	CGCAGAAGGAGCAGCTACATT	60.742	52.381	7.59	0.00	0.00	2.71
145	146	1.669779	GCAGAAGGAGCAGCTACATTG	59.330	52.381	7.59	3.04	0.00	2.82
146	147	2.679059	GCAGAAGGAGCAGCTACATTGA	60.679	50.000	7.59	0.00	0.00	2.57
147	148	3.196463	CAGAAGGAGCAGCTACATTGAG	58.804	50.000	7.59	0.00	0.00	3.02
148	149	2.170187	AGAAGGAGCAGCTACATTGAGG	59.830	50.000	7.59	0.00	0.00	3.86
149	150	0.179936	AGGAGCAGCTACATTGAGGC	59.820	55.000	7.59	0.00	0.00	4.70
150	151	0.107508	GGAGCAGCTACATTGAGGCA	60.108	55.000	0.00	0.00	0.00	4.75
151	152	1.297664	GAGCAGCTACATTGAGGCAG	58.702	55.000	0.00	0.00	0.00	4.85
152	153	0.747283	AGCAGCTACATTGAGGCAGC	60.747	55.000	0.00	12.10	38.46	5.25
153	154	1.028330	GCAGCTACATTGAGGCAGCA	61.028	55.000	13.97	0.00	38.15	4.41
154	155	1.015109	CAGCTACATTGAGGCAGCAG	58.985	55.000	0.00	0.00	36.47	4.24
155	156	0.907486	AGCTACATTGAGGCAGCAGA	59.093	50.000	0.00	0.00	36.47	4.26
156	157	1.134461	AGCTACATTGAGGCAGCAGAG	60.134	52.381	0.00	0.00	36.47	3.35
157	158	1.134580	GCTACATTGAGGCAGCAGAGA	60.135	52.381	0.00	0.00	34.13	3.10
158	159	2.823984	CTACATTGAGGCAGCAGAGAG	58.176	52.381	0.00	0.00	0.00	3.20
159	160	1.273759	ACATTGAGGCAGCAGAGAGA	58.726	50.000	0.00	0.00	0.00	3.10
160	161	1.207570	ACATTGAGGCAGCAGAGAGAG	59.792	52.381	0.00	0.00	0.00	3.20
161	162	0.178533	ATTGAGGCAGCAGAGAGAGC	59.821	55.000	0.00	0.00	0.00	4.09
162	163	1.190178	TTGAGGCAGCAGAGAGAGCA	61.190	55.000	0.00	0.00	0.00	4.26
163	164	1.190178	TGAGGCAGCAGAGAGAGCAA	61.190	55.000	0.00	0.00	0.00	3.91
164	165	0.178533	GAGGCAGCAGAGAGAGCAAT	59.821	55.000	0.00	0.00	0.00	3.56
165	166	0.107606	AGGCAGCAGAGAGAGCAATG	60.108	55.000	0.00	0.00	0.00	2.82
166	167	1.096386	GGCAGCAGAGAGAGCAATGG	61.096	60.000	0.00	0.00	0.00	3.16
167	168	0.107800	GCAGCAGAGAGAGCAATGGA	60.108	55.000	0.00	0.00	0.00	3.41
168	169	1.475392	GCAGCAGAGAGAGCAATGGAT	60.475	52.381	0.00	0.00	0.00	3.41
169	170	2.920524	CAGCAGAGAGAGCAATGGATT	58.079	47.619	0.00	0.00	0.00	3.01
170	171	3.280295	CAGCAGAGAGAGCAATGGATTT	58.720	45.455	0.00	0.00	0.00	2.17
171	172	3.695060	CAGCAGAGAGAGCAATGGATTTT	59.305	43.478	0.00	0.00	0.00	1.82
172	173	4.158025	CAGCAGAGAGAGCAATGGATTTTT	59.842	41.667	0.00	0.00	0.00	1.94
173	174	4.158025	AGCAGAGAGAGCAATGGATTTTTG	59.842	41.667	0.00	0.00	0.00	2.44
174	175	4.082354	GCAGAGAGAGCAATGGATTTTTGT	60.082	41.667	0.00	0.00	0.00	2.83
175	176	5.124457	GCAGAGAGAGCAATGGATTTTTGTA	59.876	40.000	0.00	0.00	0.00	2.41
176	177	6.349611	GCAGAGAGAGCAATGGATTTTTGTAA	60.350	38.462	0.00	0.00	0.00	2.41
177	178	7.249147	CAGAGAGAGCAATGGATTTTTGTAAG	58.751	38.462	0.00	0.00	0.00	2.34
178	179	5.958955	AGAGAGCAATGGATTTTTGTAAGC	58.041	37.500	0.00	0.00	0.00	3.09
179	180	4.737054	AGAGCAATGGATTTTTGTAAGCG	58.263	39.130	0.00	0.00	0.00	4.68
