AutoCloner

Multiple sequence alignment - TraesCS4A01G449500

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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	TraesCS4A01G449500	chr4A	100.000	2621	0	0	1	2621	715596690	715599310	0.000000e+00	4841.0
1	TraesCS4A01G449500	chr4A	94.139	1126	57	6	1	1124	715933870	715932752	0.000000e+00	1705.0
2	TraesCS4A01G449500	chr4A	96.087	869	33	1	1113	1980	715931732	715930864	0.000000e+00	1415.0
3	TraesCS4A01G449500	chr4A	84.528	879	118	8	888	1754	715954927	715955799	0.000000e+00	854.0
4	TraesCS4A01G449500	chr4A	86.250	560	69	8	2000	2552	493828775	493828217	3.730000e-168	601.0
5	TraesCS4A01G449500	chr4A	87.838	148	11	7	1763	1909	491693206	491693347	1.610000e-37	167.0
6	TraesCS4A01G449500	chr4A	78.626	131	23	4	1021	1147	725659150	725659021	6.010000e-12	82.4
7	TraesCS4A01G449500	chr2D	88.484	521	47	11	2049	2560	602634708	602635224	3.710000e-173	617.0
8	TraesCS4A01G449500	chr2D	85.167	209	20	7	493	690	619259004	619259212	1.230000e-48	204.0
9	TraesCS4A01G449500	chr2D	94.595	111	5	1	282	391	619258900	619259010	1.250000e-38	171.0
10	TraesCS4A01G449500	chr2D	96.296	54	2	0	432	485	196964885	196964938	3.590000e-14	89.8
11	TraesCS4A01G449500	chr2D	96.296	54	2	0	432	485	272802805	272802858	3.590000e-14	89.8
12	TraesCS4A01G449500	chr2D	96.296	54	2	0	432	485	630268081	630268028	3.590000e-14	89.8
13	TraesCS4A01G449500	chr2D	83.000	100	14	2	588	686	639103797	639103700	1.290000e-13	87.9
14	TraesCS4A01G449500	chr7A	87.867	511	53	7	2057	2560	288810389	288810897	2.250000e-165	592.0
15	TraesCS4A01G449500	chr7A	87.671	511	54	7	2057	2560	92462949	92463457	1.050000e-163	586.0
16	TraesCS4A01G449500	chr7A	87.230	509	60	3	2057	2560	242090231	242090739	2.260000e-160	575.0
17	TraesCS4A01G449500	chr7A	73.344	634	151	16	811	1437	17162067	17161445	4.390000e-53	219.0
18	TraesCS4A01G449500	chr7A	89.865	148	10	3	1764	1909	30155687	30155543	4.450000e-43	185.0
19	TraesCS4A01G449500	chr7A	89.865	148	10	3	1764	1909	735767050	735766906	4.450000e-43	185.0
20	TraesCS4A01G449500	chr7A	90.909	77	7	0	1905	1981	679745097	679745173	1.280000e-18	104.0
21	TraesCS4A01G449500	chr7A	96.154	52	2	0	432	483	4702026	4702077	4.650000e-13	86.1
22	TraesCS4A01G449500	chr2A	86.973	522	63	3	2044	2560	741739157	741738636	1.350000e-162	582.0
23	TraesCS4A01G449500	chr2A	90.210	286	26	2	1	284	729554959	729555244	3.190000e-99	372.0
24	TraesCS4A01G449500	chr2A	92.661	109	7	1	282	389	744339023	744339131	3.490000e-34	156.0
25	TraesCS4A01G449500	chr2A	85.106	94	13	1	586	678	485121819	485121726	7.720000e-16	95.3
26	TraesCS4A01G449500	chr6A	87.377	507	58	4	2057	2558	170616851	170617356	6.290000e-161	577.0
