AutoCloner

Multiple sequence alignment - TraesCS1A01G092200

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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	TraesCS1A01G092200	chr1A	100.000	2903	0	0	1	2903	84795977	84793075	0.000000e+00	5361.0
1	TraesCS1A01G092200	chr1A	96.114	669	13	6	1	669	85005861	85005206	0.000000e+00	1079.0
2	TraesCS1A01G092200	chr1A	94.178	292	17	0	1	292	84621664	84621955	2.050000e-121	446.0
3	TraesCS1A01G092200	chr1A	93.836	292	18	0	1	292	84484467	84484758	9.550000e-120	440.0
4	TraesCS1A01G092200	chr1A	89.091	220	14	5	486	695	84622323	84622542	6.170000e-67	265.0
5	TraesCS1A01G092200	chr1A	88.636	220	15	5	486	695	84485125	84485344	2.870000e-65	259.0
6	TraesCS1A01G092200	chr1A	89.109	101	8	3	2058	2158	281357608	281357511	3.930000e-24	122.0
7	TraesCS1A01G092200	chr1A	93.750	48	2	1	804	851	84485526	84485572	1.440000e-08	71.3
8	TraesCS1A01G092200	chr1A	93.750	48	2	1	804	851	84622727	84622773	1.440000e-08	71.3
9	TraesCS1A01G092200	chr1D	91.509	2061	95	25	3	2016	88243711	88241684	0.000000e+00	2763.0
10	TraesCS1A01G092200	chr1D	86.795	727	41	11	3	695	88281863	88281158	0.000000e+00	760.0
11	TraesCS1A01G092200	chr1D	90.186	377	27	3	2352	2719	88226486	88226111	1.560000e-132	483.0
12	TraesCS1A01G092200	chr1D	85.965	228	11	13	479	695	88215804	88216021	1.050000e-54	224.0
13	TraesCS1A01G092200	chr1D	89.216	102	8	3	2058	2157	104577202	104577302	1.090000e-24	124.0
14	TraesCS1A01G092200	chr1D	94.444	54	2	1	643	695	87905145	87905198	6.670000e-12	82.4
15	TraesCS1A01G092200	chr4D	87.925	1855	102	41	3	1811	464797268	464795490	0.000000e+00	2073.0
16	TraesCS1A01G092200	chr4D	84.486	477	49	9	2202	2654	464795206	464794731	5.710000e-122	448.0
17	TraesCS1A01G092200	chr1B	92.948	1418	63	14	689	2076	142133063	142131653	0.000000e+00	2030.0
18	TraesCS1A01G092200	chr1B	85.754	716	60	19	3	692	141845707	141846406	0.000000e+00	719.0
19	TraesCS1A01G092200	chr1B	86.441	590	53	9	2155	2719	142131602	142131015	3.180000e-174	621.0
20	TraesCS1A01G092200	chr1B	82.474	679	34	21	58	695	142133748	142133114	1.540000e-142	516.0
21	TraesCS1A01G092200	chr1B	94.792	288	15	0	3	290	142038216	142038503	1.590000e-122	449.0
22	TraesCS1A01G092200	chr1B	94.792	288	15	0	3	290	142094476	142094763	1.590000e-122	449.0
23	TraesCS1A01G092200	chr1B	93.182	176	12	0	2728	2903	142130958	142130783	2.870000e-65	259.0
