AutoCloner

Multiple sequence alignment - TraesCS5B01G009500

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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	TraesCS5B01G009500	chr5B	100.000	4800	0	0	1	4800	9355182	9359981	0.000000e+00	8865.0
1	TraesCS5B01G009500	chr5B	95.385	130	6	0	3339	3468	9367789	9367918	1.750000e-49	207.0
2	TraesCS5B01G009500	chr5A	94.446	2971	121	14	904	3868	7569351	7572283	0.000000e+00	4532.0
3	TraesCS5B01G009500	chr5A	96.087	920	15	4	1	902	57048487	57047571	0.000000e+00	1480.0
4	TraesCS5B01G009500	chr5A	89.520	687	69	2	4117	4800	7586543	7587229	0.000000e+00	867.0
5	TraesCS5B01G009500	chr5A	89.260	689	64	8	4117	4800	7577395	7578078	0.000000e+00	854.0
6	TraesCS5B01G009500	chr5A	94.191	241	11	2	3339	3576	7584670	7584910	9.820000e-97	364.0
7	TraesCS5B01G009500	chr5A	88.327	257	24	4	3656	3912	7585129	7585379	2.170000e-78	303.0
8	TraesCS5B01G009500	chr5D	95.120	1455	48	7	2415	3857	9403268	9401825	0.000000e+00	2272.0
9	TraesCS5B01G009500	chr5D	92.784	1372	92	4	904	2269	9404881	9403511	0.000000e+00	1978.0
10	TraesCS5B01G009500	chr5D	84.153	1180	154	23	1084	2246	556877988	556876825	0.000000e+00	1112.0
11	TraesCS5B01G009500	chr5D	83.433	1171	130	33	2426	3570	556876271	556875139	0.000000e+00	1029.0
12	TraesCS5B01G009500	chr5D	91.043	681	56	3	4117	4792	9453750	9454430	0.000000e+00	915.0
13	TraesCS5B01G009500	chr5D	87.830	682	66	7	4135	4800	9401456	9400776	0.000000e+00	784.0
14	TraesCS5B01G009500	chr5D	87.936	373	23	13	3339	3707	9449604	9449958	2.070000e-113	420.0
15	TraesCS5B01G009500	chr5D	89.529	191	12	5	3778	3967	9409211	9409394	8.030000e-58	235.0
16	TraesCS5B01G009500	chr5D	87.838	74	8	1	4034	4107	9453534	9453606	8.560000e-13	86.1
17	TraesCS5B01G009500	chr7B	96.848	920	11	2	1	902	620574820	620573901	0.000000e+00	1522.0
18	TraesCS5B01G009500	chr6B	96.743	921	10	2	1	903	255525249	255524331	0.000000e+00	1517.0
19	TraesCS5B01G009500	chr6B	96.739	920	12	1	1	902	326978701	326979620	0.000000e+00	1517.0
20	TraesCS5B01G009500	chr6B	96.187	918	17	4	6	905	102106280	102105363	0.000000e+00	1485.0
21	TraesCS5B01G009500	chr6B	71.875	576	125	23	1679	2237	37231633	37231078	1.080000e-26	132.0
22	TraesCS5B01G009500	chr7A	96.444	928	14	2	1	909	115022012	115022939	0.000000e+00	1513.0
23	TraesCS5B01G009500	chr7A	94.186	774	13	12	1	773	511801359	511802101	0.000000e+00	1151.0
24	TraesCS5B01G009500	chr7A	78.190	1160	203	33	1097	2237	4742503	4743631	0.000000e+00	695.0
25	TraesCS5B01G009500	chr7A	83.333	270	45	0	3132	3401	4744546	4744815	2.870000e-62	250.0
26	TraesCS5B01G009500	chr4B	95.376	930	15	5	1	902	470299358	470298429	0.000000e+00	1454.0
