AutoCloner

Multiple sequence alignment - TraesCS2D01G222000

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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	TraesCS2D01G222000	chr2D	100.000	4556	0	0	1	4556	189356014	189360569	0.000000e+00	8414.0
1	TraesCS2D01G222000	chr2D	95.703	861	31	5	2	857	431529796	431528937	0.000000e+00	1380.0
2	TraesCS2D01G222000	chr2D	74.561	228	50	8	1155	1378	189705108	189704885	4.850000e-15	93.5
3	TraesCS2D01G222000	chr2D	85.965	57	6	2	2842	2897	190112405	190112350	4.920000e-05	60.2
4	TraesCS2D01G222000	chr2D	84.746	59	7	2	3721	3778	402307957	402307900	1.770000e-04	58.4
5	TraesCS2D01G222000	chr2A	94.093	3166	126	23	854	3978	203260439	203263584	0.000000e+00	4754.0
6	TraesCS2D01G222000	chr2A	85.667	600	57	14	3969	4556	203263769	203264351	5.040000e-169	604.0
7	TraesCS2D01G222000	chr2A	88.462	234	27	0	2729	2962	203315255	203315488	2.680000e-72	283.0
8	TraesCS2D01G222000	chr2A	76.419	229	44	10	1155	1378	203537276	203537053	1.040000e-21	115.0
9	TraesCS2D01G222000	chr2A	83.505	97	15	1	4460	4556	410136116	410136211	6.280000e-14	89.8
10	TraesCS2D01G222000	chr2A	74.236	229	49	10	1155	1378	203461347	203461124	2.260000e-13	87.9
11	TraesCS2D01G222000	chr2A	74.419	215	35	15	1156	1360	203465007	203464803	1.760000e-09	75.0
12	TraesCS2D01G222000	chr2A	95.122	41	0	2	3721	3760	257770125	257770164	3.810000e-06	63.9
13	TraesCS2D01G222000	chr2A	85.965	57	6	2	2842	2897	204191646	204191591	4.920000e-05	60.2
14	TraesCS2D01G222000	chr2B	88.177	2436	181	49	1855	4213	245655269	245657674	0.000000e+00	2804.0
15	TraesCS2D01G222000	chr2B	95.050	1010	40	5	854	1860	245653599	245654601	0.000000e+00	1580.0
16	TraesCS2D01G222000	chr2B	79.762	588	86	23	2395	2962	245786336	245786910	3.300000e-106	396.0
17	TraesCS2D01G222000	chr2B	93.103	232	13	2	4278	4507	245657803	245658033	2.030000e-88	337.0
18	TraesCS2D01G222000	chr2B	89.583	144	15	0	3034	3177	245787014	245787157	2.800000e-42	183.0
19	TraesCS2D01G222000	chr2B	75.120	209	44	8	1156	1360	246004002	246003798	1.750000e-14	91.6
20	TraesCS2D01G222000	chr2B	83.505	97	16	0	4460	4556	497218104	497218008	1.750000e-14	91.6
21	TraesCS2D01G222000	chr2B	77.679	112	21	4	1160	1269	246006379	246006270	1.060000e-06	65.8
22	TraesCS2D01G222000	chr2B	85.965	57	6	2	2842	2897	246363889	246363834	4.920000e-05	60.2
23	TraesCS2D01G222000	chr6B	96.857	859	22	4	2	855	687090370	687089512	0.000000e+00	1432.0
