AutoCloner

Multiple sequence alignment - TraesCS3D01G447100

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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	TraesCS3D01G447100	chr3D	100.000	2132	0	0	1	2132	555758460	555756329	0.000000e+00	3938
1	TraesCS3D01G447100	chr3D	79.560	318	40	19	246	548	408127329	408127636	9.970000e-49	204
2	TraesCS3D01G447100	chr7D	97.294	850	23	0	1280	2129	205087542	205088391	0.000000e+00	1443
3	TraesCS3D01G447100	chr7D	96.838	854	26	1	1280	2132	419558119	419557266	0.000000e+00	1426
4	TraesCS3D01G447100	chr7D	96.479	852	30	0	1281	2132	203105795	203106646	0.000000e+00	1408
5	TraesCS3D01G447100	chr7D	96.136	854	32	1	1280	2132	161646862	161646009	0.000000e+00	1393
6	TraesCS3D01G447100	chr7D	96.023	855	32	2	1280	2132	244026053	244025199	0.000000e+00	1389
7	TraesCS3D01G447100	chr7D	95.652	46	2	0	557	602	530834313	530834358	8.160000e-10	75
8	TraesCS3D01G447100	chr4D	96.721	854	25	3	1281	2132	17889230	17890082	0.000000e+00	1419
9	TraesCS3D01G447100	chr4D	96.131	853	32	1	1280	2132	483743223	483744074	0.000000e+00	1391
10	TraesCS3D01G447100	chr4D	94.913	688	30	5	596	1280	19918090	19917405	0.000000e+00	1072
11	TraesCS3D01G447100	chr4D	86.290	248	23	9	312	548	327385341	327385094	2.100000e-65	259
12	TraesCS3D01G447100	chr4D	95.652	46	2	0	557	602	245649785	245649830	8.160000e-10	75
13	TraesCS3D01G447100	chr2D	96.702	849	27	1	1281	2129	454387207	454388054	0.000000e+00	1411
14	TraesCS3D01G447100	chr6D	96.014	853	32	2	1281	2132	302171825	302170974	0.000000e+00	1386
15	TraesCS3D01G447100	chr3B	96.948	688	17	3	596	1280	201516277	201515591	0.000000e+00	1151
16	TraesCS3D01G447100	chrUn	97.305	668	15	2	616	1280	445811485	445812152	0.000000e+00	1131
17	TraesCS3D01G447100	chrUn	96.413	669	18	6	596	1260	30305754	30306420	0.000000e+00	1098
18	TraesCS3D01G447100	chrUn	87.500	208	19	5	239	440	955091	954885	1.270000e-57	233
19	TraesCS3D01G447100	chrUn	95.652	46	2	0	557	602	327662215	327662170	8.160000e-10	75
20	TraesCS3D01G447100	chrUn	95.652	46	2	0	557	602	371049550	371049595	8.160000e-10	75
21	TraesCS3D01G447100	chr5D	96.081	689	21	6	596	1280	560874065	560873379	0.000000e+00	1118
22	TraesCS3D01G447100	chr5D	95.652	690	23	6	596	1280	6199685	6200372	0.000000e+00	1101
23	TraesCS3D01G447100	chr5D	95.646	689	24	6	596	1280	329163774	329163088	0.000000e+00	1101
24	TraesCS3D01G447100	chr5D	95.652	46	2	0	557	602	432291615	432291570	8.160000e-10	75
25	TraesCS3D01G447100	chr1D	95.791	689	23	6	596	1280	254499595	254498909	0.000000e+00	1107
26	TraesCS3D01G447100	chr1A	94.767	688	29	6	596	1280	168448973	168449656	0.000000e+00	1064
