AutoCloner

Multiple sequence alignment - TraesCS3B01G282300

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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	TraesCS3B01G282300	chr3B	100.000	3033	0	0	1	3033	452718083	452715051	0.000000e+00	5602.0
1	TraesCS3B01G282300	chr4B	95.556	2925	70	19	157	3033	24744760	24747672	0.000000e+00	4626.0
2	TraesCS3B01G282300	chr4B	88.973	1859	127	34	667	2483	24758963	24760785	0.000000e+00	2226.0
3	TraesCS3B01G282300	chr4B	86.441	1475	143	29	661	2111	24741174	24742615	0.000000e+00	1563.0
4	TraesCS3B01G282300	chr4B	82.982	570	51	12	120	662	24758303	24758853	9.840000e-130	473.0
5	TraesCS3B01G282300	chr4B	91.613	155	12	1	318	471	24739550	24739704	2.370000e-51	213.0
6	TraesCS3B01G282300	chr4B	88.679	106	9	2	226	331	24688308	24688206	3.170000e-25	126.0
7	TraesCS3B01G282300	chr4A	85.893	2403	234	54	695	3033	586683187	586680826	0.000000e+00	2462.0
8	TraesCS3B01G282300	chr4A	84.861	1691	184	41	564	2212	456437726	456436066	0.000000e+00	1639.0
9	TraesCS3B01G282300	chr4A	85.411	1604	156	41	846	2407	586700187	586698620	0.000000e+00	1594.0
10	TraesCS3B01G282300	chr4A	87.263	581	41	14	2208	2773	456420488	456419926	1.530000e-177	632.0
11	TraesCS3B01G282300	chr4A	82.278	474	30	22	157	596	586683708	586683255	7.990000e-96	361.0
12	TraesCS3B01G282300	chr4A	78.475	446	34	28	157	567	456443768	456443350	5.060000e-58	235.0
13	TraesCS3B01G282300	chr4A	92.929	99	6	1	318	415	456451808	456451710	3.150000e-30	143.0
14	TraesCS3B01G282300	chr4A	80.882	136	18	6	179	310	456451975	456451844	1.920000e-17	100.0
15	TraesCS3B01G282300	chr4A	89.706	68	6	1	57	123	586686420	586686353	5.390000e-13	86.1
16	TraesCS3B01G282300	chr4A	83.721	86	12	2	39	123	456446003	456445919	2.510000e-11	80.5
17	TraesCS3B01G282300	chr4D	88.535	1823	133	31	714	2495	14914191	14915978	0.000000e+00	2139.0
18	TraesCS3B01G282300	chr4D	86.283	1633	160	29	883	2467	14862538	14864154	0.000000e+00	1716.0
19	TraesCS3B01G282300	chr4D	87.186	1475	146	25	659	2107	14908894	14910351	0.000000e+00	1637.0
20	TraesCS3B01G282300	chr4D	86.450	1535	150	30	659	2151	14460238	14458720	0.000000e+00	1629.0
21	TraesCS3B01G282300	chr4D	84.807	1685	182	37	846	2494	14851054	14852700	0.000000e+00	1626.0
22	TraesCS3B01G282300	chr4D	87.147	778	73	10	1849	2614	14433509	14432747	0.000000e+00	857.0
23	TraesCS3B01G282300	chr4D	87.814	558	44	13	2495	3033	14918974	14919526	1.530000e-177	632.0
24	TraesCS3B01G282300	chr4D	84.890	589	41	21	120	662	14908077	14908663	4.420000e-153	551.0
