AutoCloner

Multiple sequence alignment - TraesCS5A01G471100

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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	TraesCS5A01G471100	chr5A	100.000	3263	0	0	1	3263	647580501	647577239	0.000000e+00	6026.0
1	TraesCS5A01G471100	chr5A	88.754	658	35	5	1	619	647749502	647748845	0.000000e+00	769.0
2	TraesCS5A01G471100	chr5A	90.377	530	41	2	935	1464	647748227	647747708	0.000000e+00	688.0
3	TraesCS5A01G471100	chr5A	88.101	395	47	0	1570	1964	647747560	647747166	1.370000e-128	470.0
4	TraesCS5A01G471100	chr5A	83.582	402	57	3	1586	1987	647534976	647534584	5.140000e-98	368.0
5	TraesCS5A01G471100	chr5A	88.475	295	19	6	648	941	647748772	647748492	3.120000e-90	342.0
6	TraesCS5A01G471100	chr5A	84.266	286	45	0	1227	1512	647747837	647747552	2.480000e-71	279.0
7	TraesCS5A01G471100	chr5A	87.931	58	7	0	339	396	295076430	295076373	5.840000e-08	69.4
8	TraesCS5A01G471100	chr5D	92.607	2597	129	17	688	3263	520259203	520256649	0.000000e+00	3674.0
9	TraesCS5A01G471100	chr5D	87.049	749	86	6	1227	1974	520241921	520241183	0.000000e+00	835.0
10	TraesCS5A01G471100	chr5D	84.452	611	66	12	896	1504	520242335	520241752	2.820000e-160	575.0
11	TraesCS5A01G471100	chr5D	88.716	257	26	2	1	254	520266737	520266481	8.790000e-81	311.0
12	TraesCS5A01G471100	chr5D	91.538	130	11	0	1335	1464	520258668	520258539	2.590000e-41	180.0
13	TraesCS5A01G471100	chr5D	82.796	186	28	3	1390	1573	520258364	520258181	2.610000e-36	163.0
14	TraesCS5A01G471100	chr5D	81.720	186	30	3	1390	1573	520241617	520241434	5.640000e-33	152.0
15	TraesCS5A01G471100	chr5D	87.288	118	15	0	1282	1399	520258364	520258247	5.680000e-28	135.0
16	TraesCS5A01G471100	chr5D	89.524	105	11	0	1531	1635	520258613	520258509	2.040000e-27	134.0
17	TraesCS5A01G471100	chr5D	88.506	87	9	1	387	472	330710772	330710686	1.600000e-18	104.0
18	TraesCS5A01G471100	chr5B	93.463	566	36	1	1399	1964	655484048	655483484	0.000000e+00	839.0
19	TraesCS5A01G471100	chr5B	86.561	692	55	18	712	1395	655490067	655489406	0.000000e+00	728.0
20	TraesCS5A01G471100	chr5B	82.171	645	95	10	1335	1978	655449377	655448752	1.330000e-148	536.0
21	TraesCS5A01G471100	chr5B	85.679	405	44	11	996	1399	655449596	655449205	6.510000e-112	414.0
22	TraesCS5A01G471100	chr5B	87.791	344	37	4	1	340	655491244	655490902	6.560000e-107	398.0
