AutoCloner

Multiple sequence alignment - TraesCS5B01G520300

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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	TraesCS5B01G520300	chr5B	100.000	3149	0	0	1	3149	682552618	682549470	0.000000e+00	5816
1	TraesCS5B01G520300	chr5B	97.015	67	2	0	2218	2284	546717513	546717579	2.570000e-21	113
2	TraesCS5B01G520300	chr5D	93.665	1547	67	17	686	2223	540279413	540277889	0.000000e+00	2285
3	TraesCS5B01G520300	chr5D	85.515	573	62	16	57	621	110652482	110653041	2.110000e-161	579
4	TraesCS5B01G520300	chr4A	93.204	1545	69	17	683	2210	628211365	628209840	0.000000e+00	2239
5	TraesCS5B01G520300	chr4A	84.734	583	40	21	66	622	146679275	146679834	3.570000e-149	538
6	TraesCS5B01G520300	chr7B	95.325	877	38	1	2276	3149	254118737	254117861	0.000000e+00	1389
7	TraesCS5B01G520300	chr7B	95.200	875	38	2	2278	3149	109038165	109039038	0.000000e+00	1380
8	TraesCS5B01G520300	chr7B	87.080	565	55	12	65	622	705945981	705945428	9.590000e-175	623
9	TraesCS5B01G520300	chr7B	92.857	70	5	0	2215	2284	110695259	110695328	5.560000e-18	102
10	TraesCS5B01G520300	chr6B	95.211	877	38	2	2276	3149	487542847	487543722	0.000000e+00	1384
11	TraesCS5B01G520300	chr6B	94.863	876	41	4	2277	3149	274216963	274216089	0.000000e+00	1365
12	TraesCS5B01G520300	chr6B	94.749	876	41	5	2277	3149	659253388	659252515	0.000000e+00	1358
13	TraesCS5B01G520300	chr1B	94.977	876	39	3	2277	3149	436208978	436209851	0.000000e+00	1369
14	TraesCS5B01G520300	chr1B	94.570	884	35	6	2276	3149	667267682	667266802	0.000000e+00	1354
15	TraesCS5B01G520300	chr1B	83.156	564	70	22	68	622	319470306	319469759	2.820000e-135	492
16	TraesCS5B01G520300	chr1B	95.522	67	3	0	2218	2284	486849518	486849584	1.190000e-19	108
17	TraesCS5B01G520300	chr1B	94.286	70	4	0	2215	2284	595180153	595180084	1.190000e-19	108
18	TraesCS5B01G520300	chr1B	94.203	69	4	0	2216	2284	65537743	65537675	4.300000e-19	106
19	TraesCS5B01G520300	chr1B	90.909	77	6	1	2209	2284	436208865	436208941	5.560000e-18	102
20	TraesCS5B01G520300	chr2B	94.869	877	41	3	2276	3149	631716669	631717544	0.000000e+00	1367
21	TraesCS5B01G520300	chr2B	85.409	562	59	17	66	622	776642225	776642768	2.120000e-156	562
22	TraesCS5B01G520300	chr3B	94.659	880	42	3	2274	3149	719427896	719428774	0.000000e+00	1360
23	TraesCS5B01G520300	chr3B	95.652	69	3	0	2216	2284	719427795	719427863	9.230000e-21	111
