AutoCloner

Multiple sequence alignment - TraesCS3A01G288500

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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	TraesCS3A01G288500	chr3A	100.000	6512	0	0	1	6512	516788584	516782073	0.000000e+00	12026
1	TraesCS3A01G288500	chr3A	79.250	2641	419	63	1809	4411	56560794	56558245	0.000000e+00	1722
2	TraesCS3A01G288500	chr3B	92.160	6582	363	55	16	6512	523146632	523140119	0.000000e+00	9154
3	TraesCS3A01G288500	chr3B	78.134	4244	675	137	1809	5975	69640951	69636884	0.000000e+00	2462
4	TraesCS3A01G288500	chr3D	94.760	3836	146	17	2727	6512	397186097	397182267	0.000000e+00	5919
5	TraesCS3A01G288500	chr3D	93.418	2765	114	16	1	2731	397200198	397197468	0.000000e+00	4036
6	TraesCS3A01G288500	chr2D	85.100	4396	485	100	1754	6032	192299025	192294683	0.000000e+00	4333
7	TraesCS3A01G288500	chr4A	83.004	4907	601	143	1721	6476	215127026	215131850	0.000000e+00	4226
8	TraesCS3A01G288500	chr5A	82.746	4909	613	145	1715	6476	555373696	555378517	0.000000e+00	4157
9	TraesCS3A01G288500	chr5A	82.739	4907	610	141	1721	6476	604815385	604810565	0.000000e+00	4150
10	TraesCS3A01G288500	chr5A	90.279	1687	133	20	1666	3340	644504330	644505997	0.000000e+00	2178
11	TraesCS3A01G288500	chr5A	80.761	894	125	25	770	1619	644503182	644504072	0.000000e+00	654
12	TraesCS3A01G288500	chr5A	81.047	860	115	19	849	1667	644484795	644485647	5.500000e-180	641
13	TraesCS3A01G288500	chr1D	84.845	3814	432	77	1549	5271	2860690	2864448	0.000000e+00	3707
14	TraesCS3A01G288500	chr1D	83.252	824	105	25	5265	6061	2873205	2874022	0.000000e+00	726
15	TraesCS3A01G288500	chr6B	84.105	3800	461	82	1721	5423	683642799	683639046	0.000000e+00	3539
16	TraesCS3A01G288500	chr6D	85.477	2644	291	56	1497	4083	439519924	439522531	0.000000e+00	2669
17	TraesCS3A01G288500	chr6D	84.056	2446	271	63	4098	6476	439541502	439543895	0.000000e+00	2246
18	TraesCS3A01G288500	chr6D	77.721	588	91	22	786	1353	439518777	439519344	2.260000e-84	324
19	TraesCS3A01G288500	chr7A	86.658	2226	239	46	3903	6107	301167464	301165276	0.000000e+00	2412
20	TraesCS3A01G288500	chr7D	85.676	2227	237	52	3903	6107	271057162	271054996	0.000000e+00	2270
21	TraesCS3A01G288500	chr1A	83.155	2333	307	69	3842	6107	496060131	496062444	0.000000e+00	2052
22	TraesCS3A01G288500	chr5B	85.605	917	89	24	1161	2044	97520493	97521399	0.000000e+00	922
23	TraesCS3A01G288500	chr2A	77.307	661	106	29	770	1412	571479140	571478506	3.740000e-92	350
24	TraesCS3A01G288500	chr2B	91.358	81	5	2	1	79	43288334	43288254	6.900000e-20	110