23	TraesCS5A01G471100	chr5B	83.333	120	19	1	1534	1652	655449319	655449200	3.440000e-20	110.0
24	TraesCS5A01G471100	chr5B	90.909	77	6	1	396	472	383524166	383524241	5.760000e-18	102.0
25	TraesCS5A01G471100	chr5B	90.667	75	5	1	648	720	655490323	655490249	7.450000e-17	99.0
26	TraesCS5A01G471100	chr5B	89.655	58	6	0	339	396	243421536	243421479	1.260000e-09	75.0
27	TraesCS5A01G471100	chr4D	86.260	262	31	5	3006	3263	30200191	30200451	2.480000e-71	279.0
28	TraesCS5A01G471100	chr4D	89.655	58	6	0	339	396	335774282	335774339	1.260000e-09	75.0
29	TraesCS5A01G471100	chr1B	84.942	259	30	9	3008	3262	61476802	61476549	1.500000e-63	254.0
30	TraesCS5A01G471100	chr1B	87.000	200	16	6	3069	3263	631823840	631823646	1.970000e-52	217.0
31	TraesCS5A01G471100	chr7D	83.525	261	35	6	3006	3263	482242796	482243051	1.510000e-58	237.0
32	TraesCS5A01G471100	chr7D	81.395	129	17	5	341	469	638458104	638458225	7.450000e-17	99.0
33	TraesCS5A01G471100	chr7D	85.556	90	12	1	391	480	242786768	242786856	3.470000e-15	93.5
34	TraesCS5A01G471100	chr7D	89.062	64	6	1	333	396	124529315	124529253	9.710000e-11	78.7
35	TraesCS5A01G471100	chr2B	83.396	265	33	7	3005	3263	677978658	677978399	5.440000e-58	235.0
36	TraesCS5A01G471100	chr7B	82.759	261	33	10	3006	3263	470241808	470242059	4.240000e-54	222.0
37	TraesCS5A01G471100	chr7B	84.496	129	13	5	341	469	734265597	734265476	1.590000e-23	121.0
38	TraesCS5A01G471100	chrUn	82.510	263	32	11	3006	3263	201222390	201222137	5.480000e-53	219.0
39	TraesCS5A01G471100	chrUn	79.798	198	35	1	1743	1935	153358208	153358405	4.390000e-29	139.0
40	TraesCS5A01G471100	chr3B	81.853	259	31	8	3010	3263	10921596	10921349	1.530000e-48	204.0
41	TraesCS5A01G471100	chr6D	88.356	146	17	0	1789	1934	143688785	143688930	3.350000e-40	176.0
42	TraesCS5A01G471100	chr6D	87.586	145	15	1	1789	1933	157482905	157482764	7.240000e-37	165.0
43	TraesCS5A01G471100	chr6D	87.356	87	9	2	396	480	296196932	296197018	7.450000e-17	99.0
44	TraesCS5A01G471100	chr7A	85.870	92	9	3	390	478	375877596	375877506	9.640000e-16	95.3
45	TraesCS5A01G471100	chr6A	87.209	86	8	3	397	480	421768361	421768445	9.640000e-16	95.3
46	TraesCS5A01G471100	chr6A	89.286	56	6	0	341	396	263887017	263886962	1.620000e-08	71.3
47	TraesCS5A01G471100	chr4B	89.286	56	6	0	341	396	413830724	413830779	1.620000e-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	TraesCS5A01G471100	chr5A	647577239	647580501	3262	True	6026.000000	6026	100.000000	1	3263	1	chr5A.!!$R3	3262