27	TraesCS4A01G449500	chr6A	83.131	658	68	20	1908	2560	24768607	24769226	6.330000e-156	560.0
28	TraesCS4A01G449500	chr3A	86.578	529	62	8	1992	2513	726012279	726011753	2.260000e-160	575.0
29	TraesCS4A01G449500	chr3A	95.161	62	2	1	1905	1965	10006431	10006370	2.150000e-16	97.1
30	TraesCS4A01G449500	chr3A	96.296	54	2	0	432	485	672879575	672879628	3.590000e-14	89.8
31	TraesCS4A01G449500	chr5A	87.033	509	57	7	2057	2558	467848025	467847519	1.360000e-157	566.0
32	TraesCS4A01G449500	chr5A	89.825	285	28	1	1	284	647359838	647359554	5.330000e-97	364.0
33	TraesCS4A01G449500	chr5A	88.506	87	9	1	594	679	532478369	532478455	1.280000e-18	104.0
34	TraesCS4A01G449500	chr5A	86.316	95	10	3	587	679	529126218	529126125	1.660000e-17	100.0
35	TraesCS4A01G449500	chr5A	96.429	56	2	0	1905	1960	89031772	89031717	2.780000e-15	93.5
36	TraesCS4A01G449500	chr5A	90.476	63	5	1	1903	1965	377195405	377195344	6.010000e-12	82.4
37	TraesCS4A01G449500	chr3D	91.259	286	23	2	1	284	488121183	488120898	3.160000e-104	388.0
38	TraesCS4A01G449500	chr3D	90.747	281	24	2	6	284	590752035	590751755	8.860000e-100	374.0
39	TraesCS4A01G449500	chr3D	88.926	298	25	7	1	295	582266394	582266686	6.900000e-96	361.0
40	TraesCS4A01G449500	chr3D	87.162	148	14	3	1763	1909	597172939	597172796	2.090000e-36	163.0
41	TraesCS4A01G449500	chr3D	96.296	54	2	0	432	485	559909909	559909856	3.590000e-14	89.8
42	TraesCS4A01G449500	chr4D	90.210	286	26	2	1	284	226385234	226384949	3.190000e-99	372.0
43	TraesCS4A01G449500	chr4D	89.860	286	27	2	1	284	226455326	226455041	1.480000e-97	366.0
44	TraesCS4A01G449500	chr7D	89.347	291	27	4	1	287	63397088	63396798	1.920000e-96	363.0
45	TraesCS4A01G449500	chr7D	89.189	74	7	1	1906	1978	48849184	48849111	9.990000e-15	91.6
46	TraesCS4A01G449500	chr7D	87.838	74	8	1	1906	1978	48893518	48893445	4.650000e-13	86.1
47	TraesCS4A01G449500	chrUn	89.865	148	10	3	1764	1909	305831043	305830899	4.450000e-43	185.0
48	TraesCS4A01G449500	chrUn	89.865	148	10	3	1764	1909	327652010	327651866	4.450000e-43	185.0
49	TraesCS4A01G449500	chr3B	80.159	252	45	2	2052	2302	330775570	330775323	1.600000e-42	183.0
50	TraesCS4A01G449500	chr3B	84.043	94	14	1	586	678	95574678	95574771	3.590000e-14	89.8
51	TraesCS4A01G449500	chr5B	87.248	149	17	2	1763	1909	635798174	635798026	4.490000e-38	169.0
52	TraesCS4A01G449500	chr5B	87.162	148	14	2	1763	1909	662640363	662640220	2.090000e-36	163.0
53	TraesCS4A01G449500	chr4B	90.667	75	6	1	610	683	112359809	112359883	5.970000e-17	99.0
54	TraesCS4A01G449500	chr4B	90.141	71	6	1	1901	1970	656682262	656682332	9.990000e-15	91.6
55	TraesCS4A01G449500	chr1D	90.541	74	6	1	610	682	423077176	423077103	2.150000e-16	97.1
