AutoCloner

Multiple sequence alignment - TraesCS1B01G009000

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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	TraesCS1B01G009000	chr1B	100.000	5407	0	0	1	5407	4562563	4557157	0.000000e+00	9985.0
1	TraesCS1B01G009000	chr1B	88.204	3018	320	17	1857	4863	4115469	4118461	0.000000e+00	3568.0
2	TraesCS1B01G009000	chr1B	88.693	2777	293	12	1859	4624	4482734	4479968	0.000000e+00	3369.0
3	TraesCS1B01G009000	chr1B	84.882	2626	386	7	1822	4442	3952051	3954670	0.000000e+00	2639.0
4	TraesCS1B01G009000	chr1B	87.559	1262	133	16	699	1953	4150487	4151731	0.000000e+00	1439.0
5	TraesCS1B01G009000	chr1B	82.914	1551	210	34	440	1953	4095004	4096536	0.000000e+00	1345.0
6	TraesCS1B01G009000	chr1B	82.679	1553	203	40	440	1953	4856952	4855427	0.000000e+00	1317.0
7	TraesCS1B01G009000	chr1B	86.840	1155	135	14	813	1953	687785308	687786459	0.000000e+00	1275.0
8	TraesCS1B01G009000	chr1B	82.904	854	110	21	42	891	4832510	4833331	0.000000e+00	736.0
9	TraesCS1B01G009000	chr1B	90.649	524	35	9	4890	5407	4479758	4479243	0.000000e+00	684.0
10	TraesCS1B01G009000	chr1B	89.689	514	40	10	4890	5399	4118461	4118965	1.270000e-180	643.0
11	TraesCS1B01G009000	chr1B	77.326	688	93	29	416	1082	4581569	4580924	1.110000e-91	348.0
12	TraesCS1B01G009000	chr1B	78.175	504	59	21	1	490	4538089	4537623	1.920000e-69	274.0
13	TraesCS1B01G009000	chr1B	80.380	316	37	16	4527	4824	687788995	687789303	3.280000e-52	217.0
14	TraesCS1B01G009000	chr1B	88.701	177	12	6	42	215	3941326	3941497	5.490000e-50	209.0
15	TraesCS1B01G009000	chr1B	83.019	212	27	6	4526	4734	4759007	4758802	3.330000e-42	183.0
16	TraesCS1B01G009000	chr1B	78.800	250	35	5	226	467	3940241	3940480	9.380000e-33	152.0
17	TraesCS1B01G009000	chr1B	75.829	211	42	8	350	555	4859794	4859588	1.240000e-16	99.0
18	TraesCS1B01G009000	chr1B	80.620	129	12	9	518	635	4513286	4513160	2.680000e-13	87.9
19	TraesCS1B01G009000	chr1B	83.929	56	9	0	56	111	4208859	4208914	3.000000e-03	54.7
20	TraesCS1B01G009000	chr1A	93.300	4403	221	32	1	4375	2981659	2986015	0.000000e+00	6429.0
21	TraesCS1B01G009000	chr1A	87.881	3573	368	22	1857	5407	3453784	3450255	0.000000e+00	4139.0
22	TraesCS1B01G009000	chr1A	88.425	3352	318	35	2081	5407	3680272	3676966	0.000000e+00	3976.0
23	TraesCS1B01G009000	chr1A	88.392	3334	304	34	2106	5407	2975203	2978485	0.000000e+00	3936.0
24	TraesCS1B01G009000	chr1A	84.528	1325	168	28	649	1953	3657709	3656402	0.000000e+00	1277.0
25	TraesCS1B01G009000	chr1A	84.906	212	23	6	4526	4734	3488366	3488161	7.100000e-49	206.0
26	TraesCS1B01G009000	chr1A	82.938	211	26	6	4526	4734	3669098	3668896	1.200000e-41	182.0