24	TraesCS5B01G520300	chr3B	92.958	71	5	0	2216	2286	745559892	745559822	1.540000e-18	104
25	TraesCS5B01G520300	chr7D	87.910	579	36	21	66	622	4809381	4809947	0.000000e+00	651
26	TraesCS5B01G520300	chr7D	86.643	569	56	16	65	623	104619689	104619131	2.080000e-171	612
27	TraesCS5B01G520300	chr1A	87.766	564	53	11	66	622	52840707	52841261	0.000000e+00	645
28	TraesCS5B01G520300	chr6A	87.522	561	47	16	65	621	161946109	161946650	7.410000e-176	627
29	TraesCS5B01G520300	chrUn	85.279	591	41	19	61	622	108806632	108806059	4.560000e-158	568
30	TraesCS5B01G520300	chr4B	95.522	67	3	0	2218	2284	615310310	615310376	1.190000e-19	108

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	TraesCS5B01G520300	chr5B	682549470	682552618	3148	True	5816.0	5816	100.0000	1	3149	1	chr5B.!!$R1	3148
1	TraesCS5B01G520300	chr5D	540277889	540279413	1524	True	2285.0	2285	93.6650	686	2223	1	chr5D.!!$R1	1537
2	TraesCS5B01G520300	chr5D	110652482	110653041	559	False	579.0	579	85.5150	57	621	1	chr5D.!!$F1	564
3	TraesCS5B01G520300	chr4A	628209840	628211365	1525	True	2239.0	2239	93.2040	683	2210	1	chr4A.!!$R1	1527
4	TraesCS5B01G520300	chr4A	146679275	146679834	559	False	538.0	538	84.7340	66	622	1	chr4A.!!$F1	556
5	TraesCS5B01G520300	chr7B	254117861	254118737	876	True	1389.0	1389	95.3250	2276	3149	1	chr7B.!!$R1	873
6	TraesCS5B01G520300	chr7B	109038165	109039038	873	False	1380.0	1380	95.2000	2278	3149	1	chr7B.!!$F1	871
7	TraesCS5B01G520300	chr7B	705945428	705945981	553	True	623.0	623	87.0800	65	622	1	chr7B.!!$R2	557
8	TraesCS5B01G520300	chr6B	487542847	487543722	875	False	1384.0	1384	95.2110	2276	3149	1	chr6B.!!$F1	873
9	TraesCS5B01G520300	chr6B	274216089	274216963	874	True	1365.0	1365	94.8630	2277	3149	1	chr6B.!!$R1	872
10	TraesCS5B01G520300	chr6B	659252515	659253388	873	True	1358.0	1358	94.7490	2277	3149	1	chr6B.!!$R2	872
11	TraesCS5B01G520300	chr1B	667266802	667267682	880	True	1354.0	1354	94.5700	2276	3149	1	chr1B.!!$R4	873
12	TraesCS5B01G520300	chr1B	436208865	436209851	986	False	735.5	1369	92.9430	2209	3149	2	chr1B.!!$F2	940
13	TraesCS5B01G520300	chr1B	319469759	319470306	547	True	492.0	492	83.1560	68	622	1	chr1B.!!$R2	554
14	TraesCS5B01G520300	chr2B	631716669	631717544	875	False	1367.0	1367	94.8690	2276	3149	1	chr2B.!!$F1	873
15	TraesCS5B01G520300	chr2B	776642225	776642768	543	False	562.0	562	85.4090	66	622	1	chr2B.!!$F2	556
