AutoCloner

Multiple sequence alignment - TraesCS4A01G437800

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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	TraesCS4A01G437800	chr4A	100.000	3257	0	0	1	3257	707479259	707476003	0.000000e+00	6015.0
1	TraesCS4A01G437800	chr4A	94.311	1371	61	10	1897	3257	705906546	705907909	0.000000e+00	2084.0
2	TraesCS4A01G437800	chr4A	93.399	1318	64	5	904	2219	707177748	707179044	0.000000e+00	1930.0
3	TraesCS4A01G437800	chr4A	93.399	1318	64	5	904	2219	707201273	707202569	0.000000e+00	1930.0
4	TraesCS4A01G437800	chr4A	92.559	1317	80	8	904	2219	707402822	707404121	0.000000e+00	1873.0
5	TraesCS4A01G437800	chr4A	92.045	1320	87	8	901	2219	705889347	705890649	0.000000e+00	1840.0
6	TraesCS4A01G437800	chr4A	92.126	1270	90	5	888	2152	706094825	706096089	0.000000e+00	1783.0
7	TraesCS4A01G437800	chr4A	93.410	1047	54	9	2215	3254	705959762	705960800	0.000000e+00	1537.0
8	TraesCS4A01G437800	chr4A	93.321	1048	53	10	2215	3254	706096086	706097124	0.000000e+00	1531.0
9	TraesCS4A01G437800	chr4A	91.799	378	21	6	2421	2797	707645625	707645257	4.820000e-143	518.0
10	TraesCS4A01G437800	chr4A	94.690	226	11	1	2786	3010	707643445	707643220	1.860000e-92	350.0
11	TraesCS4A01G437800	chr4A	86.916	214	14	13	2214	2421	707179072	707179277	9.090000e-56	228.0
12	TraesCS4A01G437800	chr4A	86.916	214	14	13	2214	2421	707202597	707202802	9.090000e-56	228.0
13	TraesCS4A01G437800	chr4A	97.938	97	1	1	2324	2420	707645841	707645746	2.010000e-37	167.0
14	TraesCS4A01G437800	chr4A	92.045	88	7	0	2214	2301	705890677	705890764	1.230000e-24	124.0
15	TraesCS4A01G437800	chr4A	92.208	77	2	2	2331	2404	707179273	707179348	4.440000e-19	106.0
16	TraesCS4A01G437800	chr4A	84.884	86	9	3	2581	2666	707301288	707301369	2.080000e-12	84.2
17	TraesCS4A01G437800	chrUn	92.677	1270	83	5	888	2152	220054896	220056160	0.000000e+00	1821.0
18	TraesCS4A01G437800	chrUn	93.761	577	31	2	2682	3253	343476104	343476680	0.000000e+00	861.0
19	TraesCS4A01G437800	chrUn	93.348	466	21	7	2215	2678	447800966	447801423	0.000000e+00	680.0
20	TraesCS4A01G437800	chrUn	92.857	154	7	4	2215	2367	220056157	220056307	1.520000e-53	220.0
21	TraesCS4A01G437800	chr7D	90.761	1353	99	11	888	2219	24157280	24155933	0.000000e+00	1783.0
22	TraesCS4A01G437800	chr7D	91.203	1330	83	17	904	2219	24032554	24033863	0.000000e+00	1777.0
23	TraesCS4A01G437800	chr7D	91.203	1239	99	8	959	2192	53793269	53792036	0.000000e+00	1676.0
24	TraesCS4A01G437800	chr7D	91.250	640	44	9	146	785	497789409	497790036	0.000000e+00	861.0
