AutoCloner

Multiple sequence alignment - TraesCS5B01G012500

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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	TraesCS5B01G012500	chr5B	100.000	6727	0	0	1	6727	12569107	12562381	0.000000e+00	12423
1	TraesCS5B01G012500	chr4D	95.994	6765	205	21	1	6727	65863446	65870182	0.000000e+00	10931
2	TraesCS5B01G012500	chr1D	95.952	6768	200	32	1	6727	10791260	10797994	0.000000e+00	10912
3	TraesCS5B01G012500	chr1D	95.371	6761	228	37	1	6727	466333258	466339967	0.000000e+00	10672
4	TraesCS5B01G012500	chr1D	92.829	5257	270	61	316	5525	218969473	218964277	0.000000e+00	7520
5	TraesCS5B01G012500	chr1D	95.722	4418	130	19	1	4388	108776460	108780848	0.000000e+00	7057
6	TraesCS5B01G012500	chr1D	94.635	727	16	2	1	727	58455146	58455849	0.000000e+00	1105
7	TraesCS5B01G012500	chr7D	95.755	6785	187	39	1	6727	30325229	30318488	0.000000e+00	10840
8	TraesCS5B01G012500	chr7D	93.031	2755	142	32	1	2742	59509293	59506576	0.000000e+00	3978
9	TraesCS5B01G012500	chr3D	95.319	6750	241	29	1	6727	175409260	175415957	0.000000e+00	10645
10	TraesCS5B01G012500	chr3D	91.420	5128	378	34	1629	6727	341451650	341446556	0.000000e+00	6975
11	TraesCS5B01G012500	chr2B	93.207	6683	353	43	1	6629	67256450	67263085	0.000000e+00	9732
12	TraesCS5B01G012500	chr2B	92.725	6144	322	38	30	6115	652839847	652833771	0.000000e+00	8754
13	TraesCS5B01G012500	chr2B	93.941	2195	123	10	4540	6727	95255996	95258187	0.000000e+00	3308
14	TraesCS5B01G012500	chr2B	87.561	611	43	28	1	586	608467185	608466583	0.000000e+00	676
15	TraesCS5B01G012500	chr7B	94.097	6048	288	34	736	6727	475378268	475372234	0.000000e+00	9127
16	TraesCS5B01G012500	chr6A	91.841	6471	407	76	313	6727	572216443	572222848	0.000000e+00	8913
17	TraesCS5B01G012500	chr3B	93.305	6049	326	40	736	6727	103299317	103305343	0.000000e+00	8853
18	TraesCS5B01G012500	chr3B	94.777	2757	88	21	1	2744	691323927	691326640	0.000000e+00	4242
19	TraesCS5B01G012500	chr3B	89.340	591	19	10	1	565	678512245	678512817	0.000000e+00	702
20	TraesCS5B01G012500	chr3B	88.325	591	25	14	1	565	694793940	694794512	0.000000e+00	669
21	TraesCS5B01G012500	chr4A	93.245	5833	302	45	938	6727	57406662	57412445	0.000000e+00	8504
22	TraesCS5B01G012500	chr3A	90.674	579	23	9	1	572	32218219	32217665	0.000000e+00	741
23	TraesCS5B01G012500	chr3A	95.000	180	9	0	686	865	32217636	32217457	3.970000e-72	283
24	TraesCS5B01G012500	chr3A	93.296	179	12	0	686	864	450969345	450969167	1.440000e-66	265
25	TraesCS5B01G012500	chr2A	92.069	290	18	5	301	586	614230800	614230512	2.920000e-108	403
26	TraesCS5B01G012500	chr2A	94.318	176	10	0	686	861	619869115	619869290	3.090000e-68	270