180	181	4.218417	AGAGCAATGGATTTTTGTAAGCGT	59.782	37.500	0.00	0.00	0.00	5.07
181	182	5.414454	AGAGCAATGGATTTTTGTAAGCGTA	59.586	36.000	0.00	0.00	0.00	4.42
182	183	5.399013	AGCAATGGATTTTTGTAAGCGTAC	58.601	37.500	2.53	2.53	0.00	3.67
183	184	4.262045	GCAATGGATTTTTGTAAGCGTACG	59.738	41.667	11.84	11.84	32.40	3.67
184	185	4.609691	ATGGATTTTTGTAAGCGTACGG	57.390	40.909	18.39	0.00	32.40	4.02
185	186	2.743126	TGGATTTTTGTAAGCGTACGGG	59.257	45.455	18.39	0.00	32.40	5.28
186	187	2.476686	GGATTTTTGTAAGCGTACGGGC	60.477	50.000	18.39	0.27	32.40	6.13
187	188	1.590932	TTTTTGTAAGCGTACGGGCA	58.409	45.000	18.39	0.00	32.40	5.36
188	189	1.590932	TTTTGTAAGCGTACGGGCAA	58.409	45.000	18.39	0.00	32.40	4.52
189	190	1.149987	TTTGTAAGCGTACGGGCAAG	58.850	50.000	18.39	0.00	32.40	4.01
190	191	0.033781	TTGTAAGCGTACGGGCAAGT	59.966	50.000	18.39	0.00	32.40	3.16
191	192	0.668096	TGTAAGCGTACGGGCAAGTG	60.668	55.000	18.39	0.00	32.40	3.16
192	193	1.738830	TAAGCGTACGGGCAAGTGC	60.739	57.895	18.39	0.00	41.14	4.40
203	204	4.162592	CAAGTGCCCTGACTTGCA	57.837	55.556	2.12	0.00	44.70	4.08
204	205	2.649831	CAAGTGCCCTGACTTGCAT	58.350	52.632	2.12	0.00	44.70	3.96
205	206	0.524862	CAAGTGCCCTGACTTGCATC	59.475	55.000	2.12	0.00	44.70	3.91
206	207	0.403271	AAGTGCCCTGACTTGCATCT	59.597	50.000	0.00	0.00	40.07	2.90
207	208	0.322277	AGTGCCCTGACTTGCATCTG	60.322	55.000	0.00	0.00	40.07	2.90
208	209	0.321919	GTGCCCTGACTTGCATCTGA	60.322	55.000	0.00	0.00	40.07	3.27
209	210	0.321919	TGCCCTGACTTGCATCTGAC	60.322	55.000	0.00	0.00	31.31	3.51
210	211	0.035630	GCCCTGACTTGCATCTGACT	60.036	55.000	0.00	0.00	0.00	3.41
211	212	1.735386	CCCTGACTTGCATCTGACTG	58.265	55.000	0.00	0.00	0.00	3.51
212	213	1.277273	CCCTGACTTGCATCTGACTGA	59.723	52.381	0.00	0.00	0.00	3.41
213	214	2.289882	CCCTGACTTGCATCTGACTGAA	60.290	50.000	0.00	0.00	0.00	3.02
217	218	5.821470	CCTGACTTGCATCTGACTGAATTAT	59.179	40.000	0.00	0.00	0.00	1.28
272	273	1.450312	GTCATGGAAGTGGCTCCCG	60.450	63.158	0.00	0.00	34.22	5.14
339	340	2.656698	AAAGACCAAGCCCCCACCAC	62.657	60.000	0.00	0.00	0.00	4.16
375	376	2.510906	GGCGGCATGGTAGGATGT	59.489	61.111	3.07	0.00	0.00	3.06
376	377	1.152963	GGCGGCATGGTAGGATGTT	60.153	57.895	3.07	0.00	0.00	2.71
383	384	3.435601	GGCATGGTAGGATGTTGGAGAAT	60.436	47.826	0.00	0.00	0.00	2.40
389	390	2.492025	AGGATGTTGGAGAATGGCCTA	58.508	47.619	3.32	0.00	0.00	3.93
425	426	1.205893	CTGGTGGTCAGGTAAGCTCTC	59.794	57.143	0.00	0.00	39.76	3.20
576	582	3.003173	TAGGCTGGCGCTCTTGGT	61.003	61.111	7.64	0.00	36.09	3.67
578	584	1.676678	TAGGCTGGCGCTCTTGGTAG	61.677	60.000	7.64	0.00	36.09	3.18
606	612	3.159213	TCAATTGGTGAATCTGGCTGT	57.841	42.857	5.42	0.00	31.51	4.40
622	654	1.065126	GCTGTGCCCTGAGGTTAATCT	60.065	52.381	0.00	0.00	34.57	2.40
697	729	9.396938	TGATTGTATATTTAATTTGAGCGCATG	57.603	29.630	11.47	0.00	0.00	4.06
