AutoCloner

Multiple sequence alignment - TraesCS7D01G258500

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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	TraesCS7D01G258500	chr7D	100.000	2741	0	0	1	2741	234344495	234347235	0.000000e+00	5062.0
1	TraesCS7D01G258500	chr7D	93.141	729	21	7	1042	1754	219714004	219714719	0.000000e+00	1042.0
2	TraesCS7D01G258500	chr7D	88.136	59	5	2	1459	1516	176160835	176160892	4.900000e-08	69.4
3	TraesCS7D01G258500	chr3D	98.294	1993	20	4	1	1983	456653873	456655861	0.000000e+00	3480.0
4	TraesCS7D01G258500	chr7B	94.809	732	22	6	1042	1757	180030029	180029298	0.000000e+00	1127.0
5	TraesCS7D01G258500	chr7B	87.193	367	18	6	2176	2515	206335869	206336233	9.200000e-105	390.0
6	TraesCS7D01G258500	chr7B	88.947	190	19	2	9	197	541714568	541714380	1.640000e-57	233.0
7	TraesCS7D01G258500	chr7B	85.377	212	18	6	1	200	541711651	541711861	9.950000e-50	207.0
8	TraesCS7D01G258500	chr7B	93.525	139	5	1	1984	2118	206334465	206334603	1.290000e-48	204.0
9	TraesCS7D01G258500	chr7B	80.717	223	18	14	1784	1983	541711861	541711641	1.700000e-32	150.0
10	TraesCS7D01G258500	chr7B	96.970	33	1	0	2141	2173	206334603	206334635	3.810000e-04	56.5
11	TraesCS7D01G258500	chr7A	94.239	729	26	6	1042	1754	232282935	232283663	0.000000e+00	1099.0
12	TraesCS7D01G258500	chr7A	84.848	462	21	14	2244	2669	247249518	247249966	1.170000e-113	420.0
13	TraesCS7D01G258500	chr7A	86.207	261	10	3	1984	2244	247248717	247248951	2.710000e-65	259.0
14	TraesCS7D01G258500	chr4A	91.162	792	52	13	264	1043	32462768	32461983	0.000000e+00	1059.0
15	TraesCS7D01G258500	chr4A	100.000	29	0	0	2710	2738	669858480	669858508	1.000000e-03	54.7
16	TraesCS7D01G258500	chr4B	90.886	790	37	18	264	1043	529298167	529297403	0.000000e+00	1027.0
17	TraesCS7D01G258500	chr4B	80.769	182	21	10	1784	1952	81012321	81012141	2.220000e-26	130.0
18	TraesCS7D01G258500	chr4D	90.849	754	35	16	258	1002	430794547	430793819	0.000000e+00	979.0
19	TraesCS7D01G258500	chr4D	82.297	209	26	3	1	198	487461422	487461630	1.310000e-38	171.0
20	TraesCS7D01G258500	chrUn	100.000	399	0	0	929	1327	478826297	478826695	0.000000e+00	737.0
21	TraesCS7D01G258500	chr6B	76.167	600	109	18	1106	1679	548627857	548627266	4.470000e-73	285.0
22	TraesCS7D01G258500	chr6A	76.014	592	108	16	1114	1679	504891860	504891277	2.690000e-70	276.0
23	TraesCS7D01G258500	chr6D	75.793	599	113	15	1106	1679	363870222	363869631	9.670000e-70	274.0
24	TraesCS7D01G258500	chr2B	89.000	200	22	0	1	200	739568206	739568405	5.860000e-62	248.0
