AutoCloner

Multiple sequence alignment - TraesCS5D01G422100

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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	TraesCS5D01G422100	chr5D	100.000	4264	0	0	1	4264	482141211	482145474	0.000000e+00	7875.0
1	TraesCS5D01G422100	chr5D	86.143	433	35	13	3698	4113	482151035	482151459	1.090000e-120	444.0
2	TraesCS5D01G422100	chr5D	93.571	140	5	1	88	227	482116494	482116629	5.590000e-49	206.0
3	TraesCS5D01G422100	chr5D	91.209	91	7	1	4105	4195	482164886	482164975	5.790000e-24	122.0
4	TraesCS5D01G422100	chr5D	94.118	51	3	0	4194	4244	482166736	482166786	1.270000e-10	78.7
5	TraesCS5D01G422100	chr5B	93.742	3292	127	31	1034	4264	591521737	591525010	0.000000e+00	4865.0
6	TraesCS5D01G422100	chr5B	92.121	495	34	3	545	1034	591521211	591521705	0.000000e+00	693.0
7	TraesCS5D01G422100	chr5B	88.132	455	36	6	88	534	591514782	591515226	3.780000e-145	525.0
8	TraesCS5D01G422100	chr5B	86.542	483	42	7	69	548	591520705	591521167	1.060000e-140	510.0
9	TraesCS5D01G422100	chr5B	90.820	305	27	1	547	850	591515288	591515592	1.430000e-109	407.0
10	TraesCS5D01G422100	chr5B	96.244	213	8	0	819	1031	591515593	591515805	2.440000e-92	350.0
11	TraesCS5D01G422100	chr5B	95.833	48	2	0	18	65	591520634	591520681	1.270000e-10	78.7
12	TraesCS5D01G422100	chr5B	80.734	109	9	5	287	395	591521017	591520921	1.640000e-09	75.0
13	TraesCS5D01G422100	chr5A	96.843	2819	83	2	1034	3848	601680141	601682957	0.000000e+00	4708.0
14	TraesCS5D01G422100	chr5A	91.296	494	32	6	545	1034	601679623	601680109	0.000000e+00	664.0
15	TraesCS5D01G422100	chr5A	90.578	467	26	9	88	548	601679125	601679579	1.700000e-168	603.0
16	TraesCS5D01G422100	chr5A	87.173	421	36	10	3841	4244	601682982	601683401	3.000000e-126	462.0
17	TraesCS5D01G422100	chr7A	86.790	2642	317	29	1086	3706	20492157	20494787	0.000000e+00	2916.0
18	TraesCS5D01G422100	chr7A	84.523	2578	374	22	1034	3597	20659899	20662465	0.000000e+00	2527.0
19	TraesCS5D01G422100	chr7A	84.190	2549	376	20	1034	3570	20651055	20653588	0.000000e+00	2449.0
20	TraesCS5D01G422100	chr7A	84.311	2505	369	18	1036	3533	20980856	20983343	0.000000e+00	2427.0
21	TraesCS5D01G422100	chr7A	83.340	2599	406	23	1034	3618	20966528	20969113	0.000000e+00	2375.0
22	TraesCS5D01G422100	chr7A	86.709	316	32	8	729	1034	20721311	20721626	4.080000e-90	342.0
23	TraesCS5D01G422100	chr7A	83.621	232	34	2	807	1034	20588739	20588970	9.290000e-52	215.0
24	TraesCS5D01G422100	chr7A	84.404	218	33	1	817	1034	20650807	20651023	3.340000e-51	213.0
25	TraesCS5D01G422100	chr7D	85.060	2577	362	20	1034	3597	20404553	20407119	0.000000e+00	2604.0
