AutoCloner

Multiple sequence alignment - TraesCS5A01G035300

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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	TraesCS5A01G035300	chr5A	100.000	4493	0	0	1	4493	32709473	32713965	0.000000e+00	8298.0
1	TraesCS5A01G035300	chr5A	80.572	664	116	7	2880	3532	32735561	32736222	2.410000e-137	499.0
2	TraesCS5A01G035300	chr5A	88.060	134	16	0	1823	1956	32745897	32746030	4.650000e-35	159.0
3	TraesCS5A01G035300	chr5D	95.562	3605	119	10	1	3585	42929401	42932984	0.000000e+00	5733.0
4	TraesCS5A01G035300	chr5D	82.248	2242	344	34	1294	3500	42951029	42953251	0.000000e+00	1886.0
5	TraesCS5A01G035300	chr5D	86.291	1065	146	0	2314	3378	42946003	42947067	0.000000e+00	1158.0
6	TraesCS5A01G035300	chr5D	82.126	1035	161	12	1277	2302	42944938	42945957	0.000000e+00	865.0
7	TraesCS5A01G035300	chr5D	77.358	1060	221	15	2321	3378	541953513	541952471	1.070000e-170	610.0
8	TraesCS5A01G035300	chr5D	82.181	376	44	17	4128	4488	42933762	42934129	7.300000e-78	302.0
9	TraesCS5A01G035300	chr5B	95.015	1986	76	8	1	1971	38161214	38159237	0.000000e+00	3097.0
10	TraesCS5A01G035300	chr5B	95.417	1462	65	1	1970	3429	38159143	38157682	0.000000e+00	2327.0
11	TraesCS5A01G035300	chr5B	85.185	891	129	3	2499	3387	38050600	38049711	0.000000e+00	911.0
12	TraesCS5A01G035300	chr5B	82.201	1045	166	11	2501	3528	38134793	38133752	0.000000e+00	881.0
13	TraesCS5A01G035300	chr5B	80.022	896	145	20	907	1795	38051498	38050630	2.280000e-177	632.0
14	TraesCS5A01G035300	chr5B	77.619	1050	217	14	2332	3378	684001700	684000666	4.940000e-174	621.0
15	TraesCS5A01G035300	chr5B	79.961	509	84	13	1984	2482	38133157	38132657	4.270000e-95	359.0
16	TraesCS5A01G035300	chr5B	83.117	385	61	4	2477	2859	38127787	38127405	9.250000e-92	348.0
17	TraesCS5A01G035300	chr5B	81.951	410	58	8	1903	2302	38147786	38147383	2.590000e-87	333.0
18	TraesCS5A01G035300	chr5B	90.083	121	5	4	3475	3588	38157684	38157564	2.800000e-32	150.0
19	TraesCS5A01G035300	chr4A	78.511	1061	207	14	2321	3378	627357355	627358397	0.000000e+00	676.0
20	TraesCS5A01G035300	chr4A	72.196	856	200	30	1112	1948	627360366	627361202	1.260000e-55	228.0
21	TraesCS5A01G035300	chr4A	88.043	92	5	4	3586	3672	704436861	704436771	2.210000e-18	104.0
22	TraesCS5A01G035300	chr6A	83.011	465	59	15	3684	4136	32663299	32663755	1.950000e-108	403.0
23	TraesCS5A01G035300	chr6A	82.186	494	57	16	3663	4136	36689815	36689333	3.260000e-106	396.0
24	TraesCS5A01G035300	chr6A	81.319	455	59	21	3696	4136	100428125	100428567	3.330000e-91	346.0
25	TraesCS5A01G035300	chr6A	82.134	403	54	13	3748	4136	2958252	2958650	3.350000e-86	329.0
26	TraesCS5A01G035300	chr6A	92.683	82	6	0	3586	3667	62810686	62810767	7.900000e-23	119.0
27	TraesCS5A01G035300	chr6A	86.154	65	9	0	3089	3153	598056851	598056787	2.240000e-08	71.3