25	TraesCS7D01G258500	chr2B	80.122	327	41	17	266	585	659064557	659064866	3.550000e-54	222.0
26	TraesCS7D01G258500	chr2B	81.604	212	28	4	621	831	659064873	659065074	6.070000e-37	165.0
27	TraesCS7D01G258500	chr2D	81.288	326	37	18	267	585	553330520	553330828	2.730000e-60	243.0
28	TraesCS7D01G258500	chr2D	83.511	188	20	1	48	224	187467840	187468027	6.070000e-37	165.0
29	TraesCS7D01G258500	chr2D	82.090	201	25	5	621	820	553330835	553331025	7.860000e-36	161.0
30	TraesCS7D01G258500	chr5B	88.442	199	19	4	1	197	7374	7178	1.270000e-58	237.0
31	TraesCS7D01G258500	chr5D	75.781	512	93	18	1133	1624	370120298	370120798	2.120000e-56	230.0
32	TraesCS7D01G258500	chr5D	86.869	198	26	0	1	198	483373632	483373829	3.550000e-54	222.0
33	TraesCS7D01G258500	chr5D	82.915	199	33	1	1	198	458767386	458767584	7.800000e-41	178.0
34	TraesCS7D01G258500	chr5D	96.875	32	1	0	2710	2741	557800303	557800272	1.000000e-03	54.7
35	TraesCS7D01G258500	chr2A	89.474	152	16	0	1	152	14416061	14415910	2.790000e-45	193.0
36	TraesCS7D01G258500	chr5A	100.000	32	0	0	2710	2741	621010561	621010530	2.950000e-05	60.2

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	TraesCS7D01G258500	chr7D	234344495	234347235	2740	False	5062.000000	5062	100.000000	1	2741	1	chr7D.!!$F3	2740
1	TraesCS7D01G258500	chr7D	219714004	219714719	715	False	1042.000000	1042	93.141000	1042	1754	1	chr7D.!!$F2	712
2	TraesCS7D01G258500	chr3D	456653873	456655861	1988	False	3480.000000	3480	98.294000	1	1983	1	chr3D.!!$F1	1982
3	TraesCS7D01G258500	chr7B	180029298	180030029	731	True	1127.000000	1127	94.809000	1042	1757	1	chr7B.!!$R1	715
4	TraesCS7D01G258500	chr7B	206334465	206336233	1768	False	216.833333	390	92.562667	1984	2515	3	chr7B.!!$F2	531
5	TraesCS7D01G258500	chr7A	232282935	232283663	728	False	1099.000000	1099	94.239000	1042	1754	1	chr7A.!!$F1	712
6	TraesCS7D01G258500	chr7A	247248717	247249966	1249	False	339.500000	420	85.527500	1984	2669	2	chr7A.!!$F2	685
7	TraesCS7D01G258500	chr4A	32461983	32462768	785	True	1059.000000	1059	91.162000	264	1043	1	chr4A.!!$R1	779
8	TraesCS7D01G258500	chr4B	529297403	529298167	764	True	1027.000000	1027	90.886000	264	1043	1	chr4B.!!$R2	779
9	TraesCS7D01G258500	chr4D	430793819	430794547	728	True	979.000000	979	90.849000	258	1002	1	chr4D.!!$R1	744
10	TraesCS7D01G258500	chr6B	548627266	548627857	591	True	285.000000	285	76.167000	1106	1679	1	chr6B.!!$R1	573
11	TraesCS7D01G258500	chr6A	504891277	504891860	583	True	276.000000	276	76.014000	1114	1679	1	chr6A.!!$R1	565
