AutoCloner

Multiple sequence alignment - TraesCS6A01G024200

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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	TraesCS6A01G024200	chr6A	100.000	4037	0	0	1	4037	12076818	12080854	0.000000e+00	7456
1	TraesCS6A01G024200	chr6A	84.490	2998	451	12	102	3093	12055467	12058456	0.000000e+00	2948
2	TraesCS6A01G024200	chr6D	93.647	3384	193	9	1	3377	10452160	10455528	0.000000e+00	5038
3	TraesCS6A01G024200	chr6D	93.962	265	5	2	3784	4037	10456678	10456942	1.360000e-104	390
4	TraesCS6A01G024200	chr6D	90.551	254	15	5	3372	3616	10455570	10455823	1.080000e-85	327
5	TraesCS6A01G024200	chr6D	97.183	142	3	1	3614	3754	10456536	10456677	5.210000e-59	239
6	TraesCS6A01G024200	chr6D	89.241	158	13	4	3221	3374	36811689	36811846	1.140000e-45	195
7	TraesCS6A01G024200	chr6D	88.742	151	14	3	3223	3371	428908350	428908499	8.910000e-42	182
8	TraesCS6A01G024200	chr6B	86.894	3174	390	19	1	3158	19232984	19236147	0.000000e+00	3533
9	TraesCS6A01G024200	chr6B	84.335	3211	468	20	1	3203	19240152	19243335	0.000000e+00	3110
10	TraesCS6A01G024200	chr6B	83.175	422	51	12	3368	3772	19243332	19243750	6.370000e-98	368
11	TraesCS6A01G024200	chr6B	88.158	152	17	1	3221	3371	49768922	49768771	3.210000e-41	180
12	TraesCS6A01G024200	chr6B	94.737	76	4	0	3828	3903	19537339	19537414	7.090000e-23	119
13	TraesCS6A01G024200	chr5D	80.850	3081	549	31	1	3057	33679483	33676420	0.000000e+00	2383
14	TraesCS6A01G024200	chr5D	87.662	154	18	1	3222	3374	291881916	291881763	1.150000e-40	178
15	TraesCS6A01G024200	chr5A	80.195	2560	463	29	524	3057	22211313	22208772	0.000000e+00	1879
16	TraesCS6A01G024200	chr5A	86.139	101	14	0	437	537	22220145	22220045	4.270000e-20	110
17	TraesCS6A01G024200	chr1D	81.941	1700	303	3	62	1757	203268432	203270131	0.000000e+00	1435
18	TraesCS6A01G024200	chr1D	89.677	155	13	3	3221	3373	36843400	36843553	1.140000e-45	195
19	TraesCS6A01G024200	chr1B	81.775	1701	304	5	62	1757	297057028	297058727	0.000000e+00	1419
20	TraesCS6A01G024200	chr1A	81.717	1701	305	5	62	1757	257415527	257417226	0.000000e+00	1413
21	TraesCS6A01G024200	chr4D	77.983	595	110	13	2434	3019	509482481	509481899	1.780000e-93	353
22	TraesCS6A01G024200	chr3D	88.816	152	16	1	3221	3371	91710777	91710928	6.890000e-43	185
23	TraesCS6A01G024200	chr7D	88.158	152	17	1	3221	3371	161541404	161541253	3.210000e-41	180
24	TraesCS6A01G024200	chrUn	88.158	152	15	2	3221	3371	96478374	96478225	1.150000e-40	178

