AutoCloner

Multiple sequence alignment - TraesCS3D01G366300

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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	TraesCS3D01G366300	chr3D	100.000	4667	0	0	1	4667	480421760	480417094	0.000000e+00	8619.0
1	TraesCS3D01G366300	chr3D	80.815	761	105	25	2819	3554	543811737	543810993	4.080000e-155	558.0
2	TraesCS3D01G366300	chr3D	90.323	310	20	2	593	897	268520174	268520478	9.410000e-107	398.0
3	TraesCS3D01G366300	chr3D	86.207	145	8	2	3871	4003	543810755	543810611	3.760000e-31	147.0
4	TraesCS3D01G366300	chr3B	96.138	2978	88	15	898	3858	640976895	640973928	0.000000e+00	4837.0
5	TraesCS3D01G366300	chr3B	93.878	539	20	3	4129	4667	640973596	640973071	0.000000e+00	800.0
6	TraesCS3D01G366300	chr3B	95.011	441	22	0	1	441	640980048	640979608	0.000000e+00	693.0
7	TraesCS3D01G366300	chr3B	88.415	164	9	6	429	592	640977041	640976888	6.160000e-44	189.0
8	TraesCS3D01G366300	chr3B	94.805	77	4	0	3871	3947	640973862	640973786	2.280000e-23	121.0
9	TraesCS3D01G366300	chr3B	93.939	66	3	1	4044	4108	640973733	640973668	1.070000e-16	99.0
10	TraesCS3D01G366300	chr3B	96.154	52	2	0	3970	4021	640973785	640973734	8.320000e-13	86.1
11	TraesCS3D01G366300	chr3A	95.334	2936	93	17	945	3863	623533552	623530644	0.000000e+00	4623.0
12	TraesCS3D01G366300	chr3A	94.208	518	15	3	4150	4667	623530216	623529714	0.000000e+00	776.0
13	TraesCS3D01G366300	chr3A	88.688	442	49	1	1	441	215369161	215368720	5.310000e-149	538.0
14	TraesCS3D01G366300	chr3A	95.082	244	9	3	3871	4112	623530574	623530332	9.480000e-102	381.0
15	TraesCS3D01G366300	chr3A	100.000	40	0	0	4129	4168	623530261	623530222	1.800000e-09	75.0
16	TraesCS3D01G366300	chr5D	90.769	455	29	8	4129	4574	399218600	399219050	3.110000e-166	595.0
17	TraesCS3D01G366300	chr5D	87.584	298	20	5	586	867	565937868	565937572	3.480000e-86	329.0
18	TraesCS3D01G366300	chr5D	80.080	251	25	9	3871	4098	399218038	399218286	3.740000e-36	163.0
19	TraesCS3D01G366300	chr5B	90.330	455	31	8	4129	4574	479627240	479627690	6.730000e-163	584.0
20	TraesCS3D01G366300	chr5B	88.662	441	49	1	1	440	186508794	186509234	1.910000e-148	536.0
21	TraesCS3D01G366300	chr5B	88.308	325	20	6	584	891	411542132	411542455	1.590000e-99	374.0
22	TraesCS3D01G366300	chr5B	81.275	251	22	9	3871	4098	479626677	479626925	3.710000e-41	180.0
23	TraesCS3D01G366300	chr1D	90.045	442	42	2	1	441	233776359	233776799	5.240000e-159	571.0
24	TraesCS3D01G366300	chr1D	94.839	310	11	1	593	897	188464207	188464516	3.270000e-131	479.0
