AutoCloner

Multiple sequence alignment - TraesCS3A01G239200

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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	TraesCS3A01G239200	chr3A	100.000	2900	0	0	1	2900	448700911	448703810	0.000000e+00	5356.0
1	TraesCS3A01G239200	chr3A	75.436	802	155	31	1069	1843	598553486	598554272	4.600000e-93	351.0
2	TraesCS3A01G239200	chr3A	73.924	813	171	29	1074	1858	484636979	484636180	3.660000e-74	289.0
3	TraesCS3A01G239200	chr3A	75.629	636	114	30	1089	1693	625210518	625209893	7.910000e-71	278.0
4	TraesCS3A01G239200	chr3A	90.698	43	4	0	2479	2521	738194476	738194434	1.120000e-04	58.4
5	TraesCS3A01G239200	chr3B	91.390	2172	97	37	794	2900	431039938	431042084	0.000000e+00	2892.0
6	TraesCS3A01G239200	chr3B	91.356	590	43	4	1	590	431022144	431022725	0.000000e+00	800.0
7	TraesCS3A01G239200	chr3B	89.714	525	52	1	10	532	389229140	389228616	0.000000e+00	669.0
8	TraesCS3A01G239200	chr3B	75.126	796	162	29	1069	1843	602331243	602332023	9.950000e-90	340.0
9	TraesCS3A01G239200	chr3B	75.126	796	162	29	1069	1843	602352325	602353105	9.950000e-90	340.0
10	TraesCS3A01G239200	chr3B	83.708	178	12	2	582	759	431039781	431039941	5.010000e-33	152.0
11	TraesCS3A01G239200	chr3D	96.655	1106	25	6	1016	2120	331657127	331658221	0.000000e+00	1827.0
12	TraesCS3A01G239200	chr3D	90.501	779	51	5	1	777	331654371	331655128	0.000000e+00	1007.0
13	TraesCS3A01G239200	chr3D	87.276	503	32	15	2419	2900	331667766	331668257	1.970000e-151	545.0
14	TraesCS3A01G239200	chr3D	93.289	298	17	3	2112	2407	331666960	331667256	1.230000e-118	436.0
15	TraesCS3A01G239200	chr3D	75.493	812	157	29	1074	1858	363597673	363596877	2.750000e-95	359.0
16	TraesCS3A01G239200	chr3D	75.561	802	154	31	1069	1843	455869722	455870508	9.880000e-95	357.0
17	TraesCS3A01G239200	chr6D	90.421	522	47	2	13	532	405178211	405177691	0.000000e+00	684.0
18	TraesCS3A01G239200	chr7B	89.662	532	53	1	1	530	436243343	436243874	0.000000e+00	676.0
19	TraesCS3A01G239200	chr7B	78.500	200	30	6	2486	2684	60689921	60690108	5.080000e-23	119.0
20	TraesCS3A01G239200	chr4D	89.827	521	51	1	5	523	40224764	40224244	0.000000e+00	667.0
21	TraesCS3A01G239200	chr4D	89.326	534	52	2	4	532	40153210	40153743	0.000000e+00	665.0
22	TraesCS3A01G239200	chr6A	88.951	534	54	3	1	532	103669300	103669830	0.000000e+00	654.0
23	TraesCS3A01G239200	chr1B	88.973	526	55	2	1	523	614491506	614492031	0.000000e+00	647.0
24	TraesCS3A01G239200	chr2D	80.296	203	29	7	2485	2684	553760591	553760785	3.010000e-30	143.0
25	TraesCS3A01G239200	chr5B	83.621	116	16	3	2271	2384	54395413	54395527	3.950000e-19	106.0
