AutoCloner

Multiple sequence alignment - TraesCS5B01G094000

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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	TraesCS5B01G094000	chr5B	100.000	3038	0	0	1	3038	123438952	123435915	0.000000e+00	5611.0
1	TraesCS5B01G094000	chr5B	98.109	2009	36	2	1031	3038	123219873	123217866	0.000000e+00	3498.0
2	TraesCS5B01G094000	chr5B	96.337	1283	32	12	1377	2655	123014109	123012838	0.000000e+00	2095.0
3	TraesCS5B01G094000	chr5B	90.513	1033	84	6	1043	2062	88340259	88341290	0.000000e+00	1352.0
4	TraesCS5B01G094000	chr5B	90.772	661	51	9	1	659	123024838	123024186	0.000000e+00	874.0
5	TraesCS5B01G094000	chr5B	90.758	660	51	7	2	659	123222230	123221579	0.000000e+00	872.0
6	TraesCS5B01G094000	chr5B	85.354	792	86	12	1257	2040	88211463	88212232	0.000000e+00	793.0
7	TraesCS5B01G094000	chr5B	90.598	351	33	0	1031	1381	123022482	123022132	1.650000e-127	466.0
8	TraesCS5B01G094000	chr5B	81.903	536	56	17	759	1263	88210770	88211295	6.060000e-112	414.0
9	TraesCS5B01G094000	chr5B	90.533	169	6	4	660	827	123022822	123022663	6.600000e-52	215.0
10	TraesCS5B01G094000	chr5B	89.349	169	8	4	660	827	123220213	123220054	1.430000e-48	204.0
11	TraesCS5B01G094000	chr5B	90.698	86	5	3	2560	2643	250223299	250223215	8.900000e-21	111.0
12	TraesCS5B01G094000	chr5D	88.941	1275	106	19	892	2133	78503820	78505092	0.000000e+00	1541.0
13	TraesCS5B01G094000	chr5D	91.900	642	52	0	1029	1670	78594516	78595157	0.000000e+00	898.0
14	TraesCS5B01G094000	chr5D	85.600	750	94	9	1303	2040	78371229	78371976	0.000000e+00	774.0
15	TraesCS5B01G094000	chr5D	87.745	408	48	2	1662	2068	78602935	78603341	2.740000e-130	475.0
16	TraesCS5B01G094000	chr5D	83.301	509	48	19	830	1306	78361613	78362116	4.650000e-118	435.0
17	TraesCS5B01G094000	chr5D	81.208	298	44	10	270	559	62530312	62530019	2.360000e-56	230.0
18	TraesCS5B01G094000	chr5D	85.135	222	15	8	860	1068	78594303	78594519	8.530000e-51	211.0
19	TraesCS5B01G094000	chr5D	79.348	276	39	11	2380	2642	37662002	37662272	8.660000e-41	178.0
20	TraesCS5B01G094000	chr5D	88.889	54	5	1	2623	2676	216058034	216058086	7.030000e-07	65.8
21	TraesCS5B01G094000	chr5A	91.339	1016	83	4	1029	2040	74863160	74864174	0.000000e+00	1384.0
22	TraesCS5B01G094000	chr5A	96.571	175	6	0	894	1068	74862989	74863163	1.070000e-74	291.0
23	TraesCS5B01G094000	chr5A	93.750	144	9	0	2677	2820	604994115	604994258	1.830000e-52	217.0
24	TraesCS5B01G094000	chr5A	80.435	138	18	8	121	254	548216106	548215974	2.490000e-16	97.1
25	TraesCS5B01G094000	chr7A	97.248	218	6	0	2821	3038	211292414	211292197	1.330000e-98	370.0