1	TraesCS5A01G471100	chr5A	647747166	647749502	2336	True	509.600000	769	87.994600	1	1964	5	chr5A.!!$R4	1963
2	TraesCS5A01G471100	chr5D	520256649	520259203	2554	True	857.200000	3674	88.750600	688	3263	5	chr5D.!!$R4	2575
3	TraesCS5A01G471100	chr5D	520241183	520242335	1152	True	520.666667	835	84.407000	896	1974	3	chr5D.!!$R3	1078
4	TraesCS5A01G471100	chr5B	655483484	655484048	564	True	839.000000	839	93.463000	1399	1964	1	chr5B.!!$R2	565
5	TraesCS5A01G471100	chr5B	655489406	655491244	1838	True	408.333333	728	88.339667	1	1395	3	chr5B.!!$R4	1394
6	TraesCS5A01G471100	chr5B	655448752	655449596	844	True	353.333333	536	83.727667	996	1978	3	chr5B.!!$R3	982

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
623	675	1.117150	GGAAGTACCCCACATCGCTA	58.883	55.000	0.00	0.0	0.00	4.26	F
1468	2626	1.301716	GAAACGCTCTGGCAGTGGA	60.302	57.895	15.27	0.0	36.88	4.02	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1649	2807	0.035725	CTGCATGTGCTCCCAGAAGA	60.036	55.0	6.55	0.0	42.66	2.87	R
3180	4350	0.889306	ACGGTGCTCTCCACTCTAAC	59.111	55.0	0.00	0.0	44.08	2.34	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
214	219	5.579511	GCTAGCTTTCGGTCTGTAAAATACA	59.420	40.000	7.70	0.00	37.13	2.29
354	395	6.845908	AGTTATATACTACTCCCTCGGTTCA	58.154	40.000	0.00	0.00	34.56	3.18
367	408	8.314751	ACTCCCTCGGTTCATAAATATAAGATG	58.685	37.037	0.00	0.00	0.00	2.90
390	431	9.549078	GATGTTCTAACTTTCTTAGGAATAGGG	57.451	37.037	0.00	0.00	0.00	3.53
392	433	8.319146	TGTTCTAACTTTCTTAGGAATAGGGTG	58.681	37.037	0.00	0.00	0.00	4.61
398	439	8.388656	ACTTTCTTAGGAATAGGGTGTATTCA	57.611	34.615	7.00	0.00	36.06	2.57
407	448	6.202954	GGAATAGGGTGTATTCACTCATTTCG	59.797	42.308	5.05	0.00	46.62	3.46
408	449	3.873910	AGGGTGTATTCACTCATTTCGG	58.126	45.455	5.05	0.00	46.62	4.30
421	462	8.002984	TCACTCATTTCGGTCTATATGTAACA	57.997	34.615	0.00	0.00	0.00	2.41
429	470	9.438228	TTTCGGTCTATATGTAACACATTTTGA	57.562	29.630	0.00	0.00	39.88	2.69
463	504	7.553881	AACATCTTATATTTGTGAACGGAGG	57.446	36.000	0.00	0.00	0.00	4.30
480	521	6.610075	ACGGAGGGAGTACAAAAGTAATAA	57.390	37.500	0.00	0.00	0.00	1.40
612	664	1.316651	ATCTAGACGGCGGAAGTACC	58.683	55.000	13.24	0.00	0.00	3.34
621	673	1.520787	CGGAAGTACCCCACATCGC	60.521	63.158	3.22	0.00	34.64	4.58
623	675	1.117150	GGAAGTACCCCACATCGCTA	58.883	55.000	0.00	0.00	0.00	4.26