16	TraesCS5B01G520300	chr3B	719427795	719428774	979	False	735.5	1360	95.1555	2216	3149	2	chr3B.!!$F1	933
17	TraesCS5B01G520300	chr7D	4809381	4809947	566	False	651.0	651	87.9100	66	622	1	chr7D.!!$F1	556
18	TraesCS5B01G520300	chr7D	104619131	104619689	558	True	612.0	612	86.6430	65	623	1	chr7D.!!$R1	558
19	TraesCS5B01G520300	chr1A	52840707	52841261	554	False	645.0	645	87.7660	66	622	1	chr1A.!!$F1	556
20	TraesCS5B01G520300	chr6A	161946109	161946650	541	False	627.0	627	87.5220	65	621	1	chr6A.!!$F1	556
21	TraesCS5B01G520300	chrUn	108806059	108806632	573	True	568.0	568	85.2790	61	622	1	chrUn.!!$R1	561

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
623	737	0.186386	AGCTGTATAGGAGCTCCCGT	59.814	55.0	29.54	19.85	43.54	5.28	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2533	2720	1.546476	CTTAGGCGCTATTCCTCGGAT	59.454	52.381	7.64	0.0	35.21	4.18	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	4.497473	TTTTGTTCAGAAATACAGCCCG	57.503	40.909	0.00	0.00	0.00	6.13
22	23	3.410631	TTGTTCAGAAATACAGCCCGA	57.589	42.857	0.00	0.00	0.00	5.14
23	24	2.972625	TGTTCAGAAATACAGCCCGAG	58.027	47.619	0.00	0.00	0.00	4.63
24	25	2.301870	TGTTCAGAAATACAGCCCGAGT	59.698	45.455	0.00	0.00	0.00	4.18
25	26	3.512329	TGTTCAGAAATACAGCCCGAGTA	59.488	43.478	0.00	0.00	0.00	2.59
26	27	4.020928	TGTTCAGAAATACAGCCCGAGTAA	60.021	41.667	0.00	0.00	0.00	2.24
27	28	4.811969	TCAGAAATACAGCCCGAGTAAA	57.188	40.909	0.00	0.00	0.00	2.01
28	29	5.155278	TCAGAAATACAGCCCGAGTAAAA	57.845	39.130	0.00	0.00	0.00	1.52
29	30	5.741011	TCAGAAATACAGCCCGAGTAAAAT	58.259	37.500	0.00	0.00	0.00	1.82
30	31	6.177610	TCAGAAATACAGCCCGAGTAAAATT	58.822	36.000	0.00	0.00	0.00	1.82
31	32	6.657541	TCAGAAATACAGCCCGAGTAAAATTT	59.342	34.615	0.00	0.00	0.00	1.82
32	33	7.825270	TCAGAAATACAGCCCGAGTAAAATTTA	59.175	33.333	0.00	0.00	0.00	1.40
33	34	8.621286	CAGAAATACAGCCCGAGTAAAATTTAT	58.379	33.333	0.00	0.00	0.00	1.40
34	35	9.841295	AGAAATACAGCCCGAGTAAAATTTATA	57.159	29.630	0.00	0.00	0.00	0.98
39	40	8.747538	ACAGCCCGAGTAAAATTTATATCTTT	57.252	30.769	0.00	0.00	0.00	2.52
40	41	9.185680	ACAGCCCGAGTAAAATTTATATCTTTT	57.814	29.630	0.00	0.00	0.00	2.27
41	42	9.450807	CAGCCCGAGTAAAATTTATATCTTTTG	57.549	33.333	0.00	0.00	0.00	2.44
42	43	9.403583	AGCCCGAGTAAAATTTATATCTTTTGA	57.596	29.630	0.00	0.00	0.00	2.69