26	TraesCS5D01G422100	chr7D	83.851	2545	390	19	1034	3569	20460669	20463201	0.000000e+00	2403.0
27	TraesCS5D01G422100	chr7D	86.306	314	33	7	729	1032	20404206	20404519	2.460000e-87	333.0
28	TraesCS5D01G422100	chr7D	85.388	219	31	1	817	1034	20547346	20547564	4.290000e-55	226.0
29	TraesCS5D01G422100	chr7D	81.081	111	17	4	287	395	600949141	600949249	7.600000e-13	86.1
30	TraesCS5D01G422100	chr2A	84.615	221	29	4	817	1034	733087777	733087995	9.290000e-52	215.0
31	TraesCS5D01G422100	chr4B	83.333	114	19	0	287	400	478975583	478975696	5.830000e-19	106.0
32	TraesCS5D01G422100	chr7B	80.392	102	20	0	293	394	439556106	439556207	1.270000e-10	78.7
33	TraesCS5D01G422100	chr7B	78.947	114	20	4	289	400	465122707	465122818	1.640000e-09	75.0

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	TraesCS5D01G422100	chr5D	482141211	482145474	4263	False	7875.000000	7875	100.0000	1	4264	1	chr5D.!!$F2	4263
1	TraesCS5D01G422100	chr5B	591520634	591525010	4376	False	1536.675000	4865	92.0595	18	4264	4	chr5B.!!$F2	4246
2	TraesCS5D01G422100	chr5B	591514782	591515805	1023	False	427.333333	525	91.7320	88	1031	3	chr5B.!!$F1	943
3	TraesCS5D01G422100	chr5A	601679125	601683401	4276	False	1609.250000	4708	91.4725	88	4244	4	chr5A.!!$F1	4156
4	TraesCS5D01G422100	chr7A	20492157	20494787	2630	False	2916.000000	2916	86.7900	1086	3706	1	chr7A.!!$F1	2620
5	TraesCS5D01G422100	chr7A	20659899	20662465	2566	False	2527.000000	2527	84.5230	1034	3597	1	chr7A.!!$F3	2563
6	TraesCS5D01G422100	chr7A	20980856	20983343	2487	False	2427.000000	2427	84.3110	1036	3533	1	chr7A.!!$F6	2497
7	TraesCS5D01G422100	chr7A	20966528	20969113	2585	False	2375.000000	2375	83.3400	1034	3618	1	chr7A.!!$F5	2584
8	TraesCS5D01G422100	chr7A	20650807	20653588	2781	False	1331.000000	2449	84.2970	817	3570	2	chr7A.!!$F7	2753
9	TraesCS5D01G422100	chr7D	20460669	20463201	2532	False	2403.000000	2403	83.8510	1034	3569	1	chr7D.!!$F1	2535
10	TraesCS5D01G422100	chr7D	20404206	20407119	2913	False	1468.500000	2604	85.6830	729	3597	2	chr7D.!!$F4	2868

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
249	281	0.398098	TTCATACTCCCTCCGTCCCC	60.398	60.000	0.00	0.00	0.00	4.81	F
894	1023	0.886490	GATCGGAATCGCCTTGGCAT	60.886	55.000	12.45	2.03	36.13	4.40	F
1113	1274	2.158623	TGGTCAGGAACATGATATGGGC	60.159	50.000	0.00	0.00	33.60	5.36	F
1792	1962	2.331132	GCTGCACTTGCCTCTCCAC	61.331	63.158	0.00	0.00	41.18	4.02	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1671	1841	1.067846	TCTGGAGTCCAAACATCGTCG	60.068	52.381	14.17	30.80	5.12	R