12	TraesCS7D01G258500	chr6D	363869631	363870222	591	True	274.000000	274	75.793000	1106	1679	1	chr6D.!!$R1	573
13	TraesCS7D01G258500	chr2D	553330520	553331025	505	False	202.000000	243	81.689000	267	820	2	chr2D.!!$F2	553
14	TraesCS7D01G258500	chr5D	370120298	370120798	500	False	230.000000	230	75.781000	1133	1624	1	chr5D.!!$F1	491

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
96	97	0.463654	AACTTCCAGCACACGAGCAA	60.464	50.0	0.0	0.0	36.85	3.91	F
97	98	0.882042	ACTTCCAGCACACGAGCAAG	60.882	55.0	0.0	0.0	36.85	4.01	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1327	1356	1.305802	ACTCGGGGGTGATGTAGCA	60.306	57.895	0.00	0.0	0.00	3.49	R
1842	1899	2.073232	AGCCAAGTGGATGAGCTGT	58.927	52.632	0.18	0.0	37.39	4.40	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
58	59	8.466617	TGGTTTAGTCCTTATACTTGCAAAAA	57.533	30.769	0.00	0.00	0.00	1.94
66	67	7.492344	GTCCTTATACTTGCAAAAATGGATTGG	59.508	37.037	0.00	0.00	0.00	3.16
67	68	7.398618	TCCTTATACTTGCAAAAATGGATTGGA	59.601	33.333	0.00	0.47	0.00	3.53
82	83	3.753797	GGATTGGACAGTCCTTGAACTTC	59.246	47.826	20.82	6.75	37.46	3.01
94	95	0.880278	TGAACTTCCAGCACACGAGC	60.880	55.000	0.00	0.00	0.00	5.03
95	96	0.880278	GAACTTCCAGCACACGAGCA	60.880	55.000	0.00	0.00	36.85	4.26
96	97	0.463654	AACTTCCAGCACACGAGCAA	60.464	50.000	0.00	0.00	36.85	3.91
97	98	0.882042	ACTTCCAGCACACGAGCAAG	60.882	55.000	0.00	0.00	36.85	4.01
180	181	3.911894	ACACTTAGGCCCCTACTGTTTTA	59.088	43.478	0.00	0.00	0.00	1.52
1842	1899	1.371512	CAAAATGTGCCGCGCTGAA	60.372	52.632	5.56	0.00	0.00	3.02
1844	1901	2.069465	AAAATGTGCCGCGCTGAACA	62.069	50.000	15.50	15.50	0.00	3.18
1864	1921	1.035932	GCTCATCCACTTGGCTGCAT	61.036	55.000	0.50	0.00	31.68	3.96
1994	2061	5.816258	GTGCTATTACCTCCTTAACCAACTC	59.184	44.000	0.00	0.00	0.00	3.01
2052	2123	1.071542	TGCACTGCACTAAGGCACTAA	59.928	47.619	0.00	0.00	39.25	2.24
2117	2188	1.060308	CGTATTCGCGCCCAAACAG	59.940	57.895	0.00	0.00	0.00	3.16
2118	2189	1.355796	CGTATTCGCGCCCAAACAGA	61.356	55.000	0.00	0.00	0.00	3.41
2119	2190	0.373716	GTATTCGCGCCCAAACAGAG	59.626	55.000	0.00	0.00	0.00	3.35
2120	2191	1.366111	TATTCGCGCCCAAACAGAGC	61.366	55.000	0.00	0.00	0.00	4.09
2124	2195	4.659172	CGCCCAAACAGAGCCCCA	62.659	66.667	0.00	0.00	0.00	4.96
2125	2196	2.203625	GCCCAAACAGAGCCCCAA	60.204	61.111	0.00	0.00	0.00	4.12
2126	2197	2.574018	GCCCAAACAGAGCCCCAAC	61.574	63.158	0.00	0.00	0.00	3.77
2127	2198	1.908299	CCCAAACAGAGCCCCAACC	60.908	63.158	0.00	0.00	0.00	3.77
2128	2199	1.908299	CCAAACAGAGCCCCAACCC	60.908	63.158	0.00	0.00	0.00	4.11
