AutoCloner

Multiple sequence alignment - TraesCS1D01G253100

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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	TraesCS1D01G253100	chr1D	100.000	4403	0	0	1	4403	345380395	345375993	0.000000e+00	8131.0
1	TraesCS1D01G253100	chr1D	95.130	3224	135	12	489	3693	311685181	311688401	0.000000e+00	5064.0
2	TraesCS1D01G253100	chr1A	95.070	2982	136	7	719	3693	391842273	391845250	0.000000e+00	4682.0
3	TraesCS1D01G253100	chr1A	94.513	3007	138	15	489	3469	391675628	391678633	0.000000e+00	4614.0
4	TraesCS1D01G253100	chr1A	95.161	2645	113	6	825	3469	391694081	391696710	0.000000e+00	4161.0
5	TraesCS1D01G253100	chr1A	95.123	2645	116	5	825	3469	391791567	391794198	0.000000e+00	4157.0
6	TraesCS1D01G253100	chr1A	98.361	671	11	0	3733	4403	445504180	445503510	0.000000e+00	1179.0
7	TraesCS1D01G253100	chr1A	93.790	628	22	9	1	623	391841655	391842270	0.000000e+00	928.0
8	TraesCS1D01G253100	chr1A	93.475	613	23	9	16	623	391760613	391761213	0.000000e+00	894.0
9	TraesCS1D01G253100	chr1A	89.954	219	17	2	546	759	391693826	391694044	1.210000e-70	278.0
10	TraesCS1D01G253100	chr1A	89.954	219	17	2	546	759	391791312	391791530	1.210000e-70	278.0
11	TraesCS1D01G253100	chr1A	89.593	221	18	2	544	759	391733387	391733607	4.340000e-70	276.0
12	TraesCS1D01G253100	chr1A	88.811	143	15	1	274	415	391848720	391848862	1.630000e-39	174.0
13	TraesCS1D01G253100	chr1A	89.831	59	3	2	58	116	495446314	495446259	6.110000e-09	73.1
14	TraesCS1D01G253100	chr1B	94.450	2973	126	21	469	3423	421422022	421424973	0.000000e+00	4540.0
15	TraesCS1D01G253100	chr1B	95.160	2872	128	7	825	3693	421531372	421534235	0.000000e+00	4523.0
16	TraesCS1D01G253100	chr1B	93.523	2887	160	16	825	3692	421494341	421497219	0.000000e+00	4270.0
17	TraesCS1D01G253100	chr1B	91.853	1792	116	14	1920	3692	421452509	421454289	0.000000e+00	2473.0
18	TraesCS1D01G253100	chr1B	89.270	1575	108	30	366	1933	421440186	421441706	0.000000e+00	1916.0
19	TraesCS1D01G253100	chr1B	99.255	671	5	0	3733	4403	465387726	465388396	0.000000e+00	1212.0
20	TraesCS1D01G253100	chr1B	86.792	371	27	10	309	664	421493862	421494225	1.150000e-105	394.0
21	TraesCS1D01G253100	chr1B	88.889	243	14	7	435	664	421531014	421531256	2.000000e-73	287.0
22	TraesCS1D01G253100	chr1B	87.500	128	9	1	309	436	421528885	421529005	1.650000e-29	141.0
23	TraesCS1D01G253100	chr1B	94.545	55	3	0	60	114	404967573	404967519	7.850000e-13	86.1
24	TraesCS1D01G253100	chrUn	95.049	2646	103	7	825	3461	920075	917449	0.000000e+00	4137.0
25	TraesCS1D01G253100	chrUn	89.140	221	19	2	544	759	920332	920112	2.020000e-68	270.0