26	TraesCS5B01G094000	chr7A	80.435	138	18	8	121	254	607753075	607752943	2.490000e-16	97.1
27	TraesCS5B01G094000	chr4D	97.248	218	6	0	2821	3038	123508047	123508264	1.330000e-98	370.0
28	TraesCS5B01G094000	chr4D	97.248	218	6	0	2821	3038	123737543	123737760	1.330000e-98	370.0
29	TraesCS5B01G094000	chr4D	96.789	218	7	0	2821	3038	123654746	123654963	6.190000e-97	364.0
30	TraesCS5B01G094000	chr2B	97.248	218	6	0	2821	3038	357244934	357245151	1.330000e-98	370.0
31	TraesCS5B01G094000	chr2B	75.926	216	33	15	2383	2592	558009366	558009164	3.230000e-15	93.5
32	TraesCS5B01G094000	chr1D	97.248	218	6	0	2821	3038	212467754	212467971	1.330000e-98	370.0
33	TraesCS5B01G094000	chr1D	80.374	214	26	11	2439	2642	462387478	462387685	6.790000e-32	148.0
34	TraesCS5B01G094000	chr6B	96.789	218	7	0	2821	3038	215728380	215728597	6.190000e-97	364.0
35	TraesCS5B01G094000	chr6B	82.292	288	42	7	295	576	662144864	662145148	1.090000e-59	241.0
36	TraesCS5B01G094000	chr6B	80.000	105	11	4	1619	1723	671658525	671658619	5.430000e-08	69.4
37	TraesCS5B01G094000	chr3B	96.789	218	7	0	2821	3038	39816880	39816663	6.190000e-97	364.0
38	TraesCS5B01G094000	chr3B	95.000	40	2	0	2636	2675	733416119	733416158	2.530000e-06	63.9
39	TraesCS5B01G094000	chr4A	82.201	309	47	6	274	576	575005468	575005162	3.000000e-65	259.0
40	TraesCS5B01G094000	chr4A	77.953	254	42	10	2395	2642	45737104	45737349	2.440000e-31	147.0
41	TraesCS5B01G094000	chr4A	77.907	258	37	13	2398	2642	589470866	589471116	3.160000e-30	143.0
42	TraesCS5B01G094000	chr4A	79.381	194	28	8	2388	2576	45467227	45467041	3.180000e-25	126.0
43	TraesCS5B01G094000	chr4A	82.645	121	13	7	137	254	426686878	426686763	1.930000e-17	100.0
44	TraesCS5B01G094000	chr4A	81.890	127	14	8	132	254	93131560	93131681	6.930000e-17	99.0
45	TraesCS5B01G094000	chr3D	84.173	278	29	10	2372	2642	517012054	517011785	3.890000e-64	255.0
46	TraesCS5B01G094000	chr3D	93.056	144	10	0	2677	2820	202633229	202633086	8.530000e-51	211.0
47	TraesCS5B01G094000	chr3D	79.137	278	35	13	2376	2642	126385816	126385551	1.450000e-38	171.0
48	TraesCS5B01G094000	chr3D	79.213	178	24	10	83	254	172858300	172858130	8.900000e-21	111.0
49	TraesCS5B01G094000	chr2D	81.230	309	49	8	274	576	164743265	164742960	1.090000e-59	241.0
50	TraesCS5B01G094000	chrUn	82.500	280	41	6	271	544	33187441	33187718	3.910000e-59	239.0
51	TraesCS5B01G094000	chrUn	93.056	144	10	0	2677	2820	206793358	206793215	8.530000e-51	211.0
52	TraesCS5B01G094000	chrUn	93.056	144	10	0	2677	2820	246706002	246705859	8.530000e-51	211.0
53	TraesCS5B01G094000	chrUn	93.056	144	10	0	2677	2820	266186159	266186016	8.530000e-51	211.0