2129	2200	1.908299	CAAACAGAGCCCCAACCCC	60.908	63.158	0.00	0.00	0.00	4.95
2130	2201	2.399607	AAACAGAGCCCCAACCCCA	61.400	57.895	0.00	0.00	0.00	4.96
2131	2202	2.371897	AAACAGAGCCCCAACCCCAG	62.372	60.000	0.00	0.00	0.00	4.45
2132	2203	4.748144	CAGAGCCCCAACCCCAGC	62.748	72.222	0.00	0.00	0.00	4.85
2137	2208	4.820744	CCCCAACCCCAGCCGATG	62.821	72.222	0.00	0.00	0.00	3.84
2182	3484	2.504367	AGACGGTTGCTGCTAACAAAT	58.496	42.857	13.95	2.65	32.22	2.32
2226	3528	2.579201	CGTCCGGCTCCATCAACT	59.421	61.111	0.00	0.00	0.00	3.16
2489	4388	2.489971	GGATCACCCGCGATTAATGAA	58.510	47.619	8.23	0.00	0.00	2.57
2502	4401	4.608951	GATTAATGAACGCTCGTCCTACT	58.391	43.478	0.00	0.00	0.00	2.57
2503	4402	5.559608	CGATTAATGAACGCTCGTCCTACTA	60.560	44.000	0.00	0.00	0.00	1.82
2504	4403	3.417690	AATGAACGCTCGTCCTACTAC	57.582	47.619	0.00	0.00	0.00	2.73
2511	4410	2.479656	CGCTCGTCCTACTACATCTACC	59.520	54.545	0.00	0.00	0.00	3.18
2520	4419	5.241064	TCCTACTACATCTACCGCTCAATTC	59.759	44.000	0.00	0.00	0.00	2.17
2525	4424	1.471119	TCTACCGCTCAATTCCGAGT	58.529	50.000	0.00	0.00	35.33	4.18
2531	4430	3.114065	CCGCTCAATTCCGAGTAAGTAC	58.886	50.000	0.00	0.00	35.33	2.73
2535	4434	5.220815	CGCTCAATTCCGAGTAAGTACTAGT	60.221	44.000	0.00	0.00	36.50	2.57
2537	4436	7.131565	GCTCAATTCCGAGTAAGTACTAGTAC	58.868	42.308	23.03	23.03	36.50	2.73
2538	4437	7.201679	GCTCAATTCCGAGTAAGTACTAGTACA	60.202	40.741	29.87	11.74	36.50	2.90
2546	4447	9.852091	CCGAGTAAGTACTAGTACAAATTCTTT	57.148	33.333	29.87	17.70	38.48	2.52
2630	4535	3.187227	ACACTCTAAAAATGCGCTGACAG	59.813	43.478	9.73	0.00	0.00	3.51
2631	4536	2.160417	ACTCTAAAAATGCGCTGACAGC	59.840	45.455	17.84	17.84	38.02	4.40
2632	4537	1.468520	TCTAAAAATGCGCTGACAGCC	59.531	47.619	21.55	14.34	38.18	4.85
2633	4538	1.470098	CTAAAAATGCGCTGACAGCCT	59.530	47.619	21.55	3.98	38.18	4.58
2634	4539	0.038892	AAAAATGCGCTGACAGCCTG	60.039	50.000	21.55	9.79	38.18	4.85
2635	4540	0.890542	AAAATGCGCTGACAGCCTGA	60.891	50.000	21.55	6.03	38.18	3.86
2636	4541	1.580845	AAATGCGCTGACAGCCTGAC	61.581	55.000	21.55	9.34	38.18	3.51
2637	4542	2.736579	AATGCGCTGACAGCCTGACA	62.737	55.000	21.55	14.44	38.18	3.58
2660	4565	2.273557	TCATGACATCGTGCATCACTG	58.726	47.619	0.00	0.00	33.05	3.66
2669	4574	2.680339	TCGTGCATCACTGAACAAACAA	59.320	40.909	0.00	0.00	29.14	2.83
2670	4575	3.127721	TCGTGCATCACTGAACAAACAAA	59.872	39.130	0.00	0.00	29.14	2.83
2671	4576	3.856521	CGTGCATCACTGAACAAACAAAA	59.143	39.130	0.00	0.00	29.14	2.44
2672	4577	4.503734	CGTGCATCACTGAACAAACAAAAT	59.496	37.500	0.00	0.00	29.14	1.82