27	TraesCS5B01G012500	chr2A	93.182	176	10	1	686	861	58489412	58489585	2.410000e-64	257

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	TraesCS5B01G012500	chr5B	12562381	12569107	6726	True	12423	12423	100.000	1	6727	1	chr5B.!!$R1	6726
1	TraesCS5B01G012500	chr4D	65863446	65870182	6736	False	10931	10931	95.994	1	6727	1	chr4D.!!$F1	6726
2	TraesCS5B01G012500	chr1D	10791260	10797994	6734	False	10912	10912	95.952	1	6727	1	chr1D.!!$F1	6726
3	TraesCS5B01G012500	chr1D	466333258	466339967	6709	False	10672	10672	95.371	1	6727	1	chr1D.!!$F4	6726
4	TraesCS5B01G012500	chr1D	218964277	218969473	5196	True	7520	7520	92.829	316	5525	1	chr1D.!!$R1	5209
5	TraesCS5B01G012500	chr1D	108776460	108780848	4388	False	7057	7057	95.722	1	4388	1	chr1D.!!$F3	4387
6	TraesCS5B01G012500	chr1D	58455146	58455849	703	False	1105	1105	94.635	1	727	1	chr1D.!!$F2	726
7	TraesCS5B01G012500	chr7D	30318488	30325229	6741	True	10840	10840	95.755	1	6727	1	chr7D.!!$R1	6726
8	TraesCS5B01G012500	chr7D	59506576	59509293	2717	True	3978	3978	93.031	1	2742	1	chr7D.!!$R2	2741
9	TraesCS5B01G012500	chr3D	175409260	175415957	6697	False	10645	10645	95.319	1	6727	1	chr3D.!!$F1	6726
10	TraesCS5B01G012500	chr3D	341446556	341451650	5094	True	6975	6975	91.420	1629	6727	1	chr3D.!!$R1	5098
11	TraesCS5B01G012500	chr2B	67256450	67263085	6635	False	9732	9732	93.207	1	6629	1	chr2B.!!$F1	6628
12	TraesCS5B01G012500	chr2B	652833771	652839847	6076	True	8754	8754	92.725	30	6115	1	chr2B.!!$R2	6085
13	TraesCS5B01G012500	chr2B	95255996	95258187	2191	False	3308	3308	93.941	4540	6727	1	chr2B.!!$F2	2187
14	TraesCS5B01G012500	chr2B	608466583	608467185	602	True	676	676	87.561	1	586	1	chr2B.!!$R1	585
15	TraesCS5B01G012500	chr7B	475372234	475378268	6034	True	9127	9127	94.097	736	6727	1	chr7B.!!$R1	5991
16	TraesCS5B01G012500	chr6A	572216443	572222848	6405	False	8913	8913	91.841	313	6727	1	chr6A.!!$F1	6414
17	TraesCS5B01G012500	chr3B	103299317	103305343	6026	False	8853	8853	93.305	736	6727	1	chr3B.!!$F1	5991
18	TraesCS5B01G012500	chr3B	691323927	691326640	2713	False	4242	4242	94.777	1	2744	1	chr3B.!!$F3	2743
19	TraesCS5B01G012500	chr3B	678512245	678512817	572	False	702	702	89.340	1	565	1	chr3B.!!$F2	564
20	TraesCS5B01G012500	chr3B	694793940	694794512	572	False	669	669	88.325	1	565	1	chr3B.!!$F4	564
21	TraesCS5B01G012500	chr4A	57406662	57412445	5783	False	8504	8504	93.245	938	6727	1	chr4A.!!$F1	5789
22	TraesCS5B01G012500	chr3A	32217457	32218219	762	True	512	741	92.837	1	865	2	chr3A.!!$R2	864

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
