AutoCloner

Multiple sequence alignment - TraesCS7A01G158800

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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	TraesCS7A01G158800	chr7A	100.000	3233	0	0	1	3233	114415446	114412214	0.000000e+00	5971.0
1	TraesCS7A01G158800	chr7A	94.828	3190	127	13	56	3233	114689755	114686592	0.000000e+00	4942.0
2	TraesCS7A01G158800	chr7A	86.076	79	11	0	160	238	620198897	620198975	5.750000e-13	86.1
3	TraesCS7A01G158800	chr7A	90.164	61	6	0	1	61	114700154	114700094	2.670000e-11	80.5
4	TraesCS7A01G158800	chr7B	90.388	2424	185	21	259	2668	68224416	68222027	0.000000e+00	3142.0
5	TraesCS7A01G158800	chr7B	89.564	2271	188	21	410	2667	68161313	68159079	0.000000e+00	2835.0
6	TraesCS7A01G158800	chr7B	82.281	570	53	17	2666	3233	68159124	68158601	1.770000e-122	449.0
7	TraesCS7A01G158800	chr7B	84.043	282	30	7	2666	2944	68222073	68221804	1.150000e-64	257.0
8	TraesCS7A01G158800	chr7B	90.446	157	13	2	259	414	68164244	68164089	4.230000e-49	206.0
9	TraesCS7A01G158800	chr7B	87.283	173	20	1	3061	3233	68218328	68218158	2.540000e-46	196.0
10	TraesCS7A01G158800	chr7D	91.172	1971	139	12	718	2668	109145052	109143097	0.000000e+00	2643.0
11	TraesCS7A01G158800	chr7D	78.999	1619	273	46	1057	2630	10963652	10962056	0.000000e+00	1044.0
12	TraesCS7A01G158800	chr7D	77.299	1370	232	42	1150	2459	10910337	10908987	0.000000e+00	734.0
13	TraesCS7A01G158800	chr7D	90.389	489	41	6	238	726	109145719	109145237	3.520000e-179	638.0
14	TraesCS7A01G158800	chr7D	76.013	1234	202	37	650	1820	9354413	9355615	1.310000e-153	553.0
15	TraesCS7A01G158800	chr6D	90.566	1219	103	3	997	2206	84280064	84281279	0.000000e+00	1604.0
16	TraesCS7A01G158800	chr6D	84.963	818	68	19	299	1095	84279334	84280117	0.000000e+00	778.0
17	TraesCS7A01G158800	chr6D	89.070	430	34	5	2245	2668	84281277	84281699	3.700000e-144	521.0
18	TraesCS7A01G158800	chr6D	88.942	208	17	6	414	620	429498290	429498492	5.350000e-63	252.0
19	TraesCS7A01G158800	chr6D	85.600	125	14	4	299	421	429498076	429498198	9.410000e-26	128.0
20	TraesCS7A01G158800	chr6D	91.667	72	3	1	2978	3049	84281923	84281991	2.650000e-16	97.1
21	TraesCS7A01G158800	chr4A	81.978	1193	174	21	1125	2286	728353014	728351832	0.000000e+00	974.0
22	TraesCS7A01G158800	chr4A	79.712	1321	202	44	1052	2333	729426126	729424833	0.000000e+00	894.0
23	TraesCS7A01G158800	chr4A	77.405	1372	236	48	1125	2463	729880925	729882255	0.000000e+00	749.0
24	TraesCS7A01G158800	chr4A	77.697	1233	196	37	1059	2249	731097671	731098866	0.000000e+00	680.0