25	TraesCS3D01G366300	chr1D	90.282	319	15	3	590	897	393034971	393035284	2.020000e-108	403.0
26	TraesCS3D01G366300	chr1D	92.105	38	3	0	471	508	25386830	25386867	2.000000e-03	54.7
27	TraesCS3D01G366300	chr5A	89.693	456	32	7	4129	4574	504864874	504865324	6.780000e-158	568.0
28	TraesCS3D01G366300	chr5A	90.354	311	17	5	593	897	523664125	523664428	3.380000e-106	396.0
29	TraesCS3D01G366300	chr5A	90.000	310	25	3	590	893	632776281	632775972	3.380000e-106	396.0
30	TraesCS3D01G366300	chr5A	86.905	168	18	1	2865	3028	504863354	504863521	7.970000e-43	185.0
31	TraesCS3D01G366300	chr5A	81.275	251	22	9	3871	4098	504864312	504864560	3.710000e-41	180.0
32	TraesCS3D01G366300	chr4D	89.140	442	47	1	1	441	210758712	210759153	2.450000e-152	549.0
33	TraesCS3D01G366300	chr4D	95.253	316	9	1	590	899	113170184	113170499	3.240000e-136	496.0
34	TraesCS3D01G366300	chr4D	90.462	325	21	7	584	907	397100872	397101187	2.010000e-113	420.0
35	TraesCS3D01G366300	chr6A	88.688	442	49	1	1	441	392968551	392968110	5.310000e-149	538.0
36	TraesCS3D01G366300	chr6D	88.688	442	46	2	1	441	274295594	274296032	1.910000e-148	536.0
37	TraesCS3D01G366300	chr6B	88.235	442	51	1	1	441	651939086	651938645	1.150000e-145	527.0
38	TraesCS3D01G366300	chr6B	82.991	341	34	7	583	900	207309700	207310039	2.130000e-73	287.0
39	TraesCS3D01G366300	chr7D	89.074	421	44	2	1	420	253306676	253306257	5.350000e-144	521.0
40	TraesCS3D01G366300	chr7D	91.582	297	18	4	609	899	183187175	183186880	2.020000e-108	403.0
41	TraesCS3D01G366300	chr7D	79.412	238	26	13	579	808	70184972	70184750	3.760000e-31	147.0
42	TraesCS3D01G366300	chr7D	94.595	37	2	0	471	507	619038642	619038678	1.810000e-04	58.4
43	TraesCS3D01G366300	chr2D	89.937	318	16	8	592	898	473137638	473137326	3.380000e-106	396.0
44	TraesCS3D01G366300	chr2B	86.527	334	32	6	576	897	512346336	512346004	5.740000e-94	355.0
45	TraesCS3D01G366300	chr2B	84.731	334	26	9	576	897	512345198	512344878	1.260000e-80	311.0
46	TraesCS3D01G366300	chr1A	81.424	323	40	6	584	898	385669911	385670221	3.610000e-61	246.0
47	TraesCS3D01G366300	chr7B	84.951	206	12	7	586	779	239341026	239340828	1.710000e-44	191.0

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	TraesCS3D01G366300	chr3D	480417094	480421760	4666	True	8619.000000	8619	100.000000	1	4667	1	chr3D.!!$R1	4666
1	TraesCS3D01G366300	chr3D	543810611	543811737	1126	True	352.500000	558	83.511000	2819	4003	2	chr3D.!!$R2	1184
2	TraesCS3D01G366300	chr3B	640973071	640980048	6977	True	975.014286	4837	94.048571	1	4667	7	chr3B.!!$R1	4666