1921	2091	1.586541	GCAAGCCTTTACACCTGCC	59.413	57.895	0.00	0.00	4.85	R
2376	2546	4.688879	TCACATTTAGCCTCTTGTGTAACG	59.311	41.667	7.16	42.39	3.18	R
3289	3466	0.605589	GGAAACCACCCCGTGAGAAG	60.606	60.000	0.00	35.23	2.85	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
25	26	4.569966	CCTAGCAGAGTAGCAGTCAAATTG	59.430	45.833	0.00	0.00	36.85	2.32
61	62	4.576463	ACGATTTATGGTCCTTGCATCTTC	59.424	41.667	0.00	0.00	0.00	2.87
65	66	7.173907	CGATTTATGGTCCTTGCATCTTCTTAT	59.826	37.037	0.00	0.00	0.00	1.73
67	68	8.593945	TTTATGGTCCTTGCATCTTCTTATTT	57.406	30.769	0.00	0.00	0.00	1.40
74	95	9.914131	GTCCTTGCATCTTCTTATTTTTAGTTT	57.086	29.630	0.00	0.00	0.00	2.66
78	99	8.226543	TGCATCTTCTTATTTTTAGTTTTGCG	57.773	30.769	0.00	0.00	0.00	4.85
108	129	6.075280	GCCATTAATTACGGCAATTACTACG	58.925	40.000	16.78	0.00	45.52	3.51
109	130	6.293027	GCCATTAATTACGGCAATTACTACGT	60.293	38.462	16.78	0.00	45.52	3.57
110	131	7.095691	GCCATTAATTACGGCAATTACTACGTA	60.096	37.037	16.78	0.00	45.52	3.57
111	132	8.216453	CCATTAATTACGGCAATTACTACGTAC	58.784	37.037	0.00	0.00	40.92	3.67
118	139	3.192466	GCAATTACTACGTACCACCCAG	58.808	50.000	0.00	0.00	0.00	4.45
249	281	0.398098	TTCATACTCCCTCCGTCCCC	60.398	60.000	0.00	0.00	0.00	4.81
261	293	1.524008	CCGTCCCCAAAAGCTTGTCC	61.524	60.000	0.00	0.00	0.00	4.02
264	296	2.812613	CGTCCCCAAAAGCTTGTCCTAA	60.813	50.000	0.00	0.00	0.00	2.69
297	329	3.053831	ACAGATGTACCGTCCCAAAAG	57.946	47.619	0.00	0.00	0.00	2.27
403	435	2.844348	AGATTTGTGGGACGGAGGTAAT	59.156	45.455	0.00	0.00	0.00	1.89
404	436	4.035112	AGATTTGTGGGACGGAGGTAATA	58.965	43.478	0.00	0.00	0.00	0.98
405	437	3.615224	TTTGTGGGACGGAGGTAATAC	57.385	47.619	0.00	0.00	0.00	1.89
406	438	2.537633	TGTGGGACGGAGGTAATACT	57.462	50.000	0.00	0.00	0.00	2.12
467	500	2.736721	TCAGCATTCTTGTTACGTGAGC	59.263	45.455	0.00	0.00	0.00	4.26
479	512	1.813513	ACGTGAGCAAATCCTGAAGG	58.186	50.000	0.00	0.00	0.00	3.46
513	546	2.477525	CGAGGTCTCTTAGTTACGGCAC	60.478	54.545	0.00	0.00	0.00	5.01
542	575	5.617252	TGTTGACGTTTCCTAAAGATTCCT	58.383	37.500	0.00	0.00	0.00	3.36
543	576	5.468746	TGTTGACGTTTCCTAAAGATTCCTG	59.531	40.000	0.00	0.00	0.00	3.86
563	645	6.303054	TCCTGGAACATGTCAAATAAGTTCA	58.697	36.000	0.00	0.00	40.11	3.18
620	702	4.098501	GGGCATTTATTCTTGAACCTGAGG	59.901	45.833	0.00	0.00	0.00	3.86
630	712	2.917933	TGAACCTGAGGTGTCACTTTG	58.082	47.619	4.15	0.00	35.34	2.77
676	759	7.442969	AGTTATTTGGTCGAGTGTCATTTGTTA	59.557	33.333	0.00	0.00	0.00	2.41
715	799	1.656818	AATTTGCCGCAGTCGATGGG	61.657	55.000	0.00	0.00	41.42	4.00
732	816	1.980844	GGAACTTCCCGCCACTAGT	59.019	57.895	0.00	0.00	0.00	2.57