26	TraesCS3A01G239200	chr2B	97.368	38	1	0	2484	2521	541636640	541636677	6.710000e-07	65.8
27	TraesCS3A01G239200	chr5D	88.889	45	4	1	2183	2227	73767256	73767213	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	TraesCS3A01G239200	chr3A	448700911	448703810	2899	False	5356.0	5356	100.0000	1	2900	1	chr3A.!!$F1	2899
1	TraesCS3A01G239200	chr3A	598553486	598554272	786	False	351.0	351	75.4360	1069	1843	1	chr3A.!!$F2	774
2	TraesCS3A01G239200	chr3A	484636180	484636979	799	True	289.0	289	73.9240	1074	1858	1	chr3A.!!$R1	784
3	TraesCS3A01G239200	chr3A	625209893	625210518	625	True	278.0	278	75.6290	1089	1693	1	chr3A.!!$R2	604
4	TraesCS3A01G239200	chr3B	431039781	431042084	2303	False	1522.0	2892	87.5490	582	2900	2	chr3B.!!$F4	2318
5	TraesCS3A01G239200	chr3B	431022144	431022725	581	False	800.0	800	91.3560	1	590	1	chr3B.!!$F1	589
6	TraesCS3A01G239200	chr3B	389228616	389229140	524	True	669.0	669	89.7140	10	532	1	chr3B.!!$R1	522
7	TraesCS3A01G239200	chr3B	602331243	602332023	780	False	340.0	340	75.1260	1069	1843	1	chr3B.!!$F2	774
8	TraesCS3A01G239200	chr3B	602352325	602353105	780	False	340.0	340	75.1260	1069	1843	1	chr3B.!!$F3	774
9	TraesCS3A01G239200	chr3D	331654371	331658221	3850	False	1417.0	1827	93.5780	1	2120	2	chr3D.!!$F2	2119
10	TraesCS3A01G239200	chr3D	331666960	331668257	1297	False	490.5	545	90.2825	2112	2900	2	chr3D.!!$F3	788
11	TraesCS3A01G239200	chr3D	363596877	363597673	796	True	359.0	359	75.4930	1074	1858	1	chr3D.!!$R1	784
12	TraesCS3A01G239200	chr3D	455869722	455870508	786	False	357.0	357	75.5610	1069	1843	1	chr3D.!!$F1	774
13	TraesCS3A01G239200	chr6D	405177691	405178211	520	True	684.0	684	90.4210	13	532	1	chr6D.!!$R1	519
14	TraesCS3A01G239200	chr7B	436243343	436243874	531	False	676.0	676	89.6620	1	530	1	chr7B.!!$F2	529
15	TraesCS3A01G239200	chr4D	40224244	40224764	520	True	667.0	667	89.8270	5	523	1	chr4D.!!$R1	518
16	TraesCS3A01G239200	chr4D	40153210	40153743	533	False	665.0	665	89.3260	4	532	1	chr4D.!!$F1	528
17	TraesCS3A01G239200	chr6A	103669300	103669830	530	False	654.0	654	88.9510	1	532	1	chr6A.!!$F1	531
18	TraesCS3A01G239200	chr1B	614491506	614492031	525	False	647.0	647	88.9730	1	523	1	chr1B.!!$F1	522

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
785	794	1.005332	TCAAATCTTCCATTCCCCGCA	59.995	47.619	0.0	0.0	0.0	5.69	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1988	3887	1.016627	CCACTTCATGGGCATGTACG	58.983	55.0	0.0	0.0	45.95	3.67	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
116	120	2.066262	TCATTTCCTTCGTCTTGACGC	58.934	47.619	17.11	0.00	0.00	5.19
128	132	2.536803	GTCTTGACGCGTTTCACTTGTA	59.463	45.455	15.53	0.00	0.00	2.41
