AutoCloner

Multiple sequence alignment - TraesCS2D01G366500

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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	TraesCS2D01G366500	chr2D	100.000	2767	0	0	1	2767	471062415	471065181	0.000000e+00	5110.0
1	TraesCS2D01G366500	chr2B	88.577	1926	108	52	6	1901	550396208	550398051	0.000000e+00	2235.0
2	TraesCS2D01G366500	chr2B	92.784	97	7	0	2616	2712	796526523	796526619	1.030000e-29	141.0
3	TraesCS2D01G366500	chr2A	91.194	1374	82	22	544	1901	612842871	612844221	0.000000e+00	1831.0
4	TraesCS2D01G366500	chr2A	89.454	531	15	14	1	501	612842353	612842872	1.400000e-177	632.0
5	TraesCS2D01G366500	chr3A	95.125	718	26	4	1902	2617	14058591	14059301	0.000000e+00	1123.0
6	TraesCS2D01G366500	chr3A	97.143	70	1	1	2699	2767	14059300	14059369	1.740000e-22	117.0
7	TraesCS2D01G366500	chrUn	81.555	1106	166	26	730	1824	10650721	10651799	0.000000e+00	878.0
8	TraesCS2D01G366500	chrUn	81.024	1133	174	28	730	1847	353543	354649	0.000000e+00	863.0
9	TraesCS2D01G366500	chrUn	84.157	890	119	18	993	1868	10644083	10644964	0.000000e+00	843.0
10	TraesCS2D01G366500	chrUn	81.419	1001	137	36	780	1766	10695574	10696539	0.000000e+00	773.0
11	TraesCS2D01G366500	chr7D	88.154	726	65	10	1902	2616	523436136	523435421	0.000000e+00	845.0
12	TraesCS2D01G366500	chr7D	80.000	135	23	3	2484	2617	536327162	536327031	2.270000e-16	97.1
13	TraesCS2D01G366500	chr1D	87.845	724	68	12	1902	2617	22560289	22559578	0.000000e+00	832.0
14	TraesCS2D01G366500	chr1D	80.699	1088	146	38	727	1794	35789041	35787998	0.000000e+00	787.0
15	TraesCS2D01G366500	chr1D	80.000	135	23	3	2484	2617	384138953	384138822	2.270000e-16	97.1
16	TraesCS2D01G366500	chr1D	97.297	37	1	0	1901	1937	322070388	322070352	2.300000e-06	63.9
17	TraesCS2D01G366500	chr1A	83.224	912	127	21	993	1887	34940238	34939336	0.000000e+00	813.0
18	TraesCS2D01G366500	chr1A	81.076	1004	144	34	780	1766	34891930	34890956	0.000000e+00	760.0
19	TraesCS2D01G366500	chr5B	87.569	724	61	10	1902	2616	202941981	202941278	0.000000e+00	811.0
20	TraesCS2D01G366500	chr1B	83.077	910	117	26	993	1887	55428902	55428015	0.000000e+00	793.0
21	TraesCS2D01G366500	chr1B	80.474	1055	164	34	730	1766	55242247	55241217	0.000000e+00	769.0
22	TraesCS2D01G366500	chr1B	79.651	1145	172	45	780	1899	55017382	55016274	0.000000e+00	767.0
23	TraesCS2D01G366500	chr1B	79.623	1114	177	41	730	1819	55206459	55205372	0.000000e+00	754.0
24	TraesCS2D01G366500	chr1B	88.288	111	11	2	2591	2700	503352879	503352988	6.220000e-27	132.0
25	TraesCS2D01G366500	chr6B	84.492	748	72	15	1902	2617	551952429	551953164	0.000000e+00	699.0
26	TraesCS2D01G366500	chr7B	88.427	337	32	6	1902	2233	545982758	545983092	1.540000e-107	399.0
27	TraesCS2D01G366500	chr7B	86.218	312	29	5	2310	2617	545983096	545983397	2.660000e-85	326.0
28	TraesCS2D01G366500	chr6D	83.276	293	19	10	2026	2310	2091048	2091318	2.750000e-60	243.0
