AutoCloner

Multiple sequence alignment - TraesCS6B01G008800

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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	TraesCS6B01G008800	chr6B	100.000	3145	0	0	1	3145	5716260	5713116	0.000000e+00	5808.0
1	TraesCS6B01G008800	chr6B	83.512	1777	240	25	549	2305	15105629	15107372	0.000000e+00	1609.0
2	TraesCS6B01G008800	chr6D	91.389	2671	202	16	205	2850	1540632	1537965	0.000000e+00	3633.0
3	TraesCS6B01G008800	chr6D	83.799	1753	240	20	549	2285	8140134	8141858	0.000000e+00	1624.0
4	TraesCS6B01G008800	chr6D	83.385	325	47	4	549	868	438479	438801	8.530000e-76	294.0
5	TraesCS6B01G008800	chr6D	85.714	280	35	4	2123	2399	3618463	3618186	1.100000e-74	291.0
6	TraesCS6B01G008800	chr6D	80.000	345	52	13	182	521	401864382	401864714	4.050000e-59	239.0
7	TraesCS6B01G008800	chr6D	93.966	116	6	1	49	164	1541407	1541293	1.160000e-39	174.0
8	TraesCS6B01G008800	chr6D	94.118	51	3	0	12	62	1541493	1541443	9.350000e-11	78.7
9	TraesCS6B01G008800	chr7D	92.005	1751	119	16	163	1900	558889136	558887394	0.000000e+00	2438.0
10	TraesCS6B01G008800	chr7D	90.826	1199	102	5	1946	3137	558848876	558847679	0.000000e+00	1598.0
11	TraesCS6B01G008800	chr7D	81.167	377	49	16	159	521	40116059	40116427	1.850000e-72	283.0
12	TraesCS6B01G008800	chr7D	77.892	389	58	13	968	1352	7453850	7454214	1.900000e-52	217.0
13	TraesCS6B01G008800	chr7D	88.793	116	6	6	49	164	558889278	558889170	5.470000e-28	135.0
14	TraesCS6B01G008800	chr5B	84.886	2104	265	31	589	2656	132587844	132589930	0.000000e+00	2074.0
15	TraesCS6B01G008800	chr5B	83.710	442	59	9	2668	3108	420463834	420464263	3.780000e-109	405.0
16	TraesCS6B01G008800	chr5D	83.906	2125	274	32	549	2611	119658797	119660915	0.000000e+00	1967.0
17	TraesCS6B01G008800	chr5D	79.946	369	52	18	160	521	149828461	149828814	5.210000e-63	252.0
18	TraesCS6B01G008800	chr5D	79.404	369	54	18	160	521	149840464	149840817	1.130000e-59	241.0
19	TraesCS6B01G008800	chr5A	83.597	2146	298	27	549	2656	129749106	129751235	0.000000e+00	1964.0
20	TraesCS6B01G008800	chr5A	82.900	462	64	11	2668	3126	345753196	345753645	4.890000e-108	401.0
21	TraesCS6B01G008800	chr6A	83.579	1766	242	21	549	2293	8608631	8610369	0.000000e+00	1611.0
22	TraesCS6B01G008800	chr6A	83.767	1269	169	18	549	1802	8387524	8388770	0.000000e+00	1168.0
23	TraesCS6B01G008800	chr3A	78.563	849	151	19	1569	2413	623942447	623943268	5.970000e-147	531.0
