AutoCloner

Multiple sequence alignment - TraesCS4A01G066300

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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	TraesCS4A01G066300	chr4A	100.000	2339	0	0	1	2339	63544776	63542438	0.000000e+00	4320
1	TraesCS4A01G066300	chr4A	95.556	90	3	1	2161	2249	63542558	63542469	2.420000e-30	143
2	TraesCS4A01G066300	chr4B	91.844	1741	76	27	130	1850	504944401	504942707	0.000000e+00	2368
3	TraesCS4A01G066300	chr4B	83.200	125	7	9	2	112	504944574	504944450	4.110000e-18	102
4	TraesCS4A01G066300	chr4D	94.308	1423	43	17	130	1538	405775328	405773930	0.000000e+00	2145
5	TraesCS4A01G066300	chr4D	88.630	343	16	16	1524	1850	405773914	405773579	1.680000e-106	396
6	TraesCS4A01G066300	chr4D	88.793	116	10	3	2	114	405775488	405775373	3.130000e-29	139
7	TraesCS4A01G066300	chr1B	95.876	485	20	0	1855	2339	659726163	659726647	0.000000e+00	785
8	TraesCS4A01G066300	chr1B	73.310	562	119	19	896	1437	583857564	583858114	6.640000e-41	178
9	TraesCS4A01G066300	chr1B	89.844	128	4	5	2189	2308	659726431	659726557	3.110000e-34	156
10	TraesCS4A01G066300	chr1B	95.699	93	4	0	2247	2339	356294904	356294996	1.450000e-32	150
11	TraesCS4A01G066300	chr6B	93.608	485	29	2	1856	2339	4481696	4481213	0.000000e+00	723
12	TraesCS4A01G066300	chr6B	77.753	908	196	6	424	1328	659616762	659615858	9.450000e-154	553
13	TraesCS4A01G066300	chr6B	89.404	302	24	6	1855	2156	714085928	714085635	7.890000e-100	374
14	TraesCS4A01G066300	chrUn	95.455	374	16	1	1966	2339	136329588	136329960	1.550000e-166	595
15	TraesCS4A01G066300	chrUn	89.062	128	5	5	2189	2308	136329744	136329870	1.450000e-32	150
16	TraesCS4A01G066300	chrUn	88.372	129	5	6	2123	2249	136329809	136329929	1.870000e-31	147
17	TraesCS4A01G066300	chr2B	88.866	485	33	3	1855	2339	153907179	153906716	5.600000e-161	577
18	TraesCS4A01G066300	chr2B	75.624	1042	199	44	427	1439	231234902	231233887	1.270000e-127	466
19	TraesCS4A01G066300	chr2B	74.395	1074	227	40	408	1454	390926577	390925525	1.290000e-112	416
20	TraesCS4A01G066300	chr2A	75.985	1041	197	43	427	1439	183551760	183550745	2.700000e-134	488
21	TraesCS4A01G066300	chr2A	74.882	1059	218	41	408	1439	407739491	407740528	2.760000e-119	438
22	TraesCS4A01G066300	chr2D	75.362	1035	202	42	427	1433	166608429	166609438	1.270000e-122	449
23	TraesCS4A01G066300	chr2D	74.858	1058	220	38	408	1439	323077924	323076887	2.760000e-119	438
24	TraesCS4A01G066300	chr7B	95.489	266	11	1	2075	2339	381919284	381919019	7.730000e-115	424
25	TraesCS4A01G066300	chr7B	94.796	269	14	0	2071	2339	381916792	381916524	1.000000e-113	420
