AutoCloner

Multiple sequence alignment - TraesCS6D01G048700

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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	TraesCS6D01G048700	chr6D	100.000	3269	0	0	1	3269	23633145	23629877	0.000000e+00	6037.0
1	TraesCS6D01G048700	chr6D	88.339	1355	142	12	959	2299	23642240	23640888	0.000000e+00	1613.0
2	TraesCS6D01G048700	chr6D	91.603	655	28	4	2642	3269	423442415	423443069	0.000000e+00	880.0
3	TraesCS6D01G048700	chr6B	91.031	1862	103	44	522	2338	38541935	38540093	0.000000e+00	2455.0
4	TraesCS6D01G048700	chr6B	92.516	1550	85	16	808	2341	37645157	37643623	0.000000e+00	2191.0
5	TraesCS6D01G048700	chr6B	89.877	1709	131	25	522	2216	46661485	46663165	0.000000e+00	2159.0
6	TraesCS6D01G048700	chr6B	91.667	1560	100	11	888	2435	37035364	37036905	0.000000e+00	2134.0
7	TraesCS6D01G048700	chr6B	88.487	1355	140	11	959	2299	37653007	37651655	0.000000e+00	1624.0
8	TraesCS6D01G048700	chr6B	86.813	1274	140	21	999	2258	38625755	38624496	0.000000e+00	1397.0
9	TraesCS6D01G048700	chr6B	92.973	185	13	0	2427	2611	37037101	37037285	1.490000e-68	270.0
10	TraesCS6D01G048700	chr6B	91.758	182	15	0	2428	2609	46670501	46670682	1.510000e-63	254.0
11	TraesCS6D01G048700	chr6B	82.800	250	19	11	522	747	37645534	37645285	5.530000e-48	202.0
12	TraesCS6D01G048700	chr6B	93.750	112	6	1	2231	2342	46670080	46670190	2.020000e-37	167.0
13	TraesCS6D01G048700	chr6B	90.756	119	8	2	411	526	38542078	38541960	4.370000e-34	156.0
14	TraesCS6D01G048700	chr6B	80.252	238	22	9	312	526	46661225	46661460	4.370000e-34	156.0
15	TraesCS6D01G048700	chr6B	95.652	92	4	0	2337	2428	37774643	37774552	7.310000e-32	148.0
16	TraesCS6D01G048700	chr6B	88.333	120	6	4	660	776	37789991	37789877	1.580000e-28	137.0
17	TraesCS6D01G048700	chr6B	84.076	157	9	7	59	200	46659184	46659339	1.580000e-28	137.0
18	TraesCS6D01G048700	chr6B	80.000	125	11	7	2436	2558	37040013	37040125	2.700000e-11	80.5
19	TraesCS6D01G048700	chr6B	100.000	36	0	0	1	36	38559119	38559084	2.110000e-07	67.6
20	TraesCS6D01G048700	chr6B	97.222	36	1	0	1	36	37646551	37646516	9.790000e-06	62.1
21	TraesCS6D01G048700	chr6B	100.000	31	0	0	170	200	37646200	37646170	1.270000e-04	58.4
22	TraesCS6D01G048700	chr6A	94.751	1505	70	3	847	2342	22193620	22192116	0.000000e+00	2333.0
23	TraesCS6D01G048700	chr6A	88.856	1337	131	13	974	2295	22201007	22199674	0.000000e+00	1628.0
24	TraesCS6D01G048700	chr6A	88.000	175	13	1	2445	2611	22191745	22191571	1.990000e-47	200.0
25	TraesCS6D01G048700	chr6A	80.851	282	26	13	522	776	22193918	22193638	2.570000e-46	196.0