27	TraesCS1B01G009000	chr1A	93.258	89	6	0	154	242	3583254	3583166	1.220000e-26	132.0
28	TraesCS1B01G009000	chr1A	89.000	100	7	1	1	96	3018014	3018113	2.650000e-23	121.0
29	TraesCS1B01G009000	chr1D	87.139	3600	370	39	1857	5407	620206	616651	0.000000e+00	3997.0
30	TraesCS1B01G009000	chr1D	85.006	2581	341	26	2162	4734	696761	694219	0.000000e+00	2580.0
31	TraesCS1B01G009000	chr1D	87.786	1138	137	2	808	1944	458555	459691	0.000000e+00	1330.0
32	TraesCS1B01G009000	chr1D	83.449	1444	197	28	545	1953	621618	620182	0.000000e+00	1304.0
33	TraesCS1B01G009000	chr1D	86.730	1153	140	10	813	1953	494546769	494547920	0.000000e+00	1269.0
34	TraesCS1B01G009000	chr1D	92.674	778	34	7	1	769	457644	458407	0.000000e+00	1099.0
35	TraesCS1B01G009000	chr1D	78.643	501	65	20	2	490	643214	643684	1.470000e-75	294.0
36	TraesCS1B01G009000	chr3D	86.357	2602	335	12	1857	4448	560057178	560054587	0.000000e+00	2820.0
37	TraesCS1B01G009000	chrUn	89.000	100	7	1	1	96	318173787	318173886	2.650000e-23	121.0

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	TraesCS1B01G009000	chr1B	4557157	4562563	5406	True	9985.0	9985	100.0000	1	5407	1	chr1B.!!$R3	5406
1	TraesCS1B01G009000	chr1B	3952051	3954670	2619	False	2639.0	2639	84.8820	1822	4442	1	chr1B.!!$F1	2620
2	TraesCS1B01G009000	chr1B	4115469	4118965	3496	False	2105.5	3568	88.9465	1857	5399	2	chr1B.!!$F7	3542
3	TraesCS1B01G009000	chr1B	4479243	4482734	3491	True	2026.5	3369	89.6710	1859	5407	2	chr1B.!!$R6	3548
4	TraesCS1B01G009000	chr1B	4150487	4151731	1244	False	1439.0	1439	87.5590	699	1953	1	chr1B.!!$F3	1254
5	TraesCS1B01G009000	chr1B	4095004	4096536	1532	False	1345.0	1345	82.9140	440	1953	1	chr1B.!!$F2	1513
6	TraesCS1B01G009000	chr1B	687785308	687789303	3995	False	746.0	1275	83.6100	813	4824	2	chr1B.!!$F8	4011
7	TraesCS1B01G009000	chr1B	4832510	4833331	821	False	736.0	736	82.9040	42	891	1	chr1B.!!$F5	849
8	TraesCS1B01G009000	chr1B	4855427	4859794	4367	True	708.0	1317	79.2540	350	1953	2	chr1B.!!$R7	1603
9	TraesCS1B01G009000	chr1B	4580924	4581569	645	True	348.0	348	77.3260	416	1082	1	chr1B.!!$R4	666
10	TraesCS1B01G009000	chr1A	2975203	2986015	10812	False	5182.5	6429	90.8460	1	5407	2	chr1A.!!$F2	5406
11	TraesCS1B01G009000	chr1A	3450255	3453784	3529	True	4139.0	4139	87.8810	1857	5407	1	chr1A.!!$R1	3550
12	TraesCS1B01G009000	chr1A	3676966	3680272	3306	True	3976.0	3976	88.4250	2081	5407	1	chr1A.!!$R6	3326
13	TraesCS1B01G009000	chr1A	3656402	3657709	1307	True	1277.0	1277	84.5280	649	1953	1	chr1A.!!$R4	1304
14	TraesCS1B01G009000	chr1D	616651	621618	4967	True	2650.5	3997	85.2940	545	5407	2	chr1D.!!$R2	4862