25	TraesCS3B01G282300	chr4D	81.038	559	42	21	140	662	14460953	14460423	1.320000e-103	387.0
26	TraesCS3B01G282300	chr4D	84.577	402	43	10	120	513	14867123	14867513	6.140000e-102	381.0
27	TraesCS3B01G282300	chr4D	78.634	571	66	28	512	1041	14895607	14896162	8.110000e-86	327.0
28	TraesCS3B01G282300	chr4D	84.120	233	23	5	661	884	14840237	14840010	2.370000e-51	213.0
29	TraesCS3B01G282300	chr4D	87.912	182	13	3	704	881	14850864	14851040	3.960000e-49	206.0
30	TraesCS3B01G282300	chr4D	88.889	135	12	2	155	286	14438716	14438582	2.420000e-36	163.0
31	TraesCS3B01G282300	chr4D	86.014	143	19	1	2511	2652	14854023	14854165	5.240000e-33	152.0

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	TraesCS3B01G282300	chr3B	452715051	452718083	3032	True	5602.000000	5602	100.000000	1	3033	1	chr3B.!!$R1	3032
1	TraesCS3B01G282300	chr4B	24739550	24747672	8122	False	2134.000000	4626	91.203333	157	3033	3	chr4B.!!$F1	2876
2	TraesCS3B01G282300	chr4B	24758303	24760785	2482	False	1349.500000	2226	85.977500	120	2483	2	chr4B.!!$F2	2363
3	TraesCS3B01G282300	chr4A	456436066	456437726	1660	True	1639.000000	1639	84.861000	564	2212	1	chr4A.!!$R2	1648
4	TraesCS3B01G282300	chr4A	586698620	586700187	1567	True	1594.000000	1594	85.411000	846	2407	1	chr4A.!!$R3	1561
5	TraesCS3B01G282300	chr4A	586680826	586686420	5594	True	969.700000	2462	85.959000	57	3033	3	chr4A.!!$R6	2976
6	TraesCS3B01G282300	chr4A	456419926	456420488	562	True	632.000000	632	87.263000	2208	2773	1	chr4A.!!$R1	565
7	TraesCS3B01G282300	chr4D	14908077	14919526	11449	False	1239.750000	2139	87.106250	120	3033	4	chr4D.!!$F4	2913
8	TraesCS3B01G282300	chr4D	14862538	14867513	4975	False	1048.500000	1716	85.430000	120	2467	2	chr4D.!!$F3	2347
9	TraesCS3B01G282300	chr4D	14458720	14460953	2233	True	1008.000000	1629	83.744000	140	2151	2	chr4D.!!$R4	2011
10	TraesCS3B01G282300	chr4D	14432747	14433509	762	True	857.000000	857	87.147000	1849	2614	1	chr4D.!!$R1	765
11	TraesCS3B01G282300	chr4D	14850864	14854165	3301	False	661.333333	1626	86.244333	704	2652	3	chr4D.!!$F2	1948
12	TraesCS3B01G282300	chr4D	14895607	14896162	555	False	327.000000	327	78.634000	512	1041	1	chr4D.!!$F1	529

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
105	107	0.034059	AGCTGAGTTGACACGGGAAG	59.966	55.0	0.00	0.00	0.00	3.46	F
525	4396	0.518559	GCGCTAGCAAACGTTAGCAC	60.519	55.0	16.45	7.21	41.75	4.40	F
1303	10816	0.106819	GCAAGCCCATGTCTGAGGAT	60.107	55.0	0.00	0.00	0.00	3.24	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1302	10815	0.173708	GAAGAGGAAGTCGTCGCCAT	59.826	55.0	0.00	0.0	36.02	4.40	R