54	TraesCS5B01G094000	chrUn	93.056	144	10	0	2677	2820	432754936	432754793	8.530000e-51	211.0
55	TraesCS5B01G094000	chr6A	82.609	276	42	6	269	539	56068868	56069142	3.910000e-59	239.0
56	TraesCS5B01G094000	chr6A	93.056	144	10	0	2677	2820	597219701	597219844	8.530000e-51	211.0
57	TraesCS5B01G094000	chr6A	81.159	138	17	8	121	254	108050045	108050177	5.360000e-18	102.0
58	TraesCS5B01G094000	chr6A	92.157	51	2	2	2640	2688	194459375	194459325	1.510000e-08	71.3
59	TraesCS5B01G094000	chr1B	80.456	307	49	10	277	576	32419838	32420140	1.100000e-54	224.0
60	TraesCS5B01G094000	chr1A	92.517	147	10	1	2677	2823	359901593	359901738	3.070000e-50	209.0
61	TraesCS5B01G094000	chr1A	80.603	232	33	8	2371	2594	65807737	65807964	5.210000e-38	169.0
62	TraesCS5B01G094000	chr7B	78.746	287	39	14	2372	2642	621455733	621456013	4.030000e-39	172.0
63	TraesCS5B01G094000	chr7B	87.500	56	6	1	2618	2673	695281667	695281721	2.530000e-06	63.9
64	TraesCS5B01G094000	chr3A	80.087	231	32	10	2409	2631	721673493	721673269	3.140000e-35	159.0
65	TraesCS5B01G094000	chr4B	78.652	267	35	15	2388	2642	517006847	517006591	1.130000e-34	158.0
66	TraesCS5B01G094000	chr4B	80.769	104	10	1	1620	1723	644837291	644837384	4.200000e-09	73.1
67	TraesCS5B01G094000	chr7D	77.966	177	27	10	83	254	346746892	346747061	1.930000e-17	100.0
68	TraesCS5B01G094000	chr7D	90.196	51	3	2	2639	2689	421880246	421880198	7.030000e-07	65.8
69	TraesCS5B01G094000	chr2A	92.157	51	2	2	2640	2688	474323792	474323742	1.510000e-08	71.3
70	TraesCS5B01G094000	chr2A	90.566	53	3	2	2621	2673	730128831	730128781	5.430000e-08	69.4
71	TraesCS5B01G094000	chr2A	90.385	52	3	2	2625	2676	657809346	657809297	1.950000e-07	67.6

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	TraesCS5B01G094000	chr5B	123435915	123438952	3037	True	5611.000000	5611	100.000000	1	3038	1	chr5B.!!$R2	3037
1	TraesCS5B01G094000	chr5B	123012838	123014109	1271	True	2095.000000	2095	96.337000	1377	2655	1	chr5B.!!$R1	1278
2	TraesCS5B01G094000	chr5B	123217866	123222230	4364	True	1524.666667	3498	92.738667	2	3038	3	chr5B.!!$R5	3036
3	TraesCS5B01G094000	chr5B	88340259	88341290	1031	False	1352.000000	1352	90.513000	1043	2062	1	chr5B.!!$F1	1019
4	TraesCS5B01G094000	chr5B	88210770	88212232	1462	False	603.500000	793	83.628500	759	2040	2	chr5B.!!$F2	1281
5	TraesCS5B01G094000	chr5B	123022132	123024838	2706	True	518.333333	874	90.634333	1	1381	3	chr5B.!!$R4	1380
6	TraesCS5B01G094000	chr5D	78503820	78505092	1272	False	1541.000000	1541	88.941000	892	2133	1	chr5D.!!$F4	1241
7	TraesCS5B01G094000	chr5D	78371229	78371976	747	False	774.000000	774	85.600000	1303	2040	1	chr5D.!!$F3	737