780	816	7.243604	AGTTAATTTGAAATCATGGGAGCAA	57.756	32.000	0.00	0.00	0.00	3.91
796	832	2.227865	GAGCAAGTATTTGGTTTCGGCA	59.772	45.455	4.06	0.00	44.54	5.69
837	873	6.456447	TGTCGTAAGGTGTTTAGAATTTCG	57.544	37.500	0.00	0.00	38.47	3.46
1011	1090	1.404181	GCTTCACGGATGAGCACACTA	60.404	52.381	0.00	0.00	35.83	2.74
1145	1224	3.118408	TCATGGGAAGTTGGATTCGGTAG	60.118	47.826	0.00	0.00	0.00	3.18
1361	1483	1.824852	TCATGCATGTACGAGTGTCCT	59.175	47.619	25.43	0.00	0.00	3.85
1450	1572	5.974158	CACAACCATTTGATGTTCGTTACAA	59.026	36.000	0.00	0.00	36.90	2.41
1646	1768	7.805071	GTCACAATATTCTTTGAGGAACACAAG	59.195	37.037	0.00	0.00	40.46	3.16
1704	1829	1.003580	TGCTTTAGGCTCACTCCTTGG	59.996	52.381	0.00	0.00	42.39	3.61
2060	2185	6.464222	CATCAGTTTCTTAGTACCCTGTTGA	58.536	40.000	0.00	0.00	0.00	3.18
2343	4894	2.353889	CAGTTCTGCTCGATTGGATTGG	59.646	50.000	0.00	0.00	0.00	3.16
2763	5319	2.095461	GGTGATTTCTCTTGCCCCTTC	58.905	52.381	0.00	0.00	0.00	3.46
2905	5461	5.380043	CATTATATTGGAGCAAGGACCTGT	58.620	41.667	0.00	0.00	0.00	4.00
2994	5550	0.901580	AGCTGTGGCAAGGAATTGGG	60.902	55.000	0.00	0.00	41.70	4.12
3002	5558	1.207811	GCAAGGAATTGGGGGATTGTG	59.792	52.381	0.00	0.00	0.00	3.33
3312	5872	1.013596	TAATCGGTCTGCCATTTGCG	58.986	50.000	0.00	0.00	45.60	4.85
3426	5986	9.970395	GGCATTTGATCATGTTCTATTTAATCA	57.030	29.630	0.00	0.00	0.00	2.57
3490	6071	4.202430	ACCTTACCCACAACTCTTACCTTG	60.202	45.833	0.00	0.00	0.00	3.61
3919	8206	7.371936	AGTTACTCTAGCGACATTTCATATCC	58.628	38.462	0.00	0.00	0.00	2.59
4111	8398	5.503634	TCATCCTGAAACCTGAATCTCAA	57.496	39.130	0.00	0.00	0.00	3.02
4116	8403	6.176183	TCCTGAAACCTGAATCTCAAAGATC	58.824	40.000	0.00	0.00	32.89	2.75
4152	8439	5.949952	AGACAATTAGGGTTAATTCCACACC	59.050	40.000	1.50	0.00	37.38	4.16
4155	8442	4.637387	TTAGGGTTAATTCCACACCGAA	57.363	40.909	0.00	0.00	0.00	4.30
4156	8443	3.512219	AGGGTTAATTCCACACCGAAA	57.488	42.857	0.00	0.00	0.00	3.46
4265	8570	2.041819	CCTAACCCTCCTCCCGCT	60.042	66.667	0.00	0.00	0.00	5.52
4327	8635	2.978824	GCAGTGGCCTCGTCCTTA	59.021	61.111	3.32	0.00	0.00	2.69
4603	8944	2.282180	GGGGCTTTGAAGACGGCA	60.282	61.111	0.00	0.00	33.77	5.69
4753	9094	0.752743	TCTTGCTTGGCTGCTGTTGT	60.753	50.000	0.00	0.00	0.00	3.32

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
53	54	3.217743	CTACTCCTCGACCGGCCC	61.218	72.222	0.00	0.00	0.00	5.80
54	55	2.124403	TCTACTCCTCGACCGGCC	60.124	66.667	0.00	0.00	0.00	6.13
55	56	2.821688	CGTCTACTCCTCGACCGGC	61.822	68.421	0.00	0.00	0.00	6.13
56	57	2.821688	GCGTCTACTCCTCGACCGG	61.822	68.421	0.00	0.00	0.00	5.28
57	58	1.764180	GAGCGTCTACTCCTCGACCG	61.764	65.000	0.00	0.00	0.00	4.79
58	59	0.743701	TGAGCGTCTACTCCTCGACC	60.744	60.000	0.00	0.00	35.72	4.79