3	TraesCS3D01G366300	chr3A	623529714	623533552	3838	True	1463.750000	4623	96.156000	945	4667	4	chr3A.!!$R2	3722
4	TraesCS3D01G366300	chr5D	399218038	399219050	1012	False	379.000000	595	85.424500	3871	4574	2	chr5D.!!$F1	703
5	TraesCS3D01G366300	chr5B	479626677	479627690	1013	False	382.000000	584	85.802500	3871	4574	2	chr5B.!!$F3	703
6	TraesCS3D01G366300	chr5A	504863354	504865324	1970	False	311.000000	568	85.957667	2865	4574	3	chr5A.!!$F2	1709
7	TraesCS3D01G366300	chr2B	512344878	512346336	1458	True	333.000000	355	85.629000	576	897	2	chr2B.!!$R1	321

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
62	63	0.037605	AGCATCCAAAGCAGCAAAGC	60.038	50.0	0.00	0.00	0.0	3.51	F
900	3492	0.107017	CCCATGGCCAGGACTACTTG	60.107	60.0	21.32	5.21	0.0	3.16	F
905	3497	0.176910	GGCCAGGACTACTTGAGAGC	59.823	60.0	0.00	0.00	0.0	4.09	F
907	3499	1.561643	CCAGGACTACTTGAGAGCCA	58.438	55.0	0.00	0.00	0.0	4.75	F
2981	5704	0.745486	TGTCTGATCCCGCATTGCAG	60.745	55.0	9.69	0.00	0.0	4.41	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1335	4043	1.734465	GCAACAGATCCAGAAACGGAG	59.266	52.381	0.0	0.0	38.83	4.63	R
2872	5589	0.392193	CAGTGGTGCATCCTCCAGAC	60.392	60.000	0.0	0.0	35.43	3.51	R
2981	5704	2.129555	TTGAGGCAGAAGACAGGGCC	62.130	60.000	0.0	0.0	46.77	5.80	R
3092	5821	0.324943	TTAAGACCCAGCAGCCACTC	59.675	55.000	0.0	0.0	0.00	3.51	R
4560	7837	0.882927	GTGGCGTTGTAGGACTTGCA	60.883	55.000	0.0	0.0	0.00	4.08	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
39	40	1.543358	CCAAGAGAAGGCAGAAAAGGC	59.457	52.381	0.00	0.00	0.00	4.35
62	63	0.037605	AGCATCCAAAGCAGCAAAGC	60.038	50.000	0.00	0.00	0.00	3.51
63	64	1.017701	GCATCCAAAGCAGCAAAGCC	61.018	55.000	0.00	0.00	34.23	4.35
170	171	1.068264	GCAAAGTCTGGCCAACTTAGC	60.068	52.381	24.38	14.29	35.96	3.09
180	181	3.772060	GCCAACTTAGCCAAGAATCAG	57.228	47.619	0.00	0.00	35.60	2.90
239	240	8.946085	GTATAATCTTGATGTCAAGGTCACAAA	58.054	33.333	19.50	2.53	45.84	2.83
253	254	7.337689	TCAAGGTCACAAAGATCCAATCTATTG	59.662	37.037	0.00	0.00	39.08	1.90
276	277	2.548493	GGAGAAGCTGAGAGATGATGCC	60.548	54.545	0.00	0.00	0.00	4.40
305	306	7.039434	GGATAGTGATGACAGATCTACCATTGA	60.039	40.741	9.54	0.20	0.00	2.57
313	314	5.923204	ACAGATCTACCATTGACAGATTCC	58.077	41.667	0.00	0.00	0.00	3.01
319	320	4.581309	ACCATTGACAGATTCCAGACAT	57.419	40.909	0.00	0.00	0.00	3.06
343	344	2.290896	CCTAGGGCACAAAGGTCATCAA	60.291	50.000	0.00	0.00	0.00	2.57
379	380	1.964223	ACACCAGGACTACACACTCTG	59.036	52.381	0.00	0.00	0.00	3.35
432	3012	1.150536	GTCAACTCCACCAGCCCAA	59.849	57.895	0.00	0.00	0.00	4.12