2673	4578	5.685068	CGTGCATCACTGAACAAACAAAATA	59.315	36.000	0.00	0.00	29.14	1.40
2674	4579	6.363088	CGTGCATCACTGAACAAACAAAATAT	59.637	34.615	0.00	0.00	29.14	1.28
2675	4580	7.503991	GTGCATCACTGAACAAACAAAATATG	58.496	34.615	0.00	0.00	30.42	1.78
2676	4581	7.381948	GTGCATCACTGAACAAACAAAATATGA	59.618	33.333	0.00	0.00	30.42	2.15
2677	4582	7.924947	TGCATCACTGAACAAACAAAATATGAA	59.075	29.630	0.00	0.00	0.00	2.57
2678	4583	8.928733	GCATCACTGAACAAACAAAATATGAAT	58.071	29.630	0.00	0.00	0.00	2.57
2692	4597	9.479549	ACAAAATATGAATATGAAAGGGTCTGT	57.520	29.630	0.00	0.00	0.00	3.41
2693	4598	9.956720	CAAAATATGAATATGAAAGGGTCTGTC	57.043	33.333	0.00	0.00	0.00	3.51
2694	4599	9.927081	AAAATATGAATATGAAAGGGTCTGTCT	57.073	29.630	0.00	0.00	0.00	3.41
2697	4602	6.485830	TGAATATGAAAGGGTCTGTCTAGG	57.514	41.667	0.00	0.00	0.00	3.02
2698	4603	6.202331	TGAATATGAAAGGGTCTGTCTAGGA	58.798	40.000	0.00	0.00	0.00	2.94
2699	4604	6.098409	TGAATATGAAAGGGTCTGTCTAGGAC	59.902	42.308	0.00	0.00	0.00	3.85
2700	4605	3.254093	TGAAAGGGTCTGTCTAGGACA	57.746	47.619	0.43	0.43	40.50	4.02
2701	4606	2.897969	TGAAAGGGTCTGTCTAGGACAC	59.102	50.000	0.00	0.00	37.67	3.67
2702	4607	2.696526	AAGGGTCTGTCTAGGACACA	57.303	50.000	3.18	0.00	39.36	3.72
2703	4608	2.930109	AGGGTCTGTCTAGGACACAT	57.070	50.000	3.18	0.00	39.36	3.21
2704	4609	2.741145	AGGGTCTGTCTAGGACACATC	58.259	52.381	3.18	0.00	39.36	3.06
2705	4610	2.313342	AGGGTCTGTCTAGGACACATCT	59.687	50.000	3.18	0.00	39.36	2.90
2706	4611	3.528078	AGGGTCTGTCTAGGACACATCTA	59.472	47.826	3.18	0.00	39.36	1.98
2707	4612	4.017407	AGGGTCTGTCTAGGACACATCTAA	60.017	45.833	3.18	0.00	39.36	2.10
2708	4613	4.098196	GGGTCTGTCTAGGACACATCTAAC	59.902	50.000	0.00	0.00	37.67	2.34
2709	4614	4.951094	GGTCTGTCTAGGACACATCTAACT	59.049	45.833	0.00	0.00	37.67	2.24
2710	4615	6.120905	GGTCTGTCTAGGACACATCTAACTA	58.879	44.000	0.00	0.00	37.67	2.24
2711	4616	6.773685	GGTCTGTCTAGGACACATCTAACTAT	59.226	42.308	0.00	0.00	37.67	2.12
2712	4617	7.255312	GGTCTGTCTAGGACACATCTAACTATG	60.255	44.444	0.00	0.00	37.67	2.23
2713	4618	7.283580	GTCTGTCTAGGACACATCTAACTATGT	59.716	40.741	0.00	0.00	40.75	2.29
2714	4619	7.499563	TCTGTCTAGGACACATCTAACTATGTC	59.500	40.741	0.00	0.00	38.01	3.06
2715	4620	7.116736	TGTCTAGGACACATCTAACTATGTCA	58.883	38.462	5.66	0.00	42.66	3.58
2716	4621	7.780271	TGTCTAGGACACATCTAACTATGTCAT	59.220	37.037	5.66	1.00	42.66	3.06
2717	4622	9.286170	GTCTAGGACACATCTAACTATGTCATA	57.714	37.037	5.66	2.11	42.66	2.15
2720	4625	8.948401	AGGACACATCTAACTATGTCATATCT	57.052	34.615	5.66	0.00	42.66	1.98