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	TraesCS3A01G288500	chr3A	516782073	516788584	6511	True	12026.0	12026	100.000	1	6512	1	chr3A.!!$R2	6511
1	TraesCS3A01G288500	chr3A	56558245	56560794	2549	True	1722.0	1722	79.250	1809	4411	1	chr3A.!!$R1	2602
2	TraesCS3A01G288500	chr3B	523140119	523146632	6513	True	9154.0	9154	92.160	16	6512	1	chr3B.!!$R2	6496
3	TraesCS3A01G288500	chr3B	69636884	69640951	4067	True	2462.0	2462	78.134	1809	5975	1	chr3B.!!$R1	4166
4	TraesCS3A01G288500	chr3D	397182267	397186097	3830	True	5919.0	5919	94.760	2727	6512	1	chr3D.!!$R1	3785
5	TraesCS3A01G288500	chr3D	397197468	397200198	2730	True	4036.0	4036	93.418	1	2731	1	chr3D.!!$R2	2730
6	TraesCS3A01G288500	chr2D	192294683	192299025	4342	True	4333.0	4333	85.100	1754	6032	1	chr2D.!!$R1	4278
7	TraesCS3A01G288500	chr4A	215127026	215131850	4824	False	4226.0	4226	83.004	1721	6476	1	chr4A.!!$F1	4755
8	TraesCS3A01G288500	chr5A	555373696	555378517	4821	False	4157.0	4157	82.746	1715	6476	1	chr5A.!!$F1	4761
9	TraesCS3A01G288500	chr5A	604810565	604815385	4820	True	4150.0	4150	82.739	1721	6476	1	chr5A.!!$R1	4755
10	TraesCS3A01G288500	chr5A	644503182	644505997	2815	False	1416.0	2178	85.520	770	3340	2	chr5A.!!$F3	2570
11	TraesCS3A01G288500	chr5A	644484795	644485647	852	False	641.0	641	81.047	849	1667	1	chr5A.!!$F2	818
12	TraesCS3A01G288500	chr1D	2860690	2864448	3758	False	3707.0	3707	84.845	1549	5271	1	chr1D.!!$F1	3722
13	TraesCS3A01G288500	chr1D	2873205	2874022	817	False	726.0	726	83.252	5265	6061	1	chr1D.!!$F2	796
14	TraesCS3A01G288500	chr6B	683639046	683642799	3753	True	3539.0	3539	84.105	1721	5423	1	chr6B.!!$R1	3702
15	TraesCS3A01G288500	chr6D	439541502	439543895	2393	False	2246.0	2246	84.056	4098	6476	1	chr6D.!!$F1	2378
16	TraesCS3A01G288500	chr6D	439518777	439522531	3754	False	1496.5	2669	81.599	786	4083	2	chr6D.!!$F2	3297
17	TraesCS3A01G288500	chr7A	301165276	301167464	2188	True	2412.0	2412	86.658	3903	6107	1	chr7A.!!$R1	2204
18	TraesCS3A01G288500	chr7D	271054996	271057162	2166	True	2270.0	2270	85.676	3903	6107	1	chr7D.!!$R1	2204
19	TraesCS3A01G288500	chr1A	496060131	496062444	2313	False	2052.0	2052	83.155	3842	6107	1	chr1A.!!$F1	2265
20	TraesCS3A01G288500	chr5B	97520493	97521399	906	False	922.0	922	85.605	1161	2044	1	chr5B.!!$F1	883
21	TraesCS3A01G288500	chr2A	571478506	571479140	634	True	350.0	350	77.307	770	1412	1	chr2A.!!$R1	642

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
309	313	0.319555	TCTTGTCGTCGCCAAAGAGG	60.320	55.000	0.00	0.00	41.84	3.69	F