26	TraesCS4A01G066300	chr7B	93.617	235	15	0	1856	2090	381917928	381917694	3.700000e-93	351
27	TraesCS4A01G066300	chr7B	93.617	235	15	0	1856	2090	381920423	381920189	3.700000e-93	351
28	TraesCS4A01G066300	chr7B	93.617	235	15	0	1856	2090	381942474	381942240	3.700000e-93	351
29	TraesCS4A01G066300	chr7B	94.444	90	4	1	2161	2249	381916644	381916555	1.130000e-28	137
30	TraesCS4A01G066300	chr3D	89.053	338	25	6	1855	2191	527563098	527562772	2.160000e-110	409
31	TraesCS4A01G066300	chr3B	85.546	339	39	4	1855	2191	791759313	791758983	1.720000e-91	346
32	TraesCS4A01G066300	chr1A	74.153	561	116	17	896	1437	530811163	530811713	3.050000e-49	206
33	TraesCS4A01G066300	chr1D	73.797	561	118	17	896	1437	432338659	432339209	6.600000e-46	195

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	TraesCS4A01G066300	chr4A	63542438	63544776	2338	True	2231.500000	4320	97.7780	1	2339	2	chr4A.!!$R1	2338
1	TraesCS4A01G066300	chr4B	504942707	504944574	1867	True	1235.000000	2368	87.5220	2	1850	2	chr4B.!!$R1	1848
2	TraesCS4A01G066300	chr4D	405773579	405775488	1909	True	893.333333	2145	90.5770	2	1850	3	chr4D.!!$R1	1848
3	TraesCS4A01G066300	chr6B	659615858	659616762	904	True	553.000000	553	77.7530	424	1328	1	chr6B.!!$R2	904
4	TraesCS4A01G066300	chr2B	231233887	231234902	1015	True	466.000000	466	75.6240	427	1439	1	chr2B.!!$R2	1012
5	TraesCS4A01G066300	chr2B	390925525	390926577	1052	True	416.000000	416	74.3950	408	1454	1	chr2B.!!$R3	1046
6	TraesCS4A01G066300	chr2A	183550745	183551760	1015	True	488.000000	488	75.9850	427	1439	1	chr2A.!!$R1	1012
7	TraesCS4A01G066300	chr2A	407739491	407740528	1037	False	438.000000	438	74.8820	408	1439	1	chr2A.!!$F1	1031
8	TraesCS4A01G066300	chr2D	166608429	166609438	1009	False	449.000000	449	75.3620	427	1433	1	chr2D.!!$F1	1006
9	TraesCS4A01G066300	chr2D	323076887	323077924	1037	True	438.000000	438	74.8580	408	1439	1	chr2D.!!$R1	1031
10	TraesCS4A01G066300	chr7B	381916524	381920423	3899	True	336.600000	424	94.3926	1856	2339	5	chr7B.!!$R2	483
11	TraesCS4A01G066300	chr1A	530811163	530811713	550	False	206.000000	206	74.1530	896	1437	1	chr1A.!!$F1	541

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
213	267	0.448197	TAGTTGAGCTCGCGACTGAG	59.552	55.0	20.89	0.0	39.05	3.35	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2026	2193	0.171903	AAATACGTCGCGCCTAGTGT	59.828	50.0	0.0	0.0	0.0	3.55	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
41	42	0.461548	TAGGCTCGCATTGTCAGAGG	59.538	55.000	0.00	0.00	32.96	3.69