24	TraesCS1A01G092200	chr1B	82.533	229	27	10	479	696	142102864	142103090	3.820000e-44	189.0
25	TraesCS1A01G092200	chr3B	83.111	225	14	15	482	695	535555350	535555139	1.780000e-42	183.0
26	TraesCS1A01G092200	chr4A	93.258	89	6	0	2073	2161	524080984	524080896	6.530000e-27	132.0
27	TraesCS1A01G092200	chr3D	90.816	98	9	0	2060	2157	561753954	561754051	6.530000e-27	132.0
28	TraesCS1A01G092200	chr3D	89.796	98	8	2	2072	2169	526827419	526827514	1.090000e-24	124.0
29	TraesCS1A01G092200	chr2A	90.291	103	7	2	2063	2164	716179056	716179156	6.530000e-27	132.0
30	TraesCS1A01G092200	chr7A	90.816	98	7	2	2060	2157	473897587	473897492	2.350000e-26	130.0
31	TraesCS1A01G092200	chr7A	85.714	77	8	2	2432	2505	675125291	675125367	8.620000e-11	78.7
32	TraesCS1A01G092200	chr6A	90.000	100	9	1	2063	2161	579019669	579019570	8.440000e-26	128.0
33	TraesCS1A01G092200	chr6A	91.071	56	5	0	2438	2493	377857952	377858007	3.100000e-10	76.8
34	TraesCS1A01G092200	chr3A	89.796	98	8	2	2072	2169	661044295	661044390	1.090000e-24	124.0

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	TraesCS1A01G092200	chr1A	84793075	84795977	2902	True	5361.000000	5361	100.000000	1	2903	1	chr1A.!!$R1	2902
1	TraesCS1A01G092200	chr1A	85005206	85005861	655	True	1079.000000	1079	96.114000	1	669	1	chr1A.!!$R2	668
2	TraesCS1A01G092200	chr1A	84621664	84622773	1109	False	260.766667	446	92.339667	1	851	3	chr1A.!!$F2	850
3	TraesCS1A01G092200	chr1A	84484467	84485572	1105	False	256.766667	440	92.074000	1	851	3	chr1A.!!$F1	850
4	TraesCS1A01G092200	chr1D	88241684	88243711	2027	True	2763.000000	2763	91.509000	3	2016	1	chr1D.!!$R2	2013
5	TraesCS1A01G092200	chr1D	88281158	88281863	705	True	760.000000	760	86.795000	3	695	1	chr1D.!!$R3	692
6	TraesCS1A01G092200	chr4D	464794731	464797268	2537	True	1260.500000	2073	86.205500	3	2654	2	chr4D.!!$R1	2651
7	TraesCS1A01G092200	chr1B	142130783	142133748	2965	True	856.500000	2030	88.761250	58	2903	4	chr1B.!!$R1	2845
8	TraesCS1A01G092200	chr1B	141845707	141846406	699	False	719.000000	719	85.754000	3	692	1	chr1B.!!$F1	689

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
516	751	2.093658	GGTTGAGCTTTCTATGACCGGA	60.094	50.0	9.46	0.0	0.0	5.14	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2163	2564	0.107848	TAAAGCGCACCTTAGCCTCC	60.108	55.0	11.47	0.0	32.2	4.3	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
409	464	2.096496	GCAATCAGTGATTCACCCTTCG	59.904	50.000	15.60	3.56	34.49	3.79