56	TraesCS4A01G449500	chr6D	96.296	54	2	0	432	485	429819297	429819244	3.590000e-14	89.8
57	TraesCS4A01G449500	chr5D	94.545	55	3	0	429	483	432293856	432293910	4.650000e-13	86.1
58	TraesCS4A01G449500	chr6B	93.617	47	3	0	285	331	670991057	670991103	1.300000e-08	71.3

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	TraesCS4A01G449500	chr4A	715596690	715599310	2620	False	4841	4841	100.000	1	2621	1	chr4A.!!$F2	2620
1	TraesCS4A01G449500	chr4A	715930864	715933870	3006	True	1560	1705	95.113	1	1980	2	chr4A.!!$R3	1979
2	TraesCS4A01G449500	chr4A	715954927	715955799	872	False	854	854	84.528	888	1754	1	chr4A.!!$F3	866
3	TraesCS4A01G449500	chr4A	493828217	493828775	558	True	601	601	86.250	2000	2552	1	chr4A.!!$R1	552
4	TraesCS4A01G449500	chr2D	602634708	602635224	516	False	617	617	88.484	2049	2560	1	chr2D.!!$F3	511
5	TraesCS4A01G449500	chr7A	288810389	288810897	508	False	592	592	87.867	2057	2560	1	chr7A.!!$F4	503
6	TraesCS4A01G449500	chr7A	92462949	92463457	508	False	586	586	87.671	2057	2560	1	chr7A.!!$F2	503
7	TraesCS4A01G449500	chr7A	242090231	242090739	508	False	575	575	87.230	2057	2560	1	chr7A.!!$F3	503
8	TraesCS4A01G449500	chr7A	17161445	17162067	622	True	219	219	73.344	811	1437	1	chr7A.!!$R1	626
9	TraesCS4A01G449500	chr2A	741738636	741739157	521	True	582	582	86.973	2044	2560	1	chr2A.!!$R2	516
10	TraesCS4A01G449500	chr6A	170616851	170617356	505	False	577	577	87.377	2057	2558	1	chr6A.!!$F2	501
11	TraesCS4A01G449500	chr6A	24768607	24769226	619	False	560	560	83.131	1908	2560	1	chr6A.!!$F1	652
12	TraesCS4A01G449500	chr3A	726011753	726012279	526	True	575	575	86.578	1992	2513	1	chr3A.!!$R2	521
13	TraesCS4A01G449500	chr5A	467847519	467848025	506	True	566	566	87.033	2057	2558	1	chr5A.!!$R3	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
580	582	0.101219	GGGGCAGAAAATGATGACGC	59.899	55.0	0.0	0.0	0.0	5.19	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1998	3049	0.17915	GTGTGCGCTCAAACCAAACA	60.179	50.0	14.56	0.0	0.0	2.83	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
49	50	0.539669	CCCACCAGGTTTCAAGTCCC	60.540	60.000	0.00	0.00	0.00	4.46
54	55	1.228154	AGGTTTCAAGTCCCGGTGC	60.228	57.895	0.00	0.00	0.00	5.01
69	70	1.806247	CGGTGCTCGCATTATTCCTGA	60.806	52.381	0.00	0.00	0.00	3.86
115	116	0.390472	GCTTTCAGTGGGAGGAGACG	60.390	60.000	0.00	0.00	0.00	4.18
170	171	9.107177	GACTTCATAAATCTCAAGATGACATGT	57.893	33.333	0.00	0.00	34.49	3.21
173	174	6.703165	TCATAAATCTCAAGATGACATGTCGG	59.297	38.462	20.54	7.94	34.49	4.79
178	179	1.931841	CAAGATGACATGTCGGCTCAG	59.068	52.381	20.54	11.92	0.00	3.35
182	183	0.244721	TGACATGTCGGCTCAGTCTG	59.755	55.000	20.54	0.00	0.00	3.51
