AutoCloner

Multiple sequence alignment - TraesCS3D01G047000

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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	TraesCS3D01G047000	chr3D	100.000	2765	0	0	1	2765	17646365	17643601	0.000000e+00	5107.0
1	TraesCS3D01G047000	chr3D	83.135	1684	149	62	158	1820	11351518	11353087	0.000000e+00	1411.0
2	TraesCS3D01G047000	chr3D	78.708	2400	288	96	13	2307	17373396	17375677	0.000000e+00	1395.0
3	TraesCS3D01G047000	chr3D	79.854	1504	209	57	824	2299	17516952	17515515	0.000000e+00	1013.0
4	TraesCS3D01G047000	chr3D	84.456	772	91	18	1	766	18894717	18895465	0.000000e+00	734.0
5	TraesCS3D01G047000	chr3D	82.949	434	45	11	1895	2308	11353209	11353633	5.630000e-97	364.0
6	TraesCS3D01G047000	chr3D	83.082	331	39	6	2309	2634	11353920	11354238	4.510000e-73	285.0
7	TraesCS3D01G047000	chr3D	76.695	236	39	9	2372	2597	17376002	17376231	1.740000e-22	117.0
8	TraesCS3D01G047000	chr3A	91.781	1022	52	12	880	1893	25936352	25935355	0.000000e+00	1393.0
9	TraesCS3D01G047000	chr3A	88.317	1147	79	29	669	1791	19303999	19305114	0.000000e+00	1325.0
10	TraesCS3D01G047000	chr3A	78.900	2109	281	67	38	2081	19475747	19473738	0.000000e+00	1279.0
11	TraesCS3D01G047000	chr3A	82.076	1339	163	44	824	2135	19371143	19372431	0.000000e+00	1072.0
12	TraesCS3D01G047000	chr3A	88.040	602	55	8	300	887	25937418	25936820	0.000000e+00	697.0
13	TraesCS3D01G047000	chr3A	82.529	601	66	13	1	598	19303401	19303965	2.470000e-135	492.0
14	TraesCS3D01G047000	chr3A	81.456	577	84	17	37	606	26415332	26415892	4.200000e-123	451.0
15	TraesCS3D01G047000	chr3A	83.102	432	52	14	1894	2308	25935267	25934840	9.350000e-100	374.0
16	TraesCS3D01G047000	chr3A	89.552	268	26	2	1	267	25937679	25937413	3.410000e-89	339.0
17	TraesCS3D01G047000	chr3A	85.782	211	19	5	1894	2093	19305149	19305359	2.160000e-51	213.0
18	TraesCS3D01G047000	chr3A	74.265	408	81	18	2365	2764	19473170	19472779	1.720000e-32	150.0
19	TraesCS3D01G047000	chr3A	76.786	224	43	7	2365	2585	25934292	25934075	1.740000e-22	117.0
20	TraesCS3D01G047000	chr3A	76.216	185	33	9	2365	2545	19306091	19306268	1.360000e-13	87.9
21	TraesCS3D01G047000	chrUn	90.402	1021	70	11	810	1820	37955624	37956626	0.000000e+00	1317.0
22	TraesCS3D01G047000	chrUn	90.935	695	48	4	1135	1823	392408923	392408238	0.000000e+00	920.0
23	TraesCS3D01G047000	chrUn	86.788	772	76	12	37	799	37954541	37955295	0.000000e+00	837.0
24	TraesCS3D01G047000	chrUn	86.710	775	77	12	37	802	340707391	340706634	0.000000e+00	837.0