436	3016	0.482446	AACTCCACCAGCCCAAATGA	59.518	50.000	0.00	0.00	0.00	2.57
441	3021	1.617804	CCACCAGCCCAAATGACATCT	60.618	52.381	0.00	0.00	0.00	2.90
452	3032	5.296283	CCCAAATGACATCTGATCTGAGAAC	59.704	44.000	8.37	2.93	0.00	3.01
464	3044	0.901124	CTGAGAACCAGACTCCCAGG	59.099	60.000	0.00	0.00	45.78	4.45
465	3045	0.487325	TGAGAACCAGACTCCCAGGA	59.513	55.000	0.00	0.00	33.95	3.86
466	3046	1.190643	GAGAACCAGACTCCCAGGAG	58.809	60.000	12.29	12.29	46.91	3.69
467	3047	0.907230	AGAACCAGACTCCCAGGAGC	60.907	60.000	13.78	6.80	45.54	4.70
468	3048	1.904990	GAACCAGACTCCCAGGAGCC	61.905	65.000	13.78	2.36	45.54	4.70
469	3049	3.086600	CCAGACTCCCAGGAGCCC	61.087	72.222	13.78	6.14	45.54	5.19
485	3065	2.496817	CCGTAGCACCTGAGCCTC	59.503	66.667	0.00	0.00	34.23	4.70
495	3075	2.283604	TGAGCCTCGGTAGCACCA	60.284	61.111	6.21	0.00	38.47	4.17
496	3076	2.290122	CTGAGCCTCGGTAGCACCAG	62.290	65.000	6.21	0.00	38.47	4.00
508	3088	2.485966	AGCACCAGATACTCTCCCAT	57.514	50.000	0.00	0.00	0.00	4.00
509	3089	2.045524	AGCACCAGATACTCTCCCATG	58.954	52.381	0.00	0.00	0.00	3.66
534	3114	6.500751	GGAGGGAGGGAATACATGATTACTTA	59.499	42.308	0.00	0.00	0.00	2.24
712	3304	0.514255	GAACACGTAAAAGCCCGTCC	59.486	55.000	0.00	0.00	34.59	4.79
759	3351	3.701532	TCAGGAAAACGCAAAAACGAT	57.298	38.095	0.00	0.00	36.70	3.73
766	3358	2.126110	GCAAAAACGATGGGCCCG	60.126	61.111	19.37	7.98	0.00	6.13
799	3391	1.156736	CCGGTCTTCGTGCTCAAAAT	58.843	50.000	0.00	0.00	37.11	1.82
808	3400	1.678728	CGTGCTCAAAATCTAGGCCCA	60.679	52.381	0.00	0.00	0.00	5.36
835	3427	3.314331	CAGGAGTGGTGTCGGGCT	61.314	66.667	0.00	0.00	0.00	5.19
856	3448	3.428282	CCGGGTCGGGCTTTTTCG	61.428	66.667	0.00	0.00	44.15	3.46
857	3449	3.428282	CGGGTCGGGCTTTTTCGG	61.428	66.667	0.00	0.00	0.00	4.30
858	3450	3.060000	GGGTCGGGCTTTTTCGGG	61.060	66.667	0.00	0.00	0.00	5.14
859	3451	3.744719	GGTCGGGCTTTTTCGGGC	61.745	66.667	0.00	0.00	0.00	6.13
860	3452	3.744719	GTCGGGCTTTTTCGGGCC	61.745	66.667	0.00	0.00	46.89	5.80
897	3489	2.193248	GCCCATGGCCAGGACTAC	59.807	66.667	21.32	0.65	44.06	2.73
898	3490	2.378634	GCCCATGGCCAGGACTACT	61.379	63.158	21.32	0.00	44.06	2.57
899	3491	1.926426	GCCCATGGCCAGGACTACTT	61.926	60.000	21.32	0.00	44.06	2.24
900	3492	0.107017	CCCATGGCCAGGACTACTTG	60.107	60.000	21.32	5.21	0.00	3.16
901	3493	0.911769	CCATGGCCAGGACTACTTGA	59.088	55.000	21.32	0.00	0.00	3.02
902	3494	1.134280	CCATGGCCAGGACTACTTGAG	60.134	57.143	21.32	0.00	0.00	3.02
903	3495	1.833630	CATGGCCAGGACTACTTGAGA	59.166	52.381	13.35	0.00	0.00	3.27