59	60	0.653636	CTGAGCGTCTACTCCTCGAC	59.346	60.000	0.00	0.00	35.72	4.20
60	61	1.090625	GCTGAGCGTCTACTCCTCGA	61.091	60.000	0.00	0.00	35.72	4.04
61	62	1.353804	GCTGAGCGTCTACTCCTCG	59.646	63.158	0.00	0.00	35.72	4.63
62	63	1.032657	TGGCTGAGCGTCTACTCCTC	61.033	60.000	0.00	0.00	35.72	3.71
63	64	1.000771	TGGCTGAGCGTCTACTCCT	60.001	57.895	0.00	0.00	35.72	3.69
64	65	1.139947	GTGGCTGAGCGTCTACTCC	59.860	63.158	0.00	0.00	35.72	3.85
65	66	0.179150	CAGTGGCTGAGCGTCTACTC	60.179	60.000	0.00	0.00	37.19	2.59
66	67	1.886585	CAGTGGCTGAGCGTCTACT	59.113	57.895	0.00	0.00	32.44	2.57
67	68	1.807573	GCAGTGGCTGAGCGTCTAC	60.808	63.158	0.00	0.00	36.96	2.59
68	69	2.573869	GCAGTGGCTGAGCGTCTA	59.426	61.111	0.00	0.00	36.96	2.59
87	88	2.191641	GCCTCCACCCTGAGCATC	59.808	66.667	0.00	0.00	0.00	3.91
88	89	3.790437	CGCCTCCACCCTGAGCAT	61.790	66.667	0.00	0.00	0.00	3.79
94	95	4.815973	TATGCCCGCCTCCACCCT	62.816	66.667	0.00	0.00	0.00	4.34
95	96	3.553095	GATATGCCCGCCTCCACCC	62.553	68.421	0.00	0.00	0.00	4.61
96	97	2.032681	GATATGCCCGCCTCCACC	59.967	66.667	0.00	0.00	0.00	4.61
97	98	1.302033	CTGATATGCCCGCCTCCAC	60.302	63.158	0.00	0.00	0.00	4.02
98	99	3.150949	CTGATATGCCCGCCTCCA	58.849	61.111	0.00	0.00	0.00	3.86
99	100	2.359230	GCTGATATGCCCGCCTCC	60.359	66.667	0.00	0.00	0.00	4.30
100	101	1.375268	GAGCTGATATGCCCGCCTC	60.375	63.158	0.00	0.00	0.00	4.70
101	102	2.746359	GAGCTGATATGCCCGCCT	59.254	61.111	0.00	0.00	0.00	5.52
102	103	2.715532	TTCGAGCTGATATGCCCGCC	62.716	60.000	0.00	0.00	34.22	6.13
103	104	1.287730	CTTCGAGCTGATATGCCCGC	61.288	60.000	0.00	0.00	34.22	6.13
104	105	0.668706	CCTTCGAGCTGATATGCCCG	60.669	60.000	0.00	0.00	35.52	6.13
105	106	0.952984	GCCTTCGAGCTGATATGCCC	60.953	60.000	0.00	0.00	0.00	5.36
106	107	1.287730	CGCCTTCGAGCTGATATGCC	61.288	60.000	0.00	0.00	38.10	4.40
107	108	1.895280	GCGCCTTCGAGCTGATATGC	61.895	60.000	0.00	0.00	38.10	3.14
108	109	0.598419	TGCGCCTTCGAGCTGATATG	60.598	55.000	4.18	0.00	38.10	1.78
109	110	0.319383	CTGCGCCTTCGAGCTGATAT	60.319	55.000	4.18	0.00	36.12	1.63
110	111	1.066422	CTGCGCCTTCGAGCTGATA	59.934	57.895	4.18	0.00	36.12	2.15
111	112	2.202851	CTGCGCCTTCGAGCTGAT	60.203	61.111	4.18	0.00	36.12	2.90
112	113	2.825726	CTTCTGCGCCTTCGAGCTGA	62.826	60.000	4.18	0.72	40.14	4.26
113	114	2.433145	TTCTGCGCCTTCGAGCTG	60.433	61.111	4.18	0.00	38.10	4.24
114	115	2.125753	CTTCTGCGCCTTCGAGCT	60.126	61.111	4.18	0.00	38.10	4.09
115	116	3.191539	CCTTCTGCGCCTTCGAGC	61.192	66.667	4.18	0.00	38.10	5.03
116	117	1.518133	CTCCTTCTGCGCCTTCGAG	60.518	63.158	4.18	0.00	38.10	4.04
117	118	2.573869	CTCCTTCTGCGCCTTCGA	59.426	61.111	4.18	0.00	38.10	3.71
118	119	3.191539	GCTCCTTCTGCGCCTTCG	61.192	66.667	4.18	0.00	39.07	3.79
119	120	2.046892	TGCTCCTTCTGCGCCTTC	60.047	61.111	4.18	0.00	0.00	3.46