27	TraesCS3D01G447100	chr3A	92.692	520	32	5	31	548	692700671	692700156	0.000000e+00	745
28	TraesCS3D01G447100	chr3A	81.973	294	36	15	235	513	663684032	663683741	1.270000e-57	233
29	TraesCS3D01G447100	chr1B	81.040	327	41	16	237	548	659582542	659582862	7.600000e-60	241
30	TraesCS3D01G447100	chr1B	95.652	46	2	0	557	602	633727762	633727717	8.160000e-10	75
31	TraesCS3D01G447100	chr4A	83.936	249	28	11	312	548	143695643	143695891	5.920000e-56	228
32	TraesCS3D01G447100	chr4A	80.351	285	40	11	234	506	39270711	39270431	3.590000e-48	202
33	TraesCS3D01G447100	chr4A	95.652	46	2	0	557	602	490864204	490864249	8.160000e-10	75
34	TraesCS3D01G447100	chr4B	81.221	213	32	6	234	439	521712708	521712919	4.710000e-37	165
35	TraesCS3D01G447100	chr6B	80.952	189	26	9	368	548	678599727	678599913	7.930000e-30	141
36	TraesCS3D01G447100	chr5A	77.617	277	32	14	279	546	560805909	560805654	7.930000e-30	141
37	TraesCS3D01G447100	chr7A	95.652	46	2	0	557	602	650019005	650018960	8.160000e-10	75
38	TraesCS3D01G447100	chr5B	95.652	46	2	0	557	602	429037785	429037830	8.160000e-10	75

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	TraesCS3D01G447100	chr3D	555756329	555758460	2131	True	3938	3938	100.000	1	2132	1	chr3D.!!$R1	2131
1	TraesCS3D01G447100	chr7D	205087542	205088391	849	False	1443	1443	97.294	1280	2129	1	chr7D.!!$F2	849
2	TraesCS3D01G447100	chr7D	419557266	419558119	853	True	1426	1426	96.838	1280	2132	1	chr7D.!!$R3	852
3	TraesCS3D01G447100	chr7D	203105795	203106646	851	False	1408	1408	96.479	1281	2132	1	chr7D.!!$F1	851
4	TraesCS3D01G447100	chr7D	161646009	161646862	853	True	1393	1393	96.136	1280	2132	1	chr7D.!!$R1	852
5	TraesCS3D01G447100	chr7D	244025199	244026053	854	True	1389	1389	96.023	1280	2132	1	chr7D.!!$R2	852
6	TraesCS3D01G447100	chr4D	17889230	17890082	852	False	1419	1419	96.721	1281	2132	1	chr4D.!!$F1	851
7	TraesCS3D01G447100	chr4D	483743223	483744074	851	False	1391	1391	96.131	1280	2132	1	chr4D.!!$F3	852
8	TraesCS3D01G447100	chr4D	19917405	19918090	685	True	1072	1072	94.913	596	1280	1	chr4D.!!$R1	684
9	TraesCS3D01G447100	chr2D	454387207	454388054	847	False	1411	1411	96.702	1281	2129	1	chr2D.!!$F1	848
10	TraesCS3D01G447100	chr6D	302170974	302171825	851	True	1386	1386	96.014	1281	2132	1	chr6D.!!$R1	851
11	TraesCS3D01G447100	chr3B	201515591	201516277	686	True	1151	1151	96.948	596	1280	1	chr3B.!!$R1	684
12	TraesCS3D01G447100	chrUn	445811485	445812152	667	False	1131	1131	97.305	616	1280	1	chrUn.!!$F3	664
13	TraesCS3D01G447100	chrUn	30305754	30306420	666	False	1098	1098	96.413	596	1260	1	chrUn.!!$F1	664