26	TraesCS1D01G253100	chr6A	91.619	525	39	2	3884	4403	15543271	15542747	0.000000e+00	721.0
27	TraesCS1D01G253100	chr6A	90.184	489	45	1	3899	4384	15456662	15457150	6.210000e-178	634.0
28	TraesCS1D01G253100	chr6D	91.287	505	41	1	3902	4403	14242079	14241575	0.000000e+00	686.0
29	TraesCS1D01G253100	chr6D	90.000	490	46	1	3899	4385	14201216	14201705	8.040000e-177	630.0
30	TraesCS1D01G253100	chr6D	88.753	489	52	1	3900	4385	14230595	14231083	2.930000e-166	595.0
31	TraesCS1D01G253100	chr6D	94.340	53	2	1	63	114	467150662	467150610	3.650000e-11	80.5
32	TraesCS1D01G253100	chr6B	89.328	506	49	3	3902	4403	26005429	26004925	8.040000e-177	630.0
33	TraesCS1D01G253100	chr6B	89.775	489	47	1	3899	4384	25971698	25972186	1.340000e-174	623.0
34	TraesCS1D01G253100	chr4D	93.651	63	4	0	63	125	277378601	277378539	1.300000e-15	95.3
35	TraesCS1D01G253100	chr4B	96.296	54	2	0	63	116	621432501	621432448	6.070000e-14	89.8
36	TraesCS1D01G253100	chr3D	91.045	67	4	2	63	128	533921957	533922022	6.070000e-14	89.8
37	TraesCS1D01G253100	chr2B	91.803	61	3	2	60	118	742820327	742820267	2.820000e-12	84.2

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	TraesCS1D01G253100	chr1D	345375993	345380395	4402	True	8131.000000	8131	100.000000	1	4403	1	chr1D.!!$R1	4402
1	TraesCS1D01G253100	chr1D	311685181	311688401	3220	False	5064.000000	5064	95.130000	489	3693	1	chr1D.!!$F1	3204
2	TraesCS1D01G253100	chr1A	391675628	391678633	3005	False	4614.000000	4614	94.513000	489	3469	1	chr1A.!!$F1	2980
3	TraesCS1D01G253100	chr1A	391693826	391696710	2884	False	2219.500000	4161	92.557500	546	3469	2	chr1A.!!$F4	2923
4	TraesCS1D01G253100	chr1A	391791312	391794198	2886	False	2217.500000	4157	92.538500	546	3469	2	chr1A.!!$F5	2923
5	TraesCS1D01G253100	chr1A	391841655	391848862	7207	False	1928.000000	4682	92.557000	1	3693	3	chr1A.!!$F6	3692
6	TraesCS1D01G253100	chr1A	445503510	445504180	670	True	1179.000000	1179	98.361000	3733	4403	1	chr1A.!!$R1	670
7	TraesCS1D01G253100	chr1A	391760613	391761213	600	False	894.000000	894	93.475000	16	623	1	chr1A.!!$F3	607
8	TraesCS1D01G253100	chr1B	421422022	421424973	2951	False	4540.000000	4540	94.450000	469	3423	1	chr1B.!!$F1	2954
9	TraesCS1D01G253100	chr1B	421452509	421454289	1780	False	2473.000000	2473	91.853000	1920	3692	1	chr1B.!!$F3	1772
10	TraesCS1D01G253100	chr1B	421493862	421497219	3357	False	2332.000000	4270	90.157500	309	3692	2	chr1B.!!$F5	3383
11	TraesCS1D01G253100	chr1B	421440186	421441706	1520	False	1916.000000	1916	89.270000	366	1933	1	chr1B.!!$F2	1567
