AutoCloner

Multiple sequence alignment - TraesCS3D01G445000

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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	TraesCS3D01G445000	chr3D	100.000	3736	0	0	1	3736	554327857	554331592	0.000000e+00	6900.0
1	TraesCS3D01G445000	chr3D	93.798	1951	101	12	922	2869	554216894	554218827	0.000000e+00	2915.0
2	TraesCS3D01G445000	chr3D	92.015	551	7	23	1	514	10579592	10580142	0.000000e+00	739.0
3	TraesCS3D01G445000	chr3A	94.045	2351	132	4	930	3280	690896634	690898976	0.000000e+00	3559.0
4	TraesCS3D01G445000	chr3A	93.886	1979	100	13	893	2869	690784976	690786935	0.000000e+00	2964.0
5	TraesCS3D01G445000	chr3A	92.587	1929	99	19	930	2854	690857618	690859506	0.000000e+00	2730.0
6	TraesCS3D01G445000	chr3A	92.324	482	25	7	3266	3736	690899154	690899634	0.000000e+00	675.0
7	TraesCS3D01G445000	chr3A	87.571	177	19	3	3389	3562	554389470	554389646	6.330000e-48	202.0
8	TraesCS3D01G445000	chr3B	93.936	1979	99	12	893	2869	736310976	736312935	0.000000e+00	2970.0
9	TraesCS3D01G445000	chr3B	93.264	2019	108	16	936	2940	736325015	736327019	0.000000e+00	2950.0
10	TraesCS3D01G445000	chr1D	91.124	1735	143	7	949	2681	78066974	78065249	0.000000e+00	2340.0
11	TraesCS3D01G445000	chr1D	95.054	930	9	23	1	893	38804638	38805567	0.000000e+00	1428.0
12	TraesCS3D01G445000	chr1D	89.403	670	29	28	1	632	21674293	21673628	0.000000e+00	806.0
13	TraesCS3D01G445000	chr1D	100.000	242	0	0	1	242	32228860	32228619	7.360000e-122	448.0
14	TraesCS3D01G445000	chr1D	100.000	242	0	0	1	242	485952195	485951954	7.360000e-122	448.0
15	TraesCS3D01G445000	chr1D	78.191	188	31	4	3397	3584	469828087	469827910	1.100000e-20	111.0
16	TraesCS3D01G445000	chr1B	88.779	1925	173	21	949	2852	121715450	121713548	0.000000e+00	2318.0
17	TraesCS3D01G445000	chr1B	88.421	95	10	1	3495	3588	115828587	115828681	3.050000e-21	113.0
18	TraesCS3D01G445000	chr1A	89.810	1737	161	9	949	2681	105302947	105304671	0.000000e+00	2213.0
19	TraesCS3D01G445000	chr1A	87.923	1449	173	2	1233	2681	109416571	109415125	0.000000e+00	1705.0
20	TraesCS3D01G445000	chr1A	90.572	297	26	2	970	1265	109416863	109416568	3.500000e-105	392.0
21	TraesCS3D01G445000	chr6D	95.264	929	7	23	1	892	2720275	2719347	0.000000e+00	1437.0
22	TraesCS3D01G445000	chr6D	91.241	959	18	26	1	893	32040686	32039728	0.000000e+00	1245.0
23	TraesCS3D01G445000	chr6D	99.395	661	3	1	233	892	24921273	24920613	0.000000e+00	1197.0
24	TraesCS3D01G445000	chr6D	93.008	615	6	23	1	578	9895684	9896298	0.000000e+00	863.0