28	TraesCS5A01G035300	chr6A	100.000	28	0	0	1155	1182	598189279	598189306	8.000000e-03	52.8
29	TraesCS5A01G035300	chr2B	80.943	488	63	19	3664	4136	797569989	797570461	4.270000e-95	359.0
30	TraesCS5A01G035300	chr2B	87.368	95	6	3	3580	3668	775396075	775395981	2.210000e-18	104.0
31	TraesCS5A01G035300	chr2B	87.912	91	6	1	3584	3669	536806586	536806676	7.950000e-18	102.0
32	TraesCS5A01G035300	chr7D	83.377	385	49	10	3721	4095	479018765	479018386	4.300000e-90	342.0
33	TraesCS5A01G035300	chr7D	80.134	448	62	21	3705	4136	490439314	490439750	4.370000e-80	309.0
34	TraesCS5A01G035300	chr3B	79.785	465	71	19	3661	4112	817310124	817310578	2.610000e-82	316.0
35	TraesCS5A01G035300	chr1A	79.175	485	73	21	3665	4135	531655716	531655246	1.210000e-80	311.0
36	TraesCS5A01G035300	chr1A	89.157	83	9	0	3586	3668	516456698	516456780	2.210000e-18	104.0
37	TraesCS5A01G035300	chr2A	77.027	444	76	21	3708	4136	596380595	596380163	9.720000e-57	231.0
38	TraesCS5A01G035300	chr1D	77.105	380	58	18	4128	4490	41762459	41762092	4.590000e-45	193.0
39	TraesCS5A01G035300	chr1D	89.247	93	4	4	3586	3673	275947623	275947714	1.320000e-20	111.0
40	TraesCS5A01G035300	chr2D	75.691	362	57	19	4128	4467	128446891	128446539	7.780000e-33	152.0
41	TraesCS5A01G035300	chr3A	90.244	82	8	0	3586	3667	346745202	346745121	1.710000e-19	108.0
42	TraesCS5A01G035300	chr3A	86.458	96	8	2	3576	3666	22230625	22230720	2.860000e-17	100.0
43	TraesCS5A01G035300	chr6D	87.778	90	6	2	3583	3667	469612207	469612296	2.860000e-17	100.0
44	TraesCS5A01G035300	chr6D	83.077	65	11	0	1118	1182	452585832	452585896	4.850000e-05	60.2
45	TraesCS5A01G035300	chr6B	83.824	68	11	0	3086	3153	687100455	687100388	1.040000e-06	65.8
46	TraesCS5A01G035300	chr6B	84.746	59	9	0	1124	1182	687135238	687135180	4.850000e-05	60.2
47	TraesCS5A01G035300	chr6B	84.746	59	9	0	1124	1182	687305813	687305871	4.850000e-05	60.2

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	TraesCS5A01G035300	chr5A	32709473	32713965	4492	False	8298.0	8298	100.0000	1	4493	1	chr5A.!!$F1	4492
1	TraesCS5A01G035300	chr5A	32735561	32736222	661	False	499.0	499	80.5720	2880	3532	1	chr5A.!!$F2	652
2	TraesCS5A01G035300	chr5D	42929401	42934129	4728	False	3017.5	5733	88.8715	1	4488	2	chr5D.!!$F1	4487
3	TraesCS5A01G035300	chr5D	42944938	42953251	8313	False	1303.0	1886	83.5550	1277	3500	3	chr5D.!!$F2	2223
4	TraesCS5A01G035300	chr5D	541952471	541953513	1042	True	610.0	610	77.3580	2321	3378	1	chr5D.!!$R1	1057
5	TraesCS5A01G035300	chr5B	38157564	38161214	3650	True	1858.0	3097	93.5050	1	3588	3	chr5B.!!$R6	3587
6	TraesCS5A01G035300	chr5B	38049711	38051498	1787	True	771.5	911	82.6035	907	3387	2	chr5B.!!$R4	2480
7	TraesCS5A01G035300	chr5B	684000666	684001700	1034	True	621.0	621	77.6190	2332	3378	1	chr5B.!!$R3	1046
