AutoCloner

Multiple sequence alignment - TraesCS1D01G295100

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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	TraesCS1D01G295100	chr1D	100.000	3455	0	0	1	3455	394058320	394061774	0.000000e+00	6381.0
1	TraesCS1D01G295100	chr1D	100.000	1312	0	0	3708	5019	394062027	394063338	0.000000e+00	2423.0
2	TraesCS1D01G295100	chr1B	91.539	2671	121	49	1	2639	528362018	528359421	0.000000e+00	3583.0
3	TraesCS1D01G295100	chr1B	91.828	930	62	11	3929	4849	528357741	528356817	0.000000e+00	1284.0
4	TraesCS1D01G295100	chr1B	95.584	770	34	0	2686	3455	528359100	528358331	0.000000e+00	1234.0
5	TraesCS1D01G295100	chr1B	93.165	278	18	1	1199	1475	614498855	614499132	1.680000e-109	407.0
6	TraesCS1D01G295100	chr1A	97.259	1204	28	2	1914	3113	491264277	491263075	0.000000e+00	2036.0
7	TraesCS1D01G295100	chr1A	94.883	1192	55	5	3831	5019	491250145	491248957	0.000000e+00	1858.0
8	TraesCS1D01G295100	chr1A	93.421	608	27	7	396	998	491268592	491267993	0.000000e+00	889.0
9	TraesCS1D01G295100	chr1A	97.391	345	9	0	3111	3455	491252355	491252011	5.600000e-164	588.0
10	TraesCS1D01G295100	chr1A	92.105	418	27	4	980	1392	491264686	491264270	7.240000e-163	584.0
11	TraesCS1D01G295100	chr1A	94.505	273	9	5	1	270	491268860	491268591	2.800000e-112	416.0
12	TraesCS1D01G295100	chr1A	89.820	167	12	3	713	878	271887429	271887591	5.090000e-50	209.0
13	TraesCS1D01G295100	chr1A	86.772	189	18	7	692	878	290344444	290344261	2.370000e-48	204.0
14	TraesCS1D01G295100	chr1A	82.278	158	19	9	4825	4975	199913689	199913844	1.470000e-25	128.0
15	TraesCS1D01G295100	chr1A	82.313	147	22	3	4821	4964	108355909	108355764	1.900000e-24	124.0
16	TraesCS1D01G295100	chr6D	83.871	465	55	16	4437	4890	175709498	175709953	4.640000e-115	425.0
17	TraesCS1D01G295100	chr6D	92.727	275	20	0	1199	1473	85809972	85809698	1.010000e-106	398.0
18	TraesCS1D01G295100	chr4A	93.818	275	17	0	1199	1473	618681051	618681325	1.010000e-111	414.0
19	TraesCS1D01G295100	chr4A	91.250	160	9	3	720	878	457823943	457823788	3.940000e-51	213.0
20	TraesCS1D01G295100	chr3D	91.727	278	22	1	1199	1475	34726593	34726316	7.880000e-103	385.0
21	TraesCS1D01G295100	chr3D	79.653	403	59	21	4432	4828	320640448	320640833	8.280000e-68	268.0
22	TraesCS1D01G295100	chr3B	91.007	278	24	1	1199	1476	57394227	57393951	1.710000e-99	374.0
23	TraesCS1D01G295100	chr3B	80.829	386	43	29	4518	4889	56090048	56090416	1.780000e-69	274.0