80	91	2.203195	TGCTCAGTTGGCTGCGTT	60.203	55.556	0.00	0.00	42.29	4.84	F
219	232	3.253188	TCAGTTGGCTGCATCACTTTTAC	59.747	43.478	0.50	0.00	42.29	2.01	F
1698	1901	3.009473	ACAGATGCTGAGGTATGTGGTTT	59.991	43.478	0.82	0.00	34.20	3.27	F
2858	3107	0.036105	TGCGCTTGTCCATGACATCT	60.036	50.000	9.73	0.00	42.40	2.90	F
4075	4378	0.320508	AAAGAAAGAGACGCGGGTCC	60.321	55.000	26.94	18.48	44.54	4.46	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1207	1345	0.689623	CCTCTCCCTGCTCAACACTT	59.310	55.000	0.00	0.0	0.00	3.16	R
2139	2374	5.891551	GGGGTTAGAGAGGCATTGAAATTTA	59.108	40.000	0.00	0.0	0.00	1.40	R
2874	3123	1.066929	CCCATGCATCCGATCGTATCA	60.067	52.381	15.09	6.7	0.00	2.15	R
4394	4892	0.109153	TCACTGCCATCAACTGCTGT	59.891	50.000	0.00	0.0	39.79	4.40	R
5884	6409	1.089920	GCGCATCCTTCATTCACAGT	58.910	50.000	0.30	0.0	0.00	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
80	91	2.203195	TGCTCAGTTGGCTGCGTT	60.203	55.556	0.00	0.00	42.29	4.84
218	231	3.485394	TCAGTTGGCTGCATCACTTTTA	58.515	40.909	0.50	0.00	42.29	1.52
219	232	3.253188	TCAGTTGGCTGCATCACTTTTAC	59.747	43.478	0.50	0.00	42.29	2.01
220	233	3.254166	CAGTTGGCTGCATCACTTTTACT	59.746	43.478	0.50	0.00	35.77	2.24
221	234	4.455533	CAGTTGGCTGCATCACTTTTACTA	59.544	41.667	0.50	0.00	35.77	1.82
222	235	4.697352	AGTTGGCTGCATCACTTTTACTAG	59.303	41.667	0.50	0.00	0.00	2.57
223	236	4.286297	TGGCTGCATCACTTTTACTAGT	57.714	40.909	0.00	0.00	0.00	2.57
224	237	4.651778	TGGCTGCATCACTTTTACTAGTT	58.348	39.130	0.00	0.00	0.00	2.24
225	238	4.455533	TGGCTGCATCACTTTTACTAGTTG	59.544	41.667	0.00	0.00	0.00	3.16
226	239	4.142600	GGCTGCATCACTTTTACTAGTTGG	60.143	45.833	0.00	0.00	0.00	3.77
227	240	4.672801	GCTGCATCACTTTTACTAGTTGGC	60.673	45.833	0.00	0.00	0.00	4.52
228	241	4.651778	TGCATCACTTTTACTAGTTGGCT	58.348	39.130	0.00	0.00	0.00	4.75
229	242	5.070001	TGCATCACTTTTACTAGTTGGCTT	58.930	37.500	0.00	0.00	0.00	4.35
230	243	5.048782	TGCATCACTTTTACTAGTTGGCTTG	60.049	40.000	0.00	0.00	0.00	4.01
231	244	5.393962	CATCACTTTTACTAGTTGGCTTGC	58.606	41.667	0.00	0.00	0.00	4.01
232	245	4.456535	TCACTTTTACTAGTTGGCTTGCA	58.543	39.130	0.00	0.00	0.00	4.08
233	246	5.070001	TCACTTTTACTAGTTGGCTTGCAT	58.930	37.500	0.00	0.00	0.00	3.96
234	247	5.181245	TCACTTTTACTAGTTGGCTTGCATC	59.819	40.000	0.00	0.00	0.00	3.91
235	248	5.048782	CACTTTTACTAGTTGGCTTGCATCA	60.049	40.000	0.00	0.00	0.00	3.07
236	249	5.048713	ACTTTTACTAGTTGGCTTGCATCAC	60.049	40.000	0.00	0.00	0.00	3.06
486	568	5.720371	TGCAAATTAGTACCAATGCTTGT	57.280	34.783	2.17	0.00	34.97	3.16
487	569	6.095432	TGCAAATTAGTACCAATGCTTGTT	57.905	33.333	2.17	0.00	34.97	2.83
499	582	7.671495	ACCAATGCTTGTTAATTTTCCAATC	57.329	32.000	0.00	0.00	0.00	2.67
