AutoCloner

Multiple sequence alignment - TraesCS3B01G030100

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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	TraesCS3B01G030100	chr3B	100.000	3031	0	0	1	3031	13821994	13818964	0.000000e+00	5598
1	TraesCS3B01G030100	chr3D	92.498	1333	60	17	1701	3012	4996974	4998287	0.000000e+00	1871
2	TraesCS3B01G030100	chr3D	83.661	1781	186	74	1	1701	4995143	4996898	0.000000e+00	1580
3	TraesCS3B01G030100	chr3D	86.581	1401	108	27	132	1479	9679484	9678111	0.000000e+00	1472
4	TraesCS3B01G030100	chrUn	89.077	1062	77	21	676	1701	257141447	257140389	0.000000e+00	1282
5	TraesCS3B01G030100	chrUn	89.077	1062	77	21	676	1701	279872552	279873610	0.000000e+00	1282
6	TraesCS3B01G030100	chrUn	88.769	837	56	18	1701	2517	208774532	208773714	0.000000e+00	990
7	TraesCS3B01G030100	chrUn	82.359	924	123	27	1938	2850	285726567	285725673	0.000000e+00	767
8	TraesCS3B01G030100	chrUn	92.996	514	34	2	2509	3021	208768544	208768032	0.000000e+00	749
9	TraesCS3B01G030100	chrUn	84.076	785	55	24	1	751	257142177	257141429	0.000000e+00	693
10	TraesCS3B01G030100	chrUn	86.116	605	40	15	177	751	279871980	279872570	2.000000e-171	612
11	TraesCS3B01G030100	chrUn	80.290	827	130	19	1	808	299358140	299358952	7.240000e-166	593
12	TraesCS3B01G030100	chrUn	79.594	838	130	27	1	808	309801247	309802073	2.040000e-156	562
13	TraesCS3B01G030100	chrUn	79.594	838	130	27	1	808	315209994	315210820	2.040000e-156	562
14	TraesCS3B01G030100	chrUn	83.514	552	59	24	2040	2581	34706221	34706750	1.260000e-133	486
15	TraesCS3B01G030100	chrUn	78.797	698	131	15	806	1492	306116093	306115402	1.280000e-123	453
16	TraesCS3B01G030100	chrUn	78.762	711	118	18	114	808	32290509	32289816	2.140000e-121	446
17	TraesCS3B01G030100	chrUn	83.811	488	53	18	2040	2518	265025232	265024762	9.970000e-120	440
18	TraesCS3B01G030100	chrUn	83.811	488	53	18	2040	2518	287939827	287940297	9.970000e-120	440
19	TraesCS3B01G030100	chrUn	83.607	488	54	18	2040	2518	213718683	213719153	4.640000e-118	435
20	TraesCS3B01G030100	chrUn	83.402	488	55	18	2040	2518	260319534	260320004	2.160000e-116	429
21	TraesCS3B01G030100	chrUn	78.955	670	108	23	149	808	306116771	306116125	2.790000e-115	425
22	TraesCS3B01G030100	chrUn	77.941	680	133	12	806	1478	32289784	32289115	2.810000e-110	409
23	TraesCS3B01G030100	chrUn	77.286	678	141	9	806	1478	309802105	309802774	1.320000e-103	387
24	TraesCS3B01G030100	chrUn	77.286	678	141	9	806	1478	315210852	315211521	1.320000e-103	387
25	TraesCS3B01G030100	chrUn	77.205	737	117	32	106	808	225561804	225561085	1.700000e-102	383
26	TraesCS3B01G030100	chrUn	77.162	740	118	32	103	808	237462563	237463285	1.700000e-102	383
