AutoCloner

Multiple sequence alignment - TraesCS3B01G539400

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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	TraesCS3B01G539400	chr3B	100.000	2760	0	0	1	2760	778678007	778680766	0.000000e+00	5097.0
1	TraesCS3B01G539400	chr3B	93.883	1177	54	8	920	2088	778793062	778794228	0.000000e+00	1759.0
2	TraesCS3B01G539400	chr3B	94.955	674	30	4	63	734	778791911	778792582	0.000000e+00	1053.0
3	TraesCS3B01G539400	chr3B	89.922	645	57	5	1052	1691	779135326	779135967	0.000000e+00	824.0
4	TraesCS3B01G539400	chr3B	87.163	631	69	10	994	1612	779139081	779139711	0.000000e+00	706.0
5	TraesCS3B01G539400	chr3B	85.444	687	62	15	2110	2760	778794292	778794976	0.000000e+00	680.0
6	TraesCS3B01G539400	chr3B	95.702	349	14	1	431	778	778678085	778678433	6.680000e-156	560.0
7	TraesCS3B01G539400	chr3B	95.702	349	14	1	79	427	778678437	778678784	6.680000e-156	560.0
8	TraesCS3B01G539400	chr3B	94.842	349	16	2	431	778	778791927	778792274	6.720000e-151	544.0
9	TraesCS3B01G539400	chr3B	94.771	306	14	2	79	383	778792278	778792582	2.490000e-130	475.0
10	TraesCS3B01G539400	chr3B	89.844	128	13	0	2633	2760	778768104	778768231	6.120000e-37	165.0
11	TraesCS3B01G539400	chr3B	84.375	160	24	1	21	179	779109410	779109569	3.680000e-34	156.0
12	TraesCS3B01G539400	chr3B	98.077	52	1	0	379	430	778792657	778792708	1.050000e-14	91.6
13	TraesCS3B01G539400	chr3B	96.296	54	2	0	849	902	778793012	778793065	3.790000e-14	89.8
14	TraesCS3B01G539400	chr3D	87.290	1967	160	39	843	2760	582611459	582609534	0.000000e+00	2165.0
15	TraesCS3B01G539400	chr3D	91.294	804	65	3	832	1631	582535808	582535006	0.000000e+00	1092.0
16	TraesCS3B01G539400	chr3D	87.933	721	76	8	946	1658	582250594	582249877	0.000000e+00	839.0
17	TraesCS3B01G539400	chr3D	84.975	406	44	12	426	816	582611857	582611454	1.990000e-106	396.0
18	TraesCS3B01G539400	chr3D	85.602	382	39	12	63	430	582611868	582611489	1.200000e-103	387.0
19	TraesCS3B01G539400	chr3D	80.376	372	33	15	463	818	582536138	582535791	2.120000e-61	246.0
20	TraesCS3B01G539400	chr3D	79.941	339	28	10	108	430	582536141	582535827	2.150000e-51	213.0
21	TraesCS3B01G539400	chr3D	93.151	73	5	0	1	73	582536410	582536338	1.050000e-19	108.0
22	TraesCS3B01G539400	chrUn	93.904	935	43	6	1156	2087	382449215	382450138	0.000000e+00	1399.0
23	TraesCS3B01G539400	chrUn	87.367	657	73	8	2111	2760	382450204	382450857	0.000000e+00	745.0
24	TraesCS3B01G539400	chrUn	96.676	361	9	3	377	734	41422193	41422553	5.090000e-167	597.0
25	TraesCS3B01G539400	chrUn	96.667	360	10	2	377	734	321841543	321841902	5.090000e-167	597.0
26	TraesCS3B01G539400	chrUn	96.078	306	11	1	79	383	321841597	321841902	5.310000e-137	497.0