24	TraesCS2D01G222000	chr3B	96.952	853	21	4	4	852	612806180	612805329	0.000000e+00	1426.0
25	TraesCS2D01G222000	chr1B	96.512	860	22	7	2	855	172423327	172422470	0.000000e+00	1415.0
26	TraesCS2D01G222000	chr1B	94.645	859	35	6	2	855	282044607	282043755	0.000000e+00	1321.0
27	TraesCS2D01G222000	chr1B	83.654	104	12	4	4456	4556	372966783	372966682	4.850000e-15	93.5
28	TraesCS2D01G222000	chr1B	79.389	131	18	6	4432	4556	438189491	438189618	2.920000e-12	84.2
29	TraesCS2D01G222000	chr6A	96.163	860	26	6	4	857	559445806	559446664	0.000000e+00	1399.0
30	TraesCS2D01G222000	chr4B	96.033	857	28	5	2	854	204163295	204164149	0.000000e+00	1389.0
31	TraesCS2D01G222000	chr3A	96.037	858	27	6	2	854	77711779	77710924	0.000000e+00	1389.0
32	TraesCS2D01G222000	chr3A	81.739	115	18	2	3845	3958	357300821	357300933	4.850000e-15	93.5
33	TraesCS2D01G222000	chr3A	87.013	77	6	4	3719	3793	646291916	646291842	2.920000e-12	84.2
34	TraesCS2D01G222000	chr1A	95.683	857	31	5	2	854	558982768	558981914	0.000000e+00	1373.0
35	TraesCS2D01G222000	chr1A	74.468	705	139	31	1936	2616	578197560	578198247	2.700000e-67	267.0
36	TraesCS2D01G222000	chr1A	85.075	67	6	2	3720	3786	337681794	337681732	1.060000e-06	65.8
37	TraesCS2D01G222000	chr1D	77.225	764	131	32	2751	3499	481464975	481464240	1.530000e-109	407.0
38	TraesCS2D01G222000	chr1D	74.929	702	137	33	1936	2616	481465791	481465108	7.460000e-73	285.0
39	TraesCS2D01G222000	chr5A	87.398	246	29	2	2721	2965	546236208	546235964	9.650000e-72	281.0
40	TraesCS2D01G222000	chr5A	80.576	139	24	1	1935	2070	546236934	546236796	2.240000e-18	104.0
41	TraesCS2D01G222000	chr5B	76.754	228	37	12	3721	3939	571705352	571705572	3.730000e-21	113.0
42	TraesCS2D01G222000	chr7B	84.536	97	15	0	4460	4556	400655972	400656068	3.750000e-16	97.1
43	TraesCS2D01G222000	chr4A	83.333	102	16	1	4456	4556	575483028	575483129	4.850000e-15	93.5
44	TraesCS2D01G222000	chr4A	83.673	98	15	1	4460	4556	86805975	86805878	1.750000e-14	91.6
45	TraesCS2D01G222000	chr7D	83.505	97	16	0	4460	4556	418167362	418167266	1.750000e-14	91.6
46	TraesCS2D01G222000	chrUn	93.103	58	3	1	3721	3778	102499753	102499697	2.920000e-12	84.2
47	TraesCS2D01G222000	chr7A	84.524	84	13	0	3875	3958	117604829	117604746	2.920000e-12	84.2
48	TraesCS2D01G222000	chr7A	90.000	50	3	2	3721	3769	17719112	17719160	3.810000e-06	63.9