24	TraesCS6B01G008800	chr3A	84.454	476	68	5	2668	3142	611176219	611176689	6.140000e-127	464.0
25	TraesCS6B01G008800	chr3A	84.199	462	61	12	2668	3126	742908076	742908528	3.720000e-119	438.0
26	TraesCS6B01G008800	chr7B	84.416	462	61	11	2668	3126	7263294	7263747	8.000000e-121	444.0
27	TraesCS6B01G008800	chr7B	82.900	462	63	13	2668	3126	517845581	517846029	4.890000e-108	401.0
28	TraesCS6B01G008800	chr1B	83.871	465	61	14	2668	3126	554140810	554141266	6.230000e-117	431.0
29	TraesCS6B01G008800	chr3B	83.550	462	65	11	2668	3126	770071492	770071945	3.750000e-114	422.0
30	TraesCS6B01G008800	chr3D	85.286	367	34	12	164	524	77403510	77403158	8.290000e-96	361.0
31	TraesCS6B01G008800	chr7A	78.870	407	67	11	950	1352	8381207	8381598	1.120000e-64	257.0
32	TraesCS6B01G008800	chr2D	79.946	369	52	17	163	524	143111167	143110814	5.210000e-63	252.0
33	TraesCS6B01G008800	chr2D	79.675	369	53	17	163	524	275314345	275313992	2.420000e-61	246.0

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	TraesCS6B01G008800	chr6B	5713116	5716260	3144	True	5808.000000	5808	100.000000	1	3145	1	chr6B.!!$R1	3144
1	TraesCS6B01G008800	chr6B	15105629	15107372	1743	False	1609.000000	1609	83.512000	549	2305	1	chr6B.!!$F1	1756
2	TraesCS6B01G008800	chr6D	8140134	8141858	1724	False	1624.000000	1624	83.799000	549	2285	1	chr6D.!!$F2	1736
3	TraesCS6B01G008800	chr6D	1537965	1541493	3528	True	1295.233333	3633	93.157667	12	2850	3	chr6D.!!$R2	2838
4	TraesCS6B01G008800	chr7D	558847679	558848876	1197	True	1598.000000	1598	90.826000	1946	3137	1	chr7D.!!$R1	1191
5	TraesCS6B01G008800	chr7D	558887394	558889278	1884	True	1286.500000	2438	90.399000	49	1900	2	chr7D.!!$R2	1851
6	TraesCS6B01G008800	chr5B	132587844	132589930	2086	False	2074.000000	2074	84.886000	589	2656	1	chr5B.!!$F1	2067
7	TraesCS6B01G008800	chr5D	119658797	119660915	2118	False	1967.000000	1967	83.906000	549	2611	1	chr5D.!!$F1	2062
8	TraesCS6B01G008800	chr5A	129749106	129751235	2129	False	1964.000000	1964	83.597000	549	2656	1	chr5A.!!$F1	2107
9	TraesCS6B01G008800	chr6A	8608631	8610369	1738	False	1611.000000	1611	83.579000	549	2293	1	chr6A.!!$F2	1744
10	TraesCS6B01G008800	chr6A	8387524	8388770	1246	False	1168.000000	1168	83.767000	549	1802	1	chr6A.!!$F1	1253
11	TraesCS6B01G008800	chr3A	623942447	623943268	821	False	531.000000	531	78.563000	1569	2413	1	chr3A.!!$F2	844