27	TraesCS3B01G539400	chrUn	95.765	307	11	2	79	383	41422247	41422553	6.870000e-136	494.0
28	TraesCS3B01G539400	chrUn	84.000	425	43	12	1683	2105	41591242	41591643	4.310000e-103	385.0
29	TraesCS3B01G539400	chrUn	93.981	216	10	3	514	728	41418507	41418720	9.530000e-85	324.0
30	TraesCS3B01G539400	chrUn	93.981	216	10	3	514	728	292828593	292828380	9.530000e-85	324.0
31	TraesCS3B01G539400	chrUn	93.548	217	11	3	162	377	41418506	41418720	1.230000e-83	320.0
32	TraesCS3B01G539400	chrUn	93.548	217	11	3	162	377	292828594	292828380	1.230000e-83	320.0
33	TraesCS3B01G539400	chrUn	90.871	241	14	4	919	1151	41431484	41431724	1.600000e-82	316.0
34	TraesCS3B01G539400	chrUn	90.871	241	14	4	919	1151	330746933	330747173	1.600000e-82	316.0
35	TraesCS3B01G539400	chrUn	90.871	241	14	4	919	1151	330758405	330758645	1.600000e-82	316.0
36	TraesCS3B01G539400	chrUn	89.844	128	13	0	2633	2760	292830628	292830501	6.120000e-37	165.0
37	TraesCS3B01G539400	chrUn	96.970	66	2	0	730	795	41422630	41422695	8.080000e-21	111.0
38	TraesCS3B01G539400	chrUn	96.970	66	2	0	730	795	321841977	321842042	8.080000e-21	111.0
39	TraesCS3B01G539400	chrUn	100.000	51	0	0	728	778	41422193	41422243	8.140000e-16	95.3
40	TraesCS3B01G539400	chrUn	100.000	51	0	0	728	778	321841543	321841593	8.140000e-16	95.3
41	TraesCS3B01G539400	chrUn	98.077	52	1	0	379	430	41422630	41422681	1.050000e-14	91.6
42	TraesCS3B01G539400	chrUn	98.077	52	1	0	379	430	321841977	321842028	1.050000e-14	91.6
43	TraesCS3B01G539400	chrUn	97.826	46	1	0	849	894	41431435	41431480	2.280000e-11	80.5
44	TraesCS3B01G539400	chrUn	97.826	46	1	0	849	894	330746884	330746929	2.280000e-11	80.5
45	TraesCS3B01G539400	chrUn	97.826	46	1	0	849	894	330758356	330758401	2.280000e-11	80.5
46	TraesCS3B01G539400	chrUn	100.000	29	0	0	786	814	41431409	41431437	1.000000e-03	54.7
47	TraesCS3B01G539400	chrUn	100.000	29	0	0	786	814	330746858	330746886	1.000000e-03	54.7
48	TraesCS3B01G539400	chrUn	100.000	29	0	0	786	814	330758330	330758358	1.000000e-03	54.7

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	TraesCS3B01G539400	chr3B	778678007	778680766	2759	False	2072.333333	5097	97.134667	1	2760	3	chr3B.!!$F3	2759
1	TraesCS3B01G539400	chr3B	779135326	779139711	4385	False	765.000000	824	88.542500	994	1691	2	chr3B.!!$F5	697
2	TraesCS3B01G539400	chr3B	778791911	778794976	3065	False	670.342857	1759	94.038286	63	2760	7	chr3B.!!$F4	2697
3	TraesCS3B01G539400	chr3D	582609534	582611868	2334	True	982.666667	2165	85.955667	63	2760	3	chr3D.!!$R3	2697
4	TraesCS3B01G539400	chr3D	582249877	582250594	717	True	839.000000	839	87.933000	946	1658	1	chr3D.!!$R1	712