797	886	7.452880	TTGCAGTGGCCATTCTAATAATATC	57.547	36.000	9.72	0.00	40.13	1.63
894	1023	0.886490	GATCGGAATCGCCTTGGCAT	60.886	55.000	12.45	2.03	36.13	4.40
962	1091	4.569943	CACAACTACAAGAGCTACATGGT	58.430	43.478	0.00	0.00	0.00	3.55
1110	1271	6.820335	TCTAGTTGGTCAGGAACATGATATG	58.180	40.000	0.00	0.00	0.00	1.78
1113	1274	2.158623	TGGTCAGGAACATGATATGGGC	60.159	50.000	0.00	0.00	33.60	5.36
1719	1889	6.932356	TTTGATGATTTGTCTAGGATGCTC	57.068	37.500	0.00	0.00	0.00	4.26
1792	1962	2.331132	GCTGCACTTGCCTCTCCAC	61.331	63.158	0.00	0.00	41.18	4.02
1854	2024	6.441604	AGGCATGGGATCTCTTTTGTAAAAAT	59.558	34.615	0.00	0.00	0.00	1.82
1856	2026	8.424133	GGCATGGGATCTCTTTTGTAAAAATAT	58.576	33.333	0.00	0.00	0.00	1.28
1915	2085	4.013050	GCTAAAGCCTTTGTCCAGAGAAT	58.987	43.478	0.00	0.00	34.31	2.40
1921	2091	5.006386	AGCCTTTGTCCAGAGAATTAGTTG	58.994	41.667	0.00	0.00	0.00	3.16
2213	2383	3.164269	CATCGAGGGGAGGGGTGG	61.164	72.222	0.00	0.00	0.00	4.61
2376	2546	2.140065	GCCAGAAGAACTGTTTTGGC	57.860	50.000	17.30	17.30	44.40	4.52
2509	2682	2.609459	CGAAGTGTGATTACATCAGGCC	59.391	50.000	0.00	0.00	40.53	5.19
2512	2685	3.548770	AGTGTGATTACATCAGGCCATG	58.451	45.455	5.01	2.95	40.53	3.66
2541	2714	5.066764	GTCACCATTCACTCTACTACCTCTC	59.933	48.000	0.00	0.00	0.00	3.20
2710	2887	6.753279	TGAGAAGCTTTCAAATTTGTTGACAG	59.247	34.615	17.47	3.06	31.38	3.51
3048	3225	3.421919	TCTGTGAATGCAAGTGATGGA	57.578	42.857	0.00	0.00	0.00	3.41
3156	3333	1.898472	TCTCCTCTCTTCCAAGCTGTG	59.102	52.381	0.00	0.00	0.00	3.66
3289	3466	0.798776	CACCGGAGAGCATTTGTCAC	59.201	55.000	9.46	0.00	0.00	3.67
3486	3663	1.927174	CTAGGCTTCCACGAAATCACG	59.073	52.381	0.00	0.00	39.31	4.35
3618	3800	1.067916	GCCACAAACCAGCCAACTG	59.932	57.895	0.00	0.00	44.05	3.16
3666	3859	5.663795	AAGATGTTGATGTGATACGATGC	57.336	39.130	0.00	0.00	0.00	3.91
3732	3926	2.846193	TGGGTTTCCTCTGTTTCTTCG	58.154	47.619	0.00	0.00	0.00	3.79
3739	3933	2.497675	TCCTCTGTTTCTTCGAGATGGG	59.502	50.000	0.00	0.00	0.00	4.00
3843	4041	3.712881	GTGTGCTCGGTTGTCGGC	61.713	66.667	0.00	0.00	39.77	5.54
3848	4046	3.414700	CTCGGTTGTCGGCTGTGC	61.415	66.667	0.00	0.00	39.77	4.57
3862	4093	1.626654	CTGTGCCTGTTAAGACGCGG	61.627	60.000	12.47	0.00	0.00	6.46
3868	4099	1.352156	CTGTTAAGACGCGGGTGAGC	61.352	60.000	10.96	0.00	0.00	4.26
3880	4111	0.883833	GGGTGAGCTGTGTTTCCATG	59.116	55.000	0.00	0.00	0.00	3.66
3890	4121	4.083802	GCTGTGTTTCCATGTTCAGACTAC	60.084	45.833	0.00	0.00	0.00	2.73
3891	4122	5.290493	TGTGTTTCCATGTTCAGACTACT	57.710	39.130	0.00	0.00	0.00	2.57
3919	4150	2.187946	CTGCGAGTCCCACATCCC	59.812	66.667	0.00	0.00	0.00	3.85
4012	4246	2.230750	AGGCGACAGTTACTGTAAGACC	59.769	50.000	18.63	15.83	45.44	3.85