42	43	3.096791	GCTCGCATTGTCAGAGGC	58.903	61.111	7.62	0.00	32.96	4.70
43	44	2.467826	GCTCGCATTGTCAGAGGCC	61.468	63.158	0.00	0.00	32.96	5.19
44	45	1.078918	CTCGCATTGTCAGAGGCCA	60.079	57.895	5.01	0.00	0.00	5.36
46	47	0.955428	TCGCATTGTCAGAGGCCAAC	60.955	55.000	5.01	0.00	0.00	3.77
69	79	9.912634	CAACTCCAAACAAATAGACACATAAAT	57.087	29.630	0.00	0.00	0.00	1.40
104	119	7.803279	AAACAAGAAAGACCGAAATACTCTT	57.197	32.000	0.00	0.00	0.00	2.85
109	124	7.463961	AGAAAGACCGAAATACTCTTCACTA	57.536	36.000	0.00	0.00	0.00	2.74
114	129	6.036953	AGACCGAAATACTCTTCACTACTACG	59.963	42.308	0.00	0.00	0.00	3.51
115	130	5.645497	ACCGAAATACTCTTCACTACTACGT	59.355	40.000	0.00	0.00	0.00	3.57
116	131	6.818644	ACCGAAATACTCTTCACTACTACGTA	59.181	38.462	0.00	0.00	0.00	3.57
117	132	7.497249	ACCGAAATACTCTTCACTACTACGTAT	59.503	37.037	0.00	0.00	0.00	3.06
120	135	8.853469	AAATACTCTTCACTACTACGTATTGC	57.147	34.615	0.00	0.00	0.00	3.56
182	236	1.738099	GCTGTTCCTCGTCGCATGT	60.738	57.895	0.00	0.00	0.00	3.21
183	237	1.687494	GCTGTTCCTCGTCGCATGTC	61.687	60.000	0.00	0.00	0.00	3.06
185	239	0.666274	TGTTCCTCGTCGCATGTCAC	60.666	55.000	0.00	0.00	0.00	3.67
187	241	2.812542	TTCCTCGTCGCATGTCACCG	62.813	60.000	0.00	0.00	0.00	4.94
200	254	4.500127	CATGTCACCGGTGTAATAGTTGA	58.500	43.478	32.74	8.68	0.00	3.18
213	267	0.448197	TAGTTGAGCTCGCGACTGAG	59.552	55.000	20.89	0.00	39.05	3.35
214	268	1.210413	GTTGAGCTCGCGACTGAGA	59.790	57.895	3.71	0.00	38.28	3.27
237	291	3.795561	GTGTCTGCACATCTTACACAC	57.204	47.619	0.00	0.00	44.64	3.82
238	292	2.480419	GTGTCTGCACATCTTACACACC	59.520	50.000	0.00	0.00	44.64	4.16
239	293	2.103941	TGTCTGCACATCTTACACACCA	59.896	45.455	0.00	0.00	0.00	4.17
240	294	2.738846	GTCTGCACATCTTACACACCAG	59.261	50.000	0.00	0.00	0.00	4.00
241	295	2.632512	TCTGCACATCTTACACACCAGA	59.367	45.455	0.00	0.00	0.00	3.86
242	296	2.738846	CTGCACATCTTACACACCAGAC	59.261	50.000	0.00	0.00	0.00	3.51
243	297	1.726791	GCACATCTTACACACCAGACG	59.273	52.381	0.00	0.00	0.00	4.18
244	298	2.609491	GCACATCTTACACACCAGACGA	60.609	50.000	0.00	0.00	0.00	4.20
245	299	3.245797	CACATCTTACACACCAGACGAG	58.754	50.000	0.00	0.00	0.00	4.18
246	300	3.057526	CACATCTTACACACCAGACGAGA	60.058	47.826	0.00	0.00	0.00	4.04
247	301	3.764434	ACATCTTACACACCAGACGAGAT	59.236	43.478	0.00	0.00	0.00	2.75
302	356	7.091443	TCCATCTTTCTTCTTTCTAAGTCGAC	58.909	38.462	7.70	7.70	0.00	4.20
345	399	7.687103	GCAGCCTTACATTTACATAGTAGGAGT	60.687	40.741	0.00	0.00	0.00	3.85
347	401	9.080097	AGCCTTACATTTACATAGTAGGAGTAG	57.920	37.037	0.00	0.00	0.00	2.57