24	TraesCS1D01G295100	chr6A	90.681	279	25	1	1198	1475	103248505	103248227	2.210000e-98	370.0
25	TraesCS1D01G295100	chr6A	89.080	174	12	4	707	878	7988650	7988482	5.090000e-50	209.0
26	TraesCS1D01G295100	chr6A	84.091	132	12	9	4825	4949	95204985	95205114	8.830000e-23	119.0
27	TraesCS1D01G295100	chr7D	90.288	278	26	1	1199	1475	58772104	58772381	3.690000e-96	363.0
28	TraesCS1D01G295100	chr7D	87.879	198	22	2	3989	4185	28009244	28009440	1.090000e-56	231.0
29	TraesCS1D01G295100	chr5A	83.028	436	38	21	4432	4855	632667577	632667166	3.690000e-96	363.0
30	TraesCS1D01G295100	chr5A	82.493	377	51	13	4432	4801	242948170	242947802	2.920000e-82	316.0
31	TraesCS1D01G295100	chr2A	81.156	467	60	23	4432	4890	339088497	339088051	2.880000e-92	350.0
32	TraesCS1D01G295100	chr2A	83.333	198	27	6	4827	5019	135823498	135823302	1.440000e-40	178.0
33	TraesCS1D01G295100	chr5B	83.791	364	41	16	4505	4860	153881952	153882305	3.750000e-86	329.0
34	TraesCS1D01G295100	chr2B	84.821	224	29	5	3992	4212	148235127	148234906	2.350000e-53	220.0
35	TraesCS1D01G295100	chr2B	96.970	33	0	1	557	588	651649296	651649264	3.000000e-03	54.7
36	TraesCS1D01G295100	chr3A	88.827	179	13	4	702	878	68866474	68866647	3.940000e-51	213.0
37	TraesCS1D01G295100	chr3A	91.250	160	9	3	720	878	701344488	701344643	3.940000e-51	213.0
38	TraesCS1D01G295100	chr3A	80.769	182	25	10	4821	4995	532439744	532439922	3.150000e-27	134.0
39	TraesCS1D01G295100	chr3A	81.579	152	17	10	4821	4965	359219097	359218950	1.140000e-21	115.0
40	TraesCS1D01G295100	chr5D	89.017	173	12	4	708	878	488352314	488352481	1.830000e-49	207.0
41	TraesCS1D01G295100	chr6B	81.773	203	30	6	4822	5019	698965395	698965595	4.020000e-36	163.0
42	TraesCS1D01G295100	chr4B	100.000	29	0	0	557	585	524138988	524138960	3.000000e-03	54.7

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	TraesCS1D01G295100	chr1D	394058320	394063338	5018	False	4402.000000	6381	100.000000	1	5019	2	chr1D.!!$F1	5018
1	TraesCS1D01G295100	chr1B	528356817	528362018	5201	True	2033.666667	3583	92.983667	1	4849	3	chr1B.!!$R1	4848
2	TraesCS1D01G295100	chr1A	491248957	491252355	3398	True	1223.000000	1858	96.137000	3111	5019	2	chr1A.!!$R3	1908
3	TraesCS1D01G295100	chr1A	491263075	491268860	5785	True	981.250000	2036	94.322500	1	3113	4	chr1A.!!$R4	3112

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
437	462	0.249531	TTCTTGTTCACTACGCGGCA	60.250	50.0	12.47	0.00	0.00	5.69	F
1561	4920	0.238289	GACACCAGTTGCAATCACGG	59.762	55.0	0.59	3.58	0.00	4.94	F
