AutoCloner

Multiple sequence alignment - TraesCS3D01G214400

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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	TraesCS3D01G214400	chr3D	100.000	2822	0	0	1	2822	289812520	289815341	0.000000e+00	5212.0
1	TraesCS3D01G214400	chr3B	95.963	1189	29	7	887	2068	381945653	381946829	0.000000e+00	1912.0
2	TraesCS3D01G214400	chr3B	93.795	419	26	0	2404	2822	381976369	381976787	5.130000e-177	630.0
3	TraesCS3D01G214400	chr3B	83.333	648	76	13	1	640	753943156	753943779	1.130000e-158	569.0
4	TraesCS3D01G214400	chr3B	81.426	673	92	15	217	879	597609346	597608697	1.160000e-143	520.0
5	TraesCS3D01G214400	chr3B	94.340	212	7	1	2206	2412	381976011	381976222	1.260000e-83	320.0
6	TraesCS3D01G214400	chr3B	96.089	179	7	0	2644	2822	444681942	444682120	2.750000e-75	292.0
7	TraesCS3D01G214400	chr3B	82.645	242	32	5	1833	2068	464610473	464610236	3.680000e-49	206.0
8	TraesCS3D01G214400	chr3B	100.000	34	0	0	2168	2201	381975986	381976019	2.350000e-06	63.9
9	TraesCS3D01G214400	chr1D	98.313	889	13	1	1	887	12307732	12306844	0.000000e+00	1557.0
10	TraesCS3D01G214400	chr1D	94.937	79	4	0	2068	2146	475979671	475979749	1.060000e-24	124.0
11	TraesCS3D01G214400	chr7D	98.413	882	12	2	1	880	87754269	87755150	0.000000e+00	1550.0
12	TraesCS3D01G214400	chr7D	98.064	878	13	2	1	874	2017773	2018650	0.000000e+00	1524.0
13	TraesCS3D01G214400	chr7D	94.972	179	9	0	2644	2822	36862694	36862872	5.950000e-72	281.0
14	TraesCS3D01G214400	chr7D	82.787	244	32	3	1831	2068	148155687	148155448	2.850000e-50	209.0
15	TraesCS3D01G214400	chr3A	95.842	914	38	0	921	1834	380917721	380918634	0.000000e+00	1478.0
16	TraesCS3D01G214400	chr3A	87.461	646	73	7	1	640	94114180	94113537	0.000000e+00	737.0
17	TraesCS3D01G214400	chr3A	85.604	646	85	7	1	640	393192387	393193030	0.000000e+00	671.0
18	TraesCS3D01G214400	chr3A	89.591	269	19	4	2194	2456	380918669	380918934	1.620000e-87	333.0
19	TraesCS3D01G214400	chr7A	93.715	891	26	5	1	884	44434129	44433262	0.000000e+00	1308.0
20	TraesCS3D01G214400	chr2A	92.525	883	48	9	1	879	385329631	385330499	0.000000e+00	1249.0
21	TraesCS3D01G214400	chr2A	90.698	86	8	0	2068	2153	16492047	16491962	6.390000e-22	115.0
22	TraesCS3D01G214400	chr6A	94.575	682	33	3	1	678	437499140	437499821	0.000000e+00	1051.0
23	TraesCS3D01G214400	chr6A	96.111	180	6	1	2644	2822	124892494	124892673	2.750000e-75	292.0
24	TraesCS3D01G214400	chr6A	94.350	177	9	1	703	879	437500144	437500319	1.290000e-68	270.0