348	402	8.858094	GCCTTACATTTACATAGTAGGAGTAGT	58.142	37.037	0.00	0.00	0.00	2.73
393	447	2.560861	CCGTTGGCGATGTTGTGG	59.439	61.111	0.00	0.00	41.33	4.17
394	448	2.258013	CCGTTGGCGATGTTGTGGT	61.258	57.895	0.00	0.00	41.33	4.16
395	449	1.082169	CGTTGGCGATGTTGTGGTG	60.082	57.895	0.00	0.00	41.33	4.17
717	771	2.266055	CAGGACCAGGCGAAGGAC	59.734	66.667	0.00	0.00	0.00	3.85
1459	1555	4.947147	GAACGGCCTGCACCACCA	62.947	66.667	0.00	0.00	0.00	4.17
1494	1595	7.815641	TCGTTAGAAATGCAAGATGAAATTCA	58.184	30.769	0.00	0.00	0.00	2.57
1497	1598	9.630098	GTTAGAAATGCAAGATGAAATTCAGAA	57.370	29.630	1.10	0.00	0.00	3.02
1527	1628	5.920193	ATCACGAAATGGGTCATCAAATT	57.080	34.783	0.00	0.00	0.00	1.82
1633	1782	2.159099	TCACCTAGCATGCTTTCCTACG	60.159	50.000	28.02	8.53	0.00	3.51
1673	1831	4.682860	AGTGACCGTACAAATAAAGTGTCG	59.317	41.667	0.00	0.00	0.00	4.35
1685	1844	2.933878	AAGTGTCGGAAGCGCACCAA	62.934	55.000	20.28	2.56	37.40	3.67
1780	1939	7.285629	TGTTGGACTAATGATCTACTACTCCTG	59.714	40.741	0.00	0.00	0.00	3.86
1817	1977	2.668250	CACACATGCATGTTGTCTTGG	58.332	47.619	29.48	18.11	39.39	3.61
1822	1982	1.080298	GCATGTTGTCTTGGCTGCC	60.080	57.895	12.87	12.87	0.00	4.85
1842	2009	6.561737	TGCCTCGTATAATTGAGTCTAGAG	57.438	41.667	0.00	0.00	0.00	2.43
1850	2017	8.358148	CGTATAATTGAGTCTAGAGGCCTTTAA	58.642	37.037	6.77	0.00	0.00	1.52
1870	2037	9.991906	CCTTTAAAATAGAGGTAATATCACCGA	57.008	33.333	0.00	0.00	43.84	4.69
1916	2083	6.031751	TGTTCAGTTTGGTGCTAAAACTTT	57.968	33.333	8.61	0.00	43.60	2.66
1917	2084	7.159322	TGTTCAGTTTGGTGCTAAAACTTTA	57.841	32.000	8.61	0.59	43.60	1.85
1970	2137	3.384927	GCGTGCAGATACGGTCAC	58.615	61.111	0.00	0.00	43.87	3.67
1972	2139	1.011968	GCGTGCAGATACGGTCACAA	61.012	55.000	0.00	0.00	43.87	3.33
1974	2141	1.324435	CGTGCAGATACGGTCACAATG	59.676	52.381	0.00	0.00	40.22	2.82
1976	2143	1.066215	TGCAGATACGGTCACAATGCT	60.066	47.619	0.00	0.00	33.47	3.79
1987	2154	3.797256	GGTCACAATGCTCGTATACAGAC	59.203	47.826	3.32	0.00	0.00	3.51
2011	2178	1.357420	TCAATGTGTATGGCCCCACTT	59.643	47.619	15.68	8.71	32.76	3.16
2058	2225	4.232221	CGACGTATTTTACACAGGACACT	58.768	43.478	0.00	0.00	0.00	3.55
2091	2258	4.712122	TTGTTTGTGGAAGAAGTGAACC	57.288	40.909	0.00	0.00	0.00	3.62
2093	2260	1.305201	TTGTGGAAGAAGTGAACCGC	58.695	50.000	0.00	0.00	0.00	5.68
2094	2261	0.179234	TGTGGAAGAAGTGAACCGCA	59.821	50.000	0.00	0.00	39.98	5.69
2095	2262	0.868406	GTGGAAGAAGTGAACCGCAG	59.132	55.000	0.00	0.00	33.73	5.18
2225	5808	4.320494	GCAGAAAACAGGACCACAATACTG	60.320	45.833	0.00	0.00	37.01	2.74
2321	5904	5.048852	ACATTAACAACAAAAATGGCATGCC	60.049	36.000	30.54	30.54	35.40	4.40