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
980	1702	0.254299	AATTCATCCTCCCCCACCCT	60.254	55.0	0.0	0.0	0.0	4.34	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2589	3376	0.179004	CTTGTGTGTGGTTGGCCCTA	60.179	55.0	0.0	0.0	0.0	3.53	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
78	128	2.125753	CTGCGCTCTGGTGGACTC	60.126	66.667	9.73	0.00	0.00	3.36
118	168	5.707298	CAGATAAGCCAGGTTTCTTCTTTCA	59.293	40.000	0.00	0.00	0.00	2.69
128	178	6.925718	CAGGTTTCTTCTTTCATTTTCCCTTC	59.074	38.462	0.00	0.00	0.00	3.46
134	184	6.717084	TCTTCTTTCATTTTCCCTTCCTCTTC	59.283	38.462	0.00	0.00	0.00	2.87
175	259	2.663826	TGTTTGAAAACCAGTGCCAC	57.336	45.000	3.59	0.00	38.11	5.01
371	1041	1.276138	GGATCAAAACCCTTGCCCAAG	59.724	52.381	1.05	1.05	38.14	3.61
386	1056	4.688021	TGCCCAAGTTAACAAACATCAAC	58.312	39.130	8.61	0.00	0.00	3.18
540	1210	8.031848	CAACTATTTGCTGGCAATTTAAATGT	57.968	30.769	8.86	0.34	35.70	2.71
543	1213	5.921004	TTTGCTGGCAATTTAAATGTGAC	57.079	34.783	8.86	5.51	35.70	3.67
544	1214	4.597404	TGCTGGCAATTTAAATGTGACA	57.403	36.364	14.31	14.31	0.00	3.58
545	1215	4.305769	TGCTGGCAATTTAAATGTGACAC	58.694	39.130	12.21	0.00	0.00	3.67
546	1216	4.039004	TGCTGGCAATTTAAATGTGACACT	59.961	37.500	7.20	0.00	0.00	3.55
547	1217	4.990426	GCTGGCAATTTAAATGTGACACTT	59.010	37.500	7.20	0.00	0.00	3.16
572	1248	3.102972	GCTAGATCAGGATCCATGGCTA	58.897	50.000	15.82	9.09	38.58	3.93
657	1339	0.464373	ATAGCGGAGTGGTGGCATTG	60.464	55.000	0.00	0.00	0.00	2.82
666	1348	4.298332	GAGTGGTGGCATTGTTTTTGTAG	58.702	43.478	0.00	0.00	0.00	2.74
688	1370	1.235724	GTGCCACCACTAACCTTGTC	58.764	55.000	0.00	0.00	38.93	3.18
694	1376	1.488812	ACCACTAACCTTGTCTGCACA	59.511	47.619	0.00	0.00	0.00	4.57
714	1396	5.764686	GCACAACATATAGATTGGATGGTCA	59.235	40.000	4.32	0.00	0.00	4.02
743	1425	3.787001	CGGACCCCTGCTCCTTCC	61.787	72.222	0.00	0.00	0.00	3.46
827	1511	5.229469	CGTTTCCTTGTGATGTACGATAGAC	59.771	44.000	0.00	0.00	41.38	2.59
840	1524	7.348080	TGTACGATAGACAGATTTCCAATCT	57.652	36.000	0.00	0.00	41.38	2.40
948	1665	1.322442	GCCATGGCATTTCTAGGGTC	58.678	55.000	32.08	0.00	41.49	4.46
980	1702	0.254299	AATTCATCCTCCCCCACCCT	60.254	55.000	0.00	0.00	0.00	4.34
1005	1727	1.225426	GGATCCAGCAGTGATGGCA	59.775	57.895	22.89	11.88	39.19	4.92
1021	1743	4.680237	CAACCTCAGACGCGGGCA	62.680	66.667	12.47	0.00	0.00	5.36