516	751	2.093658	GGTTGAGCTTTCTATGACCGGA	60.094	50.000	9.46	0.00	0.00	5.14
533	777	3.452627	ACCGGACTGAATCTGCTAATCTT	59.547	43.478	9.46	0.00	31.52	2.40
706	1008	7.128331	CACAACAGTAACAGATTTCACTGAAG	58.872	38.462	7.52	2.52	40.67	3.02
911	1238	3.243704	CGATCAATCCTCACCTCTTCTCC	60.244	52.174	0.00	0.00	0.00	3.71
929	1256	2.860735	CTCCGCAGTTGCAAGTCTATAC	59.139	50.000	3.08	0.00	42.21	1.47
1017	1346	1.347378	GAGATGGCTCTTCCTCATCCC	59.653	57.143	0.00	0.00	38.33	3.85
1039	1368	0.450983	GCTTCTGTCCTGCATCTTGC	59.549	55.000	0.00	0.00	45.29	4.01
1069	1414	0.392193	CCCAGGTGACTCATCAGTGC	60.392	60.000	0.00	0.00	40.21	4.40
1072	1417	1.374631	GGTGACTCATCAGTGCGCA	60.375	57.895	5.66	5.66	34.75	6.09
1084	1429	0.241749	AGTGCGCATGTGAAATGTGG	59.758	50.000	15.91	0.00	0.00	4.17
1091	1436	2.557924	GCATGTGAAATGTGGTGAAGGA	59.442	45.455	0.00	0.00	0.00	3.36
1100	1445	2.457598	TGTGGTGAAGGACTAGCTAGG	58.542	52.381	24.35	7.13	0.00	3.02
1148	1500	1.850377	TGTGCAGCGTTTCATTTTGG	58.150	45.000	0.00	0.00	0.00	3.28
1155	1507	1.269517	GCGTTTCATTTTGGTGCAGGA	60.270	47.619	0.00	0.00	0.00	3.86
1282	1634	1.301293	GGTGGCTTCTTCCTCCCTG	59.699	63.158	0.00	0.00	34.51	4.45
1287	1639	3.689002	CTTCTTCCTCCCTGCGGGC	62.689	68.421	5.85	0.00	43.94	6.13
1364	1725	4.389576	CTGCAACTTCGCGGGCAC	62.390	66.667	6.13	0.00	34.46	5.01
1779	2140	2.759973	TCGCGGCTCTTCAGGGAT	60.760	61.111	6.13	0.00	0.00	3.85
1806	2167	1.008767	GGCCTACTACAGCTACGCG	60.009	63.158	3.53	3.53	0.00	6.01
1866	2227	1.612463	GAGTACGTGGTCACCTTCTGT	59.388	52.381	0.00	0.00	0.00	3.41
1881	2242	1.990060	CTGTCCGTCCAGATGGGGT	60.990	63.158	6.07	0.00	38.05	4.95
1886	2247	1.447643	CGTCCAGATGGGGTGATCC	59.552	63.158	0.00	0.00	37.22	3.36
1906	2267	0.178967	TGTGGCCCAGATTTGAGCAA	60.179	50.000	0.00	0.00	0.00	3.91
1978	2345	8.591114	ACTCCGTATATGTATTTATACCTGCT	57.409	34.615	0.00	0.00	33.37	4.24
1979	2346	8.467598	ACTCCGTATATGTATTTATACCTGCTG	58.532	37.037	0.00	0.00	33.37	4.41
1980	2347	8.357290	TCCGTATATGTATTTATACCTGCTGT	57.643	34.615	0.00	0.00	33.37	4.40
2061	2462	6.386654	ACATGTACTATTTTCCCGCAAAAAG	58.613	36.000	0.00	1.39	37.52	2.27
2076	2477	7.225931	TCCCGCAAAAAGATAATACATGTACTC	59.774	37.037	7.96	5.82	0.00	2.59
2077	2478	7.352739	CCGCAAAAAGATAATACATGTACTCC	58.647	38.462	7.96	0.00	0.00	3.85
2078	2479	7.352739	CGCAAAAAGATAATACATGTACTCCC	58.647	38.462	7.96	0.00	0.00	4.30
2080	2481	8.560374	GCAAAAAGATAATACATGTACTCCCTC	58.440	37.037	7.96	1.63	0.00	4.30