25	TraesCS3D01G445000	chrUn	99.397	663	3	1	233	894	100509085	100508423	0.000000e+00	1201.0
26	TraesCS3D01G445000	chrUn	99.246	663	4	1	233	894	95774109	95773447	0.000000e+00	1195.0
27	TraesCS3D01G445000	chrUn	99.092	661	5	1	233	892	96541767	96542427	0.000000e+00	1186.0
28	TraesCS3D01G445000	chrUn	100.000	242	0	0	1	242	93754371	93754612	7.360000e-122	448.0
29	TraesCS3D01G445000	chr7D	99.246	663	4	1	233	894	80303129	80302467	0.000000e+00	1195.0
30	TraesCS3D01G445000	chr7D	99.244	661	4	1	233	892	38680786	38681446	0.000000e+00	1192.0
31	TraesCS3D01G445000	chr7D	99.244	661	4	1	233	892	633343695	633343035	0.000000e+00	1192.0
32	TraesCS3D01G445000	chr2D	99.092	661	5	1	233	892	569343353	569344013	0.000000e+00	1186.0
33	TraesCS3D01G445000	chr5A	82.979	188	21	6	3384	3568	135153771	135153592	3.860000e-35	159.0
34	TraesCS3D01G445000	chr5D	86.765	136	16	2	3454	3588	254825989	254826123	2.320000e-32	150.0
35	TraesCS3D01G445000	chr7A	80.916	131	20	3	3385	3514	727702281	727702155	8.540000e-17	99.0
36	TraesCS3D01G445000	chr4D	91.111	45	4	0	3423	3467	35173185	35173229	1.120000e-05	62.1

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	TraesCS3D01G445000	chr3D	554327857	554331592	3735	False	6900.0	6900	100.0000	1	3736	1	chr3D.!!$F3	3735
1	TraesCS3D01G445000	chr3D	554216894	554218827	1933	False	2915.0	2915	93.7980	922	2869	1	chr3D.!!$F2	1947
2	TraesCS3D01G445000	chr3D	10579592	10580142	550	False	739.0	739	92.0150	1	514	1	chr3D.!!$F1	513
3	TraesCS3D01G445000	chr3A	690784976	690786935	1959	False	2964.0	2964	93.8860	893	2869	1	chr3A.!!$F2	1976
4	TraesCS3D01G445000	chr3A	690857618	690859506	1888	False	2730.0	2730	92.5870	930	2854	1	chr3A.!!$F3	1924
5	TraesCS3D01G445000	chr3A	690896634	690899634	3000	False	2117.0	3559	93.1845	930	3736	2	chr3A.!!$F4	2806
6	TraesCS3D01G445000	chr3B	736310976	736312935	1959	False	2970.0	2970	93.9360	893	2869	1	chr3B.!!$F1	1976
7	TraesCS3D01G445000	chr3B	736325015	736327019	2004	False	2950.0	2950	93.2640	936	2940	1	chr3B.!!$F2	2004
8	TraesCS3D01G445000	chr1D	78065249	78066974	1725	True	2340.0	2340	91.1240	949	2681	1	chr1D.!!$R3	1732
9	TraesCS3D01G445000	chr1D	38804638	38805567	929	False	1428.0	1428	95.0540	1	893	1	chr1D.!!$F1	892
10	TraesCS3D01G445000	chr1D	21673628	21674293	665	True	806.0	806	89.4030	1	632	1	chr1D.!!$R1	631
11	TraesCS3D01G445000	chr1B	121713548	121715450	1902	True	2318.0	2318	88.7790	949	2852	1	chr1B.!!$R1	1903
12	TraesCS3D01G445000	chr1A	105302947	105304671	1724	False	2213.0	2213	89.8100	949	2681	1	chr1A.!!$F1	1732
