AutoCloner

Multiple sequence alignment - TraesCS2A01G343300

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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	TraesCS2A01G343300	chr2A	100.000	3884	0	0	1	3884	580251131	580255014	0.000000e+00	7173.0
1	TraesCS2A01G343300	chr2A	87.482	679	77	4	2207	2885	580282077	580282747	0.000000e+00	776.0
2	TraesCS2A01G343300	chr2A	86.634	621	83	0	2258	2878	580324441	580325061	0.000000e+00	688.0
3	TraesCS2A01G343300	chr2A	79.076	368	51	17	1001	1364	580322479	580322824	3.020000e-56	230.0
4	TraesCS2A01G343300	chr2A	86.034	179	23	2	1007	1184	580281237	580281414	1.420000e-44	191.0
5	TraesCS2A01G343300	chr2A	98.039	102	2	0	3065	3166	580279063	580279164	1.110000e-40	178.0
6	TraesCS2A01G343300	chr2A	94.030	67	3	1	641	706	580251709	580251775	2.470000e-17	100.0
7	TraesCS2A01G343300	chr2A	94.030	67	3	1	579	645	580251771	580251836	2.470000e-17	100.0
8	TraesCS2A01G343300	chr2D	92.953	2994	116	42	2	2973	413262987	413265907	0.000000e+00	4272.0
9	TraesCS2A01G343300	chr2D	92.618	718	51	2	3167	3884	11302192	11301477	0.000000e+00	1031.0
10	TraesCS2A01G343300	chr2D	86.892	679	81	4	2207	2885	413274495	413275165	0.000000e+00	754.0
11	TraesCS2A01G343300	chr2D	86.349	630	77	6	2258	2878	413290575	413291204	0.000000e+00	678.0
12	TraesCS2A01G343300	chr2D	78.605	631	116	13	2259	2878	413774432	413775054	2.170000e-107	399.0
13	TraesCS2A01G343300	chr2D	79.564	367	51	15	1001	1364	413288624	413288969	1.390000e-59	241.0
14	TraesCS2A01G343300	chr2D	82.083	240	37	5	1007	1245	413273629	413273863	2.370000e-47	200.0
15	TraesCS2A01G343300	chr2D	91.729	133	3	5	2962	3086	413266809	413266941	1.110000e-40	178.0
16	TraesCS2A01G343300	chr2D	92.500	80	4	1	3087	3166	413266972	413267049	3.170000e-21	113.0
17	TraesCS2A01G343300	chr2D	94.030	67	3	1	641	706	413263551	413263617	2.470000e-17	100.0
18	TraesCS2A01G343300	chr2D	94.030	67	3	1	579	645	413263613	413263678	2.470000e-17	100.0
19	TraesCS2A01G343300	chr2B	92.650	1415	73	13	567	1964	486584491	486585891	0.000000e+00	2008.0
20	TraesCS2A01G343300	chr2B	94.922	1024	44	5	2065	3087	486588628	486589644	0.000000e+00	1596.0
21	TraesCS2A01G343300	chr2B	91.798	573	21	12	1	570	486583862	486584411	0.000000e+00	774.0
22	TraesCS2A01G343300	chr2B	86.529	631	74	8	2258	2878	486770897	486771526	0.000000e+00	684.0