12	TraesCS1D01G253100	chr1B	421528885	421534235	5350	False	1650.333333	4523	90.516333	309	3693	3	chr1B.!!$F6	3384
13	TraesCS1D01G253100	chr1B	465387726	465388396	670	False	1212.000000	1212	99.255000	3733	4403	1	chr1B.!!$F4	670
14	TraesCS1D01G253100	chrUn	917449	920332	2883	True	2203.500000	4137	92.094500	544	3461	2	chrUn.!!$R1	2917
15	TraesCS1D01G253100	chr6A	15542747	15543271	524	True	721.000000	721	91.619000	3884	4403	1	chr6A.!!$R1	519
16	TraesCS1D01G253100	chr6D	14241575	14242079	504	True	686.000000	686	91.287000	3902	4403	1	chr6D.!!$R1	501
17	TraesCS1D01G253100	chr6B	26004925	26005429	504	True	630.000000	630	89.328000	3902	4403	1	chr6B.!!$R1	501

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
614	2652	0.030235	CGTAGCCGTCCATCGAATCA	59.970	55.0	0.00	0.0	42.86	2.57	F
733	2784	0.107800	CTCCTCGACCGTCTCCTACA	60.108	60.0	0.00	0.0	0.00	2.74	F
1435	3494	1.033574	CTTCCTCGAGGCCTATCGTT	58.966	55.0	27.39	0.0	43.20	3.85	F
2667	4727	0.179234	TGTGGTTTGGTGAGAGCGAA	59.821	50.0	0.00	0.0	0.00	4.70	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2379	4439	0.677288	TTTCACGAAGAGCGGAAGGA	59.323	50.0	0.00	0.00	46.49	3.36	R
2464	4524	1.271856	TATTGGACGGTCTCCTGCAA	58.728	50.0	8.23	3.82	40.26	4.08	R
3150	5219	0.462759	CGTCTTCCTCCATGGCTTCC	60.463	60.0	6.96	0.00	35.26	3.46	R
3707	5802	0.037590	GTGTTGGCTGGGTGTATGGA	59.962	55.0	0.00	0.00	0.00	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
72	73	3.700038	ACAGTGATAAAGTACTCCCTCCG	59.300	47.826	0.00	0.00	0.00	4.63
90	91	4.564821	CCTCCGTCCCAAAATAAGTTGAGA	60.565	45.833	0.00	0.00	0.00	3.27
125	126	6.052405	AGACGGAGGGAGTAGTATATACAG	57.948	45.833	15.18	0.00	0.00	2.74
126	127	5.547276	AGACGGAGGGAGTAGTATATACAGT	59.453	44.000	15.18	4.36	0.00	3.55
127	128	6.728164	AGACGGAGGGAGTAGTATATACAGTA	59.272	42.308	15.18	0.00	0.00	2.74
128	129	7.402650	AGACGGAGGGAGTAGTATATACAGTAT	59.597	40.741	15.18	0.00	0.00	2.12
129	130	8.615360	ACGGAGGGAGTAGTATATACAGTATA	57.385	38.462	15.18	2.62	0.00	1.47
153	154	7.914427	ATTACAACACCAGGAGTATATGAGA	57.086	36.000	0.00	0.00	0.00	3.27
154	155	5.599999	ACAACACCAGGAGTATATGAGAC	57.400	43.478	0.00	0.00	0.00	3.36
203	204	3.855379	GCGTAACGTCATGTCAGATACAA	59.145	43.478	0.00	0.00	42.70	2.41
205	206	5.093457	CGTAACGTCATGTCAGATACAACT	58.907	41.667	0.00	0.00	42.70	3.16
292	294	6.684686	TGGTGTACTACTAGAACATGACAAC	58.315	40.000	0.00	0.00	0.00	3.32
327	330	7.912773	GCTATTTCTTCTCAAAAGTTAGCATCC	59.087	37.037	0.00	0.00	32.01	3.51
421	431	6.477053	AGCTGCAGAATCTATCAACTTCTA	57.523	37.500	20.43	0.00	0.00	2.10
541	2564	7.716612	AGCTTCAGTTAACTGTTAAATTTGCT	58.283	30.769	29.83	22.84	44.12	3.91