13	TraesCS3D01G445000	chr1A	109415125	109416863	1738	True	1048.5	1705	89.2475	970	2681	2	chr1A.!!$R1	1711
14	TraesCS3D01G445000	chr6D	2719347	2720275	928	True	1437.0	1437	95.2640	1	892	1	chr6D.!!$R1	891
15	TraesCS3D01G445000	chr6D	32039728	32040686	958	True	1245.0	1245	91.2410	1	893	1	chr6D.!!$R3	892
16	TraesCS3D01G445000	chr6D	24920613	24921273	660	True	1197.0	1197	99.3950	233	892	1	chr6D.!!$R2	659
17	TraesCS3D01G445000	chr6D	9895684	9896298	614	False	863.0	863	93.0080	1	578	1	chr6D.!!$F1	577
18	TraesCS3D01G445000	chrUn	100508423	100509085	662	True	1201.0	1201	99.3970	233	894	1	chrUn.!!$R2	661
19	TraesCS3D01G445000	chrUn	95773447	95774109	662	True	1195.0	1195	99.2460	233	894	1	chrUn.!!$R1	661
20	TraesCS3D01G445000	chrUn	96541767	96542427	660	False	1186.0	1186	99.0920	233	892	1	chrUn.!!$F2	659
21	TraesCS3D01G445000	chr7D	80302467	80303129	662	True	1195.0	1195	99.2460	233	894	1	chr7D.!!$R1	661
22	TraesCS3D01G445000	chr7D	38680786	38681446	660	False	1192.0	1192	99.2440	233	892	1	chr7D.!!$F1	659
23	TraesCS3D01G445000	chr7D	633343035	633343695	660	True	1192.0	1192	99.2440	233	892	1	chr7D.!!$R2	659
24	TraesCS3D01G445000	chr2D	569343353	569344013	660	False	1186.0	1186	99.0920	233	892	1	chr2D.!!$F1	659

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
928	995	0.179163	GTTGCACATCCGGCTTAAGC	60.179	55.0	19.53	19.53	41.14	3.09	F
1017	1089	0.109086	CGAGATGAACCAGACGCACT	60.109	55.0	0.00	0.00	0.00	4.40	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2555	2665	0.317160	TCTCCACGATGAACGCTGTT	59.683	50.000	0.0	0.0	46.94	3.16	R
2995	3137	1.628846	AGGGAGGTTTGACGCACTTAT	59.371	47.619	0.0	0.0	0.00	1.73	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
294	332	9.296400	ACAAATTAAACAATGAACTACACACAC	57.704	29.630	0.00	0.00	0.00	3.82
478	516	2.785776	AAACCCACCACCCCCTTCC	61.786	63.158	0.00	0.00	0.00	3.46
900	967	8.904834	CCTCTTTTTCTACTAGTGTAGCTATCA	58.095	37.037	5.39	0.00	44.26	2.15
909	976	9.509855	CTACTAGTGTAGCTATCAAGTTTTCTG	57.490	37.037	5.39	0.00	39.56	3.02
910	977	7.897864	ACTAGTGTAGCTATCAAGTTTTCTGT	58.102	34.615	0.00	0.00	0.00	3.41
911	978	8.368668	ACTAGTGTAGCTATCAAGTTTTCTGTT	58.631	33.333	0.00	0.00	0.00	3.16
912	979	7.426929	AGTGTAGCTATCAAGTTTTCTGTTG	57.573	36.000	0.00	0.00	0.00	3.33
913	980	6.073003	AGTGTAGCTATCAAGTTTTCTGTTGC	60.073	38.462	0.00	0.00	0.00	4.17
914	981	5.762711	TGTAGCTATCAAGTTTTCTGTTGCA	59.237	36.000	0.00	0.00	0.00	4.08
915	982	5.113502	AGCTATCAAGTTTTCTGTTGCAC	57.886	39.130	0.00	0.00	0.00	4.57