8	TraesCS5A01G035300	chr5B	38132657	38134793	2136	True	620.0	881	81.0810	1984	3528	2	chr5B.!!$R5	1544
9	TraesCS5A01G035300	chr4A	627357355	627361202	3847	False	452.0	676	75.3535	1112	3378	2	chr4A.!!$F1	2266

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
568	589	1.527591	CGTTGTACATCACTGCATGCG	60.528	52.381	14.09	10.5	0.00	4.73	F
1228	1258	1.322936	GCTTCTTCAATCTCGACTGCG	59.677	52.381	0.00	0.0	39.35	5.18	F
1899	1931	1.547675	CCTGGGTACTTGTGCCATTGT	60.548	52.381	9.90	0.0	0.00	2.71	F
2664	9025	1.936547	GATGATTGCAGGGACGAGTTC	59.063	52.381	0.00	0.0	0.00	3.01	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1992	2125	0.244450	AACCATTGCACGCAATCAGG	59.756	50.0	14.17	15.13	43.92	3.86	R
2835	9197	0.670706	CGATCTTCAGGCGGAGATCA	59.329	55.0	20.15	0.00	37.58	2.92	R
3198	9560	1.186200	TCTGGTCGAACATCAGGAGG	58.814	55.0	2.20	0.00	0.00	4.30	R
4346	11389	1.758936	CATTGGGAGAAGATGCAGCA	58.241	50.0	4.07	0.00	0.00	4.41	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
34	35	1.548269	AGTGTGAGCCTAGCTTCAGTC	59.452	52.381	0.00	0.00	39.88	3.51
158	159	6.966435	ATGTTAGTAAATTTTGGTGCATGC	57.034	33.333	11.82	11.82	0.00	4.06
205	206	6.428083	TTGAACTGGTCAAGGTGTCTAATA	57.572	37.500	3.54	0.00	41.47	0.98
334	353	2.789208	GCATGTAGCTACGTTACGTGA	58.211	47.619	21.22	3.94	41.39	4.35
378	397	3.555168	GGGCATGATCCGAGTTAACTAGG	60.555	52.174	24.47	24.47	39.72	3.02
489	510	8.668510	ATTATGGTATTCTGCTACAACTTCTG	57.331	34.615	0.00	0.00	0.00	3.02
518	539	2.750712	GTGCTTAATTGGGACGGCTAAA	59.249	45.455	0.00	0.00	0.00	1.85
540	561	3.228453	ACAAAGTTCTACCTCCTGTCGA	58.772	45.455	0.00	0.00	0.00	4.20
568	589	1.527591	CGTTGTACATCACTGCATGCG	60.528	52.381	14.09	10.50	0.00	4.73
726	754	1.853963	ACCACCACCTAGCTAGTCAG	58.146	55.000	19.31	9.41	0.00	3.51
898	926	2.456119	GGCCGAGTCTGATTGCGTG	61.456	63.158	0.00	0.00	0.00	5.34
986	1016	3.613737	CACAATCGCCAAATTAAGCAAGG	59.386	43.478	1.10	0.00	0.00	3.61
1221	1251	2.937799	CCTCAGCAGCTTCTTCAATCTC	59.062	50.000	0.00	0.00	0.00	2.75
1228	1258	1.322936	GCTTCTTCAATCTCGACTGCG	59.677	52.381	0.00	0.00	39.35	5.18
1470	1500	6.461509	GCTTTATGGTTATTGGCTGCAATACT	60.462	38.462	0.50	0.00	0.00	2.12
1722	1754	3.879844	TGGTACAGGTTCCAGCGT	58.120	55.556	0.00	0.00	0.00	5.07
1899	1931	1.547675	CCTGGGTACTTGTGCCATTGT	60.548	52.381	9.90	0.00	0.00	2.71
1992	2125	5.613358	ACATAGCAAGCAGTTTGACTTAC	57.387	39.130	0.31	0.00	39.21	2.34
2114	2249	2.557056	CGGAGTCTGTCTTAACACTCCA	59.443	50.000	15.47	0.00	43.80	3.86
2207	2342	2.951726	TCTCGAGATGAACAGCTGTTG	58.048	47.619	35.67	19.90	38.56	3.33
2403	2578	6.368516	GCTTTTTGGCTATGCAATTACAAAGA	59.631	34.615	0.00	0.00	0.00	2.52
2493	2668	4.898607	TCAAGGCAGGTTGACACC	57.101	55.556	0.00	0.00	44.67	4.16