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	TraesCS2D01G222000	chr2D	189356014	189360569	4555	False	8414.000000	8414	100.0000	1	4556	1	chr2D.!!$F1	4555
1	TraesCS2D01G222000	chr2D	431528937	431529796	859	True	1380.000000	1380	95.7030	2	857	1	chr2D.!!$R4	855
2	TraesCS2D01G222000	chr2A	203260439	203264351	3912	False	2679.000000	4754	89.8800	854	4556	2	chr2A.!!$F4	3702
3	TraesCS2D01G222000	chr2B	245653599	245658033	4434	False	1573.666667	2804	92.1100	854	4507	3	chr2B.!!$F1	3653
4	TraesCS2D01G222000	chr2B	245786336	245787157	821	False	289.500000	396	84.6725	2395	3177	2	chr2B.!!$F2	782
5	TraesCS2D01G222000	chr6B	687089512	687090370	858	True	1432.000000	1432	96.8570	2	855	1	chr6B.!!$R1	853
6	TraesCS2D01G222000	chr3B	612805329	612806180	851	True	1426.000000	1426	96.9520	4	852	1	chr3B.!!$R1	848
7	TraesCS2D01G222000	chr1B	172422470	172423327	857	True	1415.000000	1415	96.5120	2	855	1	chr1B.!!$R1	853
8	TraesCS2D01G222000	chr1B	282043755	282044607	852	True	1321.000000	1321	94.6450	2	855	1	chr1B.!!$R2	853
9	TraesCS2D01G222000	chr6A	559445806	559446664	858	False	1399.000000	1399	96.1630	4	857	1	chr6A.!!$F1	853
10	TraesCS2D01G222000	chr4B	204163295	204164149	854	False	1389.000000	1389	96.0330	2	854	1	chr4B.!!$F1	852
11	TraesCS2D01G222000	chr3A	77710924	77711779	855	True	1389.000000	1389	96.0370	2	854	1	chr3A.!!$R1	852
12	TraesCS2D01G222000	chr1A	558981914	558982768	854	True	1373.000000	1373	95.6830	2	854	1	chr1A.!!$R2	852
13	TraesCS2D01G222000	chr1A	578197560	578198247	687	False	267.000000	267	74.4680	1936	2616	1	chr1A.!!$F1	680
14	TraesCS2D01G222000	chr1D	481464240	481465791	1551	True	346.000000	407	76.0770	1936	3499	2	chr1D.!!$R1	1563

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	Hairpin	End Stability	Orientation
739	743	0.319297	CATCATCATGCCGCGAGAGA	60.319	55.000	8.23	0.00	3.10	F
936	941	1.079819	CTCATTGCCGTGTCCGACT	60.080	57.895	0.00	35.63	4.18	F
1683	1693	1.153628	GTTCACGGACTCCATCGGG	60.154	63.158	0.00	31.96	5.14	F
2530	3256	0.109342	AGAACCTGGTGAGGCTTGTG	59.891	55.000	0.00	44.33	3.33	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2136	2833	0.106419	TTTGTCACCACAAGGGGGTC	60.106	55.0	0.00	0.00	43.54	4.46	R
2443	3169	0.739112	CTCCTTGTGCCGAGCTCTTC	60.739	60.0	12.85	3.61	0.00	2.87	R
2679	3422	0.940126	GAGTGGTGAGTGTGTGCAAG	59.060	55.0	0.00	0.00	0.00	4.01	R
4148	5259	0.099436	GCCACCAAAATGCTCGCTAG	59.901	55.0	0.00	0.00	0.00	3.42	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