192	193	1.886585	CTCAGTCTGTCGGAGGTGG	59.113	63.158	0.00	0.00	35.32	4.61
198	199	2.032620	GTCTGTCGGAGGTGGTCATAT	58.967	52.381	0.00	0.00	0.00	1.78
201	202	1.342574	TGTCGGAGGTGGTCATATGGA	60.343	52.381	2.13	0.00	0.00	3.41
215	216	5.178797	GTCATATGGATAGGGTGTATGTGC	58.821	45.833	2.13	0.00	0.00	4.57
230	231	2.203084	TGCGTGCGTTCAAAGGGA	60.203	55.556	0.00	0.00	0.00	4.20
255	256	4.299155	AGTGTATGTGCGTATGTATGAGC	58.701	43.478	0.00	0.00	0.00	4.26
275	276	1.217882	GCTTGCGTCTGTACTGTGTT	58.782	50.000	0.00	0.00	0.00	3.32
350	352	1.553248	GGTGGTTAATTGGGAAAGGGC	59.447	52.381	0.00	0.00	0.00	5.19
360	362	2.361230	GAAAGGGCGGGGGAGTTG	60.361	66.667	0.00	0.00	0.00	3.16
382	384	1.216064	TGGGGAGATGATTGGGTCAG	58.784	55.000	0.00	0.00	40.92	3.51
390	392	5.338219	GGAGATGATTGGGTCAGGATCATAG	60.338	48.000	0.00	0.00	39.81	2.23
398	400	4.141711	TGGGTCAGGATCATAGCAAGTAAC	60.142	45.833	0.00	0.00	0.00	2.50
416	418	8.560374	GCAAGTAACAAAATCAGACTAGAAACT	58.440	33.333	0.00	0.00	0.00	2.66
541	543	1.064946	CTAAGCCAGCGACTCCTCG	59.935	63.158	0.00	0.00	43.28	4.63
553	555	1.154016	CTCCTCGTTCATCGTGCGT	60.154	57.895	0.00	0.00	40.80	5.24
576	578	0.462789	GGCAGGGGCAGAAAATGATG	59.537	55.000	0.00	0.00	43.71	3.07
580	582	0.101219	GGGGCAGAAAATGATGACGC	59.899	55.000	0.00	0.00	0.00	5.19
582	584	2.288666	GGGCAGAAAATGATGACGCTA	58.711	47.619	0.00	0.00	0.00	4.26
584	586	2.285834	GGCAGAAAATGATGACGCTACG	60.286	50.000	0.00	0.00	0.00	3.51
588	590	3.859961	AGAAAATGATGACGCTACGACAG	59.140	43.478	0.00	0.00	35.01	3.51
608	610	0.907704	AATCGCTGTGGTGGGACCTA	60.908	55.000	0.00	0.00	39.58	3.08
649	651	7.490725	CGCTCCATGTTGAGATAAATCCTATAG	59.509	40.741	3.41	0.00	34.11	1.31
667	670	5.902431	CCTATAGGGGGATGAATCTCTTAGG	59.098	48.000	11.33	0.00	0.00	2.69
731	734	6.071896	CGTATCTGTGAATAGAGAGGGCATAA	60.072	42.308	0.00	0.00	28.75	1.90
758	761	3.771216	AGGAGATCCAAAATGTGCAGTT	58.229	40.909	0.92	0.00	38.89	3.16
765	768	7.709947	AGATCCAAAATGTGCAGTTATACATG	58.290	34.615	0.00	0.00	37.57	3.21
1060	1065	1.069296	TCGTTTGCATGCTTCTTTCCG	60.069	47.619	20.33	11.01	0.00	4.30
1173	2209	3.010584	ACAGCCTCAACCCAGATAATGTT	59.989	43.478	0.00	0.00	0.00	2.71
1224	2260	2.478894	GTCAAACAATCGGAGCTTCGAA	59.521	45.455	23.29	4.98	42.69	3.71
1255	2291	3.643320	CCTCAATAGCCTGGTACTCATCA	59.357	47.826	0.00	0.00	0.00	3.07
1443	2488	2.338620	CACGGAGACAACAGCGGA	59.661	61.111	0.00	0.00	0.00	5.54
1518	2563	1.583054	ACTGCGGTTCTGAACTTGAC	58.417	50.000	19.05	7.80	0.00	3.18
1845	2894	0.034059	CCGGCCTCTGCATAGTTAGG	59.966	60.000	0.00	0.00	40.13	2.69
1876	2925	0.796491	CAACACCAACACACGCACAC	60.796	55.000	0.00	0.00	0.00	3.82
1962	3011	8.810990	TTCTTGGTTTAGTTTAGTCCTTTTCA	57.189	30.769	0.00	0.00	0.00	2.69
