AutoCloner

Multiple sequence alignment - TraesCS5B01G512000

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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	TraesCS5B01G512000	chr5B	100.000	3614	0	0	1	3614	677536431	677540044	0.000000e+00	6674.0
1	TraesCS5B01G512000	chr5B	98.297	1762	12	6	866	2614	677545206	677543450	0.000000e+00	3072.0
2	TraesCS5B01G512000	chr5B	93.478	598	14	10	23	604	545590442	545589854	0.000000e+00	865.0
3	TraesCS5B01G512000	chr4A	95.779	1990	63	9	669	2651	633000211	632998236	0.000000e+00	3190.0
4	TraesCS5B01G512000	chr4A	94.442	1943	67	19	829	2754	632989512	632991430	0.000000e+00	2952.0
5	TraesCS5B01G512000	chr4A	84.848	1551	207	20	1024	2560	685834814	685836350	0.000000e+00	1537.0
6	TraesCS5B01G512000	chr4A	86.624	785	44	28	2878	3614	632991584	632992355	0.000000e+00	811.0
7	TraesCS5B01G512000	chr5D	94.298	2087	76	21	674	2738	537163224	537161159	0.000000e+00	3155.0
8	TraesCS5B01G512000	chr5D	95.369	1814	51	17	866	2657	537087904	537089706	0.000000e+00	2854.0
9	TraesCS5B01G512000	chr5D	86.500	600	45	19	3036	3614	537160785	537160201	8.520000e-176	627.0
10	TraesCS5B01G512000	chr5D	86.319	307	35	5	3308	3614	537150213	537149914	9.680000e-86	327.0
11	TraesCS5B01G512000	chr5D	81.194	335	33	21	2749	3064	537161121	537160798	3.610000e-60	243.0
12	TraesCS5B01G512000	chr5D	100.000	28	0	0	2955	2982	537160818	537160791	7.000000e-03	52.8
13	TraesCS5B01G512000	chr4D	84.729	1552	211	19	1024	2562	479540668	479542206	0.000000e+00	1530.0
14	TraesCS5B01G512000	chr4D	88.941	642	51	11	1	626	472383	473020	0.000000e+00	774.0
15	TraesCS5B01G512000	chr4B	84.377	1549	218	19	1024	2560	606764722	606766258	0.000000e+00	1498.0
16	TraesCS5B01G512000	chr4B	81.494	1540	245	30	1040	2550	624862933	624861405	0.000000e+00	1229.0
17	TraesCS5B01G512000	chr4B	94.578	664	19	4	22	670	644395890	644395229	0.000000e+00	1011.0
18	TraesCS5B01G512000	chr2A	82.376	1549	239	26	1029	2557	18358280	18359814	0.000000e+00	1317.0
19	TraesCS5B01G512000	chr5A	81.431	1551	252	32	1040	2563	670104836	670103295	0.000000e+00	1236.0
20	TraesCS5B01G512000	chr6B	96.035	681	13	2	1	667	478761760	478761080	0.000000e+00	1096.0
21	TraesCS5B01G512000	chr6B	95.161	682	19	3	1	668	49951381	49952062	0.000000e+00	1064.0
22	TraesCS5B01G512000	chr6B	95.482	664	11	6	22	669	290228361	290227701	0.000000e+00	1042.0