15	TraesCS1B01G009000	chr1D	694219	696761	2542	True	2580.0	2580	85.0060	2162	4734	1	chr1D.!!$R1	2572
16	TraesCS1B01G009000	chr1D	494546769	494547920	1151	False	1269.0	1269	86.7300	813	1953	1	chr1D.!!$F2	1140
17	TraesCS1B01G009000	chr1D	457644	459691	2047	False	1214.5	1330	90.2300	1	1944	2	chr1D.!!$F3	1943
18	TraesCS1B01G009000	chr3D	560054587	560057178	2591	True	2820.0	2820	86.3570	1857	4448	1	chr3D.!!$R1	2591

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
119	6576	1.149987	GTCGGATGTTACACGGCAAA	58.850	50.000	0.00	31.66	3.68	F
120	6577	1.532007	GTCGGATGTTACACGGCAAAA	59.468	47.619	0.00	31.66	2.44	F
662	7183	2.108425	ACGGAGGAGATATGAGTAGGCA	59.892	50.000	0.00	0.00	4.75	F
2442	11239	1.349357	AGCCTTCAGAGGAACCAACTC	59.651	52.381	0.00	46.74	3.01	F
3269	12067	1.069049	GCCAATTGTTCTTGTGGTGCT	59.931	47.619	4.43	33.43	4.40	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1350	10074	1.065709	ACACCGTGGAGACTGTTGTTT	60.066	47.619	3.03	0.00	2.83	R
1792	10516	4.958581	GGAGATTGGAATTGGACCTGAAAT	59.041	41.667	0.00	0.00	2.17	R
2524	11321	3.281727	TGCATCTAGATTTGGTGGGAC	57.718	47.619	1.33	0.00	4.46	R
3582	12380	1.014044	TGCTTCGTTGTCGGATCTGC	61.014	55.000	0.00	37.69	4.26	R
4774	13618	0.040067	CACCAGCCGAAAGAAAGTGC	60.040	55.000	0.00	0.00	4.40	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
119	6576	1.149987	GTCGGATGTTACACGGCAAA	58.850	50.000	0.00	0.00	31.66	3.68
120	6577	1.532007	GTCGGATGTTACACGGCAAAA	59.468	47.619	0.00	0.00	31.66	2.44
127	6584	3.958704	TGTTACACGGCAAAATCAACAG	58.041	40.909	0.00	0.00	0.00	3.16
309	6769	4.020573	TGTCATTTTCCTCGTACACAGGAT	60.021	41.667	10.67	0.00	39.91	3.24
346	6806	7.789349	ACTTGGGGTCCAGCATTTAATTTATAT	59.211	33.333	0.00	0.00	33.81	0.86
560	7060	9.490663	GATTACACGATCAAATAAACAAAGAGG	57.509	33.333	0.00	0.00	0.00	3.69
662	7183	2.108425	ACGGAGGAGATATGAGTAGGCA	59.892	50.000	0.00	0.00	0.00	4.75
769	7297	4.407296	AGAAAAGAGGAATAGATGGCGACT	59.593	41.667	0.00	0.00	0.00	4.18
772	7300	3.153919	AGAGGAATAGATGGCGACTCTC	58.846	50.000	0.00	0.00	0.00	3.20
786	7314	3.058846	GCGACTCTCAAGAAGGAAAAACC	60.059	47.826	0.00	0.00	39.35	3.27
860	9564	5.091261	ACACACTGAAGAATAGTCATCCC	57.909	43.478	0.00	0.00	0.00	3.85
1188	9912	2.358898	GAGCTCTTGGCAAGAAAACACA	59.641	45.455	28.27	6.86	44.79	3.72
1350	10074	5.545063	TCCTCGCATATATTGACCTTCAA	57.455	39.130	0.00	0.00	41.09	2.69
1502	10226	4.825422	CAGCTTGGTCTCTCATCTAACAA	58.175	43.478	0.00	0.00	0.00	2.83
1792	10516	6.705302	AGTCTTCAGCTTCAGTCAAATGATA	58.295	36.000	0.00	0.00	0.00	2.15
2067	10863	6.776887	ACCAAGCTAGTAGTACTATCCCTA	57.223	41.667	10.46	2.51	29.08	3.53