8	TraesCS5B01G094000	chr5D	78594303	78595157	854	False	554.500000	898	88.517500	860	1670	2	chr5D.!!$F7	810
9	TraesCS5B01G094000	chr5D	78361613	78362116	503	False	435.000000	435	83.301000	830	1306	1	chr5D.!!$F2	476
10	TraesCS5B01G094000	chr5A	74862989	74864174	1185	False	837.500000	1384	93.955000	894	2040	2	chr5A.!!$F2	1146

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
570	571	0.10339	TCGGTTCGTTGAGTGCTTCA	59.897	50.0	0.0	0.0	0.0	3.02	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2706	4425	2.579201	CGCCCTCACTGAACCGAT	59.421	61.111	0.0	0.0	0.0	4.18	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
44	45	2.231716	AACCAAGGATTAACAGGGCC	57.768	50.000	0.00	0.00	0.00	5.80
48	49	0.917333	AAGGATTAACAGGGCCGGGA	60.917	55.000	8.94	0.00	0.00	5.14
91	92	5.175126	CGATGTTAATTAAGGGTGAGTAGCG	59.825	44.000	0.00	0.00	0.00	4.26
92	93	4.186159	TGTTAATTAAGGGTGAGTAGCGC	58.814	43.478	0.00	0.00	0.00	5.92
114	115	3.809832	CCTAATTAAGCAGGGACATGTCG	59.190	47.826	19.33	7.28	0.00	4.35
148	149	4.922026	ACGCCGCGACCAAAACCT	62.922	61.111	21.79	0.00	0.00	3.50
161	162	1.128188	AAAACCTGGAGCGGAGTCCT	61.128	55.000	7.77	0.00	37.52	3.85
188	189	2.187163	GGCTCGGGCTTCACCTAC	59.813	66.667	7.48	0.00	39.10	3.18
202	203	2.171635	CCTACAAGAGGCGGTTTGC	58.828	57.895	0.00	0.00	38.96	3.68
280	281	2.105128	CGGAGGGTGCTTCTAGCG	59.895	66.667	0.00	0.00	46.26	4.26
284	285	1.935327	GAGGGTGCTTCTAGCGTCGT	61.935	60.000	0.00	0.00	46.26	4.34
290	291	1.979831	GCTTCTAGCGTCGTCGGAGT	61.980	60.000	3.90	0.00	37.56	3.85
291	292	1.284657	CTTCTAGCGTCGTCGGAGTA	58.715	55.000	3.90	0.00	37.56	2.59
312	313	0.387929	GTGTGGAGGTGTGTCTTCGA	59.612	55.000	0.00	0.00	0.00	3.71
325	326	1.676529	GTCTTCGATGGATCTCGTGGA	59.323	52.381	4.51	2.39	39.62	4.02
333	334	3.526931	TGGATCTCGTGGAATTCAGTC	57.473	47.619	7.93	0.00	0.00	3.51
373	374	2.390696	TCCGATTGGATCCGGTCTTTA	58.609	47.619	7.39	0.00	45.48	1.85
379	380	5.065988	CGATTGGATCCGGTCTTTATTTGTT	59.934	40.000	7.39	0.00	0.00	2.83
380	381	6.404293	CGATTGGATCCGGTCTTTATTTGTTT	60.404	38.462	7.39	0.00	0.00	2.83
381	382	5.637006	TGGATCCGGTCTTTATTTGTTTG	57.363	39.130	7.39	0.00	0.00	2.93
382	383	5.317808	TGGATCCGGTCTTTATTTGTTTGA	58.682	37.500	7.39	0.00	0.00	2.69
388	389	7.312154	TCCGGTCTTTATTTGTTTGATGATTG	58.688	34.615	0.00	0.00	0.00	2.67
427	428	5.639506	CCTTCTGATCTACGCTTTTCTTCAA	59.360	40.000	0.00	0.00	0.00	2.69
430	431	4.552355	TGATCTACGCTTTTCTTCAACGA	58.448	39.130	0.00	0.00	0.00	3.85
447	448	1.298041	GACGCGGTTGTTGTTGTGG	60.298	57.895	12.47	0.00	0.00	4.17
449	450	1.585002	CGCGGTTGTTGTTGTGGTG	60.585	57.895	0.00	0.00	0.00	4.17