23	TraesCS5B01G512000	chr1B	94.876	683	16	5	1	669	145572736	145572059	0.000000e+00	1050.0
24	TraesCS5B01G512000	chr2B	94.436	683	21	6	1	668	798212083	798212763	0.000000e+00	1035.0
25	TraesCS5B01G512000	chr2B	97.656	128	2	1	541	668	798212798	798212924	6.080000e-53	219.0
26	TraesCS5B01G512000	chr2B	90.244	123	9	2	544	664	102042197	102042318	1.340000e-34	158.0
27	TraesCS5B01G512000	chr2D	89.181	647	49	9	1	629	398776409	398775766	0.000000e+00	787.0
28	TraesCS5B01G512000	chr6A	84.887	708	63	16	1	669	144498693	144497991	0.000000e+00	675.0

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	TraesCS5B01G512000	chr5B	677536431	677540044	3613	False	6674.00	6674	100.000	1	3614	1	chr5B.!!$F1	3613
1	TraesCS5B01G512000	chr5B	677543450	677545206	1756	True	3072.00	3072	98.297	866	2614	1	chr5B.!!$R2	1748
2	TraesCS5B01G512000	chr5B	545589854	545590442	588	True	865.00	865	93.478	23	604	1	chr5B.!!$R1	581
3	TraesCS5B01G512000	chr4A	632998236	633000211	1975	True	3190.00	3190	95.779	669	2651	1	chr4A.!!$R1	1982
4	TraesCS5B01G512000	chr4A	632989512	632992355	2843	False	1881.50	2952	90.533	829	3614	2	chr4A.!!$F2	2785
5	TraesCS5B01G512000	chr4A	685834814	685836350	1536	False	1537.00	1537	84.848	1024	2560	1	chr4A.!!$F1	1536
6	TraesCS5B01G512000	chr5D	537087904	537089706	1802	False	2854.00	2854	95.369	866	2657	1	chr5D.!!$F1	1791
7	TraesCS5B01G512000	chr5D	537160201	537163224	3023	True	1019.45	3155	90.498	674	3614	4	chr5D.!!$R2	2940
8	TraesCS5B01G512000	chr4D	479540668	479542206	1538	False	1530.00	1530	84.729	1024	2562	1	chr4D.!!$F2	1538
9	TraesCS5B01G512000	chr4D	472383	473020	637	False	774.00	774	88.941	1	626	1	chr4D.!!$F1	625
10	TraesCS5B01G512000	chr4B	606764722	606766258	1536	False	1498.00	1498	84.377	1024	2560	1	chr4B.!!$F1	1536
11	TraesCS5B01G512000	chr4B	624861405	624862933	1528	True	1229.00	1229	81.494	1040	2550	1	chr4B.!!$R1	1510
12	TraesCS5B01G512000	chr4B	644395229	644395890	661	True	1011.00	1011	94.578	22	670	1	chr4B.!!$R2	648
13	TraesCS5B01G512000	chr2A	18358280	18359814	1534	False	1317.00	1317	82.376	1029	2557	1	chr2A.!!$F1	1528
14	TraesCS5B01G512000	chr5A	670103295	670104836	1541	True	1236.00	1236	81.431	1040	2563	1	chr5A.!!$R1	1523
15	TraesCS5B01G512000	chr6B	478761080	478761760	680	True	1096.00	1096	96.035	1	667	1	chr6B.!!$R2	666