1426	10939	0.457166	CGAAGTCCACGCGGTTCATA	60.457	55.0	12.47	0.0	0.00	2.15	R
2898	23074	0.316841	TTTTGCATTTGGACCCTCGC	59.683	50.0	0.00	0.0	0.00	5.03	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
17	18	3.978272	GCAGTGGCCTTGACTCTG	58.022	61.111	3.32	4.45	0.00	3.35
18	19	1.673665	GCAGTGGCCTTGACTCTGG	60.674	63.158	3.32	0.00	0.00	3.86
23	24	3.993535	GCCTTGACTCTGGCCTTG	58.006	61.111	3.32	0.00	43.11	3.61
24	25	2.338785	GCCTTGACTCTGGCCTTGC	61.339	63.158	3.32	0.00	43.11	4.01
25	26	1.377994	CCTTGACTCTGGCCTTGCT	59.622	57.895	3.32	0.00	0.00	3.91
26	27	0.959372	CCTTGACTCTGGCCTTGCTG	60.959	60.000	3.32	0.00	0.00	4.41
27	28	0.035881	CTTGACTCTGGCCTTGCTGA	59.964	55.000	3.32	0.00	0.00	4.26
28	29	0.694771	TTGACTCTGGCCTTGCTGAT	59.305	50.000	3.32	0.00	0.00	2.90
29	30	0.035725	TGACTCTGGCCTTGCTGATG	60.036	55.000	3.32	0.00	0.00	3.07
30	31	0.035630	GACTCTGGCCTTGCTGATGT	60.036	55.000	3.32	0.00	0.00	3.06
31	32	1.208052	GACTCTGGCCTTGCTGATGTA	59.792	52.381	3.32	0.00	0.00	2.29
32	33	1.209019	ACTCTGGCCTTGCTGATGTAG	59.791	52.381	3.32	0.00	0.00	2.74
33	34	0.543277	TCTGGCCTTGCTGATGTAGG	59.457	55.000	3.32	0.00	0.00	3.18
34	35	0.254178	CTGGCCTTGCTGATGTAGGT	59.746	55.000	3.32	0.00	0.00	3.08
35	36	1.486310	CTGGCCTTGCTGATGTAGGTA	59.514	52.381	3.32	0.00	0.00	3.08
36	37	1.486310	TGGCCTTGCTGATGTAGGTAG	59.514	52.381	3.32	0.00	0.00	3.18
37	38	1.587547	GCCTTGCTGATGTAGGTAGC	58.412	55.000	0.00	0.00	37.93	3.58
38	39	1.858091	CCTTGCTGATGTAGGTAGCG	58.142	55.000	0.00	0.00	40.24	4.26
39	40	1.539065	CCTTGCTGATGTAGGTAGCGG	60.539	57.143	0.00	0.00	40.24	5.52
40	41	0.179084	TTGCTGATGTAGGTAGCGGC	60.179	55.000	0.00	0.00	40.24	6.53
41	42	1.661821	GCTGATGTAGGTAGCGGCG	60.662	63.158	0.51	0.51	0.00	6.46
42	43	1.007271	CTGATGTAGGTAGCGGCGG	60.007	63.158	9.78	0.00	0.00	6.13
43	44	2.338984	GATGTAGGTAGCGGCGGG	59.661	66.667	9.78	0.00	0.00	6.13
44	45	3.860630	GATGTAGGTAGCGGCGGGC	62.861	68.421	9.78	0.00	44.05	6.13
105	107	0.034059	AGCTGAGTTGACACGGGAAG	59.966	55.000	0.00	0.00	0.00	3.46
107	109	0.951040	CTGAGTTGACACGGGAAGGC	60.951	60.000	0.00	0.00	0.00	4.35
108	110	1.070786	GAGTTGACACGGGAAGGCA	59.929	57.895	0.00	0.00	0.00	4.75
131	171	2.825836	CGGAAGGCCATGCAGGTC	60.826	66.667	5.01	0.00	44.66	3.85
170	2783	1.042003	GGGGGTTACTCCGGAGACTC	61.042	65.000	37.69	24.97	37.00	3.36
187	2800	0.595588	CTCGAGACAGGGATGGATCG	59.404	60.000	6.58	0.00	0.00	3.69
218	2831	1.005748	CTGACTCGCAACAGAGCCA	60.006	57.895	0.00	0.00	41.77	4.75
219	2832	0.601046	CTGACTCGCAACAGAGCCAA	60.601	55.000	0.00	0.00	41.77	4.52
223	2836	3.726517	CGCAACAGAGCCAACCGG	61.727	66.667	0.00	0.00	0.00	5.28