5	TraesCS3B01G539400	chr3D	582535006	582536410	1404	True	414.750000	1092	86.190500	1	1631	4	chr3D.!!$R2	1630
6	TraesCS3B01G539400	chrUn	382449215	382450857	1642	False	1072.000000	1399	90.635500	1156	2760	2	chrUn.!!$F7	1604
7	TraesCS3B01G539400	chrUn	41418506	41422695	4189	False	290.414286	597	96.431000	79	795	7	chrUn.!!$F2	716
8	TraesCS3B01G539400	chrUn	292828380	292830628	2248	True	269.666667	324	92.457667	162	2760	3	chrUn.!!$R1	2598

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
813	4693	0.100503	GCACCACCATTTACATCGCC	59.899	55.0	0.0	0.0	0.0	5.54	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2313	7151	0.241749	ACGCCGTCGAACATAGAACA	59.758	50.0	0.0	0.0	39.41	3.18	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
83	3747	1.584724	AGGTATTAGTGGTGCAGGCT	58.415	50.000	0.00	0.00	0.00	4.58
171	3948	3.845781	AGAGAGGAGCAAAAACACTCA	57.154	42.857	0.00	0.00	34.48	3.41
221	3998	3.557228	ACATTCCTCTGCTCTTCCATC	57.443	47.619	0.00	0.00	0.00	3.51
245	4022	3.205338	CTCACATTCACTCACACAACCA	58.795	45.455	0.00	0.00	0.00	3.67
248	4025	2.951642	ACATTCACTCACACAACCAAGG	59.048	45.455	0.00	0.00	0.00	3.61
296	4073	2.924290	GACACAACCGATCTAGCAAGTC	59.076	50.000	0.00	0.00	0.00	3.01
303	4080	2.093447	CCGATCTAGCAAGTCCCAACTT	60.093	50.000	0.00	0.00	46.80	2.66
323	4100	3.431922	TTCCCTCACACGAACGATATC	57.568	47.619	0.14	0.00	0.00	1.63
452	4229	1.273327	GGCCATTTTCACCTTGTCCTG	59.727	52.381	0.00	0.00	0.00	3.86
458	4235	0.324943	TTCACCTTGTCCTGGCTAGC	59.675	55.000	6.04	6.04	0.00	3.42
484	4261	0.529378	GCATGGGAGGCTTTGTTCAG	59.471	55.000	0.00	0.00	0.00	3.02
489	4266	1.609208	GGAGGCTTTGTTCAGCAAGA	58.391	50.000	0.00	0.00	42.10	3.02
492	4269	2.483491	GAGGCTTTGTTCAGCAAGAGAG	59.517	50.000	0.00	0.00	42.10	3.20
517	4294	2.483491	CTGCAGAAGAGAGGAGCAAAAC	59.517	50.000	8.42	0.00	34.45	2.43
518	4295	2.158769	TGCAGAAGAGAGGAGCAAAACA	60.159	45.455	0.00	0.00	31.42	2.83
519	4296	2.225255	GCAGAAGAGAGGAGCAAAACAC	59.775	50.000	0.00	0.00	0.00	3.32
520	4297	3.737850	CAGAAGAGAGGAGCAAAACACT	58.262	45.455	0.00	0.00	0.00	3.55
521	4298	3.745458	CAGAAGAGAGGAGCAAAACACTC	59.255	47.826	0.00	0.00	0.00	3.51
522	4299	2.447244	AGAGAGGAGCAAAACACTCG	57.553	50.000	0.00	0.00	34.87	4.18
599	4376	3.627123	CACATTCACTCACACAACCAAGA	59.373	43.478	0.00	0.00	0.00	3.02
604	4381	3.009723	CACTCACACAACCAAGAAGTGT	58.990	45.455	0.00	0.00	46.54	3.55
605	4382	4.081365	TCACTCACACAACCAAGAAGTGTA	60.081	41.667	0.00	0.00	44.02	2.90
606	4383	4.816385	CACTCACACAACCAAGAAGTGTAT	59.184	41.667	0.00	0.00	44.02	2.29
607	4384	5.050091	CACTCACACAACCAAGAAGTGTATC	60.050	44.000	0.00	0.00	44.02	2.24
608	4385	5.029807	TCACACAACCAAGAAGTGTATCA	57.970	39.130	0.00	0.00	44.02	2.15