16	TraesCS5B01G512000	chr6B	49951381	49952062	681	False	1064.00	1064	95.161	1	668	1	chr6B.!!$F1	667
17	TraesCS5B01G512000	chr6B	290227701	290228361	660	True	1042.00	1042	95.482	22	669	1	chr6B.!!$R1	647
18	TraesCS5B01G512000	chr1B	145572059	145572736	677	True	1050.00	1050	94.876	1	669	1	chr1B.!!$R1	668
19	TraesCS5B01G512000	chr2B	798212083	798212924	841	False	627.00	1035	96.046	1	668	2	chr2B.!!$F2	667
20	TraesCS5B01G512000	chr2D	398775766	398776409	643	True	787.00	787	89.181	1	629	1	chr2D.!!$R1	628
21	TraesCS5B01G512000	chr6A	144497991	144498693	702	True	675.00	675	84.887	1	669	1	chr6A.!!$R1	668

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
768	996	1.063717	GGAGCATGGAAATTCCCCAGA	60.064	52.381	9.87	0.0	37.08	3.86	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2619	2965	0.32121	TGTGAATATATGGCGGCCGG	60.321	55.0	29.38	8.95	0.0	6.13	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
310	315	9.063739	CCAAAATTCATTTGTGTGTTGAAAAAG	57.936	29.630	0.84	0.00	45.72	2.27
672	893	4.443034	GCGTCACATAGGAACTCCCTTAAT	60.443	45.833	0.00	0.00	44.85	1.40
679	900	9.408648	CACATAGGAACTCCCTTAATATTTTGT	57.591	33.333	0.00	0.00	44.85	2.83
683	904	8.164057	AGGAACTCCCTTAATATTTTGTCTCT	57.836	34.615	0.00	0.00	44.85	3.10
721	949	8.579006	GTTGCATTCAGATCATATTATTTCCCA	58.421	33.333	0.00	0.00	0.00	4.37
722	950	8.888836	TGCATTCAGATCATATTATTTCCCAT	57.111	30.769	0.00	0.00	0.00	4.00
723	951	8.745590	TGCATTCAGATCATATTATTTCCCATG	58.254	33.333	0.00	0.00	0.00	3.66
724	952	7.705325	GCATTCAGATCATATTATTTCCCATGC	59.295	37.037	0.00	0.00	0.00	4.06
725	953	7.707624	TTCAGATCATATTATTTCCCATGCC	57.292	36.000	0.00	0.00	0.00	4.40
726	954	5.882000	TCAGATCATATTATTTCCCATGCCG	59.118	40.000	0.00	0.00	0.00	5.69
727	955	5.066893	CAGATCATATTATTTCCCATGCCGG	59.933	44.000	0.00	0.00	0.00	6.13
768	996	1.063717	GGAGCATGGAAATTCCCCAGA	60.064	52.381	9.87	0.00	37.08	3.86
769	997	2.425392	GGAGCATGGAAATTCCCCAGAT	60.425	50.000	9.87	0.00	37.08	2.90
787	1017	4.494690	CCAGATGTAACAGCTTTACATGCG	60.495	45.833	25.59	18.96	43.39	4.73
800	1030	5.446143	TTTACATGCGGTGAAACTTCATT	57.554	34.783	0.00	0.00	39.73	2.57
921	1175	1.102154	TTCTGCACCACAACACAAGG	58.898	50.000	0.00	0.00	0.00	3.61
925	1179	1.340502	TGCACCACAACACAAGGAAGA	60.341	47.619	0.00	0.00	0.00	2.87
926	1180	1.956477	GCACCACAACACAAGGAAGAT	59.044	47.619	0.00	0.00	0.00	2.40
2571	2911	2.747686	GAGGCCCAGGACAACGAA	59.252	61.111	0.00	0.00	0.00	3.85