904	3496	1.561643	TGGCCAGGACTACTTGAGAG	58.438	55.000	0.00	0.00	0.00	3.20
905	3497	0.176910	GGCCAGGACTACTTGAGAGC	59.823	60.000	0.00	0.00	0.00	4.09
906	3498	0.176910	GCCAGGACTACTTGAGAGCC	59.823	60.000	0.00	0.00	0.00	4.70
907	3499	1.561643	CCAGGACTACTTGAGAGCCA	58.438	55.000	0.00	0.00	0.00	4.75
908	3500	1.902508	CCAGGACTACTTGAGAGCCAA	59.097	52.381	0.00	0.00	0.00	4.52
991	3583	2.448736	GAGGACCCCCAGATCCCC	60.449	72.222	0.00	0.00	35.38	4.81
1335	4043	2.127232	GAGACGGTTTTGCGCTGC	60.127	61.111	9.73	0.00	0.00	5.25
1754	4467	3.550820	TGCCGGCATCAAACATATAGTT	58.449	40.909	29.03	0.00	43.89	2.24
1838	4551	4.898320	TGCTCATCTCAGCACTAAAAAGA	58.102	39.130	0.00	0.00	44.73	2.52
1887	4600	6.993786	TTCATATGACCGACAAAGCATTAA	57.006	33.333	4.48	0.00	0.00	1.40
1914	4629	8.150945	GGTCATTACAGGTACATACTCATGATT	58.849	37.037	0.00	0.00	35.96	2.57
1958	4673	9.468491	CCATTAACTGGTGCAGAGAGATTCTCT	62.468	44.444	16.08	16.08	46.16	3.10
2050	4767	4.446719	GCTTGCTCATTTCTTTTTGAGTGG	59.553	41.667	2.30	0.00	41.16	4.00
2153	4870	5.190528	TGAAATTACTGATGAGGGAGCTTCT	59.809	40.000	0.00	0.00	0.00	2.85
2276	4993	6.020678	GCAACTGTACAATTTATTCCATTCGC	60.021	38.462	0.00	0.00	0.00	4.70
2279	4996	4.636648	TGTACAATTTATTCCATTCGCGGT	59.363	37.500	6.13	0.00	0.00	5.68
2485	5202	2.935201	GCTTGAGCAGAGTAACTGATGG	59.065	50.000	0.00	0.00	45.71	3.51
2585	5302	2.831526	ACCATGTATTTTGGCAGGAACC	59.168	45.455	0.00	0.00	37.81	3.62
2671	5388	3.358118	TCAGCATGATGCCTTCATTGAA	58.642	40.909	14.72	0.00	46.52	2.69
2792	5509	7.623999	AACTGAATCCTATCATATGACAGGT	57.376	36.000	25.79	14.31	39.68	4.00
2816	5533	1.940613	ACTCGTGTTGAAGCAAACTCC	59.059	47.619	0.00	0.00	0.00	3.85
2855	5572	3.453717	TGCCTCTACTTGAGCATCTCATT	59.546	43.478	0.00	0.00	40.39	2.57
2981	5704	0.745486	TGTCTGATCCCGCATTGCAG	60.745	55.000	9.69	0.00	0.00	4.41
3241	5978	1.048724	TCTAGGCATCTTCCACGGGG	61.049	60.000	0.00	0.00	0.00	5.73
3299	6043	3.950395	GCAGGCATTCTGGTATCTTCTTT	59.050	43.478	0.00	0.00	43.54	2.52
3382	6157	3.321968	TCCGAGTGAGCTATGTGCATAAT	59.678	43.478	0.00	0.00	45.94	1.28
3569	6350	1.081175	CTCGCGCACTTCAGTCTCA	60.081	57.895	8.75	0.00	0.00	3.27
3637	6471	7.201470	GCAATTTTGAATTAGCTAAAGACAGCC	60.201	37.037	10.85	0.00	42.84	4.85
3791	6634	8.301002	GTTTTAACAGAGGGCATTTGTGTTATA	58.699	33.333	0.00	0.00	34.46	0.98
3798	6642	6.663093	AGAGGGCATTTGTGTTATATTGTCAA	59.337	34.615	0.00	0.00	0.00	3.18
3831	6677	3.259123	GGGTTCAAATGGTTGATGCTTCT	59.741	43.478	0.88	0.00	43.29	2.85
3859	6705	9.490663	GATGTAGGATGATTTTTGTCTTAAACG	57.509	33.333	0.00	0.00	0.00	3.60