26	TraesCS6D01G048700	chr6A	94.000	100	3	3	2337	2435	22192093	22191996	7.310000e-32	148.0
27	TraesCS6D01G048700	chr6A	94.118	85	4	1	443	526	22194027	22193943	9.520000e-26	128.0
28	TraesCS6D01G048700	chr6A	86.111	108	4	3	221	318	22194264	22194158	4.460000e-19	106.0
29	TraesCS6D01G048700	chr6A	100.000	36	0	0	1	36	22194924	22194889	2.110000e-07	67.6
30	TraesCS6D01G048700	chr6A	100.000	31	0	0	170	200	22194366	22194336	1.270000e-04	58.4
31	TraesCS6D01G048700	chr3D	94.819	637	22	3	2644	3269	538408369	538407733	0.000000e+00	983.0
32	TraesCS6D01G048700	chr3D	91.862	639	37	3	2646	3269	31387376	31388014	0.000000e+00	878.0
33	TraesCS6D01G048700	chr3D	90.840	655	28	6	2647	3269	20701708	20701054	0.000000e+00	848.0
34	TraesCS6D01G048700	chr2D	92.061	655	25	4	2642	3269	41997811	41998465	0.000000e+00	896.0
35	TraesCS6D01G048700	chr1D	91.768	656	27	4	2641	3269	279085148	279084493	0.000000e+00	887.0
36	TraesCS6D01G048700	chr1D	88.467	659	29	10	2643	3269	235984097	235984740	0.000000e+00	752.0
37	TraesCS6D01G048700	chr7D	90.440	659	31	8	2643	3269	204101142	204100484	0.000000e+00	839.0
38	TraesCS6D01G048700	chr5D	87.751	449	37	8	2646	3082	356798762	356798320	2.910000e-140	508.0
39	TraesCS6D01G048700	chr3B	86.026	458	50	4	2638	3082	762018389	762018845	2.280000e-131	479.0
40	TraesCS6D01G048700	chr2B	85.120	457	52	5	2648	3090	13197111	13196657	1.380000e-123	453.0
41	TraesCS6D01G048700	chr7A	84.116	447	36	11	2646	3075	492244897	492244469	1.830000e-107	399.0
42	TraesCS6D01G048700	chr7A	97.222	36	1	0	2	37	74698396	74698431	9.790000e-06	62.1
43	TraesCS6D01G048700	chr5B	95.833	192	5	1	3080	3268	425872739	425872548	1.140000e-79	307.0
44	TraesCS6D01G048700	chr7B	97.222	36	1	0	2	37	73214958	73214923	9.790000e-06	62.1
45	TraesCS6D01G048700	chr1A	97.143	35	1	0	3	37	300580590	300580624	3.520000e-05	60.2
46	TraesCS6D01G048700	chr1B	94.595	37	2	0	1	37	330996055	330996091	1.270000e-04	58.4

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	TraesCS6D01G048700	chr6D	23629877	23633145	3268	True	6037.000000	6037	100.000000	1	3269	1	chr6D.!!$R1	3268
1	TraesCS6D01G048700	chr6D	23640888	23642240	1352	True	1613.000000	1613	88.339000	959	2299	1	chr6D.!!$R2	1340
2	TraesCS6D01G048700	chr6D	423442415	423443069	654	False	880.000000	880	91.603000	2642	3269	1	chr6D.!!$F1	627
3	TraesCS6D01G048700	chr6B	37651655	37653007	1352	True	1624.000000	1624	88.487000	959	2299	1	chr6B.!!$R1	1340
4	TraesCS6D01G048700	chr6B	38624496	38625755	1259	True	1397.000000	1397	86.813000	999	2258	1	chr6B.!!$R5	1259