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	5.086104	ACCTGTATACAGCACCTTGTAAG	57.914	43.478	24.85	11.14	42.47	2.34
41	42	4.037446	TGTGTCTATTTGTTTGGAGTTGGC	59.963	41.667	0.00	0.00	0.00	4.52
42	43	5.766150	TGTGTCTATTTGTTTGGAGTTGG	57.234	39.130	0.00	0.00	0.00	3.77
43	44	9.912634	ATTTATGTGTCTATTTGTTTGGAGTTG	57.087	29.630	0.00	0.00	0.00	3.16
69	79	8.587608	TCGGTCTTTCTTGTTTAGTATCCTTTA	58.412	33.333	0.00	0.00	0.00	1.85
70	80	7.447594	TCGGTCTTTCTTGTTTAGTATCCTTT	58.552	34.615	0.00	0.00	0.00	3.11
72	82	6.600882	TCGGTCTTTCTTGTTTAGTATCCT	57.399	37.500	0.00	0.00	0.00	3.24
73	83	7.662604	TTTCGGTCTTTCTTGTTTAGTATCC	57.337	36.000	0.00	0.00	0.00	2.59
75	85	9.939802	AGTATTTCGGTCTTTCTTGTTTAGTAT	57.060	29.630	0.00	0.00	0.00	2.12
90	105	6.183360	ACGTAGTAGTGAAGAGTATTTCGGTC	60.183	42.308	0.00	0.00	41.94	4.79
116	131	8.528643	TGCAGTTCTATATAATAGGTACGCAAT	58.471	33.333	0.00	0.00	0.00	3.56
117	132	7.888424	TGCAGTTCTATATAATAGGTACGCAA	58.112	34.615	0.00	0.00	0.00	4.85
120	135	8.521176	ACCTTGCAGTTCTATATAATAGGTACG	58.479	37.037	0.00	0.00	30.92	3.67
123	138	9.561069	CAAACCTTGCAGTTCTATATAATAGGT	57.439	33.333	0.00	0.00	33.93	3.08
159	205	2.811317	GACGAGGAACAGCAGGCG	60.811	66.667	0.00	0.00	0.00	5.52
182	236	2.829720	AGCTCAACTATTACACCGGTGA	59.170	45.455	40.21	20.46	0.00	4.02
183	237	3.187700	GAGCTCAACTATTACACCGGTG	58.812	50.000	32.83	32.83	0.00	4.94
185	239	2.460918	CGAGCTCAACTATTACACCGG	58.539	52.381	15.40	0.00	0.00	5.28
187	241	1.852895	CGCGAGCTCAACTATTACACC	59.147	52.381	15.40	0.00	0.00	4.16
200	254	0.387878	CACTTTCTCAGTCGCGAGCT	60.388	55.000	10.24	7.28	30.92	4.09
227	281	4.017126	TCATCTCGTCTGGTGTGTAAGAT	58.983	43.478	0.00	0.00	0.00	2.40
228	282	3.418047	TCATCTCGTCTGGTGTGTAAGA	58.582	45.455	0.00	0.00	0.00	2.10
229	283	3.440522	TCTCATCTCGTCTGGTGTGTAAG	59.559	47.826	0.00	0.00	0.00	2.34
230	284	3.418047	TCTCATCTCGTCTGGTGTGTAA	58.582	45.455	0.00	0.00	0.00	2.41
232	286	1.911057	TCTCATCTCGTCTGGTGTGT	58.089	50.000	0.00	0.00	0.00	3.72
233	287	2.424956	TCATCTCATCTCGTCTGGTGTG	59.575	50.000	0.00	0.00	0.00	3.82
234	288	2.687425	CTCATCTCATCTCGTCTGGTGT	59.313	50.000	0.00	0.00	0.00	4.16
235	289	2.948315	TCTCATCTCATCTCGTCTGGTG	59.052	50.000	0.00	0.00	0.00	4.17
236	290	3.289407	TCTCATCTCATCTCGTCTGGT	57.711	47.619	0.00	0.00	0.00	4.00
237	291	3.120234	CGATCTCATCTCATCTCGTCTGG	60.120	52.174	0.00	0.00	0.00	3.86
238	292	3.745458	TCGATCTCATCTCATCTCGTCTG	59.255	47.826	0.00	0.00	0.00	3.51
239	293	4.001618	TCGATCTCATCTCATCTCGTCT	57.998	45.455	0.00	0.00	0.00	4.18