53	54	9.988350	AATTTATATCTTTTGAAGTACGTGCAG	57.012	29.630	6.38	0.00	0.00	4.41
54	55	8.766000	TTTATATCTTTTGAAGTACGTGCAGA	57.234	30.769	6.38	0.00	0.00	4.26
55	56	8.942338	TTATATCTTTTGAAGTACGTGCAGAT	57.058	30.769	6.38	6.77	0.00	2.90
56	57	4.990543	TCTTTTGAAGTACGTGCAGATG	57.009	40.909	6.38	0.00	0.00	2.90
57	58	4.377021	TCTTTTGAAGTACGTGCAGATGT	58.623	39.130	6.38	0.00	0.00	3.06
58	59	4.211164	TCTTTTGAAGTACGTGCAGATGTG	59.789	41.667	6.38	0.00	0.00	3.21
59	60	2.812358	TGAAGTACGTGCAGATGTGT	57.188	45.000	6.38	0.00	0.00	3.72
60	61	3.106242	TGAAGTACGTGCAGATGTGTT	57.894	42.857	6.38	0.00	0.00	3.32
61	62	3.462982	TGAAGTACGTGCAGATGTGTTT	58.537	40.909	6.38	0.00	0.00	2.83
62	63	3.874543	TGAAGTACGTGCAGATGTGTTTT	59.125	39.130	6.38	0.00	0.00	2.43
148	149	2.044451	CTGTAAATGGGCCGGCCA	60.044	61.111	44.46	30.82	37.98	5.36
604	718	4.010224	TTAACGGGCGCCTGCAGA	62.010	61.111	35.17	17.61	45.35	4.26
623	737	0.186386	AGCTGTATAGGAGCTCCCGT	59.814	55.000	29.54	19.85	43.54	5.28
624	738	0.315568	GCTGTATAGGAGCTCCCGTG	59.684	60.000	29.54	14.17	40.87	4.94
625	739	1.693627	CTGTATAGGAGCTCCCGTGT	58.306	55.000	29.54	13.43	40.87	4.49
626	740	2.032620	CTGTATAGGAGCTCCCGTGTT	58.967	52.381	29.54	13.02	40.87	3.32
627	741	2.431057	CTGTATAGGAGCTCCCGTGTTT	59.569	50.000	29.54	12.24	40.87	2.83
628	742	2.835764	TGTATAGGAGCTCCCGTGTTTT	59.164	45.455	29.54	11.45	40.87	2.43
629	743	3.262405	TGTATAGGAGCTCCCGTGTTTTT	59.738	43.478	29.54	10.66	40.87	1.94
678	792	9.995003	TTAATTGTTTAAAGTTACGAGGTAGGA	57.005	29.630	0.00	0.00	0.00	2.94
679	793	8.907222	AATTGTTTAAAGTTACGAGGTAGGAA	57.093	30.769	0.00	0.00	0.00	3.36
680	794	9.511272	AATTGTTTAAAGTTACGAGGTAGGAAT	57.489	29.630	0.00	0.00	0.00	3.01
681	795	7.894376	TGTTTAAAGTTACGAGGTAGGAATG	57.106	36.000	0.00	0.00	0.00	2.67
707	821	2.634982	TTTCGAGTGGATTGCATTGC	57.365	45.000	0.46	0.46	0.00	3.56
719	838	3.681593	TTGCATTGCAATTGGCTAACT	57.318	38.095	19.77	0.00	43.99	2.24
748	867	4.279922	GTGTAGTTGTGGCCCAGTTAAAAT	59.720	41.667	0.00	0.00	0.00	1.82
760	879	6.547510	GGCCCAGTTAAAATCAGAATACAGAT	59.452	38.462	0.00	0.00	0.00	2.90
833	955	3.311966	GTGTAGTACACGTGGAACTTCC	58.688	50.000	24.89	17.75	39.53	3.46
860	982	3.220999	TTGGCTCGCACACGTAGCT	62.221	57.895	7.17	0.00	40.21	3.32
866	988	1.657487	CGCACACGTAGCTATCGGG	60.657	63.158	13.95	13.95	37.74	5.14
868	990	1.435925	CACACGTAGCTATCGGGCA	59.564	57.895	15.04	0.00	34.89	5.36