523	524	3.912496	ATGTTTGTCTGGATCCGATGA	57.088	42.857	7.39	2.43	0.00	2.92
526	527	1.866015	TTGTCTGGATCCGATGAGGT	58.134	50.000	7.39	0.00	41.99	3.85
531	532	0.178932	TGGATCCGATGAGGTAGGGG	60.179	60.000	7.39	0.00	41.99	4.79
559	560	1.370900	CGGTTCGTCTTCGGTTCGT	60.371	57.895	0.00	0.00	37.69	3.85
561	562	0.505655	GGTTCGTCTTCGGTTCGTTG	59.494	55.000	0.00	0.00	37.69	4.10
562	563	1.480205	GTTCGTCTTCGGTTCGTTGA	58.520	50.000	0.00	0.00	37.69	3.18
563	564	1.450905	GTTCGTCTTCGGTTCGTTGAG	59.549	52.381	0.00	0.00	37.69	3.02
564	565	0.664761	TCGTCTTCGGTTCGTTGAGT	59.335	50.000	0.00	0.00	37.69	3.41
565	566	0.776451	CGTCTTCGGTTCGTTGAGTG	59.224	55.000	0.00	0.00	0.00	3.51
566	567	0.507358	GTCTTCGGTTCGTTGAGTGC	59.493	55.000	0.00	0.00	0.00	4.40
567	568	0.387929	TCTTCGGTTCGTTGAGTGCT	59.612	50.000	0.00	0.00	0.00	4.40
569	570	1.192534	CTTCGGTTCGTTGAGTGCTTC	59.807	52.381	0.00	0.00	0.00	3.86
570	571	0.103390	TCGGTTCGTTGAGTGCTTCA	59.897	50.000	0.00	0.00	0.00	3.02
576	577	3.934457	TCGTTGAGTGCTTCATAGTCA	57.066	42.857	0.00	0.00	35.27	3.41
592	593	9.775854	CTTCATAGTCATTTAGAATCTGGATGT	57.224	33.333	0.00	0.00	0.00	3.06
621	622	8.918202	TTTTTACTCCTGATGTTCATTGTACT	57.082	30.769	0.00	0.00	0.00	2.73
622	623	7.905604	TTTACTCCTGATGTTCATTGTACTG	57.094	36.000	0.00	0.00	0.00	2.74
649	650	5.962433	TGAGATCGGAAGTTTTCTCGTAAT	58.038	37.500	2.21	0.00	36.34	1.89
650	651	6.034591	TGAGATCGGAAGTTTTCTCGTAATC	58.965	40.000	2.21	0.00	36.34	1.75
698	2067	4.081087	TGAGGTAACAGAGATTTGGCCTAC	60.081	45.833	3.32	0.00	41.41	3.18
799	2168	3.475566	TCCTAGATTTGGCATCCGAAG	57.524	47.619	0.00	0.00	29.47	3.79
823	2192	4.434545	TTAGGAGGAGACGTATAGCTGT	57.565	45.455	0.00	0.00	0.00	4.40
827	2196	0.592148	GGAGACGTATAGCTGTCGGG	59.408	60.000	0.00	0.00	40.05	5.14
855	2279	3.963383	TTTGACTTGCGTCTCTTTTCC	57.037	42.857	0.00	0.00	40.86	3.13
872	2296	1.590591	TCCATCTGGAATCGGGGAAA	58.409	50.000	0.00	0.00	42.18	3.13
873	2297	1.490490	TCCATCTGGAATCGGGGAAAG	59.510	52.381	0.00	0.00	42.18	2.62
874	2298	1.312815	CATCTGGAATCGGGGAAAGC	58.687	55.000	0.00	0.00	0.00	3.51
934	2358	0.458543	CTCGACAGATCCGTGGTTGG	60.459	60.000	0.00	0.00	0.00	3.77
1026	2484	1.272769	GACTTGGACTTGTCTACGCCT	59.727	52.381	0.61	0.00	0.00	5.52
1188	2685	0.299300	CGTTCGTGTCGAGCAACAAA	59.701	50.000	6.78	0.00	36.94	2.83
1199	2696	2.030893	CGAGCAACAAAGCATTCTTGGA	60.031	45.455	0.00	0.00	36.85	3.53
1281	2952	2.844348	GACCCATCTCCTGAACCCTAAA	59.156	50.000	0.00	0.00	0.00	1.85
1314	2985	1.244816	TCGAGCTTCCGACTCTCAAA	58.755	50.000	0.00	0.00	33.14	2.69
1329	3000	0.824595	TCAAAGACGACGAGGTCCCA	60.825	55.000	0.00	0.00	37.66	4.37
2725	4444	4.003788	CGGTTCAGTGAGGGCGGT	62.004	66.667	0.00	0.00	0.00	5.68