5	TraesCS6D01G048700	chr6B	38540093	38542078	1985	True	1305.500000	2455	90.893500	411	2338	2	chr6B.!!$R7	1927
6	TraesCS6D01G048700	chr6B	37035364	37040125	4761	False	828.166667	2134	88.213333	888	2611	3	chr6B.!!$F1	1723
7	TraesCS6D01G048700	chr6B	46659184	46663165	3981	False	817.333333	2159	84.735000	59	2216	3	chr6B.!!$F2	2157
8	TraesCS6D01G048700	chr6B	37643623	37646551	2928	True	628.375000	2191	93.134500	1	2341	4	chr6B.!!$R6	2340
9	TraesCS6D01G048700	chr6B	46670080	46670682	602	False	210.500000	254	92.754000	2231	2609	2	chr6B.!!$F3	378
10	TraesCS6D01G048700	chr6A	22199674	22201007	1333	True	1628.000000	1628	88.856000	974	2295	1	chr6A.!!$R1	1321
11	TraesCS6D01G048700	chr6A	22191571	22194924	3353	True	404.625000	2333	92.228875	1	2611	8	chr6A.!!$R2	2610
12	TraesCS6D01G048700	chr3D	538407733	538408369	636	True	983.000000	983	94.819000	2644	3269	1	chr3D.!!$R2	625
13	TraesCS6D01G048700	chr3D	31387376	31388014	638	False	878.000000	878	91.862000	2646	3269	1	chr3D.!!$F1	623
14	TraesCS6D01G048700	chr3D	20701054	20701708	654	True	848.000000	848	90.840000	2647	3269	1	chr3D.!!$R1	622
15	TraesCS6D01G048700	chr2D	41997811	41998465	654	False	896.000000	896	92.061000	2642	3269	1	chr2D.!!$F1	627
16	TraesCS6D01G048700	chr1D	279084493	279085148	655	True	887.000000	887	91.768000	2641	3269	1	chr1D.!!$R1	628
17	TraesCS6D01G048700	chr1D	235984097	235984740	643	False	752.000000	752	88.467000	2643	3269	1	chr1D.!!$F1	626
18	TraesCS6D01G048700	chr7D	204100484	204101142	658	True	839.000000	839	90.440000	2643	3269	1	chr7D.!!$R1	626

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
390	2562	0.106868	CAGCCCCTGATGAAGATGCA	60.107	55.0	0.0	0.0	32.44	3.96	F
847	3236	0.109226	CGGAACTGGACTCGAAGGTC	60.109	60.0	0.0	0.0	35.66	3.85	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1837	4276	1.065701	CACCTTGTCGTAGAGATCGGG	59.934	57.143	0.0	0.0	36.95	5.14	R
2630	5384	1.002624	GGTGCGGGGTTCAGATTGA	60.003	57.895	0.0	0.0	0.00	2.57	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
60	379	2.433604	TCATCTCAATGCTCTGGACCTC	59.566	50.000	0.00	0.00	32.58	3.85
108	446	5.418524	ACATAGCTCTAGGATGCTCTGTATG	59.581	44.000	16.31	12.97	42.20	2.39
113	451	4.281657	TCTAGGATGCTCTGTATGTGTGT	58.718	43.478	0.00	0.00	0.00	3.72
145	497	5.836898	TGGATTCGATAAAGGCCTAACTCTA	59.163	40.000	5.16	0.00	0.00	2.43
148	500	3.567164	TCGATAAAGGCCTAACTCTACCG	59.433	47.826	5.16	2.23	0.00	4.02
200	591	1.673920	GTTCGCCAAGGAAGAACACAA	59.326	47.619	17.24	0.00	42.56	3.33