2732	4637	7.835822	ACTATGTCATATCTAAGCTGATGTCC	58.164	38.462	0.00	0.00	0.00	4.02
2733	4638	6.676990	ATGTCATATCTAAGCTGATGTCCA	57.323	37.500	0.00	0.00	0.00	4.02
2734	4639	5.847304	TGTCATATCTAAGCTGATGTCCAC	58.153	41.667	0.00	0.00	0.00	4.02
2735	4640	5.600069	TGTCATATCTAAGCTGATGTCCACT	59.400	40.000	0.00	0.00	0.00	4.00
2736	4641	6.155827	GTCATATCTAAGCTGATGTCCACTC	58.844	44.000	0.00	0.00	0.00	3.51
2737	4642	6.015519	GTCATATCTAAGCTGATGTCCACTCT	60.016	42.308	0.00	0.00	0.00	3.24
2738	4643	4.669206	ATCTAAGCTGATGTCCACTCTG	57.331	45.455	0.00	0.00	0.00	3.35
2739	4644	3.435275	TCTAAGCTGATGTCCACTCTGT	58.565	45.455	0.00	0.00	0.00	3.41
2740	4645	3.834813	TCTAAGCTGATGTCCACTCTGTT	59.165	43.478	0.00	0.00	0.00	3.16

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
14	15	3.879295	ACCATCACATGCTATGCAAGTAC	59.121	43.478	0.00	0.00	43.62	2.73
25	26	6.992715	AGTATAAGGACTAAACCATCACATGC	59.007	38.462	0.00	0.00	0.00	4.06
58	59	3.331889	AGTTCAAGGACTGTCCAATCCAT	59.668	43.478	27.48	7.58	39.61	3.41
66	67	2.147150	GCTGGAAGTTCAAGGACTGTC	58.853	52.381	9.38	0.00	35.30	3.51
67	68	1.490490	TGCTGGAAGTTCAAGGACTGT	59.510	47.619	9.38	0.00	35.30	3.55
82	83	1.195448	CTAAACTTGCTCGTGTGCTGG	59.805	52.381	0.00	0.00	0.00	4.85
94	95	5.163854	CGTGATTGGCTTAGGACTAAACTTG	60.164	44.000	0.00	0.00	0.00	3.16
95	96	4.935808	CGTGATTGGCTTAGGACTAAACTT	59.064	41.667	0.00	0.00	0.00	2.66
96	97	4.020485	ACGTGATTGGCTTAGGACTAAACT	60.020	41.667	0.00	0.00	0.00	2.66
97	98	4.092968	CACGTGATTGGCTTAGGACTAAAC	59.907	45.833	10.90	0.00	0.00	2.01
180	181	1.033574	GCACTGCGGGTAGATAGAGT	58.966	55.000	0.00	0.00	0.00	3.24
713	735	2.035442	GCGAACTCCTTCAGCACCC	61.035	63.158	0.00	0.00	0.00	4.61
1327	1356	1.305802	ACTCGGGGGTGATGTAGCA	60.306	57.895	0.00	0.00	0.00	3.49
1842	1899	2.073232	AGCCAAGTGGATGAGCTGT	58.927	52.632	0.18	0.00	37.39	4.40
1864	1921	4.684724	AGTTTAGTCCTGGTCCTATCACA	58.315	43.478	0.00	0.00	0.00	3.58
1937	1995	7.567250	TCCCTGTACTTATGATGATTTAGTCCA	59.433	37.037	0.00	0.00	0.00	4.02
1994	2061	4.760715	GGTCTGATCTGATCCATTCCATTG	59.239	45.833	14.71	0.00	0.00	2.82
2120	2191	4.820744	CATCGGCTGGGGTTGGGG	62.821	72.222	0.00	0.00	0.00	4.96
2121	2192	4.820744	CCATCGGCTGGGGTTGGG	62.821	72.222	0.00	0.00	41.82	4.12
2129	2200	0.391528	TCACATCACACCATCGGCTG	60.392	55.000	0.00	0.00	0.00	4.85
2130	2201	0.543277	ATCACATCACACCATCGGCT	59.457	50.000	0.00	0.00	0.00	5.52
2131	2202	0.659427	CATCACATCACACCATCGGC	59.341	55.000	0.00	0.00	0.00	5.54
2132	2203	2.159057	TCTCATCACATCACACCATCGG	60.159	50.000	0.00	0.00	0.00	4.18