2675	3036	1.467734	GAAGCTGCAGGATGTTGAGTG	59.532	52.381	17.12	0.00	39.31	3.51
2676	3037	0.322277	AGCTGCAGGATGTTGAGTGG	60.322	55.000	17.12	0.00	39.31	4.00
2693	3054	5.745227	TGAGTGGGTCAAAGATCCTTAATC	58.255	41.667	0.00	0.00	33.22	1.75
2707	3068	9.547279	AAGATCCTTAATCTGTTGGGTAATTTT	57.453	29.630	0.00	0.00	44.26	1.82
2765	3159	2.878406	GTTTGCCGGCTCATGTATATGT	59.122	45.455	29.70	0.00	35.73	2.29
2769	3163	2.688507	CCGGCTCATGTATATGTCCAC	58.311	52.381	11.60	0.00	35.73	4.02
2770	3164	2.037121	CCGGCTCATGTATATGTCCACA	59.963	50.000	11.60	0.00	35.73	4.17
2777	3171	9.618890	GGCTCATGTATATGTCCACAATATATT	57.381	33.333	0.00	0.00	35.73	1.28
2830	3270	4.623932	AATGTGCTAGAGAGTTGGTCAA	57.376	40.909	0.00	0.00	0.00	3.18
2835	3275	5.422012	TGTGCTAGAGAGTTGGTCAATGATA	59.578	40.000	0.00	0.00	0.00	2.15
2836	3276	6.098838	TGTGCTAGAGAGTTGGTCAATGATAT	59.901	38.462	0.00	0.00	0.00	1.63
2838	3278	6.324770	TGCTAGAGAGTTGGTCAATGATATGA	59.675	38.462	0.00	0.00	0.00	2.15
2839	3279	7.015974	TGCTAGAGAGTTGGTCAATGATATGAT	59.984	37.037	0.00	0.00	0.00	2.45
2840	3280	7.331440	GCTAGAGAGTTGGTCAATGATATGATG	59.669	40.741	0.00	0.00	0.00	3.07
2841	3281	7.370905	AGAGAGTTGGTCAATGATATGATGA	57.629	36.000	0.00	0.00	0.00	2.92
2842	3282	7.443477	AGAGAGTTGGTCAATGATATGATGAG	58.557	38.462	0.00	0.00	0.00	2.90
2843	3283	5.996513	AGAGTTGGTCAATGATATGATGAGC	59.003	40.000	0.00	0.00	40.88	4.26
2844	3284	5.068636	AGTTGGTCAATGATATGATGAGCC	58.931	41.667	0.00	0.00	40.03	4.70
2845	3285	4.987963	TGGTCAATGATATGATGAGCCT	57.012	40.909	0.00	0.00	40.03	4.58
2846	3286	6.043590	AGTTGGTCAATGATATGATGAGCCTA	59.956	38.462	0.00	0.00	40.03	3.93
2847	3287	6.438186	TGGTCAATGATATGATGAGCCTAA	57.562	37.500	0.00	0.00	40.03	2.69
2848	3288	6.470278	TGGTCAATGATATGATGAGCCTAAG	58.530	40.000	0.00	0.00	40.03	2.18
2849	3289	5.353678	GGTCAATGATATGATGAGCCTAAGC	59.646	44.000	0.00	0.00	35.99	3.09
2862	3302	2.706339	CCTAAGCTGTGGCATCTCTT	57.294	50.000	0.00	0.00	41.70	2.85
2863	3303	2.559440	CCTAAGCTGTGGCATCTCTTC	58.441	52.381	0.00	0.00	41.70	2.87
2864	3304	2.200067	CTAAGCTGTGGCATCTCTTCG	58.800	52.381	0.00	0.00	41.70	3.79
2865	3305	0.322975	AAGCTGTGGCATCTCTTCGT	59.677	50.000	0.00	0.00	41.70	3.85
2866	3306	1.186200	AGCTGTGGCATCTCTTCGTA	58.814	50.000	0.00	0.00	41.70	3.43
2867	3307	1.759445	AGCTGTGGCATCTCTTCGTAT	59.241	47.619	0.00	0.00	41.70	3.06