25	TraesCS3D01G214400	chr6A	93.902	82	4	1	2068	2148	435593709	435593790	3.820000e-24	122.0
26	TraesCS3D01G214400	chr7B	83.278	909	96	23	1	879	568782059	568781177	0.000000e+00	785.0
27	TraesCS3D01G214400	chr7B	83.058	242	31	5	1833	2068	464539952	464539715	7.920000e-51	211.0
28	TraesCS3D01G214400	chrUn	92.925	212	11	2	671	879	71647104	71646894	3.530000e-79	305.0
29	TraesCS3D01G214400	chrUn	94.937	79	3	1	2068	2146	398593202	398593279	3.820000e-24	122.0
30	TraesCS3D01G214400	chr6B	95.531	179	8	0	2644	2822	601118017	601117839	1.280000e-73	287.0
31	TraesCS3D01G214400	chr4B	95.531	179	8	0	2644	2822	4206091	4206269	1.280000e-73	287.0
32	TraesCS3D01G214400	chr4B	95.531	179	8	0	2644	2822	625092128	625091950	1.280000e-73	287.0
33	TraesCS3D01G214400	chr6D	94.972	179	9	0	2644	2822	2629416	2629238	5.950000e-72	281.0
34	TraesCS3D01G214400	chr6D	94.972	179	9	0	2644	2822	201581843	201581665	5.950000e-72	281.0
35	TraesCS3D01G214400	chr2D	94.937	79	3	1	2068	2146	610488073	610488150	3.820000e-24	122.0
36	TraesCS3D01G214400	chr2D	92.683	82	6	0	2068	2149	209128668	209128749	4.940000e-23	119.0
37	TraesCS3D01G214400	chr5D	93.750	80	5	0	2068	2147	3250847	3250768	1.370000e-23	121.0
38	TraesCS3D01G214400	chr4A	92.857	84	5	1	2068	2150	589903042	589902959	1.370000e-23	121.0
39	TraesCS3D01G214400	chr1B	91.765	85	6	1	2072	2155	431010340	431010256	1.780000e-22	117.0

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	TraesCS3D01G214400	chr3D	289812520	289815341	2821	False	5212.000000	5212	100.0000	1	2822	1	chr3D.!!$F1	2821
1	TraesCS3D01G214400	chr3B	381945653	381946829	1176	False	1912.000000	1912	95.9630	887	2068	1	chr3B.!!$F1	1181
2	TraesCS3D01G214400	chr3B	753943156	753943779	623	False	569.000000	569	83.3330	1	640	1	chr3B.!!$F3	639
3	TraesCS3D01G214400	chr3B	597608697	597609346	649	True	520.000000	520	81.4260	217	879	1	chr3B.!!$R2	662
4	TraesCS3D01G214400	chr3B	381975986	381976787	801	False	337.966667	630	96.0450	2168	2822	3	chr3B.!!$F4	654
5	TraesCS3D01G214400	chr1D	12306844	12307732	888	True	1557.000000	1557	98.3130	1	887	1	chr1D.!!$R1	886
6	TraesCS3D01G214400	chr7D	87754269	87755150	881	False	1550.000000	1550	98.4130	1	880	1	chr7D.!!$F3	879
7	TraesCS3D01G214400	chr7D	2017773	2018650	877	False	1524.000000	1524	98.0640	1	874	1	chr7D.!!$F1	873
8	TraesCS3D01G214400	chr3A	380917721	380918934	1213	False	905.500000	1478	92.7165	921	2456	2	chr3A.!!$F2	1535
9	TraesCS3D01G214400	chr3A	94113537	94114180	643	True	737.000000	737	87.4610	1	640	1	chr3A.!!$R1	639