25	TraesCS4A01G437800	chr7D	85.337	416	52	4	2514	2921	24155530	24155116	3.890000e-114	422.0
26	TraesCS4A01G437800	chr7D	84.906	212	18	13	2214	2419	24033891	24034094	5.510000e-48	202.0
27	TraesCS4A01G437800	chr7D	93.333	60	2	2	748	806	460637560	460637502	1.610000e-13	87.9
28	TraesCS4A01G437800	chr7A	91.748	1236	95	5	959	2192	57219246	57218016	0.000000e+00	1711.0
29	TraesCS4A01G437800	chr7A	87.926	646	47	11	146	787	185973672	185974290	0.000000e+00	732.0
30	TraesCS4A01G437800	chr4B	95.088	794	24	3	96	876	611243465	611242674	0.000000e+00	1236.0
31	TraesCS4A01G437800	chr4B	97.895	95	2	0	6	100	611243590	611243496	7.230000e-37	165.0
32	TraesCS4A01G437800	chr4B	96.296	81	3	0	797	877	518655599	518655679	2.040000e-27	134.0
33	TraesCS4A01G437800	chr1D	91.121	642	48	4	146	787	370503324	370502692	0.000000e+00	861.0
34	TraesCS4A01G437800	chr1D	90.938	640	49	2	146	785	370353929	370353299	0.000000e+00	852.0
35	TraesCS4A01G437800	chr1D	90.343	642	51	5	146	787	370356387	370355757	0.000000e+00	832.0
36	TraesCS4A01G437800	chr1D	100.000	51	0	0	97	147	370356988	370356938	9.620000e-16	95.3
37	TraesCS4A01G437800	chr1D	98.077	52	1	0	96	147	370503924	370503873	1.240000e-14	91.6
38	TraesCS4A01G437800	chr3B	89.392	641	58	5	146	784	733632069	733631437	0.000000e+00	798.0
39	TraesCS4A01G437800	chr3B	91.916	569	45	1	147	714	691278479	691277911	0.000000e+00	795.0
40	TraesCS4A01G437800	chr3B	88.768	641	62	4	146	785	17635431	17636062	0.000000e+00	776.0
41	TraesCS4A01G437800	chr3B	81.470	313	32	14	577	889	9903553	9903839	1.950000e-57	233.0
42	TraesCS4A01G437800	chr1B	86.331	139	9	7	753	889	159161861	159161991	3.390000e-30	143.0
43	TraesCS4A01G437800	chr5B	93.902	82	4	1	797	877	693092446	693092365	4.410000e-24	122.0
44	TraesCS4A01G437800	chr3D	93.902	82	3	2	797	877	418381788	418381708	4.410000e-24	122.0
45	TraesCS4A01G437800	chr7B	92.857	84	5	1	797	880	700869204	700869122	1.590000e-23	121.0
46	TraesCS4A01G437800	chr2B	88.776	98	9	2	779	876	408313849	408313944	5.710000e-23	119.0
47	TraesCS4A01G437800	chr2B	90.698	86	8	0	790	875	232914470	232914385	7.380000e-22	115.0
48	TraesCS4A01G437800	chr5D	83.212	137	14	8	748	880	360778915	360778784	2.050000e-22	117.0
49	TraesCS4A01G437800	chr6D	80.420	143	12	13	748	875	427235000	427234859	9.620000e-16	95.3
50	TraesCS4A01G437800	chr6D	100.000	42	0	0	96	137	143375644	143375603	9.690000e-11	78.7
51	TraesCS4A01G437800	chr4D	82.222	90	16	0	3151	3240	359843236	359843147	9.690000e-11	78.7