631	683	2.752903	ACCCCACATCGCTAAATTGTTC	59.247	45.455	0.00	0.00	0.00	3.18
732	1374	2.036256	GCTGACTGCCCAATGGGT	59.964	61.111	21.02	0.00	46.51	4.51
882	1536	5.844773	AATTATTAAGGAGACCTAGCCCC	57.155	43.478	0.00	0.00	31.13	5.80
901	1563	3.774216	CCCCAGTCAAGAGAAGAGAAGAT	59.226	47.826	0.00	0.00	0.00	2.40
910	1572	5.920193	AGAGAAGAGAAGATTCCTCACTG	57.080	43.478	0.00	0.00	33.25	3.66
949	1882	2.599281	TCCACTCCGCTCGGACAA	60.599	61.111	6.95	0.00	39.76	3.18
1468	2626	1.301716	GAAACGCTCTGGCAGTGGA	60.302	57.895	15.27	0.00	36.88	4.02
1479	2637	4.100084	CAGTGGATCCAGGCCGCA	62.100	66.667	16.81	0.00	38.38	5.69
1649	2807	2.049433	CAGTTCCGGCTTCGACGT	60.049	61.111	0.00	0.00	35.61	4.34
1755	2913	4.947147	TTCTGGCGGTGGGTGCAC	62.947	66.667	8.80	8.80	0.00	4.57
1762	2920	2.194597	GGTGGGTGCACAACTCCA	59.805	61.111	20.43	13.84	33.29	3.86
2021	3179	2.766400	CGCTCGTCCAGGTCCTCTC	61.766	68.421	0.00	0.00	0.00	3.20
2124	3285	4.760047	GGCGGGCTGATGTCACGT	62.760	66.667	0.00	0.00	0.00	4.49
2333	3494	1.331214	TCTTGCTTGGCTTCCAAAGG	58.669	50.000	0.00	0.00	43.44	3.11
2347	3508	5.292589	GCTTCCAAAGGCAATGTATGATTTG	59.707	40.000	0.00	0.00	37.17	2.32
2373	3534	0.304401	CAATTTGCGCGGATCATCGA	59.696	50.000	8.83	0.00	0.00	3.59
2374	3535	1.069703	CAATTTGCGCGGATCATCGAT	60.070	47.619	8.83	0.00	0.00	3.59
2375	3536	0.792640	ATTTGCGCGGATCATCGATC	59.207	50.000	8.83	0.00	38.25	3.69
2376	3537	0.529555	TTTGCGCGGATCATCGATCA	60.530	50.000	8.83	0.00	40.50	2.92
2377	3538	0.529555	TTGCGCGGATCATCGATCAA	60.530	50.000	8.83	0.00	40.50	2.57
2378	3539	1.215014	TGCGCGGATCATCGATCAAC	61.215	55.000	8.83	0.00	40.50	3.18
2379	3540	0.941463	GCGCGGATCATCGATCAACT	60.941	55.000	8.83	0.00	40.50	3.16
2380	3541	1.056103	CGCGGATCATCGATCAACTC	58.944	55.000	0.00	0.00	40.50	3.01
2381	3542	1.423395	GCGGATCATCGATCAACTCC	58.577	55.000	0.00	0.00	40.50	3.85
2382	3543	1.269778	GCGGATCATCGATCAACTCCA	60.270	52.381	0.00	0.00	40.50	3.86
2383	3544	2.611473	GCGGATCATCGATCAACTCCAT	60.611	50.000	0.00	0.00	40.50	3.41
2384	3545	3.249091	CGGATCATCGATCAACTCCATC	58.751	50.000	0.00	0.00	40.50	3.51
2385	3546	3.249091	GGATCATCGATCAACTCCATCG	58.751	50.000	0.00	0.00	43.77	3.84
2466	3635	5.278071	CGACAACAACATTGGGTAAAGCTAA	60.278	40.000	0.00	0.00	0.00	3.09
2495	3664	3.982475	GTGCGATCCACATCTGATCTAA	58.018	45.455	8.84	0.00	44.06	2.10
2496	3665	4.371786	GTGCGATCCACATCTGATCTAAA	58.628	43.478	8.84	0.00	44.06	1.85