3863	6709	7.807680	AGGATGATTTTTGTCTTAAACGAGTC	58.192	34.615	0.00	0.00	0.00	3.36
3865	6711	8.290325	GGATGATTTTTGTCTTAAACGAGTCTT	58.710	33.333	0.00	0.00	0.00	3.01
4532	7809	4.871557	GCTGGAGATCTATGAGATGATTGC	59.128	45.833	0.00	0.00	34.53	3.56
4560	7837	8.637986	TGCACTTTCACCAATCTAAGTATTTTT	58.362	29.630	0.00	0.00	30.19	1.94

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
19	20	1.543358	GCCTTTTCTGCCTTCTCTTGG	59.457	52.381	0.00	0.00	0.00	3.61
39	40	2.157834	TGCTGCTTTGGATGCTTTTG	57.842	45.000	0.00	0.00	0.00	2.44
62	63	2.485677	CATTGGGTGCACTAGCTGG	58.514	57.895	17.98	0.00	42.74	4.85
92	93	5.070847	AGTTGGTCTTGCTTTGATTTGGATT	59.929	36.000	0.00	0.00	0.00	3.01
170	171	3.303938	TCTAGGCTCTCCTGATTCTTGG	58.696	50.000	0.00	0.00	44.08	3.61
180	181	1.271707	ACTATCCGCTCTAGGCTCTCC	60.272	57.143	0.00	0.00	39.13	3.71
231	232	6.183360	CCACAATAGATTGGATCTTTGTGACC	60.183	42.308	26.04	2.41	46.61	4.02
234	235	6.825213	TCTCCACAATAGATTGGATCTTTGTG	59.175	38.462	22.23	22.23	45.32	3.33
239	240	5.369110	AGCTTCTCCACAATAGATTGGATCT	59.631	40.000	7.16	0.00	41.20	2.75
253	254	3.719924	CATCATCTCTCAGCTTCTCCAC	58.280	50.000	0.00	0.00	0.00	4.02
276	277	5.123186	GGTAGATCTGTCATCACTATCCTCG	59.877	48.000	5.18	0.00	0.00	4.63
305	306	3.118112	CCTAGGCAATGTCTGGAATCTGT	60.118	47.826	0.00	0.00	0.00	3.41
432	3012	5.424573	TCTGGTTCTCAGATCAGATGTCATT	59.575	40.000	4.60	0.00	46.71	2.57
452	3032	3.086600	GGGCTCCTGGGAGTCTGG	61.087	72.222	18.97	0.00	45.39	3.86
464	3044	2.496817	CTCAGGTGCTACGGGCTC	59.503	66.667	4.43	0.95	42.39	4.70
465	3045	3.775654	GCTCAGGTGCTACGGGCT	61.776	66.667	4.43	0.00	42.39	5.19
466	3046	4.840005	GGCTCAGGTGCTACGGGC	62.840	72.222	0.00	0.00	42.22	6.13
467	3047	3.077556	AGGCTCAGGTGCTACGGG	61.078	66.667	0.00	0.00	0.00	5.28
468	3048	2.496817	GAGGCTCAGGTGCTACGG	59.503	66.667	10.25	0.00	0.00	4.02
469	3049	2.103143	CGAGGCTCAGGTGCTACG	59.897	66.667	15.95	0.00	0.00	3.51
477	3057	2.290122	CTGGTGCTACCGAGGCTCAG	62.290	65.000	15.95	5.63	42.58	3.35
508	3088	2.887454	TCATGTATTCCCTCCCTCCA	57.113	50.000	0.00	0.00	0.00	3.86
509	3089	4.846940	AGTAATCATGTATTCCCTCCCTCC	59.153	45.833	0.00	0.00	0.00	4.30
534	3114	3.100671	ACTCTCTAATTCGTTGGCCTCT	58.899	45.455	3.32	0.00	0.00	3.69
693	3285	0.514255	GGACGGGCTTTTACGTGTTC	59.486	55.000	0.00	0.00	44.24	3.18
695	3287	1.665599	CGGACGGGCTTTTACGTGT	60.666	57.895	0.00	0.00	44.24	4.49
735	3327	3.732471	CGTTTTTGCGTTTTCCTGAAGGA	60.732	43.478	0.00	0.00	43.73	3.36
743	3335	1.191425	GCCCATCGTTTTTGCGTTTTC	59.809	47.619	0.00	0.00	0.00	2.29