609	4386	5.620206	TCACACAACCAAGAAGTGTATCAT	58.380	37.500	0.00	0.00	44.02	2.45
610	4387	6.764379	TCACACAACCAAGAAGTGTATCATA	58.236	36.000	0.00	0.00	44.02	2.15
611	4388	7.394016	TCACACAACCAAGAAGTGTATCATAT	58.606	34.615	0.00	0.00	44.02	1.78
612	4389	7.549134	TCACACAACCAAGAAGTGTATCATATC	59.451	37.037	0.00	0.00	44.02	1.63
613	4390	7.334171	CACACAACCAAGAAGTGTATCATATCA	59.666	37.037	0.00	0.00	44.02	2.15
614	4391	7.882791	ACACAACCAAGAAGTGTATCATATCAA	59.117	33.333	0.00	0.00	44.02	2.57
615	4392	8.896744	CACAACCAAGAAGTGTATCATATCAAT	58.103	33.333	0.00	0.00	0.00	2.57
619	4396	9.988815	ACCAAGAAGTGTATCATATCAATAGAC	57.011	33.333	0.00	0.00	0.00	2.59
620	4397	9.133627	CCAAGAAGTGTATCATATCAATAGACG	57.866	37.037	0.00	0.00	30.43	4.18
621	4398	9.684448	CAAGAAGTGTATCATATCAATAGACGT	57.316	33.333	0.00	0.00	30.43	4.34
622	4399	9.900710	AAGAAGTGTATCATATCAATAGACGTC	57.099	33.333	7.70	7.70	34.12	4.34
623	4400	8.516234	AGAAGTGTATCATATCAATAGACGTCC	58.484	37.037	13.01	0.00	34.30	4.79
624	4401	7.761038	AGTGTATCATATCAATAGACGTCCA	57.239	36.000	13.01	0.00	30.43	4.02
778	4658	0.106918	GAAACCACCACACCACCTGA	60.107	55.000	0.00	0.00	0.00	3.86
783	4663	0.324614	CACCACACCACCTGATAGCA	59.675	55.000	0.00	0.00	0.00	3.49
808	4688	5.241949	AGAAAAATACGCACCACCATTTACA	59.758	36.000	0.00	0.00	0.00	2.41
809	4689	5.652994	AAAATACGCACCACCATTTACAT	57.347	34.783	0.00	0.00	0.00	2.29
810	4690	4.893424	AATACGCACCACCATTTACATC	57.107	40.909	0.00	0.00	0.00	3.06
811	4691	1.083489	ACGCACCACCATTTACATCG	58.917	50.000	0.00	0.00	0.00	3.84
812	4692	0.248054	CGCACCACCATTTACATCGC	60.248	55.000	0.00	0.00	0.00	4.58
813	4693	0.100503	GCACCACCATTTACATCGCC	59.899	55.000	0.00	0.00	0.00	5.54
818	4698	1.676006	CACCATTTACATCGCCCTTCC	59.324	52.381	0.00	0.00	0.00	3.46
819	4699	1.318576	CCATTTACATCGCCCTTCCC	58.681	55.000	0.00	0.00	0.00	3.97
820	4700	1.133792	CCATTTACATCGCCCTTCCCT	60.134	52.381	0.00	0.00	0.00	4.20
821	4701	2.222027	CATTTACATCGCCCTTCCCTC	58.778	52.381	0.00	0.00	0.00	4.30
822	4702	1.281419	TTTACATCGCCCTTCCCTCA	58.719	50.000	0.00	0.00	0.00	3.86
824	4704	1.281419	TACATCGCCCTTCCCTCAAA	58.719	50.000	0.00	0.00	0.00	2.69
825	4705	0.404040	ACATCGCCCTTCCCTCAAAA	59.596	50.000	0.00	0.00	0.00	2.44
826	4706	1.203001	ACATCGCCCTTCCCTCAAAAA	60.203	47.619	0.00	0.00	0.00	1.94
894	5010	2.803492	GCAGATGAGCCGGTTTACCTAG	60.803	54.545	1.90	0.00	0.00	3.02
917	5039	3.568430	TGCGAAGTCACTAGTTCTCTTGA	59.432	43.478	0.00	0.00	33.55	3.02
923	5045	6.909550	AGTCACTAGTTCTCTTGATGAAGT	57.090	37.500	0.00	0.00	0.00	3.01
1042	5176	2.126734	GCACGCATCACAGCCAAC	60.127	61.111	0.00	0.00	0.00	3.77
1058	5192	1.624813	CCAACCCCACAAAAGCATCAT	59.375	47.619	0.00	0.00	0.00	2.45