2497	3666	4.210120	GTGCGATCCACATCTGATCTAAAC	59.790	45.833	8.84	0.00	44.06	2.01
2498	3667	4.141959	TGCGATCCACATCTGATCTAAACA	60.142	41.667	0.00	0.00	37.15	2.83
2499	3668	4.811024	GCGATCCACATCTGATCTAAACAA	59.189	41.667	0.00	0.00	37.15	2.83
2500	3669	5.050499	GCGATCCACATCTGATCTAAACAAG	60.050	44.000	0.00	0.00	37.15	3.16
2501	3670	6.045318	CGATCCACATCTGATCTAAACAAGT	58.955	40.000	0.00	0.00	37.15	3.16
2502	3671	6.199908	CGATCCACATCTGATCTAAACAAGTC	59.800	42.308	0.00	0.00	37.15	3.01
2503	3672	6.358974	TCCACATCTGATCTAAACAAGTCA	57.641	37.500	0.00	0.00	0.00	3.41
2504	3673	6.950842	TCCACATCTGATCTAAACAAGTCAT	58.049	36.000	0.00	0.00	0.00	3.06
2505	3674	7.044181	TCCACATCTGATCTAAACAAGTCATC	58.956	38.462	0.00	0.00	0.00	2.92
2564	3733	5.733620	TTTGGAACTATGTACGAGACCTT	57.266	39.130	1.82	0.00	0.00	3.50
2613	3782	9.737427	CCTATTACTATTAGCACGATGGAATAG	57.263	37.037	0.00	0.00	37.71	1.73
2614	3783	9.239002	CTATTACTATTAGCACGATGGAATAGC	57.761	37.037	0.00	0.00	35.98	2.97
2637	3806	8.297470	AGCTTTGCTTATTTTTAGGATGATGA	57.703	30.769	0.00	0.00	33.89	2.92
2661	3831	3.477210	ACTCACTCTGAAGGTGGTTTC	57.523	47.619	0.00	0.00	35.61	2.78
2664	3834	4.080299	ACTCACTCTGAAGGTGGTTTCTTT	60.080	41.667	0.00	0.00	35.61	2.52
2674	3844	4.154942	AGGTGGTTTCTTTCATCTGCAAT	58.845	39.130	0.00	0.00	0.00	3.56
2675	3845	4.021719	AGGTGGTTTCTTTCATCTGCAATG	60.022	41.667	0.00	0.00	0.00	2.82
2694	3864	6.040054	TGCAATGAGAAATGATACCCTCAATG	59.960	38.462	0.00	0.00	38.88	2.82
2705	3875	7.062749	TGATACCCTCAATGTATACTGTTCC	57.937	40.000	4.17	0.00	0.00	3.62
2706	3876	6.844388	TGATACCCTCAATGTATACTGTTCCT	59.156	38.462	4.17	0.00	0.00	3.36
2736	3906	7.193377	TCCATTAAAAACTGTCCGTCTTAAC	57.807	36.000	0.00	0.00	0.00	2.01
2754	3924	7.975750	GTCTTAACGAAAATATTGCTCCTTCT	58.024	34.615	0.00	0.00	0.00	2.85
2761	3931	5.968387	AAATATTGCTCCTTCTTCGTACG	57.032	39.130	9.53	9.53	0.00	3.67
2782	3952	7.317269	CGTACGAAATGTTCTGTTTAGTTTCAC	59.683	37.037	10.44	0.00	0.00	3.18
2901	4071	9.931698	TCTACATCTTGTTAATTACTCCCTCTA	57.068	33.333	0.00	0.00	0.00	2.43
2959	4129	2.603953	GTGTAACCTCGACTAGCAACC	58.396	52.381	0.00	0.00	0.00	3.77
2976	4146	3.683340	GCAACCGAACTAAGGGAAAGTAG	59.317	47.826	0.00	0.00	0.00	2.57
2978	4148	4.797800	ACCGAACTAAGGGAAAGTAGTC	57.202	45.455	0.00	0.00	30.18	2.59
2988	4158	1.641577	GAAAGTAGTCGAGCGGCATT	58.358	50.000	1.45	0.00	0.00	3.56
2995	4165	4.481112	CGAGCGGCATTGTTGGGC	62.481	66.667	1.45	0.00	0.00	5.36