29	TraesCS2D01G366500	chr3B	81.641	256	36	5	2336	2589	60585442	60585688	4.670000e-48	202.0
30	TraesCS2D01G366500	chr3B	95.506	89	4	0	2616	2704	652296384	652296472	2.870000e-30	143.0
31	TraesCS2D01G366500	chr6A	94.505	91	5	0	2616	2706	568939028	568938938	1.030000e-29	141.0
32	TraesCS2D01G366500	chr4B	95.506	89	3	1	2616	2704	567009338	567009251	1.030000e-29	141.0
33	TraesCS2D01G366500	chr4B	92.708	96	5	2	2613	2708	567390998	567391091	1.340000e-28	137.0
34	TraesCS2D01G366500	chr7A	92.632	95	7	0	2616	2710	47050731	47050825	1.340000e-28	137.0
35	TraesCS2D01G366500	chr5D	89.189	111	8	4	2593	2703	395699587	395699693	4.810000e-28	135.0
36	TraesCS2D01G366500	chr5A	91.919	99	5	3	2603	2700	331942240	331942336	4.810000e-28	135.0
37	TraesCS2D01G366500	chr4D	80.000	135	23	3	2484	2617	362698586	362698717	2.270000e-16	97.1

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	TraesCS2D01G366500	chr2D	471062415	471065181	2766	False	5110.0	5110	100.0000	1	2767	1	chr2D.!!$F1	2766
1	TraesCS2D01G366500	chr2B	550396208	550398051	1843	False	2235.0	2235	88.5770	6	1901	1	chr2B.!!$F1	1895
2	TraesCS2D01G366500	chr2A	612842353	612844221	1868	False	1231.5	1831	90.3240	1	1901	2	chr2A.!!$F1	1900
3	TraesCS2D01G366500	chr3A	14058591	14059369	778	False	620.0	1123	96.1340	1902	2767	2	chr3A.!!$F1	865
4	TraesCS2D01G366500	chrUn	10650721	10651799	1078	False	878.0	878	81.5550	730	1824	1	chrUn.!!$F3	1094
5	TraesCS2D01G366500	chrUn	353543	354649	1106	False	863.0	863	81.0240	730	1847	1	chrUn.!!$F1	1117
6	TraesCS2D01G366500	chrUn	10644083	10644964	881	False	843.0	843	84.1570	993	1868	1	chrUn.!!$F2	875
7	TraesCS2D01G366500	chrUn	10695574	10696539	965	False	773.0	773	81.4190	780	1766	1	chrUn.!!$F4	986
8	TraesCS2D01G366500	chr7D	523435421	523436136	715	True	845.0	845	88.1540	1902	2616	1	chr7D.!!$R1	714
9	TraesCS2D01G366500	chr1D	22559578	22560289	711	True	832.0	832	87.8450	1902	2617	1	chr1D.!!$R1	715
10	TraesCS2D01G366500	chr1D	35787998	35789041	1043	True	787.0	787	80.6990	727	1794	1	chr1D.!!$R2	1067
11	TraesCS2D01G366500	chr1A	34939336	34940238	902	True	813.0	813	83.2240	993	1887	1	chr1A.!!$R2	894
12	TraesCS2D01G366500	chr1A	34890956	34891930	974	True	760.0	760	81.0760	780	1766	1	chr1A.!!$R1	986
13	TraesCS2D01G366500	chr5B	202941278	202941981	703	True	811.0	811	87.5690	1902	2616	1	chr5B.!!$R1	714
14	TraesCS2D01G366500	chr1B	55428015	55428902	887	True	793.0	793	83.0770	993	1887	1	chr1B.!!$R4	894
15	TraesCS2D01G366500	chr1B	55241217	55242247	1030	True	769.0	769	80.4740	730	1766	1	chr1B.!!$R3	1036
16	TraesCS2D01G366500	chr1B	55016274	55017382	1108	True	767.0	767	79.6510	780	1899	1	chr1B.!!$R1	1119
17	TraesCS2D01G366500	chr1B	55205372	55206459	1087	True	754.0	754	79.6230	730	1819	1	chr1B.!!$R2	1089
18	TraesCS2D01G366500	chr6B	551952429	551953164	735	False	699.0	699	84.4920	1902	2617	1	chr6B.!!$F1	715