2016	3067	0.528017	TTGTTTGGTTTGAGCGCACA	59.472	45.000	11.47	6.87	0.00	4.57
2032	3083	3.838550	GCGCACACTAATGTTTTTCGTAG	59.161	43.478	0.30	0.00	36.72	3.51
2036	3087	6.035220	CGCACACTAATGTTTTTCGTAGGATA	59.965	38.462	0.00	0.00	36.72	2.59
2061	3114	3.769300	TCTACACAAGCTAAGCCATCTGA	59.231	43.478	0.00	0.00	0.00	3.27
2088	3142	2.094762	ACTTGTACGTTGATGGGCTC	57.905	50.000	0.00	0.00	0.00	4.70
2101	3155	0.326522	TGGGCTCTCTATGGGCTTCA	60.327	55.000	0.00	0.00	0.00	3.02
2148	3202	8.642935	TGGGTCAAAATAAATGAACATAGTGA	57.357	30.769	0.00	0.00	36.19	3.41
2176	3230	2.127708	ACAAAGGACCTCTTGTCTGGT	58.872	47.619	13.23	0.00	43.89	4.00
2215	3270	4.082625	CCAACAAGCTATGCATCTTTCACA	60.083	41.667	0.19	0.00	0.00	3.58
2220	3275	7.478322	ACAAGCTATGCATCTTTCACATTTAG	58.522	34.615	0.19	0.00	0.00	1.85
2233	3288	8.607713	TCTTTCACATTTAGTAATCCCACCTTA	58.392	33.333	0.00	0.00	0.00	2.69
2271	3326	6.508030	TTCCCACCAGTAAATATATGAGCA	57.492	37.500	0.00	0.00	0.00	4.26
2278	3333	5.503927	CAGTAAATATATGAGCAGCCCCAT	58.496	41.667	3.67	3.67	0.00	4.00
2285	3340	0.106868	TGAGCAGCCCCATGAATCAG	60.107	55.000	0.00	0.00	0.00	2.90
2291	3346	2.008268	GCCCCATGAATCAGCCAACG	62.008	60.000	0.00	0.00	0.00	4.10
2312	3367	3.560896	CGGACGGTTAAAACAAAGGAGAA	59.439	43.478	0.00	0.00	0.00	2.87
2388	3443	8.697507	AAGGATTGTGGGCTTAAATAGAATAG	57.302	34.615	0.00	0.00	0.00	1.73
2539	3602	9.488762	AAAAGGTAGGATAATTAAAAGGAAGGG	57.511	33.333	0.00	0.00	0.00	3.95
2560	3623	1.012486	CCGTAGGCTTCAACGTGGTC	61.012	60.000	7.45	0.00	46.14	4.02
2561	3624	0.319211	CGTAGGCTTCAACGTGGTCA	60.319	55.000	0.00	0.00	34.48	4.02
2562	3625	1.145803	GTAGGCTTCAACGTGGTCAC	58.854	55.000	0.00	0.00	0.00	3.67
2605	3668	6.748132	AGAAGATCTTCTTATCTACAGCAGC	58.252	40.000	28.70	2.20	46.95	5.25
2606	3669	6.323482	AGAAGATCTTCTTATCTACAGCAGCA	59.677	38.462	28.70	0.00	46.95	4.41
2607	3670	6.477053	AGATCTTCTTATCTACAGCAGCAA	57.523	37.500	0.00	0.00	34.40	3.91
2608	3671	7.065120	AGATCTTCTTATCTACAGCAGCAAT	57.935	36.000	0.00	0.00	34.40	3.56
2609	3672	6.930164	AGATCTTCTTATCTACAGCAGCAATG	59.070	38.462	0.00	0.00	34.40	2.82
2610	3673	6.225981	TCTTCTTATCTACAGCAGCAATGA	57.774	37.500	0.00	0.00	0.00	2.57
2611	3674	6.279123	TCTTCTTATCTACAGCAGCAATGAG	58.721	40.000	0.00	0.00	0.00	2.90
2612	3675	5.604758	TCTTATCTACAGCAGCAATGAGT	57.395	39.130	0.00	0.00	0.00	3.41
2613	3676	5.982356	TCTTATCTACAGCAGCAATGAGTT	58.018	37.500	0.00	0.00	0.00	3.01
2614	3677	5.814188	TCTTATCTACAGCAGCAATGAGTTG	59.186	40.000	0.00	0.00	38.39	3.16
2615	3678	3.683365	TCTACAGCAGCAATGAGTTGA	57.317	42.857	0.00	0.00	37.53	3.18
2616	3679	4.006780	TCTACAGCAGCAATGAGTTGAA	57.993	40.909	0.00	0.00	37.53	2.69