1152	1274	4.834453	CGGGAGCAGGAGCAGCAG	62.834	72.222	0.00	0.00	45.49	4.24
1179	1301	0.905337	AGCACTACTTCCCGGAGCTT	60.905	55.000	0.73	0.00	0.00	3.74
1611	1737	1.940883	TACCACGTGGCCTGATCGAC	61.941	60.000	34.26	0.00	39.32	4.20
1752	1885	4.842091	GCGGCGGACGTGTACGAT	62.842	66.667	9.16	0.00	46.52	3.73
1803	1936	2.104331	GACATCGACATCGGCCGT	59.896	61.111	27.15	10.00	40.29	5.68
1872	2005	4.961511	GTGCTGGTGTCGCACGGA	62.962	66.667	0.00	0.00	46.81	4.69
1926	2059	4.980805	TGGACGGTGCGGCAGTTC	62.981	66.667	1.18	0.00	36.10	3.01
2156	2289	4.098501	CACCCATTTCAGCTAGGAAATTCC	59.901	45.833	3.29	3.29	43.13	3.01
2187	2320	8.965819	AGCTGATCTGTATACCTGTATATGAAG	58.034	37.037	0.00	1.05	31.45	3.02
2188	2321	7.704472	GCTGATCTGTATACCTGTATATGAAGC	59.296	40.741	0.00	6.04	31.45	3.86
2189	2322	8.650143	TGATCTGTATACCTGTATATGAAGCA	57.350	34.615	0.00	4.03	31.45	3.91
2190	2323	9.088987	TGATCTGTATACCTGTATATGAAGCAA	57.911	33.333	0.00	0.00	31.45	3.91
2195	2328	9.929180	TGTATACCTGTATATGAAGCAAAGATC	57.071	33.333	0.00	0.00	31.45	2.75
2207	2340	5.123820	TGAAGCAAAGATCTGTAAATTCCCG	59.876	40.000	0.00	0.00	0.00	5.14
2210	2343	4.496507	GCAAAGATCTGTAAATTCCCGCTC	60.497	45.833	0.00	0.00	0.00	5.03
2212	2345	2.771943	AGATCTGTAAATTCCCGCTCCA	59.228	45.455	0.00	0.00	0.00	3.86
2246	2379	1.537348	CCAACAGGCGCGCTATACTAA	60.537	52.381	32.29	0.00	0.00	2.24
2255	2388	1.371389	GCTATACTAACGCCGCGCT	60.371	57.895	13.88	2.56	0.00	5.92
2336	2516	4.215742	CCCCGCGCATACTTCGGA	62.216	66.667	8.75	0.00	45.53	4.55
2388	2568	1.214062	CGCTCTCGCACTTCCTCTT	59.786	57.895	0.00	0.00	35.30	2.85
2509	2696	1.679969	CCCCATCCCCTCCTAGTCCT	61.680	65.000	0.00	0.00	0.00	3.85
2543	2730	1.749334	GCCTCCGTCATCCGAGGAAT	61.749	60.000	7.29	0.00	39.56	3.01
2550	2737	0.827925	TCATCCGAGGAATAGCGCCT	60.828	55.000	2.29	0.00	38.81	5.52
2551	2738	0.888619	CATCCGAGGAATAGCGCCTA	59.111	55.000	2.29	0.00	35.44	3.93
2896	3086	3.448301	ACATACCCGGAGTCGTATTTTCA	59.552	43.478	0.73	0.00	33.95	2.69
2909	3099	2.844122	ATTTTCATCGCCGGTTTAGC	57.156	45.000	1.90	0.00	0.00	3.09
2924	3114	3.259064	GTTTAGCATGAGCACCGACTTA	58.741	45.455	0.00	0.00	45.49	2.24
2951	3141	1.733912	CGCATTGCAGAGAAACTAGCA	59.266	47.619	9.69	0.00	33.43	3.49

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
8	9	8.747538	ATAAATTTTACTCGGGCTGTATTTCT	57.252	30.769	0.00	0.00	0.00	2.52
13	14	9.841295	AAAGATATAAATTTTACTCGGGCTGTA	57.159	29.630	0.00	0.00	0.00	2.74