25	TraesCS7A01G158800	chr4A	80.150	801	132	17	1879	2667	728357562	728356777	1.010000e-159	573.0
26	TraesCS7A01G158800	chr4A	91.803	61	5	0	144	204	302723773	302723713	5.750000e-13	86.1
27	TraesCS7A01G158800	chr4A	90.566	53	5	0	997	1049	729819248	729819300	1.610000e-08	71.3
28	TraesCS7A01G158800	chr4A	88.462	52	6	0	996	1047	729677747	729677798	2.690000e-06	63.9
29	TraesCS7A01G158800	chr4B	79.852	1355	228	26	1062	2386	654201965	654203304	0.000000e+00	948.0
30	TraesCS7A01G158800	chr1B	83.003	353	55	5	299	650	41851749	41852097	6.730000e-82	315.0
31	TraesCS7A01G158800	chrUn	82.158	241	32	8	1	238	137834633	137834865	2.540000e-46	196.0
32	TraesCS7A01G158800	chrUn	80.000	145	23	6	98	238	37223215	37223073	5.710000e-18	102.0
33	TraesCS7A01G158800	chr1D	77.352	287	39	16	380	650	480677333	480677609	2.600000e-31	147.0
34	TraesCS7A01G158800	chr2B	80.488	164	19	11	77	236	390608881	390608727	2.640000e-21	113.0
35	TraesCS7A01G158800	chr2B	79.675	123	20	4	529	651	407216308	407216191	2.070000e-12	84.2
36	TraesCS7A01G158800	chr6B	80.137	146	19	7	298	438	138705709	138705849	2.050000e-17	100.0
37	TraesCS7A01G158800	chr5A	87.342	79	10	0	160	238	430990786	430990708	1.240000e-14	91.6
38	TraesCS7A01G158800	chr2D	87.342	79	10	0	160	238	480755728	480755806	1.240000e-14	91.6
39	TraesCS7A01G158800	chr2A	86.667	75	8	2	165	238	768994380	768994307	7.430000e-12	82.4

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	TraesCS7A01G158800	chr7A	114412214	114415446	3232	True	5971.000000	5971	100.000000	1	3233	1	chr7A.!!$R1	3232
1	TraesCS7A01G158800	chr7A	114686592	114689755	3163	True	4942.000000	4942	94.828000	56	3233	1	chr7A.!!$R2	3177
2	TraesCS7A01G158800	chr7B	68218158	68224416	6258	True	1198.333333	3142	87.238000	259	3233	3	chr7B.!!$R2	2974
3	TraesCS7A01G158800	chr7B	68158601	68164244	5643	True	1163.333333	2835	87.430333	259	3233	3	chr7B.!!$R1	2974
4	TraesCS7A01G158800	chr7D	109143097	109145719	2622	True	1640.500000	2643	90.780500	238	2668	2	chr7D.!!$R3	2430
5	TraesCS7A01G158800	chr7D	10962056	10963652	1596	True	1044.000000	1044	78.999000	1057	2630	1	chr7D.!!$R2	1573
6	TraesCS7A01G158800	chr7D	10908987	10910337	1350	True	734.000000	734	77.299000	1150	2459	1	chr7D.!!$R1	1309
7	TraesCS7A01G158800	chr7D	9354413	9355615	1202	False	553.000000	553	76.013000	650	1820	1	chr7D.!!$F1	1170
8	TraesCS7A01G158800	chr6D	84279334	84281991	2657	False	750.025000	1604	89.066500	299	3049	4	chr6D.!!$F1	2750