25	TraesCS3D01G047000	chrUn	90.000	200	19	1	1895	2093	37956769	37956968	9.830000e-65	257.0
26	TraesCS3D01G047000	chrUn	90.000	200	19	1	1895	2093	392408098	392407899	9.830000e-65	257.0
27	TraesCS3D01G047000	chrUn	84.884	172	22	2	2140	2307	37957069	37957240	1.320000e-38	171.0
28	TraesCS3D01G047000	chrUn	84.884	172	22	2	2140	2307	392407798	392407627	1.320000e-38	171.0
29	TraesCS3D01G047000	chr3B	81.227	1353	167	45	824	2135	27516542	27517848	0.000000e+00	1011.0
30	TraesCS3D01G047000	chr3B	81.161	1051	133	30	1042	2081	24941556	24942552	0.000000e+00	784.0
31	TraesCS3D01G047000	chr3B	80.874	915	129	27	37	918	24940623	24941524	0.000000e+00	678.0
32	TraesCS3D01G047000	chr3B	80.944	572	90	16	37	606	29618580	29619134	4.230000e-118	435.0
33	TraesCS3D01G047000	chr3B	82.783	424	58	9	171	594	30506686	30507094	5.630000e-97	364.0
34	TraesCS3D01G047000	chr3B	83.886	211	32	2	384	594	29615657	29615865	1.680000e-47	200.0
35	TraesCS3D01G047000	chr3B	79.221	154	23	5	616	762	27516359	27516510	6.300000e-17	99.0
36	TraesCS3D01G047000	chr4D	88.960	471	44	5	942	1411	479409539	479409076	2.390000e-160	575.0

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	TraesCS3D01G047000	chr3D	17643601	17646365	2764	True	5107.000000	5107	100.000000	1	2765	1	chr3D.!!$R2	2764
1	TraesCS3D01G047000	chr3D	17515515	17516952	1437	True	1013.000000	1013	79.854000	824	2299	1	chr3D.!!$R1	1475
2	TraesCS3D01G047000	chr3D	17373396	17376231	2835	False	756.000000	1395	77.701500	13	2597	2	chr3D.!!$F3	2584
3	TraesCS3D01G047000	chr3D	18894717	18895465	748	False	734.000000	734	84.456000	1	766	1	chr3D.!!$F1	765
4	TraesCS3D01G047000	chr3D	11351518	11354238	2720	False	686.666667	1411	83.055333	158	2634	3	chr3D.!!$F2	2476
5	TraesCS3D01G047000	chr3A	19371143	19372431	1288	False	1072.000000	1072	82.076000	824	2135	1	chr3A.!!$F1	1311
6	TraesCS3D01G047000	chr3A	19472779	19475747	2968	True	714.500000	1279	76.582500	38	2764	2	chr3A.!!$R1	2726
7	TraesCS3D01G047000	chr3A	25934075	25937679	3604	True	584.000000	1393	85.852200	1	2585	5	chr3A.!!$R2	2584
8	TraesCS3D01G047000	chr3A	19303401	19306268	2867	False	529.475000	1325	83.211000	1	2545	4	chr3A.!!$F3	2544
9	TraesCS3D01G047000	chr3A	26415332	26415892	560	False	451.000000	451	81.456000	37	606	1	chr3A.!!$F2	569
10	TraesCS3D01G047000	chrUn	340706634	340707391	757	True	837.000000	837	86.710000	37	802	1	chrUn.!!$R1	765
11	TraesCS3D01G047000	chrUn	37954541	37957240	2699	False	645.500000	1317	88.018500	37	2307	4	chrUn.!!$F1	2270