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	TraesCS6A01G024200	chr6A	12076818	12080854	4036	False	7456.0	7456	100.00000	1	4037	1	chr6A.!!$F2	4036
1	TraesCS6A01G024200	chr6A	12055467	12058456	2989	False	2948.0	2948	84.49000	102	3093	1	chr6A.!!$F1	2991
2	TraesCS6A01G024200	chr6D	10452160	10456942	4782	False	1498.5	5038	93.83575	1	4037	4	chr6D.!!$F3	4036
3	TraesCS6A01G024200	chr6B	19232984	19236147	3163	False	3533.0	3533	86.89400	1	3158	1	chr6B.!!$F1	3157
4	TraesCS6A01G024200	chr6B	19240152	19243750	3598	False	1739.0	3110	83.75500	1	3772	2	chr6B.!!$F3	3771
5	TraesCS6A01G024200	chr5D	33676420	33679483	3063	True	2383.0	2383	80.85000	1	3057	1	chr5D.!!$R1	3056
6	TraesCS6A01G024200	chr5A	22208772	22211313	2541	True	1879.0	1879	80.19500	524	3057	1	chr5A.!!$R1	2533
7	TraesCS6A01G024200	chr1D	203268432	203270131	1699	False	1435.0	1435	81.94100	62	1757	1	chr1D.!!$F2	1695
8	TraesCS6A01G024200	chr1B	297057028	297058727	1699	False	1419.0	1419	81.77500	62	1757	1	chr1B.!!$F1	1695
9	TraesCS6A01G024200	chr1A	257415527	257417226	1699	False	1413.0	1413	81.71700	62	1757	1	chr1A.!!$F1	1695
10	TraesCS6A01G024200	chr4D	509481899	509482481	582	True	353.0	353	77.98300	2434	3019	1	chr4D.!!$R1	585

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
643	654	0.107312	ACTCGCTACCGGAGAAGCTA	60.107	55.000	9.46	5.35	34.84	3.32	F
1588	1600	0.253894	TCTGTGTGATGGCCTCATGG	59.746	55.000	3.32	0.00	35.97	3.66	F
1773	1785	1.680249	GGGAATCAGCTGACAGGGAAC	60.680	57.143	20.97	5.25	0.00	3.62	F
2772	2801	1.396996	CGTTTAACAGGCTCCATTCCG	59.603	52.381	0.00	0.00	0.00	4.30	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1933	1945	0.034896	ACCACTGCTTGTAGTTCCCG	59.965	55.0	0.00	0.00	0.00	5.14	R
2648	2677	0.035915	GTCAAGGAACTCCAGGAGCC	60.036	60.0	17.31	10.65	38.49	4.70	R
2876	2911	0.534877	TTGCTGCGTGTGGTCTTGAT	60.535	50.0	0.00	0.00	0.00	2.57	R
3936	4761	0.687920	TTGGTCTTCGGTGGTATGCA	59.312	50.0	0.00	0.00	0.00	3.96	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
26	28	2.997315	CCACGGAGTCAGAGGCCA	60.997	66.667	5.01	0.00	41.61	5.36
30	32	2.286523	CGGAGTCAGAGGCCAAGGT	61.287	63.158	5.01	0.00	0.00	3.50
88	90	2.759114	CTCTCCAGCTGGGCCAAA	59.241	61.111	32.23	12.04	36.21	3.28
379	384	1.402259	CTTGTCGACCTGCGTCTCTAT	59.598	52.381	14.12	0.00	41.80	1.98
400	405	0.107897	ACAATAACCTCGCCGATGCA	60.108	50.000	0.00	0.00	37.32	3.96