27	TraesCS3B01G030100	chrUn	77.162	740	118	32	103	808	257674279	257675001	1.700000e-102	383
28	TraesCS3B01G030100	chrUn	77.162	740	118	32	103	808	279684420	279685142	1.700000e-102	383
29	TraesCS3B01G030100	chrUn	77.205	737	117	32	106	808	294339444	294338725	1.700000e-102	383
30	TraesCS3B01G030100	chrUn	88.380	284	28	3	18	299	208776465	208776185	1.350000e-88	337
31	TraesCS3B01G030100	chrUn	78.327	526	84	15	296	808	197241972	197241464	2.270000e-81	313
32	TraesCS3B01G030100	chrUn	87.719	171	9	3	1701	1871	257140107	257139949	3.990000e-44	189
33	TraesCS3B01G030100	chrUn	87.719	171	9	3	1701	1871	279873892	279874050	3.990000e-44	189
34	TraesCS3B01G030100	chrUn	76.025	317	48	14	504	808	36351837	36351537	4.070000e-29	139
35	TraesCS3B01G030100	chrUn	76.025	317	48	14	504	808	214883168	214883468	4.070000e-29	139
36	TraesCS3B01G030100	chrUn	83.051	118	13	5	1910	2026	197240155	197240044	1.920000e-17	100
37	TraesCS3B01G030100	chr3A	94.011	718	36	6	2001	2716	10879081	10879793	0.000000e+00	1081
38	TraesCS3B01G030100	chr3A	92.751	607	36	6	1099	1701	10877926	10878528	0.000000e+00	870
39	TraesCS3B01G030100	chr3A	80.290	827	130	19	1	808	11126507	11127319	7.240000e-166	593
40	TraesCS3B01G030100	chr3A	80.290	827	130	19	1	808	11135158	11135970	7.240000e-166	593
41	TraesCS3B01G030100	chr3A	80.290	827	130	19	1	808	11142030	11142842	7.240000e-166	593
42	TraesCS3B01G030100	chr3A	75.806	744	161	14	806	1543	10941130	10941860	2.870000e-95	359
43	TraesCS3B01G030100	chr3A	89.630	270	25	3	2746	3012	10879793	10880062	1.040000e-89	340
44	TraesCS3B01G030100	chr3A	84.459	296	17	13	1701	1980	10878809	10879091	6.440000e-67	265
45	TraesCS3B01G030100	chr3A	78.814	236	46	4	296	529	38136565	38136332	4.050000e-34	156
46	TraesCS3B01G030100	chr5D	93.590	78	4	1	1551	1627	188826543	188826620	6.870000e-22	115
47	TraesCS3B01G030100	chr5B	92.308	78	5	1	1551	1627	217907691	217907768	3.190000e-20	110
48	TraesCS3B01G030100	chr7A	93.243	74	4	1	1551	1623	572188311	572188384	1.150000e-19	108
49	TraesCS3B01G030100	chr4D	91.026	78	6	1	1551	1627	320026976	320027053	1.490000e-18	104
50	TraesCS3B01G030100	chr1A	89.024	82	6	3	1551	1630	449669432	449669512	6.920000e-17	99

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	TraesCS3B01G030100	chr3B	13818964	13821994	3030	True	5598.000000	5598	100.000000	1	3031	1	chr3B.!!$R1	3030
1	TraesCS3B01G030100	chr3D	4995143	4998287	3144	False	1725.500000	1871	88.079500	1	3012	2	chr3D.!!$F1	3011
2	TraesCS3B01G030100	chr3D	9678111	9679484	1373	True	1472.000000	1472	86.581000	132	1479	1	chr3D.!!$R1	1347