9	TraesCS7A01G158800	chr4A	729424833	729426126	1293	True	894.000000	894	79.712000	1052	2333	1	chr4A.!!$R2	1281
10	TraesCS7A01G158800	chr4A	728351832	728357562	5730	True	773.500000	974	81.064000	1125	2667	2	chr4A.!!$R3	1542
11	TraesCS7A01G158800	chr4A	729880925	729882255	1330	False	749.000000	749	77.405000	1125	2463	1	chr4A.!!$F3	1338
12	TraesCS7A01G158800	chr4A	731097671	731098866	1195	False	680.000000	680	77.697000	1059	2249	1	chr4A.!!$F4	1190
13	TraesCS7A01G158800	chr4B	654201965	654203304	1339	False	948.000000	948	79.852000	1062	2386	1	chr4B.!!$F1	1324

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
244	245	0.107557	GCTCAAATTTGGGGGCCATG	60.108	55.0	19.53	0.0	31.53	3.66	F
1026	4039	0.264955	AGGCGGAGAAAGGGGAGATA	59.735	55.0	0.00	0.0	0.00	1.98	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1429	4884	1.988467	GTTGTAACGGCGGTAGAGAAC	59.012	52.381	13.24	8.69	0.00	3.01	R
2387	5944	0.035317	TGACCAAGCGTTGCTCTGAT	59.965	50.000	0.00	0.00	38.25	2.90	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
21	22	2.750948	TCTTCGGGTTGTTCTTCTTCG	58.249	47.619	0.00	0.00	0.00	3.79
22	23	2.101917	TCTTCGGGTTGTTCTTCTTCGT	59.898	45.455	0.00	0.00	0.00	3.85
25	26	2.059541	CGGGTTGTTCTTCTTCGTCTC	58.940	52.381	0.00	0.00	0.00	3.36
26	27	2.414806	GGGTTGTTCTTCTTCGTCTCC	58.585	52.381	0.00	0.00	0.00	3.71
27	28	2.059541	GGTTGTTCTTCTTCGTCTCCG	58.940	52.381	0.00	0.00	0.00	4.63
29	30	0.601558	TGTTCTTCTTCGTCTCCGGG	59.398	55.000	0.00	0.00	33.95	5.73
30	31	0.736672	GTTCTTCTTCGTCTCCGGGC	60.737	60.000	0.00	0.00	33.95	6.13
31	32	1.183030	TTCTTCTTCGTCTCCGGGCA	61.183	55.000	0.00	0.00	33.95	5.36
34	35	1.874345	TTCTTCGTCTCCGGGCACTC	61.874	60.000	0.00	0.00	33.95	3.51
35	36	3.685214	CTTCGTCTCCGGGCACTCG	62.685	68.421	0.00	0.10	33.95	4.18
49	50	4.742201	CTCGGTGGTGGCGGTCAG	62.742	72.222	0.00	0.00	0.00	3.51
52	53	4.699522	GGTGGTGGCGGTCAGGTC	62.700	72.222	0.00	0.00	0.00	3.85
65	66	0.754472	TCAGGTCGTCGGGTTTCTTT	59.246	50.000	0.00	0.00	0.00	2.52
72	73	0.898326	GTCGGGTTTCTTTGGGGCAT	60.898	55.000	0.00	0.00	0.00	4.40
76	77	0.526211	GGTTTCTTTGGGGCATCGAC	59.474	55.000	0.00	0.00	0.00	4.20
152	153	2.190841	GGGTGTGTTTGTGTCCCCG	61.191	63.158	0.00	0.00	32.66	5.73
173	174	2.035783	GTTGGGCCAGGGAAGGAC	59.964	66.667	6.23	0.00	35.24	3.85
181	182	2.529389	AGGGAAGGACAAGGGCGT	60.529	61.111	0.00	0.00	0.00	5.68
244	245	0.107557	GCTCAAATTTGGGGGCCATG	60.108	55.000	19.53	0.00	31.53	3.66
742	3722	4.955811	ACGACTATCCAATCCAAGCATA	57.044	40.909	0.00	0.00	0.00	3.14