4069	4313	5.477291	ACGATACCATCCCTGAAGTATGTAG	59.523	44.000	0.00	0.00	0.00	2.74
4114	4358	5.239744	TCAGCTGCGGATGTTAAACTTAAAA	59.760	36.000	11.18	0.00	0.00	1.52
4115	4359	5.342259	CAGCTGCGGATGTTAAACTTAAAAC	59.658	40.000	0.00	0.00	0.00	2.43
4116	4360	5.009210	AGCTGCGGATGTTAAACTTAAAACA	59.991	36.000	0.00	0.00	39.73	2.83
4117	4361	5.116528	GCTGCGGATGTTAAACTTAAAACAC	59.883	40.000	0.00	0.00	38.35	3.32
4129	4373	5.635549	ACTTAAAACACTTTGATTTGCGC	57.364	34.783	0.00	0.00	0.00	6.09
4157	4403	1.208535	TGCTCGGGTATTCATTTCCGT	59.791	47.619	0.00	0.00	42.71	4.69
4159	4405	2.031683	GCTCGGGTATTCATTTCCGTTG	59.968	50.000	0.00	0.00	42.71	4.10
4169	4415	3.615155	TCATTTCCGTTGTGATATGGCA	58.385	40.909	0.00	0.00	0.00	4.92
4178	4424	4.436050	CGTTGTGATATGGCAACTGTCTTC	60.436	45.833	13.69	0.00	41.80	2.87
4195	4441	4.201871	TGTCTTCAGTTTTTGCCGTTGTAG	60.202	41.667	0.00	0.00	0.00	2.74
4208	4454	2.413837	CGTTGTAGCTTGCTACCTTGT	58.586	47.619	24.44	0.00	0.00	3.16

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	1.107114	GACTGCTACTCTGCTAGGCA	58.893	55.000	0.00	0.00	36.92	4.75
1	2	1.107114	TGACTGCTACTCTGCTAGGC	58.893	55.000	0.00	0.00	0.00	3.93
2	3	3.876274	TTTGACTGCTACTCTGCTAGG	57.124	47.619	0.00	0.00	0.00	3.02
3	4	4.033817	GCAATTTGACTGCTACTCTGCTAG	59.966	45.833	0.00	0.00	36.84	3.42
4	5	3.935203	GCAATTTGACTGCTACTCTGCTA	59.065	43.478	0.00	0.00	36.84	3.49
5	6	2.746362	GCAATTTGACTGCTACTCTGCT	59.254	45.455	0.00	0.00	36.84	4.24
6	7	2.485426	TGCAATTTGACTGCTACTCTGC	59.515	45.455	0.00	0.00	40.59	4.26
7	8	4.453478	TCTTGCAATTTGACTGCTACTCTG	59.547	41.667	0.00	0.00	40.59	3.35
8	9	4.453819	GTCTTGCAATTTGACTGCTACTCT	59.546	41.667	0.00	0.00	40.59	3.24
9	10	4.214119	TGTCTTGCAATTTGACTGCTACTC	59.786	41.667	15.76	0.00	40.59	2.59
10	11	4.136796	TGTCTTGCAATTTGACTGCTACT	58.863	39.130	15.76	0.00	40.59	2.57
11	12	4.488126	TGTCTTGCAATTTGACTGCTAC	57.512	40.909	15.76	0.00	40.59	3.58
12	13	5.710513	AATGTCTTGCAATTTGACTGCTA	57.289	34.783	15.76	0.00	40.59	3.49
13	14	4.595762	AATGTCTTGCAATTTGACTGCT	57.404	36.364	15.76	1.95	40.59	4.24
14	15	4.609783	GCAAATGTCTTGCAATTTGACTGC	60.610	41.667	21.60	16.34	44.34	4.40
15	16	5.013861	GCAAATGTCTTGCAATTTGACTG	57.986	39.130	21.60	11.86	44.34	3.51
25	26	4.266029	CCATAAATCGTGCAAATGTCTTGC	59.734	41.667	2.52	2.52	45.11	4.01
108	129	2.443416	GGGAAATCAACTGGGTGGTAC	58.557	52.381	0.00	0.00	0.00	3.34
109	130	1.356398	GGGGAAATCAACTGGGTGGTA	59.644	52.381	0.00	0.00	0.00	3.25
110	131	0.114364	GGGGAAATCAACTGGGTGGT	59.886	55.000	0.00	0.00	0.00	4.16
111	132	0.614697	GGGGGAAATCAACTGGGTGG	60.615	60.000	0.00	0.00	0.00	4.61