415	420	2.757099	GCAATCCCCCACCAGCTG	60.757	66.667	6.78	6.78	0.00	4.24
442	447	3.560105	GCTCCCTAGGATCAAGCATTTT	58.440	45.455	11.48	0.00	0.00	1.82
463	468	0.622665	ATCTGGGCTCCAACTTCCTG	59.377	55.000	0.00	0.00	30.80	3.86
465	470	0.401738	CTGGGCTCCAACTTCCTGAA	59.598	55.000	0.00	0.00	30.80	3.02
466	471	0.850100	TGGGCTCCAACTTCCTGAAA	59.150	50.000	0.00	0.00	0.00	2.69
470	475	2.693074	GGCTCCAACTTCCTGAAAAACA	59.307	45.455	0.00	0.00	0.00	2.83
471	476	3.243535	GGCTCCAACTTCCTGAAAAACAG	60.244	47.826	0.00	0.00	45.36	3.16
507	518	2.755469	GCCAATGCCCACCGTCAT	60.755	61.111	0.00	0.00	0.00	3.06
547	558	1.296715	CTACCTCACCGGCAGCTTT	59.703	57.895	0.00	0.00	35.61	3.51
586	597	0.676782	GCGGCAACATCACCTACCTT	60.677	55.000	0.00	0.00	0.00	3.50
601	612	4.153411	CCTACCTTGACCTATCGGAGAAT	58.847	47.826	0.00	0.00	43.58	2.40
602	613	4.021894	CCTACCTTGACCTATCGGAGAATG	60.022	50.000	0.00	0.00	43.58	2.67
605	616	5.394738	ACCTTGACCTATCGGAGAATGATA	58.605	41.667	0.00	0.00	43.58	2.15
610	621	6.726379	TGACCTATCGGAGAATGATATCTCT	58.274	40.000	3.98	0.00	44.30	3.10
623	634	3.980022	TGATATCTCTGGGCCAATACCAA	59.020	43.478	8.04	0.00	37.59	3.67
631	642	1.407712	GGGCCAATACCAAACTCGCTA	60.408	52.381	4.39	0.00	0.00	4.26
643	654	0.107312	ACTCGCTACCGGAGAAGCTA	60.107	55.000	9.46	5.35	34.84	3.32
676	687	4.704965	AGTACCTCAACTTGTCCTTGAAC	58.295	43.478	0.00	0.00	0.00	3.18
790	801	2.460669	GATTTTCTTGGGTCCATGCCT	58.539	47.619	0.00	0.00	0.00	4.75
967	979	0.389948	GGAGTTGTCGGCGAATGAGT	60.390	55.000	12.92	3.01	0.00	3.41
1070	1082	4.057432	CAAATTCCGGCAGTTTTGTTCAT	58.943	39.130	0.00	0.00	0.00	2.57
1304	1316	2.037136	GCAACCTCACGCAGCTCAT	61.037	57.895	0.00	0.00	0.00	2.90
1400	1412	2.174639	TCTTGGATGTCAACACCAACCT	59.825	45.455	10.95	0.00	38.52	3.50
1520	1532	0.548510	GGTAAGGGGCTGAGCTTGAT	59.451	55.000	3.72	0.00	0.00	2.57
1588	1600	0.253894	TCTGTGTGATGGCCTCATGG	59.746	55.000	3.32	0.00	35.97	3.66
1604	1616	5.688807	CCTCATGGTAGAGAATTTCATGGT	58.311	41.667	0.00	0.00	37.87	3.55
1666	1678	4.225942	TCAAGAACTGCACATCCCTATTCT	59.774	41.667	0.00	0.00	0.00	2.40
1669	1681	4.018960	AGAACTGCACATCCCTATTCTGTT	60.019	41.667	0.00	0.00	0.00	3.16
1773	1785	1.680249	GGGAATCAGCTGACAGGGAAC	60.680	57.143	20.97	5.25	0.00	3.62
1794	1806	1.805943	CTGTCGCATGATTGGTCACAA	59.194	47.619	0.00	0.00	41.59	3.33
1933	1945	2.282745	AGCTCCCAAGTTGCTGGC	60.283	61.111	0.00	0.94	35.54	4.85
1936	1948	4.659172	TCCCAAGTTGCTGGCGGG	62.659	66.667	0.00	0.00	38.34	6.13