12	TraesCS3D01G047000	chrUn	392407627	392408923	1296	True	449.333333	920	88.606333	1135	2307	3	chrUn.!!$R2	1172
13	TraesCS3D01G047000	chr3B	24940623	24942552	1929	False	731.000000	784	81.017500	37	2081	2	chr3B.!!$F2	2044
14	TraesCS3D01G047000	chr3B	27516359	27517848	1489	False	555.000000	1011	80.224000	616	2135	2	chr3B.!!$F3	1519
15	TraesCS3D01G047000	chr3B	29615657	29619134	3477	False	317.500000	435	82.415000	37	606	2	chr3B.!!$F4	569

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
435	3335	0.028374	GGAACAACACGTTTGTCCGG	59.972	55.0	13.82	0.0	38.19	5.14	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2012	5983	0.106015	AGAAACCAAGCAAGCACCCT	60.106	50.0	0.0	0.0	0.0	4.34	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
193	3087	0.394565	CCGGATCCTCCACATCTTCC	59.605	60.000	10.75	0.00	35.91	3.46
237	3131	2.338984	GACGTCCACAAGCTCGGT	59.661	61.111	3.51	0.00	0.00	4.69
357	3251	3.890147	AGAACCTCGTCTTCTACAACTGT	59.110	43.478	0.00	0.00	0.00	3.55
366	3260	2.736144	TCTACAACTGTACCAAGCCG	57.264	50.000	0.00	0.00	0.00	5.52
367	3261	1.076332	CTACAACTGTACCAAGCCGC	58.924	55.000	0.00	0.00	0.00	6.53
368	3262	0.682852	TACAACTGTACCAAGCCGCT	59.317	50.000	0.00	0.00	0.00	5.52
369	3263	0.884704	ACAACTGTACCAAGCCGCTG	60.885	55.000	0.00	0.00	0.00	5.18
370	3264	1.302511	AACTGTACCAAGCCGCTGG	60.303	57.895	0.00	0.13	42.68	4.85
435	3335	0.028374	GGAACAACACGTTTGTCCGG	59.972	55.000	13.82	0.00	38.19	5.14
436	3336	1.008329	GAACAACACGTTTGTCCGGA	58.992	50.000	0.00	0.00	38.19	5.14
556	3456	0.811281	GAATGCCAGCCACTACCAAC	59.189	55.000	0.00	0.00	0.00	3.77
585	3485	0.250081	GCGATGGATTCCTCCTCACC	60.250	60.000	3.95	0.00	42.59	4.02
589	3489	0.621571	TGGATTCCTCCTCACCTGGG	60.622	60.000	3.95	0.00	42.59	4.45
674	3596	3.342926	AGGAATCTATCTGGCCTCAGT	57.657	47.619	3.32	0.00	41.59	3.41
1045	4854	3.070576	TGCTGCTGCTCTCCGCTA	61.071	61.111	17.00	0.00	40.48	4.26
1114	4923	3.554692	GCGGCGACCTGAACATCG	61.555	66.667	12.98	0.00	41.32	3.84
1192	5001	3.349006	AGCTCAAGTGCAACGGCG	61.349	61.111	4.80	4.80	45.86	6.46
1369	5178	2.203070	GGCCCTACACCATCAGCG	60.203	66.667	0.00	0.00	0.00	5.18
1409	5218	0.700564	ATCCTCCACAACTGCACCAT	59.299	50.000	0.00	0.00	0.00	3.55
1413	5222	2.256158	CACAACTGCACCATGCCG	59.744	61.111	0.00	0.00	44.23	5.69
1414	5223	3.673484	ACAACTGCACCATGCCGC	61.673	61.111	0.00	0.00	44.23	6.53
1415	5224	3.672447	CAACTGCACCATGCCGCA	61.672	61.111	0.00	0.00	44.23	5.69
1778	5598	3.129502	CTGACAGCGCCACCATGG	61.130	66.667	11.19	11.19	41.55	3.66
1821	5664	4.333926	AGTTCTTTGATCAAGCTAATCCGC	59.666	41.667	8.41	0.00	31.70	5.54