23	TraesCS2A01G343300	chr2B	79.618	628	114	10	2258	2878	486966056	486966676	4.610000e-119	438.0
24	TraesCS2A01G343300	chr2B	81.590	239	36	4	1007	1245	486741522	486741752	1.420000e-44	191.0
25	TraesCS2A01G343300	chr2B	76.567	367	63	15	1001	1364	486768813	486769159	3.080000e-41	180.0
26	TraesCS2A01G343300	chr2B	97.015	67	1	1	579	645	486584565	486584630	1.140000e-20	111.0
27	TraesCS2A01G343300	chrUn	91.011	712	56	8	3174	3884	108916112	108915408	0.000000e+00	953.0
28	TraesCS2A01G343300	chr6D	88.858	718	76	4	3167	3884	375023639	375022926	0.000000e+00	880.0
29	TraesCS2A01G343300	chr1A	87.744	718	83	5	3167	3884	533332325	533331613	0.000000e+00	833.0
30	TraesCS2A01G343300	chr3B	86.602	724	85	10	3167	3884	23405563	23404846	0.000000e+00	789.0
31	TraesCS2A01G343300	chr3B	85.953	719	99	2	3167	3884	655338040	655338757	0.000000e+00	767.0
32	TraesCS2A01G343300	chr7B	85.593	708	95	6	3180	3884	118007553	118006850	0.000000e+00	736.0
33	TraesCS2A01G343300	chr7B	85.263	95	8	2	1067	1161	72435945	72436033	4.130000e-15	93.5
34	TraesCS2A01G343300	chr7D	90.323	496	46	2	3167	3662	572301235	572301728	0.000000e+00	649.0
35	TraesCS2A01G343300	chr5B	81.320	712	131	2	3174	3884	50247024	50246314	9.360000e-161	577.0

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	TraesCS2A01G343300	chr2A	580251131	580255014	3883	False	2457.666667	7173	96.020000	1	3884	3	chr2A.!!$F1	3883
1	TraesCS2A01G343300	chr2A	580322479	580325061	2582	False	459.000000	688	82.855000	1001	2878	2	chr2A.!!$F3	1877
2	TraesCS2A01G343300	chr2A	580279063	580282747	3684	False	381.666667	776	90.518333	1007	3166	3	chr2A.!!$F2	2159
3	TraesCS2A01G343300	chr2D	11301477	11302192	715	True	1031.000000	1031	92.618000	3167	3884	1	chr2D.!!$R1	717
4	TraesCS2A01G343300	chr2D	413262987	413267049	4062	False	952.600000	4272	93.048400	2	3166	5	chr2D.!!$F2	3164
5	TraesCS2A01G343300	chr2D	413273629	413275165	1536	False	477.000000	754	84.487500	1007	2885	2	chr2D.!!$F3	1878
6	TraesCS2A01G343300	chr2D	413288624	413291204	2580	False	459.500000	678	82.956500	1001	2878	2	chr2D.!!$F4	1877
7	TraesCS2A01G343300	chr2D	413774432	413775054	622	False	399.000000	399	78.605000	2259	2878	1	chr2D.!!$F1	619
8	TraesCS2A01G343300	chr2B	486583862	486589644	5782	False	1122.250000	2008	94.096250	1	3087	4	chr2B.!!$F3	3086
9	TraesCS2A01G343300	chr2B	486966056	486966676	620	False	438.000000	438	79.618000	2258	2878	1	chr2B.!!$F2	620