224	2837	3.365265	GCAACAGAGCCAACCGGG	61.365	66.667	6.32	0.00	40.85	5.73
294	2914	7.397892	TCTTGGCCAATCGAATATTTAAACA	57.602	32.000	20.85	0.00	0.00	2.83
420	3072	8.552034	AGAAACGAAACAAGAAGAGAACTATTG	58.448	33.333	0.00	0.00	0.00	1.90
525	4396	0.518559	GCGCTAGCAAACGTTAGCAC	60.519	55.000	16.45	7.21	41.75	4.40
541	4412	1.206610	AGCACATGTCTCTTCAGCGAT	59.793	47.619	0.00	0.00	0.00	4.58
614	4492	1.734465	AGAATAGCTTGCACGTTGCTC	59.266	47.619	10.54	0.00	45.31	4.26
618	4496	2.972505	CTTGCACGTTGCTCCGGT	60.973	61.111	0.00	0.00	45.31	5.28
619	4497	2.515057	TTGCACGTTGCTCCGGTT	60.515	55.556	0.00	0.00	45.31	4.44
723	4864	5.279657	CCCCTGAATCTCATATGATTGACGA	60.280	44.000	5.72	0.00	36.86	4.20
724	4865	5.868258	CCCTGAATCTCATATGATTGACGAG	59.132	44.000	5.72	0.00	36.86	4.18
725	4866	6.453943	CCTGAATCTCATATGATTGACGAGT	58.546	40.000	5.72	0.00	36.86	4.18
726	4867	7.309438	CCCTGAATCTCATATGATTGACGAGTA	60.309	40.741	5.72	0.00	36.86	2.59
727	4868	8.249638	CCTGAATCTCATATGATTGACGAGTAT	58.750	37.037	5.72	0.00	36.86	2.12
744	4885	2.950309	AGTATAGTAGAGGTGTGCACGG	59.050	50.000	13.13	0.00	0.00	4.94
750	4891	2.315925	AGAGGTGTGCACGGATATTG	57.684	50.000	13.13	0.00	0.00	1.90
755	4897	2.682856	GGTGTGCACGGATATTGTGAAT	59.317	45.455	13.13	0.00	39.73	2.57
779	4936	1.448985	TTCCAAGCGCAATACTCCAC	58.551	50.000	11.47	0.00	0.00	4.02
785	4942	1.550524	AGCGCAATACTCCACTGAGAA	59.449	47.619	11.47	0.00	41.42	2.87
793	4950	2.683768	ACTCCACTGAGAAACACCTCT	58.316	47.619	0.00	0.00	41.42	3.69
795	4952	3.456277	ACTCCACTGAGAAACACCTCTTT	59.544	43.478	0.00	0.00	41.42	2.52
800	4957	5.118990	CACTGAGAAACACCTCTTTCTTGA	58.881	41.667	0.00	0.00	40.01	3.02
801	4958	5.762218	CACTGAGAAACACCTCTTTCTTGAT	59.238	40.000	0.00	0.00	40.01	2.57
881	5039	4.159135	AGCCATCTCCATTTTCATCACAAC	59.841	41.667	0.00	0.00	0.00	3.32
963	10417	1.012086	ATGCATGCAGTGACGACATC	58.988	50.000	26.69	0.00	0.00	3.06
995	10481	2.869636	GCTAGCTCCATGTATCCACTGC	60.870	54.545	7.70	0.00	0.00	4.40
1014	10500	5.308237	CACTGCTCCCCTATATAAAGGACTT	59.692	44.000	0.83	0.00	39.15	3.01
1117	10612	5.886609	TCTAGCTGATCAGTCCTAGCTAAT	58.113	41.667	23.38	1.55	45.13	1.73
1240	10753	1.275291	CCTCTCCAGGACTTTTGCGTA	59.725	52.381	0.00	0.00	43.65	4.42
1302	10815	1.300963	GCAAGCCCATGTCTGAGGA	59.699	57.895	0.00	0.00	0.00	3.71
1303	10816	0.106819	GCAAGCCCATGTCTGAGGAT	60.107	55.000	0.00	0.00	0.00	3.24
1370	10883	4.367023	CGACCCCAAACGGCTCGA	62.367	66.667	1.50	0.00	31.94	4.04
1478	10991	4.424711	AACCCGCCGCACATCCAT	62.425	61.111	0.00	0.00	0.00	3.41
1547	11060	1.101331	GAATCCTTGGCAGCCTTGAG	58.899	55.000	14.15	7.97	0.00	3.02