2314	11111	5.152934	ACTCACTTTCAGGACCTTTACCTA	58.847	41.667	0.00	0.00	35.84	3.08
2442	11239	1.349357	AGCCTTCAGAGGAACCAACTC	59.651	52.381	0.00	0.00	46.74	3.01
2524	11321	5.125097	GCATCAAATAGATTCTATGGGCAGG	59.875	44.000	6.96	0.00	33.72	4.85
2691	11489	8.697507	AGATTCCACAAGAAATCTGTAGTTTT	57.302	30.769	0.00	0.00	38.21	2.43
3034	11832	6.461092	CCATAATCAGTTCAGCAGCATCATTT	60.461	38.462	0.00	0.00	0.00	2.32
3035	11833	5.401531	AATCAGTTCAGCAGCATCATTTT	57.598	34.783	0.00	0.00	0.00	1.82
3131	11929	2.552315	CAACACGGCTACTCCAAAATGT	59.448	45.455	0.00	0.00	34.01	2.71
3159	11957	6.198966	CAGCAAGTTGGTTTCTTCACAATAAC	59.801	38.462	4.45	0.00	0.00	1.89
3268	12066	1.202510	TGCCAATTGTTCTTGTGGTGC	60.203	47.619	4.43	0.00	33.43	5.01
3269	12067	1.069049	GCCAATTGTTCTTGTGGTGCT	59.931	47.619	4.43	0.00	33.43	4.40
3276	12074	2.828520	TGTTCTTGTGGTGCTTTTTGGA	59.171	40.909	0.00	0.00	0.00	3.53
3289	12087	3.303526	GCTTTTTGGAATTGTTGCTGCAG	60.304	43.478	10.11	10.11	0.00	4.41
3305	12103	5.698832	TGCTGCAGTTGTTGTCATAATAAC	58.301	37.500	16.64	0.00	0.00	1.89
3353	12151	4.576463	ACAAGAAAGTGTTACTGCTGAAGG	59.424	41.667	0.00	0.00	0.00	3.46
3405	12203	7.268199	TGATGGAAGATTAGCATTTGATGAC	57.732	36.000	0.00	0.00	0.00	3.06
3418	12216	5.345702	CATTTGATGACATTGTAAGGGCAG	58.654	41.667	0.00	0.00	27.58	4.85
3558	12356	7.862512	AGAGTTGGATGATGAAAGAAGATTC	57.137	36.000	0.00	0.00	0.00	2.52
3582	12380	6.311935	TCCGTAGTGAAATGGAAATCTTAACG	59.688	38.462	0.00	0.00	31.42	3.18
3621	12419	7.276218	CGAAGCATTGTCAAAATGTATGGATTT	59.724	33.333	0.00	0.00	0.00	2.17
3649	12447	6.851318	TCCCATCCAGCATATAAATTTCTCA	58.149	36.000	0.00	0.00	0.00	3.27
3681	12479	1.210204	TTCAGCAGGGAAGCCTCCAT	61.210	55.000	3.19	0.00	44.51	3.41
3706	12504	7.529555	TGGAATATTGGAAAATGAGGAGCTAT	58.470	34.615	0.00	0.00	0.00	2.97
3742	12540	2.119801	GCAGAAGAGAATTGCCCTGA	57.880	50.000	0.00	0.00	31.79	3.86
3959	12764	8.898761	CATAGCTCCTGGTATGTACTAGAATAG	58.101	40.741	0.00	2.11	44.86	1.73
4005	12811	7.833183	AGCATTCATCTCTATCCATTTATTCCC	59.167	37.037	0.00	0.00	0.00	3.97
4060	12866	3.860641	TGTCATACACATCTGTTGCGAT	58.139	40.909	0.00	0.00	0.00	4.58
4082	12888	9.197694	GCGATAGAGAAATGTGATGTTTATAGT	57.802	33.333	0.00	0.00	39.76	2.12
4281	13087	4.402616	TGTTTGGAATCTTCTCCCCAAT	57.597	40.909	0.00	0.00	38.34	3.16
4332	13141	2.093075	ACACTCATCCAGCCATCTTCTG	60.093	50.000	0.00	0.00	0.00	3.02
4344	13153	4.286297	CCATCTTCTGGTTCAACTACCA	57.714	45.455	0.00	0.00	45.73	3.25
4552	13376	3.206150	AGTTGACGACTCATTGCAAGTT	58.794	40.909	4.94	0.00	31.20	2.66
4582	13408	2.767960	TGTAGATTCTCCTGATGCAGCA	59.232	45.455	3.82	3.82	0.00	4.41