1065	5199	3.514645	CCACAAAAGCATCATAACAGCC	58.485	45.455	0.00	0.00	0.00	4.85
1404	5542	2.355132	CTGCTCATGCTCATGAACTTCC	59.645	50.000	12.92	2.13	46.10	3.46
1406	5544	3.015327	GCTCATGCTCATGAACTTCCTT	58.985	45.455	12.92	0.00	46.10	3.36
1478	5616	2.737376	GTGTTCACCGAGGTCCGC	60.737	66.667	0.00	0.00	36.84	5.54
1522	5660	2.626780	GCGTTTTCAGGTGGGCTCC	61.627	63.158	0.00	0.00	0.00	4.70
1781	5951	8.531622	TGAAATAAATGGTGTTGCTGTTTATG	57.468	30.769	0.00	0.00	0.00	1.90
1782	5952	8.147058	TGAAATAAATGGTGTTGCTGTTTATGT	58.853	29.630	0.00	0.00	0.00	2.29
1783	5953	7.887996	AATAAATGGTGTTGCTGTTTATGTG	57.112	32.000	0.00	0.00	0.00	3.21
1784	5954	4.935352	AATGGTGTTGCTGTTTATGTGT	57.065	36.364	0.00	0.00	0.00	3.72
1785	5955	4.935352	ATGGTGTTGCTGTTTATGTGTT	57.065	36.364	0.00	0.00	0.00	3.32
1786	5956	6.398234	AATGGTGTTGCTGTTTATGTGTTA	57.602	33.333	0.00	0.00	0.00	2.41
2011	6525	0.255890	GCTGGTGGGAGGCAAGAATA	59.744	55.000	0.00	0.00	0.00	1.75
2112	6697	2.406002	AATTGTGGGACGGTTCCGCT	62.406	55.000	19.36	0.00	43.94	5.52
2199	6797	9.117183	GTCCGTCCATTTTTACTATTAAAGGAT	57.883	33.333	0.00	0.00	27.55	3.24
2235	6833	1.133181	TCACCACATTCTGCCCTCCA	61.133	55.000	0.00	0.00	0.00	3.86
2265	6863	1.500474	TCATCGCCCTTCTCCATTCT	58.500	50.000	0.00	0.00	0.00	2.40
2269	6867	2.436417	TCGCCCTTCTCCATTCTTTTG	58.564	47.619	0.00	0.00	0.00	2.44
2271	6869	2.819608	CGCCCTTCTCCATTCTTTTGAA	59.180	45.455	0.00	0.00	43.30	2.69
2313	7151	9.737427	CATCTCTCTTACATATGTAAAACTCGT	57.263	33.333	24.65	10.63	39.70	4.18
2314	7152	9.737427	ATCTCTCTTACATATGTAAAACTCGTG	57.263	33.333	24.65	15.07	39.70	4.35
2323	7163	9.431887	ACATATGTAAAACTCGTGTTCTATGTT	57.568	29.630	6.56	0.00	34.96	2.71
2349	8667	3.326747	GGCGTCTAGTTTTCTCATGTGT	58.673	45.455	0.00	0.00	0.00	3.72
2429	9263	0.757188	CGATGGCTAGGTCCACTCCT	60.757	60.000	0.00	0.00	39.25	3.69
2456	9291	4.489771	CTCCGCCATGGTCCCACC	62.490	72.222	14.67	0.00	39.52	4.61
2462	9297	1.271840	GCCATGGTCCCACCTAGACA	61.272	60.000	14.67	0.00	39.58	3.41
2490	9325	0.674895	GCCTTGCTCACACGATCCTT	60.675	55.000	0.00	0.00	0.00	3.36
2492	9327	1.066573	CCTTGCTCACACGATCCTTCT	60.067	52.381	0.00	0.00	0.00	2.85
2550	9520	0.396060	GGAGAGGAGGCATGACCATC	59.604	60.000	0.00	0.00	43.14	3.51
2557	9527	2.027745	GGAGGCATGACCATCGACATAT	60.028	50.000	0.00	0.00	43.14	1.78
2582	9552	1.005037	TGAAGAACCGCAGCGACAT	60.005	52.632	18.75	0.72	0.00	3.06
2597	9567	4.545929	CATGCAATGCTCGAGGGA	57.454	55.556	15.58	0.00	37.62	4.20
2606	9576	2.888863	CTCGAGGGAGCAGGTGAC	59.111	66.667	3.91	0.00	32.61	3.67
2609	9902	2.997897	GAGGGAGCAGGTGACCGT	60.998	66.667	0.00	0.00	0.00	4.83