799	807	0.465705	ATTCTCATCCGGATGCACGT	59.534	50.000	35.16	19.89	38.65	4.49	F
1095	1127	1.068083	CCATGTCGCCGAGCTACAT	59.932	57.895	9.27	9.27	43.89	2.29	F
2785	3576	0.401356	TCCTCAAGCTGCCATCAACA	59.599	50.000	0.00	0.00	0.00	3.33	F
3223	4031	2.029290	GCTGTGAAAGAGAACCCTACGA	60.029	50.000	0.00	0.00	0.00	3.43	F
4862	5762	1.202348	GTTGCTCCCATTTAGTGCCAC	59.798	52.381	0.00	0.00	0.00	5.01	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1284	1323	0.249398	GAAGGGAGTAGCGGCTCAAA	59.751	55.000	5.39	0.00	37.24	2.69	R
2007	2762	1.164662	ATCAGATCATGTGGCGCTGC	61.165	55.000	7.64	0.29	0.00	5.25	R
3047	3854	1.470051	TGCTGCGTATGGTGTCTCTA	58.530	50.000	0.00	0.00	0.00	2.43	R
4339	5213	2.113139	CGGCACTTGGTTCCCTGT	59.887	61.111	0.00	0.00	0.00	4.00	R
4937	5848	1.831343	GTTGAAGCTGCAACACACAG	58.169	50.000	29.38	0.00	45.65	3.66	R
5939	6957	0.321919	ATCGCCTTGTGCACATCAGT	60.322	50.000	22.39	2.21	41.33	3.41	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
99	103	2.500098	GGGTGCTAGACATAGGTCAACA	59.500	50.000	10.58	1.79	46.80	3.33
103	107	3.260632	TGCTAGACATAGGTCAACAGCAA	59.739	43.478	21.45	10.66	44.93	3.91
128	132	3.967326	TCACGGGACTTGGAGATAATCAT	59.033	43.478	0.00	0.00	0.00	2.45
130	134	5.243954	TCACGGGACTTGGAGATAATCATAG	59.756	44.000	0.00	0.00	0.00	2.23
141	145	8.890410	TGGAGATAATCATAGAGATGACATCA	57.110	34.615	17.57	0.00	44.90	3.07
239	243	2.275418	GTTCCCCATGGGCGACAT	59.725	61.111	26.87	0.00	43.94	3.06
309	313	0.319555	TCTTGTCGTCGCCAAAGAGG	60.320	55.000	0.00	0.00	41.84	3.69
347	351	7.940850	TCTTACTGAAAGAACCAAATCAAAGG	58.059	34.615	0.00	0.00	41.35	3.11
419	423	3.631144	CAAGCGAGAAAGCACAAAATGA	58.369	40.909	0.00	0.00	40.15	2.57
538	542	3.274288	TCATACTTGTGTTGTGTGCACA	58.726	40.909	17.42	17.42	44.05	4.57
543	547	5.065704	ACTTGTGTTGTGTGCACATTTTA	57.934	34.783	24.69	7.76	44.91	1.52
637	644	1.004277	TGTATCAACACTCTTGCCCCC	59.996	52.381	0.00	0.00	0.00	5.40
646	653	3.116551	ACACTCTTGCCCCCTATAGATCT	60.117	47.826	0.00	0.00	0.00	2.75
747	754	4.590647	TCAAGAATGGGGCAATTTAACACA	59.409	37.500	0.00	0.00	0.00	3.72
799	807	0.465705	ATTCTCATCCGGATGCACGT	59.534	50.000	35.16	19.89	38.65	4.49
855	863	2.717485	GGCGCATCGTACGGTCTA	59.283	61.111	16.52	0.00	0.00	2.59
985	1017	2.314647	GCAACAACGCAGGCGACTA	61.315	57.895	21.62	0.00	40.21	2.59
1003	1035	4.214332	CGACTACGAGATCCAGAATCATGA	59.786	45.833	0.00	0.00	42.66	3.07
1082	1114	4.760047	GAGCACCGTCGGCCATGT	62.760	66.667	12.28	0.00	0.00	3.21
1095	1127	1.068083	CCATGTCGCCGAGCTACAT	59.932	57.895	9.27	9.27	43.89	2.29
1144	1178	2.124151	GGTATGGTGCCCTGCAGG	60.124	66.667	26.87	26.87	40.08	4.85