27	TraesCS5B01G009500	chr3A	94.812	906	12	9	1	902	105719272	105720146	0.000000e+00	1380.0
28	TraesCS5B01G009500	chr3A	98.812	421	5	0	482	902	696498483	696498903	0.000000e+00	750.0
29	TraesCS5B01G009500	chr2B	96.433	841	11	2	1	823	788851753	788852592	0.000000e+00	1369.0
30	TraesCS5B01G009500	chrUn	84.727	1172	149	22	1086	2246	48204651	48205803	0.000000e+00	1146.0
31	TraesCS5B01G009500	chrUn	83.234	1175	134	36	2426	3570	48206280	48207421	0.000000e+00	1020.0
32	TraesCS5B01G009500	chr4A	84.642	1172	150	22	1086	2246	605377040	605375888	0.000000e+00	1140.0
33	TraesCS5B01G009500	chr4A	83.234	1175	134	36	2426	3570	605375411	605374270	0.000000e+00	1020.0
34	TraesCS5B01G009500	chr4A	77.912	1159	208	26	1097	2237	738784341	738783213	0.000000e+00	678.0
35	TraesCS5B01G009500	chr3B	96.845	634	20	0	1	634	201890448	201889815	0.000000e+00	1061.0
36	TraesCS5B01G009500	chr3B	97.222	324	9	0	581	904	201889917	201889594	2.530000e-152	549.0
37	TraesCS5B01G009500	chr3D	78.603	229	37	3	1669	1897	600173281	600173497	1.800000e-29	141.0

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	TraesCS5B01G009500	chr5B	9355182	9359981	4799	False	8865.000000	8865	100.000000	1	4800	1	chr5B.!!$F1	4799
1	TraesCS5B01G009500	chr5A	7569351	7572283	2932	False	4532.000000	4532	94.446000	904	3868	1	chr5A.!!$F1	2964
2	TraesCS5B01G009500	chr5A	57047571	57048487	916	True	1480.000000	1480	96.087000	1	902	1	chr5A.!!$R1	901
3	TraesCS5B01G009500	chr5A	7577395	7578078	683	False	854.000000	854	89.260000	4117	4800	1	chr5A.!!$F2	683
4	TraesCS5B01G009500	chr5A	7584670	7587229	2559	False	511.333333	867	90.679333	3339	4800	3	chr5A.!!$F3	1461
5	TraesCS5B01G009500	chr5D	9400776	9404881	4105	True	1678.000000	2272	91.911333	904	4800	3	chr5D.!!$R1	3896
6	TraesCS5B01G009500	chr5D	556875139	556877988	2849	True	1070.500000	1112	83.793000	1084	3570	2	chr5D.!!$R2	2486
7	TraesCS5B01G009500	chr5D	9449604	9454430	4826	False	473.700000	915	88.939000	3339	4792	3	chr5D.!!$F2	1453
8	TraesCS5B01G009500	chr7B	620573901	620574820	919	True	1522.000000	1522	96.848000	1	902	1	chr7B.!!$R1	901
9	TraesCS5B01G009500	chr6B	255524331	255525249	918	True	1517.000000	1517	96.743000	1	903	1	chr6B.!!$R3	902
10	TraesCS5B01G009500	chr6B	326978701	326979620	919	False	1517.000000	1517	96.739000	1	902	1	chr6B.!!$F1	901
11	TraesCS5B01G009500	chr6B	102105363	102106280	917	True	1485.000000	1485	96.187000	6	905	1	chr6B.!!$R2	899
12	TraesCS5B01G009500	chr7A	115022012	115022939	927	False	1513.000000	1513	96.444000	1	909	1	chr7A.!!$F1	908
13	TraesCS5B01G009500	chr7A	511801359	511802101	742	False	1151.000000	1151	94.186000	1	773	1	chr7A.!!$F2	772