3051	4221	1.298953	ATGTACCTGTGGGCAATCCT	58.701	50.000	0.00	0.00	36.20	3.24
3056	4226	0.032813	CCTGTGGGCAATCCTCCATT	60.033	55.000	0.00	0.00	35.28	3.16
3062	4232	2.024177	TGGGCAATCCTCCATTCATCAA	60.024	45.455	0.00	0.00	36.20	2.57
3064	4234	3.257624	GGGCAATCCTCCATTCATCAATC	59.742	47.826	0.00	0.00	0.00	2.67
3077	4247	5.963214	TTCATCAATCTCCTCAAGATCCA	57.037	39.130	0.00	0.00	44.26	3.41
3151	4321	6.796426	TGTACTAGTGTCAGATATTGTCAGC	58.204	40.000	5.39	0.00	0.00	4.26
3177	4347	6.867519	TTACAGAAGAGAGAGAGAGAGAGA	57.132	41.667	0.00	0.00	0.00	3.10
3178	4348	5.350504	ACAGAAGAGAGAGAGAGAGAGAG	57.649	47.826	0.00	0.00	0.00	3.20
3179	4349	5.026121	ACAGAAGAGAGAGAGAGAGAGAGA	58.974	45.833	0.00	0.00	0.00	3.10
3180	4350	5.128499	ACAGAAGAGAGAGAGAGAGAGAGAG	59.872	48.000	0.00	0.00	0.00	3.20
3231	4401	3.977427	TCTCACGCCATACATATGACAC	58.023	45.455	10.38	0.00	35.75	3.67
3241	4411	7.083858	GCCATACATATGACACGCATTTTATT	58.916	34.615	10.38	0.00	38.44	1.40
3242	4412	7.594758	GCCATACATATGACACGCATTTTATTT	59.405	33.333	10.38	0.00	38.44	1.40

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
61	62	7.591057	GCAAACTCGCATTGATATAATTAGCAA	59.409	33.333	0.00	0.00	38.04	3.91
214	219	3.117663	ACAAACATAATACTCCGGGGCAT	60.118	43.478	0.00	0.00	0.00	4.40
367	408	8.319881	ACACCCTATTCCTAAGAAAGTTAGAAC	58.680	37.037	0.00	0.00	35.09	3.01
378	419	7.361457	TGAGTGAATACACCCTATTCCTAAG	57.639	40.000	0.00	0.00	46.99	2.18
387	428	3.263425	ACCGAAATGAGTGAATACACCCT	59.737	43.478	0.00	0.00	46.99	4.34
390	431	8.916654	CATATAGACCGAAATGAGTGAATACAC	58.083	37.037	0.00	0.00	46.24	2.90
398	439	7.778083	TGTGTTACATATAGACCGAAATGAGT	58.222	34.615	0.00	0.00	0.00	3.41
419	460	9.275398	AGATGTTTTGCATATTTCAAAATGTGT	57.725	25.926	12.92	4.74	42.89	3.72
435	476	7.753132	TCCGTTCACAAATATAAGATGTTTTGC	59.247	33.333	0.00	0.00	33.43	3.68
480	521	7.437793	TCGTATTCGGAAAAAGGTTTAATGT	57.562	32.000	0.00	0.00	37.69	2.71
612	664	2.675844	TCGAACAATTTAGCGATGTGGG	59.324	45.455	0.00	0.00	0.00	4.61
621	673	4.903638	TGCTCGTCTTCGAACAATTTAG	57.096	40.909	0.00	0.00	45.61	1.85
623	675	3.997021	AGATGCTCGTCTTCGAACAATTT	59.003	39.130	0.00	0.00	43.59	1.82
631	683	3.698382	GCCAGATGCTCGTCTTCG	58.302	61.111	0.00	0.00	36.87	3.79
640	692	0.099436	CCAAAGCGTTAGCCAGATGC	59.901	55.000	0.00	0.00	46.67	3.91
642	694	2.488153	GTTTCCAAAGCGTTAGCCAGAT	59.512	45.455	0.00	0.00	46.67	2.90