14	TraesCS3D01G447100	chr5D	560873379	560874065	686	True	1118	1118	96.081	596	1280	1	chr5D.!!$R3	684
15	TraesCS3D01G447100	chr5D	6199685	6200372	687	False	1101	1101	95.652	596	1280	1	chr5D.!!$F1	684
16	TraesCS3D01G447100	chr5D	329163088	329163774	686	True	1101	1101	95.646	596	1280	1	chr5D.!!$R1	684
17	TraesCS3D01G447100	chr1D	254498909	254499595	686	True	1107	1107	95.791	596	1280	1	chr1D.!!$R1	684
18	TraesCS3D01G447100	chr1A	168448973	168449656	683	False	1064	1064	94.767	596	1280	1	chr1A.!!$F1	684
19	TraesCS3D01G447100	chr3A	692700156	692700671	515	True	745	745	92.692	31	548	1	chr3A.!!$R2	517

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
40	41	0.03582	TTTGGTCCATAGACGGCACC	60.036	55.0	0.0	0.0	44.54	5.01	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1977	1986	0.536724	TGCTAGCATCATGGACACGT	59.463	50.0	14.93	0.0	0.0	4.49	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
22	23	2.113139	CACGAGGTGGTTGCCCTT	59.887	61.111	0.00	0.00	30.60	3.95
23	24	1.528309	CACGAGGTGGTTGCCCTTT	60.528	57.895	0.00	0.00	30.60	3.11
24	25	1.528309	ACGAGGTGGTTGCCCTTTG	60.528	57.895	0.00	0.00	30.60	2.77
25	26	2.268076	CGAGGTGGTTGCCCTTTGG	61.268	63.158	0.00	0.00	30.60	3.28
26	27	1.152546	GAGGTGGTTGCCCTTTGGT	60.153	57.895	0.00	0.00	30.60	3.67
27	28	1.152546	AGGTGGTTGCCCTTTGGTC	60.153	57.895	0.00	0.00	0.00	4.02
28	29	2.207229	GGTGGTTGCCCTTTGGTCC	61.207	63.158	0.00	0.00	0.00	4.46
29	30	1.456705	GTGGTTGCCCTTTGGTCCA	60.457	57.895	0.00	0.00	0.00	4.02
30	31	0.831711	GTGGTTGCCCTTTGGTCCAT	60.832	55.000	0.00	0.00	33.87	3.41
31	32	0.780637	TGGTTGCCCTTTGGTCCATA	59.219	50.000	0.00	0.00	0.00	2.74
32	33	1.272425	TGGTTGCCCTTTGGTCCATAG	60.272	52.381	2.45	2.45	0.00	2.23
33	34	1.005450	GGTTGCCCTTTGGTCCATAGA	59.995	52.381	10.67	0.00	0.00	1.98
34	35	2.092323	GTTGCCCTTTGGTCCATAGAC	58.908	52.381	10.67	3.68	42.73	2.59
35	36	0.251916	TGCCCTTTGGTCCATAGACG	59.748	55.000	10.67	2.23	44.54	4.18
36	37	0.463833	GCCCTTTGGTCCATAGACGG	60.464	60.000	10.67	5.73	44.54	4.79
40	41	0.035820	TTTGGTCCATAGACGGCACC	60.036	55.000	0.00	0.00	44.54	5.01
47	48	2.072487	ATAGACGGCACCCTGGCAT	61.072	57.895	0.00	0.00	43.94	4.40
107	108	2.414825	GGAAGCTCTCTTTTGCTCTTCG	59.585	50.000	0.00	0.00	38.75	3.79
118	119	4.990543	TTTGCTCTTCGACACAAGTATG	57.009	40.909	0.00	0.00	0.00	2.39
149	150	0.833949	GGTCTAGGAAGAGGCCCAAG	59.166	60.000	0.00	0.00	34.93	3.61
186	187	3.297134	ACATTCCTTGGTCAGTTGTGT	57.703	42.857	0.00	0.00	0.00	3.72
212	213	4.299155	CTCGCACCATATGTACTTAGTGG	58.701	47.826	1.24	11.99	36.06	4.00
216	217	5.238583	GCACCATATGTACTTAGTGGGATC	58.761	45.833	1.24	0.00	34.27	3.36
222	223	7.604164	CCATATGTACTTAGTGGGATCATTGAC	59.396	40.741	1.24	0.00	0.00	3.18