2656	9951	1.544724	GTTTCCAAGCTGGGCACATA	58.455	50.000	0.56	0.00	38.32	2.29
2680	9975	5.481473	ACAATGGCTCAACCTATTGACAAAT	59.519	36.000	0.00	0.00	40.01	2.32
2681	9976	5.587388	ATGGCTCAACCTATTGACAAATG	57.413	39.130	0.00	0.00	40.01	2.32
2686	9981	6.294731	GGCTCAACCTATTGACAAATGACTTT	60.295	38.462	0.00	0.00	40.01	2.66
2740	10036	3.488489	CATGGTCGTCGGAAATTGAAAC	58.512	45.455	0.00	0.00	0.00	2.78

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
83	3747	2.875296	AGCCAGCACAAGGTGAAAATA	58.125	42.857	0.00	0.00	45.95	1.40
221	3998	2.837498	TGTGTGAGTGAATGTGAGGTG	58.163	47.619	0.00	0.00	0.00	4.00
245	4022	9.386010	GACGTCTATAGATATGATACACTCCTT	57.614	37.037	8.70	0.00	0.00	3.36
248	4025	8.719560	TGGACGTCTATAGATATGATACACTC	57.280	38.462	16.46	0.00	0.00	3.51
296	4073	0.107831	TCGTGTGAGGGAAAGTTGGG	59.892	55.000	0.00	0.00	0.00	4.12
303	4080	2.223409	CGATATCGTTCGTGTGAGGGAA	60.223	50.000	17.06	0.00	34.46	3.97
323	4100	1.858041	CAGTGCTGCAGTGAAGTCG	59.142	57.895	28.90	3.81	36.99	4.18
400	4177	2.224670	GGTGTGGTGGTTTCATGTCCTA	60.225	50.000	0.00	0.00	0.00	2.94
458	4235	1.422531	AAGCCTCCCATGCTCTAGAG	58.577	55.000	15.85	15.85	38.34	2.43
467	4244	0.112995	TGCTGAACAAAGCCTCCCAT	59.887	50.000	0.00	0.00	42.83	4.00
484	4261	2.230992	TCTTCTGCAGTCTCTCTCTTGC	59.769	50.000	14.67	0.00	0.00	4.01
489	4266	2.308570	TCCTCTCTTCTGCAGTCTCTCT	59.691	50.000	14.67	0.00	0.00	3.10
492	4269	1.134946	GCTCCTCTCTTCTGCAGTCTC	59.865	57.143	14.67	0.00	0.00	3.36
530	4307	7.239763	TGTTAGGTGATTGAAGACTGACATA	57.760	36.000	0.00	0.00	0.00	2.29
531	4308	6.114187	TGTTAGGTGATTGAAGACTGACAT	57.886	37.500	0.00	0.00	0.00	3.06
599	4376	8.178313	TGGACGTCTATTGATATGATACACTT	57.822	34.615	16.46	0.00	0.00	3.16
604	4381	8.244113	GTGTCATGGACGTCTATTGATATGATA	58.756	37.037	16.46	4.49	34.95	2.15
605	4382	7.093354	GTGTCATGGACGTCTATTGATATGAT	58.907	38.462	16.46	0.00	34.95	2.45
606	4383	6.040391	TGTGTCATGGACGTCTATTGATATGA	59.960	38.462	16.46	6.03	34.95	2.15
607	4384	6.215845	TGTGTCATGGACGTCTATTGATATG	58.784	40.000	16.46	3.48	34.95	1.78
608	4385	6.405278	TGTGTCATGGACGTCTATTGATAT	57.595	37.500	16.46	0.00	34.95	1.63
609	4386	5.845391	TGTGTCATGGACGTCTATTGATA	57.155	39.130	16.46	11.11	34.95	2.15
610	4387	4.736126	TGTGTCATGGACGTCTATTGAT	57.264	40.909	16.46	0.00	34.95	2.57
611	4388	4.242475	GTTGTGTCATGGACGTCTATTGA	58.758	43.478	16.46	12.73	34.95	2.57
612	4389	3.370978	GGTTGTGTCATGGACGTCTATTG	59.629	47.826	16.46	10.62	34.95	1.90
613	4390	3.596214	GGTTGTGTCATGGACGTCTATT	58.404	45.455	16.46	0.00	34.95	1.73
614	4391	2.416836	CGGTTGTGTCATGGACGTCTAT	60.417	50.000	16.46	12.67	34.95	1.98
615	4392	1.068125	CGGTTGTGTCATGGACGTCTA	60.068	52.381	16.46	10.40	34.95	2.59