177	181	3.327757	ACCTTGATGTGAAGTTGAGGCTA	59.672	43.478	0.00	0.00	0.00	3.93
443	450	6.757897	AGGAGCAAATTTTGAACGATGATA	57.242	33.333	13.26	0.00	0.00	2.15
491	498	7.615365	TGAGCCAAATACTCAAAAGTATCCAAT	59.385	33.333	0.00	0.00	45.92	3.16
523	530	4.221262	TGTTACCGGTGAGTAGCTTGTATT	59.779	41.667	19.93	0.00	0.00	1.89
532	539	7.453838	GGTGAGTAGCTTGTATTTCGTTTTAG	58.546	38.462	0.00	0.00	0.00	1.85
593	601	4.020617	CAAGCCTCCCGGTCTGCA	62.021	66.667	0.00	0.00	0.00	4.41
610	618	2.113860	GCATACTTGCCAGACTTCCA	57.886	50.000	0.00	0.00	43.38	3.53
633	642	2.712057	AACAGCTCGCTGAAAATTGG	57.288	45.000	24.30	0.00	46.30	3.16
635	644	2.440409	ACAGCTCGCTGAAAATTGGAT	58.560	42.857	24.30	0.00	46.30	3.41
636	645	2.163010	ACAGCTCGCTGAAAATTGGATG	59.837	45.455	24.30	0.00	46.30	3.51
697	706	8.874744	TGTACAAGTATAGTCCTTCTACAAGT	57.125	34.615	0.00	0.00	0.00	3.16
698	707	9.964354	TGTACAAGTATAGTCCTTCTACAAGTA	57.036	33.333	0.00	0.00	0.00	2.24
759	768	3.305950	GCATGTGGAATTTGCACCAAGTA	60.306	43.478	17.04	0.05	37.97	2.24
760	769	4.798924	GCATGTGGAATTTGCACCAAGTAA	60.799	41.667	17.04	0.00	37.97	2.24
761	770	4.582701	TGTGGAATTTGCACCAAGTAAG	57.417	40.909	17.04	0.00	37.97	2.34
762	771	3.243704	TGTGGAATTTGCACCAAGTAAGC	60.244	43.478	17.04	0.00	37.97	3.09
763	772	2.030363	TGGAATTTGCACCAAGTAAGCG	60.030	45.455	0.00	0.00	32.93	4.68
764	773	2.227865	GGAATTTGCACCAAGTAAGCGA	59.772	45.455	0.00	0.00	0.00	4.93
765	774	3.119495	GGAATTTGCACCAAGTAAGCGAT	60.119	43.478	0.00	0.00	0.00	4.58
766	775	3.764885	ATTTGCACCAAGTAAGCGATC	57.235	42.857	0.00	0.00	0.00	3.69
767	776	2.177394	TTGCACCAAGTAAGCGATCA	57.823	45.000	0.00	0.00	0.00	2.92
768	777	2.177394	TGCACCAAGTAAGCGATCAA	57.823	45.000	0.00	0.00	0.00	2.57
769	778	2.499197	TGCACCAAGTAAGCGATCAAA	58.501	42.857	0.00	0.00	0.00	2.69
770	779	3.081061	TGCACCAAGTAAGCGATCAAAT	58.919	40.909	0.00	0.00	0.00	2.32
771	780	3.126858	TGCACCAAGTAAGCGATCAAATC	59.873	43.478	0.00	0.00	0.00	2.17
772	781	3.375299	GCACCAAGTAAGCGATCAAATCT	59.625	43.478	0.00	0.00	0.00	2.40
773	782	4.142600	GCACCAAGTAAGCGATCAAATCTT	60.143	41.667	0.00	0.00	0.00	2.40
774	783	5.563842	CACCAAGTAAGCGATCAAATCTTC	58.436	41.667	0.00	0.00	0.00	2.87
775	784	4.636206	ACCAAGTAAGCGATCAAATCTTCC	59.364	41.667	0.00	0.00	0.00	3.46
776	785	4.635765	CCAAGTAAGCGATCAAATCTTCCA	59.364	41.667	0.00	0.00	0.00	3.53
777	786	5.297776	CCAAGTAAGCGATCAAATCTTCCAT	59.702	40.000	0.00	0.00	0.00	3.41
778	787	6.183360	CCAAGTAAGCGATCAAATCTTCCATT	60.183	38.462	0.00	0.00	0.00	3.16
779	788	6.610741	AGTAAGCGATCAAATCTTCCATTC	57.389	37.500	0.00	0.00	0.00	2.67
780	789	4.907879	AAGCGATCAAATCTTCCATTCC	57.092	40.909	0.00	0.00	0.00	3.01