1042	1764	4.066490	CAAGGAGAAGATGATCATGCTCC	58.934	47.826	26.57	26.57	41.65	4.70
1066	1788	0.170784	GTCCGACGGAGAGGAGTTTC	59.829	60.000	18.98	0.00	38.30	2.78
1067	1789	1.136984	CCGACGGAGAGGAGTTTCG	59.863	63.158	8.64	0.00	0.00	3.46
1125	1869	2.501261	CGCCACATGATTGAGGATGAT	58.499	47.619	0.00	0.00	35.78	2.45
1134	1878	2.336945	TTGAGGATGATTGCGCTGAT	57.663	45.000	9.73	2.13	0.00	2.90
1235	1979	1.069765	CAGGCAACGTCTCCACTGT	59.930	57.895	8.50	0.00	46.39	3.55
1249	1993	2.768344	CTGTATCCCCCGGTGCCT	60.768	66.667	0.00	0.00	0.00	4.75
1321	2065	2.027285	TGGGACGCAGAATTCATCAAGA	60.027	45.455	8.44	0.00	0.00	3.02
1353	2097	1.195115	CCCTCTTCGACCTCATCCAA	58.805	55.000	0.00	0.00	0.00	3.53
1363	2107	9.090103	TCTTCGACCTCATCCAAGTATTATATT	57.910	33.333	0.00	0.00	0.00	1.28
1416	2163	4.775253	ACTTTTTCTTTGTGTTCCCCTTCA	59.225	37.500	0.00	0.00	0.00	3.02
1419	2166	2.131854	TCTTTGTGTTCCCCTTCAGGA	58.868	47.619	0.00	0.00	38.24	3.86
1443	2190	1.202687	CGGATCTAGATTGGGCTTGCA	60.203	52.381	6.70	0.00	0.00	4.08
1496	2243	3.596214	GACTCCACGTACAACCATCAAT	58.404	45.455	0.00	0.00	0.00	2.57
1510	2262	8.352137	ACAACCATCAATGTAGATTCAATTCA	57.648	30.769	0.00	0.00	0.00	2.57
1654	2407	7.792374	ATGTTTCACTGACATGTGTATATCC	57.208	36.000	1.15	0.00	36.43	2.59
1849	2614	3.316308	AGGTGACTTCATGTGCTGTTTTC	59.684	43.478	0.00	0.00	37.44	2.29
1885	2650	7.959651	GTCTTGTAACACATCTTAATGCAAGAG	59.040	37.037	5.12	0.00	46.37	2.85
1966	2740	1.644509	ATGGTTCTTTTTGCCCCCTC	58.355	50.000	0.00	0.00	0.00	4.30
1967	2741	0.560688	TGGTTCTTTTTGCCCCCTCT	59.439	50.000	0.00	0.00	0.00	3.69
1972	2746	0.113190	CTTTTTGCCCCCTCTCAGGT	59.887	55.000	0.00	0.00	31.93	4.00
1979	2753	1.492133	CCCCCTCTCAGGTTGCAAGA	61.492	60.000	0.00	0.00	31.93	3.02
2075	2853	6.292150	GGAGGAGATCCGTAATTTCTTCAAT	58.708	40.000	0.00	0.00	38.67	2.57
2078	2856	9.495572	GAGGAGATCCGTAATTTCTTCAATATT	57.504	33.333	0.00	0.00	42.08	1.28
2097	2875	3.671008	TTAAGAGCGACTACTTGCCAA	57.329	42.857	0.00	0.00	0.00	4.52
2115	2893	3.383223	CCAAAGGAGGAGGAGAAGATCT	58.617	50.000	0.00	0.00	0.00	2.75
2133	2911	1.461268	TGCAGGGAGAACCAGTGGA	60.461	57.895	18.40	0.00	43.89	4.02
2135	2913	1.293498	CAGGGAGAACCAGTGGACG	59.707	63.158	18.40	0.00	43.89	4.79
2174	2952	5.239306	AGTCGATGTTGTGTTGAATGAATGT	59.761	36.000	0.00	0.00	0.00	2.71
2204	2982	5.755409	TCACCATCTCAACCTTTTAGCTA	57.245	39.130	0.00	0.00	0.00	3.32