14	15	8.747538	AAAGATATAAATTTTACTCGGGCTGT	57.252	30.769	0.00	0.00	0.00	4.40
15	16	9.450807	CAAAAGATATAAATTTTACTCGGGCTG	57.549	33.333	0.00	0.00	0.00	4.85
16	17	9.403583	TCAAAAGATATAAATTTTACTCGGGCT	57.596	29.630	0.00	0.00	0.00	5.19
27	28	9.988350	CTGCACGTACTTCAAAAGATATAAATT	57.012	29.630	0.00	0.00	0.00	1.82
28	29	9.378551	TCTGCACGTACTTCAAAAGATATAAAT	57.621	29.630	0.00	0.00	0.00	1.40
29	30	8.766000	TCTGCACGTACTTCAAAAGATATAAA	57.234	30.769	0.00	0.00	0.00	1.40
30	31	8.817100	CATCTGCACGTACTTCAAAAGATATAA	58.183	33.333	0.00	0.00	0.00	0.98
31	32	7.979537	ACATCTGCACGTACTTCAAAAGATATA	59.020	33.333	0.00	0.00	0.00	0.86
32	33	6.818644	ACATCTGCACGTACTTCAAAAGATAT	59.181	34.615	0.00	0.00	0.00	1.63
33	34	6.090763	CACATCTGCACGTACTTCAAAAGATA	59.909	38.462	0.00	0.00	0.00	1.98
34	35	4.997395	ACATCTGCACGTACTTCAAAAGAT	59.003	37.500	0.00	0.00	0.00	2.40
35	36	4.211164	CACATCTGCACGTACTTCAAAAGA	59.789	41.667	0.00	0.00	0.00	2.52
36	37	4.024893	ACACATCTGCACGTACTTCAAAAG	60.025	41.667	0.00	0.00	0.00	2.27
37	38	3.874543	ACACATCTGCACGTACTTCAAAA	59.125	39.130	0.00	0.00	0.00	2.44
38	39	3.462982	ACACATCTGCACGTACTTCAAA	58.537	40.909	0.00	0.00	0.00	2.69
39	40	3.106242	ACACATCTGCACGTACTTCAA	57.894	42.857	0.00	0.00	0.00	2.69
40	41	2.812358	ACACATCTGCACGTACTTCA	57.188	45.000	0.00	0.00	0.00	3.02
41	42	4.468095	AAAACACATCTGCACGTACTTC	57.532	40.909	0.00	0.00	0.00	3.01
42	43	4.497340	CCAAAAACACATCTGCACGTACTT	60.497	41.667	0.00	0.00	0.00	2.24
43	44	3.003275	CCAAAAACACATCTGCACGTACT	59.997	43.478	0.00	0.00	0.00	2.73
44	45	3.296628	CCAAAAACACATCTGCACGTAC	58.703	45.455	0.00	0.00	0.00	3.67
45	46	2.292016	CCCAAAAACACATCTGCACGTA	59.708	45.455	0.00	0.00	0.00	3.57
46	47	1.066908	CCCAAAAACACATCTGCACGT	59.933	47.619	0.00	0.00	0.00	4.49
47	48	1.769733	CCCAAAAACACATCTGCACG	58.230	50.000	0.00	0.00	0.00	5.34
48	49	1.202510	TGCCCAAAAACACATCTGCAC	60.203	47.619	0.00	0.00	0.00	4.57
49	50	1.117994	TGCCCAAAAACACATCTGCA	58.882	45.000	0.00	0.00	0.00	4.41
50	51	2.460757	ATGCCCAAAAACACATCTGC	57.539	45.000	0.00	0.00	0.00	4.26
51	52	3.747529	GGAAATGCCCAAAAACACATCTG	59.252	43.478	0.00	0.00	0.00	2.90
52	53	3.647590	AGGAAATGCCCAAAAACACATCT	59.352	39.130	0.00	0.00	37.37	2.90
53	54	4.006780	AGGAAATGCCCAAAAACACATC	57.993	40.909	0.00	0.00	37.37	3.06
54	55	5.760484	ATAGGAAATGCCCAAAAACACAT	57.240	34.783	0.00	0.00	37.37	3.21