1634	11147	1.745232	TGCACTTCCAGTTCAACGTT	58.255	45.000	0.00	0.00	0.00	3.99
1705	15355	0.532573	ATCGTCTTCGTGCCACTCAT	59.467	50.000	0.00	0.00	38.33	2.90
1818	15469	1.614413	TCGCCGCTGGGTTTTAATTTT	59.386	42.857	0.00	0.00	34.97	1.82
1913	15566	4.453819	AGCAAAAGACATGTACTCAAGCTC	59.546	41.667	0.00	0.00	0.00	4.09
2242	15916	5.518848	AGAATGTGCAAACAAACATGAGA	57.481	34.783	0.00	0.00	37.11	3.27
2246	15928	3.947196	TGTGCAAACAAACATGAGAGACT	59.053	39.130	0.00	0.00	0.00	3.24
2898	23074	2.867472	GGTCGTTTGTCCATGCGG	59.133	61.111	0.00	0.00	0.00	5.69

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
7	8	0.959372	CAGCAAGGCCAGAGTCAAGG	60.959	60.000	5.01	0.00	0.00	3.61
8	9	0.035881	TCAGCAAGGCCAGAGTCAAG	59.964	55.000	5.01	0.00	0.00	3.02
9	10	0.694771	ATCAGCAAGGCCAGAGTCAA	59.305	50.000	5.01	0.00	0.00	3.18
10	11	0.035725	CATCAGCAAGGCCAGAGTCA	60.036	55.000	5.01	0.00	0.00	3.41
11	12	0.035630	ACATCAGCAAGGCCAGAGTC	60.036	55.000	5.01	0.00	0.00	3.36
12	13	1.209019	CTACATCAGCAAGGCCAGAGT	59.791	52.381	5.01	0.00	0.00	3.24
13	14	1.474677	CCTACATCAGCAAGGCCAGAG	60.475	57.143	5.01	0.00	0.00	3.35
14	15	0.543277	CCTACATCAGCAAGGCCAGA	59.457	55.000	5.01	0.00	0.00	3.86
15	16	0.254178	ACCTACATCAGCAAGGCCAG	59.746	55.000	5.01	0.00	33.42	4.85
16	17	1.486310	CTACCTACATCAGCAAGGCCA	59.514	52.381	5.01	0.00	33.42	5.36
17	18	1.811941	GCTACCTACATCAGCAAGGCC	60.812	57.143	0.00	0.00	35.35	5.19
18	19	1.587547	GCTACCTACATCAGCAAGGC	58.412	55.000	0.00	0.00	35.35	4.35
19	20	1.539065	CCGCTACCTACATCAGCAAGG	60.539	57.143	0.00	0.00	34.94	3.61
20	21	1.858091	CCGCTACCTACATCAGCAAG	58.142	55.000	0.00	0.00	34.94	4.01
21	22	0.179084	GCCGCTACCTACATCAGCAA	60.179	55.000	0.00	0.00	34.94	3.91
22	23	1.441729	GCCGCTACCTACATCAGCA	59.558	57.895	0.00	0.00	34.94	4.41
23	24	1.661821	CGCCGCTACCTACATCAGC	60.662	63.158	0.00	0.00	0.00	4.26
24	25	1.007271	CCGCCGCTACCTACATCAG	60.007	63.158	0.00	0.00	0.00	2.90
25	26	2.495409	CCCGCCGCTACCTACATCA	61.495	63.158	0.00	0.00	0.00	3.07
26	27	2.338984	CCCGCCGCTACCTACATC	59.661	66.667	0.00	0.00	0.00	3.06
27	28	3.925090	GCCCGCCGCTACCTACAT	61.925	66.667	0.00	0.00	0.00	2.29
30	31	4.873810	TACGCCCGCCGCTACCTA	62.874	66.667	0.00	0.00	41.76	3.08
37	38	3.993376	TTGTTAGCTACGCCCGCCG	62.993	63.158	0.00	0.00	44.21	6.46
38	39	2.125431	TTGTTAGCTACGCCCGCC	60.125	61.111	0.00	0.00	0.00	6.13
39	40	1.293267	TTGTTGTTAGCTACGCCCGC	61.293	55.000	0.00	0.00	0.00	6.13
40	41	0.719465	CTTGTTGTTAGCTACGCCCG	59.281	55.000	0.00	0.00	0.00	6.13
41	42	2.088950	TCTTGTTGTTAGCTACGCCC	57.911	50.000	0.00	0.00	0.00	6.13