1637	4997	0.037790	GCGACTCTGCCTTGAACTCT	60.038	55.0	0.00	0.00	0.00	3.24	F
2445	5810	0.108585	GGAGGACAGGCACTTTGTCA	59.891	55.0	6.89	0.00	45.23	3.58	F
3914	9275	0.094558	GTGTGTGTGTGTGTGTGTCG	59.905	55.0	0.00	0.00	0.00	4.35	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1638	4998	0.319083	TGGATCACGCGGTACAACTT	59.681	50.000	12.47	0.00	0.0	2.66	R
2445	5810	0.671781	GTCACTGCATCGCCTTGTCT	60.672	55.000	0.00	0.00	0.0	3.41	R
2782	6441	1.064017	TCCCCAAATACAGACATGGCC	60.064	52.381	0.00	0.00	0.0	5.36	R
3914	9275	0.166814	GAATCAACACAGAGGCGCAC	59.833	55.000	10.83	2.06	0.0	5.34	R
4869	10545	1.596496	CCCCTCACTTACCCCTTCAT	58.404	55.000	0.00	0.00	0.0	2.57	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
28	29	9.571810	TCATGAACTTTTTATCGAAATTGATGG	57.428	29.630	0.00	0.00	0.00	3.51
182	185	6.630443	CGTGAACAATTCTTGAGTTTGAAGAG	59.370	38.462	0.00	0.00	31.17	2.85
236	239	9.334693	GAATTCATGAACATTTCTTGAGTACAC	57.665	33.333	11.07	0.00	42.46	2.90
360	385	1.512926	CCGGTCAACCTCTTCACTTG	58.487	55.000	0.00	0.00	0.00	3.16
371	396	4.529769	ACCTCTTCACTTGTCATCTGATCA	59.470	41.667	0.00	0.00	0.00	2.92
381	406	2.102578	TCATCTGATCAAGCGACCTCA	58.897	47.619	0.00	0.00	0.00	3.86
394	419	1.586154	GACCTCACATTGTTGGGCCG	61.586	60.000	0.00	0.00	0.00	6.13
437	462	0.249531	TTCTTGTTCACTACGCGGCA	60.250	50.000	12.47	0.00	0.00	5.69
567	595	7.664082	ATGTGTGAACAAACATTTGAAAACA	57.336	28.000	11.24	8.47	40.55	2.83
821	851	7.764695	AAAAGAAAAAGAAAATACCCACACG	57.235	32.000	0.00	0.00	0.00	4.49
851	881	5.230942	CCCGTAAGATCAATGACATAGGAC	58.769	45.833	0.00	0.00	43.02	3.85
1091	4445	2.135933	GACCAGTTACTGCTGTGTGTC	58.864	52.381	6.88	4.30	34.84	3.67
1096	4450	1.404479	TTACTGCTGTGTGTCCCCGT	61.404	55.000	6.48	0.00	0.00	5.28
1146	4501	2.406616	CCAGAAAATGGGCCGACCG	61.407	63.158	0.00	0.00	46.36	4.79
1172	4527	1.048601	GATCCCCCGAAGTGCTATCA	58.951	55.000	0.00	0.00	0.00	2.15
1235	4590	1.852157	ATGCGGTGGTGTTCTCCCAT	61.852	55.000	0.00	0.00	33.76	4.00
1272	4627	1.073125	TGTTCTCATCCTTTTCCGGCA	59.927	47.619	0.00	0.00	0.00	5.69
1438	4797	7.394016	ACCATATGTGTAATCTCTGTGAACAA	58.606	34.615	1.24	0.00	0.00	2.83
1561	4920	0.238289	GACACCAGTTGCAATCACGG	59.762	55.000	0.59	3.58	0.00	4.94
1592	4952	1.808390	GGACGGGTCGAAATCACGG	60.808	63.158	1.09	0.00	35.91	4.94
1595	4955	2.822701	GGGTCGAAATCACGGGCC	60.823	66.667	0.00	0.00	0.00	5.80
1634	4994	3.016474	GCGCGACTCTGCCTTGAAC	62.016	63.158	12.10	0.00	0.00	3.18
1635	4995	1.373497	CGCGACTCTGCCTTGAACT	60.373	57.895	0.00	0.00	0.00	3.01