1864	5716	1.620822	ATTTCAAGTGCCAGTGACCC	58.379	50.000	0.00	0.00	0.00	4.46
1869	5721	0.773644	AAGTGCCAGTGACCCATTCT	59.226	50.000	0.00	0.00	0.00	2.40
1901	5844	4.385358	AAAAGCCTGACGTTTTTGATGT	57.615	36.364	0.00	0.00	0.00	3.06
1913	5858	4.739228	CGTTTTTGATGTTGCATCTGACAA	59.261	37.500	10.02	0.00	0.00	3.18
1931	5876	3.476552	ACAAAGAATCGCTGTCAGGAAA	58.523	40.909	1.14	0.00	0.00	3.13
1968	5920	1.153549	GTCGCTGTTGCTAGGAGGG	60.154	63.158	0.00	0.00	36.97	4.30
1971	5923	0.531532	CGCTGTTGCTAGGAGGGATG	60.532	60.000	0.00	0.00	36.97	3.51
2012	5983	5.872617	CACGGATATTGTGGTTTCAACTCTA	59.127	40.000	2.05	0.00	33.69	2.43
2122	6333	6.373216	TCGGTTCCTAGTCAAAATACATTTGG	59.627	38.462	1.52	0.00	46.85	3.28
2155	6401	3.486841	CAGCATTGTTCTTGGTTTCGTTG	59.513	43.478	0.00	0.00	0.00	4.10
2205	6464	4.575885	TCAATGCGCCTAGTACTTTTCTT	58.424	39.130	4.18	0.00	0.00	2.52
2207	6466	5.472137	TCAATGCGCCTAGTACTTTTCTTTT	59.528	36.000	4.18	0.00	0.00	2.27
2217	6476	3.680777	ACTTTTCTTTTCCCTGGTCCA	57.319	42.857	0.00	0.00	0.00	4.02
2261	6604	6.095300	TGTGGAAGTCAATATATTGCAACTGG	59.905	38.462	18.89	0.00	37.68	4.00
2289	6641	8.832521	TGTTGTTGAATTAGTTAGGTGTGTAAG	58.167	33.333	0.00	0.00	0.00	2.34
2308	6660	4.483476	AAGGTTGAATTGAACGCTGTAC	57.517	40.909	1.57	0.00	0.00	2.90
2351	7229	6.266330	TGGAGACTGGAGTATGATTATGACTG	59.734	42.308	0.00	0.00	0.00	3.51
2355	7233	6.987386	ACTGGAGTATGATTATGACTGCTAC	58.013	40.000	0.00	0.00	33.16	3.58
2357	7235	5.048013	TGGAGTATGATTATGACTGCTACGG	60.048	44.000	0.00	0.00	33.16	4.02
2388	7269	5.784398	TCAGGATATATTGCCACCATCAT	57.216	39.130	0.00	0.00	0.00	2.45
2454	7337	3.891366	CCAGTCACAAAAGGGAGTTTGAT	59.109	43.478	4.76	0.00	40.29	2.57
2458	7341	7.255942	CCAGTCACAAAAGGGAGTTTGATTATT	60.256	37.037	4.76	0.00	40.29	1.40
2459	7342	7.596248	CAGTCACAAAAGGGAGTTTGATTATTG	59.404	37.037	4.76	0.00	40.29	1.90
2463	7346	7.537306	CACAAAAGGGAGTTTGATTATTGTACG	59.463	37.037	4.76	0.00	40.29	3.67
2466	7349	5.425630	AGGGAGTTTGATTATTGTACGGTC	58.574	41.667	0.00	0.00	0.00	4.79
2483	7366	2.597520	GGTCGAAGCTGACAGAGTTAC	58.402	52.381	6.65	0.00	40.72	2.50
2506	7393	4.345288	CATGACAATACCAATTCAGCACG	58.655	43.478	0.00	0.00	0.00	5.34
2511	7398	4.580167	ACAATACCAATTCAGCACGCATAT	59.420	37.500	0.00	0.00	0.00	1.78
2513	7400	5.772825	ATACCAATTCAGCACGCATATTT	57.227	34.783	0.00	0.00	0.00	1.40
2529	7416	6.742718	ACGCATATTTTTCTTCTCATTTGTCG	59.257	34.615	0.00	0.00	0.00	4.35
2545	7440	1.998315	TGTCGAGCGACTACTGTACTC	59.002	52.381	21.68	0.00	44.80	2.59
2599	7495	3.369471	CGGAGTCTTCTTATGCAGGGAAA	60.369	47.826	0.00	0.00	0.00	3.13