747	3339	2.648454	GGCCCATCGTTTTTGCGT	59.352	55.556	0.00	0.00	0.00	5.24
748	3340	2.126110	GGGCCCATCGTTTTTGCG	60.126	61.111	19.95	0.00	0.00	4.85
784	3376	3.262420	GCCTAGATTTTGAGCACGAAGA	58.738	45.455	0.00	0.00	0.00	2.87
788	3380	1.017387	GGGCCTAGATTTTGAGCACG	58.983	55.000	0.84	0.00	0.00	5.34
790	3382	2.726821	CTTGGGCCTAGATTTTGAGCA	58.273	47.619	9.57	0.00	0.00	4.26
819	3411	3.314331	CAGCCCGACACCACTCCT	61.314	66.667	0.00	0.00	0.00	3.69
841	3433	3.060000	CCCGAAAAAGCCCGACCC	61.060	66.667	0.00	0.00	0.00	4.46
881	3473	0.107017	CAAGTAGTCCTGGCCATGGG	60.107	60.000	15.13	4.96	0.00	4.00
882	3474	0.911769	TCAAGTAGTCCTGGCCATGG	59.088	55.000	5.51	7.63	0.00	3.66
883	3475	1.833630	TCTCAAGTAGTCCTGGCCATG	59.166	52.381	5.51	2.84	0.00	3.66
884	3476	2.114616	CTCTCAAGTAGTCCTGGCCAT	58.885	52.381	5.51	0.00	0.00	4.40
885	3477	1.561643	CTCTCAAGTAGTCCTGGCCA	58.438	55.000	4.71	4.71	0.00	5.36
886	3478	0.176910	GCTCTCAAGTAGTCCTGGCC	59.823	60.000	0.00	0.00	0.00	5.36
887	3479	0.176910	GGCTCTCAAGTAGTCCTGGC	59.823	60.000	0.00	0.00	0.00	4.85
888	3480	1.561643	TGGCTCTCAAGTAGTCCTGG	58.438	55.000	0.00	0.00	0.00	4.45
889	3481	3.244033	CTTGGCTCTCAAGTAGTCCTG	57.756	52.381	0.00	0.00	45.81	3.86
898	3490	0.767375	AGTGCTTCCTTGGCTCTCAA	59.233	50.000	0.00	0.00	0.00	3.02
899	3491	1.276421	GTAGTGCTTCCTTGGCTCTCA	59.724	52.381	0.00	0.00	35.56	3.27
900	3492	1.276421	TGTAGTGCTTCCTTGGCTCTC	59.724	52.381	0.00	0.00	35.56	3.20
901	3493	1.352083	TGTAGTGCTTCCTTGGCTCT	58.648	50.000	0.00	0.00	37.33	4.09
902	3494	2.012673	CATGTAGTGCTTCCTTGGCTC	58.987	52.381	0.00	0.00	0.00	4.70
903	3495	1.630369	TCATGTAGTGCTTCCTTGGCT	59.370	47.619	0.00	0.00	0.00	4.75
904	3496	2.113860	TCATGTAGTGCTTCCTTGGC	57.886	50.000	0.00	0.00	0.00	4.52
905	3497	6.949352	ATTAATCATGTAGTGCTTCCTTGG	57.051	37.500	0.00	0.00	0.00	3.61
906	3498	8.437360	TGTATTAATCATGTAGTGCTTCCTTG	57.563	34.615	0.00	0.00	0.00	3.61
907	3499	9.461312	TTTGTATTAATCATGTAGTGCTTCCTT	57.539	29.630	0.00	0.00	0.00	3.36
908	3500	8.893727	GTTTGTATTAATCATGTAGTGCTTCCT	58.106	33.333	0.00	0.00	0.00	3.36
909	3501	8.673711	TGTTTGTATTAATCATGTAGTGCTTCC	58.326	33.333	0.00	0.00	0.00	3.46
912	3504	9.618890	AGATGTTTGTATTAATCATGTAGTGCT	57.381	29.630	0.00	0.00	0.00	4.40
940	3532	4.175516	CACGGCGTAGGATTTGTTAGTAA	58.824	43.478	14.22	0.00	0.00	2.24
943	3535	1.326548	GCACGGCGTAGGATTTGTTAG	59.673	52.381	14.22	0.00	0.00	2.34
991	3583	2.193248	GGGAGGGGGCGAAATGAG	59.807	66.667	0.00	0.00	0.00	2.90
1335	4043	1.734465	GCAACAGATCCAGAAACGGAG	59.266	52.381	0.00	0.00	38.83	4.63