773	3775	2.854777	CCTCTTTCTATGTTCAGCGTCG	59.145	50.000	0.00	0.00	0.00	5.12
792	3794	1.247567	GGTGATGTTGTTCCCCAGTG	58.752	55.000	0.00	0.00	0.00	3.66
793	3795	1.478654	GGTGATGTTGTTCCCCAGTGT	60.479	52.381	0.00	0.00	0.00	3.55
794	3796	1.880027	GTGATGTTGTTCCCCAGTGTC	59.120	52.381	0.00	0.00	0.00	3.67
877	3880	5.770162	GCTATCATTAGCCAAACCAAGGTAT	59.230	40.000	0.00	0.00	44.29	2.73
908	3911	2.452064	CCACAGGACCACCACCACT	61.452	63.158	0.00	0.00	38.94	4.00
1026	4039	0.264955	AGGCGGAGAAAGGGGAGATA	59.735	55.000	0.00	0.00	0.00	1.98
1158	4589	2.674852	CCTGTTCAATGTCGACCTCATG	59.325	50.000	14.12	6.86	0.00	3.07
1328	4774	0.322187	GGGTATCGCCACCACTTTGT	60.322	55.000	7.45	0.00	40.65	2.83
1429	4884	1.065273	GATGCTTGCAATGGCCTCG	59.935	57.895	3.32	0.00	40.13	4.63
1847	5384	1.204941	GTGGAAGACTATCCGTGTGCT	59.795	52.381	0.00	0.00	42.76	4.40
2010	5547	2.022195	CTGAAGCATACTGCCAGCATT	58.978	47.619	0.00	0.00	46.52	3.56
2070	5607	4.946157	GTGGTTGAGATTCATCCAGATTGT	59.054	41.667	8.68	0.00	44.34	2.71
2328	5885	4.629200	GTGTACCTCTGAATCTGCTTCAAG	59.371	45.833	0.00	0.00	43.20	3.02
2387	5944	5.450412	GCTTGTTTGATTTCCAGTTCAGACA	60.450	40.000	0.00	0.00	35.80	3.41
2494	6063	1.557371	TGGCTGTTATTCGGGACATGA	59.443	47.619	0.00	0.00	0.00	3.07
2521	6093	5.697067	AGTTTGATGGGGTTAAACTGTACA	58.303	37.500	0.00	0.00	42.86	2.90
2535	6107	0.830648	TGTACAGTGATAGGCCCTGC	59.169	55.000	0.00	0.00	0.00	4.85
2682	6262	7.624360	TGGTATTTTGTTACTGATGTGATCC	57.376	36.000	0.00	0.00	0.00	3.36
2770	6350	5.520632	TCGCTGTAGCTAATGATTCAGTAC	58.479	41.667	0.00	0.00	39.32	2.73
2875	6458	0.673644	AAGTGCCAGGTGTATGCGTC	60.674	55.000	0.00	0.00	0.00	5.19
2945	6534	3.502164	CCAGGACTGGGGCATTTAG	57.498	57.895	10.55	0.00	46.81	1.85
2946	6535	0.918983	CCAGGACTGGGGCATTTAGA	59.081	55.000	10.55	0.00	46.81	2.10
2947	6536	1.408822	CCAGGACTGGGGCATTTAGAC	60.409	57.143	10.55	0.00	46.81	2.59
2949	6538	1.095807	GGACTGGGGCATTTAGACGC	61.096	60.000	0.00	0.00	39.03	5.19
2950	6539	0.107654	GACTGGGGCATTTAGACGCT	60.108	55.000	0.00	0.00	39.39	5.07
2951	6540	0.328258	ACTGGGGCATTTAGACGCTT	59.672	50.000	0.00	0.00	39.39	4.68
2952	6541	0.734889	CTGGGGCATTTAGACGCTTG	59.265	55.000	0.00	0.00	39.39	4.01
2953	6542	0.037590	TGGGGCATTTAGACGCTTGT	59.962	50.000	0.00	0.00	39.39	3.16
2954	6543	1.173913	GGGGCATTTAGACGCTTGTT	58.826	50.000	0.00	0.00	34.79	2.83
2955	6544	1.135402	GGGGCATTTAGACGCTTGTTG	60.135	52.381	0.00	0.00	34.79	3.33
2956	6545	1.135402	GGGCATTTAGACGCTTGTTGG	60.135	52.381	0.00	0.00	0.00	3.77