2600	7496	4.195416	GGAGTCTTCTTATGCAGGGAAAG	58.805	47.826	0.00	0.00	0.00	2.62
2602	7498	3.846588	AGTCTTCTTATGCAGGGAAAGGA	59.153	43.478	0.00	0.00	0.00	3.36
2606	7502	6.153510	GTCTTCTTATGCAGGGAAAGGAAAAT	59.846	38.462	0.00	0.00	0.00	1.82
2616	7512	6.161381	CAGGGAAAGGAAAATCAACAAGATG	58.839	40.000	0.00	0.00	36.96	2.90
2634	7533	7.306013	ACAAGATGGGAGATTATAGGTGAGTA	58.694	38.462	0.00	0.00	0.00	2.59
2635	7534	7.453126	ACAAGATGGGAGATTATAGGTGAGTAG	59.547	40.741	0.00	0.00	0.00	2.57
2637	7536	5.340891	TGGGAGATTATAGGTGAGTAGCT	57.659	43.478	0.00	0.00	38.41	3.32
2638	7537	5.326069	TGGGAGATTATAGGTGAGTAGCTC	58.674	45.833	0.00	0.00	35.90	4.09
2639	7538	5.162980	TGGGAGATTATAGGTGAGTAGCTCA	60.163	44.000	0.00	0.00	38.25	4.26
2640	7539	5.775701	GGGAGATTATAGGTGAGTAGCTCAA	59.224	44.000	0.00	0.00	42.46	3.02
2641	7540	6.071616	GGGAGATTATAGGTGAGTAGCTCAAG	60.072	46.154	0.00	0.00	42.46	3.02
2642	7541	6.339587	AGATTATAGGTGAGTAGCTCAAGC	57.660	41.667	0.00	0.00	42.46	4.01
2643	7542	4.569761	TTATAGGTGAGTAGCTCAAGCG	57.430	45.455	0.00	0.00	42.46	4.68
2644	7543	2.124277	TAGGTGAGTAGCTCAAGCGA	57.876	50.000	0.00	0.00	42.46	4.93
2646	7545	0.458716	GGTGAGTAGCTCAAGCGACC	60.459	60.000	11.02	4.71	45.83	4.79
2647	7546	0.243907	GTGAGTAGCTCAAGCGACCA	59.756	55.000	11.02	6.90	45.83	4.02
2649	7548	1.550524	TGAGTAGCTCAAGCGACCAAT	59.449	47.619	11.02	0.00	45.83	3.16
2650	7549	2.028112	TGAGTAGCTCAAGCGACCAATT	60.028	45.455	11.02	0.00	45.83	2.32
2659	7558	3.649096	CGACCAATTCGGCACACA	58.351	55.556	0.00	0.00	44.60	3.72
2660	7559	2.170738	CGACCAATTCGGCACACAT	58.829	52.632	0.00	0.00	44.60	3.21
2661	7560	1.364721	CGACCAATTCGGCACACATA	58.635	50.000	0.00	0.00	44.60	2.29
2662	7561	1.939934	CGACCAATTCGGCACACATAT	59.060	47.619	0.00	0.00	44.60	1.78
2664	7563	3.181501	CGACCAATTCGGCACACATATTT	60.182	43.478	0.00	0.00	44.60	1.40
2666	7565	4.743493	ACCAATTCGGCACACATATTTTC	58.257	39.130	0.00	0.00	39.03	2.29
2667	7566	4.462483	ACCAATTCGGCACACATATTTTCT	59.538	37.500	0.00	0.00	39.03	2.52
2668	7567	5.047377	ACCAATTCGGCACACATATTTTCTT	60.047	36.000	0.00	0.00	39.03	2.52
2669	7568	5.516339	CCAATTCGGCACACATATTTTCTTC	59.484	40.000	0.00	0.00	0.00	2.87
2670	7569	6.324819	CAATTCGGCACACATATTTTCTTCT	58.675	36.000	0.00	0.00	0.00	2.85
2671	7570	5.545658	TTCGGCACACATATTTTCTTCTC	57.454	39.130	0.00	0.00	0.00	2.87
2672	7571	4.574892	TCGGCACACATATTTTCTTCTCA	58.425	39.130	0.00	0.00	0.00	3.27
2673	7572	5.185454	TCGGCACACATATTTTCTTCTCAT	58.815	37.500	0.00	0.00	0.00	2.90
2674	7573	5.647658	TCGGCACACATATTTTCTTCTCATT	59.352	36.000	0.00	0.00	0.00	2.57