614	2652	0.030235	CGTAGCCGTCCATCGAATCA	59.970	55.000	0.00	0.00	42.86	2.57
630	2673	0.394352	ATCATTTTCTTCCCGCGCCT	60.394	50.000	0.00	0.00	0.00	5.52
707	2754	3.732938	GGGTCCTGAGCCTGACAT	58.267	61.111	8.11	0.00	45.14	3.06
733	2784	0.107800	CTCCTCGACCGTCTCCTACA	60.108	60.000	0.00	0.00	0.00	2.74
782	2838	3.637273	GCAGAAGACCCACCCCGT	61.637	66.667	0.00	0.00	0.00	5.28
953	3011	2.004733	GGATCGTTTACCCACTTTCCG	58.995	52.381	0.00	0.00	0.00	4.30
1282	3340	1.079057	GTCCGGAAGAACCTGAGGC	60.079	63.158	5.23	0.00	32.74	4.70
1368	3426	4.456253	CTCCCCGTCGACGACACG	62.456	72.222	37.65	20.95	43.02	4.49
1399	3458	1.595929	GCCGGAAACCTGTTCGACA	60.596	57.895	5.05	0.00	0.00	4.35
1435	3494	1.033574	CTTCCTCGAGGCCTATCGTT	58.966	55.000	27.39	0.00	43.20	3.85
1596	3655	1.527380	GGACGAGGAGAGGCTCGAT	60.527	63.158	9.22	0.00	44.85	3.59
1626	3685	4.478195	GACGATGTCGGTGGAGTG	57.522	61.111	7.38	0.00	44.95	3.51
1686	3746	3.774528	CTGCGCCACCCTCAGCTA	61.775	66.667	4.18	0.00	0.00	3.32
1761	3821	1.153349	GACCGGCAAGACCCTCATC	60.153	63.158	0.00	0.00	33.26	2.92
2055	4115	2.444700	CTACCAACCGCCCGAACAGT	62.445	60.000	0.00	0.00	0.00	3.55
2109	4169	1.069765	CCGGGAGATCGACATTGGG	59.930	63.158	0.00	0.00	0.00	4.12
2179	4239	7.148188	CCAAAAACATGAAGCTAGCTGAAGATA	60.148	37.037	20.16	1.66	0.00	1.98
2379	4439	2.584835	TTGCACTAGGGACAAGCAAT	57.415	45.000	0.00	0.00	39.95	3.56
2403	4463	1.202486	TCCGCTCTTCGTGAAACTGTT	60.202	47.619	0.00	0.00	36.19	3.16
2449	4509	2.030027	AGATGTTGGTGGTCTGGAGA	57.970	50.000	0.00	0.00	0.00	3.71
2464	4524	2.370189	CTGGAGAGTGTCAAAAGGGAGT	59.630	50.000	0.00	0.00	0.00	3.85
2667	4727	0.179234	TGTGGTTTGGTGAGAGCGAA	59.821	50.000	0.00	0.00	0.00	4.70
2727	4787	2.508526	GCACCATGTGTCCTCTTCTTT	58.491	47.619	0.00	0.00	35.75	2.52
2799	4859	2.109181	GGTGCCGCTGATAGGGTC	59.891	66.667	0.00	0.00	0.00	4.46
2808	4868	2.103094	CGCTGATAGGGTCCTGAATCAA	59.897	50.000	0.00	0.00	0.00	2.57
2938	4998	7.222872	CCTTGATCAGCTTATCTACATTCCTT	58.777	38.462	9.25	0.00	0.00	3.36
2964	5033	0.400213	ACGTTGAATCCAGGCTCCAA	59.600	50.000	0.00	0.00	0.00	3.53
3150	5219	2.978018	GCGGCTGAAGGAAAACCCG	61.978	63.158	0.00	0.00	40.87	5.28
3357	5426	1.021390	CCGCTGCGACAGATCCTTTT	61.021	55.000	25.45	0.00	32.44	2.27
3474	5543	3.322541	TGTAAGACACGGGAAGAACATGA	59.677	43.478	0.00	0.00	0.00	3.07
3621	5710	5.517054	GCGGTACAATTCTCTTGTTCTCTAG	59.483	44.000	0.00	0.00	34.11	2.43
3698	5793	7.833786	TCTTCTTTTAAATGTACTAGCTCCGA	58.166	34.615	0.00	0.00	0.00	4.55
3699	5794	7.758528	TCTTCTTTTAAATGTACTAGCTCCGAC	59.241	37.037	0.00	0.00	0.00	4.79
3700	5795	6.927416	TCTTTTAAATGTACTAGCTCCGACA	58.073	36.000	0.00	0.00	0.00	4.35