10	TraesCS3D01G214400	chr3A	393192387	393193030	643	False	671.000000	671	85.6040	1	640	1	chr3A.!!$F1	639
11	TraesCS3D01G214400	chr7A	44433262	44434129	867	True	1308.000000	1308	93.7150	1	884	1	chr7A.!!$R1	883
12	TraesCS3D01G214400	chr2A	385329631	385330499	868	False	1249.000000	1249	92.5250	1	879	1	chr2A.!!$F1	878
13	TraesCS3D01G214400	chr6A	437499140	437500319	1179	False	660.500000	1051	94.4625	1	879	2	chr6A.!!$F3	878
14	TraesCS3D01G214400	chr7B	568781177	568782059	882	True	785.000000	785	83.2780	1	879	1	chr7B.!!$R2	878

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
913	1277	1.140407	CGCTCCAGCAGTACTAACGC	61.14	60.0	0.0	0.0	42.21	4.84	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1839	2215	0.0293	CGCTGCATTATGAAACGGGG	59.971	55.0	0.0	0.0	0.0	5.73	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
743	1106	7.561556	GCTAATGTAAATCGCTAAACGTACAT	58.438	34.615	0.00	0.00	40.91	2.29
804	1167	6.604795	CCTGATTCTGGAGATGGTAATTTGTT	59.395	38.462	3.58	0.00	0.00	2.83
913	1277	1.140407	CGCTCCAGCAGTACTAACGC	61.140	60.000	0.00	0.00	42.21	4.84
1007	1371	0.672401	CTGTACGAAACCATGGCCGT	60.672	55.000	24.23	24.23	38.82	5.68
1024	1388	1.294659	CGTGCTGCTCACCTCCTTTC	61.295	60.000	0.00	0.00	42.69	2.62
1075	1439	1.656652	CAAGAGGCCAGTTATCACCG	58.343	55.000	5.01	0.00	0.00	4.94
1102	1466	0.673644	CTTCATCTTGCCGGTCGGTT	60.674	55.000	11.25	0.00	37.65	4.44
1275	1639	2.151502	ACCTCGACATCATCTCCAGT	57.848	50.000	0.00	0.00	0.00	4.00
1393	1757	4.717629	CGCGACTCAACCTCGGCA	62.718	66.667	0.00	0.00	0.00	5.69
1458	1822	2.749044	TACGCGGCCGTCTTCTCT	60.749	61.111	28.70	3.84	46.39	3.10
1539	1913	3.791586	GCCCTGAGAGGTCTGGCC	61.792	72.222	0.00	0.00	39.86	5.36
1540	1914	3.465403	CCCTGAGAGGTCTGGCCG	61.465	72.222	0.00	0.00	43.70	6.13
1541	1915	4.154347	CCTGAGAGGTCTGGCCGC	62.154	72.222	0.00	0.00	43.70	6.53
1542	1916	4.154347	CTGAGAGGTCTGGCCGCC	62.154	72.222	1.04	1.04	43.70	6.13
1839	2215	1.408453	AATAGGCGGCAGTACTCCCC	61.408	60.000	13.08	0.00	0.00	4.81
1871	2247	9.875691	TTCATAATGCAGCGACTATAGATTTAT	57.124	29.630	6.78	0.00	0.00	1.40
1954	2335	7.223971	GTCTAGAATACCAAATGCACATCGTTA	59.776	37.037	0.00	0.00	0.00	3.18
1962	2343	2.385013	TGCACATCGTTAGCATGAGT	57.615	45.000	0.00	0.00	32.55	3.41
1968	2349	6.705825	TGCACATCGTTAGCATGAGTTATATT	59.294	34.615	0.00	0.00	32.55	1.28
1970	2351	8.070171	GCACATCGTTAGCATGAGTTATATTTT	58.930	33.333	0.00	0.00	0.00	1.82
1971	2352	9.935682	CACATCGTTAGCATGAGTTATATTTTT	57.064	29.630	0.00	0.00	0.00	1.94