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	TraesCS4A01G437800	chr4A	707476003	707479259	3256	True	6015.000000	6015	100.000000	1	3257	1	chr4A.!!$R1	3256
1	TraesCS4A01G437800	chr4A	705906546	705907909	1363	False	2084.000000	2084	94.311000	1897	3257	1	chr4A.!!$F1	1360
2	TraesCS4A01G437800	chr4A	707402822	707404121	1299	False	1873.000000	1873	92.559000	904	2219	1	chr4A.!!$F4	1315
3	TraesCS4A01G437800	chr4A	706094825	706097124	2299	False	1657.000000	1783	92.723500	888	3254	2	chr4A.!!$F6	2366
4	TraesCS4A01G437800	chr4A	705959762	705960800	1038	False	1537.000000	1537	93.410000	2215	3254	1	chr4A.!!$F2	1039
5	TraesCS4A01G437800	chr4A	707201273	707202802	1529	False	1079.000000	1930	90.157500	904	2421	2	chr4A.!!$F8	1517
6	TraesCS4A01G437800	chr4A	705889347	705890764	1417	False	982.000000	1840	92.045000	901	2301	2	chr4A.!!$F5	1400
7	TraesCS4A01G437800	chr4A	707177748	707179348	1600	False	754.666667	1930	90.841000	904	2421	3	chr4A.!!$F7	1517
8	TraesCS4A01G437800	chr4A	707643220	707645841	2621	True	345.000000	518	94.809000	2324	3010	3	chr4A.!!$R2	686
9	TraesCS4A01G437800	chrUn	220054896	220056307	1411	False	1020.500000	1821	92.767000	888	2367	2	chrUn.!!$F3	1479
10	TraesCS4A01G437800	chrUn	343476104	343476680	576	False	861.000000	861	93.761000	2682	3253	1	chrUn.!!$F1	571
11	TraesCS4A01G437800	chr7D	53792036	53793269	1233	True	1676.000000	1676	91.203000	959	2192	1	chr7D.!!$R1	1233
12	TraesCS4A01G437800	chr7D	24155116	24157280	2164	True	1102.500000	1783	88.049000	888	2921	2	chr7D.!!$R3	2033
13	TraesCS4A01G437800	chr7D	24032554	24034094	1540	False	989.500000	1777	88.054500	904	2419	2	chr7D.!!$F2	1515
14	TraesCS4A01G437800	chr7D	497789409	497790036	627	False	861.000000	861	91.250000	146	785	1	chr7D.!!$F1	639
15	TraesCS4A01G437800	chr7A	57218016	57219246	1230	True	1711.000000	1711	91.748000	959	2192	1	chr7A.!!$R1	1233
16	TraesCS4A01G437800	chr7A	185973672	185974290	618	False	732.000000	732	87.926000	146	787	1	chr7A.!!$F1	641
17	TraesCS4A01G437800	chr4B	611242674	611243590	916	True	700.500000	1236	96.491500	6	876	2	chr4B.!!$R1	870
18	TraesCS4A01G437800	chr1D	370353299	370356988	3689	True	593.100000	852	93.760333	97	787	3	chr1D.!!$R1	690
19	TraesCS4A01G437800	chr1D	370502692	370503924	1232	True	476.300000	861	94.599000	96	787	2	chr1D.!!$R2	691
20	TraesCS4A01G437800	chr3B	733631437	733632069	632	True	798.000000	798	89.392000	146	784	1	chr3B.!!$R2	638
21	TraesCS4A01G437800	chr3B	691277911	691278479	568	True	795.000000	795	91.916000	147	714	1	chr3B.!!$R1	567