120	121	2.046507	CTGCTCCTTCTGCGCCTT	60.047	61.111	4.18	0.00	0.00	4.35
121	122	4.774503	GCTGCTCCTTCTGCGCCT	62.775	66.667	4.18	0.00	0.00	5.52
122	123	3.376935	TAGCTGCTCCTTCTGCGCC	62.377	63.158	4.91	0.00	36.26	6.53
123	124	2.170434	GTAGCTGCTCCTTCTGCGC	61.170	63.158	4.91	0.00	36.26	6.09
124	125	0.179089	ATGTAGCTGCTCCTTCTGCG	60.179	55.000	4.91	0.00	36.26	5.18
125	126	1.669779	CAATGTAGCTGCTCCTTCTGC	59.330	52.381	4.91	0.00	0.00	4.26
126	127	3.196463	CTCAATGTAGCTGCTCCTTCTG	58.804	50.000	4.91	0.00	0.00	3.02
127	128	2.170187	CCTCAATGTAGCTGCTCCTTCT	59.830	50.000	4.91	0.00	0.00	2.85
128	129	2.559440	CCTCAATGTAGCTGCTCCTTC	58.441	52.381	4.91	0.00	0.00	3.46
129	130	1.407989	GCCTCAATGTAGCTGCTCCTT	60.408	52.381	4.91	0.00	0.00	3.36
130	131	0.179936	GCCTCAATGTAGCTGCTCCT	59.820	55.000	4.91	0.00	0.00	3.69
131	132	0.107508	TGCCTCAATGTAGCTGCTCC	60.108	55.000	4.91	0.00	0.00	4.70
132	133	1.297664	CTGCCTCAATGTAGCTGCTC	58.702	55.000	4.91	0.00	0.00	4.26
133	134	0.747283	GCTGCCTCAATGTAGCTGCT	60.747	55.000	7.57	7.57	44.92	4.24
134	135	1.726265	GCTGCCTCAATGTAGCTGC	59.274	57.895	0.00	11.45	42.80	5.25
135	136	1.015109	CTGCTGCCTCAATGTAGCTG	58.985	55.000	0.00	0.00	37.10	4.24
136	137	0.907486	TCTGCTGCCTCAATGTAGCT	59.093	50.000	0.00	0.00	37.10	3.32
137	138	1.134580	TCTCTGCTGCCTCAATGTAGC	60.135	52.381	0.00	0.00	36.72	3.58
138	139	2.429971	TCTCTCTGCTGCCTCAATGTAG	59.570	50.000	0.00	0.00	0.00	2.74
139	140	2.429971	CTCTCTCTGCTGCCTCAATGTA	59.570	50.000	0.00	0.00	0.00	2.29
140	141	1.207570	CTCTCTCTGCTGCCTCAATGT	59.792	52.381	0.00	0.00	0.00	2.71
141	142	1.942677	CTCTCTCTGCTGCCTCAATG	58.057	55.000	0.00	0.00	0.00	2.82
142	143	0.178533	GCTCTCTCTGCTGCCTCAAT	59.821	55.000	0.00	0.00	0.00	2.57
143	144	1.190178	TGCTCTCTCTGCTGCCTCAA	61.190	55.000	0.00	0.00	0.00	3.02
144	145	1.190178	TTGCTCTCTCTGCTGCCTCA	61.190	55.000	0.00	0.00	0.00	3.86
145	146	0.178533	ATTGCTCTCTCTGCTGCCTC	59.821	55.000	0.00	0.00	0.00	4.70
146	147	0.107606	CATTGCTCTCTCTGCTGCCT	60.108	55.000	0.00	0.00	0.00	4.75
147	148	1.096386	CCATTGCTCTCTCTGCTGCC	61.096	60.000	0.00	0.00	0.00	4.85
148	149	0.107800	TCCATTGCTCTCTCTGCTGC	60.108	55.000	0.00	0.00	0.00	5.25
149	150	2.623878	ATCCATTGCTCTCTCTGCTG	57.376	50.000	0.00	0.00	0.00	4.41
150	151	3.648507	AAATCCATTGCTCTCTCTGCT	57.351	42.857	0.00	0.00	0.00	4.24
151	152	4.082354	ACAAAAATCCATTGCTCTCTCTGC	60.082	41.667	0.00	0.00	0.00	4.26
152	153	5.640189	ACAAAAATCCATTGCTCTCTCTG	57.360	39.130	0.00	0.00	0.00	3.35
153	154	6.127786	GCTTACAAAAATCCATTGCTCTCTCT	60.128	38.462	0.00	0.00	0.00	3.10
154	155	6.032717	GCTTACAAAAATCCATTGCTCTCTC	58.967	40.000	0.00	0.00	0.00	3.20
155	156	5.392380	CGCTTACAAAAATCCATTGCTCTCT	60.392	40.000	0.00	0.00	0.00	3.10
156	157	4.795278	CGCTTACAAAAATCCATTGCTCTC	59.205	41.667	0.00	0.00	0.00	3.20