14	TraesCS5B01G009500	chr7A	4742503	4744815	2312	False	472.500000	695	80.761500	1097	3401	2	chr7A.!!$F3	2304
15	TraesCS5B01G009500	chr4B	470298429	470299358	929	True	1454.000000	1454	95.376000	1	902	1	chr4B.!!$R1	901
16	TraesCS5B01G009500	chr3A	105719272	105720146	874	False	1380.000000	1380	94.812000	1	902	1	chr3A.!!$F1	901
17	TraesCS5B01G009500	chr2B	788851753	788852592	839	False	1369.000000	1369	96.433000	1	823	1	chr2B.!!$F1	822
18	TraesCS5B01G009500	chrUn	48204651	48207421	2770	False	1083.000000	1146	83.980500	1086	3570	2	chrUn.!!$F1	2484
19	TraesCS5B01G009500	chr4A	605374270	605377040	2770	True	1080.000000	1140	83.938000	1086	3570	2	chr4A.!!$R2	2484
20	TraesCS5B01G009500	chr4A	738783213	738784341	1128	True	678.000000	678	77.912000	1097	2237	1	chr4A.!!$R1	1140
21	TraesCS5B01G009500	chr3B	201889594	201890448	854	True	805.000000	1061	97.033500	1	904	2	chr3B.!!$R1	903

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
75	76	0.165944	GCGTTGGAGTTGATTGTCGG	59.834	55.0	0.00	0.00	4.79	F
1118	1206	1.028868	GCGGCAGCATCTCCTTCTTT	61.029	55.0	3.18	44.35	2.52	F
2368	3135	0.165944	GGACGTGGATTTTCGCAGTG	59.834	55.0	0.00	0.00	3.66	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1816	1913	0.523072	CTTGATCACAACCTTGCGGG	59.477	55.0	0.00	41.89	6.13	R
2805	3727	0.318441	CACGAGCTTGTCTCCCTTGA	59.682	55.0	2.72	38.62	3.02	R
4022	6254	0.380733	TGTAGCACTACTCCGATGCG	59.619	55.0	9.12	44.25	4.73	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
75	76	0.165944	GCGTTGGAGTTGATTGTCGG	59.834	55.000	0.00	0.00	0.00	4.79
319	330	1.080974	CGTTGTAGGACGGCGAGTT	60.081	57.895	16.62	0.00	39.27	3.01
767	850	2.218953	TTGTATTCCATCGGAGTCGC	57.781	50.000	0.00	0.00	36.13	5.19
952	1035	5.780282	TGATAATTAAGAGGCAGGCTAGCTA	59.220	40.000	15.72	0.00	34.17	3.32
978	1061	5.471456	GTCCATCCAACTATAAATCAGGCAG	59.529	44.000	0.00	0.00	0.00	4.85
1017	1100	1.408340	CACACAACCACAAGCCAATCA	59.592	47.619	0.00	0.00	0.00	2.57
1118	1206	1.028868	GCGGCAGCATCTCCTTCTTT	61.029	55.000	3.18	0.00	44.35	2.52
1268	1356	3.606662	GCCGCGCTCAGGGAGATA	61.607	66.667	5.56	0.00	34.27	1.98
1340	1428	2.047274	CTGGCGGACGTGGACAAT	60.047	61.111	0.00	0.00	0.00	2.71
1769	1866	2.420372	CGAGATCGAGAACCTCAAGACA	59.580	50.000	0.00	0.00	43.02	3.41
1770	1867	3.119814	CGAGATCGAGAACCTCAAGACAA	60.120	47.826	0.00	0.00	43.02	3.18
1771	1868	4.420168	GAGATCGAGAACCTCAAGACAAG	58.580	47.826	0.00	0.00	0.00	3.16
1791	1888	2.427095	AGGATCGTGATCATGAACGTGA	59.573	45.455	21.10	9.07	40.61	4.35
1898	1995	2.345991	CACCGTGGGGTCGACAAT	59.654	61.111	18.91	0.00	46.01	2.71
1899	1996	2.032634	CACCGTGGGGTCGACAATG	61.033	63.158	18.91	7.57	46.01	2.82