781	790	3.217626	AGCGATCAAATCTTCCATTCCC	58.782	45.455	0.00	0.00	0.00	3.97
782	791	2.294512	GCGATCAAATCTTCCATTCCCC	59.705	50.000	0.00	0.00	0.00	4.81
783	792	2.549754	CGATCAAATCTTCCATTCCCCG	59.450	50.000	0.00	0.00	0.00	5.73
784	793	1.762708	TCAAATCTTCCATTCCCCGC	58.237	50.000	0.00	0.00	0.00	6.13
785	794	1.005332	TCAAATCTTCCATTCCCCGCA	59.995	47.619	0.00	0.00	0.00	5.69
786	795	1.824230	CAAATCTTCCATTCCCCGCAA	59.176	47.619	0.00	0.00	0.00	4.85
787	796	2.230130	AATCTTCCATTCCCCGCAAA	57.770	45.000	0.00	0.00	0.00	3.68
788	797	2.230130	ATCTTCCATTCCCCGCAAAA	57.770	45.000	0.00	0.00	0.00	2.44
789	798	2.002505	TCTTCCATTCCCCGCAAAAA	57.997	45.000	0.00	0.00	0.00	1.94
813	822	3.772060	AAGCGATCAAATCTTCCAAGC	57.228	42.857	0.00	0.00	0.00	4.01
816	825	2.032675	GCGATCAAATCTTCCAAGCCTC	59.967	50.000	0.00	0.00	0.00	4.70
829	838	1.172812	AAGCCTCCGTGCCAAACTTC	61.173	55.000	0.00	0.00	0.00	3.01
852	867	1.615392	AGGTACGGTAACACTGTCCAC	59.385	52.381	5.91	0.00	38.84	4.02
857	872	2.168936	ACGGTAACACTGTCCACTTTGA	59.831	45.455	0.00	0.00	30.45	2.69
861	876	5.578776	GGTAACACTGTCCACTTTGAAAAG	58.421	41.667	1.22	1.22	41.73	2.27
869	884	3.381590	GTCCACTTTGAAAAGAGCCAACT	59.618	43.478	9.71	0.00	39.31	3.16
910	925	4.950205	ACGATTCGTCCCTATAAATGGT	57.050	40.909	5.75	0.00	33.69	3.55
919	934	5.455612	CGTCCCTATAAATGGTACCCACAAT	60.456	44.000	10.07	0.81	35.80	2.71
929	944	4.108570	TGGTACCCACAATACCTCTTCAT	58.891	43.478	10.07	0.00	42.36	2.57
956	974	5.049680	CCAAGCAAATCACGTACTACAAAGT	60.050	40.000	0.00	0.00	39.91	2.66
962	980	7.411157	GCAAATCACGTACTACAAAGTATTCGT	60.411	37.037	0.00	0.00	39.89	3.85
971	989	9.737025	GTACTACAAAGTATTCGTAAAAGCTTG	57.263	33.333	0.00	0.00	40.30	4.01
979	997	5.551760	ATTCGTAAAAGCTTGACCATCTG	57.448	39.130	0.00	0.00	0.00	2.90
1009	1027	3.610114	GCTGTGACTAACAATGGCTTGTG	60.610	47.826	3.64	0.00	44.83	3.33
1955	3854	7.857389	CCATGCACTACACAATAAATCACATAC	59.143	37.037	0.00	0.00	0.00	2.39
2023	3922	2.807676	AGTGGCTAAGTTGATTTGGGG	58.192	47.619	0.00	0.00	0.00	4.96
2193	4092	7.687941	AGGATTTCAATACAAATCTGACGTT	57.312	32.000	0.00	0.00	41.00	3.99
2243	4143	2.418746	CCTCAGGTACGTCAAATCCAGG	60.419	54.545	0.00	0.00	0.00	4.45
2250	4150	1.069513	ACGTCAAATCCAGGTCGAACA	59.930	47.619	1.87	0.00	0.00	3.18
2400	4303	1.001181	TCTGGCCGTTACTTTTAGCGT	59.999	47.619	0.00	0.00	30.44	5.07
2499	4900	9.874205	CAATATTTTGACCCAAATGATAAGTGT	57.126	29.630	0.00	0.00	33.19	3.55
2509	4910	5.407084	CCAAATGATAAGTGTCACACGTGTA	59.593	40.000	22.90	2.55	39.64	2.90
2513	4914	2.303163	AAGTGTCACACGTGTAGCAA	57.697	45.000	22.90	4.60	39.64	3.91