1636	4996	1.347817	CGCGACTCTGCCTTGAACTC	61.348	60.000	0.00	0.00	0.00	3.01
1637	4997	0.037790	GCGACTCTGCCTTGAACTCT	60.038	55.000	0.00	0.00	0.00	3.24
1638	4998	1.202582	GCGACTCTGCCTTGAACTCTA	59.797	52.381	0.00	0.00	0.00	2.43
1639	4999	2.352814	GCGACTCTGCCTTGAACTCTAA	60.353	50.000	0.00	0.00	0.00	2.10
1640	5000	3.506810	CGACTCTGCCTTGAACTCTAAG	58.493	50.000	0.00	0.00	0.00	2.18
1708	5069	2.901042	CCTCTAACTCCCGCCACC	59.099	66.667	0.00	0.00	0.00	4.61
1891	5252	4.845580	CCCTCTGCGCGGCATCTT	62.846	66.667	12.58	0.00	38.13	2.40
1892	5253	3.267860	CCTCTGCGCGGCATCTTC	61.268	66.667	12.58	0.00	38.13	2.87
1893	5254	3.624300	CTCTGCGCGGCATCTTCG	61.624	66.667	12.58	0.00	38.13	3.79
1894	5255	4.435436	TCTGCGCGGCATCTTCGT	62.435	61.111	12.58	0.00	38.13	3.85
1895	5256	3.918220	CTGCGCGGCATCTTCGTC	61.918	66.667	8.83	0.00	38.13	4.20
1898	5259	3.607987	CGCGGCATCTTCGTCGAC	61.608	66.667	5.18	5.18	32.30	4.20
1899	5260	2.202623	GCGGCATCTTCGTCGACT	60.203	61.111	14.70	0.00	0.00	4.18
1900	5261	1.805945	GCGGCATCTTCGTCGACTT	60.806	57.895	14.70	0.00	0.00	3.01
1917	5278	4.616747	GACTTCTTCGACAACTTCTTCG	57.383	45.455	0.00	0.00	36.55	3.79
2445	5810	0.108585	GGAGGACAGGCACTTTGTCA	59.891	55.000	6.89	0.00	45.23	3.58
2777	6436	1.599542	ACTAACGACTACGGGTATCGC	59.400	52.381	0.00	0.00	44.46	4.58
2782	6441	2.225019	ACGACTACGGGTATCGCATTAG	59.775	50.000	0.00	0.00	44.46	1.73
3259	6918	4.771577	AGGCGATACTCTTCTCATCATGAT	59.228	41.667	1.18	1.18	0.00	2.45
3431	7090	7.935520	TGTGTGCAACTTTATGAAATTCTACA	58.064	30.769	0.00	0.00	38.04	2.74
3774	7433	6.817765	TTTTCGCTGTCAGATCCTTAATTT	57.182	33.333	3.32	0.00	0.00	1.82
3850	9207	2.277247	GCGTGTGTGTGTGTGTGC	60.277	61.111	0.00	0.00	0.00	4.57
3876	9237	3.860125	GCGTGCGTGTGTGTGTGT	61.860	61.111	0.00	0.00	0.00	3.72
3880	9241	1.669437	TGCGTGTGTGTGTGTGTGT	60.669	52.632	0.00	0.00	0.00	3.72
3884	9245	0.871722	GTGTGTGTGTGTGTGTGTGT	59.128	50.000	0.00	0.00	0.00	3.72
3905	9266	2.021243	CGTGCGTGTGTGTGTGTG	59.979	61.111	0.00	0.00	0.00	3.82
3914	9275	0.094558	GTGTGTGTGTGTGTGTGTCG	59.905	55.000	0.00	0.00	0.00	4.35
3916	9277	0.094558	GTGTGTGTGTGTGTGTCGTG	59.905	55.000	0.00	0.00	0.00	4.35
4073	9743	6.410540	CAAATCAGCTAGAAGAAACCTAGGT	58.589	40.000	9.21	9.21	43.36	3.08
4096	9766	4.899457	TGGATCACCGTCCTAACAGATTAT	59.101	41.667	0.00	0.00	39.12	1.28
4123	9793	8.518702	AGAGTTTGAATCAAAAGATTTCTAGCC	58.481	33.333	10.27	0.00	35.03	3.93
4124	9794	7.308435	AGTTTGAATCAAAAGATTTCTAGCCG	58.692	34.615	10.27	0.00	35.03	5.52