2640	2815	8.515414	GTTGCTATAAAGAAGTCCAAAGTGATT	58.485	33.333	0.00	0.00	0.00	2.57
2641	2816	8.044060	TGCTATAAAGAAGTCCAAAGTGATTG	57.956	34.615	0.00	0.00	38.84	2.67
2664	9025	1.936547	GATGATTGCAGGGACGAGTTC	59.063	52.381	0.00	0.00	0.00	3.01
2803	9165	7.225538	GGACACTATATGAGTTTCTTCATGGTG	59.774	40.741	0.00	12.40	38.25	4.17
2805	9167	6.484643	CACTATATGAGTTTCTTCATGGTGGG	59.515	42.308	0.00	0.00	38.25	4.61
2835	9197	4.279169	CACAATCTGTCACCAATTCCACTT	59.721	41.667	0.00	0.00	0.00	3.16
3198	9560	5.622346	AGAGATCCTTGTCCCATAGTTTC	57.378	43.478	0.00	0.00	0.00	2.78
3211	9573	4.122776	CCATAGTTTCCTCCTGATGTTCG	58.877	47.826	0.00	0.00	0.00	3.95
3237	9599	1.747709	ACATGCACCTGAAGATGCTC	58.252	50.000	0.00	0.00	42.55	4.26
3326	9692	3.074999	GCCTGAGCGTGAGAGGAGG	62.075	68.421	0.00	0.00	0.00	4.30
3458	9833	2.033194	CGCCGGTGGTTCTTCCTTC	61.033	63.158	7.26	0.00	37.07	3.46
3535	9913	8.746922	TTATGTTCTTGTATCGTTCGTACTTT	57.253	30.769	0.00	0.00	0.00	2.66
3588	9970	8.856153	TTTGTATGGTGTGTTTATGTGATACT	57.144	30.769	0.00	0.00	0.00	2.12
3589	9971	8.487313	TTGTATGGTGTGTTTATGTGATACTC	57.513	34.615	0.00	0.00	0.00	2.59
3590	9972	7.045416	TGTATGGTGTGTTTATGTGATACTCC	58.955	38.462	0.00	0.00	0.00	3.85
3591	9973	4.839121	TGGTGTGTTTATGTGATACTCCC	58.161	43.478	0.00	0.00	0.00	4.30
3593	9975	5.116882	GGTGTGTTTATGTGATACTCCCTC	58.883	45.833	0.00	0.00	0.00	4.30
3595	9977	5.812642	GTGTGTTTATGTGATACTCCCTCAG	59.187	44.000	0.00	0.00	0.00	3.35
3596	9978	5.483937	TGTGTTTATGTGATACTCCCTCAGT	59.516	40.000	0.00	0.00	39.41	3.41
3597	9979	6.666113	TGTGTTTATGTGATACTCCCTCAGTA	59.334	38.462	0.00	0.00	42.09	2.74
3598	9980	7.179516	TGTGTTTATGTGATACTCCCTCAGTAA	59.820	37.037	0.00	0.00	41.17	2.24
3599	9981	8.038944	GTGTTTATGTGATACTCCCTCAGTAAA	58.961	37.037	0.00	0.00	41.17	2.01
3656	10087	8.810427	TCTAAACGCTCTTATATTTGTTTACGG	58.190	33.333	0.00	0.00	32.41	4.02
3657	10088	5.978934	ACGCTCTTATATTTGTTTACGGG	57.021	39.130	0.00	0.00	0.00	5.28
3658	10089	4.812626	ACGCTCTTATATTTGTTTACGGGG	59.187	41.667	0.00	0.00	0.00	5.73
3659	10090	4.212636	CGCTCTTATATTTGTTTACGGGGG	59.787	45.833	0.00	0.00	0.00	5.40
3660	10091	5.128205	GCTCTTATATTTGTTTACGGGGGT	58.872	41.667	0.00	0.00	0.00	4.95
3661	10092	6.290605	GCTCTTATATTTGTTTACGGGGGTA	58.709	40.000	0.00	0.00	0.00	3.69
3662	10093	6.426025	GCTCTTATATTTGTTTACGGGGGTAG	59.574	42.308	0.00	0.00	0.00	3.18
3663	10094	7.436320	TCTTATATTTGTTTACGGGGGTAGT	57.564	36.000	0.00	0.00	0.00	2.73
3665	10096	8.421002	TCTTATATTTGTTTACGGGGGTAGTAC	58.579	37.037	0.00	0.00	0.00	2.73
3677	10108	3.715315	GGGGGTAGTACTAGCAAAAGGAT	59.285	47.826	28.21	0.00	35.41	3.24
3681	10112	3.821421	AGTACTAGCAAAAGGATCCGG	57.179	47.619	5.98	0.00	0.00	5.14
3682	10113	3.105283	AGTACTAGCAAAAGGATCCGGT	58.895	45.455	5.98	0.00	0.00	5.28
3683	10114	2.403252	ACTAGCAAAAGGATCCGGTG	57.597	50.000	5.98	7.04	0.00	4.94