181	182	4.992319	ACGACGACATCACTTGGAAATTTA	59.008	37.500	0.00	0.00	0.00	1.40
202	203	4.487714	AAGGCAAATGGAGAATACTCGA	57.512	40.909	0.00	0.00	43.44	4.04
567	569	6.783708	AACCAAATACAACAAACAGGAAGA	57.216	33.333	0.00	0.00	0.00	2.87
584	586	0.546267	AGACCATGGCCTCACTCACT	60.546	55.000	13.04	0.00	0.00	3.41
653	655	3.139118	GAAGAAATCGACGCCGCCG	62.139	63.158	0.00	0.00	41.14	6.46
677	679	6.446318	GCACAACATTCTAAAACTCATCCAA	58.554	36.000	0.00	0.00	0.00	3.53
739	743	0.319297	CATCATCATGCCGCGAGAGA	60.319	55.000	8.23	0.00	0.00	3.10
788	793	3.933332	GCTATGTTGTAAAGCGGTTCTCT	59.067	43.478	0.00	0.00	0.00	3.10
911	916	3.490933	GGACAAGGACTTGCTTTTCCAAC	60.491	47.826	11.73	0.00	44.03	3.77
918	923	4.290969	GACTTGCTTTTCCAACTGCTAAC	58.709	43.478	0.00	0.00	0.00	2.34
936	941	1.079819	CTCATTGCCGTGTCCGACT	60.080	57.895	0.00	0.00	35.63	4.18
957	962	7.021196	CGACTGTCAAATTTAATTGGGTGTAG	58.979	38.462	8.73	0.00	0.00	2.74
1100	1110	1.590665	CATGGACAATTTGCGGCCA	59.409	52.632	2.24	8.19	0.00	5.36
1200	1210	4.308458	CCGGACCTGTTCGCCACA	62.308	66.667	0.00	0.00	0.00	4.17
1680	1690	1.673033	CCTGTGTTCACGGACTCCATC	60.673	57.143	12.65	0.00	0.00	3.51
1683	1693	1.153628	GTTCACGGACTCCATCGGG	60.154	63.158	0.00	0.00	31.96	5.14
1862	1875	1.802069	GGAGAAGGTGAGTGCAAGTC	58.198	55.000	0.00	0.00	36.61	3.01
1911	2599	5.819379	TGCAAATCTCAACTGACCTGATATC	59.181	40.000	0.00	0.00	0.00	1.63
2136	2833	3.993081	GCCTAGCTAGCATGACATAACTG	59.007	47.826	18.83	0.00	0.00	3.16
2138	2835	5.226396	CCTAGCTAGCATGACATAACTGAC	58.774	45.833	18.83	0.00	0.00	3.51
2344	3057	7.572502	CAAGCAAACATATCTTGGAGAAAAC	57.427	36.000	0.00	0.00	34.98	2.43
2366	3092	6.254281	ACTCATCGAAATTTTGGTAAGTGG	57.746	37.500	5.58	0.00	0.00	4.00
2389	3115	4.319984	GGCTTAGTTTTAGTTGTGGTTCGG	60.320	45.833	0.00	0.00	0.00	4.30
2530	3256	0.109342	AGAACCTGGTGAGGCTTGTG	59.891	55.000	0.00	0.00	44.33	3.33
2581	3307	0.325933	TCGTCTACGAGTTCCTCCCA	59.674	55.000	0.14	0.00	44.22	4.37
2637	3363	2.234661	ACAGAATCGAATCCTGCTGTGA	59.765	45.455	10.67	0.00	35.49	3.58
2658	3401	4.398988	TGACATTTTCTCTGCAACTTGTGT	59.601	37.500	0.00	0.00	0.00	3.72
2679	3422	1.256812	ACCATTGCCTGCCTGTTTAC	58.743	50.000	0.00	0.00	0.00	2.01
2685	3432	0.039165	GCCTGCCTGTTTACTTGCAC	60.039	55.000	0.00	0.00	0.00	4.57
2706	3453	3.069729	ACACACTCACCACTCCTAGTTTC	59.930	47.826	0.00	0.00	0.00	2.78
2965	3725	1.546834	GTCGTCGGAACATAGTCAGC	58.453	55.000	0.00	0.00	0.00	4.26