916	983	4.580167	AGCTATCAAGTTTTCTGTTGCACA	59.420	37.500	0.00	0.00	0.00	4.57
917	984	5.242393	AGCTATCAAGTTTTCTGTTGCACAT	59.758	36.000	0.00	0.00	0.00	3.21
918	985	5.570589	GCTATCAAGTTTTCTGTTGCACATC	59.429	40.000	0.00	0.00	0.00	3.06
920	987	3.044986	CAAGTTTTCTGTTGCACATCCG	58.955	45.455	0.00	0.00	0.00	4.18
921	988	1.608590	AGTTTTCTGTTGCACATCCGG	59.391	47.619	0.00	0.00	0.00	5.14
922	989	0.313672	TTTTCTGTTGCACATCCGGC	59.686	50.000	0.00	0.00	0.00	6.13
923	990	0.537143	TTTCTGTTGCACATCCGGCT	60.537	50.000	0.00	0.00	0.00	5.52
924	991	0.537143	TTCTGTTGCACATCCGGCTT	60.537	50.000	0.00	0.00	0.00	4.35
925	992	0.323302	TCTGTTGCACATCCGGCTTA	59.677	50.000	0.00	0.00	0.00	3.09
926	993	1.164411	CTGTTGCACATCCGGCTTAA	58.836	50.000	0.00	0.00	0.00	1.85
927	994	1.131126	CTGTTGCACATCCGGCTTAAG	59.869	52.381	0.00	0.00	0.00	1.85
928	995	0.179163	GTTGCACATCCGGCTTAAGC	60.179	55.000	19.53	19.53	41.14	3.09
982	1054	9.663904	CCAATCAGTTACGTATTTGATTAATGG	57.336	33.333	23.51	19.83	37.98	3.16
1017	1089	0.109086	CGAGATGAACCAGACGCACT	60.109	55.000	0.00	0.00	0.00	4.40
1211	1284	1.145156	CGTCACCGAATGCCCCATA	59.855	57.895	0.00	0.00	35.63	2.74
1247	1320	0.528249	ACGTGTACCGCTTCAACGTT	60.528	50.000	0.00	0.00	41.42	3.99
1797	1907	3.781307	CGCAGATCCCGGGGTTCA	61.781	66.667	23.50	0.00	0.00	3.18
2024	2134	1.525995	CCGTGGCACCAACAAGACT	60.526	57.895	12.86	0.00	0.00	3.24
2129	2239	0.179100	TCGAGAGGTACTACGACGGG	60.179	60.000	0.00	0.00	41.55	5.28
2297	2407	3.675086	CACCTCGGTGGAGATCATG	57.325	57.895	8.22	0.00	43.27	3.07
2363	2473	2.544685	CTCCATGGCTACGACTTCTTG	58.455	52.381	6.96	0.00	0.00	3.02
2366	2476	2.615493	CCATGGCTACGACTTCTTGGTT	60.615	50.000	0.00	0.00	0.00	3.67
2408	2518	1.449601	CAATCCCAAGACGGACCCG	60.450	63.158	6.94	6.94	46.03	5.28
2420	2530	1.346722	ACGGACCCGAAGAAGTTCAAT	59.653	47.619	16.07	0.00	42.83	2.57
2432	2542	3.818773	AGAAGTTCAATTACCACAACCCG	59.181	43.478	5.50	0.00	0.00	5.28
2434	2544	0.875728	TTCAATTACCACAACCCGCG	59.124	50.000	0.00	0.00	0.00	6.46
2447	2557	4.379243	CCGCGGCTGAGGAACACT	62.379	66.667	14.67	0.00	37.19	3.55
2555	2665	0.105913	ACATCATCATGGGCATGGCA	60.106	50.000	22.06	7.72	39.24	4.92
2627	2737	0.740868	CGCCGCCAGAATTCAAGAGA	60.741	55.000	8.44	0.00	0.00	3.10
2686	2803	2.573609	ATCTGGGTAAGGACGTGCGC	62.574	60.000	0.00	0.00	0.00	6.09
2854	2992	4.776349	TCCATTGTAGTGTGTGAACTGTT	58.224	39.130	0.00	0.00	0.00	3.16
2855	2993	4.574421	TCCATTGTAGTGTGTGAACTGTTG	59.426	41.667	0.00	0.00	0.00	3.33