529	615	6.691754	TTCTCAATGTGCAAGTCTTTGTTA	57.308	33.333	0.00	0.00	36.65	2.41
587	690	4.155280	TGCAACTAGGGACGCTTATTTTTC	59.845	41.667	0.00	0.00	0.00	2.29
856	971	5.643777	GCATCATTGTAGTAGTTGGTTGTCT	59.356	40.000	0.00	0.00	0.00	3.41
889	1009	5.344743	TGGTTTTTGCATTTTGTGTCCTA	57.655	34.783	0.00	0.00	0.00	2.94
1207	1345	4.662961	CAGCCACGACCTGCACGA	62.663	66.667	1.86	0.00	34.70	4.35
1406	1551	4.844085	TGGAAAGGGAGTTGAGTCATCTTA	59.156	41.667	5.21	0.00	0.00	2.10
1416	1561	7.256012	GGAGTTGAGTCATCTTATAGGGTAAGG	60.256	44.444	5.21	0.00	0.00	2.69
1425	1571	9.447279	TCATCTTATAGGGTAAGGAAATTCTCA	57.553	33.333	0.00	0.00	0.00	3.27
1483	1642	3.354948	TTATGCAGCAGTTCTCACCAT	57.645	42.857	0.00	0.00	0.00	3.55
1698	1901	3.009473	ACAGATGCTGAGGTATGTGGTTT	59.991	43.478	0.82	0.00	34.20	3.27
1699	1902	4.012374	CAGATGCTGAGGTATGTGGTTTT	58.988	43.478	0.00	0.00	32.44	2.43
1740	1954	5.507985	GCTATTGAACAGTTCCTTGCAAACT	60.508	40.000	10.93	0.00	37.44	2.66
1811	2030	6.621596	GCACATCTGCTAGAACTTTTTGTAGG	60.622	42.308	0.00	0.00	40.63	3.18
1967	2196	6.536224	GCTTTTTCCAATACTGATCCAAATGG	59.464	38.462	0.00	0.00	0.00	3.16
2249	2484	1.546476	CAGCGGACCTCACTAAGTTCT	59.454	52.381	0.00	0.00	0.00	3.01
2353	2588	5.433051	TCAGAGGGTATTTGATCTCCCAAAT	59.567	40.000	0.00	0.00	45.52	2.32
2621	2857	3.607422	TGCTCAAGAACACAAACATCG	57.393	42.857	0.00	0.00	0.00	3.84
2750	2996	7.040409	ACCACTTCCATATGTTCTTGTTCTTTC	60.040	37.037	1.24	0.00	0.00	2.62
2754	3001	9.219603	CTTCCATATGTTCTTGTTCTTTCTGTA	57.780	33.333	1.24	0.00	0.00	2.74
2858	3107	0.036105	TGCGCTTGTCCATGACATCT	60.036	50.000	9.73	0.00	42.40	2.90
2885	3134	1.852942	CAACTGGGTGATACGATCGG	58.147	55.000	20.98	1.23	0.00	4.18
2953	3202	0.469331	TCTCTCCTGGTGTGTTCGGT	60.469	55.000	0.00	0.00	0.00	4.69
2977	3226	8.837389	GGTAAATTACAAGTGAGTTCTCTTTGT	58.163	33.333	18.76	18.76	0.00	2.83
3028	3285	5.296780	TGTTCTTTTGATGTCTGGTCACTTC	59.703	40.000	0.00	0.00	0.00	3.01
3478	3760	3.383505	GGCATCCAAGTTACCAATAACCC	59.616	47.826	0.00	0.00	41.54	4.11
3479	3761	3.066203	GCATCCAAGTTACCAATAACCCG	59.934	47.826	0.00	0.00	41.54	5.28
3600	3887	6.459670	TGTAGTTGCGAGAATACAGGATTA	57.540	37.500	0.00	0.00	0.00	1.75
4034	4335	3.324268	ACAACATCCATCAATGCAAACCA	59.676	39.130	0.00	0.00	0.00	3.67
4039	4340	0.609151	CATCAATGCAAACCAGGGCA	59.391	50.000	0.00	0.00	45.23	5.36
4069	4370	2.290641	TGCTCCAAAAAGAAAGAGACGC	59.709	45.455	0.00	0.00	0.00	5.19
4075	4378	0.320508	AAAGAAAGAGACGCGGGTCC	60.321	55.000	26.94	18.48	44.54	4.46
4091	4394	4.430908	CGGGTCCACTATACAAGAAGAAC	58.569	47.826	0.00	0.00	0.00	3.01
4154	4457	3.691118	GGAAGCAGCAATAGATGTTGACA	59.309	43.478	0.00	0.00	42.37	3.58