2868	3308	2.131183	GCTGTGGCATCTCTTCGTATC	58.869	52.381	0.00	0.00	38.54	2.24
2869	3309	2.748605	CTGTGGCATCTCTTCGTATCC	58.251	52.381	0.00	0.00	0.00	2.59
2870	3310	1.067060	TGTGGCATCTCTTCGTATCCG	59.933	52.381	0.00	0.00	0.00	4.18
2871	3311	1.337071	GTGGCATCTCTTCGTATCCGA	59.663	52.381	0.00	0.00	42.41	4.55
2872	3312	2.029828	GTGGCATCTCTTCGTATCCGAT	60.030	50.000	0.00	0.00	43.80	4.18
2873	3313	2.229062	TGGCATCTCTTCGTATCCGATC	59.771	50.000	0.00	0.00	43.80	3.69
2874	3314	2.416162	GGCATCTCTTCGTATCCGATCC	60.416	54.545	0.00	0.00	43.80	3.36
2878	3318	3.816994	TCTCTTCGTATCCGATCCAAGA	58.183	45.455	0.00	0.00	43.80	3.02
2902	3342	4.837860	ACCTCAAGACTCTCTTCAGTCAAT	59.162	41.667	3.56	0.00	44.73	2.57
2989	3430	9.308000	TCACTGGTTACTTATTGGATTTGATTT	57.692	29.630	0.00	0.00	0.00	2.17
2990	3431	9.357652	CACTGGTTACTTATTGGATTTGATTTG	57.642	33.333	0.00	0.00	0.00	2.32
2991	3432	9.308000	ACTGGTTACTTATTGGATTTGATTTGA	57.692	29.630	0.00	0.00	0.00	2.69
3038	3524	5.580297	GCTAGTCAAGAGTCTCCTTCATTTG	59.420	44.000	0.00	0.00	0.00	2.32
3106	3592	3.008375	TGGAGTGAAGTCATCTTCCAAGG	59.992	47.826	8.73	0.00	46.66	3.61
3121	3607	5.191722	TCTTCCAAGGTTATGACTAAGGCAT	59.808	40.000	0.00	0.00	0.00	4.40
3203	3700	6.391227	ACCAAATAGAACAAAAGGTGTCAG	57.609	37.500	0.00	0.00	40.60	3.51
3212	3709	2.256117	AAAGGTGTCAGTCGGGAAAG	57.744	50.000	0.00	0.00	0.00	2.62
3217	3714	1.343465	GTGTCAGTCGGGAAAGGAAGA	59.657	52.381	0.00	0.00	0.00	2.87
3233	3731	6.704056	AAGGAAGAAAGAGGTCATTAGGAA	57.296	37.500	0.00	0.00	0.00	3.36
3234	3732	6.306643	AGGAAGAAAGAGGTCATTAGGAAG	57.693	41.667	0.00	0.00	0.00	3.46
3288	3786	7.012327	GCACATCTGTTGGTTTAGCTTGATATA	59.988	37.037	0.00	0.00	0.00	0.86
3289	3787	9.060347	CACATCTGTTGGTTTAGCTTGATATAT	57.940	33.333	0.00	0.00	0.00	0.86
3290	3788	9.632638	ACATCTGTTGGTTTAGCTTGATATATT	57.367	29.630	0.00	0.00	0.00	1.28
3291	3789	9.888878	CATCTGTTGGTTTAGCTTGATATATTG	57.111	33.333	0.00	0.00	0.00	1.90
3304	3802	9.759473	AGCTTGATATATTGGCACCTTATTTAT	57.241	29.630	0.00	0.00	0.00	1.40
3338	3857	2.014010	ATTGCAACCCACCAACTCAT	57.986	45.000	0.00	0.00	0.00	2.90
3425	3944	8.887717	GGTGAAGAAGATCATTGGCATATATAC	58.112	37.037	0.00	0.00	0.00	1.47
3426	3945	9.664332	GTGAAGAAGATCATTGGCATATATACT	57.336	33.333	0.00	0.00	0.00	2.12
3482	4001	6.015940	AGTCAACTCAAATCAACCTCAAATCC	60.016	38.462	0.00	0.00	0.00	3.01