2068	2449	8.243426	TGACTTTCAAAAACATCTATATGCACC	58.757	33.333	0.00	0.00	36.50	5.01
2069	2450	8.353423	ACTTTCAAAAACATCTATATGCACCT	57.647	30.769	0.00	0.00	36.50	4.00
2070	2451	8.462016	ACTTTCAAAAACATCTATATGCACCTC	58.538	33.333	0.00	0.00	36.50	3.85
2071	2452	6.603237	TCAAAAACATCTATATGCACCTCG	57.397	37.500	0.00	0.00	36.50	4.63
2072	2453	6.345298	TCAAAAACATCTATATGCACCTCGA	58.655	36.000	0.00	0.00	36.50	4.04
2073	2454	6.479990	TCAAAAACATCTATATGCACCTCGAG	59.520	38.462	5.13	5.13	36.50	4.04
2074	2455	5.791336	AAACATCTATATGCACCTCGAGA	57.209	39.130	15.71	0.00	36.50	4.04
2075	2456	5.791336	AACATCTATATGCACCTCGAGAA	57.209	39.130	15.71	0.00	36.50	2.87
2076	2457	5.991933	ACATCTATATGCACCTCGAGAAT	57.008	39.130	15.71	4.64	36.50	2.40
2077	2458	7.468141	AACATCTATATGCACCTCGAGAATA	57.532	36.000	15.71	6.76	36.50	1.75
2078	2459	7.468141	ACATCTATATGCACCTCGAGAATAA	57.532	36.000	15.71	0.00	36.50	1.40
2079	2460	8.072321	ACATCTATATGCACCTCGAGAATAAT	57.928	34.615	15.71	5.00	36.50	1.28
2080	2461	8.535335	ACATCTATATGCACCTCGAGAATAATT	58.465	33.333	15.71	0.00	36.50	1.40
2090	2471	9.612620	GCACCTCGAGAATAATTAATAAAATGG	57.387	33.333	15.71	0.00	0.00	3.16
2091	2472	9.612620	CACCTCGAGAATAATTAATAAAATGGC	57.387	33.333	15.71	0.00	0.00	4.40
2092	2473	8.793592	ACCTCGAGAATAATTAATAAAATGGCC	58.206	33.333	15.71	0.00	0.00	5.36
2093	2474	7.962918	CCTCGAGAATAATTAATAAAATGGCCG	59.037	37.037	15.71	0.00	0.00	6.13
2094	2475	7.302524	TCGAGAATAATTAATAAAATGGCCGC	58.697	34.615	0.00	0.00	0.00	6.53
2095	2476	7.041030	TCGAGAATAATTAATAAAATGGCCGCA	60.041	33.333	0.00	0.00	0.00	5.69
2096	2477	7.754924	CGAGAATAATTAATAAAATGGCCGCAT	59.245	33.333	0.00	0.00	0.00	4.73
2097	2478	8.761575	AGAATAATTAATAAAATGGCCGCATG	57.238	30.769	0.00	0.00	0.00	4.06
2098	2479	6.966435	ATAATTAATAAAATGGCCGCATGC	57.034	33.333	7.91	7.91	40.16	4.06
2099	2480	3.808466	TTAATAAAATGGCCGCATGCA	57.192	38.095	19.57	0.00	43.89	3.96
2100	2481	2.914695	AATAAAATGGCCGCATGCAT	57.085	40.000	19.57	0.00	43.89	3.96
2101	2482	2.443887	ATAAAATGGCCGCATGCATC	57.556	45.000	19.57	8.10	43.89	3.91
2102	2483	1.401761	TAAAATGGCCGCATGCATCT	58.598	45.000	19.57	0.00	43.89	2.90
2103	2484	0.538118	AAAATGGCCGCATGCATCTT	59.462	45.000	19.57	0.28	43.89	2.40
2104	2485	0.103572	AAATGGCCGCATGCATCTTC	59.896	50.000	19.57	2.63	43.89	2.87
2105	2486	1.741327	AATGGCCGCATGCATCTTCC	61.741	55.000	19.57	10.69	43.89	3.46
2106	2487	2.829914	GGCCGCATGCATCTTCCA	60.830	61.111	19.57	0.00	43.89	3.53
2107	2488	2.719979	GCCGCATGCATCTTCCAG	59.280	61.111	19.57	0.00	40.77	3.86