2688	7587	8.760980	TTTCTTCTCATTTTCCTTTGGTTCTA	57.239	30.769	0.00	0.00	0.00	2.10
2690	7589	8.166422	TCTTCTCATTTTCCTTTGGTTCTAAC	57.834	34.615	0.00	0.00	0.00	2.34
2735	7634	5.989477	CAGAATATGGAGAACAAGGTGGTA	58.011	41.667	0.00	0.00	0.00	3.25
2741	7640	5.055265	TGGAGAACAAGGTGGTAAAATCA	57.945	39.130	0.00	0.00	0.00	2.57
2743	7642	4.825085	GGAGAACAAGGTGGTAAAATCACA	59.175	41.667	0.00	0.00	36.90	3.58
2749	7648	4.989279	AGGTGGTAAAATCACATGATGC	57.011	40.909	0.00	0.00	36.90	3.91
2751	7650	4.771577	AGGTGGTAAAATCACATGATGCAA	59.228	37.500	0.00	0.00	36.90	4.08
2757	7656	9.368674	TGGTAAAATCACATGATGCAAAATTAG	57.631	29.630	0.00	0.00	34.49	1.73
2761	7660	8.470040	AAATCACATGATGCAAAATTAGTCAC	57.530	30.769	0.00	0.00	34.49	3.67
2764	7663	7.604549	TCACATGATGCAAAATTAGTCACATT	58.395	30.769	0.00	0.00	0.00	2.71

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
193	3087	2.046892	CAGGGAGCCGTTGTGGAG	60.047	66.667	0.00	0.00	42.00	3.86
237	3131	1.715862	CGCCGGAGAGATCGAAGTCA	61.716	60.000	5.05	0.00	0.00	3.41
261	3155	1.671054	CGGGACATGGCAACGAGTT	60.671	57.895	9.04	0.00	42.51	3.01
263	3157	2.100631	GTCGGGACATGGCAACGAG	61.101	63.158	16.63	0.00	42.51	4.18
264	3158	2.047655	GTCGGGACATGGCAACGA	60.048	61.111	12.85	12.85	42.51	3.85
265	3159	3.487202	CGTCGGGACATGGCAACG	61.487	66.667	0.00	4.44	42.51	4.10
435	3335	1.213799	GTTGTACCGACCTCCCGTC	59.786	63.158	0.00	0.00	38.21	4.79
436	3336	2.629656	CGTTGTACCGACCTCCCGT	61.630	63.158	0.00	0.00	0.00	5.28
444	3344	2.981560	GCCGGACTCGTTGTACCGA	61.982	63.158	5.05	0.00	46.94	4.69
556	3456	1.799403	GAATCCATCGCTGATGAGCTG	59.201	52.381	16.69	0.00	42.09	4.24
661	3583	4.590647	CAGATAAGGAACTGAGGCCAGATA	59.409	45.833	5.01	0.00	43.02	1.98
674	3596	1.352622	ATGGCCCGGCAGATAAGGAA	61.353	55.000	12.58	0.00	0.00	3.36
698	3632	0.534412	TTGCCAACCCGCCATTAATG	59.466	50.000	8.58	8.58	0.00	1.90
764	3737	1.312371	ATTTGTGGGATGCCGTTCCG	61.312	55.000	0.00	0.00	36.58	4.30
985	4791	1.049855	GGCATGGATTGGATTGGGCA	61.050	55.000	0.00	0.00	0.00	5.36
1020	4826	4.098722	AGCAGCAGCAGGAGGAGC	62.099	66.667	3.17	0.00	45.49	4.70
1077	4886	1.557269	ATCTCTTGGGCGAGCAGGTT	61.557	55.000	0.00	0.00	0.00	3.50
1078	4887	1.992277	ATCTCTTGGGCGAGCAGGT	60.992	57.895	0.00	0.00	0.00	4.00
1114	4923	2.125106	CAGCCAGAACGGGTAGGC	60.125	66.667	0.94	0.94	46.49	3.93
1369	5178	2.669240	CACCTCCCGGTTCTTCCC	59.331	66.667	0.00	0.00	42.13	3.97
1390	5199	0.700564	ATGGTGCAGTTGTGGAGGAT	59.299	50.000	0.00	0.00	0.00	3.24
1560	5380	2.045731	TCGCCATCCGGAAAACCC	60.046	61.111	9.01	0.00	37.59	4.11
