AutoCloner

Multiple sequence alignment - TraesCS4D01G298500

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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	TraesCS4D01G298500	chr4D	100.000	2857	0	0	1	2857	467822313	467819457	0.000000e+00	5276
1	TraesCS4D01G298500	chr4D	94.217	709	37	4	1	707	93440964	93441670	0.000000e+00	1079
2	TraesCS4D01G298500	chr4D	83.712	264	20	14	2092	2351	467681882	467681638	7.960000e-56	228
3	TraesCS4D01G298500	chr4D	91.216	148	10	3	2710	2855	489505322	489505468	6.240000e-47	198
4	TraesCS4D01G298500	chr4B	90.175	1140	62	22	767	1864	586070469	586069338	0.000000e+00	1439
5	TraesCS4D01G298500	chr4B	90.417	720	56	7	55	771	602652724	602652015	0.000000e+00	935
6	TraesCS4D01G298500	chr4B	91.511	589	45	5	2271	2857	586048962	586048377	0.000000e+00	806
7	TraesCS4D01G298500	chr4B	95.238	168	5	1	2109	2276	586068953	586068789	2.180000e-66	263
8	TraesCS4D01G298500	chr4B	88.000	200	24	0	1168	1367	586237194	586236995	1.320000e-58	237
9	TraesCS4D01G298500	chr5D	96.076	739	26	2	34	771	423274758	423275494	0.000000e+00	1201
10	TraesCS4D01G298500	chr5D	92.895	760	44	7	13	770	407316604	407317355	0.000000e+00	1096
11	TraesCS4D01G298500	chr5D	91.768	741	50	6	34	770	524595883	524596616	0.000000e+00	1020
12	TraesCS4D01G298500	chr5D	85.057	174	26	0	1189	1362	412960785	412960958	8.130000e-41	178
13	TraesCS4D01G298500	chr3D	92.894	774	44	5	1	770	80218546	80217780	0.000000e+00	1114
14	TraesCS4D01G298500	chr3D	86.577	149	15	4	2709	2855	598908163	598908308	2.950000e-35	159
15	TraesCS4D01G298500	chr2B	92.913	762	39	9	10	770	54460496	54459749	0.000000e+00	1094
16	TraesCS4D01G298500	chr4A	93.664	726	38	5	1170	1892	3342244	3342964	0.000000e+00	1079
17	TraesCS4D01G298500	chr4A	87.114	745	52	14	2007	2709	3343246	3343988	0.000000e+00	804
18	TraesCS4D01G298500	chr4A	91.605	405	26	5	767	1167	3341804	3342204	1.160000e-153	553
19	TraesCS4D01G298500	chr4A	88.587	184	20	1	1182	1365	3276912	3277094	3.700000e-54	222
20	TraesCS4D01G298500	chr1B	92.297	753	39	8	18	768	684864553	684863818	0.000000e+00	1051
21	TraesCS4D01G298500	chr5A	92.537	737	42	7	37	770	700172075	700171349	0.000000e+00	1044
22	TraesCS4D01G298500	chr3A	89.515	763	66	10	10	768	80609975	80609223	0.000000e+00	953
23	TraesCS4D01G298500	chr3A	90.935	706	37	8	66	770	725341854	725342533	0.000000e+00	924
24	TraesCS4D01G298500	chr5B	85.057	174	26	0	1189	1362	497504690	497504863	8.130000e-41	178
25	TraesCS4D01G298500	chr6D	85.714	147	18	3	2710	2854	4371553	4371698	4.930000e-33	152