229	230	1.812571	GTGGGATCATTGACACGCTTT	59.187	47.619	0.00	0.00	0.00	3.51
238	239	0.817634	TGACACGCTTTTGGGTCAGG	60.818	55.000	0.00	0.00	44.11	3.86
245	246	0.754957	CTTTTGGGTCAGGGTGTGCA	60.755	55.000	0.00	0.00	0.00	4.57
262	263	3.308323	TGTGCAAAATCGAACAAAAAGCC	59.692	39.130	0.00	0.00	0.00	4.35
266	267	5.106555	TGCAAAATCGAACAAAAAGCCAAAA	60.107	32.000	0.00	0.00	0.00	2.44
267	268	5.797434	GCAAAATCGAACAAAAAGCCAAAAA	59.203	32.000	0.00	0.00	0.00	1.94
269	270	7.305361	GCAAAATCGAACAAAAAGCCAAAAATC	60.305	33.333	0.00	0.00	0.00	2.17
270	271	5.574815	ATCGAACAAAAAGCCAAAAATCG	57.425	34.783	0.00	0.00	0.00	3.34
272	273	5.103000	TCGAACAAAAAGCCAAAAATCGAA	58.897	33.333	0.00	0.00	34.32	3.71
273	274	5.004916	TCGAACAAAAAGCCAAAAATCGAAC	59.995	36.000	0.00	0.00	34.32	3.95
314	316	7.219726	CCAAAATTTTTCGTTTTCCCATGTTTG	59.780	33.333	0.00	0.00	0.00	2.93
442	444	2.031508	CGGTTCAAAGCGTAATGGTTGT	60.032	45.455	6.20	0.00	44.15	3.32
444	446	3.733727	GGTTCAAAGCGTAATGGTTGTTG	59.266	43.478	0.00	0.00	38.56	3.33
473	475	1.354031	TCTGGCCCATTTAGTGCTTCA	59.646	47.619	0.00	0.00	0.00	3.02
491	493	5.355071	TGCTTCAGTTTATGTGATTAGCCTG	59.645	40.000	0.00	0.00	0.00	4.85
508	510	2.162408	GCCTGACTGCTTATCCAACAAC	59.838	50.000	0.00	0.00	0.00	3.32
513	515	4.275689	TGACTGCTTATCCAACAACACTTG	59.724	41.667	0.00	0.00	0.00	3.16
558	560	8.442632	TTTTCTCATTATGATTAGCCTGACTG	57.557	34.615	0.00	0.00	0.00	3.51
559	561	5.545588	TCTCATTATGATTAGCCTGACTGC	58.454	41.667	0.00	0.00	0.00	4.40
560	562	4.309933	TCATTATGATTAGCCTGACTGCG	58.690	43.478	0.00	0.00	36.02	5.18
561	563	3.819564	TTATGATTAGCCTGACTGCGT	57.180	42.857	0.00	0.00	36.02	5.24
562	564	2.698855	ATGATTAGCCTGACTGCGTT	57.301	45.000	0.00	0.00	36.02	4.84
563	565	2.472695	TGATTAGCCTGACTGCGTTT	57.527	45.000	0.00	0.00	36.02	3.60
564	566	2.778299	TGATTAGCCTGACTGCGTTTT	58.222	42.857	0.00	0.00	36.02	2.43
565	567	2.742053	TGATTAGCCTGACTGCGTTTTC	59.258	45.455	0.00	0.00	36.02	2.29
579	581	3.385079	CGTTTTCGCTGGGATTAGTTC	57.615	47.619	0.00	0.00	36.22	3.01
580	582	3.000727	CGTTTTCGCTGGGATTAGTTCT	58.999	45.455	0.00	0.00	36.22	3.01
581	583	3.435671	CGTTTTCGCTGGGATTAGTTCTT	59.564	43.478	0.00	0.00	36.22	2.52
582	584	4.669197	CGTTTTCGCTGGGATTAGTTCTTG	60.669	45.833	0.00	0.00	36.22	3.02
583	585	3.695830	TTCGCTGGGATTAGTTCTTGT	57.304	42.857	0.00	0.00	0.00	3.16
584	586	3.695830	TCGCTGGGATTAGTTCTTGTT	57.304	42.857	0.00	0.00	0.00	2.83
585	587	4.015872	TCGCTGGGATTAGTTCTTGTTT	57.984	40.909	0.00	0.00	0.00	2.83
586	588	3.751175	TCGCTGGGATTAGTTCTTGTTTG	59.249	43.478	0.00	0.00	0.00	2.93
587	589	3.502211	CGCTGGGATTAGTTCTTGTTTGT	59.498	43.478	0.00	0.00	0.00	2.83