2971	3731	1.935873	CGGAACATAGTCAGCACCATG	59.064	52.381	0.00	0.00	0.00	3.66
2990	3758	2.984562	TGCATATTCGAACTCAGGCAA	58.015	42.857	11.64	0.00	0.00	4.52
2992	3760	2.285834	GCATATTCGAACTCAGGCAACG	60.286	50.000	0.00	0.00	46.39	4.10
2993	3761	3.186909	CATATTCGAACTCAGGCAACGA	58.813	45.455	0.00	0.00	46.39	3.85
3019	3798	7.097192	TCGTGCAGAGAAACTAACTGAATTAT	58.903	34.615	0.00	0.00	34.07	1.28
3203	3995	4.354155	GGTACGTGCTGTTGCTCA	57.646	55.556	3.01	0.00	40.48	4.26
3219	4018	7.095857	GCTGTTGCTCAGTATCTGAATATGTAC	60.096	40.741	10.20	0.00	45.23	2.90
3513	4314	1.364171	CGATCACCCGGTCATCTCC	59.636	63.158	0.00	0.00	0.00	3.71
3566	4367	7.441157	TGGAGTGTCTATTTAACAAGTTCAGTG	59.559	37.037	0.00	0.00	0.00	3.66
3701	4502	3.265791	GAGAGATGTCGTTCAAGGCAAT	58.734	45.455	0.00	0.00	0.00	3.56
3759	4561	3.473647	CCTCCGGCCTCTGCATCA	61.474	66.667	0.00	0.00	40.13	3.07
3763	4565	3.207669	CGGCCTCTGCATCAAGCC	61.208	66.667	0.00	7.03	44.83	4.35
3778	4580	0.604578	AAGCCATGCACACAACCATC	59.395	50.000	0.00	0.00	0.00	3.51
3788	4590	7.862372	CCATGCACACAACCATCTTTATTATAC	59.138	37.037	0.00	0.00	0.00	1.47
3864	4666	4.587262	TGGTGGCGATCTATGTTACTACAT	59.413	41.667	0.00	0.00	46.49	2.29
3866	4668	5.047943	GGTGGCGATCTATGTTACTACATCT	60.048	44.000	0.00	0.00	43.81	2.90
3919	4721	3.289836	CCAATGCACACCATCTAATCCA	58.710	45.455	0.00	0.00	31.43	3.41
4010	5006	9.750125	GACCTTTTACAAGAATCATTTTGTTCT	57.250	29.630	4.08	0.00	38.41	3.01
4058	5068	3.192422	TGTCTTGGTATGCGGGAAAAATG	59.808	43.478	0.00	0.00	0.00	2.32
4072	5086	5.516339	CGGGAAAAATGTATGCAAGACAATC	59.484	40.000	8.69	5.77	0.00	2.67
4113	5127	6.358178	AGAACCTGATATCGTTCTCTCTACA	58.642	40.000	16.07	0.00	44.12	2.74
4148	5259	0.246635	ATAGGCCGTGTGTGACTGTC	59.753	55.000	0.00	0.00	0.00	3.51
4157	5268	0.241213	GTGTGACTGTCTAGCGAGCA	59.759	55.000	9.51	0.00	0.00	4.26
4203	5314	2.932614	CCTCTGTTCTACTGAAATGGCG	59.067	50.000	0.00	0.00	33.52	5.69
4220	5331	0.109132	GCGAGGAAAATTGCCTGTGG	60.109	55.000	0.00	0.00	35.44	4.17
4231	5342	1.277579	TGCCTGTGGGTTATAACGGA	58.722	50.000	9.46	0.00	34.45	4.69
4262	5373	7.033185	CAGGGTTAAAACACTATTATGGCAAC	58.967	38.462	0.00	0.00	41.69	4.17
4263	5374	6.153851	AGGGTTAAAACACTATTATGGCAACC	59.846	38.462	0.00	0.00	41.84	3.77
4270	5381	9.651913	AAAACACTATTATGGCAACCAAAATAG	57.348	29.630	0.00	3.63	36.95	1.73
4276	5387	3.399440	TGGCAACCAAAATAGGCAAAG	57.601	42.857	0.00	0.00	33.37	2.77
4334	5445	1.520120	ACTCGTCCTGCATGCATCG	60.520	57.895	22.97	23.65	0.00	3.84