42	43	3.241995	CGATTCTTGTTGTTAGCTACGCC	60.242	47.826	0.00	0.00	0.00	5.68
43	44	3.241995	CCGATTCTTGTTGTTAGCTACGC	60.242	47.826	0.00	0.00	0.00	4.42
44	45	3.924686	ACCGATTCTTGTTGTTAGCTACG	59.075	43.478	0.00	0.00	0.00	3.51
45	46	6.327934	TCTACCGATTCTTGTTGTTAGCTAC	58.672	40.000	0.00	0.00	0.00	3.58
46	47	6.519679	TCTACCGATTCTTGTTGTTAGCTA	57.480	37.500	0.00	0.00	0.00	3.32
47	48	5.401531	TCTACCGATTCTTGTTGTTAGCT	57.598	39.130	0.00	0.00	0.00	3.32
48	49	6.476243	TTTCTACCGATTCTTGTTGTTAGC	57.524	37.500	0.00	0.00	0.00	3.09
49	50	8.029642	ACATTTCTACCGATTCTTGTTGTTAG	57.970	34.615	0.00	0.00	0.00	2.34
50	51	7.972832	ACATTTCTACCGATTCTTGTTGTTA	57.027	32.000	0.00	0.00	0.00	2.41
51	52	6.877611	ACATTTCTACCGATTCTTGTTGTT	57.122	33.333	0.00	0.00	0.00	2.83
52	53	6.710744	AGAACATTTCTACCGATTCTTGTTGT	59.289	34.615	0.00	0.00	38.49	3.32
53	54	7.133891	AGAACATTTCTACCGATTCTTGTTG	57.866	36.000	0.00	0.00	38.49	3.33
54	55	7.094762	GGAAGAACATTTCTACCGATTCTTGTT	60.095	37.037	1.98	0.00	39.61	2.83
55	56	6.371825	GGAAGAACATTTCTACCGATTCTTGT	59.628	38.462	1.98	0.00	39.61	3.16
56	57	6.595716	AGGAAGAACATTTCTACCGATTCTTG	59.404	38.462	1.98	0.00	39.61	3.02
57	58	6.712276	AGGAAGAACATTTCTACCGATTCTT	58.288	36.000	0.00	0.00	39.61	2.52
58	59	6.301169	AGGAAGAACATTTCTACCGATTCT	57.699	37.500	0.00	0.00	39.61	2.40
59	60	6.819146	AGAAGGAAGAACATTTCTACCGATTC	59.181	38.462	0.00	0.00	39.61	2.52
105	107	3.443925	GGCCTTCCGCTTCTTGCC	61.444	66.667	0.00	0.00	38.78	4.52
107	109	1.805254	CATGGCCTTCCGCTTCTTG	59.195	57.895	3.32	0.00	37.74	3.02
108	110	2.048603	GCATGGCCTTCCGCTTCTT	61.049	57.895	3.32	0.00	37.74	2.52
116	118	2.825836	CGGACCTGCATGGCCTTC	60.826	66.667	12.50	0.00	40.22	3.46
145	185	2.672908	GGAGTAACCCCCGGTTGG	59.327	66.667	0.00	2.64	46.35	3.77
170	2783	1.662608	CCGATCCATCCCTGTCTCG	59.337	63.158	0.00	0.00	0.00	4.04
294	2914	2.600729	CCCTGCCTGTCTCCTTGCT	61.601	63.158	0.00	0.00	0.00	3.91
420	3072	1.104577	CCTGGCTACGGTCTCTCTCC	61.105	65.000	0.00	0.00	0.00	3.71
441	3098	0.974010	TACCTACCCTGAACGGCTGG	60.974	60.000	0.00	0.00	35.50	4.85
525	4396	4.176271	TGTGTAATCGCTGAAGAGACATG	58.824	43.478	0.00	0.00	0.00	3.21
541	4412	4.931002	GCCGGTTTATCTGTAGTTGTGTAA	59.069	41.667	1.90	0.00	0.00	2.41
614	4492	3.606687	ACTTGCTAATTGGTCTAACCGG	58.393	45.455	0.00	0.00	42.58	5.28
618	4496	3.687698	GCCGAACTTGCTAATTGGTCTAA	59.312	43.478	0.00	0.00	0.00	2.10
619	4497	3.055385	AGCCGAACTTGCTAATTGGTCTA	60.055	43.478	0.00	0.00	37.28	2.59
662	4540	1.144708	TGCCAGGGTCTTCATTCAACA	59.855	47.619	0.00	0.00	0.00	3.33
723	4864	2.950309	CCGTGCACACCTCTACTATACT	59.050	50.000	18.64	0.00	0.00	2.12