2108	2489	1.820906	GCCGCATGCATCTTCCAGA	60.821	57.895	19.57	0.00	40.77	3.86
2109	2490	1.170919	GCCGCATGCATCTTCCAGAT	61.171	55.000	19.57	0.00	40.77	2.90
2117	2498	1.595466	CATCTTCCAGATGCAGAGGC	58.405	55.000	0.84	0.00	44.69	4.70
2118	2499	0.473326	ATCTTCCAGATGCAGAGGCC	59.527	55.000	0.00	0.00	40.13	5.19
2119	2500	1.523258	CTTCCAGATGCAGAGGCCG	60.523	63.158	0.00	0.00	40.13	6.13
2120	2501	2.937379	CTTCCAGATGCAGAGGCCGG	62.937	65.000	0.00	0.00	40.13	6.13
2121	2502	3.790437	CCAGATGCAGAGGCCGGT	61.790	66.667	1.90	0.00	40.13	5.28
2122	2503	2.513204	CAGATGCAGAGGCCGGTG	60.513	66.667	1.90	0.00	40.13	4.94
2123	2504	2.685017	AGATGCAGAGGCCGGTGA	60.685	61.111	11.28	0.00	40.13	4.02
2124	2505	2.068821	AGATGCAGAGGCCGGTGAT	61.069	57.895	11.28	2.61	40.13	3.06
2125	2506	1.596477	GATGCAGAGGCCGGTGATC	60.596	63.158	11.28	0.00	40.13	2.92
2126	2507	2.315781	GATGCAGAGGCCGGTGATCA	62.316	60.000	11.28	0.00	40.13	2.92
2127	2508	1.703014	ATGCAGAGGCCGGTGATCAT	61.703	55.000	11.28	3.67	40.13	2.45
2128	2509	1.596477	GCAGAGGCCGGTGATCATC	60.596	63.158	11.28	0.00	0.00	2.92
2129	2510	1.070445	CAGAGGCCGGTGATCATCC	59.930	63.158	1.90	1.25	0.00	3.51
2130	2511	1.074926	AGAGGCCGGTGATCATCCT	60.075	57.895	1.90	3.56	0.00	3.24
2131	2512	1.118356	AGAGGCCGGTGATCATCCTC	61.118	60.000	19.85	19.85	42.68	3.71
2132	2513	1.383109	AGGCCGGTGATCATCCTCA	60.383	57.895	1.90	0.00	0.00	3.86
2133	2514	0.765903	AGGCCGGTGATCATCCTCAT	60.766	55.000	1.90	0.00	0.00	2.90
2134	2515	0.109342	GGCCGGTGATCATCCTCATT	59.891	55.000	1.90	0.00	0.00	2.57
2135	2516	1.477558	GGCCGGTGATCATCCTCATTT	60.478	52.381	1.90	0.00	0.00	2.32
2136	2517	2.301346	GCCGGTGATCATCCTCATTTT	58.699	47.619	1.90	0.00	0.00	1.82
2137	2518	2.291741	GCCGGTGATCATCCTCATTTTC	59.708	50.000	1.90	0.00	0.00	2.29
2138	2519	2.880890	CCGGTGATCATCCTCATTTTCC	59.119	50.000	0.00	0.00	0.00	3.13
2139	2520	3.544684	CGGTGATCATCCTCATTTTCCA	58.455	45.455	0.00	0.00	0.00	3.53
2140	2521	3.947196	CGGTGATCATCCTCATTTTCCAA	59.053	43.478	0.00	0.00	0.00	3.53
2141	2522	4.398988	CGGTGATCATCCTCATTTTCCAAA	59.601	41.667	0.00	0.00	0.00	3.28
2142	2523	5.105797	CGGTGATCATCCTCATTTTCCAAAA	60.106	40.000	0.00	0.00	0.00	2.44
2143	2524	6.572119	CGGTGATCATCCTCATTTTCCAAAAA	60.572	38.462	0.00	0.00	0.00	1.94
2215	2604	2.100605	GCTGTAGGCTGTAGCTGTTT	57.899	50.000	15.02	0.00	41.70	2.83
2338	2733	6.672147	AGTGACACTTGCAATCTTATTCAAC	58.328	36.000	1.07	0.00	0.00	3.18
2377	2772	7.226523	ACACCTGGTTTTTCTTTTCATATTTGC	59.773	33.333	0.00	0.00	0.00	3.68
2444	2994	1.136110	ACAGTTTTTGCCTGGGTTTCG	59.864	47.619	0.00	0.00	34.16	3.46