4335	5446	2.879070	CTCGTCCTGCATGCATCGC	61.879	63.158	22.97	12.66	0.00	4.58
4397	5514	2.516225	GCCCCGGATGTTAGGCAC	60.516	66.667	0.73	0.00	45.07	5.01
4511	5631	5.674525	ACATGGTTGTCATAGTAGGTCATG	58.325	41.667	0.00	0.00	36.51	3.07
4521	5641	7.097192	GTCATAGTAGGTCATGTTTTCTGTCA	58.903	38.462	0.00	0.00	0.00	3.58
4527	5647	4.758674	AGGTCATGTTTTCTGTCACTCATG	59.241	41.667	0.00	0.00	35.47	3.07
4535	5655	6.646653	TGTTTTCTGTCACTCATGTACATCTC	59.353	38.462	5.07	0.00	0.00	2.75
4537	5657	5.826601	TCTGTCACTCATGTACATCTCTC	57.173	43.478	5.07	0.00	0.00	3.20
4538	5658	4.333926	TCTGTCACTCATGTACATCTCTCG	59.666	45.833	5.07	0.00	0.00	4.04
4552	5672	2.876091	TCTCTCGCGGTTTTATGACAG	58.124	47.619	6.13	0.00	0.00	3.51

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
30	31	2.981560	CTTGTCGCGCATGGCCTTT	61.982	57.895	8.75	0.00	38.94	3.11
31	32	3.434319	CTTGTCGCGCATGGCCTT	61.434	61.111	8.75	0.00	38.94	4.35
181	182	4.192317	GTCGAGTATTCTCCATTTGCCTT	58.808	43.478	0.00	0.00	37.40	4.35
202	203	2.043227	GTCCCTATAAGCAGAGCCTGT	58.957	52.381	4.45	0.00	33.43	4.00
442	444	6.183360	CCATGCTTTGACCATTCTCCAAATAT	60.183	38.462	0.00	0.00	0.00	1.28
567	569	1.487976	CATAGTGAGTGAGGCCATGGT	59.512	52.381	14.67	0.00	0.00	3.55
584	586	5.125356	CAGATGACCCAACATACAAGCATA	58.875	41.667	0.00	0.00	0.00	3.14
653	655	6.012658	TGGATGAGTTTTAGAATGTTGTGC	57.987	37.500	0.00	0.00	0.00	4.57
657	659	7.461749	TCCTCTTGGATGAGTTTTAGAATGTT	58.538	34.615	0.00	0.00	37.46	2.71
677	679	2.681778	CACGTCCTGGCCTCCTCT	60.682	66.667	3.32	0.00	0.00	3.69
739	743	4.932200	TCAACAAAAGGTGCAAACGAATTT	59.068	33.333	0.00	0.00	0.00	1.82
788	793	9.847224	AATTAAGAAGGAGAGTTTTGAGTACAA	57.153	29.630	0.00	0.00	0.00	2.41
911	916	1.394917	GACACGGCAATGAGTTAGCAG	59.605	52.381	0.00	0.00	0.00	4.24
918	923	3.474806	GTCGGACACGGCAATGAG	58.525	61.111	2.62	0.00	45.76	2.90
936	941	9.757227	CTTTTCTACACCCAATTAAATTTGACA	57.243	29.630	0.00	0.00	0.00	3.58
957	962	2.229062	GGGAAGTTGGTGCTAGCTTTTC	59.771	50.000	17.23	9.86	0.00	2.29
1073	1083	4.024048	CGCAAATTGTCCATGGGTATACTC	60.024	45.833	13.02	0.00	0.00	2.59
1100	1110	2.731691	CTTGGCCGTGTAGGTGCTGT	62.732	60.000	0.00	0.00	43.70	4.40
1394	1404	1.007038	TTGTAGGTGGTGTCGTCGC	60.007	57.895	0.00	0.00	0.00	5.19
1636	1646	1.131126	CCATGTCTTGATGTTCACGGC	59.869	52.381	0.00	0.00	0.00	5.68
1680	1690	2.124151	CCAAGAATCCTGGCCCCG	60.124	66.667	0.00	0.00	0.00	5.73
1683	1693	0.552848	TCATCCCAAGAATCCTGGCC	59.447	55.000	0.00	0.00	0.00	5.36