22	TraesCS4A01G437800	chr3B	17635431	17636062	631	False	776.000000	776	88.768000	146	785	1	chr3B.!!$F2	639

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
840	3903	0.167251	CAGCGAAAAATAACCGGCGT	59.833	50.0	6.01	0.0	0.0	5.68	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2335	5499	1.203313	AGGACTGTAGGAGAAGGGCAA	60.203	52.381	0.0	0.0	0.0	4.52	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
65	66	3.636231	TCTTGGCTCCGTGGGTGG	61.636	66.667	0.00	0.00	0.00	4.61
211	799	3.807538	GACCTCGCGTCCGCACTA	61.808	66.667	12.58	0.00	42.06	2.74
310	3356	0.677731	CGACATCCACCTTGCCATGT	60.678	55.000	0.00	0.00	32.02	3.21
330	3376	0.251922	ATGTCAAGGTTGCATGGCCT	60.252	50.000	3.32	0.00	36.51	5.19
691	3741	4.811557	CGGTATGGAAAGTTCTGATCCTTC	59.188	45.833	0.00	0.00	34.24	3.46
748	3798	0.179174	GCGAAACTAAACCGGCATGG	60.179	55.000	0.00	0.00	46.41	3.66
836	3899	6.937886	AATAAAACCAGCGAAAAATAACCG	57.062	33.333	0.00	0.00	0.00	4.44
840	3903	0.167251	CAGCGAAAAATAACCGGCGT	59.833	50.000	6.01	0.00	0.00	5.68
858	3921	2.603560	GCGTACTATTCACCAACTGCTC	59.396	50.000	0.00	0.00	0.00	4.26
863	3926	7.423199	CGTACTATTCACCAACTGCTCTATTA	58.577	38.462	0.00	0.00	0.00	0.98
878	3941	8.506168	CTGCTCTATTAGGAGTAGAGATTAGG	57.494	42.308	12.90	0.00	45.10	2.69
879	3942	8.220898	TGCTCTATTAGGAGTAGAGATTAGGA	57.779	38.462	12.90	0.00	45.10	2.94
880	3943	8.325787	TGCTCTATTAGGAGTAGAGATTAGGAG	58.674	40.741	12.90	0.00	45.10	3.69
881	3944	8.326529	GCTCTATTAGGAGTAGAGATTAGGAGT	58.673	40.741	12.90	0.00	45.10	3.85
886	3949	9.624037	ATTAGGAGTAGAGATTAGGAGTAGAGA	57.376	37.037	0.00	0.00	0.00	3.10
927	3999	9.477484	GATGAAGAAAATCGCTCTATAAAGGTA	57.523	33.333	0.00	0.00	0.00	3.08
957	4029	4.817063	CGGCAGCGGCACAATTCG	62.817	66.667	11.88	0.00	43.71	3.34
971	4043	5.107875	GGCACAATTCGATTCAAAACAAGAC	60.108	40.000	0.00	0.00	0.00	3.01
1015	4087	1.355796	CGCCATGCATGCAAACAAGG	61.356	55.000	26.68	20.67	0.00	3.61
1092	4164	4.667420	CGCAAGTACAAGGACGGT	57.333	55.556	0.00	0.00	0.00	4.83
1194	4266	3.103911	GTCGTCGACAAGGCCACG	61.104	66.667	20.28	4.85	32.09	4.94
1381	4453	1.844771	CGTCGTGTCGGTGGAGTACA	61.845	60.000	0.00	0.00	0.00	2.90
1830	4911	2.836154	GTGGCTGGGAAGGACACA	59.164	61.111	0.00	0.00	41.90	3.72
1866	4947	3.203442	GACCTGTCGGACCGCATA	58.797	61.111	9.66	0.00	0.00	3.14
2103	5192	1.816224	GACGTGTTTGGGTATGGCATT	59.184	47.619	4.78	0.00	0.00	3.56
2225	5365	2.437359	GATGCCTGCTGCGGTTCT	60.437	61.111	7.82	0.00	45.60	3.01
2335	5499	0.552615	AGGGTCTGGCCAAAGGGTAT	60.553	55.000	7.01	0.00	39.65	2.73