643	695	1.877443	GTTTCCAAAGCGTTAGCCAGA	59.123	47.619	0.00	0.00	46.67	3.86
644	696	1.068541	GGTTTCCAAAGCGTTAGCCAG	60.069	52.381	0.00	0.00	46.67	4.85
645	697	0.955905	GGTTTCCAAAGCGTTAGCCA	59.044	50.000	0.00	0.00	46.67	4.75
882	1536	6.071447	TGAGGAATCTTCTCTTCTCTTGACTG	60.071	42.308	0.00	0.00	32.78	3.51
901	1563	2.357881	CGCTGCTGCAGTGAGGAA	60.358	61.111	33.35	0.00	43.78	3.36
949	1882	4.367039	TTCCCGAGAACAAGATTCCTTT	57.633	40.909	0.00	0.00	0.00	3.11
1207	2149	4.699522	GACGACCAGGTGGGCCAC	62.700	72.222	28.69	28.69	41.34	5.01
1210	2152	4.394712	CAGGACGACCAGGTGGGC	62.395	72.222	6.71	2.04	42.05	5.36
1211	2153	4.394712	GCAGGACGACCAGGTGGG	62.395	72.222	6.71	0.00	44.81	4.61
1212	2154	4.394712	GGCAGGACGACCAGGTGG	62.395	72.222	6.71	0.00	38.94	4.61
1479	2637	1.741770	GAAACTGATGCTCGCGGGT	60.742	57.895	8.30	0.00	0.00	5.28
1485	2643	0.729690	GGAAGCCGAAACTGATGCTC	59.270	55.000	0.00	0.00	32.62	4.26
1649	2807	0.035725	CTGCATGTGCTCCCAGAAGA	60.036	55.000	6.55	0.00	42.66	2.87
1755	2913	2.514592	ATGCCGGCGATGGAGTTG	60.515	61.111	23.90	0.00	0.00	3.16
1759	2917	4.916293	GCTGATGCCGGCGATGGA	62.916	66.667	23.90	3.26	34.60	3.41
1948	3106	2.045926	CCAGCAGTACCAGGCCAC	60.046	66.667	5.01	0.00	0.00	5.01
1952	3110	0.179062	GATCTGCCAGCAGTACCAGG	60.179	60.000	18.61	0.00	43.96	4.45
2373	3534	7.002250	AGATTATCATCACGATGGAGTTGAT	57.998	36.000	7.17	4.63	39.24	2.57
2374	3535	6.410942	AGATTATCATCACGATGGAGTTGA	57.589	37.500	7.17	0.00	39.24	3.18
2375	3536	7.488187	AAAGATTATCATCACGATGGAGTTG	57.512	36.000	7.17	0.00	39.24	3.16
2376	3537	7.554118	ACAAAAGATTATCATCACGATGGAGTT	59.446	33.333	7.17	0.00	39.24	3.01
2377	3538	7.050377	ACAAAAGATTATCATCACGATGGAGT	58.950	34.615	7.17	0.00	39.24	3.85
2378	3539	7.488187	ACAAAAGATTATCATCACGATGGAG	57.512	36.000	7.17	0.00	39.24	3.86
2379	3540	7.864108	AACAAAAGATTATCATCACGATGGA	57.136	32.000	7.17	0.00	39.24	3.41
2466	3635	2.760634	TGTGGATCGCACTACATTGT	57.239	45.000	13.32	0.00	0.00	2.71
2495	3664	8.138074	GCTTTTCTAAAAGAAGGATGACTTGTT	58.862	33.333	17.25	0.00	46.39	2.83
2496	3665	7.285401	TGCTTTTCTAAAAGAAGGATGACTTGT	59.715	33.333	17.25	0.00	46.39	3.16
2497	3666	7.651808	TGCTTTTCTAAAAGAAGGATGACTTG	58.348	34.615	17.25	0.00	46.39	3.16
2498	3667	7.823745	TGCTTTTCTAAAAGAAGGATGACTT	57.176	32.000	17.25	0.00	46.39	3.01
2499	3668	7.667219	TCATGCTTTTCTAAAAGAAGGATGACT	59.333	33.333	17.25	0.00	46.36	3.41