1723	5543	3.319198	GCACTTCTCGGGGTGGGA	61.319	66.667	0.00	0.00	34.41	4.37
1821	5664	2.173356	TGAGGGGAATGAATACCAGCAG	59.827	50.000	0.00	0.00	0.00	4.24
1901	5844	3.076621	AGCGATTCTTTGTCAGATGCAA	58.923	40.909	0.00	0.00	30.53	4.08
1913	5858	4.008074	TCTTTTCCTGACAGCGATTCTT	57.992	40.909	0.00	0.00	0.00	2.52
1927	5872	6.592348	CGTAAAACGCAGTAAATCTTTTCC	57.408	37.500	0.00	0.00	45.00	3.13
1968	5920	4.025396	CGTGTCCAATCAGCATTCTACATC	60.025	45.833	0.00	0.00	0.00	3.06
1971	5923	2.609459	CCGTGTCCAATCAGCATTCTAC	59.391	50.000	0.00	0.00	0.00	2.59
2012	5983	0.106015	AGAAACCAAGCAAGCACCCT	60.106	50.000	0.00	0.00	0.00	4.34
2122	6333	6.583806	CCAAGAACAATGCTGACTAATTCAAC	59.416	38.462	0.00	0.00	32.21	3.18
2155	6401	6.419771	GCGAATACAGGAATAGTTTACTTGC	58.580	40.000	0.00	0.00	0.00	4.01
2192	6447	5.938710	GGACCAGGGAAAAGAAAAGTACTAG	59.061	44.000	0.00	0.00	0.00	2.57
2205	6464	1.422024	TCGAAACATGGACCAGGGAAA	59.578	47.619	11.48	0.00	0.00	3.13
2207	6466	1.060729	TTCGAAACATGGACCAGGGA	58.939	50.000	11.48	0.00	0.00	4.20
2261	6604	7.477494	ACACACCTAACTAATTCAACAACAAC	58.523	34.615	0.00	0.00	0.00	3.32
2289	6641	4.483476	AAGTACAGCGTTCAATTCAACC	57.517	40.909	0.00	0.00	0.00	3.77
2332	7210	6.089476	CGTAGCAGTCATAATCATACTCCAG	58.911	44.000	0.00	0.00	0.00	3.86
2334	7212	5.183331	TCCGTAGCAGTCATAATCATACTCC	59.817	44.000	0.00	0.00	0.00	3.85
2351	7229	3.795623	TCCTGAAGTACATTCCGTAGC	57.204	47.619	0.00	0.00	37.08	3.58
2355	7233	6.313905	GGCAATATATCCTGAAGTACATTCCG	59.686	42.308	0.00	0.00	37.08	4.30
2357	7235	7.119846	GGTGGCAATATATCCTGAAGTACATTC	59.880	40.741	0.00	0.00	38.50	2.67
2392	7273	8.691797	TCCAGCAAAGGGTAAATTTCATATTAC	58.308	33.333	0.00	0.00	0.00	1.89
2393	7274	8.830915	TCCAGCAAAGGGTAAATTTCATATTA	57.169	30.769	0.00	0.00	0.00	0.98
2397	7278	6.625532	AATCCAGCAAAGGGTAAATTTCAT	57.374	33.333	0.00	0.00	0.00	2.57
2407	7288	2.528564	TGAGGAAAATCCAGCAAAGGG	58.471	47.619	0.00	0.00	39.61	3.95
2409	7290	6.101997	GGTTAATGAGGAAAATCCAGCAAAG	58.898	40.000	0.00	0.00	39.61	2.77
2454	7337	3.057386	TGTCAGCTTCGACCGTACAATAA	60.057	43.478	2.02	0.00	34.88	1.40
2458	7341	0.240145	CTGTCAGCTTCGACCGTACA	59.760	55.000	2.02	0.00	34.88	2.90
2459	7342	0.520404	TCTGTCAGCTTCGACCGTAC	59.480	55.000	2.02	0.00	34.88	3.67
2463	7346	2.597520	GTAACTCTGTCAGCTTCGACC	58.402	52.381	2.02	0.00	34.88	4.79
2466	7349	2.724977	TGGTAACTCTGTCAGCTTCG	57.275	50.000	0.00	0.00	37.61	3.79
2483	7366	4.675510	GTGCTGAATTGGTATTGTCATGG	58.324	43.478	0.00	0.00	0.00	3.66