206	644	2.689983	CCAAGGAAGAACACAAGCAAGT	59.310	45.455	0.00	0.00	0.00	3.16
217	659	1.339438	ACAAGCAAGTCTCCATGCGAT	60.339	47.619	0.00	0.00	46.98	4.58
291	743	2.329379	GGCGTAGAGAGTCAACACTTG	58.671	52.381	0.00	0.00	30.63	3.16
349	2521	1.365028	TCCTTACCCTTCCTGCTACCT	59.635	52.381	0.00	0.00	0.00	3.08
356	2528	2.025887	CCCTTCCTGCTACCTTTCACAT	60.026	50.000	0.00	0.00	0.00	3.21
387	2559	1.358830	CCCCAGCCCCTGATGAAGAT	61.359	60.000	0.00	0.00	32.44	2.40
390	2562	0.106868	CAGCCCCTGATGAAGATGCA	60.107	55.000	0.00	0.00	32.44	3.96
392	2564	0.182061	GCCCCTGATGAAGATGCAGA	59.818	55.000	0.00	0.00	0.00	4.26
396	2568	3.552875	CCCTGATGAAGATGCAGACATT	58.447	45.455	0.00	0.00	36.35	2.71
428	2657	2.275134	TTTCTGAGCCAGCAACATCA	57.725	45.000	0.00	0.00	0.00	3.07
527	2787	1.257743	AGCAGGCGAAGTACTTGAGA	58.742	50.000	14.14	0.00	0.00	3.27
538	2798	8.136165	GGCGAAGTACTTGAGATAGAATAAAGA	58.864	37.037	14.14	0.00	0.00	2.52
577	2842	9.617523	ATCAATATAAAAATTCAAAGGGGCAAG	57.382	29.630	0.00	0.00	0.00	4.01
579	2844	8.882736	CAATATAAAAATTCAAAGGGGCAAGTC	58.117	33.333	0.00	0.00	0.00	3.01
583	2848	1.703411	TTCAAAGGGGCAAGTCCAAG	58.297	50.000	0.00	0.00	36.21	3.61
592	2857	1.666189	GGCAAGTCCAAGTAATCTCGC	59.334	52.381	0.00	0.00	34.01	5.03
597	2862	2.103263	AGTCCAAGTAATCTCGCCCATC	59.897	50.000	0.00	0.00	0.00	3.51
599	2864	2.103094	TCCAAGTAATCTCGCCCATCAG	59.897	50.000	0.00	0.00	0.00	2.90
669	2934	9.715123	CGCTGATCACATAATTAATACACAAAA	57.285	29.630	0.00	0.00	0.00	2.44
845	3234	1.215647	CCGGAACTGGACTCGAAGG	59.784	63.158	0.00	0.00	0.00	3.46
846	3235	1.533469	CCGGAACTGGACTCGAAGGT	61.533	60.000	0.00	0.00	0.00	3.50
847	3236	0.109226	CGGAACTGGACTCGAAGGTC	60.109	60.000	0.00	0.00	35.66	3.85
848	3237	0.109226	GGAACTGGACTCGAAGGTCG	60.109	60.000	0.00	0.00	42.10	4.79
949	3355	2.870161	CGGCTGTCTTCGTCGTCG	60.870	66.667	0.00	0.00	38.55	5.12
1931	4370	2.438434	GCGGTTCATGGTCCCCAG	60.438	66.667	0.00	0.00	36.75	4.45
1956	4395	0.664761	AGTTCACGACCGAGTTCGAA	59.335	50.000	2.59	0.00	41.78	3.71
2097	4537	2.932234	CGAGGTGGACGAGCAAGGT	61.932	63.158	0.00	0.00	0.00	3.50
2274	4715	6.472686	AATCCTCTCGCTAACTGAGTAAAT	57.527	37.500	0.00	0.00	34.99	1.40
2342	4793	5.356470	GTGCTGATCTCCATTAAAAAGAGCT	59.644	40.000	0.00	0.00	0.00	4.09
2343	4794	5.948162	TGCTGATCTCCATTAAAAAGAGCTT	59.052	36.000	0.00	0.00	0.00	3.74
2344	4795	6.127814	TGCTGATCTCCATTAAAAAGAGCTTG	60.128	38.462	0.00	0.00	0.00	4.01
2345	4796	6.094603	GCTGATCTCCATTAAAAAGAGCTTGA	59.905	38.462	0.00	0.00	0.00	3.02
2346	4797	7.201803	GCTGATCTCCATTAAAAAGAGCTTGAT	60.202	37.037	0.00	0.00	0.00	2.57