55	56	5.559148	AATAGGAAATGCCCAAAAACACA	57.441	34.783	0.00	0.00	37.37	3.72
56	57	5.181056	CCAAATAGGAAATGCCCAAAAACAC	59.819	40.000	0.00	0.00	41.22	3.32
57	58	5.312079	CCAAATAGGAAATGCCCAAAAACA	58.688	37.500	0.00	0.00	41.22	2.83
58	59	4.155826	GCCAAATAGGAAATGCCCAAAAAC	59.844	41.667	0.00	0.00	41.22	2.43
59	60	4.331108	GCCAAATAGGAAATGCCCAAAAA	58.669	39.130	0.00	0.00	41.22	1.94
60	61	3.618507	CGCCAAATAGGAAATGCCCAAAA	60.619	43.478	0.00	0.00	41.22	2.44
61	62	2.093764	CGCCAAATAGGAAATGCCCAAA	60.094	45.455	0.00	0.00	41.22	3.28
62	63	1.480137	CGCCAAATAGGAAATGCCCAA	59.520	47.619	0.00	0.00	41.22	4.12
148	149	0.103208	CGAGAACCAGCGCCTAGATT	59.897	55.000	2.29	0.00	0.00	2.40
235	280	8.652810	AAAAAGTTCATCCATTTTCAAGACAG	57.347	30.769	0.00	0.00	0.00	3.51
471	581	8.923270	TGAAATGGAGAAAGGTTTACAGATTTT	58.077	29.630	0.00	0.00	0.00	1.82
549	663	3.083349	TGCTAGCATGGTCCGGCT	61.083	61.111	14.93	12.05	43.94	5.52
555	669	2.513204	CAGCGCTGCTAGCATGGT	60.513	61.111	26.68	16.36	42.58	3.55
632	746	8.647796	CAATTAAAGAATTTATAGGGGTTCCCC	58.352	37.037	18.61	18.61	41.95	4.81
633	747	9.209048	ACAATTAAAGAATTTATAGGGGTTCCC	57.791	33.333	0.00	0.00	40.76	3.97
652	766	9.995003	TCCTACCTCGTAACTTTAAACAATTAA	57.005	29.630	0.00	0.00	0.00	1.40
653	767	9.995003	TTCCTACCTCGTAACTTTAAACAATTA	57.005	29.630	0.00	0.00	0.00	1.40
654	768	8.907222	TTCCTACCTCGTAACTTTAAACAATT	57.093	30.769	0.00	0.00	0.00	2.32
655	769	8.943002	CATTCCTACCTCGTAACTTTAAACAAT	58.057	33.333	0.00	0.00	0.00	2.71
656	770	7.933033	ACATTCCTACCTCGTAACTTTAAACAA	59.067	33.333	0.00	0.00	0.00	2.83
657	771	7.444299	ACATTCCTACCTCGTAACTTTAAACA	58.556	34.615	0.00	0.00	0.00	2.83
658	772	7.895975	ACATTCCTACCTCGTAACTTTAAAC	57.104	36.000	0.00	0.00	0.00	2.01
659	773	8.907222	AAACATTCCTACCTCGTAACTTTAAA	57.093	30.769	0.00	0.00	0.00	1.52
660	774	8.907222	AAAACATTCCTACCTCGTAACTTTAA	57.093	30.769	0.00	0.00	0.00	1.52
661	775	8.907222	AAAAACATTCCTACCTCGTAACTTTA	57.093	30.769	0.00	0.00	0.00	1.85
662	776	7.812690	AAAAACATTCCTACCTCGTAACTTT	57.187	32.000	0.00	0.00	0.00	2.66
719	838	1.294138	GCCACAACTACACGGCCTA	59.706	57.895	0.00	0.00	38.67	3.93
726	845	3.579534	TTTAACTGGGCCACAACTACA	57.420	42.857	0.00	0.00	0.00	2.74
748	867	5.378230	AGCAAATGGGATCTGTATTCTGA	57.622	39.130	0.00	0.00	0.00	3.27
760	879	1.704628	TCCACAGAGAAGCAAATGGGA	59.295	47.619	0.00	0.00	0.00	4.37