4151	9821	1.080569	GCCATTGTGTTTGCCTCCG	60.081	57.895	0.00	0.00	0.00	4.63
4159	9829	0.249868	TGTTTGCCTCCGTCAGACAG	60.250	55.000	0.41	0.00	0.00	3.51
4160	9830	0.951040	GTTTGCCTCCGTCAGACAGG	60.951	60.000	0.41	1.86	0.00	4.00
4185	9855	7.035612	GGAGTAAATTGAACATCACCAATTCC	58.964	38.462	0.00	0.00	40.78	3.01
4201	9871	4.142816	CCAATTCCGTGAGCTAAGTGAAAG	60.143	45.833	0.00	0.00	0.00	2.62
4354	10024	2.436109	GGGTTGCTTCTGGGCTGA	59.564	61.111	0.00	0.00	0.00	4.26
4359	10029	1.758440	TTGCTTCTGGGCTGACGACT	61.758	55.000	0.00	0.00	0.00	4.18
4466	10138	0.618458	TCTTCACGAATTGGAGGGGG	59.382	55.000	0.00	0.00	30.47	5.40
4491	10165	2.158813	TGAGGAGGGACACAAAGAACAC	60.159	50.000	0.00	0.00	0.00	3.32
4671	10347	4.645535	TGAGTCTTGAAGATTCACTTGGG	58.354	43.478	15.24	0.00	36.27	4.12
4701	10377	3.375699	TCCCTTAGGAGGTCTTGATGAC	58.624	50.000	0.00	0.00	41.85	3.06
4869	10545	6.200114	GGGGGAGTATATATAGTACAAGCCA	58.800	44.000	11.26	0.00	0.00	4.75
4885	10561	1.561542	AGCCATGAAGGGGTAAGTGAG	59.438	52.381	0.00	0.00	36.76	3.51
4898	10574	0.475044	AAGTGAGGGGCAAAACGGTA	59.525	50.000	0.00	0.00	0.00	4.02
4906	10582	1.248101	GGCAAAACGGTACATGGGCT	61.248	55.000	0.00	0.00	0.00	5.19
4964	10640	2.346365	GGAACGGCCGGAAGTTCT	59.654	61.111	31.76	2.42	44.33	3.01
5000	10676	3.830192	GCAAGCTTCCGGGCATGG	61.830	66.667	0.00	0.00	32.45	3.66

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
335	340	0.613777	AAGAGGTTGACCGGGATCAC	59.386	55.000	6.32	0.00	42.08	3.06
360	385	2.159184	TGAGGTCGCTTGATCAGATGAC	60.159	50.000	12.36	12.36	0.00	3.06
371	396	1.238439	CCAACAATGTGAGGTCGCTT	58.762	50.000	0.00	0.00	0.00	4.68
381	406	2.282887	GGTCCGGCCCAACAATGT	60.283	61.111	0.00	0.00	0.00	2.71
431	456	0.028242	TAAGTGTTTGTTGTGCCGCG	59.972	50.000	0.00	0.00	0.00	6.46
437	462	3.136626	AGCTCCTCCTAAGTGTTTGTTGT	59.863	43.478	0.00	0.00	0.00	3.32
611	639	7.712797	TCCAAGAAGTGTTAGGAAATTTCAAC	58.287	34.615	19.49	15.45	0.00	3.18
690	719	7.391016	CCATTGAAAAACTGTTCGTCTTTTTC	58.609	34.615	7.55	7.55	41.32	2.29
704	733	5.624509	GCCCTAGACATTCCCATTGAAAAAC	60.625	44.000	0.00	0.00	36.33	2.43
808	837	3.617284	GGGAGATTCGTGTGGGTATTTT	58.383	45.455	0.00	0.00	0.00	1.82
821	851	4.991687	GTCATTGATCTTACGGGGAGATTC	59.008	45.833	0.00	0.00	34.13	2.52
851	881	6.806388	TGCCATATGTATTGCACATCTAAG	57.194	37.500	1.24	0.00	44.99	2.18
1071	4425	2.135933	GACACACAGCAGTAACTGGTC	58.864	52.381	0.00	0.00	40.40	4.02
1146	4501	2.640184	CACTTCGGGGGATCTAAAACC	58.360	52.381	0.00	0.00	0.00	3.27
1172	4527	1.303317	GAGGCGACCAAACCCACAT	60.303	57.895	0.00	0.00	0.00	3.21