2347	4798	9.334947	CTGATCTCCATTAAAAAGAGCTTGATA	57.665	33.333	0.00	0.00	0.00	2.15
2348	4799	9.113838	TGATCTCCATTAAAAAGAGCTTGATAC	57.886	33.333	0.00	0.00	0.00	2.24
2349	4800	9.113838	GATCTCCATTAAAAAGAGCTTGATACA	57.886	33.333	0.00	0.00	0.00	2.29
2350	4801	9.638176	ATCTCCATTAAAAAGAGCTTGATACAT	57.362	29.630	0.00	0.00	0.00	2.29
2351	4802	9.466497	TCTCCATTAAAAAGAGCTTGATACATT	57.534	29.630	0.00	0.00	0.00	2.71
2381	4876	1.957668	TCATGTCCCAGATCAATGCG	58.042	50.000	0.00	0.00	0.00	4.73
2399	4894	2.035961	TGCGAGGGCATAAGTATGACTC	59.964	50.000	4.20	8.24	46.21	3.36
2439	5177	8.394971	TGAAAAAGAAAGCTCATTGTAGATCA	57.605	30.769	0.00	0.00	0.00	2.92
2461	5207	1.074727	TGGGGATCCAACACAAACGAT	59.925	47.619	15.23	0.00	40.73	3.73
2470	5216	3.562141	CCAACACAAACGATAACAGTCCA	59.438	43.478	0.00	0.00	0.00	4.02
2471	5217	4.523813	CAACACAAACGATAACAGTCCAC	58.476	43.478	0.00	0.00	0.00	4.02
2490	5236	1.067635	ACGCAACCAAAAGGATGATGC	60.068	47.619	0.00	0.00	32.83	3.91
2494	5240	3.841643	CAACCAAAAGGATGATGCTGAC	58.158	45.455	0.00	0.00	0.00	3.51
2551	5305	4.803588	GCAACAATTGTGATTCCCCAATGT	60.804	41.667	12.82	0.00	31.89	2.71
2612	5366	9.937175	GTACCATTTTTCTTTCTCATATGTAGC	57.063	33.333	1.90	0.00	0.00	3.58
2613	5367	8.814038	ACCATTTTTCTTTCTCATATGTAGCT	57.186	30.769	1.90	0.00	0.00	3.32
2615	5369	9.727627	CCATTTTTCTTTCTCATATGTAGCTTC	57.272	33.333	1.90	0.00	0.00	3.86
2619	5373	8.484641	TTTCTTTCTCATATGTAGCTTCACTG	57.515	34.615	1.90	0.00	0.00	3.66
2620	5374	7.175347	TCTTTCTCATATGTAGCTTCACTGT	57.825	36.000	1.90	0.00	0.00	3.55
2621	5375	7.615403	TCTTTCTCATATGTAGCTTCACTGTT	58.385	34.615	1.90	0.00	0.00	3.16
2623	5377	5.111989	TCTCATATGTAGCTTCACTGTTGC	58.888	41.667	1.90	0.00	0.00	4.17
2624	5378	4.191544	TCATATGTAGCTTCACTGTTGCC	58.808	43.478	1.90	0.00	0.00	4.52
2625	5379	2.867109	ATGTAGCTTCACTGTTGCCT	57.133	45.000	0.00	0.00	0.00	4.75
2626	5380	1.882912	TGTAGCTTCACTGTTGCCTG	58.117	50.000	0.00	0.00	0.00	4.85
2627	5381	1.160137	GTAGCTTCACTGTTGCCTGG	58.840	55.000	0.00	0.00	0.00	4.45
2630	5384	1.202976	AGCTTCACTGTTGCCTGGATT	60.203	47.619	0.00	0.00	0.00	3.01
2631	5385	1.200948	GCTTCACTGTTGCCTGGATTC	59.799	52.381	0.00	0.00	0.00	2.52
2632	5386	2.507484	CTTCACTGTTGCCTGGATTCA	58.493	47.619	0.00	0.00	0.00	2.57
2633	5387	2.655090	TCACTGTTGCCTGGATTCAA	57.345	45.000	0.00	0.00	0.00	2.69
2634	5388	3.159213	TCACTGTTGCCTGGATTCAAT	57.841	42.857	0.00	0.00	0.00	2.57
2635	5389	3.084039	TCACTGTTGCCTGGATTCAATC	58.916	45.455	0.00	0.00	0.00	2.67
2636	5390	3.087031	CACTGTTGCCTGGATTCAATCT	58.913	45.455	0.00	0.00	0.00	2.40