2133	2204	2.862536	GTCTCATCACATCACACCATCG	59.137	50.000	0.00	0.00	0.00	3.84
2134	2205	2.862536	CGTCTCATCACATCACACCATC	59.137	50.000	0.00	0.00	0.00	3.51
2135	2206	2.897436	CGTCTCATCACATCACACCAT	58.103	47.619	0.00	0.00	0.00	3.55
2136	2207	1.672737	GCGTCTCATCACATCACACCA	60.673	52.381	0.00	0.00	0.00	4.17
2137	2208	1.002366	GCGTCTCATCACATCACACC	58.998	55.000	0.00	0.00	0.00	4.16
2138	2209	1.657594	CAGCGTCTCATCACATCACAC	59.342	52.381	0.00	0.00	0.00	3.82
2139	2210	1.404583	CCAGCGTCTCATCACATCACA	60.405	52.381	0.00	0.00	0.00	3.58
2226	3528	0.036483	TCGCTCACATGGCAAAGCTA	60.036	50.000	0.00	0.54	32.55	3.32
2412	4310	1.238625	TGAAACGGACGGAATTGCCC	61.239	55.000	0.00	0.00	0.00	5.36
2489	4388	2.328819	AGATGTAGTAGGACGAGCGT	57.671	50.000	0.00	0.00	0.00	5.07
2502	4401	2.953648	TCGGAATTGAGCGGTAGATGTA	59.046	45.455	0.00	0.00	0.00	2.29
2503	4402	1.754803	TCGGAATTGAGCGGTAGATGT	59.245	47.619	0.00	0.00	0.00	3.06
2504	4403	2.223829	ACTCGGAATTGAGCGGTAGATG	60.224	50.000	0.00	0.00	39.68	2.90
2511	4410	4.030134	AGTACTTACTCGGAATTGAGCG	57.970	45.455	0.00	0.00	39.68	5.03
2520	4419	9.852091	AAAGAATTTGTACTAGTACTTACTCGG	57.148	33.333	28.56	0.00	36.60	4.63
2553	4454	5.745294	GCGATAATCGTACAAAACTGTCCTA	59.255	40.000	0.00	0.00	42.81	2.94
2567	4468	0.313043	ATTCGGTCCGCGATAATCGT	59.687	50.000	8.23	0.00	42.81	3.73
2575	4476	3.564027	GCCTCAATTCGGTCCGCG	61.564	66.667	6.34	0.00	0.00	6.46
2630	4535	2.133553	CGATGTCATGAGATGTCAGGC	58.866	52.381	10.56	0.00	35.66	4.85
2631	4536	3.121544	CACGATGTCATGAGATGTCAGG	58.878	50.000	10.56	0.00	35.66	3.86
2632	4537	2.538861	GCACGATGTCATGAGATGTCAG	59.461	50.000	10.56	1.87	35.66	3.51
2633	4538	2.094078	TGCACGATGTCATGAGATGTCA	60.094	45.455	10.56	0.00	37.02	3.58
2634	4539	2.543641	TGCACGATGTCATGAGATGTC	58.456	47.619	10.56	0.00	0.00	3.06
2635	4540	2.678471	TGCACGATGTCATGAGATGT	57.322	45.000	10.56	6.14	0.00	3.06
2636	4541	3.059800	GTGATGCACGATGTCATGAGATG	60.060	47.826	10.56	5.53	0.00	2.90
2637	4542	3.129109	GTGATGCACGATGTCATGAGAT	58.871	45.455	4.78	4.78	0.00	2.75
2671	4576	8.820831	CCTAGACAGACCCTTTCATATTCATAT	58.179	37.037	0.00	0.00	0.00	1.78
2672	4577	8.010697	TCCTAGACAGACCCTTTCATATTCATA	58.989	37.037	0.00	0.00	0.00	2.15
2673	4578	6.846505	TCCTAGACAGACCCTTTCATATTCAT	59.153	38.462	0.00	0.00	0.00	2.57
2674	4579	6.098409	GTCCTAGACAGACCCTTTCATATTCA	59.902	42.308	0.00	0.00	32.09	2.57
2675	4580	6.098409	TGTCCTAGACAGACCCTTTCATATTC	59.902	42.308	0.00	0.00	37.67	1.75
2676	4581	5.964477	TGTCCTAGACAGACCCTTTCATATT	59.036	40.000	0.00	0.00	37.67	1.28