1907	2004	2.264794	GTCGACAATGACCCGCCT	59.735	61.111	11.55	0.00	32.61	5.52
1966	2063	4.161295	CGCCGGCAAGGAGGATCA	62.161	66.667	28.98	0.00	45.00	2.92
2060	2157	1.821136	GGGGAGAAATCCAAGCAAGTG	59.179	52.381	0.00	0.00	0.00	3.16
2121	2218	1.874019	CAGATCTTCGACACGGCCG	60.874	63.158	26.86	26.86	0.00	6.13
2320	2925	9.657121	GATTATTACTACTTCTTTACGCGTACT	57.343	33.333	20.44	0.00	0.00	2.73
2366	3133	1.086696	ATGGACGTGGATTTTCGCAG	58.913	50.000	0.00	0.00	0.00	5.18
2367	3134	0.250124	TGGACGTGGATTTTCGCAGT	60.250	50.000	0.00	0.00	0.00	4.40
2368	3135	0.165944	GGACGTGGATTTTCGCAGTG	59.834	55.000	0.00	0.00	0.00	3.66
2371	3138	1.086696	CGTGGATTTTCGCAGTGGAT	58.913	50.000	0.00	0.00	0.00	3.41
2372	3139	1.468520	CGTGGATTTTCGCAGTGGATT	59.531	47.619	0.00	0.00	0.00	3.01
2373	3140	2.095263	CGTGGATTTTCGCAGTGGATTT	60.095	45.455	0.00	0.00	0.00	2.17
2375	3142	3.920412	GTGGATTTTCGCAGTGGATTTTC	59.080	43.478	0.00	0.00	0.00	2.29
2376	3143	3.171277	GGATTTTCGCAGTGGATTTTCG	58.829	45.455	0.00	0.00	0.00	3.46
2378	3145	0.947960	TTTCGCAGTGGATTTTCGCA	59.052	45.000	0.00	0.00	0.00	5.10
2379	3146	1.164411	TTCGCAGTGGATTTTCGCAT	58.836	45.000	0.00	0.00	0.00	4.73
2380	3147	1.164411	TCGCAGTGGATTTTCGCATT	58.836	45.000	0.00	0.00	0.00	3.56
2381	3148	1.539388	TCGCAGTGGATTTTCGCATTT	59.461	42.857	0.00	0.00	0.00	2.32
2382	3149	1.650153	CGCAGTGGATTTTCGCATTTG	59.350	47.619	0.00	0.00	0.00	2.32
2383	3150	2.668001	CGCAGTGGATTTTCGCATTTGA	60.668	45.455	0.00	0.00	0.00	2.69
2385	3152	4.671377	GCAGTGGATTTTCGCATTTGATA	58.329	39.130	0.00	0.00	0.00	2.15
2699	3606	2.511600	CGGCCTTCACCATCGACC	60.512	66.667	0.00	0.00	0.00	4.79
2776	3698	4.329545	GCCCTCACCGACAAGCCA	62.330	66.667	0.00	0.00	0.00	4.75
2804	3726	3.157680	CCTTCCCGTCCACCAACT	58.842	61.111	0.00	0.00	0.00	3.16
2805	3727	1.454539	CCTTCCCGTCCACCAACTT	59.545	57.895	0.00	0.00	0.00	2.66
2812	3734	0.107831	CGTCCACCAACTTCAAGGGA	59.892	55.000	0.00	0.00	0.00	4.20
2980	3914	1.613630	ACCCAGGGAAGACTGCGAT	60.614	57.895	14.54	0.00	37.16	4.58
3614	4562	4.227134	CCAGGGTCTCCATCCGCG	62.227	72.222	0.00	0.00	34.83	6.46
3615	4563	4.899239	CAGGGTCTCCATCCGCGC	62.899	72.222	0.00	0.00	34.83	6.86
3763	5169	2.302157	GGAGGAGAAGGTTTCTTTCCGA	59.698	50.000	7.24	0.00	40.87	4.55
3783	5189	4.917415	CCGATTTCATGTCCTTGTTGTTTC	59.083	41.667	0.00	0.00	0.00	2.78
3787	5193	5.913137	TTCATGTCCTTGTTGTTTCTTGT	57.087	34.783	0.00	0.00	0.00	3.16
3877	5283	1.648467	GGCTGACCGGCTAAAGCTTG	61.648	60.000	15.30	0.00	41.70	4.01
4041	6273	0.380733	CGCATCGGAGTAGTGCTACA	59.619	55.000	11.39	0.00	38.48	2.74
4045	6277	3.676324	GCATCGGAGTAGTGCTACAACTT	60.676	47.826	11.39	0.00	38.48	2.66