2899	4618	1.482177	CGGATCCTCCCTCATTCTCCT	60.482	57.143	10.75	0.00	31.13	3.69

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
44	45	0.037605	GTCACTTACAGTGGGTCCCG	60.038	60.000	2.65	0.00	45.94	5.14
48	49	1.887198	CGAGAGTCACTTACAGTGGGT	59.113	52.381	4.09	0.00	45.94	4.51
57	58	7.042335	CCCTTAATTAACATCGAGAGTCACTT	58.958	38.462	0.00	0.00	0.00	3.16
67	68	5.175126	CGCTACTCACCCTTAATTAACATCG	59.825	44.000	0.00	0.00	0.00	3.84
91	92	3.555966	ACATGTCCCTGCTTAATTAGGC	58.444	45.455	12.39	12.39	32.58	3.93
92	93	3.809832	CGACATGTCCCTGCTTAATTAGG	59.190	47.826	20.03	0.00	0.00	2.69
114	115	4.966787	TGCAAACCCCGGCAGACC	62.967	66.667	0.00	0.00	34.58	3.85
188	189	2.629656	CCCTGCAAACCGCCTCTTG	61.630	63.158	0.00	0.00	41.33	3.02
209	210	3.636231	CTCCAACGGGACCAGCCA	61.636	66.667	0.00	0.00	38.64	4.75
213	214	3.636231	CCAGCTCCAACGGGACCA	61.636	66.667	0.00	0.00	38.64	4.02
280	281	1.154338	CCACACGTACTCCGACGAC	60.154	63.158	2.55	0.00	45.82	4.34
284	285	1.073722	ACCTCCACACGTACTCCGA	59.926	57.895	0.00	0.00	40.70	4.55
290	291	1.338973	GAAGACACACCTCCACACGTA	59.661	52.381	0.00	0.00	0.00	3.57
291	292	0.104304	GAAGACACACCTCCACACGT	59.896	55.000	0.00	0.00	0.00	4.49
312	313	3.452264	TGACTGAATTCCACGAGATCCAT	59.548	43.478	2.27	0.00	0.00	3.41
325	326	4.273480	CCGAAGACAAACACTGACTGAATT	59.727	41.667	0.00	0.00	30.01	2.17
333	334	1.948104	TCCACCGAAGACAAACACTG	58.052	50.000	0.00	0.00	0.00	3.66
357	358	6.435904	TCAAACAAATAAAGACCGGATCCAAT	59.564	34.615	9.46	0.00	0.00	3.16
373	374	7.288810	ACCTACACACAATCATCAAACAAAT	57.711	32.000	0.00	0.00	0.00	2.32
379	380	4.979335	TCCAACCTACACACAATCATCAA	58.021	39.130	0.00	0.00	0.00	2.57
380	381	4.632327	TCCAACCTACACACAATCATCA	57.368	40.909	0.00	0.00	0.00	3.07
381	382	4.576463	GGATCCAACCTACACACAATCATC	59.424	45.833	6.95	0.00	0.00	2.92
382	383	4.228210	AGGATCCAACCTACACACAATCAT	59.772	41.667	15.82	0.00	38.65	2.45
388	389	3.260884	TCAGAAGGATCCAACCTACACAC	59.739	47.826	15.82	0.00	39.62	3.82
427	428	2.101835	ACAACAACAACCGCGTCGT	61.102	52.632	4.92	0.00	0.00	4.34
430	431	2.041686	ACCACAACAACAACCGCGT	61.042	52.632	4.92	0.00	0.00	6.01
447	448	1.224592	CCCCATAGGACCAGCACAC	59.775	63.158	0.00	0.00	38.24	3.82
449	450	0.331616	AAACCCCATAGGACCAGCAC	59.668	55.000	0.00	0.00	39.89	4.40
523	524	2.838225	CCGTCATCGCCCCTACCT	60.838	66.667	0.00	0.00	35.54	3.08
544	545	1.066002	ACTCAACGAACCGAAGACGAA	59.934	47.619	0.00	0.00	42.66	3.85
546	547	0.776451	CACTCAACGAACCGAAGACG	59.224	55.000	0.00	0.00	39.43	4.18
548	549	0.387929	AGCACTCAACGAACCGAAGA	59.612	50.000	0.00	0.00	0.00	2.87
553	554	3.326747	ACTATGAAGCACTCAACGAACC	58.673	45.455	0.00	0.00	37.67	3.62