810	932	2.309613	AGTTCCACGTGTACTACACCA	58.690	47.619	15.65	0.00	45.93	4.17
833	955	3.479269	GCGAGCCAAGAACGACGG	61.479	66.667	0.00	0.00	0.00	4.79
880	1002	3.477530	AGAAGGTTTGTTTTCTAGCGCT	58.522	40.909	17.26	17.26	32.13	5.92
889	1011	1.407618	GTGGGCGAAGAAGGTTTGTTT	59.592	47.619	0.00	0.00	0.00	2.83
969	1091	0.577269	CTATCTTGCGCGGTTGCTAC	59.423	55.000	8.83	0.00	39.65	3.58
980	1102	5.334724	GCCATCAACTAATCAGCTATCTTGC	60.335	44.000	0.00	0.00	0.00	4.01
1152	1274	1.642952	GGAAGTAGTGCTGCTGCTGC	61.643	60.000	22.51	22.51	40.11	5.25
1872	2005	4.235762	AACACCCGCAGCGTCAGT	62.236	61.111	15.05	5.25	0.00	3.41
2156	2289	4.343526	ACAGGTATACAGATCAGCTCCAAG	59.656	45.833	5.01	0.00	0.00	3.61
2187	2320	3.378427	AGCGGGAATTTACAGATCTTTGC	59.622	43.478	0.00	0.00	0.00	3.68
2188	2321	4.035675	GGAGCGGGAATTTACAGATCTTTG	59.964	45.833	0.00	0.00	0.00	2.77
2189	2322	4.200092	GGAGCGGGAATTTACAGATCTTT	58.800	43.478	0.00	0.00	0.00	2.52
2190	2323	3.199946	TGGAGCGGGAATTTACAGATCTT	59.800	43.478	0.00	0.00	0.00	2.40
2195	2328	2.403252	ACTGGAGCGGGAATTTACAG	57.597	50.000	0.00	0.00	0.00	2.74
2210	2343	3.937706	CTGTTGGAGATGCTCTAAACTGG	59.062	47.826	0.00	0.00	33.06	4.00
2212	2345	3.620966	GCCTGTTGGAGATGCTCTAAACT	60.621	47.826	0.00	0.00	33.06	2.66
2246	2379	3.381169	CTAATTTGCAGCGCGGCGT	62.381	57.895	26.78	13.11	36.28	5.68
2255	2388	3.668491	GCGCTAAAACCGACTAATTTGCA	60.668	43.478	0.00	0.00	0.00	4.08
2285	2462	1.791662	CGCGCCCAACTCGTTTTAT	59.208	52.632	0.00	0.00	0.00	1.40
2388	2568	3.407967	GATGGGGGTGGAAGCGGA	61.408	66.667	0.00	0.00	33.03	5.54
2487	2674	3.444417	TAGGAGGGGATGGGGCGA	61.444	66.667	0.00	0.00	0.00	5.54
2533	2720	1.546476	CTTAGGCGCTATTCCTCGGAT	59.454	52.381	7.64	0.00	35.21	4.18
2668	2855	6.467723	ACGAACTCATCTACAATGTTCAAC	57.532	37.500	0.00	0.00	37.46	3.18
2712	2899	7.082316	TCCTCCTCCTCTTCCATATCAAATTA	58.918	38.462	0.00	0.00	0.00	1.40
2791	2981	4.837093	ATTTTCTCTCGACCCATAACCA	57.163	40.909	0.00	0.00	0.00	3.67
2896	3086	1.160329	GCTCATGCTAAACCGGCGAT	61.160	55.000	9.30	0.00	36.03	4.58
2909	3099	2.868583	CCTGAATAAGTCGGTGCTCATG	59.131	50.000	0.00	0.00	0.00	3.07
2924	3114	0.393402	TCTCTGCAATGCGCCTGAAT	60.393	50.000	4.18	0.00	41.33	2.57
2951	3141	0.966179	GGAAAAACCGGTCATGGCTT	59.034	50.000	8.04	0.00	0.00	4.35
3103	3293	0.798159	GCGCTTGACACACATGATGA	59.202	50.000	0.00	0.00	0.00	2.92

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.