588	590	4.693566	CGCTGGGATTAGTTCTTGTTTGTA	59.306	41.667	0.00	0.00	0.00	2.41
589	591	5.354234	CGCTGGGATTAGTTCTTGTTTGTAT	59.646	40.000	0.00	0.00	0.00	2.29
590	592	6.537301	CGCTGGGATTAGTTCTTGTTTGTATA	59.463	38.462	0.00	0.00	0.00	1.47
591	593	7.226720	CGCTGGGATTAGTTCTTGTTTGTATAT	59.773	37.037	0.00	0.00	0.00	0.86
592	594	8.560374	GCTGGGATTAGTTCTTGTTTGTATATC	58.440	37.037	0.00	0.00	0.00	1.63
593	595	8.974060	TGGGATTAGTTCTTGTTTGTATATCC	57.026	34.615	0.00	0.00	0.00	2.59
594	596	8.778059	TGGGATTAGTTCTTGTTTGTATATCCT	58.222	33.333	0.00	0.00	0.00	3.24
595	597	9.628500	GGGATTAGTTCTTGTTTGTATATCCTT	57.372	33.333	0.00	0.00	0.00	3.36
764	766	6.349280	GGAATATAGCGAATAAAGCCATTGCA	60.349	38.462	0.00	0.00	41.13	4.08
769	771	2.539476	GAATAAAGCCATTGCAACCCG	58.461	47.619	0.00	0.00	41.13	5.28
847	851	3.396260	TCAGTAAACTACCTGCACCAC	57.604	47.619	0.00	0.00	0.00	4.16
882	886	7.364851	GGCCTAGGTTTAGAACTATCTTCAACT	60.365	40.741	11.31	0.00	37.10	3.16
1293	1301	2.370281	ACGTATTGTGACAGCCTGAG	57.630	50.000	0.00	0.00	0.00	3.35
1454	1463	1.065126	CCCCTTCTGATCCACCTCAAC	60.065	57.143	0.00	0.00	0.00	3.18
1778	1787	0.554792	ATGGCTAGCCTCCAAAGCAT	59.445	50.000	33.07	13.86	38.01	3.79
1977	1986	1.768275	AGAGTTCACATGGTGACCACA	59.232	47.619	6.40	0.00	42.60	4.17
1992	2001	0.674581	CCACACGTGTCCATGATGCT	60.675	55.000	20.49	0.00	0.00	3.79
2001	2010	1.209383	CCATGATGCTAGCATGCGC	59.791	57.895	34.16	19.97	41.30	6.09
2081	2090	1.732917	CCAAGCGTGCCAAACTTCA	59.267	52.632	0.00	0.00	0.00	3.02
2089	2098	1.412343	GTGCCAAACTTCACCACCATT	59.588	47.619	0.00	0.00	0.00	3.16
2113	2122	2.674177	CGTCTCAACGGCATTAACTCCT	60.674	50.000	0.00	0.00	45.21	3.69

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
13	14	3.205419	GTCTATGGACCAAAGGGCAACC	61.205	54.545	0.00	0.00	46.86	3.77
14	15	2.092323	GTCTATGGACCAAAGGGCAAC	58.908	52.381	0.00	0.00	37.90	4.17
15	16	1.339631	CGTCTATGGACCAAAGGGCAA	60.340	52.381	0.00	0.00	39.15	4.52
16	17	0.251916	CGTCTATGGACCAAAGGGCA	59.748	55.000	0.00	0.00	39.15	5.36
17	18	0.463833	CCGTCTATGGACCAAAGGGC	60.464	60.000	0.00	0.00	39.15	5.19
18	19	0.463833	GCCGTCTATGGACCAAAGGG	60.464	60.000	0.00	3.82	39.15	3.95
19	20	0.251916	TGCCGTCTATGGACCAAAGG	59.748	55.000	0.00	0.19	39.15	3.11
20	21	1.369625	GTGCCGTCTATGGACCAAAG	58.630	55.000	0.00	0.00	39.15	2.77
21	22	0.035820	GGTGCCGTCTATGGACCAAA	60.036	55.000	0.00	0.00	39.15	3.28
22	23	1.600107	GGTGCCGTCTATGGACCAA	59.400	57.895	0.00	0.00	39.15	3.67
23	24	2.363975	GGGTGCCGTCTATGGACCA	61.364	63.158	3.33	0.00	39.15	4.02
24	25	2.064581	AGGGTGCCGTCTATGGACC	61.065	63.158	3.33	0.00	39.15	4.46
25	26	1.144057	CAGGGTGCCGTCTATGGAC	59.856	63.158	0.00	0.00	38.97	4.02