26	TraesCS4D01G298500	chr6D	88.889	81	7	2	2735	2813	459937451	459937531	6.510000e-17	99
27	TraesCS4D01G298500	chr6B	84.354	147	20	3	2710	2854	8227639	8227494	1.070000e-29	141
28	TraesCS4D01G298500	chr3B	97.561	82	2	0	1	82	85628309	85628390	1.070000e-29	141
29	TraesCS4D01G298500	chr3B	94.118	85	5	0	1	85	25224093	25224177	2.310000e-26	130

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	TraesCS4D01G298500	chr4D	467819457	467822313	2856	True	5276	5276	100.000000	1	2857	1	chr4D.!!$R2	2856
1	TraesCS4D01G298500	chr4D	93440964	93441670	706	False	1079	1079	94.217000	1	707	1	chr4D.!!$F1	706
2	TraesCS4D01G298500	chr4B	602652015	602652724	709	True	935	935	90.417000	55	771	1	chr4B.!!$R3	716
3	TraesCS4D01G298500	chr4B	586068789	586070469	1680	True	851	1439	92.706500	767	2276	2	chr4B.!!$R4	1509
4	TraesCS4D01G298500	chr4B	586048377	586048962	585	True	806	806	91.511000	2271	2857	1	chr4B.!!$R1	586
5	TraesCS4D01G298500	chr5D	423274758	423275494	736	False	1201	1201	96.076000	34	771	1	chr5D.!!$F3	737
6	TraesCS4D01G298500	chr5D	407316604	407317355	751	False	1096	1096	92.895000	13	770	1	chr5D.!!$F1	757
7	TraesCS4D01G298500	chr5D	524595883	524596616	733	False	1020	1020	91.768000	34	770	1	chr5D.!!$F4	736
8	TraesCS4D01G298500	chr3D	80217780	80218546	766	True	1114	1114	92.894000	1	770	1	chr3D.!!$R1	769
9	TraesCS4D01G298500	chr2B	54459749	54460496	747	True	1094	1094	92.913000	10	770	1	chr2B.!!$R1	760
10	TraesCS4D01G298500	chr4A	3341804	3343988	2184	False	812	1079	90.794333	767	2709	3	chr4A.!!$F2	1942
11	TraesCS4D01G298500	chr1B	684863818	684864553	735	True	1051	1051	92.297000	18	768	1	chr1B.!!$R1	750
12	TraesCS4D01G298500	chr5A	700171349	700172075	726	True	1044	1044	92.537000	37	770	1	chr5A.!!$R1	733
13	TraesCS4D01G298500	chr3A	80609223	80609975	752	True	953	953	89.515000	10	768	1	chr3A.!!$R1	758
14	TraesCS4D01G298500	chr3A	725341854	725342533	679	False	924	924	90.935000	66	770	1	chr3A.!!$F1	704

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
908	945	0.170116	CTGCTCTGAGGTCGTCACTC	59.83	60.0	6.83	0.0	35.55	3.51	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2608	2945	0.106918	ACGGGTTTGAGTGCAAAGGA	60.107	50.0	0.0	0.0	44.12	3.36	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
272	275	2.789213	TCCATGAAGATGCCGTTGAAA	58.211	42.857	0.00	0.00	0.00	2.69
335	338	2.468301	TGAGGAGAGGGAGGAAGATG	57.532	55.000	0.00	0.00	0.00	2.90
377	380	3.349927	TCGTCTTCCGAAGATAAGGACA	58.650	45.455	13.92	0.00	44.03	4.02
391	406	1.546961	AGGACAAGGACGAAGACGAT	58.453	50.000	0.00	0.00	42.66	3.73