1270	1309	9.914131	GAATGCATAGTATAGATGTGTTGTCTA	57.086	33.333	0.00	0.00	33.09	2.59
1284	1323	5.010282	GTGTTGTCTATTCAGGGGTTTCAT	58.990	41.667	0.00	0.00	0.00	2.57
1449	1543	2.314852	TGGAGGACTAGATTCCCAGTGA	59.685	50.000	0.00	0.00	36.12	3.41
1490	1587	5.646360	ACTATTTGGTTCGTCAAGTTATGGG	59.354	40.000	0.00	0.00	0.00	4.00
1498	1631	4.963373	TCGTCAAGTTATGGGTTTCTTGA	58.037	39.130	0.00	0.00	42.21	3.02
1619	2138	2.472723	GCGTTTTGCTGCATGTAATTGC	60.473	45.455	1.84	4.08	43.07	3.56
1652	2172	2.416747	TCTTTGAGCTGATTGTGTCGG	58.583	47.619	0.00	0.00	36.23	4.79
1800	2549	8.916654	CCATCGCTTTCTGTAGTAATTGTATAG	58.083	37.037	0.00	0.00	0.00	1.31
1928	2683	1.987704	AACACTTGCGCGAAGTTGCA	61.988	50.000	12.10	0.00	42.70	4.08
2007	2762	0.994995	CACGAGCATCTCACCTTTCG	59.005	55.000	0.00	0.00	0.00	3.46
2330	3097	6.493115	TCCACAACATTTATCACAAGAATGGT	59.507	34.615	0.00	0.00	35.60	3.55
2387	3154	3.234353	TCGAGCTAGGAATGATGATGGT	58.766	45.455	0.00	0.00	0.00	3.55
2525	3292	2.487762	TGAATTCGCTTGGGATGAACAC	59.512	45.455	0.04	0.00	0.00	3.32
2616	3393	3.984732	GGGTTGGGGGCTGCTTCT	61.985	66.667	0.00	0.00	0.00	2.85
2785	3576	0.401356	TCCTCAAGCTGCCATCAACA	59.599	50.000	0.00	0.00	0.00	3.33
2899	3690	2.418083	GGCAAAGCCTCATTCGGGG	61.418	63.158	0.00	0.00	46.69	5.73
3030	3837	8.361139	TCTTGTTTCTTTTTGTTTTGTGTCCTA	58.639	29.630	0.00	0.00	0.00	2.94
3040	3847	5.302360	TGTTTTGTGTCCTATAGTTTCGCT	58.698	37.500	0.00	0.00	0.00	4.93
3047	3854	4.705507	TGTCCTATAGTTTCGCTCTCTGTT	59.294	41.667	0.00	0.00	0.00	3.16
3223	4031	2.029290	GCTGTGAAAGAGAACCCTACGA	60.029	50.000	0.00	0.00	0.00	3.43
3414	4254	6.702449	TCATATGGTAAGTTGCATCCCTAT	57.298	37.500	2.13	0.00	0.00	2.57
3501	4341	8.245491	TCTACGACAAGCACACAAAACTATATA	58.755	33.333	0.00	0.00	0.00	0.86
3503	4343	7.515643	ACGACAAGCACACAAAACTATATAAC	58.484	34.615	0.00	0.00	0.00	1.89
3540	4380	2.105134	TCTCCAAGTTCTTACGGGCAAA	59.895	45.455	0.00	0.00	0.00	3.68
3667	4507	3.005554	CTCCTCACAGCAATGTTGTAGG	58.994	50.000	1.68	10.11	0.00	3.18
3692	4532	4.096681	AGTCAGATGGTCATGGTTGTAGA	58.903	43.478	0.00	0.00	0.00	2.59
3879	4727	3.745975	CCTTGCACGATGTTTTGAGACTA	59.254	43.478	0.00	0.00	0.00	2.59
3891	4739	8.697507	ATGTTTTGAGACTACAAAGGAGAAAT	57.302	30.769	0.00	0.00	40.15	2.17
4204	5064	5.012458	CCTCTATGGCTCCATTATCAAGTGA	59.988	44.000	6.73	0.00	37.82	3.41
4339	5213	4.040461	AGAGCCAGTTGTTCTAGTTAGCAA	59.960	41.667	0.00	0.00	0.00	3.91
4404	5278	3.910568	AGGATGAGAAGAAGCTCAAGG	57.089	47.619	0.00	0.00	46.94	3.61
4462	5336	8.454106	CGGATCAAAGTACAAGAAAATCAAGAT	58.546	33.333	0.00	0.00	0.00	2.40