2507	3057	1.134788	CGGAGCCCTAAGAAACACGAT	60.135	52.381	0.00	0.00	0.00	3.73
2510	3060	3.756963	GGAGCCCTAAGAAACACGATTTT	59.243	43.478	0.00	0.00	0.00	1.82
2562	3112	3.261580	TGCACAGTCCTTCGTTGATATG	58.738	45.455	0.00	0.00	0.00	1.78
2563	3113	3.262420	GCACAGTCCTTCGTTGATATGT	58.738	45.455	0.00	0.00	0.00	2.29
2602	3152	5.458452	CACGAGAGCAAGATAATGAGACTTC	59.542	44.000	0.00	0.00	0.00	3.01
2606	3156	6.339730	AGAGCAAGATAATGAGACTTCACAG	58.660	40.000	0.00	0.00	35.83	3.66
2648	3198	2.231716	ACTAATTTTGGCCCCACCTC	57.768	50.000	0.00	0.00	40.22	3.85
2668	3218	0.038166	ACTGGATGGGCGAAACACAT	59.962	50.000	0.00	0.00	0.00	3.21
2713	3263	3.802948	ACAACGGCTCTCTACCATTAG	57.197	47.619	0.00	0.00	0.00	1.73
2724	3274	2.941064	TCTACCATTAGTGACGACCTCG	59.059	50.000	0.00	0.00	46.33	4.63
2757	3307	2.924290	GAGACACGCACCTTATCTCAAC	59.076	50.000	0.00	0.00	36.60	3.18
2800	3350	4.122776	CAATCTAATGAGAAGGTCACCCG	58.877	47.826	0.00	0.00	38.28	5.28
2816	3366	0.790814	CCCGTCTTTTGCGAGAAGAC	59.209	55.000	13.58	13.58	45.96	3.01

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
743	1106	4.469945	CACATAAAAGTCAGACCTCCCCTA	59.530	45.833	0.00	0.00	0.00	3.53
804	1167	6.262720	AGTTAAACGTACACAGGCCAAATAAA	59.737	34.615	5.01	0.00	0.00	1.40
874	1238	6.094881	GGAGCGCTACATATCTTCTCTATCTT	59.905	42.308	16.75	0.00	0.00	2.40
884	1248	1.271934	CTGCTGGAGCGCTACATATCT	59.728	52.381	25.49	0.00	45.83	1.98
913	1277	4.497006	GCTGGTTGATCGATTGATTCTTGG	60.497	45.833	0.00	0.00	34.09	3.61
1007	1371	1.376466	GGAAAGGAGGTGAGCAGCA	59.624	57.895	0.00	0.00	0.00	4.41
1075	1439	1.092345	GGCAAGATGAAGGACGAGGC	61.092	60.000	0.00	0.00	0.00	4.70
1102	1466	0.882927	GCCGGTAAGTTGTGCTCACA	60.883	55.000	1.90	0.00	39.98	3.58
1214	1578	2.126417	CTCGTCGTGGAAGTGGTCGT	62.126	60.000	0.00	0.00	0.00	4.34
1275	1639	0.461548	CATAGAGGAAGCCGCTGTCA	59.538	55.000	0.00	0.00	33.89	3.58
1308	1672	4.201679	CAGACCCGCGCCGACATA	62.202	66.667	0.00	0.00	0.00	2.29
1335	1699	1.410083	GCCATGATGAGGGCCTTGTTA	60.410	52.381	7.89	0.00	43.69	2.41
1539	1913	4.457496	AGGATGTGGCTCACGGCG	62.457	66.667	4.80	4.80	42.94	6.46
1540	1914	2.821366	CAGGATGTGGCTCACGGC	60.821	66.667	0.00	0.00	37.14	5.68
1541	1915	2.821366	GCAGGATGTGGCTCACGG	60.821	66.667	0.00	0.00	39.31	4.94
1542	1916	2.267006	AGCAGGATGTGGCTCACG	59.733	61.111	0.00	0.00	39.31	4.35
1546	1920	2.996395	CTGGAGCAGGATGTGGCT	59.004	61.111	0.00	0.00	44.48	4.75
1819	2195	1.335145	GGGAGTACTGCCGCCTATTA	58.665	55.000	18.47	0.00	0.00	0.98