240	294	4.492409	CGATCGATCTCATCTCATCTCGTC	60.492	50.000	22.43	0.00	0.00	4.20
241	295	3.370672	CGATCGATCTCATCTCATCTCGT	59.629	47.826	22.43	0.00	0.00	4.18
242	296	3.616379	TCGATCGATCTCATCTCATCTCG	59.384	47.826	22.43	6.85	0.00	4.04
243	297	5.739752	ATCGATCGATCTCATCTCATCTC	57.260	43.478	24.60	0.00	0.00	2.75
244	298	7.622893	TTTATCGATCGATCTCATCTCATCT	57.377	36.000	32.50	8.99	36.17	2.90
245	299	6.414694	GCTTTATCGATCGATCTCATCTCATC	59.585	42.308	32.50	9.38	36.17	2.92
246	300	6.095300	AGCTTTATCGATCGATCTCATCTCAT	59.905	38.462	32.50	9.73	36.17	2.90
247	301	5.414144	AGCTTTATCGATCGATCTCATCTCA	59.586	40.000	32.50	11.23	36.17	3.27
302	356	3.371063	CCTGCCTGCCTGCACAAG	61.371	66.667	0.00	0.00	36.04	3.16
345	399	3.311106	CACCGTCTGAAAAGCGTTACTA	58.689	45.455	0.00	0.00	0.00	1.82
347	401	1.193874	CCACCGTCTGAAAAGCGTTAC	59.806	52.381	0.00	0.00	0.00	2.50
348	402	1.504359	CCACCGTCTGAAAAGCGTTA	58.496	50.000	0.00	0.00	0.00	3.18
350	404	2.251642	GCCACCGTCTGAAAAGCGT	61.252	57.895	0.00	0.00	0.00	5.07
351	405	2.556287	GCCACCGTCTGAAAAGCG	59.444	61.111	0.00	0.00	0.00	4.68
352	406	2.251642	ACGCCACCGTCTGAAAAGC	61.252	57.895	0.00	0.00	46.39	3.51
393	447	2.355481	GACGACGACCACCACCAC	60.355	66.667	0.00	0.00	0.00	4.16
394	448	3.968568	CGACGACGACCACCACCA	61.969	66.667	0.00	0.00	42.66	4.17
395	449	3.886329	GACGACGACGACCACCACC	62.886	68.421	15.32	0.00	42.66	4.61
717	771	3.411351	GTGTGCACCTACGTGGCG	61.411	66.667	15.69	0.00	40.61	5.69
1314	1407	1.296392	CACGAGCAAGATCCACCCA	59.704	57.895	0.00	0.00	0.00	4.51
1458	1554	4.607235	GCATTTCTAACGAAACGAACTGTG	59.393	41.667	0.00	0.00	41.58	3.66
1459	1555	4.271533	TGCATTTCTAACGAAACGAACTGT	59.728	37.500	0.00	0.00	41.58	3.55
1460	1556	4.768145	TGCATTTCTAACGAAACGAACTG	58.232	39.130	0.00	0.00	41.58	3.16
1461	1557	5.235616	TCTTGCATTTCTAACGAAACGAACT	59.764	36.000	0.00	0.00	41.58	3.01
1481	1577	7.912949	TTTCACGTTTCTGAATTTCATCTTG	57.087	32.000	0.00	0.00	30.19	3.02
1483	1579	7.805071	GTGATTTCACGTTTCTGAATTTCATCT	59.195	33.333	0.00	0.00	37.10	2.90
1484	1580	7.932526	GTGATTTCACGTTTCTGAATTTCATC	58.067	34.615	0.00	0.00	37.10	2.92
1485	1581	7.858052	GTGATTTCACGTTTCTGAATTTCAT	57.142	32.000	0.00	0.00	37.10	2.57
1673	1831	0.392461	TGATAGGTTGGTGCGCTTCC	60.392	55.000	9.73	12.17	0.00	3.46
1685	1844	3.850752	AGAGATTCCGATGGTGATAGGT	58.149	45.455	0.00	0.00	0.00	3.08
1773	1932	2.092861	AGAACTAGCTCGAGCAGGAGTA	60.093	50.000	36.87	19.88	45.16	2.59
1774	1933	1.099689	GAACTAGCTCGAGCAGGAGT	58.900	55.000	36.87	30.30	45.16	3.85
1775	1934	1.065401	CAGAACTAGCTCGAGCAGGAG	59.935	57.143	36.87	29.69	45.16	3.69