118	139	1.627834	TGGCAATTGGGGGAAATCAAC	59.372	47.619	7.72	0.00	0.00	3.18
249	281	7.706179	TCTTGACAAATTTAGGACAAGCTTTTG	59.294	33.333	12.61	0.00	35.97	2.44
264	296	7.103641	ACGGTACATCTGTATCTTGACAAATT	58.896	34.615	0.00	0.00	33.34	1.82
297	329	5.584253	TGTAGACAGATCTAAGACAAGCC	57.416	43.478	0.00	0.00	39.20	4.35
349	381	9.261180	ACATTTATCTAAATACGGATGTCTGTG	57.739	33.333	4.77	0.00	36.70	3.66
384	416	3.778629	AGTATTACCTCCGTCCCACAAAT	59.221	43.478	0.00	0.00	0.00	2.32
388	420	4.210331	TCTAAGTATTACCTCCGTCCCAC	58.790	47.826	0.00	0.00	0.00	4.61
403	435	4.018490	TGTGGTGCCGTATCTTCTAAGTA	58.982	43.478	0.00	0.00	0.00	2.24
404	436	2.829720	TGTGGTGCCGTATCTTCTAAGT	59.170	45.455	0.00	0.00	0.00	2.24
405	437	3.187700	GTGTGGTGCCGTATCTTCTAAG	58.812	50.000	0.00	0.00	0.00	2.18
406	438	2.563620	TGTGTGGTGCCGTATCTTCTAA	59.436	45.455	0.00	0.00	0.00	2.10
467	500	2.292267	CGATGTCCCCTTCAGGATTTG	58.708	52.381	0.00	0.00	38.48	2.32
542	575	8.298854	CAGAATGAACTTATTTGACATGTTCCA	58.701	33.333	0.00	0.00	39.69	3.53
543	576	8.299570	ACAGAATGAACTTATTTGACATGTTCC	58.700	33.333	0.00	0.00	39.69	3.62
563	645	7.530426	AAATTTGAGGCAAGTAAGACAGAAT	57.470	32.000	0.00	0.00	0.00	2.40
620	702	1.571460	CTCTGCCGCAAAGTGACAC	59.429	57.895	0.00	0.00	0.00	3.67
641	724	3.491639	TCGACCAAATAACTGAACACACG	59.508	43.478	0.00	0.00	0.00	4.49
644	727	4.510340	ACACTCGACCAAATAACTGAACAC	59.490	41.667	0.00	0.00	0.00	3.32
715	799	2.180432	AAACTAGTGGCGGGAAGTTC	57.820	50.000	0.00	0.00	31.15	3.01
759	843	4.046462	CCACTGCAAAATGAACAAGTGAG	58.954	43.478	2.32	0.00	0.00	3.51
766	854	2.460757	ATGGCCACTGCAAAATGAAC	57.539	45.000	8.16	0.00	40.13	3.18
797	886	0.404040	TTTGGTGGTGGCCTTCCTAG	59.596	55.000	16.22	0.00	0.00	3.02
894	1023	1.234615	GCTTGGTTTGCCGCTCTACA	61.235	55.000	0.00	0.00	37.67	2.74
1110	1271	4.929819	TTTCAGGTAAAAACAAGAGCCC	57.070	40.909	0.00	0.00	0.00	5.19
1113	1274	5.753438	GCCCTTTTTCAGGTAAAAACAAGAG	59.247	40.000	0.00	0.00	41.13	2.85
1566	1736	9.809096	TTAGATAGAACACTGACATCATCTTTC	57.191	33.333	0.00	0.00	0.00	2.62
1671	1841	1.067846	TCTGGAGTCCAAACATCGTCG	60.068	52.381	14.17	0.00	30.80	5.12
1792	1962	8.635877	AAAGCTTCTAGTGTTAAGATATGTCG	57.364	34.615	0.00	0.00	0.00	4.35
1894	2064	6.881602	ACTAATTCTCTGGACAAAGGCTTTAG	59.118	38.462	12.95	6.66	0.00	1.85
1915	2085	2.107552	AGCCTTTACACCTGCCAACTAA	59.892	45.455	0.00	0.00	0.00	2.24
1921	2091	1.586541	GCAAGCCTTTACACCTGCC	59.413	57.895	0.00	0.00	0.00	4.85
2213	2383	6.102663	TCTGCTACTTCTTCTAATGTGCTTC	58.897	40.000	0.00	0.00	0.00	3.86
2376	2546	4.688879	TCACATTTAGCCTCTTGTGTAACG	59.311	41.667	7.16	0.00	42.39	3.18