2602	5005	1.340405	ACTGAAGCTTGCCATCCGAAT	60.340	47.619	2.10	0.00	0.00	3.34
2604	5007	2.945008	CTGAAGCTTGCCATCCGAATAA	59.055	45.455	2.10	0.00	0.00	1.40
2605	5008	2.945008	TGAAGCTTGCCATCCGAATAAG	59.055	45.455	2.10	0.00	0.00	1.73
2611	5014	5.127682	AGCTTGCCATCCGAATAAGAAATTT	59.872	36.000	0.00	0.00	0.00	1.82
2612	5015	6.321181	AGCTTGCCATCCGAATAAGAAATTTA	59.679	34.615	0.00	0.00	0.00	1.40
2618	5021	7.274250	GCCATCCGAATAAGAAATTTATCATGC	59.726	37.037	0.00	0.00	0.00	4.06
2662	5071	2.863740	TCGCGTCACTAAATTGCCATAG	59.136	45.455	5.77	0.00	0.00	2.23
2672	5081	8.801299	TCACTAAATTGCCATAGAAAACATTCA	58.199	29.630	0.00	0.00	0.00	2.57
2751	5186	9.725019	TCACATCAACTAATAAGACAGTTTGAT	57.275	29.630	0.00	0.00	32.72	2.57
2794	5229	1.391485	GTCTCACGACGACTAAGCGTA	59.609	52.381	0.00	0.00	45.72	4.42
2796	5231	2.093310	TCTCACGACGACTAAGCGTAAG	59.907	50.000	0.00	0.00	45.72	2.34
2842	5278	0.390603	CCCAACAGTATTCGGTCGCA	60.391	55.000	0.00	0.00	0.00	5.10
2881	5317	0.543749	GGGAGCACCAGAGCACTAAT	59.456	55.000	1.58	0.00	39.85	1.73

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
116	120	3.745975	TGAAGGCATCTACAAGTGAAACG	59.254	43.478	0.00	0.00	45.86	3.60
128	132	3.504906	CACAAGTTGACATGAAGGCATCT	59.495	43.478	10.54	0.00	36.86	2.90
177	181	3.326747	GCACTTCGTCTATTCAAGTGGT	58.673	45.455	11.84	0.00	44.83	4.16
249	253	4.226168	AGGAGACAAAGATCCCTCGAAAAT	59.774	41.667	0.00	0.00	36.14	1.82
250	254	3.583086	AGGAGACAAAGATCCCTCGAAAA	59.417	43.478	0.00	0.00	36.14	2.29
340	344	9.970395	TCTACAATAACTTCACTCGAAAAGTTA	57.030	29.630	20.64	20.64	46.38	2.24
443	450	7.624360	TCAAAGTGTTACATTCTTGACAAGT	57.376	32.000	14.75	0.00	0.00	3.16
491	498	1.141254	TCACCGGTAACAAGCCTCAAA	59.859	47.619	6.87	0.00	0.00	2.69
523	530	3.655486	TCAACATCCTCGCTAAAACGAA	58.345	40.909	0.00	0.00	42.39	3.85
532	539	3.265791	ACTTCTGATTCAACATCCTCGC	58.734	45.455	0.00	0.00	0.00	5.03
593	601	4.640771	TTTCTGGAAGTCTGGCAAGTAT	57.359	40.909	0.00	0.00	33.76	2.12
603	611	1.195674	GCGAGCTGTTTTCTGGAAGTC	59.804	52.381	0.00	0.00	33.76	3.01
610	618	4.293415	CAATTTTCAGCGAGCTGTTTTCT	58.707	39.130	22.47	5.65	43.96	2.52
633	642	6.131264	TGGGCATATTGATATTGGGATCATC	58.869	40.000	0.00	0.00	35.77	2.92
635	644	5.533333	TGGGCATATTGATATTGGGATCA	57.467	39.130	0.00	0.00	33.96	2.92
636	645	5.716228	TGTTGGGCATATTGATATTGGGATC	59.284	40.000	0.00	0.00	0.00	3.36
684	693	6.154021	TGTTGGGACTATACTTGTAGAAGGAC	59.846	42.308	4.45	0.00	32.95	3.85
685	694	6.258354	TGTTGGGACTATACTTGTAGAAGGA	58.742	40.000	4.45	0.00	32.95	3.36
686	695	6.540438	TGTTGGGACTATACTTGTAGAAGG	57.460	41.667	4.45	0.00	32.95	3.46
692	701	9.920946	ATCATTAATTGTTGGGACTATACTTGT	57.079	29.630	0.00	0.00	0.00	3.16