451	466	5.007921	ACTTGATTTGCATTTTGAACTTGGC	59.992	36.000	0.00	0.00	0.00	4.52
511	526	6.364435	GGCATGAACTTTTCTTCATCAACTTC	59.636	38.462	0.00	0.00	38.57	3.01
586	602	3.872459	TTTTGGGTCCAAAATGCCATT	57.128	38.095	20.27	0.00	46.80	3.16
639	658	1.812525	TTTTTGCGCTGTGCTGGAA	59.187	47.368	14.92	4.18	46.63	3.53
709	740	0.655733	CACGCAAAACCAGACGAACT	59.344	50.000	0.00	0.00	0.00	3.01
710	741	0.935196	ACGCAAAACCAGACGAACTC	59.065	50.000	0.00	0.00	0.00	3.01
712	743	1.305201	GCAAAACCAGACGAACTCCA	58.695	50.000	0.00	0.00	0.00	3.86
760	792	2.946762	GAAGCACGGCTGTTGGAC	59.053	61.111	0.00	0.00	39.62	4.02
792	824	2.098117	CCGCCATGAATTTTGGAGACTC	59.902	50.000	11.47	0.00	36.26	3.36
802	834	3.151022	GGAGACTCTGCCCCCTCG	61.151	72.222	1.74	0.00	0.00	4.63
876	913	2.107343	AACACTACCGCACGCACA	59.893	55.556	0.00	0.00	0.00	4.57
893	930	1.884579	CACAACCTTGATCAAGCTGCT	59.115	47.619	27.01	14.25	37.11	4.24
902	939	0.175302	ATCAAGCTGCTCTGAGGTCG	59.825	55.000	1.00	0.00	0.00	4.79
906	943	1.445238	GCTGCTCTGAGGTCGTCAC	60.445	63.158	6.83	0.00	0.00	3.67
907	944	1.872197	GCTGCTCTGAGGTCGTCACT	61.872	60.000	6.83	0.00	0.00	3.41
908	945	0.170116	CTGCTCTGAGGTCGTCACTC	59.830	60.000	6.83	0.00	35.55	3.51
909	946	0.537371	TGCTCTGAGGTCGTCACTCA	60.537	55.000	6.83	0.00	42.31	3.41
910	947	0.598562	GCTCTGAGGTCGTCACTCAA	59.401	55.000	6.83	0.91	43.74	3.02
911	948	1.402194	GCTCTGAGGTCGTCACTCAAG	60.402	57.143	6.83	8.57	43.74	3.02
912	949	1.883275	CTCTGAGGTCGTCACTCAAGT	59.117	52.381	0.00	0.00	43.74	3.16
914	951	2.812591	TCTGAGGTCGTCACTCAAGTAC	59.187	50.000	7.59	0.00	43.74	2.73
923	960	5.114721	GTCGTCACTCAAGTACGTAAGAAAC	59.885	44.000	0.00	0.00	43.62	2.78
994	1034	2.739292	GTACACACAGCGAGAAGTGAA	58.261	47.619	12.98	0.00	39.03	3.18
1006	1046	3.364366	CGAGAAGTGAACAAAGATGTGCC	60.364	47.826	0.00	0.00	40.46	5.01
1368	1445	1.219393	CTCAACTTCCCCTCCTCGC	59.781	63.158	0.00	0.00	0.00	5.03
1373	1450	4.649705	TTCCCCTCCTCGCCCACA	62.650	66.667	0.00	0.00	0.00	4.17
1374	1451	4.649705	TCCCCTCCTCGCCCACAA	62.650	66.667	0.00	0.00	0.00	3.33
1375	1452	4.410400	CCCCTCCTCGCCCACAAC	62.410	72.222	0.00	0.00	0.00	3.32
1376	1453	3.636231	CCCTCCTCGCCCACAACA	61.636	66.667	0.00	0.00	0.00	3.33
1517	1594	3.706373	GCCCTGCCGGACTTCTCA	61.706	66.667	5.05	0.00	0.00	3.27
1692	1769	3.612860	CGACCAACTGTTAGATCCTTTCG	59.387	47.826	0.00	0.00	0.00	3.46
1712	1789	1.083489	TGTTCGATGACCAATTCGGC	58.917	50.000	0.00	0.00	39.03	5.54
1812	1889	1.743252	CTCTGGAGCTTTGGCGACC	60.743	63.158	0.00	0.00	44.37	4.79
1864	1947	5.558307	CGTGCAAGTAGAGTAGTACTGTAC	58.442	45.833	23.60	23.60	43.09	2.90