4552	5438	9.823647	GGAAATTGAGTAAGTATCATCTTCTCA	57.176	33.333	0.00	0.00	33.91	3.27
4668	5565	4.140536	CAGGCCTCCTTTCATTAGGATTC	58.859	47.826	0.00	0.00	43.24	2.52
4702	5599	5.995897	ACATTACCTACACCAACTTTCAGAC	59.004	40.000	0.00	0.00	0.00	3.51
4777	5674	7.769272	TTGAAACCTTCAACATTGAACAATC	57.231	32.000	2.89	1.68	44.21	2.67
4862	5762	1.202348	GTTGCTCCCATTTAGTGCCAC	59.798	52.381	0.00	0.00	0.00	5.01
4937	5848	8.094548	ACTTTTTCTTATGTTTTTCTATGCCCC	58.905	33.333	0.00	0.00	0.00	5.80
5006	5918	3.475566	AGTGTTTGTGCAAGAGAGCTA	57.524	42.857	0.00	0.00	34.99	3.32
5014	5926	1.199615	GCAAGAGAGCTAAGGAGGGT	58.800	55.000	0.00	0.00	0.00	4.34
5052	5964	8.383175	TCCAGATTTCAGTTTTTGACCTAGTAT	58.617	33.333	0.00	0.00	34.94	2.12
5380	6323	9.121517	CATGTGTTCAAAATCTTGATAGTGAAC	57.878	33.333	20.64	20.64	41.22	3.18
5554	6525	6.881602	GTGGATTTATCTTCTCTCAAACCAGT	59.118	38.462	0.00	0.00	0.00	4.00
5726	6709	7.340122	TGATTGTGGATTGTTTTCAACACTA	57.660	32.000	0.00	0.00	42.94	2.74
5939	6957	1.455849	CTGAACAAGGTCTGCCCCA	59.544	57.895	0.00	0.00	34.57	4.96
6009	7028	2.671914	GCATTGAAGAAGGCGATTGCAA	60.672	45.455	7.38	0.00	45.35	4.08
6010	7029	3.577667	CATTGAAGAAGGCGATTGCAAA	58.422	40.909	1.71	0.00	45.35	3.68
6066	7091	9.104965	GTTAATACATTATTGCCAGTAGTGTGA	57.895	33.333	5.77	0.00	0.00	3.58
6107	7136	7.092716	GTCAAATGAACTCCATGTAAAGCAAT	58.907	34.615	0.00	0.00	35.24	3.56
6128	7178	1.260544	GCTTGGCTGGAATGGTTCTT	58.739	50.000	0.00	0.00	0.00	2.52
6194	7244	2.289756	TGTTGGAAGCTATAACCGTGCA	60.290	45.455	0.00	0.00	0.00	4.57
6264	7316	9.196552	CTCAACCTTTTCAAGTTTTATGGAATC	57.803	33.333	0.00	0.00	0.00	2.52
6315	7368	8.445275	TTCATGTGTGTTTTTCTAGTATGTGT	57.555	30.769	0.00	0.00	0.00	3.72
6378	7431	7.517614	TGTCAGCAACAATGTTAAGGAATTA	57.482	32.000	0.00	0.00	34.03	1.40
6379	7432	8.121305	TGTCAGCAACAATGTTAAGGAATTAT	57.879	30.769	0.00	0.00	34.03	1.28
6494	7558	7.625553	CAGCTTTGACATAATACTAGAAGCAC	58.374	38.462	0.00	0.00	40.36	4.40

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
12	15	6.210522	ACCTTCCATCCCTAACTAATACACT	58.789	40.000	0.00	0.00	0.00	3.55
141	145	4.318332	CATCTGTTACCGGCATACATCAT	58.682	43.478	0.00	0.00	0.00	2.45
147	151	0.833949	TGGCATCTGTTACCGGCATA	59.166	50.000	0.00	0.00	0.00	3.14
153	157	2.638480	TAGCCATGGCATCTGTTACC	57.362	50.000	37.18	4.97	44.88	2.85
239	243	1.483415	GTAGGTTTAGGTCATCGCCCA	59.517	52.381	0.00	0.00	0.00	5.36
245	249	4.323562	GCAGTGAAGGTAGGTTTAGGTCAT	60.324	45.833	0.00	0.00	0.00	3.06
312	316	5.862924	TCTTTCAGTAAGATGCCGAAAAG	57.137	39.130	0.00	0.00	37.96	2.27