2450	5826	4.522789	GCCCATTAATTACCGAACATGGAT	59.477	41.667	11.58	0.00	34.21	3.41
2512	5891	4.968812	TCATAAACAGGTGTCATGCATG	57.031	40.909	21.07	21.07	0.00	4.06
2623	6006	9.561069	GTACATGTAATATTGGATTCTCAAGGT	57.439	33.333	7.25	0.00	0.00	3.50
2691	6078	2.590291	TGTGTCCGTGCGTTGCAT	60.590	55.556	0.00	0.00	41.91	3.96
2733	6120	9.185680	AGAGTCATAAAATTTATAACCCCACAC	57.814	33.333	0.00	0.00	0.00	3.82
2779	6170	8.704668	GGAAATCCAACCTACCATCAATTTTAT	58.295	33.333	0.00	0.00	35.64	1.40
2971	8186	3.281727	TTTGTGATCTGGAGGGCATAC	57.718	47.619	0.00	0.00	0.00	2.39
3024	8239	1.947456	ACGTGTTTTTCTCCTCTTGGC	59.053	47.619	0.00	0.00	0.00	4.52
3037	8252	1.336440	CTCTTGGCGATCACGATCTCT	59.664	52.381	5.55	0.00	42.66	3.10
3038	8253	1.751351	TCTTGGCGATCACGATCTCTT	59.249	47.619	5.55	0.00	42.66	2.85
3042	8257	1.127701	GCGATCACGATCTCTTGAGC	58.872	55.000	5.55	0.00	42.66	4.26
3050	8265	1.925847	CGATCTCTTGAGCACTTCTGC	59.074	52.381	0.00	0.00	44.63	4.26
3090	8309	1.658686	GACTCCTCCTGACGTGCGAT	61.659	60.000	0.00	0.00	0.00	4.58
3112	8331	1.227527	CAACGAGCAGTGGGTCACA	60.228	57.895	0.00	0.00	41.62	3.58
3181	8400	3.533606	AGAAGATGAGGTGTTCGATGG	57.466	47.619	0.00	0.00	35.38	3.51
3192	8411	3.050619	GTGTTCGATGGCCTAGTAATCG	58.949	50.000	14.52	14.52	43.47	3.34
3199	8418	4.082733	CGATGGCCTAGTAATCGATGAAGA	60.083	45.833	15.37	0.00	44.57	2.87

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
2	3	4.790962	ATGCTGCCTCCGCACTGG	62.791	66.667	0.00	0.00	41.12	4.00
3	4	3.506096	CATGCTGCCTCCGCACTG	61.506	66.667	0.00	0.00	41.12	3.66
4	5	3.709633	TCATGCTGCCTCCGCACT	61.710	61.111	0.00	0.00	41.12	4.40
15	16	1.220206	CTTGCCTCTCCGTCATGCT	59.780	57.895	0.00	0.00	0.00	3.79
65	66	0.675522	CCCCACGTACAACATCCACC	60.676	60.000	0.00	0.00	0.00	4.61
211	799	1.686110	GGATGTCCCCGGTCTCAGT	60.686	63.158	0.00	0.00	0.00	3.41
296	3342	1.632920	TGACATACATGGCAAGGTGGA	59.367	47.619	0.00	0.00	44.23	4.02
310	3356	1.005805	AGGCCATGCAACCTTGACATA	59.994	47.619	5.01	0.00	29.74	2.29
379	3425	0.811616	CTCCACTTCGCCATAGCACC	60.812	60.000	0.00	0.00	39.83	5.01
605	3652	8.542953	TCAATCACGATCAATCTCTAAAAATCG	58.457	33.333	0.00	0.00	41.17	3.34
609	3656	9.605275	AGAATCAATCACGATCAATCTCTAAAA	57.395	29.630	0.00	0.00	0.00	1.52
748	3798	2.071636	TTTTTCGTCCCCTCCCCCAC	62.072	60.000	0.00	0.00	0.00	4.61
769	3819	2.030628	CCGTGGTTTATTTTCGCTGGTT	60.031	45.455	0.00	0.00	0.00	3.67
770	3820	1.538075	CCGTGGTTTATTTTCGCTGGT	59.462	47.619	0.00	0.00	0.00	4.00
772	3822	2.413634	GGTCCGTGGTTTATTTTCGCTG	60.414	50.000	0.00	0.00	0.00	5.18
773	3823	1.808343	GGTCCGTGGTTTATTTTCGCT	59.192	47.619	0.00	0.00	0.00	4.93