2617	3680	4.582869	TCTACAGCAGCAATGAGTTGAAT	58.417	39.130	0.00	0.00	37.53	2.57
2618	3681	5.733676	TCTACAGCAGCAATGAGTTGAATA	58.266	37.500	0.00	0.00	37.53	1.75
2619	3682	4.959596	ACAGCAGCAATGAGTTGAATAG	57.040	40.909	0.00	0.00	37.53	1.73
2620	3683	3.128242	ACAGCAGCAATGAGTTGAATAGC	59.872	43.478	0.00	0.00	37.53	2.97

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
49	50	0.583438	CAGGAATAATGCGAGCACCG	59.417	55.000	0.00	0.00	42.21	4.94
87	88	1.207089	CCCACTGAAAGCGTATCTCCA	59.793	52.381	0.00	0.00	37.60	3.86
90	91	1.482593	CCTCCCACTGAAAGCGTATCT	59.517	52.381	0.00	0.00	37.60	1.98
133	134	2.417339	TATGAAGTCATCGTAGGCGC	57.583	50.000	0.00	0.00	37.76	6.53
140	141	8.486383	GTCATCTTGAGATTTATGAAGTCATCG	58.514	37.037	0.00	0.00	33.62	3.84
170	171	2.033602	TCCGACAGACTGAGCCGA	59.966	61.111	10.08	0.00	0.00	5.54
173	174	1.214062	CACCTCCGACAGACTGAGC	59.786	63.158	10.08	0.00	0.00	4.26
178	179	1.471119	TATGACCACCTCCGACAGAC	58.529	55.000	0.00	0.00	0.00	3.51
182	183	1.410004	TCCATATGACCACCTCCGAC	58.590	55.000	3.65	0.00	0.00	4.79
192	193	5.178797	GCACATACACCCTATCCATATGAC	58.821	45.833	3.65	0.00	0.00	3.06
198	199	1.138069	CACGCACATACACCCTATCCA	59.862	52.381	0.00	0.00	0.00	3.41
201	202	0.529773	CGCACGCACATACACCCTAT	60.530	55.000	0.00	0.00	0.00	2.57
215	216	0.443869	CTCATCCCTTTGAACGCACG	59.556	55.000	0.00	0.00	0.00	5.34
230	231	6.084326	TCATACATACGCACATACACTCAT	57.916	37.500	0.00	0.00	0.00	2.90
255	256	0.939577	ACACAGTACAGACGCAAGCG	60.940	55.000	13.50	13.50	46.03	4.68
287	289	5.276440	ACTGATCCTATTCACCTTCTCTGT	58.724	41.667	0.00	0.00	0.00	3.41
296	298	8.908786	TGATTTCCATAACTGATCCTATTCAC	57.091	34.615	0.00	0.00	0.00	3.18
350	352	2.270874	CTCCCCAATCAACTCCCCCG	62.271	65.000	0.00	0.00	0.00	5.73
360	362	2.175499	TGACCCAATCATCTCCCCAATC	59.825	50.000	0.00	0.00	29.99	2.67
382	384	8.125448	GTCTGATTTTGTTACTTGCTATGATCC	58.875	37.037	0.00	0.00	0.00	3.36
390	392	8.560374	AGTTTCTAGTCTGATTTTGTTACTTGC	58.440	33.333	0.00	0.00	0.00	4.01
473	475	4.916870	TGAACTCACGTACGATATGGAAG	58.083	43.478	24.41	6.87	0.00	3.46
482	484	4.219143	TGGCTATATGAACTCACGTACG	57.781	45.455	15.01	15.01	0.00	3.67
483	485	5.983720	ACATTGGCTATATGAACTCACGTAC	59.016	40.000	0.00	0.00	0.00	3.67
484	486	5.983118	CACATTGGCTATATGAACTCACGTA	59.017	40.000	0.00	0.00	0.00	3.57
485	487	4.811024	CACATTGGCTATATGAACTCACGT	59.189	41.667	0.00	0.00	0.00	4.49
486	488	4.212004	CCACATTGGCTATATGAACTCACG	59.788	45.833	0.00	0.00	0.00	4.35
541	543	4.147322	CCGCCACGCACGATGAAC	62.147	66.667	0.00	0.00	0.00	3.18
588	590	1.745489	GGTCCCACCACAGCGATTC	60.745	63.158	0.00	0.00	38.42	2.52
608	610	1.520494	GAGCGCATCCACATCATCAT	58.480	50.000	11.47	0.00	0.00	2.45