1874	1957	7.949903	AGAGTAGTACTGTACTGTATCATCG	57.050	40.000	26.45	0.00	39.81	3.84
1880	1963	5.158101	ACTGTACTGTATCATCGAAGACG	57.842	43.478	3.21	0.00	42.51	4.18
1892	1975	2.286872	TCGAAGACGACAGGATAGGAC	58.713	52.381	0.00	0.00	43.81	3.85
1895	1978	2.810870	AGACGACAGGATAGGACACT	57.189	50.000	0.00	0.00	0.00	3.55
1896	1979	2.645802	AGACGACAGGATAGGACACTC	58.354	52.381	0.00	0.00	0.00	3.51
1897	1980	1.331138	GACGACAGGATAGGACACTCG	59.669	57.143	0.00	0.00	0.00	4.18
1898	1981	0.663688	CGACAGGATAGGACACTCGG	59.336	60.000	0.00	0.00	0.00	4.63
1899	1982	1.746171	CGACAGGATAGGACACTCGGA	60.746	57.143	0.00	0.00	0.00	4.55
1914	2049	2.631062	ACTCGGACACACCTTGTTGATA	59.369	45.455	0.00	0.00	39.17	2.15
1922	2057	5.491982	ACACACCTTGTTGATAATCTCTCC	58.508	41.667	0.00	0.00	33.09	3.71
1923	2058	4.878397	CACACCTTGTTGATAATCTCTCCC	59.122	45.833	0.00	0.00	0.00	4.30
1926	2061	5.130145	CACCTTGTTGATAATCTCTCCCTCT	59.870	44.000	0.00	0.00	0.00	3.69
1928	2063	6.903534	ACCTTGTTGATAATCTCTCCCTCTTA	59.096	38.462	0.00	0.00	0.00	2.10
1976	2111	4.201960	TGTTGATGCTGTAAAAACTTCGCA	60.202	37.500	0.00	0.00	0.00	5.10
1988	2123	3.603158	AACTTCGCAGTTTTGGGTTTT	57.397	38.095	0.00	0.00	40.66	2.43
1991	2126	3.132111	ACTTCGCAGTTTTGGGTTTTCAT	59.868	39.130	0.00	0.00	38.34	2.57
1992	2127	3.090952	TCGCAGTTTTGGGTTTTCATG	57.909	42.857	0.00	0.00	38.34	3.07
1993	2128	2.428890	TCGCAGTTTTGGGTTTTCATGT	59.571	40.909	0.00	0.00	38.34	3.21
1996	2131	3.245048	GCAGTTTTGGGTTTTCATGTTCG	59.755	43.478	0.00	0.00	0.00	3.95
1997	2132	4.677584	CAGTTTTGGGTTTTCATGTTCGA	58.322	39.130	0.00	0.00	0.00	3.71
1998	2133	4.502645	CAGTTTTGGGTTTTCATGTTCGAC	59.497	41.667	0.00	0.00	0.00	4.20
1999	2134	4.401202	AGTTTTGGGTTTTCATGTTCGACT	59.599	37.500	0.00	0.00	0.00	4.18
2004	2139	4.582656	TGGGTTTTCATGTTCGACTTCAAT	59.417	37.500	0.00	0.00	0.00	2.57
2005	2140	4.917415	GGGTTTTCATGTTCGACTTCAATG	59.083	41.667	0.00	0.00	0.00	2.82
2008	2275	6.577427	GGTTTTCATGTTCGACTTCAATGTAC	59.423	38.462	0.00	0.00	0.00	2.90
2028	2295	2.619646	ACTAAAACCGTTTCCGTGCAAT	59.380	40.909	0.00	0.00	0.00	3.56
2056	2327	1.681780	CCTGCCCGGTTGTGATTATGT	60.682	52.381	0.00	0.00	0.00	2.29
2057	2328	2.091541	CTGCCCGGTTGTGATTATGTT	58.908	47.619	0.00	0.00	0.00	2.71
2058	2329	2.088423	TGCCCGGTTGTGATTATGTTC	58.912	47.619	0.00	0.00	0.00	3.18
2059	2330	1.404035	GCCCGGTTGTGATTATGTTCC	59.596	52.381	0.00	0.00	0.00	3.62
2061	2332	1.668751	CCGGTTGTGATTATGTTCCCG	59.331	52.381	0.00	0.00	0.00	5.14
2062	2333	2.352388	CGGTTGTGATTATGTTCCCGT	58.648	47.619	0.00	0.00	0.00	5.28