3520	4039	8.116753	CGAGTCAACCAAAATCATTGATAGTAC	58.883	37.037	0.00	0.00	34.98	2.73
3521	4040	9.167311	GAGTCAACCAAAATCATTGATAGTACT	57.833	33.333	0.00	0.00	34.98	2.73
3532	4051	7.751047	TCATTGATAGTACTAAACGAACTGC	57.249	36.000	6.70	0.00	0.00	4.40
3550	4069	1.021968	GCACAAACTGGAAACGAGGT	58.978	50.000	0.00	0.00	0.00	3.85
3559	4078	1.628340	TGGAAACGAGGTGATCCACAT	59.372	47.619	0.00	0.00	37.05	3.21

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
672	893	9.166173	CAACCTATCAACATCAGAGACAAAATA	57.834	33.333	0.00	0.00	0.00	1.40
679	900	4.824479	TGCAACCTATCAACATCAGAGA	57.176	40.909	0.00	0.00	0.00	3.10
683	904	5.499313	TCTGAATGCAACCTATCAACATCA	58.501	37.500	0.00	0.00	0.00	3.07
727	955	5.541845	TCCATCGTTGACAAGGATATCATC	58.458	41.667	19.93	0.00	34.50	2.92
768	996	3.126858	CACCGCATGTAAAGCTGTTACAT	59.873	43.478	19.75	19.75	43.97	2.29
769	997	2.482336	CACCGCATGTAAAGCTGTTACA	59.518	45.455	17.80	17.80	38.99	2.41
787	1017	1.128692	CCGCGAGAATGAAGTTTCACC	59.871	52.381	8.23	0.00	40.49	4.02
800	1030	2.516460	GTCTAGGCTCCCGCGAGA	60.516	66.667	8.23	0.00	38.52	4.04
837	1067	3.994392	GGTGTCACCGCGAATATTGATAT	59.006	43.478	8.23	0.00	0.00	1.63
984	1273	1.064783	CATGATGCTGCTGCTGCTG	59.935	57.895	27.67	16.73	40.48	4.41
985	1274	2.121538	CCATGATGCTGCTGCTGCT	61.122	57.895	27.67	15.76	40.48	4.24
986	1275	2.413351	CCATGATGCTGCTGCTGC	59.587	61.111	22.51	22.51	40.48	5.25
987	1276	2.413351	GCCATGATGCTGCTGCTG	59.587	61.111	17.00	6.37	40.48	4.41
988	1277	3.209812	CGCCATGATGCTGCTGCT	61.210	61.111	17.00	2.26	40.48	4.24
989	1278	4.925576	GCGCCATGATGCTGCTGC	62.926	66.667	8.89	8.89	40.20	5.25
990	1279	4.607606	CGCGCCATGATGCTGCTG	62.608	66.667	0.00	0.00	0.00	4.41
2618	2964	1.376683	TGAATATATGGCGGCCGGC	60.377	57.895	41.79	41.79	42.51	6.13
2619	2965	0.321210	TGTGAATATATGGCGGCCGG	60.321	55.000	29.38	8.95	0.00	6.13
2620	2966	1.196808	GTTGTGAATATATGGCGGCCG	59.803	52.381	24.05	24.05	0.00	6.13
2666	3027	3.331889	AGGATCTTTGACCCACTCAACAT	59.668	43.478	0.00	0.00	38.70	2.71
2675	3036	5.358160	CCAACAGATTAAGGATCTTTGACCC	59.642	44.000	0.00	0.00	42.55	4.46
2676	3037	5.358160	CCCAACAGATTAAGGATCTTTGACC	59.642	44.000	0.00	0.00	42.55	4.02
2707	3068	6.522233	TTAAGCGTGTACGTATCACAAAAA	57.478	33.333	20.53	10.81	42.22	1.94
2777	3171	8.735692	TGCAAGTTGATTGATTGATGTAGATA	57.264	30.769	7.16	0.00	41.83	1.98
2778	3172	7.634671	TGCAAGTTGATTGATTGATGTAGAT	57.365	32.000	7.16	0.00	41.83	1.98