19	TraesCS2D01G366500	chr7B	545982758	545983397	639	False	362.5	399	87.3225	1902	2617	2	chr7B.!!$F1	715

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
537	574	0.179215	CCGTGCGCAGATGTTTTCTC	60.179	55.0	12.22	0.0	29.93	2.87	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1938	2084	0.321671	CGGTGGGCGGATGAGATTAT	59.678	55.0	0.0	0.0	0.0	1.28	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
24	25	1.946768	GGCGGAGTGCTAATAAATGCA	59.053	47.619	0.00	0.00	45.43	3.96
152	166	0.818445	GATGAGACCCTCCGCGTCTA	60.818	60.000	4.92	0.00	40.67	2.59
275	304	0.671163	GTCACGCGTGGGGTAAATGA	60.671	55.000	36.41	13.35	0.00	2.57
278	307	1.135803	CACGCGTGGGGTAAATGAAAG	60.136	52.381	31.15	0.00	0.00	2.62
336	373	4.452733	CGGGGAACGCTCCACTCC	62.453	72.222	5.41	0.00	43.89	3.85
413	450	4.697352	TGCAGCTTAAGATTGAACCTCTTC	59.303	41.667	6.67	0.00	34.81	2.87
449	486	5.602978	ACTACTCCTTAGAGAGAGAGAGAGG	59.397	48.000	5.06	0.00	43.39	3.69
451	488	3.973973	CTCCTTAGAGAGAGAGAGAGGGA	59.026	52.174	0.00	0.00	43.39	4.20
455	492	2.412591	AGAGAGAGAGAGAGGGAGAGG	58.587	57.143	0.00	0.00	0.00	3.69
456	493	1.421646	GAGAGAGAGAGAGGGAGAGGG	59.578	61.905	0.00	0.00	0.00	4.30
457	494	1.010793	AGAGAGAGAGAGGGAGAGGGA	59.989	57.143	0.00	0.00	0.00	4.20
458	495	1.421646	GAGAGAGAGAGGGAGAGGGAG	59.578	61.905	0.00	0.00	0.00	4.30
460	497	1.421646	GAGAGAGAGGGAGAGGGAGAG	59.578	61.905	0.00	0.00	0.00	3.20
461	498	1.010793	AGAGAGAGGGAGAGGGAGAGA	59.989	57.143	0.00	0.00	0.00	3.10
462	499	1.850345	GAGAGAGGGAGAGGGAGAGAA	59.150	57.143	0.00	0.00	0.00	2.87
463	500	2.243736	GAGAGAGGGAGAGGGAGAGAAA	59.756	54.545	0.00	0.00	0.00	2.52
508	545	1.939974	TACCAGATCGCAAGCATGAC	58.060	50.000	0.00	0.00	37.18	3.06
531	568	3.121030	GCTTCCGTGCGCAGATGT	61.121	61.111	12.22	0.00	0.00	3.06
532	569	2.680913	GCTTCCGTGCGCAGATGTT	61.681	57.895	12.22	0.00	0.00	2.71
533	570	1.868997	CTTCCGTGCGCAGATGTTT	59.131	52.632	12.22	0.00	0.00	2.83
534	571	0.238289	CTTCCGTGCGCAGATGTTTT	59.762	50.000	12.22	0.00	0.00	2.43
535	572	0.237235	TTCCGTGCGCAGATGTTTTC	59.763	50.000	12.22	0.00	0.00	2.29
536	573	0.602638	TCCGTGCGCAGATGTTTTCT	60.603	50.000	12.22	0.00	33.90	2.52
537	574	0.179215	CCGTGCGCAGATGTTTTCTC	60.179	55.000	12.22	0.00	29.93	2.87
538	575	0.792640	CGTGCGCAGATGTTTTCTCT	59.207	50.000	12.22	0.00	29.93	3.10
539	576	1.195448	CGTGCGCAGATGTTTTCTCTT	59.805	47.619	12.22	0.00	29.93	2.85
540	577	2.411748	CGTGCGCAGATGTTTTCTCTTA	59.588	45.455	12.22	0.00	29.93	2.10
599	636	9.238368	AGCACTTTAATAATGTGTTTAAGCCTA	57.762	29.630	16.82	0.00	38.43	3.93
632	679	0.248907	GCATCGCCTAGCTACGACAA	60.249	55.000	8.45	0.00	41.76	3.18
633	680	1.478137	CATCGCCTAGCTACGACAAC	58.522	55.000	8.45	0.00	41.76	3.32
634	681	1.100510	ATCGCCTAGCTACGACAACA	58.899	50.000	8.45	0.00	41.76	3.33
635	682	0.450583	TCGCCTAGCTACGACAACAG	59.549	55.000	2.56	0.00	32.45	3.16
636	683	0.450583	CGCCTAGCTACGACAACAGA	59.549	55.000	0.00	0.00	0.00	3.41