2063	2334	2.095213	CGGTTGTGATTATGTTCCCGTG	59.905	50.000	0.00	0.00	0.00	4.94
2065	2336	4.255301	GGTTGTGATTATGTTCCCGTGTA	58.745	43.478	0.00	0.00	0.00	2.90
2103	2378	5.830912	TGTGTGCATTTCTTCCTACTTTTG	58.169	37.500	0.00	0.00	0.00	2.44
2115	2390	7.816640	TCTTCCTACTTTTGTATCAACAATGC	58.183	34.615	0.00	0.00	44.85	3.56
2419	2755	1.684386	CTTCTCCATCCGAGCAGCCT	61.684	60.000	0.00	0.00	38.62	4.58
2461	2798	0.836400	TTTGTCTTCCTCCTCCCGCT	60.836	55.000	0.00	0.00	0.00	5.52
2464	2801	0.973496	GTCTTCCTCCTCCCGCTTCT	60.973	60.000	0.00	0.00	0.00	2.85
2480	2817	1.203523	CTTCTGACGAACCCTCTCTGG	59.796	57.143	0.00	0.00	0.00	3.86
2482	2819	1.533033	TGACGAACCCTCTCTGGCA	60.533	57.895	0.00	0.00	0.00	4.92
2524	2861	2.221169	GCCACTTGTGACTGTCATCAA	58.779	47.619	14.37	16.79	0.00	2.57
2582	2919	1.889829	CCTAGTCATCCCTCTAAGCCG	59.110	57.143	0.00	0.00	0.00	5.52
2608	2945	0.539051	CTTCTCCGGCTCTGGTGAAT	59.461	55.000	11.35	0.00	39.87	2.57
2619	2956	2.746362	CTCTGGTGAATCCTTTGCACTC	59.254	50.000	0.00	0.00	37.07	3.51
2709	3046	2.650116	ATGTTCTGGCTCGGCTCGT	61.650	57.895	0.00	0.00	0.00	4.18
2712	3049	2.867855	TTCTGGCTCGGCTCGTTGT	61.868	57.895	0.00	0.00	0.00	3.32
2719	3056	1.324736	GCTCGGCTCGTTGTTAATGAG	59.675	52.381	6.45	6.45	45.34	2.90
2746	3083	8.760980	TTTCTCAATTTTAGAAAGGTCCTCAA	57.239	30.769	8.14	0.00	37.89	3.02
2831	3169	3.119029	CCTCGGATCATGCATTGGTTTTT	60.119	43.478	0.00	0.00	0.00	1.94
2845	3183	6.019559	GCATTGGTTTTTCAGACTCTGTTTTC	60.020	38.462	5.94	0.00	32.61	2.29

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
64	65	2.440796	CGAAGCCACCCATGCCAT	60.441	61.111	0.00	0.00	0.00	4.40
272	275	1.234615	CCGACGGTGTTGGCAAGATT	61.235	55.000	5.48	0.00	29.56	2.40
335	338	1.884926	CTTCCGCCTCCGAAGATGC	60.885	63.158	0.00	0.00	36.29	3.91
371	374	1.325355	TCGTCTTCGTCCTTGTCCTT	58.675	50.000	0.00	0.00	38.33	3.36
374	377	2.251893	GTCATCGTCTTCGTCCTTGTC	58.748	52.381	0.00	0.00	38.33	3.18
376	379	1.135774	TCGTCATCGTCTTCGTCCTTG	60.136	52.381	0.00	0.00	38.33	3.61
377	380	1.130749	CTCGTCATCGTCTTCGTCCTT	59.869	52.381	0.00	0.00	38.33	3.36
391	406	3.961480	AAGACACATCAATCCTCGTCA	57.039	42.857	0.00	0.00	0.00	4.35
451	466	1.475280	CATGCCCACAAGTTCATCCAG	59.525	52.381	0.00	0.00	0.00	3.86
571	587	3.871485	TGCATAAATGGCATTTTGGACC	58.129	40.909	28.56	14.02	36.11	4.46
586	602	3.215568	CGCCGGGGCATTGCATAA	61.216	61.111	11.39	0.00	42.06	1.90
709	740	0.533308	AAACTAGTTTGCCGCGTGGA	60.533	50.000	21.76	0.35	37.49	4.02
710	741	0.309612	AAAACTAGTTTGCCGCGTGG	59.690	50.000	21.22	11.67	38.77	4.94
712	743	2.350102	GCTAAAAACTAGTTTGCCGCGT	60.350	45.455	21.22	1.86	32.36	6.01