1780	1939	0.804156	GTGCCAGAACTAGCTCGAGC	60.804	60.000	30.01	30.01	42.49	5.03
1817	1977	3.983741	AGACTCAATTATACGAGGCAGC	58.016	45.455	0.00	0.00	39.96	5.25
1822	1982	5.708230	AGGCCTCTAGACTCAATTATACGAG	59.292	44.000	0.00	0.00	35.30	4.18
1842	2009	9.011095	GGTGATATTACCTCTATTTTAAAGGCC	57.989	37.037	9.39	0.00	37.74	5.19
1850	2017	9.529823	TGACTATCGGTGATATTACCTCTATTT	57.470	33.333	14.25	0.00	38.62	1.40
1851	2018	9.702253	ATGACTATCGGTGATATTACCTCTATT	57.298	33.333	14.25	1.20	38.62	1.73
1853	2020	9.833917	CTATGACTATCGGTGATATTACCTCTA	57.166	37.037	14.25	5.31	38.62	2.43
1854	2021	8.549731	TCTATGACTATCGGTGATATTACCTCT	58.450	37.037	14.25	4.47	38.62	3.69
1916	2083	7.648039	AGGTGACCACAAAACTGTATTTTTA	57.352	32.000	3.63	0.00	0.00	1.52
1917	2084	6.538945	AGGTGACCACAAAACTGTATTTTT	57.461	33.333	3.63	0.00	0.00	1.94
1925	2092	4.638865	GTCAAGTTAGGTGACCACAAAACT	59.361	41.667	3.63	5.17	39.62	2.66
1970	2137	7.873739	TTGATATGTCTGTATACGAGCATTG	57.126	36.000	9.91	0.00	0.00	2.82
1972	2139	7.543520	CACATTGATATGTCTGTATACGAGCAT	59.456	37.037	0.00	5.00	43.07	3.79
1974	2141	6.863645	ACACATTGATATGTCTGTATACGAGC	59.136	38.462	0.00	0.00	43.07	5.03
1976	2143	9.840427	CATACACATTGATATGTCTGTATACGA	57.160	33.333	0.00	0.00	43.07	3.43
1987	2154	3.507233	GTGGGGCCATACACATTGATATG	59.493	47.826	16.67	0.00	37.54	1.78
2011	2178	0.736636	AGTGTCGTTCGTCACTGACA	59.263	50.000	19.79	2.02	42.30	3.58
2026	2193	0.171903	AAATACGTCGCGCCTAGTGT	59.828	50.000	0.00	0.00	0.00	3.55
2072	2239	2.540973	GCGGTTCACTTCTTCCACAAAC	60.541	50.000	0.00	0.00	0.00	2.93
2079	2246	0.944311	TCGCTGCGGTTCACTTCTTC	60.944	55.000	23.03	0.00	0.00	2.87
2090	2257	5.839262	TCTATAAAAATACATCGCTGCGG	57.161	39.130	23.03	9.56	0.00	5.69
2091	2258	7.638295	TGTTTTCTATAAAAATACATCGCTGCG	59.362	33.333	17.25	17.25	36.37	5.18
2093	2260	9.221775	GGTGTTTTCTATAAAAATACATCGCTG	57.778	33.333	10.78	0.00	36.37	5.18
2094	2261	9.174166	AGGTGTTTTCTATAAAAATACATCGCT	57.826	29.630	10.78	0.00	36.37	4.93
2095	2262	9.783256	AAGGTGTTTTCTATAAAAATACATCGC	57.217	29.630	10.78	0.00	36.37	4.58
2137	3225	1.173043	TATTGCGGGCCTGTTTTCTG	58.827	50.000	14.55	0.00	0.00	3.02
2202	3348	3.821033	AGTATTGTGGTCCTGTTTTCTGC	59.179	43.478	0.00	0.00	0.00	4.26
2225	5808	8.560576	AAGTTTTAATGTTCGCATATATGTGC	57.439	30.769	19.44	14.00	41.65	4.57
2273	5856	5.296748	TCGCATATATGTGCAGTATTGTGT	58.703	37.500	22.27	0.00	45.30	3.72
2299	5882	5.068636	TGGCATGCCATTTTTGTTGTTAAT	58.931	33.333	35.59	0.00	41.89	1.40

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.