10	TraesCS2A01G343300	chr2B	486768813	486771526	2713	False	432.000000	684	81.548000	1001	2878	2	chr2B.!!$F4	1877
11	TraesCS2A01G343300	chrUn	108915408	108916112	704	True	953.000000	953	91.011000	3174	3884	1	chrUn.!!$R1	710
12	TraesCS2A01G343300	chr6D	375022926	375023639	713	True	880.000000	880	88.858000	3167	3884	1	chr6D.!!$R1	717
13	TraesCS2A01G343300	chr1A	533331613	533332325	712	True	833.000000	833	87.744000	3167	3884	1	chr1A.!!$R1	717
14	TraesCS2A01G343300	chr3B	23404846	23405563	717	True	789.000000	789	86.602000	3167	3884	1	chr3B.!!$R1	717
15	TraesCS2A01G343300	chr3B	655338040	655338757	717	False	767.000000	767	85.953000	3167	3884	1	chr3B.!!$F1	717
16	TraesCS2A01G343300	chr7B	118006850	118007553	703	True	736.000000	736	85.593000	3180	3884	1	chr7B.!!$R1	704
17	TraesCS2A01G343300	chr5B	50246314	50247024	710	True	577.000000	577	81.320000	3174	3884	1	chr5B.!!$R1	710

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
464	469	1.140052	TGGAAGCAGAAACCACTTCGA	59.860	47.619	0.0	0.0	40.57	3.71	F
1766	3007	1.518792	GCTCGACGGGAAAGCCTAC	60.519	63.158	0.0	0.0	0.00	3.18	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2310	7211	1.659954	GCGGATGCTGAGCTCGTAG	60.660	63.158	9.64	2.68	38.39	3.51	R
3144	9025	0.107831	GCCTGTAATATGCCCGTCCA	59.892	55.000	0.00	0.00	0.00	4.02	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	79	4.097437	GGCAATTCTTCTGATCTGCATTCA	59.903	41.667	0.00	0.00	34.03	2.57
135	136	8.946085	CCAATAAGCCGTGTGTATTTGATATAT	58.054	33.333	0.00	0.00	0.00	0.86
333	336	8.058915	CGCTTCTTACTTTCTTATTAGTCATGC	58.941	37.037	0.00	0.00	0.00	4.06
334	337	8.058915	GCTTCTTACTTTCTTATTAGTCATGCG	58.941	37.037	0.00	0.00	0.00	4.73
462	467	3.130340	TGTTTGGAAGCAGAAACCACTTC	59.870	43.478	0.00	0.00	39.25	3.01
463	468	1.593196	TGGAAGCAGAAACCACTTCG	58.407	50.000	0.00	0.00	40.57	3.79
464	469	1.140052	TGGAAGCAGAAACCACTTCGA	59.860	47.619	0.00	0.00	40.57	3.71
465	470	2.224523	TGGAAGCAGAAACCACTTCGAT	60.225	45.455	0.00	0.00	40.57	3.59
466	471	2.160417	GGAAGCAGAAACCACTTCGATG	59.840	50.000	0.00	0.00	40.57	3.84
470	475	2.413453	GCAGAAACCACTTCGATGTCTC	59.587	50.000	0.13	0.00	39.22	3.36
487	502	3.056250	TGTCTCTCAGCCTGATTGAACTC	60.056	47.826	0.00	0.00	0.00	3.01
550	565	2.825532	TGCCTGAAGGAAATACTTTGCC	59.174	45.455	0.00	0.00	37.39	4.52
563	578	6.809630	AATACTTTGCCTCTCAGAAAAGAC	57.190	37.500	4.61	0.00	34.47	3.01