157	158	4.218417	ACGCTTACAAAAATCCATTGCTCT	59.782	37.500	0.00	0.00	0.00	4.09
158	159	4.485163	ACGCTTACAAAAATCCATTGCTC	58.515	39.130	0.00	0.00	0.00	4.26
159	160	4.519540	ACGCTTACAAAAATCCATTGCT	57.480	36.364	0.00	0.00	0.00	3.91
160	161	4.262045	CGTACGCTTACAAAAATCCATTGC	59.738	41.667	0.52	0.00	0.00	3.56
161	162	4.791163	CCGTACGCTTACAAAAATCCATTG	59.209	41.667	10.49	0.00	0.00	2.82
162	163	4.142556	CCCGTACGCTTACAAAAATCCATT	60.143	41.667	10.49	0.00	0.00	3.16
163	164	3.375922	CCCGTACGCTTACAAAAATCCAT	59.624	43.478	10.49	0.00	0.00	3.41
164	165	2.743126	CCCGTACGCTTACAAAAATCCA	59.257	45.455	10.49	0.00	0.00	3.41
165	166	2.476686	GCCCGTACGCTTACAAAAATCC	60.477	50.000	10.49	0.00	0.00	3.01
166	167	2.160022	TGCCCGTACGCTTACAAAAATC	59.840	45.455	10.49	0.00	0.00	2.17
167	168	2.152830	TGCCCGTACGCTTACAAAAAT	58.847	42.857	10.49	0.00	0.00	1.82
168	169	1.590932	TGCCCGTACGCTTACAAAAA	58.409	45.000	10.49	0.00	0.00	1.94
169	170	1.532007	CTTGCCCGTACGCTTACAAAA	59.468	47.619	10.49	0.00	0.00	2.44
170	171	1.149987	CTTGCCCGTACGCTTACAAA	58.850	50.000	10.49	0.00	0.00	2.83
171	172	0.033781	ACTTGCCCGTACGCTTACAA	59.966	50.000	10.49	9.65	0.00	2.41
172	173	0.668096	CACTTGCCCGTACGCTTACA	60.668	55.000	10.49	1.56	0.00	2.41
173	174	1.963190	GCACTTGCCCGTACGCTTAC	61.963	60.000	10.49	0.00	34.31	2.34
174	175	1.738830	GCACTTGCCCGTACGCTTA	60.739	57.895	10.49	0.00	34.31	3.09
175	176	3.047877	GCACTTGCCCGTACGCTT	61.048	61.111	10.49	0.00	34.31	4.68
187	188	0.403271	AGATGCAAGTCAGGGCACTT	59.597	50.000	0.00	0.00	43.75	3.16
188	189	0.322277	CAGATGCAAGTCAGGGCACT	60.322	55.000	0.00	0.00	43.75	4.40
189	190	0.321919	TCAGATGCAAGTCAGGGCAC	60.322	55.000	0.00	0.00	43.75	5.01
190	191	0.321919	GTCAGATGCAAGTCAGGGCA	60.322	55.000	0.00	0.00	45.23	5.36
191	192	0.035630	AGTCAGATGCAAGTCAGGGC	60.036	55.000	0.00	0.00	0.00	5.19
192	193	1.277273	TCAGTCAGATGCAAGTCAGGG	59.723	52.381	0.00	0.00	0.00	4.45
193	194	2.756840	TCAGTCAGATGCAAGTCAGG	57.243	50.000	0.00	0.00	0.00	3.86
194	195	6.716438	CATAATTCAGTCAGATGCAAGTCAG	58.284	40.000	0.00	0.00	0.00	3.51
195	196	5.065602	GCATAATTCAGTCAGATGCAAGTCA	59.934	40.000	0.00	0.00	41.98	3.41
196	197	5.508872	GCATAATTCAGTCAGATGCAAGTC	58.491	41.667	0.00	0.00	41.98	3.01
197	198	4.034858	CGCATAATTCAGTCAGATGCAAGT	59.965	41.667	7.62	0.00	42.41	3.16
198	199	4.524749	CGCATAATTCAGTCAGATGCAAG	58.475	43.478	7.62	0.00	42.41	4.01
199	200	3.313249	CCGCATAATTCAGTCAGATGCAA	59.687	43.478	7.62	0.00	42.41	4.08
200	201	2.874086	CCGCATAATTCAGTCAGATGCA	59.126	45.455	7.62	0.00	42.41	3.96
201	202	2.350197	GCCGCATAATTCAGTCAGATGC	60.350	50.000	0.00	0.00	39.59	3.91
202	203	2.096565	CGCCGCATAATTCAGTCAGATG	60.097	50.000	0.00	0.00	0.00	2.90