3	TraesCS3B01G030100	chrUn	285725673	285726567	894	True	767.000000	767	82.359000	1938	2850	1	chrUn.!!$R5	912
4	TraesCS3B01G030100	chrUn	208768032	208768544	512	True	749.000000	749	92.996000	2509	3021	1	chrUn.!!$R2	512
5	TraesCS3B01G030100	chrUn	257139949	257142177	2228	True	721.333333	1282	86.957333	1	1871	3	chrUn.!!$R10	1870
6	TraesCS3B01G030100	chrUn	279871980	279874050	2070	False	694.333333	1282	87.637333	177	1871	3	chrUn.!!$F10	1694
7	TraesCS3B01G030100	chrUn	208773714	208776465	2751	True	663.500000	990	88.574500	18	2517	2	chrUn.!!$R9	2499
8	TraesCS3B01G030100	chrUn	299358140	299358952	812	False	593.000000	593	80.290000	1	808	1	chrUn.!!$F9	807
9	TraesCS3B01G030100	chrUn	34706221	34706750	529	False	486.000000	486	83.514000	2040	2581	1	chrUn.!!$F1	541
10	TraesCS3B01G030100	chrUn	309801247	309802774	1527	False	474.500000	562	78.440000	1	1478	2	chrUn.!!$F11	1477
11	TraesCS3B01G030100	chrUn	315209994	315211521	1527	False	474.500000	562	78.440000	1	1478	2	chrUn.!!$F12	1477
12	TraesCS3B01G030100	chrUn	306115402	306116771	1369	True	439.000000	453	78.876000	149	1492	2	chrUn.!!$R11	1343
13	TraesCS3B01G030100	chrUn	32289115	32290509	1394	True	427.500000	446	78.351500	114	1478	2	chrUn.!!$R7	1364
14	TraesCS3B01G030100	chrUn	225561085	225561804	719	True	383.000000	383	77.205000	106	808	1	chrUn.!!$R3	702
15	TraesCS3B01G030100	chrUn	237462563	237463285	722	False	383.000000	383	77.162000	103	808	1	chrUn.!!$F4	705
16	TraesCS3B01G030100	chrUn	257674279	257675001	722	False	383.000000	383	77.162000	103	808	1	chrUn.!!$F5	705
17	TraesCS3B01G030100	chrUn	279684420	279685142	722	False	383.000000	383	77.162000	103	808	1	chrUn.!!$F7	705
18	TraesCS3B01G030100	chrUn	294338725	294339444	719	True	383.000000	383	77.205000	106	808	1	chrUn.!!$R6	702
19	TraesCS3B01G030100	chrUn	197240044	197241972	1928	True	206.500000	313	80.689000	296	2026	2	chrUn.!!$R8	1730
20	TraesCS3B01G030100	chr3A	10877926	10880062	2136	False	639.000000	1081	90.212750	1099	3012	4	chr3A.!!$F5	1913
21	TraesCS3B01G030100	chr3A	11126507	11127319	812	False	593.000000	593	80.290000	1	808	1	chr3A.!!$F2	807
22	TraesCS3B01G030100	chr3A	11135158	11135970	812	False	593.000000	593	80.290000	1	808	1	chr3A.!!$F3	807
23	TraesCS3B01G030100	chr3A	11142030	11142842	812	False	593.000000	593	80.290000	1	808	1	chr3A.!!$F4	807
24	TraesCS3B01G030100	chr3A	10941130	10941860	730	False	359.000000	359	75.806000	806	1543	1	chr3A.!!$F1	737

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
833	1039	0.945265	CCCGCCTTTGCACATGTTTG	60.945	55.0	0.0	0.0	37.32	2.93	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2030	2573	1.552337	CATCCTATGTATCGCCTGCCT	59.448	52.381	0.0	0.0	0.0	4.75	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