2957	6546	1.810151	GGCATTTAGACGCTTGTTGGA	59.190	47.619	0.00	0.00	0.00	3.53
2958	6547	2.227865	GGCATTTAGACGCTTGTTGGAA	59.772	45.455	0.00	0.00	0.00	3.53
2959	6548	3.305064	GGCATTTAGACGCTTGTTGGAAA	60.305	43.478	0.00	0.00	0.00	3.13
2960	6549	4.295051	GCATTTAGACGCTTGTTGGAAAA	58.705	39.130	0.00	0.00	0.00	2.29
2961	6550	4.382754	GCATTTAGACGCTTGTTGGAAAAG	59.617	41.667	0.00	0.00	0.00	2.27
2962	6551	5.519722	CATTTAGACGCTTGTTGGAAAAGT	58.480	37.500	0.00	0.00	0.00	2.66
2963	6552	4.806342	TTAGACGCTTGTTGGAAAAGTC	57.194	40.909	0.00	0.00	0.00	3.01
2964	6553	2.919228	AGACGCTTGTTGGAAAAGTCT	58.081	42.857	0.00	0.00	33.27	3.24
2965	6554	2.872858	AGACGCTTGTTGGAAAAGTCTC	59.127	45.455	0.00	0.00	32.77	3.36
2966	6555	2.612212	GACGCTTGTTGGAAAAGTCTCA	59.388	45.455	0.00	0.00	0.00	3.27
2967	6556	2.354821	ACGCTTGTTGGAAAAGTCTCAC	59.645	45.455	0.00	0.00	0.00	3.51
2968	6557	2.354510	CGCTTGTTGGAAAAGTCTCACA	59.645	45.455	0.00	0.00	0.00	3.58
3049	10029	4.421948	CGTTATCCGCTCTTAACTGAAGT	58.578	43.478	0.00	0.00	36.45	3.01
3051	10031	3.528597	ATCCGCTCTTAACTGAAGTCC	57.471	47.619	0.00	0.00	36.45	3.85
3090	10070	0.249699	CCTTGTGGCTGTACACGTCA	60.250	55.000	0.00	0.00	44.21	4.35
3096	10076	1.301423	GGCTGTACACGTCAAAACCA	58.699	50.000	0.00	0.00	0.00	3.67
3147	10127	3.947868	ACATTGTCAGACTCCCAGATTG	58.052	45.455	1.31	0.00	0.00	2.67
3149	10129	3.685139	TTGTCAGACTCCCAGATTGTC	57.315	47.619	1.31	0.00	0.00	3.18
3153	10133	3.095332	TCAGACTCCCAGATTGTCTCAG	58.905	50.000	0.00	0.00	38.80	3.35

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	3.128349	CGAAGAAGAACAACCCGAAGAA	58.872	45.455	0.00	0.00	0.00	2.52
3	4	2.101917	AGACGAAGAAGAACAACCCGAA	59.898	45.455	0.00	0.00	0.00	4.30
4	5	1.684983	AGACGAAGAAGAACAACCCGA	59.315	47.619	0.00	0.00	0.00	5.14
5	6	2.059541	GAGACGAAGAAGAACAACCCG	58.940	52.381	0.00	0.00	0.00	5.28
35	36	4.699522	GACCTGACCGCCACCACC	62.700	72.222	0.00	0.00	0.00	4.61
38	39	4.736896	GACGACCTGACCGCCACC	62.737	72.222	0.00	0.00	0.00	4.61
43	44	3.216944	AAACCCGACGACCTGACCG	62.217	63.158	0.00	0.00	0.00	4.79
44	45	1.373873	GAAACCCGACGACCTGACC	60.374	63.158	0.00	0.00	0.00	4.02
45	46	0.033090	AAGAAACCCGACGACCTGAC	59.967	55.000	0.00	0.00	0.00	3.51
46	47	0.754472	AAAGAAACCCGACGACCTGA	59.246	50.000	0.00	0.00	0.00	3.86
47	48	0.865769	CAAAGAAACCCGACGACCTG	59.134	55.000	0.00	0.00	0.00	4.00
48	49	0.250166	CCAAAGAAACCCGACGACCT	60.250	55.000	0.00	0.00	0.00	3.85
49	50	1.232621	CCCAAAGAAACCCGACGACC	61.233	60.000	0.00	0.00	0.00	4.79