3701	5796	7.380536	TCTTTTAAATGTACTAGCTCCGACAA	58.619	34.615	0.00	0.00	0.00	3.18
3702	5797	8.038944	TCTTTTAAATGTACTAGCTCCGACAAT	58.961	33.333	0.00	0.00	0.00	2.71
3703	5798	7.534085	TTTAAATGTACTAGCTCCGACAATG	57.466	36.000	0.00	0.00	0.00	2.82
3704	5799	5.339008	AAATGTACTAGCTCCGACAATGA	57.661	39.130	0.00	0.00	0.00	2.57
3707	5802	4.207955	TGTACTAGCTCCGACAATGATCT	58.792	43.478	0.00	0.00	0.00	2.75
3708	5803	4.276183	TGTACTAGCTCCGACAATGATCTC	59.724	45.833	0.00	0.00	0.00	2.75
3712	5807	3.234353	AGCTCCGACAATGATCTCCATA	58.766	45.455	0.00	0.00	34.45	2.74
3713	5808	3.006323	AGCTCCGACAATGATCTCCATAC	59.994	47.826	0.00	0.00	34.45	2.39
3714	5809	3.243873	GCTCCGACAATGATCTCCATACA	60.244	47.826	0.00	0.00	34.45	2.29
3715	5810	4.302455	CTCCGACAATGATCTCCATACAC	58.698	47.826	0.00	0.00	34.45	2.90
3716	5811	3.069586	TCCGACAATGATCTCCATACACC	59.930	47.826	0.00	0.00	34.45	4.16
3717	5812	3.393800	CGACAATGATCTCCATACACCC	58.606	50.000	0.00	0.00	34.45	4.61
3718	5813	3.181466	CGACAATGATCTCCATACACCCA	60.181	47.826	0.00	0.00	34.45	4.51
3719	5814	4.384056	GACAATGATCTCCATACACCCAG	58.616	47.826	0.00	0.00	34.45	4.45
3720	5815	3.144506	CAATGATCTCCATACACCCAGC	58.855	50.000	0.00	0.00	34.45	4.85
3722	5817	1.131638	GATCTCCATACACCCAGCCA	58.868	55.000	0.00	0.00	0.00	4.75
3723	5818	1.490490	GATCTCCATACACCCAGCCAA	59.510	52.381	0.00	0.00	0.00	4.52
3724	5819	0.618458	TCTCCATACACCCAGCCAAC	59.382	55.000	0.00	0.00	0.00	3.77
3725	5820	0.327924	CTCCATACACCCAGCCAACA	59.672	55.000	0.00	0.00	0.00	3.33
3726	5821	0.037590	TCCATACACCCAGCCAACAC	59.962	55.000	0.00	0.00	0.00	3.32
3727	5822	0.965363	CCATACACCCAGCCAACACC	60.965	60.000	0.00	0.00	0.00	4.16
3728	5823	1.002624	ATACACCCAGCCAACACCG	60.003	57.895	0.00	0.00	0.00	4.94
3729	5824	2.478335	ATACACCCAGCCAACACCGG	62.478	60.000	0.00	0.00	0.00	5.28
3766	5861	9.144747	TGAAAAGAAATTCAATCAAAACGAACA	57.855	25.926	0.00	0.00	36.42	3.18
3862	6062	3.308530	GACTCGGAAAGCAAAACCAATG	58.691	45.455	0.00	0.00	0.00	2.82

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
43	44	7.068839	AGGGAGTACTTTATCACTGTGAGTATG	59.931	40.741	16.46	10.45	0.00	2.39
90	91	3.581332	TCCCTCCGTCTCAAAATAAGTGT	59.419	43.478	0.00	0.00	0.00	3.55
127	128	9.601810	TCTCATATACTCCTGGTGTTGTAATAT	57.398	33.333	6.73	2.02	0.00	1.28
128	129	8.857098	GTCTCATATACTCCTGGTGTTGTAATA	58.143	37.037	6.73	0.00	0.00	0.98
129	130	7.344612	TGTCTCATATACTCCTGGTGTTGTAAT	59.655	37.037	6.73	0.00	0.00	1.89
134	135	5.663106	ACATGTCTCATATACTCCTGGTGTT	59.337	40.000	6.73	0.00	0.00	3.32
137	138	5.710646	AGACATGTCTCATATACTCCTGGT	58.289	41.667	22.89	0.00	34.17	4.00
166	167	5.126108	CGTTACGCGTACTACTAGTTGTA	57.874	43.478	20.44	12.37	35.54	2.41