616	4393	0.319555	CGGTTGTGTCATGGACGTCT	60.320	55.000	16.46	0.00	34.95	4.18
617	4394	0.319211	TCGGTTGTGTCATGGACGTC	60.319	55.000	7.13	7.13	34.95	4.34
618	4395	0.320374	ATCGGTTGTGTCATGGACGT	59.680	50.000	0.00	0.00	34.95	4.34
619	4396	0.999406	GATCGGTTGTGTCATGGACG	59.001	55.000	0.00	0.00	34.95	4.79
620	4397	2.386661	AGATCGGTTGTGTCATGGAC	57.613	50.000	0.00	0.00	0.00	4.02
621	4398	2.159099	GCTAGATCGGTTGTGTCATGGA	60.159	50.000	0.00	0.00	0.00	3.41
622	4399	2.205074	GCTAGATCGGTTGTGTCATGG	58.795	52.381	0.00	0.00	0.00	3.66
623	4400	2.892374	TGCTAGATCGGTTGTGTCATG	58.108	47.619	0.00	0.00	0.00	3.07
624	4401	3.055819	ACTTGCTAGATCGGTTGTGTCAT	60.056	43.478	1.04	0.00	0.00	3.06
778	4658	4.142469	GGTGGTGCGTATTTTTCTTGCTAT	60.142	41.667	0.00	0.00	0.00	2.97
783	4663	4.864704	AATGGTGGTGCGTATTTTTCTT	57.135	36.364	0.00	0.00	0.00	2.52
827	4707	2.094442	CCGGGCGATGTAAATGGTTTTT	60.094	45.455	0.00	0.00	0.00	1.94
829	4709	1.099689	CCGGGCGATGTAAATGGTTT	58.900	50.000	0.00	0.00	0.00	3.27
830	4710	1.381165	GCCGGGCGATGTAAATGGTT	61.381	55.000	1.81	0.00	0.00	3.67
832	4712	2.551912	GGCCGGGCGATGTAAATGG	61.552	63.158	14.21	0.00	0.00	3.16
833	4713	1.785041	CTGGCCGGGCGATGTAAATG	61.785	60.000	24.45	0.80	0.00	2.32
834	4714	1.525995	CTGGCCGGGCGATGTAAAT	60.526	57.895	24.45	0.00	0.00	1.40
836	4716	4.169696	CCTGGCCGGGCGATGTAA	62.170	66.667	20.35	3.02	0.00	2.41
894	5010	3.562567	AGAGAACTAGTGACTTCGCAC	57.437	47.619	0.00	0.00	39.05	5.34
917	5039	2.288579	TGTGTTCGGCTCGTTACTTCAT	60.289	45.455	0.00	0.00	0.00	2.57
923	5045	5.472478	AGAGATATATGTGTTCGGCTCGTTA	59.528	40.000	0.00	0.00	0.00	3.18
999	5133	3.120782	GTGCGTACGCTAGTATTTATGCC	59.879	47.826	36.99	7.27	42.51	4.40
1042	5176	3.676873	GCTGTTATGATGCTTTTGTGGGG	60.677	47.826	0.00	0.00	0.00	4.96
1058	5192	2.366266	AGTAGTCGGTGTTTGGCTGTTA	59.634	45.455	0.00	0.00	0.00	2.41
1065	5199	2.036733	TCCCTTGAGTAGTCGGTGTTTG	59.963	50.000	0.00	0.00	0.00	2.93
1105	5240	2.701780	GCGAGGAGGACGAAGAGCA	61.702	63.158	0.00	0.00	0.00	4.26
1239	5377	1.628238	TTGGAGGTGTTGGTCGTGGT	61.628	55.000	0.00	0.00	0.00	4.16
1404	5542	1.231958	TACTTGCCGGCGGTGAAAAG	61.232	55.000	28.82	24.76	0.00	2.27
1406	5544	1.962306	GTACTTGCCGGCGGTGAAA	60.962	57.895	28.82	17.93	0.00	2.69
1478	5616	2.278206	CCGACGACAGCCATCTCG	60.278	66.667	0.00	0.00	35.96	4.04
1659	5797	3.565764	AACAGCAGCCAGAGCATATAA	57.434	42.857	0.00	0.00	43.56	0.98
1781	5951	5.707411	ACAACGACTTGTAACACTAACAC	57.293	39.130	0.00	0.00	38.95	3.32
1782	5952	6.101332	AGAACAACGACTTGTAACACTAACA	58.899	36.000	0.00	0.00	39.88	2.41
1783	5953	6.579491	AGAACAACGACTTGTAACACTAAC	57.421	37.500	0.00	0.00	39.88	2.34
1784	5954	7.037438	AGAAGAACAACGACTTGTAACACTAA	58.963	34.615	0.00	0.00	39.88	2.24