4643	13469	4.504826	GGGTTTTCCACGTAAAAATGTGTG	59.495	41.667	10.21	0.00	42.91	3.82
4645	13471	5.230516	GGTTTTCCACGTAAAAATGTGTGTC	59.769	40.000	10.21	0.00	40.31	3.67
4646	13472	4.555348	TTCCACGTAAAAATGTGTGTCC	57.445	40.909	0.00	0.00	34.28	4.02
4647	13473	3.542648	TCCACGTAAAAATGTGTGTCCA	58.457	40.909	0.00	0.00	34.28	4.02
4676	13507	9.177608	CCCATGTTCTTGATATTTCTCTGTTTA	57.822	33.333	0.00	0.00	0.00	2.01
4725	13556	6.926272	GCATAAATATAATTTGGTTTGCGGGA	59.074	34.615	0.00	0.00	0.00	5.14
4768	13612	8.441572	AGACTGTACTGTAGACATAGTATCCAT	58.558	37.037	5.27	0.00	31.87	3.41
4774	13618	8.354711	ACTGTAGACATAGTATCCATATGTGG	57.645	38.462	1.19	1.19	42.48	4.17
4791	13635	1.172180	TGGCACTTTCTTTCGGCTGG	61.172	55.000	0.00	0.00	0.00	4.85
4814	13659	3.756434	TGTCTGCAGGGTACTTAAAATGC	59.244	43.478	15.13	0.00	0.00	3.56
4868	13716	9.770097	CTATTGCTCTCATAACCTAAAGATTGA	57.230	33.333	0.00	0.00	0.00	2.57
4901	13761	0.248907	CGGTACCATGTAGTCCTGCG	60.249	60.000	13.54	0.00	0.00	5.18
4904	13764	2.268298	GTACCATGTAGTCCTGCGTTG	58.732	52.381	0.00	0.00	0.00	4.10
4917	13780	6.588204	AGTCCTGCGTTGTTTATTCCATATA	58.412	36.000	0.00	0.00	0.00	0.86
4918	13781	7.224297	AGTCCTGCGTTGTTTATTCCATATAT	58.776	34.615	0.00	0.00	0.00	0.86
4951	13814	7.573968	AGATAAATTATCTTGGACCAAGCAC	57.426	36.000	26.79	10.79	42.70	4.40
4970	13833	3.543494	GCACGAACAATCACAATGCATAC	59.457	43.478	0.00	0.00	0.00	2.39
5056	13929	8.333186	GCAATATACCAAGTAAAAGGACTTACG	58.667	37.037	0.00	0.00	37.57	3.18
5085	13958	3.204606	TGTAGGGCAGGAGTATGTAGTCT	59.795	47.826	0.00	0.00	0.00	3.24
5165	14047	3.792401	GACACGTTATCATGTCATCCCA	58.208	45.455	0.00	0.00	43.89	4.37
5176	14059	9.913310	TTATCATGTCATCCCACTTTATTGTTA	57.087	29.630	0.00	0.00	0.00	2.41
5227	14110	3.181479	CCAAGCAGGAATGATCACAATGG	60.181	47.826	0.00	0.00	41.22	3.16
5302	14189	6.435428	AGGTGCATAAAACAAGAAAAGTACG	58.565	36.000	0.00	0.00	0.00	3.67
5343	14231	2.097110	TACGGAGGATTGTAGGGCAT	57.903	50.000	0.00	0.00	0.00	4.40
5350	14238	2.442878	AGGATTGTAGGGCATGCATACA	59.557	45.455	23.59	23.59	0.00	2.29
5359	14247	3.077359	GGGCATGCATACATAGTCCTTC	58.923	50.000	21.36	0.00	33.67	3.46
5366	14258	6.656632	TGCATACATAGTCCTTCTCCTTAG	57.343	41.667	0.00	0.00	0.00	2.18
5383	14275	3.328931	CCTTAGGGATGGAGCATATGTGT	59.671	47.826	4.29	0.00	33.58	3.72

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
119	6576	1.094785	GCCCATGTACGCTGTTGATT	58.905	50.000	0.00	0.00	0.00	2.57
120	6577	0.748005	GGCCCATGTACGCTGTTGAT	60.748	55.000	0.00	0.00	0.00	2.57
375	6835	2.279935	TTCCGTGCTGGTGGTAAAAT	57.720	45.000	0.00	0.00	39.52	1.82
559	7059	4.881850	CCTGTGGTTGGTTTGATAGTATCC	59.118	45.833	7.69	0.00	0.00	2.59