2637	5391	3.087031	ACTGTTGCCTGGATTCAATCTG	58.913	45.455	0.00	0.00	0.00	2.90
2638	5392	3.245016	ACTGTTGCCTGGATTCAATCTGA	60.245	43.478	0.00	0.00	0.00	3.27
2639	5393	3.760151	CTGTTGCCTGGATTCAATCTGAA	59.240	43.478	0.00	0.00	41.09	3.02
2983	5819	2.473457	GCGTTTTTGCCCGGATCTA	58.527	52.632	0.73	0.00	0.00	1.98
2994	5830	4.221422	GGATCTAGTGGGCGCGCA	62.221	66.667	34.42	24.55	0.00	6.09

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
36	37	4.657504	AGGTCCAGAGCATTGAGATGAATA	59.342	41.667	0.00	0.00	35.16	1.75
60	379	2.679837	AGTCATTGCAAACCAGCTATCG	59.320	45.455	1.71	0.00	34.99	2.92
120	458	5.308237	AGAGTTAGGCCTTTATCGAATCCAT	59.692	40.000	12.58	0.00	0.00	3.41
145	497	5.892119	TCTCCTTATTGAAGACTATGACGGT	59.108	40.000	0.00	0.00	34.25	4.83
148	500	6.987404	GGGTTCTCCTTATTGAAGACTATGAC	59.013	42.308	0.00	0.00	34.25	3.06
217	659	2.288152	GCTTTCAAGGGCACGATGAAAA	60.288	45.455	19.15	7.78	41.14	2.29
267	709	1.077805	TTGACTCTCTACGCCCCCA	59.922	57.895	0.00	0.00	0.00	4.96
364	2536	4.851252	ATCAGGGGCTGGGGGAGG	62.851	72.222	0.00	0.00	31.51	4.30
365	2537	3.496160	CATCAGGGGCTGGGGGAG	61.496	72.222	0.00	0.00	31.51	4.30
390	2562	4.475016	AGAAATAGGTACTGGGCAATGTCT	59.525	41.667	0.00	0.00	41.52	3.41
392	2564	4.227300	TCAGAAATAGGTACTGGGCAATGT	59.773	41.667	0.00	0.00	41.52	2.71
479	2708	9.846248	TGTCATCATTGAGTTATCTATATGACG	57.154	33.333	0.00	0.00	36.28	4.35
552	2812	8.601546	ACTTGCCCCTTTGAATTTTTATATTGA	58.398	29.630	0.00	0.00	0.00	2.57
577	2842	2.158957	TGATGGGCGAGATTACTTGGAC	60.159	50.000	0.00	0.00	0.00	4.02
579	2844	2.103094	TCTGATGGGCGAGATTACTTGG	59.897	50.000	0.00	0.00	0.00	3.61
583	2848	4.585955	TTAGTCTGATGGGCGAGATTAC	57.414	45.455	0.00	0.00	0.00	1.89
592	2857	5.221185	CCTTGCATTGATTTAGTCTGATGGG	60.221	44.000	0.00	0.00	0.00	4.00
597	2862	4.946157	AGGTCCTTGCATTGATTTAGTCTG	59.054	41.667	0.00	0.00	0.00	3.51
599	2864	6.349300	TCTAGGTCCTTGCATTGATTTAGTC	58.651	40.000	0.00	0.00	0.00	2.59
628	2893	3.882131	AGCGGTGCTGATATTTGGT	57.118	47.368	0.00	0.00	37.57	3.67
689	2981	8.950210	GCAGGAGTATATTAATTGCACACATAT	58.050	33.333	0.00	0.00	0.00	1.78
690	2982	7.390440	GGCAGGAGTATATTAATTGCACACATA	59.610	37.037	7.98	0.00	0.00	2.29
691	2983	6.207417	GGCAGGAGTATATTAATTGCACACAT	59.793	38.462	7.98	0.00	0.00	3.21
692	2984	5.530915	GGCAGGAGTATATTAATTGCACACA	59.469	40.000	7.98	0.00	0.00	3.72
693	2985	5.530915	TGGCAGGAGTATATTAATTGCACAC	59.469	40.000	7.98	0.00	0.00	3.82
845	3234	0.179000	ATGGGCTGATGGACTTCGAC	59.821	55.000	0.00	0.00	0.00	4.20
846	3235	0.911769	AATGGGCTGATGGACTTCGA	59.088	50.000	0.00	0.00	0.00	3.71