1876	2562	7.436080	TCAGTTGAGATTTGCAAATTTGAACTC	59.564	33.333	30.94	26.43	35.74	3.01
2136	2833	0.106419	TTTGTCACCACAAGGGGGTC	60.106	55.000	0.00	0.00	43.54	4.46
2138	2835	1.452145	CGTTTGTCACCACAAGGGGG	61.452	60.000	0.00	0.00	43.54	5.40
2337	3050	9.118236	CTTACCAAAATTTCGATGAGTTTTCTC	57.882	33.333	0.00	0.00	46.33	2.87
2344	3057	5.640732	CCCACTTACCAAAATTTCGATGAG	58.359	41.667	0.00	0.00	0.00	2.90
2366	3092	4.319984	CCGAACCACAACTAAAACTAAGCC	60.320	45.833	0.00	0.00	0.00	4.35
2389	3115	1.610886	GGGAGAGTACCCTGTGCAAAC	60.611	57.143	0.00	0.00	45.90	2.93
2443	3169	0.739112	CTCCTTGTGCCGAGCTCTTC	60.739	60.000	12.85	3.61	0.00	2.87
2581	3307	1.481871	TCTTATCGAGGCTCCGGTTT	58.518	50.000	9.32	0.00	0.00	3.27
2637	3363	4.989279	ACACAAGTTGCAGAGAAAATGT	57.011	36.364	1.81	0.00	0.00	2.71
2658	3401	2.008242	AAACAGGCAGGCAATGGTAA	57.992	45.000	0.00	0.00	0.00	2.85
2679	3422	0.940126	GAGTGGTGAGTGTGTGCAAG	59.060	55.000	0.00	0.00	0.00	4.01
2685	3432	3.555168	GGAAACTAGGAGTGGTGAGTGTG	60.555	52.174	0.00	0.00	0.00	3.82
2706	3453	1.336887	CGTGTCTACCACAGGTTCAGG	60.337	57.143	0.00	0.00	44.78	3.86
2965	3725	3.249320	CCTGAGTTCGAATATGCATGGTG	59.751	47.826	10.16	0.00	0.00	4.17
2971	3731	2.285834	CGTTGCCTGAGTTCGAATATGC	60.286	50.000	0.00	1.19	0.00	3.14
2981	3749	1.738099	GCACGATCGTTGCCTGAGT	60.738	57.895	20.14	0.00	0.00	3.41
2982	3750	1.690283	CTGCACGATCGTTGCCTGAG	61.690	60.000	27.73	19.38	0.00	3.35
2990	3758	3.057456	AGTTAGTTTCTCTGCACGATCGT	60.057	43.478	16.60	16.60	0.00	3.73
2992	3760	4.486090	TCAGTTAGTTTCTCTGCACGATC	58.514	43.478	0.00	0.00	0.00	3.69
2993	3761	4.521130	TCAGTTAGTTTCTCTGCACGAT	57.479	40.909	0.00	0.00	0.00	3.73
3019	3798	1.227823	CGCTGGAACAACAGGGTGA	60.228	57.895	0.00	0.00	43.87	4.02
3219	4018	5.122239	TGAGCCAAACATTCTTTCTGATACG	59.878	40.000	0.00	0.00	0.00	3.06
3513	4314	2.421314	TGCACGGACACAGTGGAG	59.579	61.111	5.31	0.00	39.80	3.86
3566	4367	4.806330	CATGAGGCATGAATTAATCTGCC	58.194	43.478	20.80	20.80	43.81	4.85
3744	4546	2.586245	CTTGATGCAGAGGCCGGA	59.414	61.111	5.05	0.00	40.13	5.14
3746	4548	3.207669	GGCTTGATGCAGAGGCCG	61.208	66.667	5.97	0.00	45.15	6.13
3759	4561	0.604578	GATGGTTGTGTGCATGGCTT	59.395	50.000	0.00	0.00	0.00	4.35
3763	4565	8.623903	AGTATAATAAAGATGGTTGTGTGCATG	58.376	33.333	0.00	0.00	0.00	4.06
3818	4620	9.699410	ACCAAGATGACTTTGGATTGATTTATA	57.301	29.630	10.72	0.00	33.70	0.98