560	7060	5.741011	TCCTGTGGTTGGTTTGATAGTATC	58.259	41.667	2.97	2.97	0.00	2.24
662	7183	0.179119	GAAGGGTACACGCAGCGTAT	60.179	55.000	22.49	13.25	38.32	3.06
769	7297	4.127171	CAGACGGTTTTTCCTTCTTGAGA	58.873	43.478	0.00	0.00	41.23	3.27
772	7300	2.287608	GGCAGACGGTTTTTCCTTCTTG	60.288	50.000	0.00	0.00	41.23	3.02
860	9564	1.962822	TTGAGTGGAAGCTGCTGCG	60.963	57.895	1.35	0.00	45.42	5.18
1188	9912	2.116125	GACCAGTTGCAGGGCCTT	59.884	61.111	1.32	0.00	0.00	4.35
1350	10074	1.065709	ACACCGTGGAGACTGTTGTTT	60.066	47.619	3.03	0.00	0.00	2.83
1792	10516	4.958581	GGAGATTGGAATTGGACCTGAAAT	59.041	41.667	0.00	0.00	0.00	2.17
2067	10863	5.041191	AGCCGGTTATCTGATTTTGATCT	57.959	39.130	1.90	0.00	0.00	2.75
2314	11111	4.473444	CTGCCCCCTGAACATATATTTGT	58.527	43.478	0.00	0.00	0.00	2.83
2524	11321	3.281727	TGCATCTAGATTTGGTGGGAC	57.718	47.619	1.33	0.00	0.00	4.46
2703	11501	8.954950	ATTGGTTAGATGATAAGTTCAGTCTG	57.045	34.615	0.00	0.00	37.89	3.51
3034	11832	2.036217	CCATGCTTGCAAAAGAGGACAA	59.964	45.455	0.00	0.00	0.00	3.18
3035	11833	1.614903	CCATGCTTGCAAAAGAGGACA	59.385	47.619	0.00	0.00	0.00	4.02
3131	11929	4.219507	TGTGAAGAAACCAACTTGCTGAAA	59.780	37.500	0.00	0.00	0.00	2.69
3268	12066	3.872771	ACTGCAGCAACAATTCCAAAAAG	59.127	39.130	15.27	0.00	0.00	2.27
3269	12067	3.871485	ACTGCAGCAACAATTCCAAAAA	58.129	36.364	15.27	0.00	0.00	1.94
3276	12074	3.189285	GACAACAACTGCAGCAACAATT	58.811	40.909	15.27	0.00	0.00	2.32
3289	12087	8.013378	ACAACTAAGCGTTATTATGACAACAAC	58.987	33.333	0.00	0.00	33.63	3.32
3305	12103	6.134061	GGTTTTCTCTTGTTACAACTAAGCG	58.866	40.000	0.00	0.00	0.00	4.68
3353	12151	4.225267	TCCAAACAGAGAATAGGTCCCTTC	59.775	45.833	0.00	0.00	0.00	3.46
3405	12203	2.421424	GTCTTCTGCTGCCCTTACAATG	59.579	50.000	0.00	0.00	0.00	2.82
3418	12216	3.760537	ACTTATCGTCGAAGTCTTCTGC	58.239	45.455	10.81	2.70	31.36	4.26
3558	12356	6.475207	CGTTAAGATTTCCATTTCACTACGG	58.525	40.000	0.00	0.00	0.00	4.02
3582	12380	1.014044	TGCTTCGTTGTCGGATCTGC	61.014	55.000	0.00	0.00	37.69	4.26
3649	12447	3.319405	CCCTGCTGAATGTAGTCGTAGAT	59.681	47.826	0.00	0.00	40.67	1.98
3681	12479	5.769835	AGCTCCTCATTTTCCAATATTCCA	58.230	37.500	0.00	0.00	0.00	3.53
3706	12504	5.711506	TCTTCTGCCAATCTAATTGCTTTGA	59.288	36.000	0.00	0.00	38.92	2.69
3712	12510	6.696148	GCAATTCTCTTCTGCCAATCTAATTG	59.304	38.462	0.00	0.00	39.94	2.32
3738	12536	1.271001	TGAGCCACATCAGTTGTCAGG	60.271	52.381	0.00	0.00	36.00	3.86
3741	12539	1.198637	GCTTGAGCCACATCAGTTGTC	59.801	52.381	0.00	0.00	36.00	3.18
3742	12540	1.242076	GCTTGAGCCACATCAGTTGT	58.758	50.000	0.00	0.00	39.91	3.32
3852	12650	1.128692	GTGCCGAAATCCGAGACAAAG	59.871	52.381	0.00	0.00	41.76	2.77