203	204	2.138320	CGCCGCATAATTCAGTCAGAT	58.862	47.619	0.00	0.00	0.00	2.90
204	205	1.136110	TCGCCGCATAATTCAGTCAGA	59.864	47.619	0.00	0.00	0.00	3.27
205	206	1.570813	TCGCCGCATAATTCAGTCAG	58.429	50.000	0.00	0.00	0.00	3.51
206	207	1.933181	CTTCGCCGCATAATTCAGTCA	59.067	47.619	0.00	0.00	0.00	3.41
207	208	1.333258	GCTTCGCCGCATAATTCAGTC	60.333	52.381	0.00	0.00	0.00	3.51
208	209	0.657840	GCTTCGCCGCATAATTCAGT	59.342	50.000	0.00	0.00	0.00	3.41
209	210	0.940126	AGCTTCGCCGCATAATTCAG	59.060	50.000	0.00	0.00	0.00	3.02
210	211	0.937304	GAGCTTCGCCGCATAATTCA	59.063	50.000	0.00	0.00	0.00	2.57
211	212	0.235926	GGAGCTTCGCCGCATAATTC	59.764	55.000	0.00	0.00	0.00	2.17
212	213	0.463654	TGGAGCTTCGCCGCATAATT	60.464	50.000	0.00	0.00	0.00	1.40
213	214	1.146041	TGGAGCTTCGCCGCATAAT	59.854	52.632	0.00	0.00	0.00	1.28
264	265	2.444706	CCTCAGATCCGGGAGCCA	60.445	66.667	9.01	0.00	0.00	4.75
272	273	4.933064	CCGCGCGACCTCAGATCC	62.933	72.222	34.63	0.00	0.00	3.36
320	321	2.399607	TGGTGGGGGCTTGGTCTTT	61.400	57.895	0.00	0.00	0.00	2.52
375	376	2.168521	CGAACTCTAGGCCATTCTCCAA	59.831	50.000	5.01	0.00	0.00	3.53
376	377	1.757118	CGAACTCTAGGCCATTCTCCA	59.243	52.381	5.01	0.00	0.00	3.86
383	384	1.890894	GAGCACGAACTCTAGGCCA	59.109	57.895	5.01	0.00	33.69	5.36
557	560	2.887568	CAAGAGCGCCAGCCTACG	60.888	66.667	2.29	0.00	46.67	3.51
559	562	1.676678	CTACCAAGAGCGCCAGCCTA	61.677	60.000	2.29	0.00	46.67	3.93
606	612	1.839994	CTCCAGATTAACCTCAGGGCA	59.160	52.381	0.00	0.00	35.63	5.36
622	654	2.124768	TCCATCCAGGTGCCTCCA	59.875	61.111	0.00	0.00	39.02	3.86
780	816	4.279671	TGAAACATGCCGAAACCAAATACT	59.720	37.500	0.00	0.00	0.00	2.12
796	832	6.282199	ACGACATCTAACTACCTGAAACAT	57.718	37.500	0.00	0.00	0.00	2.71
837	873	3.181523	GGTTCGCAACGTTTCTCTTATCC	60.182	47.826	0.00	0.00	0.00	2.59
1011	1090	4.333926	GCAAACTTCCTTATCGATTGCTCT	59.666	41.667	1.71	0.00	38.79	4.09
1103	1182	6.403636	CCATGAATACAGGTTGTAGAAGTTGC	60.404	42.308	0.00	0.00	36.14	4.17
1105	1184	6.012858	TCCCATGAATACAGGTTGTAGAAGTT	60.013	38.462	0.00	0.00	36.14	2.66
1145	1224	2.633481	AGTCGGCTTTCCCCATATCTAC	59.367	50.000	0.00	0.00	0.00	2.59
1361	1483	0.740868	GTAGCAACCTGATCAGCGCA	60.741	55.000	23.61	12.28	0.00	6.09
1450	1572	1.212935	CCAATGAACCTTCTCCCCGAT	59.787	52.381	0.00	0.00	0.00	4.18
1600	1722	0.389391	CCTGTTGACAGTCGTGGTCT	59.611	55.000	10.03	0.00	42.27	3.85
1625	1747	6.899393	TGCTTGTGTTCCTCAAAGAATATT	57.101	33.333	0.00	0.00	0.00	1.28
1626	1748	6.899393	TTGCTTGTGTTCCTCAAAGAATAT	57.101	33.333	0.00	0.00	0.00	1.28
1646	1768	3.545703	AGTTAGTGCATACCTGGATTGC	58.454	45.455	15.44	15.44	36.91	3.56
1689	1814	0.324943	GTTGCCAAGGAGTGAGCCTA	59.675	55.000	0.00	0.00	37.26	3.93
1704	1829	6.931281	TCATCCTTATGATAGCTAAGTGTTGC	59.069	38.462	0.00	0.00	37.20	4.17