178	179	7.142574	TGTATCTGACATGACGTTACGCGTA	62.143	44.000	16.41	16.41	43.48	4.42
179	180	6.433099	TGTATCTGACATGACGTTACGCGT	62.433	45.833	19.17	19.17	45.14	6.01
180	181	4.027706	TGTATCTGACATGACGTTACGCG	61.028	47.826	3.53	3.53	38.91	6.01
181	182	3.431856	TGTATCTGACATGACGTTACGC	58.568	45.455	4.09	0.00	31.20	4.42
182	183	5.093457	AGTTGTATCTGACATGACGTTACG	58.907	41.667	2.19	2.19	38.07	3.18
183	184	6.323266	AGAGTTGTATCTGACATGACGTTAC	58.677	40.000	0.00	1.28	38.07	2.50
184	185	6.510879	AGAGTTGTATCTGACATGACGTTA	57.489	37.500	0.00	0.00	38.07	3.18
185	186	5.392767	AGAGTTGTATCTGACATGACGTT	57.607	39.130	0.00	0.00	38.07	3.99
215	217	8.928448	ACCTAAGTGCTCATATCTTCAATTCTA	58.072	33.333	0.00	0.00	0.00	2.10
292	294	9.535270	CTTTTGAGAAGAAATAGCTCTTAAACG	57.465	33.333	0.00	0.00	35.76	3.60
421	431	9.969001	AACACTGTTATTTATTATACTGGGTGT	57.031	29.630	0.00	0.00	33.95	4.16
541	2564	3.385384	CGCCCAGCTCCTCTGTCA	61.385	66.667	0.00	0.00	41.25	3.58
614	2652	0.966179	AAAAGGCGCGGGAAGAAAAT	59.034	45.000	8.83	0.00	0.00	1.82
630	2673	2.739292	CGAGACACGGACTGAAGAAAA	58.261	47.619	0.00	0.00	38.46	2.29
953	3011	5.672856	CGATTCGATTCGATTGTTTTCCTTC	59.327	40.000	21.74	0.00	41.62	3.46
980	3038	3.131478	GATGGGACGCGGGTTTGG	61.131	66.667	12.47	0.00	0.00	3.28
1368	3426	4.918201	CCGGCGATCCCTTGGAGC	62.918	72.222	9.30	0.00	34.05	4.70
1369	3427	2.252072	TTTCCGGCGATCCCTTGGAG	62.252	60.000	9.30	0.00	34.05	3.86
1399	3458	2.560158	GGAAGTAGGGTCTCAGGAAGGT	60.560	54.545	0.00	0.00	0.00	3.50
1435	3494	0.793617	AGGTCTCCTTTCCTGAGGGA	59.206	55.000	0.00	0.00	40.36	4.20
1558	3617	2.654079	CCCGCTTGACAGGCTCTCT	61.654	63.158	8.03	0.00	0.00	3.10
1560	3619	2.604686	TCCCGCTTGACAGGCTCT	60.605	61.111	8.03	0.00	0.00	4.09
1626	3685	1.153005	CTGGGCCATCTGCTTCCTC	60.153	63.158	6.72	0.00	40.92	3.71
1686	3746	2.183478	TCACACCGATGCACTTGAAT	57.817	45.000	0.00	0.00	0.00	2.57
1779	3839	0.951040	AGAAGAAGGCGCCTGTTTCG	60.951	55.000	33.60	0.00	0.00	3.46
2055	4115	2.302260	CTTCTGAGAGCAGGGTCGATA	58.698	52.381	0.00	0.00	42.53	2.92
2179	4239	2.234661	TCGAGACATGCTCCAGTTCAAT	59.765	45.455	10.34	0.00	40.70	2.57
2379	4439	0.677288	TTTCACGAAGAGCGGAAGGA	59.323	50.000	0.00	0.00	46.49	3.36
2403	4463	5.067674	CCAAGAGACATTTGGAACTTCAACA	59.932	40.000	0.00	0.00	46.42	3.33
2449	4509	2.301346	CTGCAACTCCCTTTTGACACT	58.699	47.619	0.00	0.00	0.00	3.55
2464	4524	1.271856	TATTGGACGGTCTCCTGCAA	58.728	50.000	8.23	3.82	40.26	4.08
2667	4727	1.538047	AAATCTCACGCACATTGGCT	58.462	45.000	0.00	0.00	0.00	4.75
2727	4787	1.534805	GCAATCGAGTCGAGCTCATCA	60.535	52.381	21.36	0.00	44.33	3.07