4052	9268	3.386726	AGTAGTGCTACAACTTGTGACCA	59.613	43.478	11.39	0.00	38.48	4.02
4053	9269	3.492102	AGTGCTACAACTTGTGACCAT	57.508	42.857	4.57	0.00	0.00	3.55
4058	9274	1.878953	ACAACTTGTGACCATCGGAC	58.121	50.000	0.00	0.00	0.00	4.79
4064	9280	2.362503	TGACCATCGGACCTCGCT	60.363	61.111	0.00	0.00	39.05	4.93
4103	9319	1.167851	CATGGTTGTCGTCATGCCTT	58.832	50.000	0.00	0.00	35.07	4.35
4109	9325	4.015406	TCGTCATGCCTTGCCGGT	62.015	61.111	1.90	0.00	34.25	5.28
4114	9330	3.727258	ATGCCTTGCCGGTGCCTA	61.727	61.111	1.90	0.00	36.33	3.93
4115	9331	3.704231	ATGCCTTGCCGGTGCCTAG	62.704	63.158	1.90	0.00	36.33	3.02
4128	9481	2.104331	CCTAGAACACGCGGCGAT	59.896	61.111	30.94	13.88	0.00	4.58
4132	9485	2.495366	TAGAACACGCGGCGATTGGT	62.495	55.000	30.94	16.98	0.00	3.67
4145	9498	2.165437	GCGATTGGTAGAAATTTGGGCA	59.835	45.455	0.00	0.00	0.00	5.36
4163	9516	1.305802	ATGTCCACCGGTGCCTAGA	60.306	57.895	29.75	17.77	0.00	2.43
4185	9538	5.839606	AGAGTCGCCCTTTCTAATTATACCT	59.160	40.000	0.00	0.00	0.00	3.08
4304	9659	3.469008	TTGTGTACACCTCCTTGACTG	57.531	47.619	22.91	0.00	0.00	3.51
4305	9660	2.673258	TGTGTACACCTCCTTGACTGA	58.327	47.619	22.91	0.00	0.00	3.41
4312	9667	7.707035	GTGTACACCTCCTTGACTGAATAATAG	59.293	40.741	15.42	0.00	0.00	1.73
4355	9714	7.658179	TCTCAATCACATTCAACAACTCTAC	57.342	36.000	0.00	0.00	0.00	2.59
4369	9728	5.294356	ACAACTCTACGCATGTTACTTTGA	58.706	37.500	0.00	0.00	0.00	2.69
4449	9817	3.438781	CCTCTGCAATACGGCAAAAAGTA	59.561	43.478	0.00	0.00	44.40	2.24
4460	9828	6.870971	ACGGCAAAAAGTAGTTCAATTCTA	57.129	33.333	0.00	0.00	0.00	2.10
4483	9852	9.066892	TCTACCATGTTCCATCATAAAATAAGC	57.933	33.333	0.00	0.00	0.00	3.09
4537	9906	7.168637	ACACGGACGAATACAATGTACATTATC	59.831	37.037	20.39	14.39	0.00	1.75
4629	10001	2.669781	TGGGGATTTCAGCATTCCATC	58.330	47.619	0.00	0.00	0.00	3.51
4715	10089	5.937540	TCGGAAGCTGTTTGAAATTGATCTA	59.062	36.000	0.00	0.00	0.00	1.98
4765	10140	1.532868	CAGCAACAACTGTAGCCTCAC	59.467	52.381	0.00	0.00	32.78	3.51
4788	10163	3.928754	TCCCAGCTAGTCATCCATAAGT	58.071	45.455	0.00	0.00	0.00	2.24
4792	10167	5.295950	CCAGCTAGTCATCCATAAGTTGAG	58.704	45.833	0.00	0.00	0.00	3.02

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
75	76	1.522580	GGCTGTGCGATCTCTTCCC	60.523	63.158	0.00	0.00	0.00	3.97
952	1035	5.611374	CCTGATTTATAGTTGGATGGACGT	58.389	41.667	0.00	0.00	0.00	4.34
978	1061	0.032815	GGTTAGATGAGGCTCTCCGC	59.967	60.000	16.72	2.41	37.47	5.54
1017	1100	5.816777	GCTAGCTCTTCTTCACTTGATGATT	59.183	40.000	7.70	0.00	37.11	2.57
1118	1206	2.609610	GGTGGCCTGTAGGTCCCA	60.610	66.667	3.32	0.00	39.61	4.37
1196	1284	2.282251	TCGTCGGTGAGCAGGAGT	60.282	61.111	0.00	0.00	0.00	3.85