2779	3173	7.080353	CTGCAAGTTGATTGATTGATGTAGA	57.920	36.000	7.16	0.00	41.83	2.59
2817	3257	7.370905	TCATCATATCATTGACCAACTCTCT	57.629	36.000	0.00	0.00	0.00	3.10
2843	3283	2.559440	GAAGAGATGCCACAGCTTAGG	58.441	52.381	0.00	0.00	40.80	2.69
2844	3284	2.200067	CGAAGAGATGCCACAGCTTAG	58.800	52.381	0.00	0.00	40.80	2.18
2845	3285	1.550524	ACGAAGAGATGCCACAGCTTA	59.449	47.619	0.00	0.00	40.80	3.09
2846	3286	0.322975	ACGAAGAGATGCCACAGCTT	59.677	50.000	0.00	0.00	40.80	3.74
2847	3287	1.186200	TACGAAGAGATGCCACAGCT	58.814	50.000	0.00	0.00	40.80	4.24
2848	3288	2.131183	GATACGAAGAGATGCCACAGC	58.869	52.381	0.00	0.00	40.48	4.40
2849	3289	2.748605	GGATACGAAGAGATGCCACAG	58.251	52.381	0.00	0.00	0.00	3.66
2850	3290	2.890808	GGATACGAAGAGATGCCACA	57.109	50.000	0.00	0.00	0.00	4.17
2864	3304	4.099573	TCTTGAGGTTCTTGGATCGGATAC	59.900	45.833	0.00	0.00	0.00	2.24
2865	3305	4.099573	GTCTTGAGGTTCTTGGATCGGATA	59.900	45.833	0.00	0.00	0.00	2.59
2866	3306	3.107601	TCTTGAGGTTCTTGGATCGGAT	58.892	45.455	0.00	0.00	0.00	4.18
2867	3307	2.233922	GTCTTGAGGTTCTTGGATCGGA	59.766	50.000	0.00	0.00	0.00	4.55
2868	3308	2.234908	AGTCTTGAGGTTCTTGGATCGG	59.765	50.000	0.00	0.00	0.00	4.18
2869	3309	3.194542	AGAGTCTTGAGGTTCTTGGATCG	59.805	47.826	0.00	0.00	0.00	3.69
2870	3310	4.466015	AGAGAGTCTTGAGGTTCTTGGATC	59.534	45.833	0.00	0.00	0.00	3.36
2871	3311	4.424842	AGAGAGTCTTGAGGTTCTTGGAT	58.575	43.478	0.00	0.00	0.00	3.41
2872	3312	3.850752	AGAGAGTCTTGAGGTTCTTGGA	58.149	45.455	0.00	0.00	0.00	3.53
2873	3313	4.039730	TGAAGAGAGTCTTGAGGTTCTTGG	59.960	45.833	0.00	0.00	36.73	3.61
2874	3314	5.207110	TGAAGAGAGTCTTGAGGTTCTTG	57.793	43.478	0.00	0.00	36.73	3.02
2878	3318	4.219115	TGACTGAAGAGAGTCTTGAGGTT	58.781	43.478	7.85	0.00	41.17	3.50
2914	3354	7.119699	CACCTCAGAGTGCAATTATAGTTTGAA	59.880	37.037	0.00	0.00	0.00	2.69
2989	3430	8.198109	GCCTAGAACTACTCACAGAATTAATCA	58.802	37.037	0.00	0.00	0.00	2.57
2990	3431	8.417884	AGCCTAGAACTACTCACAGAATTAATC	58.582	37.037	0.00	0.00	0.00	1.75
2991	3432	8.312669	AGCCTAGAACTACTCACAGAATTAAT	57.687	34.615	0.00	0.00	0.00	1.40
2992	3433	7.719871	AGCCTAGAACTACTCACAGAATTAA	57.280	36.000	0.00	0.00	0.00	1.40
2993	3434	8.053963	ACTAGCCTAGAACTACTCACAGAATTA	58.946	37.037	5.58	0.00	0.00	1.40
2998	3439	5.186942	TGACTAGCCTAGAACTACTCACAG	58.813	45.833	5.58	0.00	0.00	3.66