1235	4590	5.186215	TGAGAACAACCGTCATACCAAGATA	59.814	40.000	0.00	0.00	0.00	1.98
1291	4650	3.478857	AACATAGTCCACAAACGTCCA	57.521	42.857	0.00	0.00	0.00	4.02
1398	4757	2.961526	ATGGTCACCATACGAGACAC	57.038	50.000	7.87	0.00	43.19	3.67
1475	4834	2.415512	GGAAAATCGTATATGGCGCTCC	59.584	50.000	7.64	0.00	0.00	4.70
1476	4835	3.064207	TGGAAAATCGTATATGGCGCTC	58.936	45.455	7.64	0.00	0.00	5.03
1519	4878	1.139734	CGTCAGCACCGTCATAGCT	59.860	57.895	0.00	0.00	39.63	3.32
1577	4937	3.192922	GCCCGTGATTTCGACCCG	61.193	66.667	0.00	0.00	0.00	5.28
1587	4947	1.202879	ACTGAAAAATCTGGCCCGTGA	60.203	47.619	0.00	0.00	0.00	4.35
1592	4952	2.291605	ACCCCTACTGAAAAATCTGGCC	60.292	50.000	0.00	0.00	0.00	5.36
1595	4955	3.127030	GCGAACCCCTACTGAAAAATCTG	59.873	47.826	0.00	0.00	0.00	2.90
1625	4985	4.638304	GGTACAACTTAGAGTTCAAGGCA	58.362	43.478	0.00	0.00	36.03	4.75
1634	4994	2.624316	TCACGCGGTACAACTTAGAG	57.376	50.000	12.47	0.00	0.00	2.43
1635	4995	2.159338	GGATCACGCGGTACAACTTAGA	60.159	50.000	12.47	0.00	0.00	2.10
1636	4996	2.190981	GGATCACGCGGTACAACTTAG	58.809	52.381	12.47	0.00	0.00	2.18
1637	4997	1.545136	TGGATCACGCGGTACAACTTA	59.455	47.619	12.47	0.00	0.00	2.24
1638	4998	0.319083	TGGATCACGCGGTACAACTT	59.681	50.000	12.47	0.00	0.00	2.66
1639	4999	0.389426	GTGGATCACGCGGTACAACT	60.389	55.000	12.47	0.00	0.00	3.16
1640	5000	1.356527	GGTGGATCACGCGGTACAAC	61.357	60.000	12.47	1.31	34.83	3.32
1708	5069	1.523938	GGCGCTTAGGGTTAGGCTG	60.524	63.158	7.64	0.00	30.21	4.85
1808	5169	3.114616	CGCCAGTTCCTGCAGACG	61.115	66.667	17.39	0.00	0.00	4.18
1895	5256	7.046852	GTCGAAGAAGTTGTCGAAGAAGTCG	62.047	48.000	9.25	0.00	46.91	4.18
1896	5257	4.146788	GTCGAAGAAGTTGTCGAAGAAGTC	59.853	45.833	9.25	0.00	46.91	3.01
1897	5258	4.043073	GTCGAAGAAGTTGTCGAAGAAGT	58.957	43.478	9.25	0.00	46.91	3.01
1898	5259	4.042398	TGTCGAAGAAGTTGTCGAAGAAG	58.958	43.478	9.25	0.00	46.91	2.85
1899	5260	4.036567	TGTCGAAGAAGTTGTCGAAGAA	57.963	40.909	9.25	0.00	46.91	2.52
1900	5261	3.703286	TGTCGAAGAAGTTGTCGAAGA	57.297	42.857	9.25	0.00	46.91	2.87
1906	5267	3.871594	CCTTCTGTTGTCGAAGAAGTTGT	59.128	43.478	18.60	0.00	45.24	3.32
1915	5276	1.300620	CCGTGCCTTCTGTTGTCGA	60.301	57.895	0.00	0.00	0.00	4.20
1917	5278	1.166531	AAGCCGTGCCTTCTGTTGTC	61.167	55.000	0.00	0.00	0.00	3.18
2154	5515	1.810030	GATCGAACACGAGGTGCCC	60.810	63.158	0.00	0.00	39.38	5.36
2445	5810	0.671781	GTCACTGCATCGCCTTGTCT	60.672	55.000	0.00	0.00	0.00	3.41
2777	6436	4.279169	CCCAAATACAGACATGGCCTAATG	59.721	45.833	3.32	2.28	0.00	1.90