760	792	2.174363	TCATGGCGGATAAGAGCATG	57.826	50.000	0.00	0.00	34.54	4.06
876	913	2.039480	TCAGAGCAGCTTGATCAAGGTT	59.961	45.455	32.13	21.59	45.80	3.50
893	930	1.982660	ACTTGAGTGACGACCTCAGA	58.017	50.000	0.00	0.00	39.91	3.27
902	939	5.401674	CCTGTTTCTTACGTACTTGAGTGAC	59.598	44.000	0.00	0.00	0.00	3.67
906	943	4.879598	ACCCTGTTTCTTACGTACTTGAG	58.120	43.478	0.00	0.00	0.00	3.02
907	944	4.942761	ACCCTGTTTCTTACGTACTTGA	57.057	40.909	0.00	0.00	0.00	3.02
908	945	4.624452	GCTACCCTGTTTCTTACGTACTTG	59.376	45.833	0.00	0.00	0.00	3.16
909	946	4.616835	CGCTACCCTGTTTCTTACGTACTT	60.617	45.833	0.00	0.00	0.00	2.24
910	947	3.119708	CGCTACCCTGTTTCTTACGTACT	60.120	47.826	0.00	0.00	0.00	2.73
911	948	3.119849	TCGCTACCCTGTTTCTTACGTAC	60.120	47.826	0.00	0.00	0.00	3.67
912	949	3.081061	TCGCTACCCTGTTTCTTACGTA	58.919	45.455	0.00	0.00	0.00	3.57
914	951	2.257034	GTCGCTACCCTGTTTCTTACG	58.743	52.381	0.00	0.00	0.00	3.18
923	960	2.490217	CTGTCGGTCGCTACCCTG	59.510	66.667	1.10	0.00	43.54	4.45
948	985	0.459585	AAGGTATACGTGCCTGCGTG	60.460	55.000	0.00	0.00	45.33	5.34
994	1034	2.281484	ACCGCGGCACATCTTTGT	60.281	55.556	28.58	0.00	36.15	2.83
1092	1132	2.493907	AAGCAGCCTCGAAGTCGTCC	62.494	60.000	0.00	0.00	40.80	4.79
1187	1264	4.814294	CGGACGCCCCTGTACTGC	62.814	72.222	0.00	0.00	0.00	4.40
1263	1340	2.347490	GAAGGTGCCGAGCCAGAA	59.653	61.111	0.00	0.00	0.00	3.02
1368	1445	3.977244	GGGTGCGCTTGTTGTGGG	61.977	66.667	9.73	0.00	0.00	4.61
1373	1450	3.119193	CACTTGGGTGCGCTTGTT	58.881	55.556	9.73	0.00	36.61	2.83
1394	1471	2.431260	GTCGGTTTCGCGGCTACA	60.431	61.111	6.13	0.00	36.13	2.74
1586	1663	2.878429	CCCAGGTCGACGACAGAG	59.122	66.667	27.77	16.44	33.68	3.35
1589	1666	3.680786	CTGCCCAGGTCGACGACA	61.681	66.667	27.77	6.85	33.68	4.35
1671	1748	4.389077	CACGAAAGGATCTAACAGTTGGTC	59.611	45.833	0.00	0.00	0.00	4.02
1692	1769	1.202031	GCCGAATTGGTCATCGAACAC	60.202	52.381	0.00	0.00	41.43	3.32
1712	1789	0.320247	ACGAGCTGCTGTCCAAGAAG	60.320	55.000	7.01	0.00	34.10	2.85
1812	1889	1.226802	CCTCGGCGAGACAGTCATG	60.227	63.158	36.47	14.39	0.00	3.07
1874	1957	3.018149	AGTGTCCTATCCTGTCGTCTTC	58.982	50.000	0.00	0.00	0.00	2.87
1880	1963	1.677052	GTCCGAGTGTCCTATCCTGTC	59.323	57.143	0.00	0.00	0.00	3.51
1892	1975	0.937304	CAACAAGGTGTGTCCGAGTG	59.063	55.000	0.00	0.00	40.60	3.51
1895	1978	3.755112	TTATCAACAAGGTGTGTCCGA	57.245	42.857	0.00	0.00	40.60	4.55
1896	1979	4.253685	AGATTATCAACAAGGTGTGTCCG	58.746	43.478	0.00	0.00	40.60	4.79
1897	1980	5.491982	AGAGATTATCAACAAGGTGTGTCC	58.508	41.667	0.00	0.00	40.60	4.02