634	636	7.996758	TTCATCCCCCTATAGGATTTATCTC	57.003	40.000	21.07	0.00	41.52	2.75
649	651	7.511028	CCTATATACCTAAGAGATTCATCCCCC	59.489	44.444	0.00	0.00	0.00	5.40
731	734	6.662755	TGCACATTTTGGATCTCCTAGTATT	58.337	36.000	0.00	0.00	36.82	1.89
1060	1065	2.355837	TTGAGCAGCGACGACCAC	60.356	61.111	0.00	0.00	0.00	4.16
1131	2167	3.016474	GCTCGAGGCGTTCTTGCAC	62.016	63.158	15.58	0.00	36.28	4.57
1224	2260	2.703007	CAGGCTATTGAGGTCCTTAGCT	59.297	50.000	17.03	0.00	37.72	3.32
1255	2291	2.421529	GGCCTTTAAGGATGTCGATGGT	60.422	50.000	16.18	0.00	37.67	3.55
1443	2488	1.823610	GGTAGCTCAAAGGACGGTAGT	59.176	52.381	0.00	0.00	0.00	2.73
1506	2551	5.046376	TGGCATATCTCTGTCAAGTTCAGAA	60.046	40.000	0.00	0.00	40.68	3.02
1757	2806	5.627503	GCCAATAAAATCCACCTTTGAGCAT	60.628	40.000	0.00	0.00	0.00	3.79
1763	2812	7.125391	TCTATGAGCCAATAAAATCCACCTTT	58.875	34.615	0.00	0.00	0.00	3.11
1764	2813	6.672593	TCTATGAGCCAATAAAATCCACCTT	58.327	36.000	0.00	0.00	0.00	3.50
1793	2842	5.945784	TCTTTGGGTTTGTATCCTCTTGATG	59.054	40.000	0.00	0.00	34.76	3.07
1801	2850	6.349860	GGTGTGTATTCTTTGGGTTTGTATCC	60.350	42.308	0.00	0.00	0.00	2.59
1845	2894	0.743688	TGGTGTTGGTTGTGTGCATC	59.256	50.000	0.00	0.00	0.00	3.91
1855	2904	1.675972	TGCGTGTGTTGGTGTTGGT	60.676	52.632	0.00	0.00	0.00	3.67
1984	3033	6.766944	TCAAACCAAACAAAATCAATGATGCT	59.233	30.769	0.00	0.00	0.00	3.79
1985	3034	6.957150	TCAAACCAAACAAAATCAATGATGC	58.043	32.000	0.00	0.00	0.00	3.91
1986	3035	7.073265	GCTCAAACCAAACAAAATCAATGATG	58.927	34.615	0.00	0.00	0.00	3.07
1988	3037	5.233902	CGCTCAAACCAAACAAAATCAATGA	59.766	36.000	0.00	0.00	0.00	2.57
1989	3038	5.433855	CGCTCAAACCAAACAAAATCAATG	58.566	37.500	0.00	0.00	0.00	2.82
1990	3039	4.024977	GCGCTCAAACCAAACAAAATCAAT	60.025	37.500	0.00	0.00	0.00	2.57
1998	3049	0.179150	GTGTGCGCTCAAACCAAACA	60.179	50.000	14.56	0.00	0.00	2.83
2016	3067	7.783042	AGAGCTATCCTACGAAAAACATTAGT	58.217	34.615	0.00	0.00	0.00	2.24
2061	3114	1.965643	TCAACGTACAAGTACCTGGCT	59.034	47.619	4.89	0.00	32.61	4.75
2088	3142	4.321601	CGGTCTCTATTGAAGCCCATAGAG	60.322	50.000	9.14	9.14	42.24	2.43
2101	3155	7.093509	ACCCAATTAATTTTTGCGGTCTCTATT	60.094	33.333	0.00	0.00	0.00	1.73
2138	3192	8.017946	GTCCTTTGTTCAATTCTCACTATGTTC	58.982	37.037	0.00	0.00	0.00	3.18
2144	3198	5.053978	AGGTCCTTTGTTCAATTCTCACT	57.946	39.130	0.00	0.00	0.00	3.41
2148	3202	5.449553	ACAAGAGGTCCTTTGTTCAATTCT	58.550	37.500	11.48	0.00	31.42	2.40
2220	3275	8.674607	CATTGTAAAAGAGTAAGGTGGGATTAC	58.325	37.037	0.00	0.00	34.08	1.89
2233	3288	5.640147	TGGTGGGAATCATTGTAAAAGAGT	58.360	37.500	0.00	0.00	0.00	3.24
2271	3326	0.685458	GTTGGCTGATTCATGGGGCT	60.685	55.000	0.00	0.00	0.00	5.19
2278	3333	1.375396	CCGTCCGTTGGCTGATTCA	60.375	57.895	0.00	0.00	0.00	2.57