1992	2004	4.027437	GCAATGGGTTCTGGGGTAAATTA	58.973	43.478	0.00	0.00	0.00	1.40
2092	2104	2.622942	TCTGTCATTGAAACCTGTTGCC	59.377	45.455	0.00	0.00	0.00	4.52
2222	2238	7.301868	ACAATTTTAGTGGTGTCATTCCATT	57.698	32.000	0.00	0.00	37.30	3.16
2342	2370	2.035961	TGGAACAACTCTCGTCTTGGAG	59.964	50.000	0.00	0.00	31.92	3.86
2360	2388	6.828273	TCTTGGAGAACAACATCTTCTGAAAA	59.172	34.615	0.00	0.00	34.76	2.29
2601	2630	4.307432	GTCTCCGATTCTTGAACTTGTCA	58.693	43.478	0.00	0.00	0.00	3.58
2616	2645	5.852738	ACTTGTCAAGAAATGATCTGTCG	57.147	39.130	19.53	0.00	40.97	4.35
2618	2647	4.535526	TGTCAAGAAATGATCTGTCGGA	57.464	40.909	0.00	0.00	40.97	4.55
2629	2658	5.707242	TGATCTGTCGGATAGTATTCCAC	57.293	43.478	1.55	0.00	35.34	4.02
2692	2721	3.399330	TCATGGAACGAACTTTCAGGTC	58.601	45.455	0.00	0.00	0.00	3.85
2728	2757	3.410631	TCTCAAATTTGCCGTACCTCA	57.589	42.857	13.54	0.00	0.00	3.86
2754	2783	4.514066	GTGTTAAATCTCTCCAACAACCGT	59.486	41.667	0.00	0.00	33.04	4.83
2760	2789	4.139859	TCTCTCCAACAACCGTTTAACA	57.860	40.909	0.00	0.00	31.13	2.41
2764	2793	1.679153	CCAACAACCGTTTAACAGGCT	59.321	47.619	6.03	0.00	31.13	4.58
2772	2801	1.396996	CGTTTAACAGGCTCCATTCCG	59.603	52.381	0.00	0.00	0.00	4.30
2875	2910	0.764890	TTGTCTGGGTGAGGGAACTG	59.235	55.000	0.00	0.00	44.43	3.16
2876	2911	0.105194	TGTCTGGGTGAGGGAACTGA	60.105	55.000	0.00	0.00	44.43	3.41
2877	2912	1.280457	GTCTGGGTGAGGGAACTGAT	58.720	55.000	0.00	0.00	44.43	2.90
2889	2924	2.069273	GGAACTGATCAAGACCACACG	58.931	52.381	0.00	0.00	0.00	4.49
3006	3041	1.918957	CCATGGAGGGTTTCCTTCTCT	59.081	52.381	5.56	0.00	46.92	3.10
3067	3102	4.843728	TCCTCAGGTGTAATGTGGATTTC	58.156	43.478	0.00	0.00	35.86	2.17
3111	3146	6.324819	CAAGTGACCAAATAATAGCAGGTTG	58.675	40.000	0.00	0.00	31.57	3.77
3209	3253	6.092807	GTCTGCTTGAAAATAAGTACTCCCTG	59.907	42.308	0.00	0.00	0.00	4.45
3210	3254	5.876357	TGCTTGAAAATAAGTACTCCCTGT	58.124	37.500	0.00	0.00	0.00	4.00
3211	3255	5.705441	TGCTTGAAAATAAGTACTCCCTGTG	59.295	40.000	0.00	0.00	0.00	3.66
3212	3256	5.705905	GCTTGAAAATAAGTACTCCCTGTGT	59.294	40.000	0.00	0.00	0.00	3.72
3213	3257	6.206829	GCTTGAAAATAAGTACTCCCTGTGTT	59.793	38.462	0.00	0.00	0.00	3.32
3214	3258	7.573283	GCTTGAAAATAAGTACTCCCTGTGTTC	60.573	40.741	0.00	0.00	0.00	3.18
3215	3259	6.235664	TGAAAATAAGTACTCCCTGTGTTCC	58.764	40.000	0.00	0.00	0.00	3.62
3216	3260	6.043938	TGAAAATAAGTACTCCCTGTGTTCCT	59.956	38.462	0.00	0.00	0.00	3.36
3217	3261	7.236019	TGAAAATAAGTACTCCCTGTGTTCCTA	59.764	37.037	0.00	0.00	0.00	2.94