724	4865	2.947652	TCCGTGCACACCTCTACTATAC	59.052	50.000	18.64	0.00	0.00	1.47
725	4866	3.286329	TCCGTGCACACCTCTACTATA	57.714	47.619	18.64	0.00	0.00	1.31
726	4867	2.139323	TCCGTGCACACCTCTACTAT	57.861	50.000	18.64	0.00	0.00	2.12
727	4868	2.139323	ATCCGTGCACACCTCTACTA	57.861	50.000	18.64	0.00	0.00	1.82
744	4885	5.273944	GCTTGGAAACGGATTCACAATATC	58.726	41.667	0.36	0.00	39.98	1.63
750	4891	0.454452	GCGCTTGGAAACGGATTCAC	60.454	55.000	0.00	0.00	39.98	3.18
755	4897	0.800012	GTATTGCGCTTGGAAACGGA	59.200	50.000	9.73	0.00	0.00	4.69
779	4936	6.709846	AGAATCAAGAAAGAGGTGTTTCTCAG	59.290	38.462	2.84	0.58	44.38	3.35
785	4942	5.237344	CGAACAGAATCAAGAAAGAGGTGTT	59.763	40.000	0.00	0.00	0.00	3.32
793	4950	4.274950	GGACCAACGAACAGAATCAAGAAA	59.725	41.667	0.00	0.00	0.00	2.52
795	4952	3.399330	GGACCAACGAACAGAATCAAGA	58.601	45.455	0.00	0.00	0.00	3.02
800	4957	2.879103	ATGGGACCAACGAACAGAAT	57.121	45.000	0.00	0.00	0.00	2.40
801	4958	2.649531	AATGGGACCAACGAACAGAA	57.350	45.000	0.00	0.00	0.00	3.02
881	5039	0.174845	TTACTTGCGTCGGGATCAGG	59.825	55.000	0.00	0.00	0.00	3.86
963	10417	1.071228	TGGAGCTAGCTATGCATGTGG	59.929	52.381	19.38	0.46	0.00	4.17
995	10481	8.207545	GCATATGAAGTCCTTTATATAGGGGAG	58.792	40.741	6.97	0.00	32.26	4.30
1014	10500	3.111484	TGAGTGGTGGTAAGGCATATGA	58.889	45.455	6.97	0.00	0.00	2.15
1130	10632	1.202698	GGAGTACCCCATGCTTGCTAG	60.203	57.143	0.00	0.00	0.00	3.42
1240	10753	1.377725	CTTGCCATCAAGGTCGGCT	60.378	57.895	0.00	0.00	46.39	5.52
1249	10762	2.268920	GAGACCGCCTTGCCATCA	59.731	61.111	0.00	0.00	0.00	3.07
1302	10815	0.173708	GAAGAGGAAGTCGTCGCCAT	59.826	55.000	0.00	0.00	36.02	4.40
1303	10816	0.894184	AGAAGAGGAAGTCGTCGCCA	60.894	55.000	0.00	0.00	38.60	5.69
1426	10939	0.457166	CGAAGTCCACGCGGTTCATA	60.457	55.000	12.47	0.00	0.00	2.15
1547	11060	0.896226	AGTAGAGCTTGTTCCCGGAC	59.104	55.000	0.73	0.00	0.00	4.79
1634	11147	1.684734	GGAGGCCTCGGTCTTACCA	60.685	63.158	26.36	0.00	38.47	3.25
1705	15355	1.221840	GGATTGGAGCCGAAGAGCA	59.778	57.895	0.00	0.00	34.23	4.26
1913	15566	0.813610	TGCATGCGAGATTAACCCGG	60.814	55.000	14.09	0.00	0.00	5.73
2194	15862	5.242434	AGATTGCTACAATACGTGGAACAA	58.758	37.500	0.00	0.00	44.16	2.83
2242	15916	1.139058	GGGATGTTCCGTGCATAGTCT	59.861	52.381	0.00	0.00	37.43	3.24
2246	15928	4.846551	CGGGATGTTCCGTGCATA	57.153	55.556	0.00	0.00	44.60	3.14
2362	16062	6.358974	TGATGATACACTTCTCAACAAGGA	57.641	37.500	0.00	0.00	0.00	3.36
2898	23074	0.316841	TTTTGCATTTGGACCCTCGC	59.683	50.000	0.00	0.00	0.00	5.03

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.