2885	3027	6.323225	GTCCAGTAGCTATAGGGTTCAGTTTA	59.677	42.308	12.80	0.00	0.00	2.01
2888	3030	7.494952	CCAGTAGCTATAGGGTTCAGTTTAAAC	59.505	40.741	10.47	10.47	0.00	2.01
2992	3134	2.546778	GAAACCACGTCAGAGTGTTGA	58.453	47.619	0.00	0.00	40.33	3.18
2995	3137	4.330944	AACCACGTCAGAGTGTTGATAA	57.669	40.909	0.00	0.00	40.33	1.75
3043	3185	7.680442	TCGTTTGATCTAAATCCAATTGTCA	57.320	32.000	4.43	0.00	0.00	3.58
3179	3321	6.485830	TTGGTTGGATCACAAAATTTGGTA	57.514	33.333	10.71	0.00	41.58	3.25
3188	3330	3.639094	CACAAAATTTGGTAGGGGTGTGA	59.361	43.478	10.71	0.00	37.84	3.58
3242	3384	1.466856	GCTGATCTGCCCATGTTTCA	58.533	50.000	13.26	0.00	0.00	2.69
3288	3621	0.836606	TTTCCATCGCATAGCCCTCA	59.163	50.000	0.00	0.00	0.00	3.86
3306	3639	4.506625	CCCTCACCAAAACTCTGTAATGGA	60.507	45.833	8.15	0.00	35.16	3.41
3347	3680	5.477637	GTGATATACCTCTAGAAGTGGGGTC	59.522	48.000	4.14	0.00	33.33	4.46
3348	3681	2.842645	TACCTCTAGAAGTGGGGTCC	57.157	55.000	4.14	0.00	33.33	4.46
3358	3691	2.530661	TGGGGTCCCATTGGTCGT	60.531	61.111	10.98	0.00	41.89	4.34
3408	3741	2.945984	CACATGTGTGGCACGGAC	59.054	61.111	18.03	7.16	42.10	4.79
3493	3826	5.486526	TGTCAAACATGGCAACTTTCTTTT	58.513	33.333	0.00	0.00	37.61	2.27
3591	3931	0.663153	GGATTGCTTCGTACCATGGC	59.337	55.000	13.04	0.00	0.00	4.40
3605	3945	3.711863	ACCATGGCACTTATCATTTGGT	58.288	40.909	13.04	0.00	0.00	3.67
3637	3977	5.713025	ACAGTGGATGTGAATTTTATGTGC	58.287	37.500	0.00	0.00	41.91	4.57
3676	4016	5.534207	TGAAACTGAGGCAAATGATTTGT	57.466	34.783	18.12	0.37	42.56	2.83
3678	4018	4.525912	AACTGAGGCAAATGATTTGTCC	57.474	40.909	17.95	17.83	46.09	4.02
3697	4040	8.893563	TTTGTCCCATTCATTAAATAAGGAGT	57.106	30.769	0.00	0.00	32.38	3.85
3729	4072	0.409092	ACATGAACCCAATGCCAGGA	59.591	50.000	0.00	0.00	0.00	3.86
3731	4074	1.205417	CATGAACCCAATGCCAGGAAC	59.795	52.381	0.00	0.00	0.00	3.62
3732	4075	0.187117	TGAACCCAATGCCAGGAACA	59.813	50.000	0.00	0.00	0.00	3.18
3734	4077	1.273327	GAACCCAATGCCAGGAACAAG	59.727	52.381	0.00	0.00	0.00	3.16
3735	4078	1.187567	ACCCAATGCCAGGAACAAGC	61.188	55.000	0.00	0.00	0.00	4.01

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
294	332	8.785468	TTCATGTGTCATTGATAAAATATGCG	57.215	30.769	0.00	0.00	0.00	4.73
478	516	4.024556	ACTCAGCTCACTTCACAATTTTCG	60.025	41.667	0.00	0.00	0.00	3.46
909	976	0.179163	GCTTAAGCCGGATGTGCAAC	60.179	55.000	17.00	0.00	34.31	4.17
910	977	0.322456	AGCTTAAGCCGGATGTGCAA	60.322	50.000	23.71	0.00	43.38	4.08
911	978	0.322456	AAGCTTAAGCCGGATGTGCA	60.322	50.000	23.71	0.00	43.38	4.57