41	42	2.701006	CACGCGCCTAAATCCACG	59.299	61.111	5.73	0.00	0.00	4.94
68	69	2.830370	GATTGAGGCGGGCCAAGG	60.830	66.667	12.97	0.00	38.92	3.61
111	119	2.464403	CCTCCATCCCCATCCCCAC	61.464	68.421	0.00	0.00	0.00	4.61
422	460	3.647771	GGACCCCAGTTTCCGGCT	61.648	66.667	0.00	0.00	0.00	5.52
454	492	1.529010	CACCACTGGAAGCTGCCAA	60.529	57.895	16.33	0.00	37.52	4.52
632	685	3.251571	GCGTCCTCGTCATAAACTTTCT	58.748	45.455	0.00	0.00	39.49	2.52
635	688	3.060895	GTCCTCGTCATAAACTTTCTGCG	59.939	47.826	0.00	0.00	0.00	5.18
636	689	2.222819	CCTCGTCATAAACTTTCTGCGC	60.223	50.000	0.00	0.00	0.00	6.09
637	690	2.409012	TCGTCATAAACTTTCTGCGCA	58.591	42.857	10.98	10.98	0.00	6.09
638	691	2.803386	TCGTCATAAACTTTCTGCGCAA	59.197	40.909	13.05	0.00	0.00	4.85
639	692	3.248841	TCGTCATAAACTTTCTGCGCAAA	59.751	39.130	13.05	2.27	0.00	3.68
640	693	3.357823	CGTCATAAACTTTCTGCGCAAAC	59.642	43.478	13.05	0.00	0.00	2.93
641	694	4.537015	GTCATAAACTTTCTGCGCAAACT	58.463	39.130	13.05	0.00	0.00	2.66
642	695	4.976116	GTCATAAACTTTCTGCGCAAACTT	59.024	37.500	13.05	1.82	0.00	2.66
643	696	5.458779	GTCATAAACTTTCTGCGCAAACTTT	59.541	36.000	13.05	7.97	0.00	2.66
833	1039	0.945265	CCCGCCTTTGCACATGTTTG	60.945	55.000	0.00	0.00	37.32	2.93
903	1109	8.478877	ACTCCACCTAAGTTTTATCATACTGAG	58.521	37.037	0.00	0.00	0.00	3.35
1002	1211	1.089920	GGCACAACCTAGCTGTGATG	58.910	55.000	21.21	0.74	45.80	3.07
1065	1282	1.493446	AGCCATCAGATCATTCAGGCA	59.507	47.619	15.44	0.00	42.90	4.75
1113	1330	2.022764	TGTCTCACAATGGCCATACG	57.977	50.000	21.15	16.03	0.00	3.06
1223	1440	3.347077	ACCTGCTCAGATTGAAGGAAG	57.653	47.619	4.29	0.00	30.73	3.46
1309	1529	4.098960	ACGACGGTGTCTATATGGTTCAAT	59.901	41.667	0.00	0.00	0.00	2.57
1311	1531	5.051039	CGACGGTGTCTATATGGTTCAATTG	60.051	44.000	0.00	0.00	0.00	2.32
1333	1553	9.635520	AATTGAAGTTGATGCAATCTAGAAAAG	57.364	29.630	0.00	0.00	45.81	2.27
1341	1561	7.362662	TGATGCAATCTAGAAAAGTTTGTGAC	58.637	34.615	0.00	0.00	45.81	3.67
1342	1562	6.072112	TGCAATCTAGAAAAGTTTGTGACC	57.928	37.500	0.00	0.00	37.27	4.02
1467	1687	5.029807	TCCGTACATGGATGCTCAAATAA	57.970	39.130	0.00	0.00	31.53	1.40
1518	1754	8.340757	TCCTTATGGTTTCATTTAATACACCCT	58.659	33.333	0.00	0.00	34.96	4.34
1569	1805	5.670792	AACCCGTCTCACAATATAAGACA	57.329	39.130	0.00	0.00	39.49	3.41
1580	1816	9.630098	CTCACAATATAAGACATTTTTGCAAGT	57.370	29.630	0.00	0.00	0.00	3.16
1589	1825	8.748380	AAGACATTTTTGCAAGTTATCTTAGC	57.252	30.769	0.00	0.00	32.07	3.09
1649	1885	2.237143	TGCCTTCATCCTTGTGAGGTAG	59.763	50.000	0.00	0.00	43.97	3.18
1750	2276	6.810911	TGACATAAATTCTAGACTCTGCCTC	58.189	40.000	0.00	0.00	0.00	4.70