2500	3669	7.820648	TCATGCTTTTCTAAAAGAAGGATGAC	58.179	34.615	17.25	0.30	46.36	3.06
2502	3671	9.298774	GATTCATGCTTTTCTAAAAGAAGGATG	57.701	33.333	17.25	9.27	42.16	3.51
2503	3672	8.186821	CGATTCATGCTTTTCTAAAAGAAGGAT	58.813	33.333	17.25	7.21	42.16	3.24
2504	3673	7.174946	ACGATTCATGCTTTTCTAAAAGAAGGA	59.825	33.333	17.25	11.90	46.39	3.36
2505	3674	7.308435	ACGATTCATGCTTTTCTAAAAGAAGG	58.692	34.615	17.25	9.88	46.39	3.46
2564	3733	2.607038	CGTCGATATGATTCGGCCAAGA	60.607	50.000	2.24	0.00	40.53	3.02
2613	3782	8.193438	AGTCATCATCCTAAAAATAAGCAAAGC	58.807	33.333	0.00	0.00	0.00	3.51
2637	3806	3.577919	ACCACCTTCAGAGTGAGTAAGT	58.422	45.455	0.00	0.00	37.42	2.24
2640	3809	4.223953	AGAAACCACCTTCAGAGTGAGTA	58.776	43.478	0.00	0.00	37.42	2.59
2641	3810	3.041946	AGAAACCACCTTCAGAGTGAGT	58.958	45.455	0.00	0.00	37.42	3.41
2661	3831	7.861372	GGTATCATTTCTCATTGCAGATGAAAG	59.139	37.037	11.14	3.70	31.50	2.62
2664	3834	5.766670	GGGTATCATTTCTCATTGCAGATGA	59.233	40.000	10.01	10.01	0.00	2.92
2674	3844	9.159254	AGTATACATTGAGGGTATCATTTCTCA	57.841	33.333	5.50	0.00	37.89	3.27
2675	3845	9.429359	CAGTATACATTGAGGGTATCATTTCTC	57.571	37.037	5.50	0.00	37.89	2.87
2736	3906	5.470845	ACGAAGAAGGAGCAATATTTTCG	57.529	39.130	11.23	11.23	41.16	3.46
2754	3924	7.467557	AACTAAACAGAACATTTCGTACGAA	57.532	32.000	26.00	26.00	34.02	3.85
2782	3952	8.017946	CCTCTTGAAAAGGAACGATTTAAAGAG	58.982	37.037	14.41	14.41	45.98	2.85
2959	4129	4.660105	CTCGACTACTTTCCCTTAGTTCG	58.340	47.826	0.00	0.00	0.00	3.95
2976	4146	2.480555	CCAACAATGCCGCTCGAC	59.519	61.111	0.00	0.00	0.00	4.20
2978	4148	4.481112	GCCCAACAATGCCGCTCG	62.481	66.667	0.00	0.00	0.00	5.03
2988	4158	1.916506	TCGGAAAATCATGCCCAACA	58.083	45.000	0.00	0.00	0.00	3.33
3051	4221	5.963214	TCTTGAGGAGATTGATGAATGGA	57.037	39.130	0.00	0.00	0.00	3.41
3056	4226	5.745181	GCATGGATCTTGAGGAGATTGATGA	60.745	44.000	0.00	0.00	45.17	2.92
3064	4234	3.773418	ATCTGCATGGATCTTGAGGAG	57.227	47.619	0.00	0.00	0.00	3.69
3151	4321	7.824289	TCTCTCTCTCTCTCTCTTCTGTAAAAG	59.176	40.741	0.00	0.00	0.00	2.27
3177	4347	2.452505	GGTGCTCTCCACTCTAACTCT	58.547	52.381	0.00	0.00	44.08	3.24
3178	4348	1.133407	CGGTGCTCTCCACTCTAACTC	59.867	57.143	0.00	0.00	44.08	3.01
3179	4349	1.178276	CGGTGCTCTCCACTCTAACT	58.822	55.000	0.00	0.00	44.08	2.24
3180	4350	0.889306	ACGGTGCTCTCCACTCTAAC	59.111	55.000	0.00	0.00	44.08	2.34

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.