4269	4683	4.640647	GGACAAACAAGAAGAGGACAAAGT	59.359	41.667	0.00	0.00	0.00	2.66
4300	4717	5.187967	GGAGGACAAGGAAGAAGATAGTGAA	59.812	44.000	0.00	0.00	0.00	3.18
4344	4764	1.778383	AGGCCAAAGAGGGGGACAA	60.778	57.895	5.01	0.00	38.09	3.18
4394	4892	0.693049	GAGGGGAGAAGACAAAGGCA	59.307	55.000	0.00	0.00	0.00	4.75
4397	4895	1.528129	GGGAGAAGACAAAGGCACAG	58.472	55.000	0.00	0.00	0.00	3.66
4408	4906	1.530013	AAGGCACAGCAGTTGATGGC	61.530	55.000	2.21	2.86	35.42	4.40
4631	5144	7.041721	CAGGAGCACACTACAGATGTTAATTA	58.958	38.462	0.00	0.00	0.00	1.40
4802	5316	9.512588	AAGATATGTGTGAGAAGATCAACTTTT	57.487	29.630	0.00	0.00	40.43	2.27
5063	5578	2.113807	AGATGGTGAGTGCAGATGCTA	58.886	47.619	6.35	0.00	42.66	3.49
5124	5639	1.674221	GCCAACTGTAGTGAGCAGAGG	60.674	57.143	0.00	0.00	37.40	3.69
5200	5715	2.245287	AGTCCCACCAAAACCACCTAAA	59.755	45.455	0.00	0.00	0.00	1.85
5201	5716	3.116900	AGTCCCACCAAAACCACCTAAAT	60.117	43.478	0.00	0.00	0.00	1.40
5213	5728	9.921637	CAAAACCACCTAAATAGCAAAAGATTA	57.078	29.630	0.00	0.00	0.00	1.75
5308	5824	4.670199	CAGCCATTGATGCAGGGA	57.330	55.556	0.00	0.00	0.00	4.20
5491	6009	3.162666	CATAGGGATGCTTCAATGCCAT	58.837	45.455	1.64	0.00	40.37	4.40
5524	6042	5.104485	GGAGGTGATCCTACTACCAAATTGT	60.104	44.000	2.33	0.00	45.24	2.71
5768	6293	4.098960	GTCTTATCATGGTGACGGGTTCTA	59.901	45.833	0.00	0.00	0.00	2.10
5884	6409	0.465460	GTGTGAGTTGGACCCAGCAA	60.465	55.000	5.71	0.00	0.00	3.91
5909	6434	0.679002	AATGAAGGATGCGCTGCTGT	60.679	50.000	9.73	0.00	0.00	4.40
6111	6636	5.289083	ACAAGAAGAAGACTTTCAGCTCT	57.711	39.130	0.00	0.00	36.39	4.09
6152	6677	4.439057	CTTTACGCTGCCCTCTTGTATTA	58.561	43.478	0.00	0.00	0.00	0.98
6305	6831	2.597455	ACAGGGCTTTTAGTTGCACAT	58.403	42.857	0.00	0.00	34.58	3.21
6313	6839	4.084900	GCTTTTAGTTGCACATTGTTCTGC	60.085	41.667	0.00	0.00	0.00	4.26
6645	7184	2.845659	TGAGGGAGGCCTTTCATCTAA	58.154	47.619	6.77	0.00	0.00	2.10

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
218	231	2.867109	AGTGATGCAAGCCAACTAGT	57.133	45.000	0.00	0.00	0.00	2.57
219	232	4.510038	AAAAGTGATGCAAGCCAACTAG	57.490	40.909	0.00	0.00	0.00	2.57
220	233	5.070001	AGTAAAAGTGATGCAAGCCAACTA	58.930	37.500	0.00	0.00	0.00	2.24
221	234	3.891366	AGTAAAAGTGATGCAAGCCAACT	59.109	39.130	0.00	0.00	0.00	3.16
222	235	4.243007	AGTAAAAGTGATGCAAGCCAAC	57.757	40.909	0.00	0.00	0.00	3.77
223	236	5.070001	ACTAGTAAAAGTGATGCAAGCCAA	58.930	37.500	0.00	0.00	0.00	4.52
224	237	4.651778	ACTAGTAAAAGTGATGCAAGCCA	58.348	39.130	0.00	0.00	0.00	4.75
225	238	5.393962	CAACTAGTAAAAGTGATGCAAGCC	58.606	41.667	0.00	0.00	0.00	4.35
226	239	5.393962	CCAACTAGTAAAAGTGATGCAAGC	58.606	41.667	0.00	0.00	0.00	4.01