2782	6441	1.064017	TCCCCAAATACAGACATGGCC	60.064	52.381	0.00	0.00	0.00	5.36
3237	6896	4.511617	TCATGATGAGAAGAGTATCGCC	57.488	45.455	0.00	0.00	42.67	5.54
3834	9191	2.021243	CGCACACACACACACACG	59.979	61.111	0.00	0.00	0.00	4.49
3860	9217	2.021243	CACACACACACACGCACG	59.979	61.111	0.00	0.00	0.00	5.34
3864	9221	0.179227	CACACACACACACACACACG	60.179	55.000	0.00	0.00	0.00	4.49
3866	9223	0.871057	CACACACACACACACACACA	59.129	50.000	0.00	0.00	0.00	3.72
3872	9233	1.669437	ACGCACACACACACACACA	60.669	52.632	0.00	0.00	0.00	3.72
3876	9237	3.858989	CGCACGCACACACACACA	61.859	61.111	0.00	0.00	0.00	3.72
3880	9241	3.858989	CACACGCACGCACACACA	61.859	61.111	0.00	0.00	0.00	3.72
3884	9245	3.858989	CACACACACGCACGCACA	61.859	61.111	0.00	0.00	0.00	4.57
3905	9266	3.702555	GAGGCGCACGACACACAC	61.703	66.667	10.83	0.00	0.00	3.82
3914	9275	0.166814	GAATCAACACAGAGGCGCAC	59.833	55.000	10.83	2.06	0.00	5.34
3916	9277	0.166814	GTGAATCAACACAGAGGCGC	59.833	55.000	0.00	0.00	40.11	6.53
4073	9743	2.225382	TCTGTTAGGACGGTGATCCA	57.775	50.000	0.00	0.00	41.73	3.41
4151	9821	5.305585	TGTTCAATTTACTCCCTGTCTGAC	58.694	41.667	0.00	0.00	0.00	3.51
4159	9829	5.975693	TTGGTGATGTTCAATTTACTCCC	57.024	39.130	0.00	0.00	0.00	4.30
4160	9830	7.035612	GGAATTGGTGATGTTCAATTTACTCC	58.964	38.462	0.00	0.00	41.80	3.85
4185	9855	3.433274	TGATTGCTTTCACTTAGCTCACG	59.567	43.478	0.00	0.00	39.38	4.35
4201	9871	5.640732	ACTGGATATGTTTTCGTTGATTGC	58.359	37.500	0.00	0.00	0.00	3.56
4298	9968	2.586792	GGATCGCACTGAAGCCCT	59.413	61.111	0.00	0.00	0.00	5.19
4354	10024	5.007724	CCAAGCTTTTGAAGAAGTTAGTCGT	59.992	40.000	0.00	0.00	0.00	4.34
4359	10029	5.240844	GGTAGCCAAGCTTTTGAAGAAGTTA	59.759	40.000	0.00	0.00	40.44	2.24
4466	10138	3.551846	TCTTTGTGTCCCTCCTCAAAAC	58.448	45.455	0.00	0.00	31.07	2.43
4491	10165	2.722094	TGATTTCTCCATGTTTCCCCG	58.278	47.619	0.00	0.00	0.00	5.73
4645	10320	6.171921	CAAGTGAATCTTCAAGACTCATCCT	58.828	40.000	1.11	0.00	32.76	3.24
4701	10377	5.274279	GGGAGAAGGATTCCCCAAGTGAG	62.274	56.522	0.00	0.00	46.11	3.51
4869	10545	1.596496	CCCCTCACTTACCCCTTCAT	58.404	55.000	0.00	0.00	0.00	2.57
4885	10561	1.600511	CCCATGTACCGTTTTGCCCC	61.601	60.000	0.00	0.00	0.00	5.80
4906	10582	4.908687	AGCAGTGTGTTCGGCGCA	62.909	61.111	10.83	0.00	34.05	6.09
4946	10622	2.745100	GAACTTCCGGCCGTTCCC	60.745	66.667	26.12	4.00	34.83	3.97
4947	10623	2.033194	CAGAACTTCCGGCCGTTCC	61.033	63.158	26.12	6.74	40.18	3.62

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.