3819	4621	8.472413	CACCAAGATGACTTTGGATTGATTTAT	58.528	33.333	10.72	0.00	33.70	1.40
3820	4622	7.093814	CCACCAAGATGACTTTGGATTGATTTA	60.094	37.037	10.72	0.00	36.60	1.40
3821	4623	6.295462	CCACCAAGATGACTTTGGATTGATTT	60.295	38.462	10.72	0.00	36.60	2.17
3842	4644	4.579454	TGTAGTAACATAGATCGCCACC	57.421	45.455	0.00	0.00	0.00	4.61
3866	4668	9.431887	GGTTAAGACACATCATCAAACTAGTAA	57.568	33.333	0.00	0.00	0.00	2.24
3889	4691	1.032014	GTGTGCATTGGTGTGAGGTT	58.968	50.000	0.00	0.00	0.00	3.50
3958	4760	1.000896	GTTGCAGTAGGGGGCATGT	60.001	57.895	0.00	0.00	40.17	3.21
4113	5127	1.064685	CCTATGGCTTTCGGGTCCTTT	60.065	52.381	0.00	0.00	0.00	3.11
4148	5259	0.099436	GCCACCAAAATGCTCGCTAG	59.901	55.000	0.00	0.00	0.00	3.42
4157	5268	0.887933	CGTTAGCCTGCCACCAAAAT	59.112	50.000	0.00	0.00	0.00	1.82
4203	5314	1.632589	ACCCACAGGCAATTTTCCTC	58.367	50.000	0.00	0.00	36.11	3.71
4216	5327	3.055021	TGCATCTTCCGTTATAACCCACA	60.055	43.478	10.01	0.00	0.00	4.17
4217	5328	3.537580	TGCATCTTCCGTTATAACCCAC	58.462	45.455	10.01	0.00	0.00	4.61
4220	5331	3.139077	CCCTGCATCTTCCGTTATAACC	58.861	50.000	10.01	0.00	0.00	2.85
4231	5342	8.686334	CATAATAGTGTTTTAACCCTGCATCTT	58.314	33.333	0.00	0.00	0.00	2.40
4262	5373	9.874205	TCATATTTTCTTCTTTGCCTATTTTGG	57.126	29.630	0.00	0.00	0.00	3.28
4268	5379	8.877864	TCCTTTCATATTTTCTTCTTTGCCTA	57.122	30.769	0.00	0.00	0.00	3.93
4269	5380	7.781324	TCCTTTCATATTTTCTTCTTTGCCT	57.219	32.000	0.00	0.00	0.00	4.75
4270	5381	8.876790	CAATCCTTTCATATTTTCTTCTTTGCC	58.123	33.333	0.00	0.00	0.00	4.52
4276	5387	9.132521	CACACACAATCCTTTCATATTTTCTTC	57.867	33.333	0.00	0.00	0.00	2.87
4319	5430	2.893895	AGCGATGCATGCAGGACG	60.894	61.111	26.69	27.39	33.85	4.79
4334	5445	2.019984	CCTGGCAGGATCTTAAACAGC	58.980	52.381	29.96	0.00	37.67	4.40
4335	5446	3.634397	TCCTGGCAGGATCTTAAACAG	57.366	47.619	32.01	2.22	40.06	3.16
4397	5514	2.442643	GTGGGGCCATCATGGTGG	60.443	66.667	21.48	21.48	40.46	4.61
4437	5555	3.657448	TACACCATGCGCTCACCGG	62.657	63.158	9.73	0.00	37.44	5.28
4474	5594	4.640201	ACAACCATGTATCAATACAGGTGC	59.360	41.667	17.46	0.00	45.46	5.01
4477	5597	7.933577	ACTATGACAACCATGTATCAATACAGG	59.066	37.037	8.66	8.14	45.46	4.00
4511	5631	6.870965	AGAGATGTACATGAGTGACAGAAAAC	59.129	38.462	14.43	0.00	0.00	2.43
4521	5641	1.335182	CCGCGAGAGATGTACATGAGT	59.665	52.381	14.43	0.00	0.00	3.41
4527	5647	4.206609	GTCATAAAACCGCGAGAGATGTAC	59.793	45.833	8.23	2.06	0.00	2.90

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.