50	51	1.232621	CCCCAAAGAAACCCGACGAC	61.233	60.000	0.00	0.00	0.00	4.34
51	52	1.071814	CCCCAAAGAAACCCGACGA	59.928	57.895	0.00	0.00	0.00	4.20
52	53	2.622962	GCCCCAAAGAAACCCGACG	61.623	63.158	0.00	0.00	0.00	5.12
53	54	0.898326	ATGCCCCAAAGAAACCCGAC	60.898	55.000	0.00	0.00	0.00	4.79
54	55	0.610785	GATGCCCCAAAGAAACCCGA	60.611	55.000	0.00	0.00	0.00	5.14
65	66	2.690510	TCCATGGTCGATGCCCCA	60.691	61.111	12.58	0.00	34.66	4.96
72	73	1.075970	CTCCCTCCTCCATGGTCGA	60.076	63.158	12.58	7.47	37.07	4.20
76	77	1.003442	TCCACTCCCTCCTCCATGG	59.997	63.158	4.97	4.97	37.10	3.66
168	169	1.675641	GATGCACGCCCTTGTCCTT	60.676	57.895	0.00	0.00	0.00	3.36
244	245	3.046993	CGCGTAACGGACACAAAAC	57.953	52.632	0.00	0.00	38.44	2.43
531	3316	3.788227	ATGCCACCACAAACTAAGAGA	57.212	42.857	0.00	0.00	0.00	3.10
697	3482	9.916397	CGTAGATACAAACATAAAAATGACCTC	57.084	33.333	0.00	0.00	0.00	3.85
742	3722	6.664816	TGAACATAGAAAGAGGAAATTGGCAT	59.335	34.615	0.00	0.00	0.00	4.40
773	3775	1.247567	CACTGGGGAACAACATCACC	58.752	55.000	0.00	0.00	43.65	4.02
792	3794	1.535833	TCACTTCTCAGAGGACGGAC	58.464	55.000	0.00	0.00	0.00	4.79
793	3795	2.163509	CTTCACTTCTCAGAGGACGGA	58.836	52.381	0.00	0.00	0.00	4.69
794	3796	1.889829	ACTTCACTTCTCAGAGGACGG	59.110	52.381	0.00	0.00	0.00	4.79
877	3880	1.192146	CCTGTGGGGAGTCGGAAAGA	61.192	60.000	0.00	0.00	37.23	2.52
908	3911	2.230266	GCTGAGAAAAATTAACCCGGCA	59.770	45.455	0.00	0.00	0.00	5.69
1026	4039	1.244019	GCTTGGCGTTCCACTCCAAT	61.244	55.000	0.00	0.00	41.56	3.16
1429	4884	1.988467	GTTGTAACGGCGGTAGAGAAC	59.012	52.381	13.24	8.69	0.00	3.01
1847	5384	7.982761	ATAGTACCAAATTTTGAACCGTACA	57.017	32.000	19.50	11.34	31.34	2.90
2070	5607	2.886523	CTGAGCCAGGAAAATTGTGTCA	59.113	45.455	0.00	0.00	0.00	3.58
2304	5858	3.055819	TGAAGCAGATTCAGAGGTACACC	60.056	47.826	0.00	0.00	43.09	4.16
2387	5944	0.035317	TGACCAAGCGTTGCTCTGAT	59.965	50.000	0.00	0.00	38.25	2.90
2494	6063	6.370453	ACAGTTTAACCCCATCAAACTAAGT	58.630	36.000	0.00	0.00	39.78	2.24
2521	6093	1.132721	TGGATAGCAGGGCCTATCACT	60.133	52.381	5.28	4.11	43.46	3.41
2578	6156	5.420725	ACACTAGCAGGTTGACAATATGA	57.579	39.130	6.74	0.00	0.00	2.15
2712	6292	7.346751	AGAATTTCACAAAGGAAGTGCTTTA	57.653	32.000	0.00	0.00	36.93	1.85
2875	6458	5.561532	CGCAAGCTTATATGATGGACCAAAG	60.562	44.000	0.00	0.00	0.00	2.77
2905	6493	2.231235	CACCTGCCAACAAAATCCTACC	59.769	50.000	0.00	0.00	0.00	3.18
2934	6523	0.037590	ACAAGCGTCTAAATGCCCCA	59.962	50.000	0.00	0.00	38.23	4.96
2938	6527	3.552604	TTCCAACAAGCGTCTAAATGC	57.447	42.857	0.00	0.00	37.71	3.56