700	709	9.308000	TGTAGAAAATCATTAATTGTTGGGACT	57.692	29.630	0.00	0.00	0.00	3.85
701	710	9.921637	TTGTAGAAAATCATTAATTGTTGGGAC	57.078	29.630	0.00	0.00	0.00	4.46
759	768	3.633986	GGGAATGGAAGATTTGATCGCTT	59.366	43.478	0.00	0.00	0.00	4.68
760	769	3.217626	GGGAATGGAAGATTTGATCGCT	58.782	45.455	0.00	0.00	0.00	4.93
761	770	2.294512	GGGGAATGGAAGATTTGATCGC	59.705	50.000	0.00	0.00	0.00	4.58
762	771	2.549754	CGGGGAATGGAAGATTTGATCG	59.450	50.000	0.00	0.00	0.00	3.69
763	772	2.294512	GCGGGGAATGGAAGATTTGATC	59.705	50.000	0.00	0.00	0.00	2.92
764	773	2.310538	GCGGGGAATGGAAGATTTGAT	58.689	47.619	0.00	0.00	0.00	2.57
765	774	1.005332	TGCGGGGAATGGAAGATTTGA	59.995	47.619	0.00	0.00	0.00	2.69
766	775	1.473258	TGCGGGGAATGGAAGATTTG	58.527	50.000	0.00	0.00	0.00	2.32
767	776	2.230130	TTGCGGGGAATGGAAGATTT	57.770	45.000	0.00	0.00	0.00	2.17
768	777	2.230130	TTTGCGGGGAATGGAAGATT	57.770	45.000	0.00	0.00	0.00	2.40
769	778	2.230130	TTTTGCGGGGAATGGAAGAT	57.770	45.000	0.00	0.00	0.00	2.40
770	779	2.002505	TTTTTGCGGGGAATGGAAGA	57.997	45.000	0.00	0.00	0.00	2.87
790	799	4.925646	GCTTGGAAGATTTGATCGCTTTTT	59.074	37.500	0.00	0.00	0.00	1.94
791	800	4.488879	GCTTGGAAGATTTGATCGCTTTT	58.511	39.130	0.00	0.00	0.00	2.27
792	801	3.119352	GGCTTGGAAGATTTGATCGCTTT	60.119	43.478	0.00	0.00	0.00	3.51
793	802	2.424956	GGCTTGGAAGATTTGATCGCTT	59.575	45.455	0.00	0.00	0.00	4.68
794	803	2.019984	GGCTTGGAAGATTTGATCGCT	58.980	47.619	0.00	0.00	0.00	4.93
795	804	2.019984	AGGCTTGGAAGATTTGATCGC	58.980	47.619	0.00	0.00	0.00	4.58
796	805	2.615912	GGAGGCTTGGAAGATTTGATCG	59.384	50.000	0.00	0.00	0.00	3.69
803	812	1.078143	GCACGGAGGCTTGGAAGAT	60.078	57.895	0.00	0.00	0.00	2.40
813	822	0.323629	TAGGAAGTTTGGCACGGAGG	59.676	55.000	0.00	0.00	0.00	4.30
816	825	0.036306	ACCTAGGAAGTTTGGCACGG	59.964	55.000	17.98	0.00	0.00	4.94
829	838	2.424956	GGACAGTGTTACCGTACCTAGG	59.575	54.545	7.41	7.41	0.00	3.02
852	867	4.654091	TTGGAGTTGGCTCTTTTCAAAG	57.346	40.909	0.00	0.00	41.38	2.77
857	872	4.391405	CAAGTTTGGAGTTGGCTCTTTT	57.609	40.909	0.00	0.00	41.38	2.27
910	925	3.181469	GCGATGAAGAGGTATTGTGGGTA	60.181	47.826	0.00	0.00	0.00	3.69
919	934	0.901827	TGCTTGGCGATGAAGAGGTA	59.098	50.000	0.00	0.00	0.00	3.08
929	944	0.793861	GTACGTGATTTGCTTGGCGA	59.206	50.000	0.00	0.00	0.00	5.54
956	974	5.584649	CCAGATGGTCAAGCTTTTACGAATA	59.415	40.000	0.00	0.00	0.00	1.75
984	1002	1.128692	GCCATTGTTAGTCACAGCGAC	59.871	52.381	0.00	0.00	45.77	5.19
1009	1027	3.517500	AGGAGAGGAGACCATTTGAGTTC	59.482	47.826	0.00	0.00	0.00	3.01
1204	3010	2.264794	GTGTCCGGCGAGGTTGAT	59.735	61.111	9.30	0.00	41.99	2.57