3685	10116	2.039879	ACTAGCAAAAGGATCCGGTGTT	59.960	45.455	5.98	6.53	0.00	3.32
3687	10118	0.388520	GCAAAAGGATCCGGTGTTGC	60.389	55.000	21.04	21.04	35.13	4.17
3690	10121	0.958822	AAAGGATCCGGTGTTGCAAC	59.041	50.000	22.83	22.83	0.00	4.17
3691	10122	1.234615	AAGGATCCGGTGTTGCAACG	61.235	55.000	23.79	12.65	44.86	4.10
3767	10198	9.634021	ATCACTGAGATGTACTATAACTCTCAA	57.366	33.333	0.00	0.00	41.14	3.02
3843	10274	8.948853	TCGTGAATATTTTTCAAACTCATGAC	57.051	30.769	0.00	0.00	0.00	3.06
3845	10276	7.807433	CGTGAATATTTTTCAAACTCATGACCA	59.193	33.333	0.00	0.00	0.00	4.02
3854	10285	7.397892	TTCAAACTCATGACCACTTTTACAA	57.602	32.000	0.00	0.00	0.00	2.41
3991	10699	6.592798	TTTCTAGAACGAACGAACATTGTT	57.407	33.333	4.18	0.63	0.00	2.83
4083	10860	6.203647	TGCATGATCATTTTCTAAATCAGCG	58.796	36.000	5.16	0.00	32.09	5.18
4086	10863	7.594015	GCATGATCATTTTCTAAATCAGCGAAT	59.406	33.333	5.16	0.00	32.09	3.34
4139	10916	8.748380	AAGTCAAGCATAGTTTTTGAATAAGC	57.252	30.769	0.00	0.00	33.10	3.09
4140	10917	7.885297	AGTCAAGCATAGTTTTTGAATAAGCA	58.115	30.769	0.00	0.00	33.10	3.91
4141	10918	8.359642	AGTCAAGCATAGTTTTTGAATAAGCAA	58.640	29.630	0.00	0.00	33.10	3.91
4143	10920	8.977505	TCAAGCATAGTTTTTGAATAAGCAAAC	58.022	29.630	0.00	0.00	37.48	2.93
4263	11185	8.263854	TGGAACCTTTTTAATTCCAAACCATA	57.736	30.769	5.22	0.00	46.93	2.74
4361	11404	2.467826	GCGTGCTGCATCTTCTCCC	61.468	63.158	5.27	0.00	45.45	4.30
4363	11406	0.674581	CGTGCTGCATCTTCTCCCAA	60.675	55.000	5.27	0.00	0.00	4.12
4364	11407	1.760192	GTGCTGCATCTTCTCCCAAT	58.240	50.000	5.27	0.00	0.00	3.16
4375	11418	2.704464	TCTCCCAATGCAGATCACAG	57.296	50.000	0.00	0.00	0.00	3.66
4376	11419	1.911357	TCTCCCAATGCAGATCACAGT	59.089	47.619	0.00	0.00	0.00	3.55
4378	11421	3.713248	TCTCCCAATGCAGATCACAGTAT	59.287	43.478	0.00	0.00	0.00	2.12
4379	11422	4.901250	TCTCCCAATGCAGATCACAGTATA	59.099	41.667	0.00	0.00	0.00	1.47
4380	11423	5.011431	TCTCCCAATGCAGATCACAGTATAG	59.989	44.000	0.00	0.00	0.00	1.31
4381	11424	4.040829	TCCCAATGCAGATCACAGTATAGG	59.959	45.833	0.00	0.00	0.00	2.57
4382	11425	4.040829	CCCAATGCAGATCACAGTATAGGA	59.959	45.833	0.00	0.00	0.00	2.94
4383	11426	5.236282	CCAATGCAGATCACAGTATAGGAG	58.764	45.833	0.00	0.00	0.00	3.69
4384	11427	5.236282	CAATGCAGATCACAGTATAGGAGG	58.764	45.833	0.00	0.00	0.00	4.30
4385	11428	3.916035	TGCAGATCACAGTATAGGAGGT	58.084	45.455	0.00	0.00	0.00	3.85
4387	11430	3.257127	GCAGATCACAGTATAGGAGGTCC	59.743	52.174	0.00	0.00	0.00	4.46
4409	11452	3.942439	GGATGGGTCGGCCTAGGC	61.942	72.222	26.55	26.55	41.06	3.93
4430	11473	1.977056	GGGATTCCCCGGTATGAAAC	58.023	55.000	11.02	0.00	44.02	2.78
4466	11510	8.939932	TCACTTATATGTGATATTGGTGGGTAA	58.060	33.333	15.48	0.00	41.43	2.85
4467	11511	8.999431	CACTTATATGTGATATTGGTGGGTAAC	58.001	37.037	12.29	0.00	40.12	2.50