3874	12672	3.933861	ATCGGGCTTAAGAATCCTTGT	57.066	42.857	6.67	0.00	33.94	3.16
3959	12764	3.365767	GCTTCTGATGTGAGAAACAAGGC	60.366	47.826	0.00	0.00	43.61	4.35
4005	12811	8.380644	ACAAAAGTGTCGACAATATTAGAATCG	58.619	33.333	21.95	5.03	29.49	3.34
4018	12824	2.351726	AGTTCTGCACAAAAGTGTCGAC	59.648	45.455	9.11	9.11	35.07	4.20
4082	12888	3.292460	CTCTAACACAACCACCCCAAAA	58.708	45.455	0.00	0.00	0.00	2.44
4281	13087	2.676121	CCGCATGGTTGGCCTTGA	60.676	61.111	3.32	0.00	41.07	3.02
4332	13141	3.153919	TGAAAGGCATGGTAGTTGAACC	58.846	45.455	0.00	0.00	40.19	3.62
4344	13153	2.862541	TGTAAGTGCACTGAAAGGCAT	58.137	42.857	22.49	4.17	41.07	4.40
4430	13244	3.467374	AGAAATCTGAATCGGCCTCTC	57.533	47.619	0.00	0.00	0.00	3.20
4552	13376	9.494271	GCATCAGGAGAATCTACAAATACATAA	57.506	33.333	0.00	0.00	33.73	1.90
4567	13393	3.144657	TCTTTTGCTGCATCAGGAGAA	57.855	42.857	1.84	0.00	34.74	2.87
4577	13403	1.001378	ACAACGGTGATCTTTTGCTGC	60.001	47.619	7.88	0.00	0.00	5.25
4643	13469	2.859165	TCAAGAACATGGGACTGGAC	57.141	50.000	0.00	0.00	0.00	4.02
4645	13471	6.125029	AGAAATATCAAGAACATGGGACTGG	58.875	40.000	0.00	0.00	0.00	4.00
4646	13472	7.012138	CAGAGAAATATCAAGAACATGGGACTG	59.988	40.741	0.00	0.00	0.00	3.51
4647	13473	7.052873	CAGAGAAATATCAAGAACATGGGACT	58.947	38.462	0.00	0.00	0.00	3.85
4676	13507	6.091713	GCATTGTTAGAAATCAGCAAGCAAAT	59.908	34.615	0.00	0.00	0.00	2.32
4768	13612	1.810151	GCCGAAAGAAAGTGCCACATA	59.190	47.619	0.00	0.00	0.00	2.29
4774	13618	0.040067	CACCAGCCGAAAGAAAGTGC	60.040	55.000	0.00	0.00	0.00	4.40
4791	13635	4.379499	GCATTTTAAGTACCCTGCAGACAC	60.379	45.833	17.39	9.68	0.00	3.67
4931	13794	4.331968	TCGTGCTTGGTCCAAGATAATTT	58.668	39.130	31.94	0.00	43.42	1.82
4934	13797	3.071479	GTTCGTGCTTGGTCCAAGATAA	58.929	45.455	31.94	17.03	43.42	1.75
4951	13814	3.780279	CGTGTATGCATTGTGATTGTTCG	59.220	43.478	3.54	0.00	0.00	3.95
4970	13833	4.165779	GCTTACATTCATTTGGTTCCGTG	58.834	43.478	0.00	0.00	0.00	4.94
5056	13929	1.615424	TCCTGCCCTACAACCCTCC	60.615	63.158	0.00	0.00	0.00	4.30
5165	14047	9.975218	ACTTTGATACCCAGATAACAATAAAGT	57.025	29.630	0.00	0.00	0.00	2.66
5227	14110	3.466836	GTTTACGCATCGAACACTTGAC	58.533	45.455	0.00	0.00	0.00	3.18
5271	14154	8.815565	TTTCTTGTTTTATGCACCTATATCCA	57.184	30.769	0.00	0.00	0.00	3.41
5302	14189	6.966066	CGTAAGCTCTTTTACCTAGTACTGTC	59.034	42.308	5.39	0.00	31.33	3.51
5343	14231	5.540337	CCTAAGGAGAAGGACTATGTATGCA	59.460	44.000	0.00	0.00	36.08	3.96
5366	14258	2.107204	AGGAACACATATGCTCCATCCC	59.893	50.000	17.10	5.35	42.72	3.85
5383	14275	2.505819	GCTCCATCCTAAGGACAAGGAA	59.494	50.000	0.00	0.00	46.06	3.36

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.