2081	2482	9.057089	CAAAAAGATAATACATGTACTCCCTCC	57.943	37.037	7.96	0.00	0.00	4.30
2082	2483	6.591750	AAGATAATACATGTACTCCCTCCG	57.408	41.667	7.96	0.00	0.00	4.63
2083	2484	5.642165	AGATAATACATGTACTCCCTCCGT	58.358	41.667	7.96	0.00	0.00	4.69
2084	2485	5.711036	AGATAATACATGTACTCCCTCCGTC	59.289	44.000	7.96	0.00	0.00	4.79
2085	2486	2.062971	TACATGTACTCCCTCCGTCC	57.937	55.000	0.08	0.00	0.00	4.79
2086	2487	0.686769	ACATGTACTCCCTCCGTCCC	60.687	60.000	0.00	0.00	0.00	4.46
2093	2494	2.488836	ACTCCCTCCGTCCCAAAATAT	58.511	47.619	0.00	0.00	0.00	1.28
2095	2496	4.042174	ACTCCCTCCGTCCCAAAATATAA	58.958	43.478	0.00	0.00	0.00	0.98
2096	2497	4.102681	ACTCCCTCCGTCCCAAAATATAAG	59.897	45.833	0.00	0.00	0.00	1.73
2097	2498	4.300345	TCCCTCCGTCCCAAAATATAAGA	58.700	43.478	0.00	0.00	0.00	2.10
2098	2499	4.722781	TCCCTCCGTCCCAAAATATAAGAA	59.277	41.667	0.00	0.00	0.00	2.52
2099	2500	4.820173	CCCTCCGTCCCAAAATATAAGAAC	59.180	45.833	0.00	0.00	0.00	3.01
2100	2501	4.510340	CCTCCGTCCCAAAATATAAGAACG	59.490	45.833	0.00	0.00	0.00	3.95
2101	2502	5.088680	TCCGTCCCAAAATATAAGAACGT	57.911	39.130	0.00	0.00	0.00	3.99
2102	2503	5.490159	TCCGTCCCAAAATATAAGAACGTT	58.510	37.500	0.00	0.00	0.00	3.99
2103	2504	5.939296	TCCGTCCCAAAATATAAGAACGTTT	59.061	36.000	0.46	0.00	0.00	3.60
2104	2505	6.430616	TCCGTCCCAAAATATAAGAACGTTTT	59.569	34.615	0.46	0.00	0.00	2.43
2105	2506	7.040548	TCCGTCCCAAAATATAAGAACGTTTTT	60.041	33.333	9.22	9.22	0.00	1.94
2106	2507	8.235905	CCGTCCCAAAATATAAGAACGTTTTTA	58.764	33.333	13.02	13.02	0.00	1.52
2107	2508	9.609950	CGTCCCAAAATATAAGAACGTTTTTAA	57.390	29.630	14.41	5.85	0.00	1.52
2181	2582	1.377333	GGAGGCTAAGGTGCGCTTT	60.377	57.895	9.73	0.00	0.00	3.51
2182	2583	0.107848	GGAGGCTAAGGTGCGCTTTA	60.108	55.000	9.73	1.62	0.00	1.85
2204	2625	1.135972	CGCGCTGCTCTTTATTTGTGT	60.136	47.619	5.56	0.00	0.00	3.72
2208	2629	4.337763	CGCTGCTCTTTATTTGTGTGATC	58.662	43.478	0.00	0.00	0.00	2.92
2264	2692	5.983540	TGCTTTTGGTTTGGTTTTATCTGT	58.016	33.333	0.00	0.00	0.00	3.41
2265	2693	5.814705	TGCTTTTGGTTTGGTTTTATCTGTG	59.185	36.000	0.00	0.00	0.00	3.66
2269	2697	5.923733	TGGTTTGGTTTTATCTGTGTTGT	57.076	34.783	0.00	0.00	0.00	3.32
2276	2704	6.119536	TGGTTTTATCTGTGTTGTCTTGAGT	58.880	36.000	0.00	0.00	0.00	3.41
2281	2709	8.506168	TTTATCTGTGTTGTCTTGAGTTTTCT	57.494	30.769	0.00	0.00	0.00	2.52
2329	2761	6.307077	GCACGGATTTTCAATGTAAAAGGTAC	59.693	38.462	0.00	0.00	32.20	3.34