26	27	2.063979	CCAGGGTGCCGTCTATGGA	61.064	63.158	0.00	0.00	0.00	3.41
27	28	2.505982	CCAGGGTGCCGTCTATGG	59.494	66.667	0.00	0.00	0.00	2.74
28	29	2.203070	GCCAGGGTGCCGTCTATG	60.203	66.667	0.00	0.00	0.00	2.23
29	30	2.072487	ATGCCAGGGTGCCGTCTAT	61.072	57.895	0.00	0.00	0.00	1.98
30	31	2.687200	ATGCCAGGGTGCCGTCTA	60.687	61.111	0.00	0.00	0.00	2.59
31	32	4.415150	CATGCCAGGGTGCCGTCT	62.415	66.667	0.00	0.00	0.00	4.18
32	33	4.722700	ACATGCCAGGGTGCCGTC	62.723	66.667	0.00	0.00	0.00	4.79
34	35	4.720902	TCACATGCCAGGGTGCCG	62.721	66.667	0.00	0.00	35.04	5.69
35	36	2.283101	TTCACATGCCAGGGTGCC	60.283	61.111	0.00	0.00	35.04	5.01
36	37	0.682209	ATCTTCACATGCCAGGGTGC	60.682	55.000	0.00	0.00	35.04	5.01
47	48	3.623703	AGGCATTGCATGTATCTTCACA	58.376	40.909	11.39	0.00	0.00	3.58
107	108	4.504461	CGATAACTGAGCCATACTTGTGTC	59.496	45.833	0.00	0.00	0.00	3.67
118	119	2.584236	TCCTAGACCGATAACTGAGCC	58.416	52.381	0.00	0.00	0.00	4.70
186	187	0.031585	GTACATATGGTGCGAGCCGA	59.968	55.000	7.80	0.00	0.00	5.54
212	213	2.415893	CCCAAAAGCGTGTCAATGATCC	60.416	50.000	0.00	0.00	0.00	3.36
216	217	1.336440	TGACCCAAAAGCGTGTCAATG	59.664	47.619	0.00	0.00	34.98	2.82
222	223	1.528309	ACCCTGACCCAAAAGCGTG	60.528	57.895	0.00	0.00	0.00	5.34
229	230	0.324738	TTTTGCACACCCTGACCCAA	60.325	50.000	0.00	0.00	0.00	4.12
238	239	4.781883	GCTTTTTGTTCGATTTTGCACACC	60.782	41.667	0.00	0.00	0.00	4.16
245	246	6.904543	CGATTTTTGGCTTTTTGTTCGATTTT	59.095	30.769	0.00	0.00	0.00	1.82
279	281	8.873215	AAAACGAAAAATTTTGGTTTGGTTTT	57.127	23.077	24.67	19.12	44.07	2.43
290	292	7.254137	CCAAACATGGGAAAACGAAAAATTTT	58.746	30.769	0.00	0.00	31.96	1.82
314	316	7.010460	CAGATTTCAAAACTGAAACTGAAACCC	59.990	37.037	16.58	0.00	39.78	4.11
421	423	2.031508	ACAACCATTACGCTTTGAACCG	60.032	45.455	0.00	0.00	0.00	4.44
432	434	7.753580	GCCAGAAAATACTACAACAACCATTAC	59.246	37.037	0.00	0.00	0.00	1.89
442	444	7.122055	CACTAAATGGGCCAGAAAATACTACAA	59.878	37.037	13.78	0.00	0.00	2.41
444	446	6.459710	GCACTAAATGGGCCAGAAAATACTAC	60.460	42.308	13.78	0.00	39.71	2.73
473	475	4.878397	GCAGTCAGGCTAATCACATAAACT	59.122	41.667	0.00	0.00	0.00	2.66
491	493	4.275936	ACAAGTGTTGTTGGATAAGCAGTC	59.724	41.667	0.00	0.00	42.22	3.51
536	538	5.545588	GCAGTCAGGCTAATCATAATGAGA	58.454	41.667	0.00	0.00	0.00	3.27
548	550	1.289109	GCGAAAACGCAGTCAGGCTA	61.289	55.000	9.66	0.00	45.00	3.93
549	551	2.607892	GCGAAAACGCAGTCAGGCT	61.608	57.895	9.66	0.00	45.00	4.58
550	552	2.127232	GCGAAAACGCAGTCAGGC	60.127	61.111	9.66	0.00	45.00	4.85
551	553	1.205064	CAGCGAAAACGCAGTCAGG	59.795	57.895	16.32	0.00	45.00	3.86
552	554	1.205064	CCAGCGAAAACGCAGTCAG	59.795	57.895	16.32	1.78	45.00	3.51