613	711	7.268586	GCATACAAGGAGAAAACTAGATGAGA	58.731	38.462	0.00	0.00	0.00	3.27
716	814	2.279784	CGGGAGATGAAGCGAGCC	60.280	66.667	0.00	0.00	0.00	4.70
844	942	5.532779	ACTTGATCAAGAGTTTTGACTTCCC	59.467	40.000	36.15	0.00	40.79	3.97
1158	2330	3.462678	GGAGCCACCCTCGTCTCC	61.463	72.222	0.00	0.00	41.71	3.71
1266	2442	5.637006	TGTTGTTGTTCTTGTTGCTTAGT	57.363	34.783	0.00	0.00	0.00	2.24
1276	2454	5.647589	TCTTGTTGCTTAGTAGGTCATACG	58.352	41.667	0.00	0.00	39.55	3.06
1360	2541	5.410924	TGTAAGATCACGAATTCCTCTGTG	58.589	41.667	0.00	2.47	32.94	3.66
1363	2544	4.899502	AGATCACGAATTCCTCTGTGTTT	58.100	39.130	9.95	1.92	33.24	2.83
1364	2545	5.308825	AGATCACGAATTCCTCTGTGTTTT	58.691	37.500	9.95	0.00	33.24	2.43
1365	2546	5.765182	AGATCACGAATTCCTCTGTGTTTTT	59.235	36.000	9.95	0.00	33.24	1.94
1517	2722	2.185004	ACACGCACAGCTAAAAGGAT	57.815	45.000	0.00	0.00	0.00	3.24
1518	2723	3.328382	ACACGCACAGCTAAAAGGATA	57.672	42.857	0.00	0.00	0.00	2.59
1519	2724	3.670625	ACACGCACAGCTAAAAGGATAA	58.329	40.909	0.00	0.00	0.00	1.75
1520	2725	4.069304	ACACGCACAGCTAAAAGGATAAA	58.931	39.130	0.00	0.00	0.00	1.40
1536	2741	7.732222	AAGGATAAATAAAACAATGCAGGGA	57.268	32.000	0.00	0.00	0.00	4.20
1540	2745	7.814587	GGATAAATAAAACAATGCAGGGATAGC	59.185	37.037	0.00	0.00	0.00	2.97
1766	3007	1.518792	GCTCGACGGGAAAGCCTAC	60.519	63.158	0.00	0.00	0.00	3.18
1812	3056	2.632377	ACTCCATTCACGGTATGCTTG	58.368	47.619	0.00	0.00	0.00	4.01
1814	3058	2.609459	CTCCATTCACGGTATGCTTGAC	59.391	50.000	0.00	0.00	0.00	3.18
1820	3064	2.299013	TCACGGTATGCTTGACACTTCT	59.701	45.455	0.00	0.00	0.00	2.85
1852	3096	9.853177	ACTTCCTTTATTTATAATGGGAGTGAG	57.147	33.333	19.85	10.98	46.51	3.51
1853	3097	9.853177	CTTCCTTTATTTATAATGGGAGTGAGT	57.147	33.333	11.81	0.00	37.93	3.41
1854	3098	9.627123	TTCCTTTATTTATAATGGGAGTGAGTG	57.373	33.333	12.08	0.00	37.85	3.51
1948	3214	3.179265	CAAGGAGTACGTGCGCGG	61.179	66.667	25.20	6.07	43.45	6.46
2059	5959	3.356290	GGCCACATGTCCAAAGTTCTAT	58.644	45.455	0.00	0.00	0.00	1.98
2060	5960	4.523083	GGCCACATGTCCAAAGTTCTATA	58.477	43.478	0.00	0.00	0.00	1.31
2061	5961	4.576463	GGCCACATGTCCAAAGTTCTATAG	59.424	45.833	0.00	0.00	0.00	1.31
2092	6001	5.576447	TCTTGCACGTCAGTTGATCTATA	57.424	39.130	0.00	0.00	0.00	1.31
2102	6011	8.197439	ACGTCAGTTGATCTATATTCATGACAA	58.803	33.333	0.00	0.00	34.80	3.18