2354	2800	9.814899	ACAAATCAAACAAACACATATTCAAGA	57.185	25.926	0.00	0.00	0.00	3.02
2366	2812	0.754217	ATTCAAGATGGCATGGCGCT	60.754	50.000	15.27	11.52	41.91	5.92
2475	2921	1.601903	TGTTGCGATGTTGTTGGAGAC	59.398	47.619	0.00	0.00	0.00	3.36
2476	2922	1.601903	GTTGCGATGTTGTTGGAGACA	59.398	47.619	0.00	0.00	39.83	3.41
2496	2942	4.579869	ACAATATTTGTTCCGAGAGCAGT	58.420	39.130	0.00	0.00	42.22	4.40
2546	2992	9.667107	CTTGACTTGACTATACCAATTAAGGAA	57.333	33.333	0.00	0.00	0.00	3.36
2616	3062	7.110043	TGCTCAATGTTAATTGCCATAATGA	57.890	32.000	0.00	0.00	42.55	2.57
2670	3117	7.637709	GTATTGAACCAATTCTGAAAACCAC	57.362	36.000	0.00	0.00	35.54	4.16
2690	3137	4.421058	CACGTCCTCAATCGATGAAACTA	58.579	43.478	0.00	0.00	37.67	2.24
2704	3151	7.231607	TCGATGAAACTAAAACGATAGCAAAC	58.768	34.615	0.00	0.00	42.67	2.93
2726	3173	1.286880	GCACATGCACCCAGTGAAC	59.713	57.895	12.81	0.00	41.59	3.18
2728	3175	0.594602	CACATGCACCCAGTGAACAG	59.405	55.000	0.00	0.00	35.23	3.16
2735	3230	1.302832	CCCAGTGAACAGGAGCACC	60.303	63.158	0.00	0.00	35.67	5.01
2757	3252	4.423732	CAAAAGAAATACCGGCATTCCAG	58.576	43.478	0.00	0.00	0.00	3.86
2759	3254	3.366052	AGAAATACCGGCATTCCAGTT	57.634	42.857	0.00	0.00	0.00	3.16
2773	3268	5.177696	GCATTCCAGTTGATATCGTAACTCC	59.822	44.000	5.66	0.00	35.08	3.85
2856	3351	0.668535	AAACTTTCTTGAGCACGGGC	59.331	50.000	0.00	0.00	41.61	6.13

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
409	464	8.629158	TCATGTAATTTCCATGCTACAATAACC	58.371	33.333	11.14	0.00	39.60	2.85
516	751	7.750229	TTTCAACAAGATTAGCAGATTCAGT	57.250	32.000	0.00	0.00	0.00	3.41
698	1000	4.090761	AGTGCCATCTTTTCTTCAGTGA	57.909	40.909	0.00	0.00	0.00	3.41
706	1008	9.937175	GTAATTATCTGTTAGTGCCATCTTTTC	57.063	33.333	0.00	0.00	0.00	2.29
911	1238	4.394795	GTTTGTATAGACTTGCAACTGCG	58.605	43.478	0.00	0.00	45.83	5.18
929	1256	6.480524	TGAACTGATATGAAACGAGGTTTG	57.519	37.500	0.00	0.00	35.77	2.93
1010	1339	0.179936	GGACAGAAGCAGGGGATGAG	59.820	60.000	0.00	0.00	0.00	2.90
1013	1342	1.919600	GCAGGACAGAAGCAGGGGAT	61.920	60.000	0.00	0.00	0.00	3.85
1017	1346	0.252479	AGATGCAGGACAGAAGCAGG	59.748	55.000	0.00	0.00	42.14	4.85
1039	1368	3.007920	ACCTGGGAGAGCCAGCAG	61.008	66.667	0.00	0.00	35.15	4.24
1069	1414	2.587956	CTTCACCACATTTCACATGCG	58.412	47.619	0.00	0.00	0.00	4.73
1072	1417	4.104383	AGTCCTTCACCACATTTCACAT	57.896	40.909	0.00	0.00	0.00	3.21