2799	4859	3.056536	TCTCGGTGAGAAGTTGATTCAGG	60.057	47.826	0.00	0.00	40.67	3.86
2808	4868	0.811915	CGTCCATCTCGGTGAGAAGT	59.188	55.000	0.00	0.00	42.27	3.01
2938	4998	1.522668	CTGGATTCAACGTCAGGCAA	58.477	50.000	0.00	0.00	0.00	4.52
2964	5033	1.213926	CTAAGGCAGGCCCTGAAGATT	59.786	52.381	16.85	5.21	45.62	2.40
3150	5219	0.462759	CGTCTTCCTCCATGGCTTCC	60.463	60.000	6.96	0.00	35.26	3.46
3357	5426	1.960040	CTGCCGTGGTAGAGGATGCA	61.960	60.000	0.00	0.00	0.00	3.96
3598	5687	6.853720	TCTAGAGAACAAGAGAATTGTACCG	58.146	40.000	0.00	0.00	31.50	4.02
3621	5710	0.179018	AATACCCTTGATGCGGCCTC	60.179	55.000	0.00	0.00	0.00	4.70
3693	5788	4.302455	GTGTATGGAGATCATTGTCGGAG	58.698	47.826	0.00	0.00	37.30	4.63
3696	5791	3.181466	TGGGTGTATGGAGATCATTGTCG	60.181	47.826	0.00	0.00	37.30	4.35
3698	5793	3.434167	GCTGGGTGTATGGAGATCATTGT	60.434	47.826	0.00	0.00	37.30	2.71
3699	5794	3.144506	GCTGGGTGTATGGAGATCATTG	58.855	50.000	0.00	0.00	37.30	2.82
3700	5795	2.107204	GGCTGGGTGTATGGAGATCATT	59.893	50.000	0.00	0.00	37.30	2.57
3701	5796	1.701847	GGCTGGGTGTATGGAGATCAT	59.298	52.381	0.00	0.00	39.78	2.45
3702	5797	1.131638	GGCTGGGTGTATGGAGATCA	58.868	55.000	0.00	0.00	0.00	2.92
3703	5798	1.131638	TGGCTGGGTGTATGGAGATC	58.868	55.000	0.00	0.00	0.00	2.75
3704	5799	1.212935	GTTGGCTGGGTGTATGGAGAT	59.787	52.381	0.00	0.00	0.00	2.75
3707	5802	0.037590	GTGTTGGCTGGGTGTATGGA	59.962	55.000	0.00	0.00	0.00	3.41
3708	5803	0.965363	GGTGTTGGCTGGGTGTATGG	60.965	60.000	0.00	0.00	0.00	2.74
3712	5807	4.579384	CCGGTGTTGGCTGGGTGT	62.579	66.667	0.00	0.00	0.00	4.16
3720	5815	3.801068	TTTGGAGGGCCGGTGTTGG	62.801	63.158	1.90	0.00	36.79	3.77
3722	5817	2.203437	GTTTGGAGGGCCGGTGTT	60.203	61.111	1.90	0.00	36.79	3.32
3723	5818	3.175710	AGTTTGGAGGGCCGGTGT	61.176	61.111	1.90	0.00	36.79	4.16
3724	5819	2.672996	CAGTTTGGAGGGCCGGTG	60.673	66.667	1.90	0.00	36.79	4.94
3725	5820	2.002018	TTTCAGTTTGGAGGGCCGGT	62.002	55.000	1.90	0.00	36.79	5.28
3726	5821	0.825840	TTTTCAGTTTGGAGGGCCGG	60.826	55.000	0.00	0.00	36.79	6.13
3727	5822	0.598065	CTTTTCAGTTTGGAGGGCCG	59.402	55.000	0.00	0.00	36.79	6.13
3728	5823	1.995376	TCTTTTCAGTTTGGAGGGCC	58.005	50.000	0.00	0.00	0.00	5.80
3729	5824	4.607293	ATTTCTTTTCAGTTTGGAGGGC	57.393	40.909	0.00	0.00	0.00	5.19
3730	5825	6.160576	TGAATTTCTTTTCAGTTTGGAGGG	57.839	37.500	0.00	0.00	32.07	4.30
3731	5826	7.927629	TGATTGAATTTCTTTTCAGTTTGGAGG	59.072	33.333	0.00	0.00	36.97	4.30
3766	5861	1.714899	GAGTGGCGTGTTTGTGCTGT	61.715	55.000	0.00	0.00	0.00	4.40
3895	6576	0.676184	CATCTCCGATGTGATCCGGT	59.324	55.000	0.00	0.00	45.48	5.28

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.