2122	6031	8.109705	TGACAACTCGGTGTAAAATACTACTA	57.890	34.615	0.00	0.00	0.00	1.82
2123	6032	8.023128	TGACAACTCGGTGTAAAATACTACTAC	58.977	37.037	0.00	0.00	0.00	2.73
2124	6033	7.885297	ACAACTCGGTGTAAAATACTACTACA	58.115	34.615	0.00	0.00	0.00	2.74
2125	6034	7.809806	ACAACTCGGTGTAAAATACTACTACAC	59.190	37.037	3.54	3.54	43.00	2.90
2178	6091	6.703165	TGCAATACAGTAGCATATTCTCTGTG	59.297	38.462	13.52	0.00	39.27	3.66
2190	7091	8.887717	AGCATATTCTCTGTGTTAGAAAATCAC	58.112	33.333	0.00	0.00	36.60	3.06
2193	7094	7.588143	ATTCTCTGTGTTAGAAAATCACTCG	57.412	36.000	0.00	0.00	36.60	4.18
2527	7431	1.153901	ACCATGTACGACTTCCGCG	60.154	57.895	0.00	0.00	43.32	6.46
2563	7467	2.880879	CGCACATGGAGGTCGTCG	60.881	66.667	0.00	0.00	0.00	5.12
2860	7788	1.282248	CCAGGTGTACAAGCACGACG	61.282	60.000	0.00	0.00	40.08	5.12
2958	7886	6.131264	TGATTATCCTCATTGCAATGAACCT	58.869	36.000	34.91	25.00	44.20	3.50
2961	7889	3.282021	TCCTCATTGCAATGAACCTAGC	58.718	45.455	34.91	0.00	44.20	3.42
3006	8847	6.798427	ATGCTATATGACGACCAATATCCT	57.202	37.500	0.00	0.00	0.00	3.24
3007	8848	5.965922	TGCTATATGACGACCAATATCCTG	58.034	41.667	0.00	0.00	0.00	3.86
3008	8849	5.105351	TGCTATATGACGACCAATATCCTGG	60.105	44.000	0.00	0.00	42.68	4.45
3009	8850	4.826274	ATATGACGACCAATATCCTGGG	57.174	45.455	0.00	0.00	41.16	4.45
3053	8904	0.248539	CTCTCCCGTCGGATTCGTTC	60.249	60.000	14.39	0.00	37.60	3.95
3145	9026	3.141002	GCACACCAGAAATGCTACATG	57.859	47.619	0.00	0.00	36.40	3.21
3160	9041	3.556213	GCTACATGGACGGGCATATTACA	60.556	47.826	0.00	0.00	0.00	2.41
3172	9053	4.935352	GCATATTACAGGCCAATTGGAA	57.065	40.909	29.02	13.16	37.39	3.53
3316	9197	1.202891	AGGAAGTACACCTGGGCAAAC	60.203	52.381	10.19	0.00	36.30	2.93
3344	9225	4.210331	GCCTGAACCCACATATGAGAAAT	58.790	43.478	10.38	0.00	0.00	2.17
3366	9247	9.428097	GAAATTTGACAGAATTTTAATCTGCCT	57.572	29.630	0.00	0.00	46.56	4.75
3398	9280	4.827789	AGACAAATACCCCCTAGCTATGA	58.172	43.478	0.00	0.00	0.00	2.15
3439	9321	3.467483	AGATATCTGACCACACCCCTCTA	59.533	47.826	3.89	0.00	0.00	2.43
3616	9503	5.495926	ACATCAGACAGAAAATCAGAGGT	57.504	39.130	0.00	0.00	0.00	3.85
3619	9506	5.551305	TCAGACAGAAAATCAGAGGTTGA	57.449	39.130	0.00	0.00	40.85	3.18
3728	9617	5.543507	ATGGTCTTAGTGCTCAAGATAGG	57.456	43.478	4.69	0.00	34.67	2.57
3741	9630	5.990996	GCTCAAGATAGGGAGATTCAGAAAG	59.009	44.000	0.00	0.00	32.87	2.62
3742	9631	6.491714	TCAAGATAGGGAGATTCAGAAAGG	57.508	41.667	0.00	0.00	0.00	3.11