2939	6528	5.519722	ACTTTTCCAACAAGCGTCTAAATG	58.480	37.500	0.00	0.00	0.00	2.32
2940	6529	5.531287	AGACTTTTCCAACAAGCGTCTAAAT	59.469	36.000	0.00	0.00	0.00	1.40
2943	6532	4.056050	GAGACTTTTCCAACAAGCGTCTA	58.944	43.478	0.00	0.00	31.11	2.59
2944	6533	2.872858	GAGACTTTTCCAACAAGCGTCT	59.127	45.455	0.00	0.00	33.39	4.18
2945	6534	2.612212	TGAGACTTTTCCAACAAGCGTC	59.388	45.455	0.00	0.00	0.00	5.19
2946	6535	2.354821	GTGAGACTTTTCCAACAAGCGT	59.645	45.455	0.00	0.00	0.00	5.07
2947	6536	2.354510	TGTGAGACTTTTCCAACAAGCG	59.645	45.455	0.00	0.00	0.00	4.68
2949	6538	6.049149	TCTAGTGTGAGACTTTTCCAACAAG	58.951	40.000	0.00	0.00	35.96	3.16
2950	6539	5.984725	TCTAGTGTGAGACTTTTCCAACAA	58.015	37.500	0.00	0.00	35.96	2.83
2951	6540	5.607939	TCTAGTGTGAGACTTTTCCAACA	57.392	39.130	0.00	0.00	35.96	3.33
2952	6541	6.920569	TTTCTAGTGTGAGACTTTTCCAAC	57.079	37.500	0.00	0.00	35.96	3.77
2953	6542	7.054124	ACATTTCTAGTGTGAGACTTTTCCAA	58.946	34.615	0.00	0.00	35.96	3.53
2954	6543	6.591935	ACATTTCTAGTGTGAGACTTTTCCA	58.408	36.000	0.00	0.00	35.96	3.53
2955	6544	8.603242	TTACATTTCTAGTGTGAGACTTTTCC	57.397	34.615	0.00	0.00	35.96	3.13
2957	6546	9.003658	CCATTACATTTCTAGTGTGAGACTTTT	57.996	33.333	0.00	0.00	35.96	2.27
2958	6547	7.119846	GCCATTACATTTCTAGTGTGAGACTTT	59.880	37.037	0.00	0.00	35.96	2.66
2959	6548	6.595716	GCCATTACATTTCTAGTGTGAGACTT	59.404	38.462	0.00	0.00	35.96	3.01
2960	6549	6.109359	GCCATTACATTTCTAGTGTGAGACT	58.891	40.000	0.00	0.00	38.88	3.24
2961	6550	5.294552	GGCCATTACATTTCTAGTGTGAGAC	59.705	44.000	0.00	0.00	0.00	3.36
2962	6551	5.045942	TGGCCATTACATTTCTAGTGTGAGA	60.046	40.000	0.00	0.00	0.00	3.27
2963	6552	5.185454	TGGCCATTACATTTCTAGTGTGAG	58.815	41.667	0.00	0.00	0.00	3.51
2964	6553	5.172687	TGGCCATTACATTTCTAGTGTGA	57.827	39.130	0.00	0.00	0.00	3.58
2965	6554	5.589855	TCATGGCCATTACATTTCTAGTGTG	59.410	40.000	17.92	0.00	0.00	3.82
2966	6555	5.754782	TCATGGCCATTACATTTCTAGTGT	58.245	37.500	17.92	0.00	0.00	3.55
2967	6556	6.095300	TGTTCATGGCCATTACATTTCTAGTG	59.905	38.462	17.92	0.92	0.00	2.74
2968	6557	6.186957	TGTTCATGGCCATTACATTTCTAGT	58.813	36.000	17.92	0.00	0.00	2.57
3051	10031	1.497991	CACATCAGCCGTATTACCCG	58.502	55.000	0.00	0.00	0.00	5.28
3085	10065	0.956902	GCCGGGTATGGTTTTGACGT	60.957	55.000	2.18	0.00	0.00	4.34
3090	10070	1.254975	GCCTTGCCGGGTATGGTTTT	61.255	55.000	16.50	0.00	0.00	2.43
3096	10076	0.039035	TTTTCTGCCTTGCCGGGTAT	59.961	50.000	2.18	0.00	0.00	2.73

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.