2677	4582	5.364157	GTGTCCTAGACAGACCCTTTCATAT	59.636	44.000	0.00	0.00	43.57	1.78
2678	4583	4.710375	GTGTCCTAGACAGACCCTTTCATA	59.290	45.833	0.00	0.00	43.57	2.15
2679	4584	3.515901	GTGTCCTAGACAGACCCTTTCAT	59.484	47.826	0.00	0.00	43.57	2.57
2680	4585	2.897969	GTGTCCTAGACAGACCCTTTCA	59.102	50.000	0.00	0.00	43.57	2.69
2681	4586	2.897969	TGTGTCCTAGACAGACCCTTTC	59.102	50.000	0.00	0.00	43.57	2.62
2682	4587	2.972348	TGTGTCCTAGACAGACCCTTT	58.028	47.619	0.00	0.00	43.57	3.11
2683	4588	2.696526	TGTGTCCTAGACAGACCCTT	57.303	50.000	0.00	0.00	43.57	3.95
2684	4589	2.313342	AGATGTGTCCTAGACAGACCCT	59.687	50.000	0.00	0.00	43.57	4.34
2685	4590	2.741145	AGATGTGTCCTAGACAGACCC	58.259	52.381	0.00	0.00	43.57	4.46
2686	4591	4.951094	AGTTAGATGTGTCCTAGACAGACC	59.049	45.833	0.00	0.00	43.57	3.85
2687	4592	7.283580	ACATAGTTAGATGTGTCCTAGACAGAC	59.716	40.741	0.00	0.00	43.57	3.51
2688	4593	7.347252	ACATAGTTAGATGTGTCCTAGACAGA	58.653	38.462	0.00	0.00	43.57	3.41
2689	4594	7.283354	TGACATAGTTAGATGTGTCCTAGACAG	59.717	40.741	0.00	0.00	43.57	3.51
2690	4595	7.116736	TGACATAGTTAGATGTGTCCTAGACA	58.883	38.462	0.00	0.00	40.18	3.41
2691	4596	7.569639	TGACATAGTTAGATGTGTCCTAGAC	57.430	40.000	0.00	0.00	40.18	2.59
2695	4600	8.948401	AGATATGACATAGTTAGATGTGTCCT	57.052	34.615	0.98	0.00	40.18	3.85
2706	4611	8.310382	GGACATCAGCTTAGATATGACATAGTT	58.690	37.037	0.98	0.00	0.00	2.24
2707	4612	7.452813	TGGACATCAGCTTAGATATGACATAGT	59.547	37.037	0.98	0.00	0.00	2.12
2708	4613	7.758980	GTGGACATCAGCTTAGATATGACATAG	59.241	40.741	0.98	0.00	0.00	2.23
2709	4614	7.452813	AGTGGACATCAGCTTAGATATGACATA	59.547	37.037	0.00	0.00	0.00	2.29
2710	4615	6.269538	AGTGGACATCAGCTTAGATATGACAT	59.730	38.462	0.00	0.00	0.00	3.06
2711	4616	5.600069	AGTGGACATCAGCTTAGATATGACA	59.400	40.000	0.00	0.00	0.00	3.58
2712	4617	6.015519	AGAGTGGACATCAGCTTAGATATGAC	60.016	42.308	0.00	0.00	0.00	3.06
2713	4618	6.015603	CAGAGTGGACATCAGCTTAGATATGA	60.016	42.308	0.00	0.00	0.00	2.15
2714	4619	6.157904	CAGAGTGGACATCAGCTTAGATATG	58.842	44.000	0.00	0.00	0.00	1.78
2715	4620	5.837979	ACAGAGTGGACATCAGCTTAGATAT	59.162	40.000	0.00	0.00	0.00	1.63
2716	4621	5.204292	ACAGAGTGGACATCAGCTTAGATA	58.796	41.667	0.00	0.00	0.00	1.98
2717	4622	4.029520	ACAGAGTGGACATCAGCTTAGAT	58.970	43.478	0.00	0.00	0.00	1.98
2718	4623	3.435275	ACAGAGTGGACATCAGCTTAGA	58.565	45.455	0.00	0.00	0.00	2.10
2719	4624	3.883830	ACAGAGTGGACATCAGCTTAG	57.116	47.619	0.00	0.00	0.00	2.18

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.