1785	5955	6.567050	AGAAGAACAACGACTTGTAACACTA	58.433	36.000	0.00	0.00	39.88	2.74
1786	5956	5.416947	AGAAGAACAACGACTTGTAACACT	58.583	37.500	0.00	0.00	39.88	3.55
1823	5993	5.071250	TCAACTATCCACACCGCCTAATAAT	59.929	40.000	0.00	0.00	0.00	1.28
1824	5994	4.406326	TCAACTATCCACACCGCCTAATAA	59.594	41.667	0.00	0.00	0.00	1.40
1825	5995	3.962063	TCAACTATCCACACCGCCTAATA	59.038	43.478	0.00	0.00	0.00	0.98
1826	5996	2.769663	TCAACTATCCACACCGCCTAAT	59.230	45.455	0.00	0.00	0.00	1.73
2011	6525	6.294473	CCTTCTTGGCACTGTTATATCAGAT	58.706	40.000	16.10	0.00	38.63	2.90
2069	6584	5.350365	TGTTTTCTATCCGATGTACAACAGC	59.650	40.000	0.00	0.00	0.00	4.40
2112	6697	7.929785	AGAGAAAACCAACACTAATTCGAACTA	59.070	33.333	0.00	0.00	0.00	2.24
2199	6797	3.071479	GGTGAGGCGAATGTTTCAACTA	58.929	45.455	0.00	0.00	0.00	2.24
2209	6807	1.742761	CAGAATGTGGTGAGGCGAAT	58.257	50.000	0.00	0.00	0.00	3.34
2235	6833	6.039829	GGAGAAGGGCGATGAAGAAAAATAAT	59.960	38.462	0.00	0.00	0.00	1.28
2284	7122	7.934120	AGTTTTACATATGTAAGAGAGATGGGC	59.066	37.037	23.65	8.92	41.03	5.36
2313	7151	0.241749	ACGCCGTCGAACATAGAACA	59.758	50.000	0.00	0.00	39.41	3.18
2314	7152	0.912528	GACGCCGTCGAACATAGAAC	59.087	55.000	0.00	0.00	39.41	3.01
2321	7161	1.384742	GAAAACTAGACGCCGTCGAAC	59.615	52.381	12.13	0.00	37.67	3.95
2323	7163	0.877071	AGAAAACTAGACGCCGTCGA	59.123	50.000	12.13	5.64	37.67	4.20
2355	8673	4.273318	AGGAGATGATTGGTTTGGTAAGC	58.727	43.478	0.00	0.00	0.00	3.09
2365	8684	1.627834	GGGAGCCTAGGAGATGATTGG	59.372	57.143	14.75	0.00	0.00	3.16
2429	9263	2.434843	ATGGCGGAGGATTCGAGCA	61.435	57.895	0.00	0.00	42.19	4.26
2456	9291	2.279517	GGCGGCGATGGTGTCTAG	60.280	66.667	12.98	0.00	0.00	2.43
2490	9325	0.830444	ACGAGCAAGGTGGTGGTAGA	60.830	55.000	0.00	0.00	35.13	2.59
2492	9327	1.369692	CACGAGCAAGGTGGTGGTA	59.630	57.895	6.53	0.00	34.67	3.25
2522	9491	1.001503	CCTCCTCTCCTCCACTGCT	59.998	63.158	0.00	0.00	0.00	4.24
2525	9494	0.690411	CATGCCTCCTCTCCTCCACT	60.690	60.000	0.00	0.00	0.00	4.00
2550	9520	4.917998	CGGTTCTTCAGACCATATATGTCG	59.082	45.833	11.73	0.05	0.00	4.35
2557	9527	1.405526	GCTGCGGTTCTTCAGACCATA	60.406	52.381	0.00	0.00	32.26	2.74
2597	9567	3.941188	CCACCACGGTCACCTGCT	61.941	66.667	0.00	0.00	0.00	4.24
2656	9951	4.032960	TGTCAATAGGTTGAGCCATTGT	57.967	40.909	9.11	0.00	44.58	2.71
2680	9975	0.469144	GGTCAAGGGGGCAAAAGTCA	60.469	55.000	0.00	0.00	0.00	3.41
2681	9976	1.185618	GGGTCAAGGGGGCAAAAGTC	61.186	60.000	0.00	0.00	0.00	3.01
2686	9981	1.078347	GATTGGGTCAAGGGGGCAA	59.922	57.895	0.00	0.00	0.00	4.52
2723	10018	2.148768	AGGGTTTCAATTTCCGACGAC	58.851	47.619	0.00	0.00	0.00	4.34

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.