2506	7393	7.044445	GCTCGACAAATGAGAAGAAAAATATGC	60.044	37.037	0.00	0.00	35.43	3.14
2511	7398	4.509970	TCGCTCGACAAATGAGAAGAAAAA	59.490	37.500	0.00	0.00	35.43	1.94
2513	7400	3.428870	GTCGCTCGACAAATGAGAAGAAA	59.571	43.478	16.47	0.00	44.02	2.52
2578	7474	3.914426	TTCCCTGCATAAGAAGACTCC	57.086	47.619	0.00	0.00	0.00	3.85
2599	7495	5.261040	TCTCCCATCTTGTTGATTTTCCT	57.739	39.130	0.00	0.00	32.05	3.36
2600	7496	6.535963	AATCTCCCATCTTGTTGATTTTCC	57.464	37.500	0.00	0.00	32.05	3.13
2602	7498	9.359653	CCTATAATCTCCCATCTTGTTGATTTT	57.640	33.333	0.00	0.00	32.05	1.82
2606	7502	6.615316	TCACCTATAATCTCCCATCTTGTTGA	59.385	38.462	0.00	0.00	0.00	3.18
2616	7512	5.326069	TGAGCTACTCACCTATAATCTCCC	58.674	45.833	0.00	0.00	35.39	4.30
2634	7533	2.460330	CGAATTGGTCGCTTGAGCT	58.540	52.632	1.07	0.00	44.14	4.09
2643	7542	4.370364	AAATATGTGTGCCGAATTGGTC	57.630	40.909	0.00	0.00	41.21	4.02
2644	7543	4.462483	AGAAAATATGTGTGCCGAATTGGT	59.538	37.500	0.00	0.00	41.21	3.67
2646	7545	6.324819	AGAAGAAAATATGTGTGCCGAATTG	58.675	36.000	0.00	0.00	0.00	2.32
2647	7546	6.150976	TGAGAAGAAAATATGTGTGCCGAATT	59.849	34.615	0.00	0.00	0.00	2.17
2649	7548	5.000591	TGAGAAGAAAATATGTGTGCCGAA	58.999	37.500	0.00	0.00	0.00	4.30
2650	7549	4.574892	TGAGAAGAAAATATGTGTGCCGA	58.425	39.130	0.00	0.00	0.00	5.54
2652	7551	7.276438	GGAAAATGAGAAGAAAATATGTGTGCC	59.724	37.037	0.00	0.00	0.00	5.01
2654	7553	9.918630	AAGGAAAATGAGAAGAAAATATGTGTG	57.081	29.630	0.00	0.00	0.00	3.82
2657	7556	9.933723	CCAAAGGAAAATGAGAAGAAAATATGT	57.066	29.630	0.00	0.00	0.00	2.29
2658	7557	9.933723	ACCAAAGGAAAATGAGAAGAAAATATG	57.066	29.630	0.00	0.00	0.00	1.78
2660	7559	9.981114	GAACCAAAGGAAAATGAGAAGAAAATA	57.019	29.630	0.00	0.00	0.00	1.40
2661	7560	8.708378	AGAACCAAAGGAAAATGAGAAGAAAAT	58.292	29.630	0.00	0.00	0.00	1.82
2662	7561	8.078060	AGAACCAAAGGAAAATGAGAAGAAAA	57.922	30.769	0.00	0.00	0.00	2.29
2664	7563	8.630037	GTTAGAACCAAAGGAAAATGAGAAGAA	58.370	33.333	0.00	0.00	0.00	2.52
2688	7587	2.578021	ACAATATGGAGCACTGGAGGTT	59.422	45.455	0.00	0.00	0.00	3.50
2690	7589	3.495100	GGTACAATATGGAGCACTGGAGG	60.495	52.174	0.00	0.00	0.00	4.30
2691	7590	3.134623	TGGTACAATATGGAGCACTGGAG	59.865	47.826	0.00	0.00	33.08	3.86
2695	7594	5.636903	ATTCTGGTACAATATGGAGCACT	57.363	39.130	0.00	0.00	33.08	4.40
2726	7625	5.104374	GCATCATGTGATTTTACCACCTTG	58.896	41.667	0.00	0.00	33.80	3.61
2731	7630	9.368674	CTAATTTTGCATCATGTGATTTTACCA	57.631	29.630	0.00	0.00	31.21	3.25
2735	7634	8.928733	GTGACTAATTTTGCATCATGTGATTTT	58.071	29.630	0.00	0.00	31.21	1.82

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.