912	979	1.663695	TAAGCTTAAGCCGGATGTGC	58.336	50.000	23.71	4.39	43.38	4.57
913	980	2.476619	CGATAAGCTTAAGCCGGATGTG	59.523	50.000	23.71	4.73	43.38	3.21
914	981	2.102588	ACGATAAGCTTAAGCCGGATGT	59.897	45.455	23.71	14.12	43.38	3.06
915	982	2.731976	GACGATAAGCTTAAGCCGGATG	59.268	50.000	23.71	13.49	43.38	3.51
916	983	2.628657	AGACGATAAGCTTAAGCCGGAT	59.371	45.455	23.71	14.14	43.38	4.18
917	984	2.029623	AGACGATAAGCTTAAGCCGGA	58.970	47.619	23.71	9.79	43.38	5.14
918	985	2.510768	AGACGATAAGCTTAAGCCGG	57.489	50.000	23.71	10.91	43.38	6.13
920	987	5.993106	AATCAAGACGATAAGCTTAAGCC	57.007	39.130	23.71	7.58	36.14	4.35
921	988	7.701809	ACTAATCAAGACGATAAGCTTAAGC	57.298	36.000	20.09	20.09	35.88	3.09
925	992	9.088512	CAGTTAACTAATCAAGACGATAAGCTT	57.911	33.333	8.04	3.48	32.51	3.74
926	993	8.251721	ACAGTTAACTAATCAAGACGATAAGCT	58.748	33.333	8.04	0.00	32.51	3.74
927	994	8.408743	ACAGTTAACTAATCAAGACGATAAGC	57.591	34.615	8.04	0.00	32.51	3.09
982	1054	0.792640	CTCGTGCACCTGAACATCAC	59.207	55.000	12.15	0.00	0.00	3.06
1017	1089	1.674359	ATCTTGGTCGTGTTGCACAA	58.326	45.000	0.00	0.00	33.40	3.33
1061	1134	4.175337	ATGTCGATGGTGGGGCCG	62.175	66.667	0.00	0.00	41.21	6.13
1280	1382	2.654877	CGGAGGCAGGTAACGTGT	59.345	61.111	0.00	0.00	46.39	4.49
1668	1770	2.736995	CGCGACGGTCACCATGTT	60.737	61.111	0.00	0.00	0.00	2.71
2009	2119	1.723608	CGCAAGTCTTGTTGGTGCCA	61.724	55.000	14.03	0.00	31.41	4.92
2129	2239	2.033194	GTACAGGCCACTTGTCCGC	61.033	63.158	5.01	0.00	0.00	5.54
2408	2518	5.562113	CGGGTTGTGGTAATTGAACTTCTTC	60.562	44.000	0.00	0.00	0.00	2.87
2432	2542	2.031163	ACAGTGTTCCTCAGCCGC	59.969	61.111	0.00	0.00	0.00	6.53
2434	2544	1.227943	TGCACAGTGTTCCTCAGCC	60.228	57.895	1.61	0.00	0.00	4.85
2555	2665	0.317160	TCTCCACGATGAACGCTGTT	59.683	50.000	0.00	0.00	46.94	3.16
2649	2759	6.044871	ACCCAGATTAATTAGCTCTATGGCTT	59.955	38.462	0.00	0.00	42.97	4.35
2841	2979	1.816224	ACCAACCAACAGTTCACACAC	59.184	47.619	0.00	0.00	36.18	3.82
2855	2993	2.633481	CCCTATAGCTACTGGACCAACC	59.367	54.545	13.68	0.00	39.54	3.77
2867	3009	6.154021	TCTCGTTTAAACTGAACCCTATAGCT	59.846	38.462	16.01	0.00	0.00	3.32
2868	3010	6.335777	TCTCGTTTAAACTGAACCCTATAGC	58.664	40.000	16.01	0.00	0.00	2.97
2869	3011	6.979238	CCTCTCGTTTAAACTGAACCCTATAG	59.021	42.308	16.01	0.00	0.00	1.31
2870	3012	6.438425	ACCTCTCGTTTAAACTGAACCCTATA	59.562	38.462	16.01	0.00	0.00	1.31
2871	3013	5.247792	ACCTCTCGTTTAAACTGAACCCTAT	59.752	40.000	16.01	0.00	0.00	2.57
2872	3014	4.590222	ACCTCTCGTTTAAACTGAACCCTA	59.410	41.667	16.01	0.20	0.00	3.53