227	240	5.182001	AGCCAACTAGTAAAAGTGATGCAAG	59.818	40.000	0.00	0.00	0.00	4.01
228	241	5.048782	CAGCCAACTAGTAAAAGTGATGCAA	60.049	40.000	0.00	0.00	0.00	4.08
229	242	4.455533	CAGCCAACTAGTAAAAGTGATGCA	59.544	41.667	0.00	0.00	0.00	3.96
230	243	4.455877	ACAGCCAACTAGTAAAAGTGATGC	59.544	41.667	0.00	0.00	0.00	3.91
231	244	6.204688	TGAACAGCCAACTAGTAAAAGTGATG	59.795	38.462	0.00	0.00	0.00	3.07
232	245	6.296026	TGAACAGCCAACTAGTAAAAGTGAT	58.704	36.000	0.00	0.00	0.00	3.06
233	246	5.676552	TGAACAGCCAACTAGTAAAAGTGA	58.323	37.500	0.00	0.00	0.00	3.41
234	247	6.560253	ATGAACAGCCAACTAGTAAAAGTG	57.440	37.500	0.00	0.00	0.00	3.16
235	248	7.883311	ACATATGAACAGCCAACTAGTAAAAGT	59.117	33.333	10.38	0.00	0.00	2.66
236	249	8.268850	ACATATGAACAGCCAACTAGTAAAAG	57.731	34.615	10.38	0.00	0.00	2.27
499	582	8.807667	AAGACTTGCACATTGAGAAAAATTAG	57.192	30.769	0.00	0.00	0.00	1.73
529	615	4.344679	ACACATGAAAACAACCACATCCAT	59.655	37.500	0.00	0.00	0.00	3.41
587	690	3.194116	AGCAACCATCAGTGCTAATTTGG	59.806	43.478	0.00	0.00	33.04	3.28
678	791	5.641209	AGCTCAGTAAGATAACTTGTGCAAG	59.359	40.000	10.09	10.09	43.79	4.01
889	1009	8.753497	TGATCTACAGACATCTACACATAAGT	57.247	34.615	0.00	0.00	0.00	2.24
1207	1345	0.689623	CCTCTCCCTGCTCAACACTT	59.310	55.000	0.00	0.00	0.00	3.16
1598	1800	6.595326	CCAGTGATGTCAACTATAAAGAAGCA	59.405	38.462	0.00	0.00	0.00	3.91
1699	1902	9.243637	GTTCAATAGCTCATAAACACACAAAAA	57.756	29.630	0.00	0.00	0.00	1.94
1811	2030	7.871463	ACTAAGAAAATATACGATACCTGGCAC	59.129	37.037	0.00	0.00	0.00	5.01
2139	2374	5.891551	GGGGTTAGAGAGGCATTGAAATTTA	59.108	40.000	0.00	0.00	0.00	1.40
2249	2484	1.374947	GCTGGTAGGACTGCACCAA	59.625	57.895	0.00	0.00	44.06	3.67
2353	2588	8.832735	ACTAAATATCTGACTTTTTGACCCCTA	58.167	33.333	3.78	0.00	0.00	3.53
2621	2857	4.267349	TGTGTTCTACTACAAAGAGGCC	57.733	45.455	0.00	0.00	0.00	5.19
2754	3001	9.672673	ATGAGTATTTCAGCAAACTATAACTGT	57.327	29.630	0.00	0.00	39.68	3.55
2872	3121	1.995484	CATGCATCCGATCGTATCACC	59.005	52.381	15.09	0.00	0.00	4.02
2874	3123	1.066929	CCCATGCATCCGATCGTATCA	60.067	52.381	15.09	6.70	0.00	2.15
2885	3134	6.314896	GCAATTAGAGTACTATCCCATGCATC	59.685	42.308	0.00	0.00	0.00	3.91
3384	3666	8.216423	TCCGTGTATCTATACTCCTCTTTAAGT	58.784	37.037	2.07	0.00	34.41	2.24
3403	3685	2.986979	TGGCGTCTGCTCCGTGTA	60.987	61.111	0.00	0.00	42.25	2.90
3422	3704	2.032979	GCTTGCAAAATTCCACCAAACG	60.033	45.455	0.00	0.00	0.00	3.60
3479	3761	1.165270	AACACTAACCTGCGGATTGC	58.835	50.000	0.00	0.00	46.70	3.56
3600	3887	6.003950	ACTAAACATACATCACAGCCAACTT	58.996	36.000	0.00	0.00	0.00	2.66
3719	4009	1.308047	TGCACTGTGGCACAAACTAG	58.692	50.000	22.31	11.88	44.16	2.57