1084	1429	3.560896	CGAGTACCTAGCTAGTCCTTCAC	59.439	52.174	19.31	7.55	0.00	3.18
1091	1436	2.171027	AGCAGTCGAGTACCTAGCTAGT	59.829	50.000	19.31	10.02	31.68	2.57
1100	1445	0.435008	CAAACGCAGCAGTCGAGTAC	59.565	55.000	0.00	0.00	0.00	2.73
1266	1618	2.959484	CGCAGGGAGGAAGAAGCCA	61.959	63.158	0.00	0.00	0.00	4.75
1866	2227	1.002921	ATCACCCCATCTGGACGGA	59.997	57.895	0.00	0.00	37.39	4.69
1886	2247	2.187073	GCTCAAATCTGGGCCACAG	58.813	57.895	0.00	10.15	43.96	3.66
1978	2345	7.762382	TGTCAACACAAAATATTACACACACA	58.238	30.769	0.00	0.00	0.00	3.72
1979	2346	8.795786	ATGTCAACACAAAATATTACACACAC	57.204	30.769	0.00	0.00	35.64	3.82
2061	2462	5.105837	GGACGGAGGGAGTACATGTATTATC	60.106	48.000	9.18	7.84	0.00	1.75
2076	2477	4.699925	TCTTATATTTTGGGACGGAGGG	57.300	45.455	0.00	0.00	0.00	4.30
2077	2478	4.510340	CGTTCTTATATTTTGGGACGGAGG	59.490	45.833	0.00	0.00	0.00	4.30
2078	2479	5.114081	ACGTTCTTATATTTTGGGACGGAG	58.886	41.667	0.00	0.00	0.00	4.63
2080	2481	5.806366	AACGTTCTTATATTTTGGGACGG	57.194	39.130	0.00	0.00	0.00	4.79
2081	2482	9.609950	TTAAAAACGTTCTTATATTTTGGGACG	57.390	29.630	0.00	0.00	0.00	4.79
2139	2540	9.931698	TCCAAATAGTACTTCCTCTGTCTTATA	57.068	33.333	0.00	0.00	0.00	0.98
2140	2541	8.840200	TCCAAATAGTACTTCCTCTGTCTTAT	57.160	34.615	0.00	0.00	0.00	1.73
2141	2542	7.342284	CCTCCAAATAGTACTTCCTCTGTCTTA	59.658	40.741	0.00	0.00	0.00	2.10
2142	2543	6.155393	CCTCCAAATAGTACTTCCTCTGTCTT	59.845	42.308	0.00	0.00	0.00	3.01
2143	2544	5.659079	CCTCCAAATAGTACTTCCTCTGTCT	59.341	44.000	0.00	0.00	0.00	3.41
2144	2545	5.682730	GCCTCCAAATAGTACTTCCTCTGTC	60.683	48.000	0.00	0.00	0.00	3.51
2145	2546	4.162509	GCCTCCAAATAGTACTTCCTCTGT	59.837	45.833	0.00	0.00	0.00	3.41
2146	2547	4.407296	AGCCTCCAAATAGTACTTCCTCTG	59.593	45.833	0.00	0.00	0.00	3.35
2147	2548	4.625963	AGCCTCCAAATAGTACTTCCTCT	58.374	43.478	0.00	0.00	0.00	3.69
2148	2549	6.463190	CCTTAGCCTCCAAATAGTACTTCCTC	60.463	46.154	0.00	0.00	0.00	3.71
2149	2550	5.367060	CCTTAGCCTCCAAATAGTACTTCCT	59.633	44.000	0.00	0.00	0.00	3.36
2150	2551	5.130643	ACCTTAGCCTCCAAATAGTACTTCC	59.869	44.000	0.00	0.00	0.00	3.46
2151	2552	6.049790	CACCTTAGCCTCCAAATAGTACTTC	58.950	44.000	0.00	0.00	0.00	3.01
2152	2553	5.629366	GCACCTTAGCCTCCAAATAGTACTT	60.629	44.000	0.00	0.00	0.00	2.24
2153	2554	4.141688	GCACCTTAGCCTCCAAATAGTACT	60.142	45.833	0.00	0.00	0.00	2.73
2163	2564	0.107848	TAAAGCGCACCTTAGCCTCC	60.108	55.000	11.47	0.00	32.20	4.30
2181	2582	1.663643	CAAATAAAGAGCAGCGCGGTA	59.336	47.619	11.92	0.00	0.00	4.02