1268	1356	1.075601	TCTTTCCCATGAAGGCCAGT	58.924	50.000	5.01	0.00	35.39	4.00
1327	1415	2.358125	TGCCATTGTCCACGTCCG	60.358	61.111	0.00	0.00	0.00	4.79
1385	1473	2.673341	AGGTGCAGCGTCTCGAGA	60.673	61.111	12.08	12.08	0.00	4.04
1430	1518	1.072159	GCTCAGCACCTTCACCACT	59.928	57.895	0.00	0.00	0.00	4.00
1604	1701	0.543410	TCCTGTACACCACGGTCCAT	60.543	55.000	0.00	0.00	0.00	3.41
1769	1866	3.119137	TCACGTTCATGATCACGATCCTT	60.119	43.478	23.06	1.28	39.76	3.36
1770	1867	2.427095	TCACGTTCATGATCACGATCCT	59.573	45.455	23.06	1.62	39.76	3.24
1771	1868	2.809446	TCACGTTCATGATCACGATCC	58.191	47.619	23.06	0.00	39.76	3.36
1816	1913	0.523072	CTTGATCACAACCTTGCGGG	59.477	55.000	0.00	0.00	41.89	6.13
1898	1995	2.745037	GTGTTGGTAGGCGGGTCA	59.255	61.111	0.00	0.00	0.00	4.02
1899	1996	2.046604	GGTGTTGGTAGGCGGGTC	60.047	66.667	0.00	0.00	0.00	4.46
1907	2004	2.663520	CACGCTGCGGTGTTGGTA	60.664	61.111	26.95	0.00	33.47	3.25
1961	2058	1.520787	CACCGGCGTTACCTGATCC	60.521	63.158	6.01	0.00	35.61	3.36
2060	2157	1.153958	GCGCTCCACCTTCATTTGC	60.154	57.895	0.00	0.00	0.00	3.68
2304	2909	9.823098	CAATATATAGAGTACGCGTAAAGAAGT	57.177	33.333	22.44	2.67	0.00	3.01
2305	2910	9.275231	CCAATATATAGAGTACGCGTAAAGAAG	57.725	37.037	22.44	2.34	0.00	2.85
2308	2913	6.471519	GGCCAATATATAGAGTACGCGTAAAG	59.528	42.308	22.44	0.30	0.00	1.85
2311	2916	4.034394	CGGCCAATATATAGAGTACGCGTA	59.966	45.833	16.41	16.41	0.00	4.42
2313	2918	3.360533	CGGCCAATATATAGAGTACGCG	58.639	50.000	3.53	3.53	0.00	6.01
2314	2919	3.490419	CCCGGCCAATATATAGAGTACGC	60.490	52.174	2.24	0.00	0.00	4.42
2320	2925	2.261729	TGTGCCCGGCCAATATATAGA	58.738	47.619	7.03	0.00	0.00	1.98
2396	3163	9.674824	GATTTTCTTATTATCCTGCAGACATTG	57.325	33.333	17.39	0.00	0.00	2.82
2416	3187	3.935203	TCCTCTCGATGCTTGTGATTTTC	59.065	43.478	0.00	0.00	0.00	2.29
2699	3606	1.153309	TCATGATCTGCACCGGCTG	60.153	57.895	0.00	0.00	41.91	4.85
2776	3698	2.040544	CGGGAAGGCGCAGTTGAAT	61.041	57.895	10.83	0.00	0.00	2.57
2804	3726	1.048601	ACGAGCTTGTCTCCCTTGAA	58.951	50.000	0.00	0.00	38.62	2.69
2805	3727	0.318441	CACGAGCTTGTCTCCCTTGA	59.682	55.000	2.72	0.00	38.62	3.02
2980	3914	2.379972	GAGGAGGAGAAGACGATCCAA	58.620	52.381	0.00	0.00	38.12	3.53
3058	3992	3.387225	GAAGTAGCCGGGGTCCAGC	62.387	68.421	2.18	0.00	0.00	4.85
3614	4562	0.456142	GATGAAAACGAAAGGGGCGC	60.456	55.000	0.00	0.00	0.00	6.53
3615	4563	0.878416	TGATGAAAACGAAAGGGGCG	59.122	50.000	0.00	0.00	0.00	6.13
3616	4564	1.402852	GCTGATGAAAACGAAAGGGGC	60.403	52.381	0.00	0.00	0.00	5.80
3617	4565	1.202348	GGCTGATGAAAACGAAAGGGG	59.798	52.381	0.00	0.00	0.00	4.79
3763	5169	6.757947	CACAAGAAACAACAAGGACATGAAAT	59.242	34.615	0.00	0.00	0.00	2.17