3218	3262	7.563724	AAATAAGTACTCCCTGTGTTCCTAA	57.436	36.000	0.00	0.00	0.00	2.69
3219	3263	7.563724	AATAAGTACTCCCTGTGTTCCTAAA	57.436	36.000	0.00	0.00	0.00	1.85
3259	3303	9.692325	AGTTCTTTTAGAGATTTCAATATGGCT	57.308	29.630	0.00	0.00	33.49	4.75
3282	3326	6.038603	GCTACATATGGAGCAAAATGAGTGAA	59.961	38.462	31.23	0.00	38.62	3.18
3342	3390	8.114331	TGTAGTCCGTAGTGAAATCTCTTAAA	57.886	34.615	0.00	0.00	0.00	1.52
3346	3394	7.813627	AGTCCGTAGTGAAATCTCTTAAAAGTC	59.186	37.037	0.00	0.00	0.00	3.01
3391	3486	7.119846	GGAGTAATGAGTATTGCCACCATATTC	59.880	40.741	0.00	0.00	31.50	1.75
3400	3495	4.248174	TGCCACCATATTCAAATCCTGA	57.752	40.909	0.00	0.00	0.00	3.86
3426	3521	7.684062	ATTACAACATTAAGCATCGATTTGC	57.316	32.000	2.71	2.71	43.09	3.68
3574	3683	0.523072	GCATCAGCACATCAAACGGT	59.477	50.000	0.00	0.00	41.58	4.83
3604	3713	3.241530	ACCGAAGCTGTGCCTCCA	61.242	61.111	0.00	0.00	0.00	3.86
3609	3718	3.951769	AAGCTGTGCCTCCATGCCC	62.952	63.158	0.00	0.00	0.00	5.36
3745	4570	2.926242	TCGTTGGAGGTGGGGGAC	60.926	66.667	0.00	0.00	0.00	4.46
3764	4589	3.220999	CTTGACGGCGAGGTGGACA	62.221	63.158	16.62	0.00	0.00	4.02
3907	4732	1.424493	CCAGCAAGACGAGGAATCGC	61.424	60.000	0.00	0.00	36.44	4.58
3936	4761	3.202829	TCGTTTTAACCTTCCTGCACT	57.797	42.857	0.00	0.00	0.00	4.40
4019	4855	2.359975	GGTTCCACCAAGCCTCCG	60.360	66.667	0.00	0.00	38.42	4.63
4031	4867	0.036306	AGCCTCCGGTCGTGAATTTT	59.964	50.000	0.00	0.00	0.00	1.82

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
10	12	1.079543	CTTGGCCTCTGACTCCGTG	60.080	63.158	3.32	0.00	0.00	4.94
19	21	0.980231	CTAGGAGCACCTTGGCCTCT	60.980	60.000	8.39	0.00	45.36	3.69
26	28	2.183679	CTTCCAGTCTAGGAGCACCTT	58.816	52.381	8.39	0.00	45.36	3.50
30	32	0.978146	GGCCTTCCAGTCTAGGAGCA	60.978	60.000	0.00	0.00	39.25	4.26
238	243	0.814410	TGGCGCCGACAAAGTTGTTA	60.814	50.000	23.90	0.00	42.43	2.41
379	384	2.206750	GCATCGGCGAGGTTATTGTTA	58.793	47.619	23.12	0.00	0.00	2.41
400	405	2.988839	GCTCAGCTGGTGGGGGATT	61.989	63.158	15.13	0.00	0.00	3.01
415	420	0.470833	TGATCCTAGGGAGCCTGCTC	60.471	60.000	9.46	10.68	37.30	4.26
442	447	0.620556	GGAAGTTGGAGCCCAGATCA	59.379	55.000	0.00	0.00	33.81	2.92
463	468	1.886886	TGCGGTAGTCCCTGTTTTTC	58.113	50.000	0.00	0.00	0.00	2.29
465	470	1.142262	ACTTGCGGTAGTCCCTGTTTT	59.858	47.619	0.00	0.00	0.00	2.43
466	471	0.763035	ACTTGCGGTAGTCCCTGTTT	59.237	50.000	0.00	0.00	0.00	2.83