3848	4144	9.442047	AAAAGATTCAGTACTGATTCAGTTAGG	57.558	33.333	33.26	13.20	42.59	2.69
4018	4319	1.559368	CCCTGGTTTGCATTGATGGA	58.441	50.000	0.00	0.00	0.00	3.41
4039	4340	1.203052	CTTTTTGGAGCATGGCGTGAT	59.797	47.619	11.71	3.20	0.00	3.06
4047	4348	3.057946	GCGTCTCTTTCTTTTTGGAGCAT	60.058	43.478	0.00	0.00	0.00	3.79
4069	4370	4.081862	TGTTCTTCTTGTATAGTGGACCCG	60.082	45.833	0.00	0.00	0.00	5.28
4075	4378	9.046296	ACAAACTCTTGTTCTTCTTGTATAGTG	57.954	33.333	0.00	0.00	43.45	2.74
4091	4394	5.059161	TGACTCATCCTCAACAAACTCTTG	58.941	41.667	0.00	0.00	38.61	3.02
4154	4457	1.464608	CGCATTTGTGTCCTCGTCATT	59.535	47.619	0.00	0.00	0.00	2.57
4269	4683	2.927007	TCTTCCTTGTCCTCCTCCTCTA	59.073	50.000	0.00	0.00	0.00	2.43
4300	4717	1.360852	TCTTCTTCCTCCTCCTCTGCT	59.639	52.381	0.00	0.00	0.00	4.24
4344	4764	1.342174	CAATTGCTGCACCTTTGTCCT	59.658	47.619	0.00	0.00	0.00	3.85
4394	4892	0.109153	TCACTGCCATCAACTGCTGT	59.891	50.000	0.00	0.00	39.79	4.40
4397	4895	1.085091	CTCTCACTGCCATCAACTGC	58.915	55.000	0.00	0.00	0.00	4.40
4408	4906	3.428725	CGTCATCTTCTTCCCTCTCACTG	60.429	52.174	0.00	0.00	0.00	3.66
4631	5144	4.799564	TGTCTTTCCAGCAAGTTTTGTT	57.200	36.364	0.00	0.00	0.00	2.83
4802	5316	2.373169	AGAACAGGCTCTTGTCAATGGA	59.627	45.455	0.00	0.00	0.00	3.41
5063	5578	6.948309	ACAGCTTCCTTGACCATATTTACTTT	59.052	34.615	0.00	0.00	0.00	2.66
5124	5639	1.978617	CCTGTGATGGTGGTTGGCC	60.979	63.158	0.00	0.00	0.00	5.36
5308	5824	2.440409	CAACCTAGCAGAACTTGGCAT	58.560	47.619	0.00	0.00	44.36	4.40
5475	5993	2.689471	TGTGTATGGCATTGAAGCATCC	59.311	45.455	4.78	0.00	35.83	3.51
5524	6042	3.706373	GCTGGCTCTTGGGGACGA	61.706	66.667	0.00	0.00	0.00	4.20
5718	6237	3.170717	TCTTCGTATGGGTTCAAGGACT	58.829	45.455	0.00	0.00	0.00	3.85
5768	6293	1.812571	GGTCAAAAGATGGTGCATCGT	59.187	47.619	0.00	0.00	44.67	3.73
5846	6371	7.609146	ACTCACACTCATCAATACAAATCACAT	59.391	33.333	0.00	0.00	0.00	3.21
5884	6409	1.089920	GCGCATCCTTCATTCACAGT	58.910	50.000	0.30	0.00	0.00	3.55
5909	6434	1.752498	CTATTGCCTTGCCAGCATCAA	59.248	47.619	0.00	0.00	40.59	2.57
6111	6636	3.423539	AGCTTGTTCACTGCCTCATTA	57.576	42.857	0.00	0.00	0.00	1.90
6152	6677	0.904865	TCCTTCGTGATGCCTGACCT	60.905	55.000	0.00	0.00	0.00	3.85
6305	6831	5.234757	GTGCATGAAATTGAAAGCAGAACAA	59.765	36.000	0.00	0.00	32.03	2.83
6387	6921	6.013379	CCATACCTAATTATCTCAGGGCTGAA	60.013	42.308	0.00	0.00	39.39	3.02
6404	6940	7.195374	AGAAATGTAGAAAGCACCATACCTA	57.805	36.000	0.00	0.00	0.00	3.08
6448	6984	1.462616	CCATTGAACCGGCTTCATCA	58.537	50.000	16.70	5.57	38.74	3.07
6645	7184	3.659183	AGCATGGCTCAAACTCCTTAT	57.341	42.857	0.00	0.00	30.62	1.73

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.