1917	3789	3.134127	GCATGGTCGCACTTCCCC	61.134	66.667	0.00	0.00	0.00	4.81
1986	3885	2.419436	CCACTTCATGGGCATGTACGTA	60.419	50.000	0.00	0.00	45.95	3.57
1987	3886	1.678728	CCACTTCATGGGCATGTACGT	60.679	52.381	0.00	0.00	45.95	3.57
1988	3887	1.016627	CCACTTCATGGGCATGTACG	58.983	55.000	0.00	0.00	45.95	3.67
2023	3922	1.443802	GCCCGCTCTTATTATCCAGC	58.556	55.000	0.00	0.00	0.00	4.85
2058	3957	5.301045	ACACCAAGCATCCATATCATTTCTG	59.699	40.000	0.00	0.00	0.00	3.02
2193	4092	9.131791	GTCAGATTTTTAGCCCTAAAATATCCA	57.868	33.333	12.48	0.72	42.48	3.41
2243	4143	4.846137	GCGATTAATTGCCATATGTTCGAC	59.154	41.667	15.79	0.00	0.00	4.20
2250	4150	5.003160	TGCTACAGCGATTAATTGCCATAT	58.997	37.500	21.75	9.28	45.83	1.78
2400	4303	8.670135	CACGATATGTATCCACAAGGTTTTAAA	58.330	33.333	0.00	0.00	38.42	1.52
2423	4824	2.317689	CGCTGATTAGTGCGCACG	59.682	61.111	32.94	19.44	45.50	5.34
2464	4865	6.678568	TGGGTCAAAATATTGGTTGATGTT	57.321	33.333	5.99	0.00	36.23	2.71
2499	4900	1.202475	TGCTTCTTGCTACACGTGTGA	60.202	47.619	30.83	16.12	43.37	3.58
2509	4910	2.048603	GGCCGGATTGCTTCTTGCT	61.049	57.895	5.05	0.00	43.37	3.91
2513	4914	2.273449	CAGGGCCGGATTGCTTCT	59.727	61.111	5.05	0.00	0.00	2.85
2575	4977	5.296748	GGATGGCAAGCTTCAGTTTTTAAA	58.703	37.500	0.00	0.00	0.00	1.52
2577	4979	3.057596	CGGATGGCAAGCTTCAGTTTTTA	60.058	43.478	0.00	0.00	0.00	1.52
2588	4991	4.574599	ATTTCTTATTCGGATGGCAAGC	57.425	40.909	0.00	0.00	0.00	4.01
2618	5021	8.328864	GCGAGGATGATAACTTTAGTTGTTAAG	58.671	37.037	5.41	0.00	38.90	1.85
2634	5037	3.735237	ATTTAGTGACGCGAGGATGAT	57.265	42.857	15.93	0.00	0.00	2.45
2662	5071	4.691685	TGCATGGCAATTCTGAATGTTTTC	59.308	37.500	3.22	0.00	34.76	2.29
2672	5081	3.306502	CCTGAAAAGTGCATGGCAATTCT	60.307	43.478	4.30	0.00	46.02	2.40
2794	5229	3.127548	CCATCATGCAGTCTTTAACGCTT	59.872	43.478	0.00	0.00	0.00	4.68
2796	5231	2.677836	TCCATCATGCAGTCTTTAACGC	59.322	45.455	0.00	0.00	0.00	4.84
2798	5233	3.684788	ACGTCCATCATGCAGTCTTTAAC	59.315	43.478	0.00	0.00	0.00	2.01
2799	5234	3.684305	CACGTCCATCATGCAGTCTTTAA	59.316	43.478	0.00	0.00	0.00	1.52
2800	5235	3.261580	CACGTCCATCATGCAGTCTTTA	58.738	45.455	0.00	0.00	0.00	1.85
2801	5236	2.079158	CACGTCCATCATGCAGTCTTT	58.921	47.619	0.00	0.00	0.00	2.52
2802	5237	1.730501	CACGTCCATCATGCAGTCTT	58.269	50.000	0.00	0.00	0.00	3.01
2803	5238	0.742281	GCACGTCCATCATGCAGTCT	60.742	55.000	0.00	0.00	39.23	3.24
2804	5239	1.709147	GGCACGTCCATCATGCAGTC	61.709	60.000	0.00	0.00	41.27	3.51
2805	5240	1.746615	GGCACGTCCATCATGCAGT	60.747	57.895	0.00	0.00	41.27	4.40
2842	5278	4.104738	TCCCAGTTCTTGAAATCTTGACCT	59.895	41.667	0.00	0.00	0.00	3.85

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.