314	318	4.454504	GGTTCTTTCAGTAAGATGCCGAAA	59.545	41.667	0.00	0.00	42.32	3.46
320	324	9.403110	CTTTGATTTGGTTCTTTCAGTAAGATG	57.597	33.333	0.00	0.00	42.32	2.90
347	351	6.793349	TGCGTAGATCTCTTAGTAAAACCTC	58.207	40.000	0.00	0.00	0.00	3.85
444	448	7.014038	GGACATTCTCAGAATCAAAAGGCATAT	59.986	37.037	0.00	0.00	0.00	1.78
483	487	4.024048	GGCAACAAACAGAAATTCTCGAGA	60.024	41.667	12.08	12.08	0.00	4.04
543	547	9.341078	ACAAATGGAGTGCATTTAAAGAAATTT	57.659	25.926	20.54	0.00	32.73	1.82
700	707	7.167302	TGACATAGAAAAAGCAAAAACGACATG	59.833	33.333	0.00	0.00	0.00	3.21
747	754	1.429687	AGTGAGTACTCCTCCCTGTGT	59.570	52.381	20.11	0.00	39.65	3.72
812	820	1.659794	GACGGCATGCAAGTTGGTT	59.340	52.632	21.36	0.00	0.00	3.67
817	825	1.815421	GATCCGACGGCATGCAAGT	60.815	57.895	21.36	18.59	0.00	3.16
855	863	0.622665	CCCCTGGTCAGAAAGCATCT	59.377	55.000	0.00	0.00	39.68	2.90
985	1017	2.035193	CCGTCATGATTCTGGATCTCGT	59.965	50.000	0.00	0.00	35.69	4.18
1082	1114	2.782222	GGGTCATGTAGCTCGGCGA	61.782	63.158	10.14	10.14	0.00	5.54
1119	1153	2.506065	GGCACCATACCTCTCGTCT	58.494	57.895	0.00	0.00	0.00	4.18
1144	1178	1.405463	GGGGGAGAAAAATGATGCGAC	59.595	52.381	0.00	0.00	0.00	5.19
1238	1273	5.480422	ACATCTATACTATGCATTCGACCCA	59.520	40.000	3.54	0.00	0.00	4.51
1270	1309	2.833943	GGCTCAAATGAAACCCCTGAAT	59.166	45.455	0.00	0.00	0.00	2.57
1284	1323	0.249398	GAAGGGAGTAGCGGCTCAAA	59.751	55.000	5.39	0.00	37.24	2.69
1477	1574	5.181245	ACATCAAGAAACCCATAACTTGACG	59.819	40.000	0.00	0.00	46.87	4.35
1652	2172	5.466819	AGAAAAACTAAACAATTAGCCGCC	58.533	37.500	0.00	0.00	41.92	6.13
1800	2549	5.715434	AATGTATTGGGTACAAACACCAC	57.285	39.130	0.00	0.00	45.87	4.16
1928	2683	8.691661	TCTTGCTAGGATTAAGTTTTGTCTTT	57.308	30.769	0.00	0.00	0.00	2.52
2007	2762	1.164662	ATCAGATCATGTGGCGCTGC	61.165	55.000	7.64	0.29	0.00	5.25
2330	3097	2.701423	TGTATGCGTAATTGGAGCCCTA	59.299	45.455	0.00	0.00	0.00	3.53
2387	3154	5.030147	ACCCATGACCTCTTTGTAGTATCA	58.970	41.667	0.00	0.00	0.00	2.15
2525	3292	5.747565	TCTCTCATTGCAACACTTAAAACG	58.252	37.500	0.00	0.00	0.00	3.60
2616	3393	3.409570	AGAAGTATACCGCGAGCATAGA	58.590	45.455	8.23	0.00	0.00	1.98
2785	3576	7.178983	TGGAAGAGAATAATTCAATTGGTGCTT	59.821	33.333	5.42	0.00	0.00	3.91
2899	3690	5.019498	CACACAAAAACTTACACGACACTC	58.981	41.667	0.00	0.00	0.00	3.51
3047	3854	1.470051	TGCTGCGTATGGTGTCTCTA	58.530	50.000	0.00	0.00	0.00	2.43
3223	4031	0.475044	TCCGTTGGGTTGCTACCTTT	59.525	50.000	17.03	0.00	44.38	3.11
3501	4341	3.317149	GGAGACCCTTTTAACTTTGCGTT	59.683	43.478	0.00	0.00	39.64	4.84