553	555	2.250939	CCCAGCGAAAACGCAGTCA	61.251	57.895	16.32	0.00	45.00	3.41
554	556	1.298859	ATCCCAGCGAAAACGCAGTC	61.299	55.000	16.32	0.00	45.00	3.51
556	558	1.062587	CTAATCCCAGCGAAAACGCAG	59.937	52.381	16.32	8.53	37.35	5.18
557	559	1.083489	CTAATCCCAGCGAAAACGCA	58.917	50.000	16.32	0.00	37.35	5.24
558	560	1.084289	ACTAATCCCAGCGAAAACGC	58.916	50.000	6.50	6.50	0.00	4.84
559	561	3.000727	AGAACTAATCCCAGCGAAAACG	58.999	45.455	0.00	0.00	0.00	3.60
560	562	4.215613	ACAAGAACTAATCCCAGCGAAAAC	59.784	41.667	0.00	0.00	0.00	2.43
561	563	4.394729	ACAAGAACTAATCCCAGCGAAAA	58.605	39.130	0.00	0.00	0.00	2.29
562	564	4.015872	ACAAGAACTAATCCCAGCGAAA	57.984	40.909	0.00	0.00	0.00	3.46
563	565	3.695830	ACAAGAACTAATCCCAGCGAA	57.304	42.857	0.00	0.00	0.00	4.70
564	566	3.695830	AACAAGAACTAATCCCAGCGA	57.304	42.857	0.00	0.00	0.00	4.93
565	567	3.502211	ACAAACAAGAACTAATCCCAGCG	59.498	43.478	0.00	0.00	0.00	5.18
566	568	6.759497	ATACAAACAAGAACTAATCCCAGC	57.241	37.500	0.00	0.00	0.00	4.85
567	569	9.057089	GGATATACAAACAAGAACTAATCCCAG	57.943	37.037	0.00	0.00	0.00	4.45
568	570	8.778059	AGGATATACAAACAAGAACTAATCCCA	58.222	33.333	0.00	0.00	31.50	4.37
569	571	9.628500	AAGGATATACAAACAAGAACTAATCCC	57.372	33.333	0.00	0.00	31.50	3.85
693	695	3.731652	TTCTTCCGTTTTACTGGACGA	57.268	42.857	0.00	0.00	41.53	4.20
764	766	2.356432	GGGACTACCTTTTATGCGGGTT	60.356	50.000	0.00	0.00	34.86	4.11
769	771	3.021695	GTTGGGGGACTACCTTTTATGC	58.978	50.000	0.00	0.00	40.03	3.14
806	810	7.343357	ACTGAAACCCTTGAATTCGGAATATA	58.657	34.615	3.22	0.00	34.34	0.86
847	851	4.320870	TCTAAACCTAGGCCAAAACGAAG	58.679	43.478	9.30	0.00	0.00	3.79
1003	1007	4.705337	TGGCGACTAAAGTTGTTGTTTT	57.295	36.364	0.00	0.00	0.00	2.43
1101	1105	4.202020	CCGTGTTCTTCGAATGGATCTCTA	60.202	45.833	0.00	0.00	0.00	2.43
1260	1267	7.280428	TGTCACAATACGTTCCTTTTAGTTTCA	59.720	33.333	0.00	0.00	0.00	2.69
1293	1301	3.511540	AGGCAAATAAGAGAGGGCAAAAC	59.488	43.478	0.00	0.00	0.00	2.43
1669	1678	3.909732	AGAAACCACCATTTCTGTCCAA	58.090	40.909	0.09	0.00	45.22	3.53
1778	1787	3.015145	GCTGGGAGTTGGGGGCTA	61.015	66.667	0.00	0.00	0.00	3.93
1977	1986	0.536724	TGCTAGCATCATGGACACGT	59.463	50.000	14.93	0.00	0.00	4.49
2001	2010	4.447069	ACTCAGAGCGCGTCGACG	62.447	66.667	32.57	32.57	43.27	5.12
2065	2074	1.034838	TGGTGAAGTTTGGCACGCTT	61.035	50.000	2.82	2.82	35.91	4.68
2081	2090	2.457366	GTTGAGACGAGAATGGTGGT	57.543	50.000	0.00	0.00	0.00	4.16
2102	2111	1.065126	AGCACCAGGAGGAGTTAATGC	60.065	52.381	0.00	0.00	38.69	3.56
2113	2122	4.147449	CATCGGCGAGCACCAGGA	62.147	66.667	17.22	0.00	0.00	3.86

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.