4479	11526	2.303175	GTGGGTAACTGCAACTTTGGA	58.697	47.619	0.00	0.00	0.00	3.53

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
34	35	1.971695	GCTTCCAAGTCCCAACCGG	60.972	63.158	0.00	0.00	0.00	5.28
76	77	3.730059	AGATAGGATAGTCTGGGACCAGT	59.270	47.826	17.34	2.68	43.96	4.00
152	153	1.028130	TTGTGAAGAAACCGCATGCA	58.972	45.000	19.57	0.00	0.00	3.96
158	159	3.568007	TCCCAGAAATTGTGAAGAAACCG	59.432	43.478	0.00	0.00	0.00	4.44
426	447	9.764363	GGTATCATGTATCTGTTTGAGTCATAA	57.236	33.333	0.00	0.00	0.00	1.90
431	452	7.187824	ACTGGTATCATGTATCTGTTTGAGT	57.812	36.000	0.00	0.00	0.00	3.41
489	510	3.378427	GTCCCAATTAAGCACATCTGGAC	59.622	47.826	0.00	0.00	33.69	4.02
518	539	3.640029	TCGACAGGAGGTAGAACTTTGTT	59.360	43.478	0.00	0.00	0.00	2.83
540	561	3.938963	CAGTGATGTACAACGGGCTAAAT	59.061	43.478	0.00	0.00	0.00	1.40
610	631	3.774766	TGAGTCAAAGCCTCAGCCTAATA	59.225	43.478	0.00	0.00	41.25	0.98
726	754	7.067008	AGCTGGTGTATGTATGTTAAAATGGTC	59.933	37.037	0.00	0.00	0.00	4.02
946	975	0.178767	TGTTGAGTGTGCTGACTGCT	59.821	50.000	5.87	0.00	43.37	4.24
1018	1048	2.724520	CCAGAGCTGGTGTTTGCTT	58.275	52.632	8.38	0.00	45.53	3.91
1030	1060	3.118592	AGGTAGAGCATTACAACCAGAGC	60.119	47.826	0.00	0.00	32.43	4.09
1221	1251	1.566018	GGGAGGTGTTTTCGCAGTCG	61.566	60.000	0.00	0.00	0.00	4.18
1228	1258	2.265904	GCGGGTGGGAGGTGTTTTC	61.266	63.158	0.00	0.00	0.00	2.29
1451	1481	3.947196	CAGAGTATTGCAGCCAATAACCA	59.053	43.478	0.00	0.00	43.48	3.67
1470	1500	0.923358	AACCACCAACAAGACCCAGA	59.077	50.000	0.00	0.00	0.00	3.86
1899	1931	4.140354	CCCTCGTAACCAGGGGAA	57.860	61.111	0.00	0.00	46.54	3.97
1929	1961	3.624410	AGTTACCTTGACAACCGTTGTTC	59.376	43.478	17.81	11.44	45.52	3.18
1992	2125	0.244450	AACCATTGCACGCAATCAGG	59.756	50.000	14.17	15.13	43.92	3.86
2114	2249	5.052693	TGCATTTACAATCATAGCCTCCT	57.947	39.130	0.00	0.00	0.00	3.69
2174	2309	2.562635	TCTCGAGAATACAGAGGTCGG	58.437	52.381	14.01	0.00	33.16	4.79
2207	2342	3.851098	ACGAGAGTTGAACTTGCCTATC	58.149	45.455	0.00	0.00	46.40	2.08
2268	2403	7.600065	AGATGTTTCAACTCATCAAATCAAGG	58.400	34.615	7.68	0.00	41.74	3.61
2341	2516	1.092921	ACAACGGCAGAAACGCTCAA	61.093	50.000	0.00	0.00	34.00	3.02
2493	2668	1.990799	TTTCTGTGAGTATGCGGACG	58.009	50.000	0.00	0.00	0.00	4.79
2640	2815	1.485895	TCGTCCCTGCAATCATCATCA	59.514	47.619	0.00	0.00	0.00	3.07
2641	2816	2.141517	CTCGTCCCTGCAATCATCATC	58.858	52.381	0.00	0.00	0.00	2.92
2664	9025	7.096065	TGCGACAAGATTATGATCTCATTTACG	60.096	37.037	0.00	3.60	41.78	3.18
2803	9165	1.065199	TGACAGATTGTGATCAGGCCC	60.065	52.381	0.00	0.00	34.60	5.80
2805	9167	2.012673	GGTGACAGATTGTGATCAGGC	58.987	52.381	0.00	0.00	34.60	4.85
2835	9197	0.670706	CGATCTTCAGGCGGAGATCA	59.329	55.000	20.15	0.00	37.58	2.92
3162	9524	2.698274	GGATCTCTTCTCCTTGGAGGAC	59.302	54.545	15.81	0.00	40.06	3.85