3503	4343	2.882137	TGGAGACCCTTTTAACTTTGCG	59.118	45.455	0.00	0.00	0.00	4.85
3519	4359	1.344065	TGCCCGTAAGAACTTGGAGA	58.656	50.000	0.00	0.00	43.02	3.71
3667	4507	2.119801	ACCATGACCATCTGACTTGC	57.880	50.000	0.00	0.00	0.00	4.01
3692	4532	4.914581	ACCTTCTCCCTAGAACTTTCCTTT	59.085	41.667	0.00	0.00	36.80	3.11
3809	4655	2.743718	CCCAGCTCAACCACGTCT	59.256	61.111	0.00	0.00	0.00	4.18
3843	4689	2.682856	GTGCAAGGTTCTCACTGACAAA	59.317	45.455	0.00	0.00	0.00	2.83
3879	4727	3.891366	CCACTGGACAATTTCTCCTTTGT	59.109	43.478	0.00	0.00	38.71	2.83
3891	4739	5.491070	CTCAATATCTTCACCACTGGACAA	58.509	41.667	0.71	0.00	0.00	3.18
4204	5064	2.365635	AGGGCATACCGGCAGTCT	60.366	61.111	0.00	0.00	46.96	3.24
4339	5213	2.113139	CGGCACTTGGTTCCCTGT	59.887	61.111	0.00	0.00	0.00	4.00
4404	5278	3.601435	GACTCCCTACTCTTTTCTTGCC	58.399	50.000	0.00	0.00	0.00	4.52
4462	5336	3.861276	TTGCTTCCGTCTTCGAATCTA	57.139	42.857	0.00	0.00	39.71	1.98
4702	5599	3.334751	TGCGTGGCTTCAACGACG	61.335	61.111	0.00	0.00	34.93	5.12
4777	5674	4.621460	TCTTCTGCTTATTTGAAGACGACG	59.379	41.667	0.00	0.00	40.54	5.12
4937	5848	1.831343	GTTGAAGCTGCAACACACAG	58.169	50.000	29.38	0.00	45.65	3.66
5006	5918	2.101640	AATTTTGGCACACCCTCCTT	57.898	45.000	0.00	0.00	39.29	3.36
5014	5926	5.163322	ACTGAAATCTGGAAATTTTGGCACA	60.163	36.000	0.00	0.00	0.00	4.57
5148	6069	7.255625	GGATGGTGAAGAAAAGCTAGAAAAAGT	60.256	37.037	0.00	0.00	0.00	2.66
5380	6323	4.755123	ACTAAAACTTCAGACACATTCGGG	59.245	41.667	0.00	0.00	0.00	5.14
5544	6515	0.607489	CAGGGGCAGACTGGTTTGAG	60.607	60.000	4.26	0.00	32.38	3.02
5554	6525	1.553690	GGTAGTCAAGCAGGGGCAGA	61.554	60.000	0.00	0.00	44.61	4.26
5726	6709	3.754323	TGCCGTCGAAATTTTCCAAGTAT	59.246	39.130	3.61	0.00	0.00	2.12
5939	6957	0.321919	ATCGCCTTGTGCACATCAGT	60.322	50.000	22.39	2.21	41.33	3.41
6037	7062	9.935682	CACTACTGGCAATAATGTATTAACAAG	57.064	33.333	0.00	0.00	39.58	3.16
6041	7066	9.845740	ATCACACTACTGGCAATAATGTATTAA	57.154	29.630	0.00	0.00	0.00	1.40
6107	7136	0.968405	GAACCATTCCAGCCAAGCAA	59.032	50.000	0.00	0.00	0.00	3.91
6154	7204	9.906660	TTCCAACAAAATCACTGAAACATATAC	57.093	29.630	0.00	0.00	0.00	1.47
6194	7244	2.456577	ACTTGCTTCCAACAAACCACT	58.543	42.857	0.00	0.00	0.00	4.00
6264	7316	8.702163	AACATTTGTAACAAAAACTGAGAAGG	57.298	30.769	0.00	0.00	0.00	3.46
6315	7368	6.403866	ACAATTTGTGACAAGATAAGGCAA	57.596	33.333	0.15	0.00	0.00	4.52
6378	7431	4.701651	TCATGAGCATGCTTCCTCTAAT	57.298	40.909	23.61	4.66	38.65	1.73
6379	7432	4.492494	TTCATGAGCATGCTTCCTCTAA	57.508	40.909	23.61	9.14	38.65	2.10

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.