2207	2985	5.705441	CACCATCTCAACCTTTTAGCTACAA	59.295	40.000	0.00	0.00	0.00	2.41
2265	3044	5.104900	AGTCTATGAGGTGGTGTCATTAACC	60.105	44.000	0.00	0.00	36.11	2.85
2270	3049	6.134535	TGAGGTGGTGTCATTAACCTATTT	57.865	37.500	4.53	0.00	43.12	1.40
2273	3052	7.181305	TGAGGTGGTGTCATTAACCTATTTAGA	59.819	37.037	4.53	0.00	43.12	2.10
2278	3057	9.802039	TGGTGTCATTAACCTATTTAGAGTTTT	57.198	29.630	0.00	0.00	38.60	2.43
2286	3065	6.648879	ACCTATTTAGAGTTTTTGCTTGCA	57.351	33.333	0.00	0.00	0.00	4.08
2417	3198	0.038166	TCCAGCCAATCTGAACCCAC	59.962	55.000	0.00	0.00	45.72	4.61
2420	3205	2.092212	CCAGCCAATCTGAACCCACTAT	60.092	50.000	0.00	0.00	45.72	2.12
2489	3275	6.331845	TGACATGATGTTGCATAAACCATTC	58.668	36.000	0.00	0.00	38.06	2.67
2496	3282	4.023963	TGTTGCATAAACCATTCGAAACGA	60.024	37.500	0.00	0.00	38.06	3.85
2516	3303	9.952341	GAAACGAAACATAGCCATAAAATTTTC	57.048	29.630	6.72	0.00	0.00	2.29
2573	3360	1.143684	GCTCATATCCTGGGAAGCCAA	59.856	52.381	0.00	0.00	0.00	4.52
2589	3376	2.084546	GCCAAACGATAGACCAGCTTT	58.915	47.619	0.00	0.00	41.38	3.51
2602	3389	0.539438	CAGCTTTAGGGCCAACCACA	60.539	55.000	6.18	0.00	43.89	4.17
2611	3398	2.498056	GCCAACCACACACAAGGGG	61.498	63.158	0.00	0.00	0.00	4.79
2689	3476	9.595823	AATCATGATGAAGAAACATGGAATTTC	57.404	29.630	9.46	0.00	40.86	2.17
2715	3502	3.912496	ATCATGAGATTCACCCAACGA	57.088	42.857	0.09	0.00	0.00	3.85
2724	3511	2.851263	TCACCCAACGAGTGCTATTT	57.149	45.000	0.00	0.00	35.14	1.40
2833	3620	5.163814	CGGAGGCTAAAAGACAATCAAAGAG	60.164	44.000	0.00	0.00	0.00	2.85
2844	3631	8.558973	AAGACAATCAAAGAGAGAATAACCTG	57.441	34.615	0.00	0.00	0.00	4.00
2943	3730	4.968259	TCATACCTATGATTCCCAAACCG	58.032	43.478	0.00	0.00	37.76	4.44
2958	3745	3.425625	CCAAACCGTCAAACATATGGTCG	60.426	47.826	7.80	0.21	35.11	4.79
2973	3760	3.478857	TGGTCGAACCACACTACAAAT	57.521	42.857	0.00	0.00	44.79	2.32
3011	3798	9.706846	GCAAATAAGTTCATTGGAATAAATTGC	57.293	29.630	0.00	0.00	35.05	3.56
3066	3853	7.894376	TTCTGGTAAACGGTTATACTCAAAG	57.106	36.000	0.00	0.00	0.00	2.77
3077	3864	6.703607	CGGTTATACTCAAAGCTTCATCTGAT	59.296	38.462	0.00	0.00	0.00	2.90
3079	3866	7.351223	GTTATACTCAAAGCTTCATCTGATGC	58.649	38.462	12.78	9.39	43.17	3.91
3087	3874	2.950309	GCTTCATCTGATGCAGAACCAT	59.050	45.455	19.29	0.00	44.04	3.55
3137	3924	7.870954	GTGAATTCCATTGCATTGATGATATGT	59.129	33.333	10.14	0.00	0.00	2.29
3138	3925	8.425703	TGAATTCCATTGCATTGATGATATGTT	58.574	29.630	10.14	0.00	0.00	2.71