1763	2289	5.086104	ACTCTGCCTCGCTTTCTTATAAA	57.914	39.130	0.00	0.00	0.00	1.40
1809	2335	7.887495	AGAGAGCTAAATTCTTCATTTGAGGTT	59.113	33.333	0.00	0.00	35.71	3.50
1810	2336	7.824672	AGAGCTAAATTCTTCATTTGAGGTTG	58.175	34.615	0.00	0.00	35.71	3.77
1811	2337	6.393171	AGCTAAATTCTTCATTTGAGGTTGC	58.607	36.000	0.00	0.00	35.71	4.17
1812	2338	6.210185	AGCTAAATTCTTCATTTGAGGTTGCT	59.790	34.615	0.00	0.00	35.71	3.91
1813	2339	7.394359	AGCTAAATTCTTCATTTGAGGTTGCTA	59.606	33.333	0.00	0.00	35.71	3.49
1814	2340	8.193438	GCTAAATTCTTCATTTGAGGTTGCTAT	58.807	33.333	0.00	0.00	35.71	2.97
1817	2343	7.814264	ATTCTTCATTTGAGGTTGCTATAGG	57.186	36.000	1.04	0.00	0.00	2.57
1818	2344	6.313519	TCTTCATTTGAGGTTGCTATAGGT	57.686	37.500	1.04	0.00	0.00	3.08
1819	2345	6.721318	TCTTCATTTGAGGTTGCTATAGGTT	58.279	36.000	1.04	0.00	0.00	3.50
1855	2381	9.630098	ACATTACACTGCTTTCAAGAATATTTG	57.370	29.630	0.00	0.00	0.00	2.32
1862	2388	5.406175	TGCTTTCAAGAATATTTGCTGCAAC	59.594	36.000	15.72	3.04	30.63	4.17
1901	2441	8.690680	AGTTACGAGAAGTCAGCTATTTAAAG	57.309	34.615	0.00	0.00	0.00	1.85
1902	2442	8.521176	AGTTACGAGAAGTCAGCTATTTAAAGA	58.479	33.333	0.00	0.00	0.00	2.52
1903	2443	9.303537	GTTACGAGAAGTCAGCTATTTAAAGAT	57.696	33.333	0.00	0.00	0.00	2.40
1906	2446	9.871238	ACGAGAAGTCAGCTATTTAAAGATAAA	57.129	29.630	0.00	0.00	35.57	1.40
2030	2573	7.280876	GGTTATGATAGAGCTGAAATGTTGTGA	59.719	37.037	0.00	0.00	0.00	3.58
2033	2576	2.157738	AGAGCTGAAATGTTGTGAGGC	58.842	47.619	0.00	0.00	0.00	4.70
2054	2599	3.444034	GCAGGCGATACATAGGATGACTA	59.556	47.826	0.00	0.00	35.80	2.59
2109	2655	6.154706	GGTTCACCAGGTAAGAAGATCTTCTA	59.845	42.308	32.89	20.03	41.41	2.10
2214	2767	8.023021	TCAAACTACTGTCCATTCAGCTATAT	57.977	34.615	0.00	0.00	38.84	0.86
2215	2768	9.143155	TCAAACTACTGTCCATTCAGCTATATA	57.857	33.333	0.00	0.00	38.84	0.86
2217	2770	8.713708	AACTACTGTCCATTCAGCTATATAGT	57.286	34.615	11.38	0.00	38.84	2.12
2219	2772	6.352016	ACTGTCCATTCAGCTATATAGTGG	57.648	41.667	11.38	10.15	38.84	4.00
2239	2792	4.006989	TGGTTCACGCTTGCTAATAACAT	58.993	39.130	0.00	0.00	0.00	2.71
2246	2799	6.592220	TCACGCTTGCTAATAACATAGACAAA	59.408	34.615	0.00	0.00	0.00	2.83
2488	3047	6.287525	AGGGTTTATTTTGTTGTCATTGGTG	58.712	36.000	0.00	0.00	0.00	4.17
2600	3162	9.061435	TGATCTTGAATTTGTACACACATGTTA	57.939	29.630	0.00	0.00	40.48	2.41
2610	3172	7.284518	TGTACACACATGTTATTCATACACG	57.715	36.000	0.00	0.00	40.48	4.49
2899	3468	3.003394	TCAGCCCCAAAGTATCACATG	57.997	47.619	0.00	0.00	0.00	3.21
3002	3571	1.160137	GGTTGTTGCTGCTGTCTAGG	58.840	55.000	0.00	0.00	0.00	3.02
3012	3581	4.937620	TGCTGCTGTCTAGGATTTTGTAAG	59.062	41.667	0.00	0.00	0.00	2.34