1898	1981	5.582665	GGAGAGATTATCAACAAGGTGTGTC	59.417	44.000	0.00	0.00	40.60	3.67
1899	1982	5.491982	GGAGAGATTATCAACAAGGTGTGT	58.508	41.667	0.00	0.00	44.64	3.72
1961	2096	4.502645	CCCAAAACTGCGAAGTTTTTACAG	59.497	41.667	28.11	17.84	46.15	2.74
1976	2111	4.401202	AGTCGAACATGAAAACCCAAAACT	59.599	37.500	0.00	0.00	0.00	2.66
1985	2120	7.490962	AGTACATTGAAGTCGAACATGAAAA	57.509	32.000	0.00	0.00	0.00	2.29
1988	2123	8.492748	GTTTTAGTACATTGAAGTCGAACATGA	58.507	33.333	0.00	0.00	0.00	3.07
1991	2126	6.074195	CGGTTTTAGTACATTGAAGTCGAACA	60.074	38.462	0.00	0.00	0.00	3.18
1992	2127	6.074142	ACGGTTTTAGTACATTGAAGTCGAAC	60.074	38.462	0.00	0.00	0.00	3.95
1993	2128	5.984926	ACGGTTTTAGTACATTGAAGTCGAA	59.015	36.000	0.00	0.00	0.00	3.71
1996	2131	7.073883	GGAAACGGTTTTAGTACATTGAAGTC	58.926	38.462	7.65	0.00	0.00	3.01
1997	2132	6.962686	GGAAACGGTTTTAGTACATTGAAGT	58.037	36.000	7.65	0.00	0.00	3.01
2044	2315	6.759827	AGTATACACGGGAACATAATCACAAC	59.240	38.462	5.50	0.00	0.00	3.32
2056	2327	5.452255	AGGAGTATCAAGTATACACGGGAA	58.548	41.667	5.50	0.00	42.63	3.97
2057	2328	5.057843	AGGAGTATCAAGTATACACGGGA	57.942	43.478	5.50	0.00	42.63	5.14
2058	2329	5.068723	ACAAGGAGTATCAAGTATACACGGG	59.931	44.000	5.50	0.00	42.63	5.28
2059	2330	5.977725	CACAAGGAGTATCAAGTATACACGG	59.022	44.000	5.50	0.00	42.63	4.94
2061	2332	6.255887	GCACACAAGGAGTATCAAGTATACAC	59.744	42.308	5.50	0.00	42.63	2.90
2062	2333	6.071051	TGCACACAAGGAGTATCAAGTATACA	60.071	38.462	5.50	0.00	42.63	2.29
2063	2334	6.338146	TGCACACAAGGAGTATCAAGTATAC	58.662	40.000	0.00	0.00	40.80	1.47
2065	2336	5.420725	TGCACACAAGGAGTATCAAGTAT	57.579	39.130	0.00	0.00	36.25	2.12
2103	2378	3.691118	TCAAGAGCAGGCATTGTTGATAC	59.309	43.478	8.46	0.00	0.00	2.24
2115	2390	7.772332	ATTTAGTTTACGTATCAAGAGCAGG	57.228	36.000	0.00	0.00	0.00	4.85
2461	2798	1.257743	CCAGAGAGGGTTCGTCAGAA	58.742	55.000	0.00	0.00	0.00	3.02
2464	2801	1.533033	TGCCAGAGAGGGTTCGTCA	60.533	57.895	0.00	0.00	38.09	4.35
2482	2819	3.575351	GACAGGTGCTTCGCTCGGT	62.575	63.158	0.00	0.00	0.00	4.69
2582	2919	0.968393	AGAGCCGGAGAAGAGGACAC	60.968	60.000	5.05	0.00	0.00	3.67
2608	2945	0.106918	ACGGGTTTGAGTGCAAAGGA	60.107	50.000	0.00	0.00	44.12	3.36
2619	2956	2.148768	GTAAGGAGGTTGACGGGTTTG	58.851	52.381	0.00	0.00	0.00	2.93
2732	3069	9.667107	CACAGTAAATATTTGAGGACCTTTCTA	57.333	33.333	11.05	0.00	0.00	2.10
2736	3073	8.706322	AAACACAGTAAATATTTGAGGACCTT	57.294	30.769	11.05	0.00	0.00	3.50
2749	3086	9.921637	TGAAAACAAGAAGAAAACACAGTAAAT	57.078	25.926	0.00	0.00	0.00	1.40

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.