3139	3926	9.268268	GAATTCCATTGCATTGATGATATGTTT	57.732	29.630	10.14	0.00	0.00	2.83
3140	3927	8.601845	ATTCCATTGCATTGATGATATGTTTG	57.398	30.769	10.14	0.00	0.00	2.93
3141	3928	5.986741	TCCATTGCATTGATGATATGTTTGC	59.013	36.000	10.14	0.00	0.00	3.68
3142	3929	5.178623	CCATTGCATTGATGATATGTTTGCC	59.821	40.000	10.14	0.00	0.00	4.52
3143	3930	5.601583	TTGCATTGATGATATGTTTGCCT	57.398	34.783	0.00	0.00	0.00	4.75
3144	3931	6.712179	TTGCATTGATGATATGTTTGCCTA	57.288	33.333	0.00	0.00	0.00	3.93

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
41	42	1.153409	CCCTGCTGCTAGAGTGCTG	60.153	63.158	0.00	0.00	35.44	4.41
151	201	4.453819	TGGCACTGGTTTTCAAACAAAAAG	59.546	37.500	4.85	0.00	40.63	2.27
156	206	1.895798	TGTGGCACTGGTTTTCAAACA	59.104	42.857	19.83	0.00	40.63	2.83
157	207	2.094234	AGTGTGGCACTGGTTTTCAAAC	60.094	45.455	19.83	4.25	43.63	2.93
161	245	2.024414	AGAAGTGTGGCACTGGTTTTC	58.976	47.619	19.83	13.80	44.62	2.29
175	259	9.276590	TGGCAACATATATATTTCAGAGAAGTG	57.723	33.333	0.00	0.00	46.17	3.16
308	977	7.414814	TTTTCAACGAATTAATTGGGCTTTC	57.585	32.000	13.84	0.00	0.00	2.62
371	1041	7.924103	AATTCCTTCGTTGATGTTTGTTAAC	57.076	32.000	0.00	0.00	34.75	2.01
496	1166	4.451435	AGTTGCATCTAGAATCATCATGCG	59.549	41.667	0.00	0.00	42.35	4.73
533	1203	7.823799	TGATCTAGCATGAAGTGTCACATTTAA	59.176	33.333	5.62	0.00	36.31	1.52
535	1205	6.175471	TGATCTAGCATGAAGTGTCACATTT	58.825	36.000	5.62	0.00	36.31	2.32
536	1206	5.737860	TGATCTAGCATGAAGTGTCACATT	58.262	37.500	5.62	0.00	36.31	2.71
537	1207	5.349061	TGATCTAGCATGAAGTGTCACAT	57.651	39.130	5.62	0.00	36.31	3.21
539	1209	4.118410	CCTGATCTAGCATGAAGTGTCAC	58.882	47.826	0.00	0.00	36.31	3.67
540	1210	4.026052	TCCTGATCTAGCATGAAGTGTCA	58.974	43.478	0.00	2.23	38.41	3.58
543	1213	4.040095	TGGATCCTGATCTAGCATGAAGTG	59.960	45.833	14.23	0.00	37.92	3.16
544	1214	4.229639	TGGATCCTGATCTAGCATGAAGT	58.770	43.478	14.23	0.00	37.92	3.01
545	1215	4.886496	TGGATCCTGATCTAGCATGAAG	57.114	45.455	14.23	0.00	37.92	3.02
546	1216	4.019591	CCATGGATCCTGATCTAGCATGAA	60.020	45.833	14.23	0.00	37.27	2.57
547	1217	3.518303	CCATGGATCCTGATCTAGCATGA	59.482	47.826	14.23	0.00	37.27	3.07
657	1339	3.380320	AGTGGTGGCACTTCTACAAAAAC	59.620	43.478	18.45	0.00	29.93	2.43
666	1348	1.880027	CAAGGTTAGTGGTGGCACTTC	59.120	52.381	18.45	10.71	36.68	3.01
681	1363	5.420725	TCTATATGTTGTGCAGACAAGGT	57.579	39.130	6.90	0.43	42.87	3.50