470	475	0.896226	GAGAACTTGCGGTAGTCCCT	59.104	55.000	0.00	0.00	0.00	4.20
471	476	0.458025	CGAGAACTTGCGGTAGTCCC	60.458	60.000	0.00	0.00	0.00	4.46
507	518	2.723273	TGAGGTAGAGCGACATGAAGA	58.277	47.619	0.00	0.00	0.00	2.87
601	612	3.597182	TGGTATTGGCCCAGAGATATCA	58.403	45.455	0.00	0.00	0.00	2.15
602	613	4.640771	TTGGTATTGGCCCAGAGATATC	57.359	45.455	0.00	0.00	32.49	1.63
605	616	2.582636	AGTTTGGTATTGGCCCAGAGAT	59.417	45.455	0.00	0.00	32.49	2.75
610	621	0.963355	GCGAGTTTGGTATTGGCCCA	60.963	55.000	0.00	0.00	0.00	5.36
623	634	0.966370	AGCTTCTCCGGTAGCGAGTT	60.966	55.000	17.33	0.00	40.15	3.01
631	642	1.551019	GGTTGGGTAGCTTCTCCGGT	61.551	60.000	0.00	0.00	0.00	5.28
643	654	2.105993	GTTGAGGTACTTGAGGTTGGGT	59.894	50.000	0.00	0.00	41.55	4.51
671	682	4.379174	GCCAGAGAAGGCGTTCAA	57.621	55.556	20.38	0.00	46.12	2.69
790	801	3.638627	TGAGTTCAAGAGCTCTCAACTGA	59.361	43.478	31.48	25.02	39.11	3.41
1105	1117	1.792949	CTTCCCAGTGAACGAGTTTCG	59.207	52.381	0.00	0.00	46.93	3.46
1304	1316	0.901124	GAAGAAGAGCTCCAGCCTCA	59.099	55.000	10.93	0.00	43.38	3.86
1313	1325	1.696336	TGAGCTGGTTGAAGAAGAGCT	59.304	47.619	0.00	0.00	42.69	4.09
1400	1412	1.659794	GGCAGCTCGCTTTCCAAAA	59.340	52.632	7.85	0.00	41.91	2.44
1554	1566	1.291588	CAGACTCTGCGGCAGTTCT	59.708	57.895	27.63	24.79	32.61	3.01
1604	1616	2.811431	CCGCTGAAGTTGTTATGGTTCA	59.189	45.455	0.00	0.00	0.00	3.18
1611	1623	2.822306	CGAGCCGCTGAAGTTGTTA	58.178	52.632	0.00	0.00	0.00	2.41
1666	1678	3.117701	TGGTTCTGGTCCAATCTCAAACA	60.118	43.478	0.00	0.00	31.50	2.83
1669	1681	3.874383	TTGGTTCTGGTCCAATCTCAA	57.126	42.857	0.00	0.00	39.62	3.02
1773	1785	0.729116	GTGACCAATCATGCGACAGG	59.271	55.000	0.00	0.00	37.14	4.00
1794	1806	7.062322	TGGATAGAATTGTTAGATTGGTGCAT	58.938	34.615	0.00	0.00	0.00	3.96
1933	1945	0.034896	ACCACTGCTTGTAGTTCCCG	59.965	55.000	0.00	0.00	0.00	5.14
1936	1948	6.821665	TCCATAAATACCACTGCTTGTAGTTC	59.178	38.462	0.00	0.00	0.00	3.01
1992	2004	3.093057	ACTCAAGCTTGTCGAGATAGGT	58.907	45.455	25.19	8.95	0.00	3.08
1996	2008	2.560542	AGTCACTCAAGCTTGTCGAGAT	59.439	45.455	25.19	7.16	0.00	2.75
2092	2104	5.431420	AGATCTAGTGTGATGAGCTTACG	57.569	43.478	0.00	0.00	0.00	3.18
2222	2238	6.013379	AGATTAGAAAGCTGGGATATCTCGA	58.987	40.000	2.05	0.00	0.00	4.04
2342	2370	6.441274	TCATGCTTTTCAGAAGATGTTGTTC	58.559	36.000	0.00	0.00	0.00	3.18
2360	2388	3.079578	CTCAGTTGGACAACATCATGCT	58.920	45.455	16.58	0.00	43.47	3.79
2601	2630	8.091449	GGAATACTATCCGACAGATCATTTCTT	58.909	37.037	0.00	0.00	36.33	2.52