3769	9661	6.058833	GGAGGAAAGAACTGAAAGATATCCC	58.941	44.000	0.00	0.00	37.43	3.85
3851	9743	8.435982	GGAGACTCTAATACTAGGTACTACCAA	58.564	40.741	8.01	0.00	41.95	3.67

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
78	79	1.003355	CTGACTGGACCGGCATGTT	60.003	57.895	0.00	0.00	0.00	2.71
135	136	9.995003	AATAATCCACAAGCAAATAAGAAACAA	57.005	25.926	0.00	0.00	0.00	2.83
186	187	2.489938	TACAAAACCCTGCCTAGCTG	57.510	50.000	0.00	0.00	0.00	4.24
187	188	3.518992	TTTACAAAACCCTGCCTAGCT	57.481	42.857	0.00	0.00	0.00	3.32
247	249	1.003233	ACCTGGACGTCCCAAGATTTC	59.997	52.381	31.19	3.87	46.07	2.17
250	252	1.192428	GTACCTGGACGTCCCAAGAT	58.808	55.000	31.19	13.15	46.07	2.40
251	253	0.113776	AGTACCTGGACGTCCCAAGA	59.886	55.000	31.19	12.20	46.07	3.02
252	254	1.749634	CTAGTACCTGGACGTCCCAAG	59.250	57.143	31.19	21.91	46.07	3.61
333	336	1.076332	GATTTCGACACCCCAAGACG	58.924	55.000	0.00	0.00	0.00	4.18
334	337	1.076332	CGATTTCGACACCCCAAGAC	58.924	55.000	0.00	0.00	43.02	3.01
409	414	4.910956	GCATGGAGTGCGTAGACA	57.089	55.556	0.00	0.00	45.23	3.41
417	422	4.778534	AAAGAAACATCTGCATGGAGTG	57.221	40.909	14.43	13.44	33.82	3.51
418	423	5.069516	ACAAAAAGAAACATCTGCATGGAGT	59.930	36.000	14.43	0.00	33.82	3.85
419	424	5.535333	ACAAAAAGAAACATCTGCATGGAG	58.465	37.500	8.12	8.12	33.82	3.86
462	467	2.100418	TCAATCAGGCTGAGAGACATCG	59.900	50.000	23.24	4.87	0.00	3.84
463	468	3.815856	TCAATCAGGCTGAGAGACATC	57.184	47.619	23.24	0.00	0.00	3.06
464	469	3.518705	AGTTCAATCAGGCTGAGAGACAT	59.481	43.478	23.24	10.47	0.00	3.06
465	470	2.902486	AGTTCAATCAGGCTGAGAGACA	59.098	45.455	23.24	10.44	0.00	3.41
466	471	3.520569	GAGTTCAATCAGGCTGAGAGAC	58.479	50.000	23.24	16.87	0.00	3.36
470	475	2.662006	TCGAGTTCAATCAGGCTGAG	57.338	50.000	23.24	10.36	0.00	3.35
487	502	4.775058	AGATTAGCAGTAGCAGGTATCG	57.225	45.455	0.00	0.00	45.49	2.92
550	565	4.238761	TGGTACACGTCTTTTCTGAGAG	57.761	45.455	0.00	0.00	0.00	3.20
613	711	1.789523	TTAGGGCGGCTAGTCTCAAT	58.210	50.000	9.56	0.00	0.00	2.57
716	814	1.331214	ATGGCGGCTAATCCCAAATG	58.669	50.000	11.43	0.00	31.43	2.32
844	942	0.177604	CTCTGCCAGCTCCTACTTGG	59.822	60.000	0.00	0.00	35.06	3.61
1158	2330	2.808315	CCATCAGGGACGAGGACG	59.192	66.667	0.00	0.00	45.75	4.79
1266	2442	6.839124	TCCTACAAGAAAACGTATGACCTA	57.161	37.500	0.00	0.00	0.00	3.08
1276	2454	5.067283	TCAGCCAAGTTTCCTACAAGAAAAC	59.933	40.000	0.00	0.00	37.49	2.43