688	1370	5.766670	ACCATCCAATCTATATGTTGTGCAG	59.233	40.000	0.00	0.00	0.00	4.41
694	1376	8.497745	ACTTTCTGACCATCCAATCTATATGTT	58.502	33.333	0.00	0.00	0.00	2.71
714	1396	1.371558	GGGTCCGAGCACACTTTCT	59.628	57.895	0.00	0.00	0.00	2.52
827	1511	2.789092	GCAACGCGAGATTGGAAATCTG	60.789	50.000	15.93	2.22	0.00	2.90
948	1665	2.967887	GGATGAATTTGGGATTGGGGAG	59.032	50.000	0.00	0.00	0.00	4.30
980	1702	0.758734	CACTGCTGGATCCGGGATTA	59.241	55.000	22.38	2.98	0.00	1.75
1005	1727	3.883744	CTTGCCCGCGTCTGAGGTT	62.884	63.158	4.92	0.00	32.31	3.50
1021	1743	3.715315	TGGAGCATGATCATCTTCTCCTT	59.285	43.478	29.57	2.72	40.42	3.36
1024	1746	4.309099	GACTGGAGCATGATCATCTTCTC	58.691	47.826	13.85	11.99	0.00	2.87
1042	1764	2.751913	CCTCTCCGTCGGACGACTG	61.752	68.421	30.33	18.66	46.05	3.51
1056	1778	0.905337	CCTCCACCCGAAACTCCTCT	60.905	60.000	0.00	0.00	0.00	3.69
1066	1788	3.391382	GACCACCTCCTCCACCCG	61.391	72.222	0.00	0.00	0.00	5.28
1067	1789	2.203938	TGACCACCTCCTCCACCC	60.204	66.667	0.00	0.00	0.00	4.61
1134	1878	1.809133	TGGGTATCGGGATGGCTTTA	58.191	50.000	0.00	0.00	0.00	1.85
1235	1979	2.445845	CAGAGGCACCGGGGGATA	60.446	66.667	5.47	0.00	0.00	2.59
1249	1993	1.287815	CCACGGTGTTAGACGCAGA	59.712	57.895	7.45	0.00	0.00	4.26
1276	2020	2.114616	CTTGAGGTCCTCAGCTATGGT	58.885	52.381	20.86	0.00	41.75	3.55
1279	2023	3.896888	CAGATCTTGAGGTCCTCAGCTAT	59.103	47.826	20.86	15.15	41.75	2.97
1321	2065	0.706433	AAGAGGGTGGCATGGTTGAT	59.294	50.000	0.00	0.00	0.00	2.57
1416	2163	3.235200	CCCAATCTAGATCCGAGTTCCT	58.765	50.000	5.51	0.00	0.00	3.36
1419	2166	2.683768	AGCCCAATCTAGATCCGAGTT	58.316	47.619	5.51	0.00	0.00	3.01
1481	2228	6.403049	TGAATCTACATTGATGGTTGTACGT	58.597	36.000	0.00	0.00	0.00	3.57
1496	2243	8.397906	GTCCATTCGAATTGAATTGAATCTACA	58.602	33.333	13.03	0.00	45.06	2.74
1654	2407	6.407202	AGCTTCCTAGGTTACACATAACAAG	58.593	40.000	9.08	1.43	42.26	3.16
1744	2499	4.887655	TGAGTAGTCTGATCTTTCCGCATA	59.112	41.667	0.00	0.00	0.00	3.14
1849	2614	9.950680	AAGATGTGTTACAAGACAATAAAACAG	57.049	29.630	0.00	0.00	35.71	3.16
1916	2688	9.809096	TGTCAAAGAGAAGCATTAGTCTATAAG	57.191	33.333	0.00	0.00	0.00	1.73
1966	2740	3.616956	TGAGGTATCTTGCAACCTGAG	57.383	47.619	12.56	0.00	46.22	3.35
1967	2741	3.582647	TCTTGAGGTATCTTGCAACCTGA	59.417	43.478	12.56	1.16	46.22	3.86
1972	2746	5.188434	CCTTGATCTTGAGGTATCTTGCAA	58.812	41.667	0.00	0.00	0.00	4.08