2885	3027	3.428589	GCCAGTTCGTATACCTCTCGTTT	60.429	47.826	0.00	0.00	0.00	3.60
2888	3030	1.948145	AGCCAGTTCGTATACCTCTCG	59.052	52.381	0.00	0.00	0.00	4.04
2980	3122	5.577164	ACGCACTTATTATCAACACTCTGAC	59.423	40.000	0.00	0.00	0.00	3.51
2985	3127	6.348213	GGTTTGACGCACTTATTATCAACACT	60.348	38.462	0.00	0.00	0.00	3.55
2986	3128	5.793457	GGTTTGACGCACTTATTATCAACAC	59.207	40.000	0.00	0.00	0.00	3.32
2992	3134	4.080526	AGGGAGGTTTGACGCACTTATTAT	60.081	41.667	0.00	0.00	0.00	1.28
2995	3137	1.628846	AGGGAGGTTTGACGCACTTAT	59.371	47.619	0.00	0.00	0.00	1.73
3043	3185	5.990996	CCTTTTGGTTTGCAGTATGATTTGT	59.009	36.000	0.00	0.00	33.78	2.83
3117	3259	7.500559	GCATCAAGATTCCCATTTTACTAGTCT	59.499	37.037	0.00	0.00	0.00	3.24
3121	3263	8.537728	AATGCATCAAGATTCCCATTTTACTA	57.462	30.769	0.00	0.00	0.00	1.82
3131	3273	6.205101	AGAGTCAAAATGCATCAAGATTCC	57.795	37.500	0.00	0.00	0.00	3.01
3179	3321	1.228367	CTGCTTGCTTCACACCCCT	60.228	57.895	0.00	0.00	0.00	4.79
3188	3330	2.123769	TGTGGTGGCTGCTTGCTT	60.124	55.556	0.00	0.00	42.39	3.91
3203	3345	2.518349	CCCACAAAGTGCGGGTGT	60.518	61.111	0.00	0.00	35.03	4.16
3242	3384	4.382685	CCCTCTATACACGACCATGTTTGT	60.383	45.833	0.00	0.00	33.85	2.83
3254	3396	5.770417	CGATGGAAAGTACCCTCTATACAC	58.230	45.833	0.00	0.00	0.00	2.90
3288	3621	8.877864	TTATGAATCCATTACAGAGTTTTGGT	57.122	30.769	0.00	0.00	34.31	3.67
3316	3649	8.145122	CACTTCTAGAGGTATATCACTTTTCCC	58.855	40.741	7.25	0.00	0.00	3.97
3347	3680	5.828299	AAATATGTGTAACGACCAATGGG	57.172	39.130	3.55	0.00	42.39	4.00
3408	3741	1.440850	CGTTCGCAGTTGCCATGTG	60.441	57.895	0.00	0.00	37.91	3.21
3435	3768	4.623932	TCCTCATGTCACTAAACTTGCT	57.376	40.909	0.00	0.00	0.00	3.91
3476	3809	4.503643	CCATCCAAAAGAAAGTTGCCATGT	60.504	41.667	0.00	0.00	0.00	3.21
3488	3821	7.654022	AAACTGAAACTTACCATCCAAAAGA	57.346	32.000	0.00	0.00	0.00	2.52
3568	3902	0.322322	TGGTACGAAGCAATCCGGTT	59.678	50.000	0.00	0.00	38.27	4.44
3572	3906	0.663153	GCCATGGTACGAAGCAATCC	59.337	55.000	14.67	0.00	36.53	3.01
3605	3945	9.442047	AAAATTCACATCCACTGTTTACAAAAA	57.558	25.926	0.00	0.00	35.29	1.94
3646	3986	7.669427	TCATTTGCCTCAGTTTCATACAAAAT	58.331	30.769	0.00	0.00	0.00	1.82
3653	3993	6.105397	ACAAATCATTTGCCTCAGTTTCAT	57.895	33.333	10.21	0.00	44.39	2.57
3676	4016	7.559897	GTCCAACTCCTTATTTAATGAATGGGA	59.440	37.037	0.00	0.00	33.24	4.37
3678	4018	8.292444	TGTCCAACTCCTTATTTAATGAATGG	57.708	34.615	0.00	0.00	0.00	3.16
3697	4040	4.956700	TGGGTTCATGTAACTTTTGTCCAA	59.043	37.500	0.00	0.00	38.23	3.53

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.