847	3236	1.019673	CAATGGGCTGATGGACTTCG	58.980	55.000	0.00	0.00	0.00	3.79
848	3237	1.747355	CACAATGGGCTGATGGACTTC	59.253	52.381	0.00	0.00	0.00	3.01
849	3238	1.843368	CACAATGGGCTGATGGACTT	58.157	50.000	0.00	0.00	0.00	3.01
850	3239	0.682209	GCACAATGGGCTGATGGACT	60.682	55.000	0.00	0.00	0.00	3.85
851	3240	0.966875	TGCACAATGGGCTGATGGAC	60.967	55.000	9.57	0.00	0.00	4.02
852	3241	0.966875	GTGCACAATGGGCTGATGGA	60.967	55.000	13.17	0.00	0.00	3.41
932	3325	2.870161	CGACGACGAAGACAGCCG	60.870	66.667	0.00	0.00	42.66	5.52
933	3326	2.267681	ATCCGACGACGAAGACAGCC	62.268	60.000	9.28	0.00	42.66	4.85
934	3327	0.862283	GATCCGACGACGAAGACAGC	60.862	60.000	9.28	0.00	42.66	4.40
935	3328	0.586748	CGATCCGACGACGAAGACAG	60.587	60.000	9.28	0.00	42.66	3.51
1320	3748	2.755876	ATCGCCGGAGCTCTGTGA	60.756	61.111	21.06	19.31	36.60	3.58
1324	3752	2.811101	CTTGATCGCCGGAGCTCT	59.189	61.111	14.64	0.00	36.60	4.09
1326	3754	3.023949	AAGCTTGATCGCCGGAGCT	62.024	57.895	5.05	6.42	46.71	4.09
1329	3757	1.447838	GACAAGCTTGATCGCCGGA	60.448	57.895	32.50	0.00	0.00	5.14
1531	3959	2.103042	GGATGCGCTGCTTCGTCTT	61.103	57.895	9.73	0.00	34.22	3.01
1532	3960	2.510238	GGATGCGCTGCTTCGTCT	60.510	61.111	9.73	0.00	34.22	4.18
1642	4078	4.764336	CGGCGCGGTGAAGACGTA	62.764	66.667	8.83	0.00	0.00	3.57
1837	4276	1.065701	CACCTTGTCGTAGAGATCGGG	59.934	57.143	0.00	0.00	36.95	5.14
1931	4370	1.137513	CTCGGTCGTGAACTTGAACC	58.862	55.000	0.00	0.00	0.00	3.62
1965	4404	1.081892	CACCAAGCTTCCTCATGTCG	58.918	55.000	0.00	0.00	0.00	4.35
2006	4446	1.078848	ACCATGCCTGAGAAGTCGC	60.079	57.895	0.00	0.00	0.00	5.19
2190	4630	2.028130	TCAACCACGGCAAACAAGAAT	58.972	42.857	0.00	0.00	0.00	2.40
2342	4793	8.467963	ACATGATTTGCTGGATAATGTATCAA	57.532	30.769	0.00	0.00	36.91	2.57
2343	4794	7.175467	GGACATGATTTGCTGGATAATGTATCA	59.825	37.037	0.00	0.00	36.91	2.15
2344	4795	7.362401	GGGACATGATTTGCTGGATAATGTATC	60.362	40.741	0.00	0.00	30.37	2.24
2345	4796	6.435277	GGGACATGATTTGCTGGATAATGTAT	59.565	38.462	0.00	0.00	30.37	2.29
2346	4797	5.769662	GGGACATGATTTGCTGGATAATGTA	59.230	40.000	0.00	0.00	30.37	2.29
2347	4798	4.586001	GGGACATGATTTGCTGGATAATGT	59.414	41.667	0.00	0.00	32.43	2.71
2348	4799	4.585581	TGGGACATGATTTGCTGGATAATG	59.414	41.667	0.00	0.00	0.00	1.90
2349	4800	4.806892	TGGGACATGATTTGCTGGATAAT	58.193	39.130	0.00	0.00	0.00	1.28
2350	4801	4.079844	TCTGGGACATGATTTGCTGGATAA	60.080	41.667	0.00	0.00	38.20	1.75
2351	4802	3.459227	TCTGGGACATGATTTGCTGGATA	59.541	43.478	0.00	0.00	38.20	2.59
2352	4803	2.242965	TCTGGGACATGATTTGCTGGAT	59.757	45.455	0.00	0.00	38.20	3.41