774	3824	1.536331	TGGTCCGTGGTTTATTTTCGC	59.464	47.619	0.00	0.00	0.00	4.70
775	3825	2.160813	CCTGGTCCGTGGTTTATTTTCG	59.839	50.000	0.00	0.00	0.00	3.46
776	3826	2.490509	CCCTGGTCCGTGGTTTATTTTC	59.509	50.000	0.00	0.00	0.00	2.29
777	3827	2.158430	ACCCTGGTCCGTGGTTTATTTT	60.158	45.455	0.00	0.00	0.00	1.82
836	3899	1.664151	GCAGTTGGTGAATAGTACGCC	59.336	52.381	0.00	0.00	38.27	5.68
840	3903	7.783119	TCCTAATAGAGCAGTTGGTGAATAGTA	59.217	37.037	0.00	0.00	0.00	1.82
863	3926	9.624037	TTATCTCTACTCCTAATCTCTACTCCT	57.376	37.037	0.00	0.00	0.00	3.69
876	3939	5.127491	CCACGTCTCTTTATCTCTACTCCT	58.873	45.833	0.00	0.00	0.00	3.69
877	3940	4.261280	GCCACGTCTCTTTATCTCTACTCC	60.261	50.000	0.00	0.00	0.00	3.85
878	3941	4.553156	CGCCACGTCTCTTTATCTCTACTC	60.553	50.000	0.00	0.00	0.00	2.59
879	3942	3.312973	CGCCACGTCTCTTTATCTCTACT	59.687	47.826	0.00	0.00	0.00	2.57
880	3943	3.311871	TCGCCACGTCTCTTTATCTCTAC	59.688	47.826	0.00	0.00	0.00	2.59
881	3944	3.538591	TCGCCACGTCTCTTTATCTCTA	58.461	45.455	0.00	0.00	0.00	2.43
882	3945	2.366533	TCGCCACGTCTCTTTATCTCT	58.633	47.619	0.00	0.00	0.00	3.10
883	3946	2.846039	TCGCCACGTCTCTTTATCTC	57.154	50.000	0.00	0.00	0.00	2.75
884	3947	2.688446	TCATCGCCACGTCTCTTTATCT	59.312	45.455	0.00	0.00	0.00	1.98
885	3948	3.079960	TCATCGCCACGTCTCTTTATC	57.920	47.619	0.00	0.00	0.00	1.75
886	3949	3.130516	TCTTCATCGCCACGTCTCTTTAT	59.869	43.478	0.00	0.00	0.00	1.40
892	3955	2.163818	TTTTCTTCATCGCCACGTCT	57.836	45.000	0.00	0.00	0.00	4.18
945	4017	1.975837	TTTGAATCGAATTGTGCCGC	58.024	45.000	0.00	0.00	0.00	6.53
946	4018	3.304257	TGTTTTGAATCGAATTGTGCCG	58.696	40.909	0.00	0.00	0.00	5.69
947	4019	4.981674	TCTTGTTTTGAATCGAATTGTGCC	59.018	37.500	0.00	0.00	0.00	5.01
948	4020	5.687285	AGTCTTGTTTTGAATCGAATTGTGC	59.313	36.000	0.00	0.00	0.00	4.57
949	4021	7.096477	GGAAGTCTTGTTTTGAATCGAATTGTG	60.096	37.037	0.00	0.00	0.00	3.33
950	4022	6.918022	GGAAGTCTTGTTTTGAATCGAATTGT	59.082	34.615	0.00	0.00	0.00	2.71
951	4023	6.917477	TGGAAGTCTTGTTTTGAATCGAATTG	59.083	34.615	0.00	0.00	0.00	2.32
952	4024	7.038154	TGGAAGTCTTGTTTTGAATCGAATT	57.962	32.000	0.00	0.00	0.00	2.17
953	4025	6.633500	TGGAAGTCTTGTTTTGAATCGAAT	57.367	33.333	0.00	0.00	0.00	3.34
954	4026	6.443934	TTGGAAGTCTTGTTTTGAATCGAA	57.556	33.333	0.00	0.00	0.00	3.71
955	4027	6.094881	ACTTTGGAAGTCTTGTTTTGAATCGA	59.905	34.615	0.00	0.00	37.02	3.59
957	4029	9.581099	TTTACTTTGGAAGTCTTGTTTTGAATC	57.419	29.630	0.00	0.00	41.77	2.52
971	4043	4.276926	AGTTGAGCTGCTTTACTTTGGAAG	59.723	41.667	2.53	0.00	0.00	3.46