1839	2215	0.029300	CGCTGCATTATGAAACGGGG	59.971	55.000	0.00	0.00	0.00	5.73
1920	2301	8.803235	TGCATTTGGTATTCTAGACGTATCTAT	58.197	33.333	0.00	0.00	36.81	1.98
1928	2309	5.523916	ACGATGTGCATTTGGTATTCTAGAC	59.476	40.000	0.00	0.00	0.00	2.59
2064	2445	9.612620	CCATTTTATTAATTATTCTCGAGGTGC	57.387	33.333	13.56	0.00	0.00	5.01
2068	2449	7.481798	GCGGCCATTTTATTAATTATTCTCGAG	59.518	37.037	5.93	5.93	0.00	4.04
2069	2450	7.041030	TGCGGCCATTTTATTAATTATTCTCGA	60.041	33.333	2.24	0.00	0.00	4.04
2070	2451	7.081349	TGCGGCCATTTTATTAATTATTCTCG	58.919	34.615	2.24	0.00	0.00	4.04
2071	2452	8.863049	CATGCGGCCATTTTATTAATTATTCTC	58.137	33.333	2.24	0.00	0.00	2.87
2072	2453	7.331687	GCATGCGGCCATTTTATTAATTATTCT	59.668	33.333	0.00	0.00	36.11	2.40
2073	2454	7.117523	TGCATGCGGCCATTTTATTAATTATTC	59.882	33.333	14.09	0.00	43.89	1.75
2074	2455	6.933521	TGCATGCGGCCATTTTATTAATTATT	59.066	30.769	14.09	0.00	43.89	1.40
2075	2456	6.462500	TGCATGCGGCCATTTTATTAATTAT	58.538	32.000	14.09	0.00	43.89	1.28
2076	2457	5.847304	TGCATGCGGCCATTTTATTAATTA	58.153	33.333	14.09	0.00	43.89	1.40
2077	2458	4.701765	TGCATGCGGCCATTTTATTAATT	58.298	34.783	14.09	0.00	43.89	1.40
2078	2459	4.333913	TGCATGCGGCCATTTTATTAAT	57.666	36.364	14.09	0.00	43.89	1.40
2079	2460	3.808466	TGCATGCGGCCATTTTATTAA	57.192	38.095	14.09	0.00	43.89	1.40
2080	2461	3.573538	AGATGCATGCGGCCATTTTATTA	59.426	39.130	14.09	0.00	43.89	0.98
2081	2462	2.366266	AGATGCATGCGGCCATTTTATT	59.634	40.909	14.09	0.00	43.89	1.40
2082	2463	1.965643	AGATGCATGCGGCCATTTTAT	59.034	42.857	14.09	0.00	43.89	1.40
2083	2464	1.401761	AGATGCATGCGGCCATTTTA	58.598	45.000	14.09	0.00	43.89	1.52
2084	2465	0.538118	AAGATGCATGCGGCCATTTT	59.462	45.000	14.09	0.00	43.89	1.82
2085	2466	0.103572	GAAGATGCATGCGGCCATTT	59.896	50.000	14.09	1.35	43.89	2.32
2086	2467	1.737816	GAAGATGCATGCGGCCATT	59.262	52.632	14.09	3.15	43.89	3.16
2087	2468	2.198287	GGAAGATGCATGCGGCCAT	61.198	57.895	14.09	0.00	43.89	4.40
2088	2469	2.829914	GGAAGATGCATGCGGCCA	60.830	61.111	14.09	0.00	43.89	5.36
2089	2470	2.829914	TGGAAGATGCATGCGGCC	60.830	61.111	14.09	9.89	43.89	6.13
2090	2471	1.820906	TCTGGAAGATGCATGCGGC	60.821	57.895	14.09	7.38	38.67	6.53
2091	2472	4.545929	TCTGGAAGATGCATGCGG	57.454	55.556	14.09	0.00	38.67	5.69
2101	2482	1.523258	CGGCCTCTGCATCTGGAAG	60.523	63.158	0.00	0.00	40.13	3.46
2102	2483	2.586245	CGGCCTCTGCATCTGGAA	59.414	61.111	0.00	0.00	40.13	3.53
2103	2484	3.473647	CCGGCCTCTGCATCTGGA	61.474	66.667	0.00	0.00	40.13	3.86
2104	2485	3.790437	ACCGGCCTCTGCATCTGG	61.790	66.667	0.00	0.00	40.13	3.86