1979	2753	4.366267	ACAGACCCTTGATCTTGAGGTAT	58.634	43.478	0.00	0.00	0.00	2.73
2075	2853	4.994907	TGGCAAGTAGTCGCTCTTAATA	57.005	40.909	0.00	0.00	0.00	0.98
2078	2856	3.585862	CTTTGGCAAGTAGTCGCTCTTA	58.414	45.455	0.00	0.00	0.00	2.10
2083	2861	1.079503	CTCCTTTGGCAAGTAGTCGC	58.920	55.000	0.00	0.00	0.00	5.19
2097	2875	2.292785	TGCAGATCTTCTCCTCCTCCTT	60.293	50.000	0.00	0.00	0.00	3.36
2115	2893	1.461268	TCCACTGGTTCTCCCTGCA	60.461	57.895	0.00	0.00	35.64	4.41
2133	2911	2.743126	CGACTCTCCTCTACTGAAACGT	59.257	50.000	0.00	0.00	0.00	3.99
2135	2913	4.396790	ACATCGACTCTCCTCTACTGAAAC	59.603	45.833	0.00	0.00	0.00	2.78
2174	2952	8.934023	AAAAGGTTGAGATGGTGAATACTAAA	57.066	30.769	0.00	0.00	0.00	1.85
2236	3014	2.043115	ACACCACCTCATAGACTCCAGA	59.957	50.000	0.00	0.00	0.00	3.86
2265	3044	8.746922	TTCATGCAAGCAAAAACTCTAAATAG	57.253	30.769	0.00	0.00	0.00	1.73
2270	3049	9.709495	AAATTATTCATGCAAGCAAAAACTCTA	57.291	25.926	0.00	0.00	0.00	2.43
2326	3107	7.542025	AAGCTTAGGAAAATGCTAAGATGTTG	58.458	34.615	18.95	0.00	44.30	3.33
2372	3153	5.300034	AGAAAATGTTGCTTGACATGAGTGA	59.700	36.000	0.00	0.00	40.03	3.41
2489	3275	7.734538	AATTTTATGGCTATGTTTCGTTTCG	57.265	32.000	0.00	0.00	0.00	3.46
2516	3303	8.956426	ACCTTGTACCATCAATAACTGTTTATG	58.044	33.333	0.00	0.00	0.00	1.90
2521	3308	7.103641	CACTACCTTGTACCATCAATAACTGT	58.896	38.462	0.00	0.00	0.00	3.55
2544	3331	0.839946	AGGATATGAGCCACCCACAC	59.160	55.000	0.00	0.00	0.00	3.82
2573	3360	2.158943	GCCCTAAAGCTGGTCTATCGTT	60.159	50.000	0.00	0.00	0.00	3.85
2589	3376	0.179004	CTTGTGTGTGGTTGGCCCTA	60.179	55.000	0.00	0.00	0.00	3.53
2602	3389	4.354987	AGGATAATATCATGCCCCTTGTGT	59.645	41.667	2.41	0.00	0.00	3.72
2611	3398	5.365025	TCCTCAGCCTAGGATAATATCATGC	59.635	44.000	14.75	0.00	40.86	4.06
2689	3476	6.968904	CGTTGGGTGAATCTCATGATTTTAAG	59.031	38.462	0.00	0.00	42.43	1.85
3040	3827	8.851541	TTTGAGTATAACCGTTTACCAGAATT	57.148	30.769	0.00	0.00	0.00	2.17
3052	3839	6.042777	TCAGATGAAGCTTTGAGTATAACCG	58.957	40.000	0.00	0.00	0.00	4.44
3054	3841	7.011763	TGCATCAGATGAAGCTTTGAGTATAAC	59.988	37.037	15.12	0.00	39.29	1.89
3059	3846	3.682696	TGCATCAGATGAAGCTTTGAGT	58.317	40.909	15.12	0.00	39.29	3.41
3066	3853	2.362736	TGGTTCTGCATCAGATGAAGC	58.637	47.619	15.12	9.64	40.39	3.86
3077	3864	4.842574	TGCACTAGATTTATGGTTCTGCA	58.157	39.130	0.00	0.00	0.00	4.41

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.