1364	2545	5.638783	TCTGAAACGGCGAAAACTTAAAAA	58.361	33.333	16.62	0.00	0.00	1.94
1365	2546	5.232610	TCTGAAACGGCGAAAACTTAAAA	57.767	34.783	16.62	0.00	0.00	1.52
1367	2548	3.303526	GCTCTGAAACGGCGAAAACTTAA	60.304	43.478	16.62	0.00	0.00	1.85
1438	2626	3.484557	GCGGTAATAACACATGGTCAACG	60.485	47.826	0.00	0.00	0.00	4.10
1517	2722	7.652524	TGCTATCCCTGCATTGTTTTATTTA	57.347	32.000	0.00	0.00	35.31	1.40
1518	2723	6.543430	TGCTATCCCTGCATTGTTTTATTT	57.457	33.333	0.00	0.00	35.31	1.40
1519	2724	6.155049	AGTTGCTATCCCTGCATTGTTTTATT	59.845	34.615	0.00	0.00	40.34	1.40
1520	2725	5.658190	AGTTGCTATCCCTGCATTGTTTTAT	59.342	36.000	0.00	0.00	40.34	1.40
1534	2739	6.736123	TCTCTCGTTATTACAGTTGCTATCC	58.264	40.000	0.00	0.00	0.00	2.59
1536	2741	8.251721	AGTTTCTCTCGTTATTACAGTTGCTAT	58.748	33.333	0.00	0.00	0.00	2.97
1540	2745	7.639162	ACAGTTTCTCTCGTTATTACAGTTG	57.361	36.000	0.00	0.00	0.00	3.16
1655	2863	4.574013	TGATTGGAAACATTGCACAAAACC	59.426	37.500	0.00	0.00	42.32	3.27
1766	3007	3.302968	GTCGTTACGGAAGAGACGG	57.697	57.895	4.53	0.00	40.94	4.79
1835	3079	7.013655	GCATGTTCACTCACTCCCATTATAAAT	59.986	37.037	0.00	0.00	0.00	1.40
1852	3096	4.201851	ACAAGATGATTAGCGCATGTTCAC	60.202	41.667	11.47	2.74	28.09	3.18
1853	3097	3.940852	ACAAGATGATTAGCGCATGTTCA	59.059	39.130	11.47	7.52	28.09	3.18
1854	3098	4.277258	CACAAGATGATTAGCGCATGTTC	58.723	43.478	11.47	0.98	28.09	3.18
2059	5959	6.684686	ACTGACGTGCAAGAAAATAGTACTA	58.315	36.000	6.65	4.77	0.00	1.82
2060	5960	5.539048	ACTGACGTGCAAGAAAATAGTACT	58.461	37.500	6.65	0.00	0.00	2.73
2061	5961	5.840940	ACTGACGTGCAAGAAAATAGTAC	57.159	39.130	6.65	0.00	0.00	2.73
2092	6001	6.817765	ATTTTACACCGAGTTGTCATGAAT	57.182	33.333	0.00	0.00	0.00	2.57
2122	6031	7.661040	CAAATTTGACTTCTTGGATAAGGTGT	58.339	34.615	13.08	0.00	34.59	4.16
2123	6032	6.587608	GCAAATTTGACTTCTTGGATAAGGTG	59.412	38.462	22.31	0.00	34.59	4.00
2124	6033	6.267471	TGCAAATTTGACTTCTTGGATAAGGT	59.733	34.615	22.31	0.00	34.59	3.50
2125	6034	6.690530	TGCAAATTTGACTTCTTGGATAAGG	58.309	36.000	22.31	0.00	34.59	2.69
2178	6091	6.798959	AGTACGTACACGAGTGATTTTCTAAC	59.201	38.462	26.55	0.00	43.02	2.34
2190	7091	2.928757	AGCTCTACAGTACGTACACGAG	59.071	50.000	26.55	22.56	43.02	4.18
2192	7093	2.669924	TCAGCTCTACAGTACGTACACG	59.330	50.000	26.55	18.87	46.33	4.49
2193	7094	3.683822	AGTCAGCTCTACAGTACGTACAC	59.316	47.826	26.55	12.08	0.00	2.90