1026	4098	1.162698	TACGTCCGTCCTTCTCAGTG	58.837	55.000	0.00	0.00	0.00	3.66
1028	4100	1.538512	TGTTACGTCCGTCCTTCTCAG	59.461	52.381	0.00	0.00	0.00	3.35
1092	4164	2.447250	CGTAAGAAACGCTCGATGCTA	58.553	47.619	0.00	0.00	46.10	3.49
1108	4180	0.032952	AGCACGAAAGGACTGCGTAA	59.967	50.000	0.00	0.00	36.37	3.18
1119	4191	3.033764	GACGACGCCAGCACGAAA	61.034	61.111	11.91	0.00	36.70	3.46
1253	4325	1.404843	GTAGATGACGAGGGGAAGCT	58.595	55.000	0.00	0.00	0.00	3.74
1296	4368	4.803426	CGGCCGAAAGCGCTCTCT	62.803	66.667	24.07	0.00	45.17	3.10
1381	4453	0.396001	GGGAACTCCGGAGCTAGACT	60.396	60.000	31.56	7.90	36.71	3.24
1655	4727	3.680786	CACCCTCGCTGTCGTCCA	61.681	66.667	0.00	0.00	36.96	4.02
1855	4936	1.357690	GATCACGTATGCGGTCCGA	59.642	57.895	17.49	0.00	43.45	4.55
1885	4966	2.265904	CCTGCATCATCCATGGCCG	61.266	63.158	6.96	0.00	32.37	6.13
1890	4971	2.114625	CGCCCCTGCATCATCCAT	59.885	61.111	0.00	0.00	37.32	3.41
2103	5192	3.089838	CCCCAGGACTTCATGGCA	58.910	61.111	4.32	0.00	45.74	4.92
2225	5365	1.410882	TGTTGATCACACGAGTCCACA	59.589	47.619	0.00	0.00	0.00	4.17
2312	5452	1.763770	CTTTGGCCAGACCCTCTGT	59.236	57.895	5.11	0.00	42.80	3.41
2335	5499	1.203313	AGGACTGTAGGAGAAGGGCAA	60.203	52.381	0.00	0.00	0.00	4.52
2450	5826	9.709495	AGATAAACCACACAACTTACGTATAAA	57.291	29.630	0.00	0.00	0.00	1.40
2512	5891	8.863872	AGGGAAGGCATACAATATACATTTAC	57.136	34.615	0.00	0.00	0.00	2.01
2691	6078	4.515361	TGACTCTTTTGTTGTTAACCCGA	58.485	39.130	2.48	0.00	0.00	5.14
2725	6112	7.394923	TGAATTCGAATTATTTTAGTGTGGGGT	59.605	33.333	22.78	0.00	0.00	4.95
2739	6126	6.096282	GGTTGGATTTCCCTGAATTCGAATTA	59.904	38.462	22.78	6.55	35.38	1.40
2971	8186	7.066645	TGAGTTCATGCATAATTCAAAGAGGAG	59.933	37.037	0.00	0.00	0.00	3.69
3024	8239	2.115595	GTGCTCAAGAGATCGTGATCG	58.884	52.381	0.32	0.00	42.48	3.69
3050	8265	1.081892	CCATCGCCACTTCTGTCTTG	58.918	55.000	0.00	0.00	0.00	3.02
3061	8280	3.838271	GAGGAGTCGCCATCGCCA	61.838	66.667	0.00	0.00	40.02	5.69
3077	8296	4.492160	GCCGATCGCACGTCAGGA	62.492	66.667	10.32	0.00	37.47	3.86
3090	8309	4.680237	CCCACTGCTCGTTGCCGA	62.680	66.667	0.00	0.00	42.00	5.54
3097	8316	2.047844	CCTGTGACCCACTGCTCG	60.048	66.667	0.00	0.00	35.11	5.03
3112	8331	0.322546	GTCTTCCATTCCAACGCCCT	60.323	55.000	0.00	0.00	0.00	5.19
3181	8400	4.321378	GGACCTCTTCATCGATTACTAGGC	60.321	50.000	11.66	6.55	0.00	3.93
3192	8411	1.616374	GATCTCCGGGACCTCTTCATC	59.384	57.143	0.00	0.00	0.00	2.92
3199	8418	1.000019	TCGTTGATCTCCGGGACCT	60.000	57.895	0.00	0.00	0.00	3.85

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.