2182	2583	0.447801	CAAATAAAGAGCAGCGCGGT	59.552	50.000	4.23	4.23	0.00	5.68
2191	2592	8.562892	ACAAGAGTTGATCACACAAATAAAGAG	58.437	33.333	0.00	0.00	0.00	2.85
2204	2625	7.389803	TGTCAAAGAAAACAAGAGTTGATCA	57.610	32.000	0.00	0.00	38.17	2.92
2208	2629	5.954335	ACCTGTCAAAGAAAACAAGAGTTG	58.046	37.500	0.00	0.00	38.17	3.16
2243	2670	7.333174	ACAACACAGATAAAACCAAACCAAAAG	59.667	33.333	0.00	0.00	0.00	2.27
2254	2682	8.911247	AAAACTCAAGACAACACAGATAAAAC	57.089	30.769	0.00	0.00	0.00	2.43
2306	2735	7.513371	TGTACCTTTTACATTGAAAATCCGT	57.487	32.000	0.00	0.00	0.00	4.69
2348	2780	3.199551	GCGCCATGCCATCTTGAA	58.800	55.556	0.00	0.00	37.76	2.69
2453	2899	0.306228	TCCAACAACATCGCAACACG	59.694	50.000	0.00	0.00	45.62	4.49
2475	2921	4.393062	ACACTGCTCTCGGAACAAATATTG	59.607	41.667	0.00	0.00	0.00	1.90
2476	2922	4.393062	CACACTGCTCTCGGAACAAATATT	59.607	41.667	0.00	0.00	0.00	1.28
2559	3005	9.136323	GAATAGGGACACTAAAATGAATGGAAT	57.864	33.333	0.00	0.00	34.79	3.01
2616	3062	1.550976	GCAGTAGCCTGGAGTTGTACT	59.449	52.381	0.00	0.00	39.22	2.73
2654	3100	2.884639	AGGACGTGGTTTTCAGAATTGG	59.115	45.455	0.00	0.00	0.00	3.16
2660	3106	2.157668	CGATTGAGGACGTGGTTTTCAG	59.842	50.000	0.00	0.00	0.00	3.02
2666	3113	1.182667	TCATCGATTGAGGACGTGGT	58.817	50.000	0.00	0.00	28.20	4.16
2670	3117	6.241385	GTTTTAGTTTCATCGATTGAGGACG	58.759	40.000	0.00	0.00	34.07	4.79
2719	3166	1.679139	TTTGGTGCTCCTGTTCACTG	58.321	50.000	6.34	0.00	33.91	3.66
2721	3168	2.297701	TCTTTTGGTGCTCCTGTTCAC	58.702	47.619	6.34	0.00	34.23	3.18
2722	3169	2.727123	TCTTTTGGTGCTCCTGTTCA	57.273	45.000	6.34	0.00	34.23	3.18
2723	3170	4.590850	ATTTCTTTTGGTGCTCCTGTTC	57.409	40.909	6.34	0.00	34.23	3.18
2724	3171	4.280929	GGTATTTCTTTTGGTGCTCCTGTT	59.719	41.667	6.34	0.00	34.23	3.16
2726	3173	3.119849	CGGTATTTCTTTTGGTGCTCCTG	60.120	47.826	6.34	0.00	34.23	3.86
2728	3175	2.163613	CCGGTATTTCTTTTGGTGCTCC	59.836	50.000	0.00	0.00	0.00	4.70
2735	3230	4.423732	CTGGAATGCCGGTATTTCTTTTG	58.576	43.478	22.39	8.17	35.70	2.44
2757	3252	5.231568	CAGGTTTCGGAGTTACGATATCAAC	59.768	44.000	3.12	0.75	43.11	3.18
2759	3254	4.400251	ACAGGTTTCGGAGTTACGATATCA	59.600	41.667	3.12	0.00	43.11	2.15
2773	3268	9.893305	AAATTATTTAAGTTCTCACAGGTTTCG	57.107	29.630	0.00	0.00	0.00	3.46
2875	3370	8.488308	AGGTAGTTTTTGAAGAGTAGGAGTTA	57.512	34.615	0.00	0.00	0.00	2.24

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.