559	560	9.102757	GATTCTAAATGACTATGAAGCACTCAA	57.897	33.333	0.00	0.00	37.67	3.02
561	562	8.763356	CAGATTCTAAATGACTATGAAGCACTC	58.237	37.037	0.00	0.00	0.00	3.51
562	563	7.714377	CCAGATTCTAAATGACTATGAAGCACT	59.286	37.037	0.00	0.00	0.00	4.40
563	564	7.712639	TCCAGATTCTAAATGACTATGAAGCAC	59.287	37.037	0.00	0.00	0.00	4.40
564	565	7.795047	TCCAGATTCTAAATGACTATGAAGCA	58.205	34.615	0.00	0.00	0.00	3.91
565	566	8.719648	CATCCAGATTCTAAATGACTATGAAGC	58.280	37.037	2.68	0.00	0.00	3.86
566	567	9.775854	ACATCCAGATTCTAAATGACTATGAAG	57.224	33.333	12.15	0.00	0.00	3.02
603	604	3.264193	AGGCAGTACAATGAACATCAGGA	59.736	43.478	0.00	0.00	0.00	3.86
620	621	2.393271	AACTTCCGATCTCAAGGCAG	57.607	50.000	5.72	0.00	0.00	4.85
621	622	2.859165	AAACTTCCGATCTCAAGGCA	57.141	45.000	5.72	0.00	0.00	4.75
622	623	3.339141	AGAAAACTTCCGATCTCAAGGC	58.661	45.455	5.72	0.00	0.00	4.35
649	650	4.862371	GGGTTTAGTCCCCATTGTAATGA	58.138	43.478	6.18	0.00	42.15	2.57
728	2097	3.329814	ACGGGACTCCCTAAAATCTGTTT	59.670	43.478	12.62	0.00	42.67	2.83
729	2098	2.910977	ACGGGACTCCCTAAAATCTGTT	59.089	45.455	12.62	0.00	42.67	3.16
730	2099	2.236395	CACGGGACTCCCTAAAATCTGT	59.764	50.000	12.62	0.00	42.67	3.41
735	2104	1.203212	TCCTCACGGGACTCCCTAAAA	60.203	52.381	12.62	0.00	42.67	1.52
736	2105	0.410663	TCCTCACGGGACTCCCTAAA	59.589	55.000	12.62	0.00	42.67	1.85
799	2168	5.474189	ACAGCTATACGTCTCCTCCTAATTC	59.526	44.000	0.00	0.00	0.00	2.17
827	2196	1.281656	CGCAAGTCAAAACCGGACC	59.718	57.895	9.46	0.00	35.89	4.46
855	2279	1.312815	GCTTTCCCCGATTCCAGATG	58.687	55.000	0.00	0.00	0.00	2.90
872	2296	5.656900	ATATATATATAGGGGGCTGGGCT	57.343	43.478	3.27	0.00	0.00	5.19
873	2297	5.363005	CGTATATATATATAGGGGGCTGGGC	59.637	48.000	18.63	3.42	31.10	5.36
874	2298	6.500336	ACGTATATATATATAGGGGGCTGGG	58.500	44.000	25.41	7.94	36.14	4.45
934	2358	2.359230	AAGCGGCACAAGGCTCTC	60.359	61.111	1.45	0.00	44.01	3.20
1026	2484	2.743664	CAAATCCATCGCTGACAACAGA	59.256	45.455	0.00	0.00	46.03	3.41
1188	2685	1.448540	CGGCGTCTCCAAGAATGCT	60.449	57.895	0.00	0.00	31.04	3.79
1281	2952	2.028130	AGCTCGATTCTTGATCCGTCT	58.972	47.619	0.00	0.00	0.00	4.18
1314	2985	2.052690	CCATGGGACCTCGTCGTCT	61.053	63.158	2.85	0.00	32.65	4.18
1329	3000	4.314440	ACGCACCTGCACGTCCAT	62.314	61.111	0.00	0.00	38.28	3.41
2706	4425	2.579201	CGCCCTCACTGAACCGAT	59.421	61.111	0.00	0.00	0.00	4.18
2725	4444	0.871722	CCATTTGGTGACTTTCGCGA	59.128	50.000	3.71	3.71	0.00	5.87
2834	4553	1.195115	CAACCGGGATCTCCTTGAGA	58.805	55.000	6.32	0.00	43.20	3.27
2899	4618	3.808466	AGCGTCTTATCAAGATCTGCA	57.192	42.857	0.00	0.00	40.18	4.41

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.