2105	2486	2.321263	ATCACCGGCCTCTGCATCTG	62.321	60.000	0.00	0.00	40.13	2.90
2106	2487	2.037620	GATCACCGGCCTCTGCATCT	62.038	60.000	0.00	0.00	40.13	2.90
2107	2488	1.596477	GATCACCGGCCTCTGCATC	60.596	63.158	0.00	0.00	40.13	3.91
2108	2489	1.703014	ATGATCACCGGCCTCTGCAT	61.703	55.000	0.00	0.00	40.13	3.96
2109	2490	2.315781	GATGATCACCGGCCTCTGCA	62.316	60.000	0.00	0.00	40.13	4.41
2110	2491	1.596477	GATGATCACCGGCCTCTGC	60.596	63.158	0.00	0.00	0.00	4.26
2111	2492	1.070445	GGATGATCACCGGCCTCTG	59.930	63.158	0.00	0.00	0.00	3.35
2112	2493	1.074926	AGGATGATCACCGGCCTCT	60.075	57.895	0.00	0.00	0.00	3.69
2113	2494	1.369321	GAGGATGATCACCGGCCTC	59.631	63.158	15.68	15.68	38.45	4.70
2114	2495	0.765903	ATGAGGATGATCACCGGCCT	60.766	55.000	0.00	2.49	30.46	5.19
2115	2496	0.109342	AATGAGGATGATCACCGGCC	59.891	55.000	0.00	0.00	30.46	6.13
2116	2497	1.972872	AAATGAGGATGATCACCGGC	58.027	50.000	0.00	1.02	30.46	6.13
2117	2498	2.880890	GGAAAATGAGGATGATCACCGG	59.119	50.000	0.00	0.00	30.46	5.28
2118	2499	3.544684	TGGAAAATGAGGATGATCACCG	58.455	45.455	0.00	0.00	30.46	4.94
2119	2500	5.920193	TTTGGAAAATGAGGATGATCACC	57.080	39.130	0.00	1.52	30.46	4.02
2211	2600	7.687941	ACACTTTCTTTCTTCTCTTGAAACA	57.312	32.000	0.00	0.00	31.21	2.83
2215	2604	7.687941	AACAACACTTTCTTTCTTCTCTTGA	57.312	32.000	0.00	0.00	0.00	3.02
2377	2772	7.031226	TCTGAATTTGGTCTTTGTTCTTCAG	57.969	36.000	0.00	0.00	39.61	3.02
2444	2994	4.022849	AGAGAGTTGCATGTTTAGTTTGCC	60.023	41.667	0.00	0.00	35.51	4.52
2545	3095	4.033358	GCTTCACATATCAACGAAGGACTG	59.967	45.833	0.00	0.00	36.27	3.51
2576	3126	3.131046	TCTCATTATCTTGCTCTCGTGCA	59.869	43.478	0.00	0.00	41.65	4.57
2581	3131	6.336566	TGTGAAGTCTCATTATCTTGCTCTC	58.663	40.000	0.00	0.00	33.05	3.20
2594	3144	4.866508	ATTTACGTCCTGTGAAGTCTCA	57.133	40.909	0.00	0.00	34.86	3.27
2602	3152	4.816385	AGCATGGAATATTTACGTCCTGTG	59.184	41.667	0.00	0.00	32.28	3.66
2606	3156	7.376615	AGTAGTAGCATGGAATATTTACGTCC	58.623	38.462	0.00	0.00	0.00	4.79
2634	3184	1.152567	CAGTGAGGTGGGGCCAAAA	60.153	57.895	4.39	0.00	40.61	2.44
2648	3198	0.888736	TGTGTTTCGCCCATCCAGTG	60.889	55.000	0.00	0.00	0.00	3.66
2713	3263	1.986378	CAATCTTGTCGAGGTCGTCAC	59.014	52.381	0.00	0.00	37.16	3.67
2724	3274	1.127582	GCGTGTCTCTGCAATCTTGTC	59.872	52.381	0.00	0.00	0.00	3.18
2796	3346	0.391597	TCTTCTCGCAAAAGACGGGT	59.608	50.000	0.00	0.00	31.39	5.28
2800	3350	2.662700	TCTCGTCTTCTCGCAAAAGAC	58.337	47.619	11.08	11.08	45.90	3.01

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.