3013	3582	4.938226	GCTGCTGTCTAGGATTTTGTAAGT	59.062	41.667	0.00	0.00	0.00	2.24
3017	3586	6.426937	TGCTGTCTAGGATTTTGTAAGTGTTC	59.573	38.462	0.00	0.00	0.00	3.18
3021	3590	6.371825	GTCTAGGATTTTGTAAGTGTTCCTGG	59.628	42.308	0.00	0.00	35.33	4.45
3022	3591	3.826729	AGGATTTTGTAAGTGTTCCTGGC	59.173	43.478	0.00	0.00	32.48	4.85
3023	3592	3.826729	GGATTTTGTAAGTGTTCCTGGCT	59.173	43.478	0.00	0.00	0.00	4.75
3024	3593	4.280929	GGATTTTGTAAGTGTTCCTGGCTT	59.719	41.667	0.00	0.00	0.00	4.35
3025	3594	4.647424	TTTTGTAAGTGTTCCTGGCTTG	57.353	40.909	0.00	0.00	0.00	4.01
3026	3595	3.290948	TTGTAAGTGTTCCTGGCTTGT	57.709	42.857	0.00	0.00	0.00	3.16
3027	3596	2.846193	TGTAAGTGTTCCTGGCTTGTC	58.154	47.619	0.00	0.00	0.00	3.18
3028	3597	1.798813	GTAAGTGTTCCTGGCTTGTCG	59.201	52.381	0.00	0.00	0.00	4.35
3029	3598	0.180406	AAGTGTTCCTGGCTTGTCGT	59.820	50.000	0.00	0.00	0.00	4.34
3030	3599	0.180406	AGTGTTCCTGGCTTGTCGTT	59.820	50.000	0.00	0.00	0.00	3.85

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
41	42	2.171725	GCCTCAATCGCGTGGGTAC	61.172	63.158	5.77	0.00	0.00	3.34
53	54	4.033776	CTCCTTGGCCCGCCTCAA	62.034	66.667	7.35	0.00	36.94	3.02
111	119	1.354337	CGTCTTCACTGGCGTGGATG	61.354	60.000	9.05	2.96	41.53	3.51
292	300	1.081376	CGTCGTCTTCAAGCGGACT	60.081	57.895	6.23	0.00	0.00	3.85
294	302	1.081641	GTCGTCGTCTTCAAGCGGA	60.082	57.895	2.13	0.00	0.00	5.54
405	443	3.623703	GAGCCGGAAACTGGGGTCC	62.624	68.421	5.05	0.00	43.35	4.46
422	460	4.704833	GGTGCTGGCAGAAGCGGA	62.705	66.667	20.86	0.00	46.65	5.54
449	487	1.821216	GAAGAAACCGAGGATTGGCA	58.179	50.000	0.00	0.00	46.70	4.92
454	492	1.263356	TCCACGAAGAAACCGAGGAT	58.737	50.000	0.00	0.00	40.75	3.24
635	688	1.190763	CACATTGCGCAGAAAGTTTGC	59.809	47.619	11.31	0.00	38.18	3.68
636	689	1.190763	GCACATTGCGCAGAAAGTTTG	59.809	47.619	11.31	3.59	31.71	2.93
637	690	1.490621	GCACATTGCGCAGAAAGTTT	58.509	45.000	11.31	0.00	31.71	2.66
638	691	3.184094	GCACATTGCGCAGAAAGTT	57.816	47.368	11.31	0.00	31.71	2.66
639	692	4.950744	GCACATTGCGCAGAAAGT	57.049	50.000	11.31	5.17	31.71	2.66
720	892	1.811266	CCGGTGATGAAGCTGTCCG	60.811	63.158	0.00	0.00	38.05	4.79
833	1039	0.680280	TACACCGGTCTCTGAGGAGC	60.680	60.000	2.59	1.07	39.31	4.70
903	1109	8.129211	GCATTACCAATAAGTGAACCATAACTC	58.871	37.037	0.00	0.00	0.00	3.01
1002	1211	0.178068	TTGTAATGGGAGGCGCTCTC	59.822	55.000	7.64	12.39	41.71	3.20
1065	1282	0.250901	GACCAACAGCACCATCCACT	60.251	55.000	0.00	0.00	0.00	4.00
1113	1330	4.248058	CCTCCTTTTGCCACATTTGAATC	58.752	43.478	0.00	0.00	0.00	2.52
1223	1440	6.831868	TCCCAGTATAAATAACTTTGCCTTCC	59.168	38.462	0.00	0.00	0.00	3.46
1309	1529	8.169977	ACTTTTCTAGATTGCATCAACTTCAA	57.830	30.769	0.00	0.00	0.00	2.69