2285	3340	0.662085	TGTTTTAACCGTCCGTTGGC	59.338	50.000	0.00	0.00	35.79	4.52
2291	3346	4.336153	TGTTCTCCTTTGTTTTAACCGTCC	59.664	41.667	0.00	0.00	0.00	4.79
2312	3367	1.066143	CGCCCTAAACATGAGGACTGT	60.066	52.381	0.00	0.00	35.99	3.55
2388	3443	9.285770	CTTTCTTTAATTAGCCATCCGTTTAAC	57.714	33.333	0.00	0.00	0.00	2.01
2436	3495	7.967890	AAGCCCACAATCTTTCTTTTAATTG	57.032	32.000	0.00	0.00	35.68	2.32
2485	3547	5.592688	TCAAATCCTTCCTTTAATTAGCCCG	59.407	40.000	0.00	0.00	0.00	6.13
2539	3602	1.012486	CCACGTTGAAGCCTACGGAC	61.012	60.000	0.00	0.00	43.81	4.79
2565	3628	4.292178	CTCTCCCTCCGGCGATGC	62.292	72.222	9.30	0.00	0.00	3.91
2566	3629	2.081425	CTTCTCTCCCTCCGGCGATG	62.081	65.000	9.30	0.00	0.00	3.84
2567	3630	1.830408	CTTCTCTCCCTCCGGCGAT	60.830	63.158	9.30	0.00	0.00	4.58
2568	3631	2.285889	ATCTTCTCTCCCTCCGGCGA	62.286	60.000	9.30	0.00	0.00	5.54
2569	3632	1.801309	GATCTTCTCTCCCTCCGGCG	61.801	65.000	0.00	0.00	0.00	6.46
2570	3633	0.469144	AGATCTTCTCTCCCTCCGGC	60.469	60.000	0.00	0.00	0.00	6.13
2571	3634	1.960689	GAAGATCTTCTCTCCCTCCGG	59.039	57.143	25.26	0.00	36.69	5.14
2572	3635	2.944129	AGAAGATCTTCTCTCCCTCCG	58.056	52.381	28.70	0.00	46.13	4.63
2582	3645	6.511416	TGCTGCTGTAGATAAGAAGATCTTC	58.489	40.000	25.20	25.20	37.89	2.87
2583	3646	6.477053	TGCTGCTGTAGATAAGAAGATCTT	57.523	37.500	7.95	7.95	40.35	2.40
2584	3647	6.477053	TTGCTGCTGTAGATAAGAAGATCT	57.523	37.500	0.00	0.00	39.54	2.75
2585	3648	6.927936	TCATTGCTGCTGTAGATAAGAAGATC	59.072	38.462	0.00	0.00	0.00	2.75
2586	3649	6.824553	TCATTGCTGCTGTAGATAAGAAGAT	58.175	36.000	0.00	0.00	0.00	2.40
2587	3650	6.127225	ACTCATTGCTGCTGTAGATAAGAAGA	60.127	38.462	0.00	0.00	0.00	2.87
2588	3651	6.047870	ACTCATTGCTGCTGTAGATAAGAAG	58.952	40.000	0.00	0.00	0.00	2.85
2589	3652	5.982356	ACTCATTGCTGCTGTAGATAAGAA	58.018	37.500	0.00	0.00	0.00	2.52
2590	3653	5.604758	ACTCATTGCTGCTGTAGATAAGA	57.395	39.130	0.00	0.00	0.00	2.10
2591	3654	5.814188	TCAACTCATTGCTGCTGTAGATAAG	59.186	40.000	0.00	0.00	35.63	1.73
2592	3655	5.733676	TCAACTCATTGCTGCTGTAGATAA	58.266	37.500	0.00	0.00	35.63	1.75
2593	3656	5.343307	TCAACTCATTGCTGCTGTAGATA	57.657	39.130	0.00	0.00	35.63	1.98
2594	3657	4.212143	TCAACTCATTGCTGCTGTAGAT	57.788	40.909	0.00	0.00	35.63	1.98
2595	3658	3.683365	TCAACTCATTGCTGCTGTAGA	57.317	42.857	0.00	0.00	35.63	2.59
2596	3659	4.959596	ATTCAACTCATTGCTGCTGTAG	57.040	40.909	0.00	0.00	35.63	2.74
2597	3660	4.333649	GCTATTCAACTCATTGCTGCTGTA	59.666	41.667	0.00	0.00	35.63	2.74
2598	3661	3.128242	GCTATTCAACTCATTGCTGCTGT	59.872	43.478	0.00	0.00	35.63	4.40
2599	3662	3.692576	GCTATTCAACTCATTGCTGCTG	58.307	45.455	0.00	0.00	35.63	4.41

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.