2353	4804	1.634973	TCTGGGACATGATTTGCTGGA	59.365	47.619	0.00	0.00	38.20	3.86
2354	4805	2.133281	TCTGGGACATGATTTGCTGG	57.867	50.000	0.00	0.00	38.20	4.85
2355	4806	3.284617	TGATCTGGGACATGATTTGCTG	58.715	45.455	0.00	0.00	38.20	4.41
2356	4807	3.657398	TGATCTGGGACATGATTTGCT	57.343	42.857	0.00	0.00	38.20	3.91
2357	4808	4.617959	CATTGATCTGGGACATGATTTGC	58.382	43.478	0.00	0.00	38.20	3.68
2358	4809	4.617959	GCATTGATCTGGGACATGATTTG	58.382	43.478	0.00	0.00	38.20	2.32
2381	4876	3.070159	TGCAGAGTCATACTTATGCCCTC	59.930	47.826	12.71	7.28	39.20	4.30
2399	4894	2.582728	TTTCAGTTGCCAGTTTGCAG	57.417	45.000	0.00	0.00	43.21	4.41
2439	5177	1.892474	CGTTTGTGTTGGATCCCCATT	59.108	47.619	9.90	0.00	43.12	3.16
2443	5189	3.754323	TGTTATCGTTTGTGTTGGATCCC	59.246	43.478	9.90	0.00	0.00	3.85
2461	5207	2.039818	TTTGGTTGCGTGGACTGTTA	57.960	45.000	0.00	0.00	0.00	2.41
2470	5216	1.067635	GCATCATCCTTTTGGTTGCGT	60.068	47.619	0.00	0.00	38.77	5.24
2471	5217	1.203052	AGCATCATCCTTTTGGTTGCG	59.797	47.619	0.00	0.00	38.77	4.85
2509	5255	5.163571	TGTTGCATGTTTCAGCTAGAACAAA	60.164	36.000	15.45	5.81	35.56	2.83
2611	5365	1.200948	GAATCCAGGCAACAGTGAAGC	59.799	52.381	0.00	0.00	41.41	3.86
2612	5366	2.507484	TGAATCCAGGCAACAGTGAAG	58.493	47.619	0.00	0.00	41.41	3.02
2613	5367	2.655090	TGAATCCAGGCAACAGTGAA	57.345	45.000	0.00	0.00	41.41	3.18
2615	5369	3.087031	AGATTGAATCCAGGCAACAGTG	58.913	45.455	0.75	0.00	41.41	3.66
2616	5370	3.087031	CAGATTGAATCCAGGCAACAGT	58.913	45.455	0.75	0.00	41.41	3.55
2617	5371	3.349927	TCAGATTGAATCCAGGCAACAG	58.650	45.455	0.75	0.00	41.41	3.16
2619	5373	3.119352	GGTTCAGATTGAATCCAGGCAAC	60.119	47.826	0.75	0.00	38.79	4.17
2620	5374	3.091545	GGTTCAGATTGAATCCAGGCAA	58.908	45.455	0.75	0.00	38.79	4.52
2621	5375	2.726821	GGTTCAGATTGAATCCAGGCA	58.273	47.619	0.75	0.00	38.79	4.75
2627	5381	1.401905	GTGCGGGGTTCAGATTGAATC	59.598	52.381	0.00	0.00	38.79	2.52
2630	5384	1.002624	GGTGCGGGGTTCAGATTGA	60.003	57.895	0.00	0.00	0.00	2.57
2631	5385	2.046285	GGGTGCGGGGTTCAGATTG	61.046	63.158	0.00	0.00	0.00	2.67
2632	5386	2.355115	GGGTGCGGGGTTCAGATT	59.645	61.111	0.00	0.00	0.00	2.40
2633	5387	4.096003	CGGGTGCGGGGTTCAGAT	62.096	66.667	0.00	0.00	0.00	2.90
2777	5540	1.226802	CATGCGTGACGGGAGAGAG	60.227	63.158	7.25	0.00	0.00	3.20
2971	5807	3.642078	CCCACTAGATCCGGGCAA	58.358	61.111	0.00	0.00	31.89	4.52
2975	5811	4.647615	CGCGCCCACTAGATCCGG	62.648	72.222	0.00	0.00	0.00	5.14
3076	6877	2.045045	CCCTTCATGCCGCCAGAA	60.045	61.111	0.00	0.00	0.00	3.02

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.