3829	5235	6.538381	AGCAAACATTGACCCTTTACAAAAAG	59.462	34.615	0.00	0.00	41.57	2.27
3830	5236	6.410540	AGCAAACATTGACCCTTTACAAAAA	58.589	32.000	0.00	0.00	0.00	1.94
3912	5318	7.179269	GGGTTGAGGGGCATATACAATAATAA	58.821	38.462	0.00	0.00	0.00	1.40
3914	5320	5.518367	GGGGTTGAGGGGCATATACAATAAT	60.518	44.000	0.00	0.00	0.00	1.28
3915	5321	4.202631	GGGGTTGAGGGGCATATACAATAA	60.203	45.833	0.00	0.00	0.00	1.40
3922	6152	3.133365	GCGGGGTTGAGGGGCATAT	62.133	63.158	0.00	0.00	0.00	1.78
3929	6159	3.737172	CTTTGCGCGGGGTTGAGG	61.737	66.667	8.83	0.00	0.00	3.86
4022	6254	0.380733	TGTAGCACTACTCCGATGCG	59.619	55.000	9.12	0.00	44.25	4.73
4041	6273	1.002087	GAGGTCCGATGGTCACAAGTT	59.998	52.381	0.00	0.00	0.00	2.66
4045	6277	3.001902	GCGAGGTCCGATGGTCACA	62.002	63.158	0.00	0.00	41.76	3.58
4052	9268	2.065470	TAGCCCTAGCGAGGTCCGAT	62.065	60.000	12.29	0.00	46.67	4.18
4053	9269	2.749584	TAGCCCTAGCGAGGTCCGA	61.750	63.158	12.29	0.00	46.67	4.55
4103	9319	2.345991	GTGTTCTAGGCACCGGCA	59.654	61.111	0.00	0.00	43.71	5.69
4112	9328	1.631072	CAATCGCCGCGTGTTCTAG	59.369	57.895	13.39	0.00	0.00	2.43
4113	9329	1.807981	CCAATCGCCGCGTGTTCTA	60.808	57.895	13.39	0.00	0.00	2.10
4114	9330	2.495366	TACCAATCGCCGCGTGTTCT	62.495	55.000	13.39	0.00	0.00	3.01
4115	9331	2.020836	CTACCAATCGCCGCGTGTTC	62.021	60.000	13.39	0.00	0.00	3.18
4128	9481	3.513515	GGACATGCCCAAATTTCTACCAA	59.486	43.478	0.00	0.00	0.00	3.67
4132	9485	3.096092	GGTGGACATGCCCAAATTTCTA	58.904	45.455	0.75	0.00	38.06	2.10
4145	9498	1.305802	TCTAGGCACCGGTGGACAT	60.306	57.895	34.58	19.50	0.00	3.06
4163	9516	6.099269	TCAAGGTATAATTAGAAAGGGCGACT	59.901	38.462	0.00	0.00	0.00	4.18
4185	9538	9.817809	GTTTATATCCTCATAGAACACAGTCAA	57.182	33.333	0.00	0.00	0.00	3.18
4258	9613	2.625790	GCGATGTCTCCCTAGATCAAGT	59.374	50.000	0.00	0.00	33.30	3.16
4304	9659	7.023575	CGAATGCCCATTTACAGCTATTATTC	58.976	38.462	0.00	0.00	0.00	1.75
4305	9660	6.714810	TCGAATGCCCATTTACAGCTATTATT	59.285	34.615	0.00	0.00	0.00	1.40
4312	9667	2.880890	AGATCGAATGCCCATTTACAGC	59.119	45.455	0.00	0.00	0.00	4.40
4355	9714	6.408858	AACTATCAGTCAAAGTAACATGCG	57.591	37.500	0.00	0.00	0.00	4.73
4369	9728	7.888021	TGATGTTGTTGGGAAATAACTATCAGT	59.112	33.333	0.00	0.00	0.00	3.41
4483	9852	3.358707	TGAGCAGCAAGTTGAACAATG	57.641	42.857	7.16	0.00	0.00	2.82
4590	9962	6.740693	TCCCCAATTTTATTTCTCATCTCCA	58.259	36.000	0.00	0.00	0.00	3.86
4629	10001	1.444895	GCTCCAAAGCGCATGGTTG	60.445	57.895	25.64	20.70	39.10	3.77
4715	10089	5.310451	AGCAACTTTCCATTGATTTTGCAT	58.690	33.333	6.22	0.00	40.23	3.96
4765	10140	4.285517	ACTTATGGATGACTAGCTGGGATG	59.714	45.833	0.85	0.00	0.00	3.51

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.