3171	9533	2.472029	TGGGACAAGGATCTCTTCTCC	58.528	52.381	8.69	8.69	39.10	3.71
3198	9560	1.186200	TCTGGTCGAACATCAGGAGG	58.814	55.000	2.20	0.00	0.00	4.30
3211	9573	1.808945	CTTCAGGTGCATGTTCTGGTC	59.191	52.381	0.00	0.00	0.00	4.02
3326	9692	3.982372	TTCATCGTCGGCCTGTCGC	62.982	63.158	0.00	0.00	0.00	5.19
3390	9756	3.716195	TCACCATCACCGGCCTGG	61.716	66.667	14.28	14.28	46.41	4.45
3411	9777	1.202580	CCTCCACCGAAGTCATCATCC	60.203	57.143	0.00	0.00	0.00	3.51
3458	9833	2.202797	CATCTGTCACCTCGGCCG	60.203	66.667	22.12	22.12	0.00	6.13
3535	9913	4.213694	ACAAACACACAAACTGTTCGTACA	59.786	37.500	0.00	0.00	30.34	2.90
3588	9970	8.867097	ACGCTCTTATATTTATTTACTGAGGGA	58.133	33.333	0.00	0.00	36.36	4.20
3589	9971	9.490379	AACGCTCTTATATTTATTTACTGAGGG	57.510	33.333	0.00	0.00	37.76	4.30
3631	10062	8.060090	CCCGTAAACAAATATAAGAGCGTTTAG	58.940	37.037	0.00	0.00	31.53	1.85
3633	10064	6.183360	CCCCGTAAACAAATATAAGAGCGTTT	60.183	38.462	0.00	0.00	0.00	3.60
3634	10065	5.295045	CCCCGTAAACAAATATAAGAGCGTT	59.705	40.000	0.00	0.00	0.00	4.84
3635	10066	4.812626	CCCCGTAAACAAATATAAGAGCGT	59.187	41.667	0.00	0.00	0.00	5.07
3636	10067	4.212636	CCCCCGTAAACAAATATAAGAGCG	59.787	45.833	0.00	0.00	0.00	5.03
3637	10068	5.128205	ACCCCCGTAAACAAATATAAGAGC	58.872	41.667	0.00	0.00	0.00	4.09
3638	10069	7.503549	ACTACCCCCGTAAACAAATATAAGAG	58.496	38.462	0.00	0.00	0.00	2.85
3639	10070	7.436320	ACTACCCCCGTAAACAAATATAAGA	57.564	36.000	0.00	0.00	0.00	2.10
3640	10071	8.424133	AGTACTACCCCCGTAAACAAATATAAG	58.576	37.037	0.00	0.00	0.00	1.73
3641	10072	8.317776	AGTACTACCCCCGTAAACAAATATAA	57.682	34.615	0.00	0.00	0.00	0.98
3642	10073	7.912778	AGTACTACCCCCGTAAACAAATATA	57.087	36.000	0.00	0.00	0.00	0.86
3645	10076	5.395657	GCTAGTACTACCCCCGTAAACAAAT	60.396	44.000	0.00	0.00	0.00	2.32
3647	10078	3.447229	GCTAGTACTACCCCCGTAAACAA	59.553	47.826	0.00	0.00	0.00	2.83
3648	10079	3.023832	GCTAGTACTACCCCCGTAAACA	58.976	50.000	0.00	0.00	0.00	2.83
3649	10080	3.023832	TGCTAGTACTACCCCCGTAAAC	58.976	50.000	0.00	0.00	0.00	2.01
3650	10081	3.380471	TGCTAGTACTACCCCCGTAAA	57.620	47.619	0.00	0.00	0.00	2.01
3651	10082	3.380471	TTGCTAGTACTACCCCCGTAA	57.620	47.619	0.00	0.00	0.00	3.18
3654	10085	2.159000	CCTTTTGCTAGTACTACCCCCG	60.159	54.545	0.00	0.00	0.00	5.73
3655	10086	3.109928	TCCTTTTGCTAGTACTACCCCC	58.890	50.000	0.00	0.00	0.00	5.40
3656	10087	4.202336	GGATCCTTTTGCTAGTACTACCCC	60.202	50.000	3.84	0.00	0.00	4.95
3657	10088	4.501058	CGGATCCTTTTGCTAGTACTACCC	60.501	50.000	10.75	0.00	0.00	3.69
3658	10089	4.501058	CCGGATCCTTTTGCTAGTACTACC	60.501	50.000	10.75	0.00	0.00	3.18
3659	10090	4.099113	ACCGGATCCTTTTGCTAGTACTAC	59.901	45.833	9.46	0.00	0.00	2.73
3660	10091	4.098960	CACCGGATCCTTTTGCTAGTACTA	59.901	45.833	9.46	1.89	0.00	1.82