1583	4291	7.254455	CGAAACTATGTACTGGAAATCATGGTC	60.254	40.741	0.00	0.00	32.51	4.02
1754	4467	4.718774	AGCTTCTCCAGACTATCAATGGAA	59.281	41.667	0.00	0.00	42.40	3.53
1836	4549	8.061304	TCCTCCCAAATCTAGCAAATTTAATCT	58.939	33.333	0.00	0.00	0.00	2.40
1838	4551	8.608185	TTCCTCCCAAATCTAGCAAATTTAAT	57.392	30.769	0.00	0.00	0.00	1.40
1887	4600	6.839134	TCATGAGTATGTACCTGTAATGACCT	59.161	38.462	0.00	0.00	35.73	3.85
1958	4673	5.717178	ACTAGATGAGACAAGGTTAGCAGAA	59.283	40.000	0.00	0.00	0.00	3.02
1960	4675	5.590530	ACTAGATGAGACAAGGTTAGCAG	57.409	43.478	0.00	0.00	0.00	4.24
2050	4767	8.866956	ACTATAAATTAATACTCCATTACGCGC	58.133	33.333	5.73	0.00	0.00	6.86
2153	4870	4.339872	TCTTGTAAACGCCTTAAGGACA	57.660	40.909	26.21	16.46	37.39	4.02
2276	4993	2.766313	TGAACTTCAGAATCACCACCG	58.234	47.619	0.00	0.00	0.00	4.94
2279	4996	6.962182	AGGAATATGAACTTCAGAATCACCA	58.038	36.000	4.32	0.00	0.00	4.17
2515	5232	4.217334	TGAGGCTTAGATATCTCAGCTTCG	59.783	45.833	30.37	6.26	46.14	3.79
2763	5480	8.370940	TGTCATATGATAGGATTCAGTTTCTCC	58.629	37.037	9.02	0.00	0.00	3.71
2792	5509	3.438781	AGTTTGCTTCAACACGAGTGAAA	59.561	39.130	10.50	1.09	0.00	2.69
2816	5533	4.109050	GAGGCAGAGACAGTATTTTCTCG	58.891	47.826	0.00	0.00	42.72	4.04
2855	5572	7.674348	TCCTCCAGACTTAGACTTTCAAGATAA	59.326	37.037	0.00	0.00	0.00	1.75
2872	5589	0.392193	CAGTGGTGCATCCTCCAGAC	60.392	60.000	0.00	0.00	35.43	3.51
2981	5704	2.129555	TTGAGGCAGAAGACAGGGCC	62.130	60.000	0.00	0.00	46.77	5.80
3092	5821	0.324943	TTAAGACCCAGCAGCCACTC	59.675	55.000	0.00	0.00	0.00	3.51
3299	6043	5.781306	TGAAGTTACATCACCCTTACCTACA	59.219	40.000	0.00	0.00	0.00	2.74
3411	6191	8.677300	TGCTGTATTTTATCCTTTGATCTGTTC	58.323	33.333	0.00	0.00	32.18	3.18
3637	6471	7.697691	AGAAGCACTATTTAATCAAATGACGG	58.302	34.615	0.00	0.00	35.88	4.79
3798	6642	3.261390	CCATTTGAACCCATGGTCACATT	59.739	43.478	11.73	0.00	36.01	2.71
3859	6705	5.858381	TGCACCTCATGGATAATAAGACTC	58.142	41.667	0.00	0.00	37.04	3.36
3863	6709	4.392047	TGCTGCACCTCATGGATAATAAG	58.608	43.478	0.00	0.00	37.04	1.73
3865	6711	4.645863	ATGCTGCACCTCATGGATAATA	57.354	40.909	3.57	0.00	37.04	0.98
3867	6713	3.301794	AATGCTGCACCTCATGGATAA	57.698	42.857	3.57	0.00	37.04	1.75
4037	6977	3.755378	CACCAGCTGCTTGTTTCTTATCT	59.245	43.478	8.66	0.00	0.00	1.98
4052	6992	5.534207	TGAACAATTCAATTTCACCAGCT	57.466	34.783	0.00	0.00	36.59	4.24
4532	7809	4.074970	ACTTAGATTGGTGAAAGTGCAGG	58.925	43.478	0.00	0.00	31.20	4.85
4560	7837	0.882927	GTGGCGTTGTAGGACTTGCA	60.883	55.000	0.00	0.00	0.00	4.08

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.