3038	3524	7.337938	AGTACTCAGGGACTAAGAAGTACTAC	58.662	42.308	10.39	0.00	42.42	2.73
3106	3592	4.051922	CGGTCTGATGCCTTAGTCATAAC	58.948	47.826	0.00	0.00	0.00	1.89
3121	3607	6.531503	AGAAAGTTAGATGATTCGGTCTGA	57.468	37.500	2.61	0.00	0.00	3.27
3177	3664	8.294954	TGACACCTTTTGTTCTATTTGGTTTA	57.705	30.769	0.00	0.00	39.17	2.01
3179	3666	6.379988	ACTGACACCTTTTGTTCTATTTGGTT	59.620	34.615	0.00	0.00	39.17	3.67
3180	3667	5.891551	ACTGACACCTTTTGTTCTATTTGGT	59.108	36.000	0.00	0.00	39.17	3.67
3181	3668	6.391227	ACTGACACCTTTTGTTCTATTTGG	57.609	37.500	0.00	0.00	39.17	3.28
3186	3683	3.493699	CCCGACTGACACCTTTTGTTCTA	60.494	47.826	0.00	0.00	39.17	2.10
3203	3700	2.038689	ACCTCTTTCTTCCTTTCCCGAC	59.961	50.000	0.00	0.00	0.00	4.79
3212	3709	5.877564	CACTTCCTAATGACCTCTTTCTTCC	59.122	44.000	0.00	0.00	0.00	3.46
3217	3714	5.770162	CCAAACACTTCCTAATGACCTCTTT	59.230	40.000	0.00	0.00	0.00	2.52
3233	3731	2.653726	TGATGCAGACAACCAAACACT	58.346	42.857	0.00	0.00	0.00	3.55
3234	3732	3.435105	TTGATGCAGACAACCAAACAC	57.565	42.857	5.23	0.00	0.00	3.32
3288	3786	9.920946	TTCTTTCTCTATAAATAAGGTGCCAAT	57.079	29.630	0.00	0.00	0.00	3.16
3289	3787	9.747898	TTTCTTTCTCTATAAATAAGGTGCCAA	57.252	29.630	0.00	0.00	0.00	4.52
3290	3788	9.920946	ATTTCTTTCTCTATAAATAAGGTGCCA	57.079	29.630	0.00	0.00	0.00	4.92
3304	3802	6.945435	TGGGTTGCAATACATTTCTTTCTCTA	59.055	34.615	0.59	0.00	0.00	2.43
3307	3805	5.279456	GGTGGGTTGCAATACATTTCTTTCT	60.279	40.000	0.59	0.00	0.00	2.52
3425	3944	3.139077	GACCTTGACCCAACACAAGTAG	58.861	50.000	0.00	0.00	40.98	2.57
3426	3945	2.506231	TGACCTTGACCCAACACAAGTA	59.494	45.455	0.00	0.00	40.98	2.24
3427	3946	1.283613	TGACCTTGACCCAACACAAGT	59.716	47.619	0.00	0.00	40.98	3.16
3472	3991	6.007703	TCGGTTAATTTCTTGGATTTGAGGT	58.992	36.000	0.00	0.00	0.00	3.85
3482	4001	5.682943	TGGTTGACTCGGTTAATTTCTTG	57.317	39.130	0.00	0.00	0.00	3.02
3520	4039	3.311322	TCCAGTTTGTGCAGTTCGTTTAG	59.689	43.478	0.00	0.00	0.00	1.85
3521	4040	3.271729	TCCAGTTTGTGCAGTTCGTTTA	58.728	40.909	0.00	0.00	0.00	2.01
3522	4041	2.088423	TCCAGTTTGTGCAGTTCGTTT	58.912	42.857	0.00	0.00	0.00	3.60
3532	4051	2.285083	TCACCTCGTTTCCAGTTTGTG	58.715	47.619	0.00	0.00	0.00	3.33
3550	4069	0.697658	TGCCCTTGTGATGTGGATCA	59.302	50.000	0.00	0.00	36.16	2.92
3559	4078	1.299648	CCGGATCTTGCCCTTGTGA	59.700	57.895	0.00	0.00	0.00	3.58

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.