1311	1531	8.909671	CAAACTTTTCTAGATTGCATCAACTTC	58.090	33.333	0.00	0.00	31.10	3.01
1446	1666	4.816385	AGTTATTTGAGCATCCATGTACGG	59.184	41.667	0.00	0.00	0.00	4.02
1467	1687	9.694137	GATATAAGTCCGTTAATCTAGCAAAGT	57.306	33.333	0.00	0.00	0.00	2.66
1525	1761	7.660208	GGGTTTGAGTATATTGGACGATAACAT	59.340	37.037	0.00	0.00	0.00	2.71
1533	1769	5.019785	AGACGGGTTTGAGTATATTGGAC	57.980	43.478	0.00	0.00	0.00	4.02
1548	1784	5.871396	ATGTCTTATATTGTGAGACGGGT	57.129	39.130	1.83	0.00	44.20	5.28
1569	1805	9.762933	TTTCAAGCTAAGATAACTTGCAAAAAT	57.237	25.926	0.00	0.00	40.45	1.82
1813	2339	9.929180	CAGTGTAATGTATACATAGCAACCTAT	57.071	33.333	18.56	2.76	35.10	2.57
1814	2340	7.870954	GCAGTGTAATGTATACATAGCAACCTA	59.129	37.037	18.56	3.21	35.10	3.08
1815	2341	6.706270	GCAGTGTAATGTATACATAGCAACCT	59.294	38.462	18.56	11.24	35.10	3.50
1816	2342	6.706270	AGCAGTGTAATGTATACATAGCAACC	59.294	38.462	18.56	9.50	35.10	3.77
1817	2343	7.715265	AGCAGTGTAATGTATACATAGCAAC	57.285	36.000	18.56	13.76	35.10	4.17
1818	2344	8.731275	AAAGCAGTGTAATGTATACATAGCAA	57.269	30.769	18.56	2.98	35.10	3.91
1819	2345	7.984617	TGAAAGCAGTGTAATGTATACATAGCA	59.015	33.333	18.56	16.20	35.10	3.49
1835	2361	5.061808	GCAGCAAATATTCTTGAAAGCAGTG	59.938	40.000	0.00	0.00	0.00	3.66
1862	2388	9.464714	ACTTCTCGTAACTATATATGTTGCTTG	57.535	33.333	0.00	0.00	0.00	4.01
2013	2556	2.157738	GCCTCACAACATTTCAGCTCT	58.842	47.619	0.00	0.00	0.00	4.09
2030	2573	1.552337	CATCCTATGTATCGCCTGCCT	59.448	52.381	0.00	0.00	0.00	4.75
2033	2576	5.592282	AGATAGTCATCCTATGTATCGCCTG	59.408	44.000	0.00	0.00	36.47	4.85
2054	2599	3.630769	CACATTAGCACATCAAGGCAGAT	59.369	43.478	0.00	0.00	0.00	2.90
2109	2655	8.732531	CAATTCAAATCCCACAAAAGCATATTT	58.267	29.630	0.00	0.00	0.00	1.40
2115	2661	6.183360	ACAAACAATTCAAATCCCACAAAAGC	60.183	34.615	0.00	0.00	0.00	3.51
2161	2708	1.826054	CACCCACAGTGGCCGAAAA	60.826	57.895	14.98	0.00	43.26	2.29
2214	2767	2.823924	TTAGCAAGCGTGAACCACTA	57.176	45.000	2.99	0.00	31.34	2.74
2215	2768	2.185004	ATTAGCAAGCGTGAACCACT	57.815	45.000	2.99	0.00	31.34	4.00
2217	2770	3.403968	TGTTATTAGCAAGCGTGAACCA	58.596	40.909	2.99	0.00	0.00	3.67
2219	2772	6.035650	TGTCTATGTTATTAGCAAGCGTGAAC	59.964	38.462	2.99	0.00	0.00	3.18
2239	2792	8.012957	ACACCACCATTTTTATTGTTTGTCTA	57.987	30.769	0.00	0.00	0.00	2.59
2246	2799	4.141620	TGGCAACACCACCATTTTTATTGT	60.142	37.500	0.00	0.00	46.36	2.71
2899	3468	4.276460	CGTTACACAAAAGCACCAAGTAC	58.724	43.478	0.00	0.00	0.00	2.73
3002	3571	5.221244	ACAAGCCAGGAACACTTACAAAATC	60.221	40.000	0.00	0.00	0.00	2.17
3012	3581	2.702847	AACGACAAGCCAGGAACAC	58.297	52.632	0.00	0.00	0.00	3.32

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.