2310	7211	1.659954	GCGGATGCTGAGCTCGTAG	60.660	63.158	9.64	2.68	38.39	3.51
2811	7739	1.063811	GATCGACGACGGGAACTCC	59.936	63.158	7.55	0.00	40.21	3.85
2860	7788	5.123027	CCTAATTGGAGAACTTGAAGAGCAC	59.877	44.000	0.00	0.00	38.35	4.40
2937	7865	5.532406	GCTAGGTTCATTGCAATGAGGATAA	59.468	40.000	33.96	21.06	45.35	1.75
2961	7889	9.057089	AGCATTTCCGTATAGAAAAGATAAAGG	57.943	33.333	0.00	0.00	39.11	3.11
3053	8904	1.308069	CCTGGGCCAAGATTCGTGTG	61.308	60.000	9.44	0.00	0.00	3.82
3120	9001	1.202855	AGCATTTCTGGTGTGCTGACT	60.203	47.619	0.00	0.00	46.60	3.41
3121	9002	1.242076	AGCATTTCTGGTGTGCTGAC	58.758	50.000	0.00	0.00	46.60	3.51
3122	9003	3.731716	AGCATTTCTGGTGTGCTGA	57.268	47.368	0.00	0.00	46.60	4.26
3125	9006	2.159338	CCATGTAGCATTTCTGGTGTGC	60.159	50.000	0.00	0.00	39.10	4.57
3144	9025	0.107831	GCCTGTAATATGCCCGTCCA	59.892	55.000	0.00	0.00	0.00	4.02
3145	9026	0.605589	GGCCTGTAATATGCCCGTCC	60.606	60.000	0.00	0.00	39.30	4.79
3160	9041	1.149133	AGTCCCCTTCCAATTGGCCT	61.149	55.000	20.33	3.69	34.44	5.19
3166	9047	7.882755	TGATAAGATTAAAGTCCCCTTCCAAT	58.117	34.615	0.00	0.00	0.00	3.16
3167	9048	7.183839	TCTGATAAGATTAAAGTCCCCTTCCAA	59.816	37.037	0.00	0.00	0.00	3.53
3168	9049	6.676632	TCTGATAAGATTAAAGTCCCCTTCCA	59.323	38.462	0.00	0.00	0.00	3.53
3169	9050	7.138054	TCTGATAAGATTAAAGTCCCCTTCC	57.862	40.000	0.00	0.00	0.00	3.46
3170	9051	9.634021	ATTTCTGATAAGATTAAAGTCCCCTTC	57.366	33.333	0.00	0.00	0.00	3.46
3316	9197	1.843368	ATGTGGGTTCAGGCAGATTG	58.157	50.000	0.00	0.00	0.00	2.67
3344	9225	7.950512	TCAAGGCAGATTAAAATTCTGTCAAA	58.049	30.769	10.84	0.00	38.45	2.69
3366	9247	4.775253	GGGGGTATTTGTCTTTCCAATCAA	59.225	41.667	0.00	0.00	0.00	2.57
3398	9280	2.245546	TCTCCCTTTCCATGGCATTCAT	59.754	45.455	6.96	0.00	36.31	2.57
3439	9321	8.458573	TTTTGTGATTACCAGTGTCTAACAAT	57.541	30.769	0.00	0.00	0.00	2.71
3468	9351	3.509442	TCAAATCTGAAAATGGGCTGGT	58.491	40.909	0.00	0.00	0.00	4.00
3563	9450	0.881796	GTTTGCCACCTGTCTAAGCC	59.118	55.000	0.00	0.00	0.00	4.35
3728	9617	3.264450	TCCTCCAACCTTTCTGAATCTCC	59.736	47.826	0.00	0.00	0.00	3.71
3741	9630	4.461198	TCTTTCAGTTCTTTCCTCCAACC	58.539	43.478	0.00	0.00	0.00	3.77
3742	9631	7.066404	GGATATCTTTCAGTTCTTTCCTCCAAC	59.934	40.741	2.05	0.00	0.00	3.77
3769	9661	6.256321	CAGCCATTTAATTTCCTCCATTTTCG	59.744	38.462	0.00	0.00	0.00	3.46

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.