2616	2645	4.520492	CCAATGCTTGGTGGAATACTATCC	59.480	45.833	6.74	0.00	45.93	2.59
2640	2669	1.068352	ACTCCAGGAGCCCCAAACTT	61.068	55.000	17.31	0.00	32.04	2.66
2648	2677	0.035915	GTCAAGGAACTCCAGGAGCC	60.036	60.000	17.31	10.65	38.49	4.70
2692	2721	0.689623	GAGATGCTGGGTGGGATAGG	59.310	60.000	0.00	0.00	0.00	2.57
2728	2757	5.531287	GGTTGTTGGAGAGATTTAACACACT	59.469	40.000	0.00	0.00	33.25	3.55
2754	2783	2.706890	GTCGGAATGGAGCCTGTTAAA	58.293	47.619	0.00	0.00	0.00	1.52
2760	2789	3.470888	CCCGTCGGAATGGAGCCT	61.471	66.667	14.39	0.00	32.79	4.58
2764	2793	2.038329	ACTCCCCGTCGGAATGGA	59.962	61.111	14.39	10.26	41.40	3.41
2772	2801	0.680280	TCTGTAGCTGACTCCCCGTC	60.680	60.000	0.00	0.00	43.14	4.79
2875	2910	0.950555	TGCTGCGTGTGGTCTTGATC	60.951	55.000	0.00	0.00	0.00	2.92
2876	2911	0.534877	TTGCTGCGTGTGGTCTTGAT	60.535	50.000	0.00	0.00	0.00	2.57
2877	2912	1.153269	TTGCTGCGTGTGGTCTTGA	60.153	52.632	0.00	0.00	0.00	3.02
2889	2924	2.738521	TCGCTTCCGAGTTGCTGC	60.739	61.111	0.00	0.00	38.82	5.25
3006	3041	5.295787	ACTGCACAACTTATCAAGAAAACGA	59.704	36.000	0.00	0.00	0.00	3.85
3111	3146	5.047377	TCTGAAATGGCCAACTGGTTATTTC	60.047	40.000	10.96	13.32	42.76	2.17
3246	3290	7.177184	TGCTCCATATGTAGCCATATTGAAAT	58.823	34.615	16.73	0.00	41.35	2.17
3259	3303	7.557358	ACATTCACTCATTTTGCTCCATATGTA	59.443	33.333	1.24	0.00	0.00	2.29
3342	3390	9.392259	CTCCCTCCGTTTTTAAATATAAGACTT	57.608	33.333	0.00	0.00	0.00	3.01
3391	3486	9.421806	TGCTTAATGTTGTAATTTCAGGATTTG	57.578	29.630	0.00	0.00	0.00	2.32
3400	3495	8.594687	GCAAATCGATGCTTAATGTTGTAATTT	58.405	29.630	0.00	0.00	43.06	1.82
3426	3521	8.472683	TTGGTACTTGTTTTTGTTGAATGAAG	57.527	30.769	0.00	0.00	0.00	3.02
3556	3665	1.805943	TCACCGTTTGATGTGCTGATG	59.194	47.619	0.00	0.00	32.51	3.07
3745	4570	3.691342	TCCACCTCGCCGTCAAGG	61.691	66.667	0.00	0.00	44.97	3.61
3755	4580	2.432628	CGAGGCGTTGTCCACCTC	60.433	66.667	0.00	0.00	45.44	3.85
3780	4605	4.415332	TTCCGACTGCTCGCCGTC	62.415	66.667	3.73	3.73	38.70	4.79
3781	4606	4.421479	CTTCCGACTGCTCGCCGT	62.421	66.667	0.00	0.00	38.70	5.68
3782	4607	4.421479	ACTTCCGACTGCTCGCCG	62.421	66.667	0.00	0.00	38.70	6.46
3793	4618	2.119655	ATCTCCCGTCCGACTTCCG	61.120	63.158	0.00	0.00	38.18	4.30
3907	4732	7.013529	CAGGAAGGTTAAAACGATTAAACGAG	58.986	38.462	12.41	0.00	37.03	4.18
3936	4761	0.687920	TTGGTCTTCGGTGGTATGCA	59.312	50.000	0.00	0.00	0.00	3.96

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.