1864	1989	2.224719	ACTCTTTCAGGCTGAGTTGCAT	60.225	45.455	17.91	0.47	37.76	3.96
2060	2185	7.039082	AGTGTTGTGGCCATTTAATACTGAAAT	60.039	33.333	20.75	5.21	0.00	2.17
2292	4843	7.554118	AGAATACTGTGTGCTGCATAACTAAAT	59.446	33.333	5.27	0.85	0.00	1.40
2343	4894	5.874810	TGATTTACCAGAGTACATGAACTGC	59.125	40.000	0.00	0.00	0.00	4.40
2511	5064	4.393062	CAGAGGAAACGCAGAAATGTACAT	59.607	41.667	1.41	1.41	0.00	2.29
2905	5461	0.178932	CATGGTATCCCCCTCCTCGA	60.179	60.000	0.00	0.00	0.00	4.04
2925	5481	1.061546	TTTTACCAGGTTCGCCTCCT	58.938	50.000	0.00	0.00	46.86	3.69
2978	5534	1.229145	CCCCCAATTCCTTGCCACA	60.229	57.895	0.00	0.00	0.00	4.17
3002	5558	4.992688	TGTTGAACACAACTGAATGGAAC	58.007	39.130	12.95	0.00	42.74	3.62
3295	5855	1.078497	TCGCAAATGGCAGACCGAT	60.078	52.632	0.00	0.00	45.17	4.18
3312	5872	4.725790	AAAATGCAGCCCTAATTCACTC	57.274	40.909	0.00	0.00	0.00	3.51
3426	5986	2.727798	ACGACGAAACGAACGAAATGAT	59.272	40.909	0.00	0.00	35.48	2.45
3427	5987	2.118683	ACGACGAAACGAACGAAATGA	58.881	42.857	0.00	0.00	35.48	2.57
3428	5988	2.548497	ACGACGAAACGAACGAAATG	57.452	45.000	0.00	0.00	35.48	2.32
3429	5989	2.097250	GGAACGACGAAACGAACGAAAT	60.097	45.455	0.00	7.28	35.48	2.17
3430	5990	1.255084	GGAACGACGAAACGAACGAAA	59.745	47.619	0.00	0.00	35.48	3.46
3431	5991	0.845768	GGAACGACGAAACGAACGAA	59.154	50.000	0.00	0.00	35.48	3.85
3432	5992	0.248417	TGGAACGACGAAACGAACGA	60.248	50.000	0.00	0.00	35.48	3.85
3433	5993	0.780002	ATGGAACGACGAAACGAACG	59.220	50.000	0.00	0.00	36.70	3.95
3435	5995	1.421382	GGATGGAACGACGAAACGAA	58.579	50.000	0.00	0.00	37.03	3.85
3671	7924	1.134946	GCAATTACGGAAGCCAGCAAT	59.865	47.619	0.00	0.00	0.00	3.56
4111	8398	9.790344	CTAATTGTCTATCAATGAAGGGATCTT	57.210	33.333	0.00	0.00	44.85	2.40
4152	8439	1.560923	CTATGCTGGGACGTCTTTCG	58.439	55.000	16.46	3.08	46.00	3.46
4155	8442	1.522569	GCCTATGCTGGGACGTCTT	59.477	57.895	16.46	0.00	33.53	3.01
4156	8443	2.786495	CGCCTATGCTGGGACGTCT	61.786	63.158	16.46	0.00	34.43	4.18
4319	8627	4.424566	GTGCGCGGGTAAGGACGA	62.425	66.667	8.83	0.00	0.00	4.20
4446	8785	3.395702	ATCCACCGCGCCAGGTTA	61.396	61.111	4.02	0.00	43.00	2.85
4522	8863	1.077357	AGAGATCGAGACAGGGCGT	60.077	57.895	0.00	0.00	0.00	5.68
4590	8931	1.205064	CACGCTGCCGTCTTCAAAG	59.795	57.895	0.00	0.00	46.39	2.77
4603	8944	2.126307	CGCTGCAGTAGACACGCT	60.126	61.111	16.64	0.00	0.00	5.07
4673	9014	1.816537	GGCGACAGGAGCACATCTA	59.183	57.895	0.00	0.00	36.08	1.98
4674	9015	2.581354	GGCGACAGGAGCACATCT	59.419	61.111	0.00	0.00	36.08	2.90
4700	9041	2.672996	GCCATTGGCGGTCACTGT	60.673	61.111	12.82	0.00	39.62	3.55
4740	9081	2.813901	GGCAACAACAGCAGCCAA	59.186	55.556	0.00	0.00	46.26	4.52
4753	9094	2.272146	GGGAATGAGGAGCGGCAA	59.728	61.111	1.45	0.00	0.00	4.52

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.