2541	2714	7.763528	GTCATATATCTTGACTCCTTGCATAGG	59.236	40.741	10.15	8.22	40.26	2.57
2710	2887	8.997621	TGTATGTCAGATTTACAAAGGTCTAC	57.002	34.615	0.00	0.00	0.00	2.59
3048	3225	6.966534	ACATTCAACAAGAGAACCTCATTT	57.033	33.333	0.00	0.00	32.06	2.32
3156	3333	5.859205	ATTCATACAAATTCTGCCCTTCC	57.141	39.130	0.00	0.00	0.00	3.46
3289	3466	0.605589	GGAAACCACCCCGTGAGAAG	60.606	60.000	0.00	0.00	35.23	2.85
3666	3859	2.418197	CCGGTGACACCTACATAACCAG	60.418	54.545	22.14	2.69	35.66	4.00
3732	3926	2.093235	AGAAAGTGCAGTAGCCCATCTC	60.093	50.000	0.00	0.00	41.13	2.75
3811	4005	2.411748	AGCACACGATCAACACATTACG	59.588	45.455	0.00	0.00	0.00	3.18
3843	4041	1.626654	CCGCGTCTTAACAGGCACAG	61.627	60.000	4.92	0.00	0.00	3.66
3848	4046	0.736325	CTCACCCGCGTCTTAACAGG	60.736	60.000	4.92	0.00	0.00	4.00
3850	4048	1.373748	GCTCACCCGCGTCTTAACA	60.374	57.895	4.92	0.00	0.00	2.41
3851	4049	1.080025	AGCTCACCCGCGTCTTAAC	60.080	57.895	4.92	0.00	34.40	2.01
3853	4051	2.273179	ACAGCTCACCCGCGTCTTA	61.273	57.895	4.92	0.00	34.40	2.10
3854	4052	3.616721	ACAGCTCACCCGCGTCTT	61.617	61.111	4.92	0.00	34.40	3.01
3855	4053	4.363990	CACAGCTCACCCGCGTCT	62.364	66.667	4.92	0.00	34.40	4.18
3857	4055	3.750373	AAACACAGCTCACCCGCGT	62.750	57.895	4.92	0.00	34.40	6.01
3868	4099	5.178252	CAGTAGTCTGAACATGGAAACACAG	59.822	44.000	0.00	0.00	43.59	3.66
3880	4111	0.389166	AGCGCTGCAGTAGTCTGAAC	60.389	55.000	10.39	0.00	43.76	3.18
3906	4137	2.185310	AACAGCGGGATGTGGGACTC	62.185	60.000	0.00	0.00	32.52	3.36
3919	4150	0.925267	CAAGCACACGAACAACAGCG	60.925	55.000	0.00	0.00	0.00	5.18
3999	4233	5.952033	ACTCAATCTCGGTCTTACAGTAAC	58.048	41.667	0.00	0.00	0.00	2.50
4012	4246	7.850003	GCAATATGAAAAGAAGACTCAATCTCG	59.150	37.037	0.00	0.00	36.27	4.04
4069	4313	4.092821	TGAAATAGCACACACGAATAGCAC	59.907	41.667	0.00	0.00	0.00	4.40
4114	4358	6.034898	GCATTATTAAGCGCAAATCAAAGTGT	59.965	34.615	11.47	0.00	0.00	3.55
4115	4359	6.254157	AGCATTATTAAGCGCAAATCAAAGTG	59.746	34.615	11.47	2.93	35.48	3.16
4116	4360	6.332630	AGCATTATTAAGCGCAAATCAAAGT	58.667	32.000	11.47	0.00	35.48	2.66
4117	4361	6.344468	CGAGCATTATTAAGCGCAAATCAAAG	60.344	38.462	11.47	2.07	35.48	2.77
4129	4373	8.237267	GGAAATGAATACCCGAGCATTATTAAG	58.763	37.037	0.00	0.00	31.30	1.85
4157	4403	4.650734	TGAAGACAGTTGCCATATCACAA	58.349	39.130	0.00	0.00	0.00	3.33
4159	4405	4.871993	CTGAAGACAGTTGCCATATCAC	57.128	45.455	0.00	0.00	39.11	3.06
4178	4424	2.774439	AGCTACAACGGCAAAAACTG	57.226	45.000	0.00	0.00	0.00	3.16
4195	4441	3.990318	AAACAGAACAAGGTAGCAAGC	57.010	42.857	0.00	0.00	0.00	4.01

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.