3661	10092	3.105283	ACCGGATCCTTTTGCTAGTACT	58.895	45.455	9.46	0.00	0.00	2.73
3662	10093	3.195661	CACCGGATCCTTTTGCTAGTAC	58.804	50.000	9.46	0.00	0.00	2.73
3663	10094	2.835764	ACACCGGATCCTTTTGCTAGTA	59.164	45.455	9.46	0.00	0.00	1.82
3665	10096	2.403252	ACACCGGATCCTTTTGCTAG	57.597	50.000	9.46	0.00	0.00	3.42
3677	10108	4.858680	TGCCGTTGCAACACCGGA	62.859	61.111	28.01	13.55	46.66	5.14
3714	10145	5.361571	AGCAAAATGTGATCATGGCTATTGA	59.638	36.000	0.00	0.00	36.07	2.57
3715	10146	5.462068	CAGCAAAATGTGATCATGGCTATTG	59.538	40.000	0.00	1.97	36.07	1.90
3716	10147	5.597806	CAGCAAAATGTGATCATGGCTATT	58.402	37.500	0.00	0.00	36.07	1.73
3717	10148	4.500887	GCAGCAAAATGTGATCATGGCTAT	60.501	41.667	0.00	0.00	36.07	2.97
3718	10149	3.181484	GCAGCAAAATGTGATCATGGCTA	60.181	43.478	0.00	0.00	36.07	3.93
3719	10150	2.418197	GCAGCAAAATGTGATCATGGCT	60.418	45.455	0.00	0.00	37.29	4.75
3728	10159	3.057806	TCTCAGTGATGCAGCAAAATGTG	60.058	43.478	6.05	7.46	0.00	3.21
3801	10232	7.953305	ATTCACGATTTCAAATATGTTCACG	57.047	32.000	0.00	0.00	0.00	4.35
3819	10250	7.807433	TGGTCATGAGTTTGAAAAATATTCACG	59.193	33.333	0.00	0.00	0.00	4.35
3832	10263	8.647143	AATTTGTAAAAGTGGTCATGAGTTTG	57.353	30.769	0.00	0.00	0.00	2.93
3836	10267	9.311916	TCAAAAATTTGTAAAAGTGGTCATGAG	57.688	29.630	0.00	0.00	39.18	2.90
3961	10669	7.140705	TGTTCGTTCGTTCTAGAAATGTTCTA	58.859	34.615	6.78	0.00	41.14	2.10
3971	10679	8.756376	TTTAAAACAATGTTCGTTCGTTCTAG	57.244	30.769	0.00	0.00	0.00	2.43
3977	10685	8.111224	ACCAATTTTTAAAACAATGTTCGTTCG	58.889	29.630	0.00	0.00	0.00	3.95
4120	10897	9.492973	AATGTTTGCTTATTCAAAAACTATGCT	57.507	25.926	0.00	0.00	37.65	3.79
4306	11341	4.589675	TCCGGGCGGCCTGTTTTT	62.590	61.111	27.04	0.00	34.68	1.94
4320	11362	4.720902	TGCACCAGCCCATGTCCG	62.721	66.667	0.00	0.00	41.13	4.79
4346	11389	1.758936	CATTGGGAGAAGATGCAGCA	58.241	50.000	4.07	0.00	0.00	4.41
4361	11404	5.221601	ACCTCCTATACTGTGATCTGCATTG	60.222	44.000	0.00	0.00	0.00	2.82
4363	11406	4.487804	ACCTCCTATACTGTGATCTGCAT	58.512	43.478	0.00	0.00	0.00	3.96
4364	11407	3.891977	GACCTCCTATACTGTGATCTGCA	59.108	47.826	0.00	0.00	0.00	4.41
4391	11434	3.616721	CCTAGGCCGACCCATCCG	61.617	72.222	0.00	0.00	36.11	4.18
4392	11435	3.942439	GCCTAGGCCGACCCATCC	61.942	72.222	24.19	0.00	36.11	3.51
4393	11436	4.301027	CGCCTAGGCCGACCCATC	62.301	72.222	28.09	0.00	37.98	3.51
4453	11497	4.316025	AGTTGCAGTTACCCACCAATAT	57.684	40.909	0.00	0.00	0.00	1.28
4454	11498	3.799432	AGTTGCAGTTACCCACCAATA	57.201	42.857	0.00	0.00	0.00	1.90
4463	11507	4.893424	TTGTCTCCAAAGTTGCAGTTAC	57.107	40.909	0.00	0.00	0.00	2.50
4466	11510	4.202151	GGAAATTGTCTCCAAAGTTGCAGT	60.202	41.667	0.00	0.00	33.44	4.40
4467	11511	4.301628	GGAAATTGTCTCCAAAGTTGCAG	58.698	43.478	0.00	0.00	33.44	4.41

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.