637	684	1.135489	CGCCTAGCTACGACAACAGAA	60.135	52.381	0.00	0.00	0.00	3.02
638	685	2.670229	CGCCTAGCTACGACAACAGAAA	60.670	50.000	0.00	0.00	0.00	2.52
639	686	2.666994	GCCTAGCTACGACAACAGAAAC	59.333	50.000	0.00	0.00	0.00	2.78
640	687	3.859627	GCCTAGCTACGACAACAGAAACA	60.860	47.826	0.00	0.00	0.00	2.83
641	688	3.673809	CCTAGCTACGACAACAGAAACAC	59.326	47.826	0.00	0.00	0.00	3.32
642	689	2.124903	AGCTACGACAACAGAAACACG	58.875	47.619	0.00	0.00	0.00	4.49
643	690	1.856597	GCTACGACAACAGAAACACGT	59.143	47.619	0.00	0.00	37.68	4.49
644	691	2.097541	GCTACGACAACAGAAACACGTC	60.098	50.000	0.00	0.00	35.66	4.34
645	692	1.283736	ACGACAACAGAAACACGTCC	58.716	50.000	0.00	0.00	0.00	4.79
646	693	0.580104	CGACAACAGAAACACGTCCC	59.420	55.000	0.00	0.00	0.00	4.46
647	694	0.942252	GACAACAGAAACACGTCCCC	59.058	55.000	0.00	0.00	0.00	4.81
648	695	0.544697	ACAACAGAAACACGTCCCCT	59.455	50.000	0.00	0.00	0.00	4.79
649	696	1.764134	ACAACAGAAACACGTCCCCTA	59.236	47.619	0.00	0.00	0.00	3.53
650	697	2.171027	ACAACAGAAACACGTCCCCTAA	59.829	45.455	0.00	0.00	0.00	2.69
651	698	3.207778	CAACAGAAACACGTCCCCTAAA	58.792	45.455	0.00	0.00	0.00	1.85
652	699	3.564053	ACAGAAACACGTCCCCTAAAA	57.436	42.857	0.00	0.00	0.00	1.52
653	700	3.888583	ACAGAAACACGTCCCCTAAAAA	58.111	40.909	0.00	0.00	0.00	1.94
699	746	6.832384	ACTTGATCAAACCATGCATATCTCTT	59.168	34.615	9.88	0.00	0.00	2.85
745	794	0.249322	ATCGATTAGTTGGCCGTCGG	60.249	55.000	6.99	6.99	33.46	4.79
860	925	3.000872	CGACACAACAAACACAAATGCTG	60.001	43.478	0.00	0.00	0.00	4.41
869	939	1.812571	ACACAAATGCTGTTCGATCCC	59.187	47.619	0.00	0.00	35.47	3.85
871	941	1.271871	ACAAATGCTGTTCGATCCCCA	60.272	47.619	0.00	0.00	32.99	4.96
950	1039	2.681848	GCATCAGCACAATCACTAGCTT	59.318	45.455	0.00	0.00	41.58	3.74
988	1084	2.415512	GCACACCCGATTTAGTGAGAAC	59.584	50.000	0.00	0.00	37.43	3.01
1108	1213	1.517257	GTCGCTGACAGGACATCCG	60.517	63.158	15.25	5.64	42.08	4.18
1545	1683	8.027189	ACAAGTTGTTCTCAAAAGTTCTTAACC	58.973	33.333	1.64	0.00	35.20	2.85
1562	1700	5.663556	TCTTAACCAAGGGGATGTTTTTGTT	59.336	36.000	0.00	0.00	38.05	2.83
1669	1807	3.434167	GGAGTGATCACCATAGCCAATGT	60.434	47.826	22.21	0.00	33.34	2.71
1695	1833	0.259356	TGCATCCAAGCCATCCATCA	59.741	50.000	0.00	0.00	0.00	3.07
1696	1834	1.342175	TGCATCCAAGCCATCCATCAA	60.342	47.619	0.00	0.00	0.00	2.57
1938	2084	2.599757	ATGAGCACAGCTGAGCCCA	61.600	57.895	29.15	25.36	39.88	5.36
1940	2086	1.266867	TGAGCACAGCTGAGCCCATA	61.267	55.000	29.15	12.68	39.88	2.74
1954	2100	0.692476	CCCATAATCTCATCCGCCCA	59.308	55.000	0.00	0.00	0.00	5.36
1956	2102	1.611673	CCATAATCTCATCCGCCCACC	60.612	57.143	0.00	0.00	0.00	4.61
2018	2165	3.496130	AGAATGCTGCGTATTGTAGATGC	59.504	43.478	0.00	0.00	30.84	3.91
2045	2192	1.144503	AGATGGGCCTGCCTCATTTAG	59.855	52.381	4.53	0.00	36.10	1.85
2200	2353	7.968405	AGCTTACGAATTTGAATACATTTGACC	59.032	33.333	0.00	0.00	0.00	4.02
2438	2623	1.614903	TCAGCAGGTGCAAATTGGAAG	59.385	47.619	4.48	0.00	45.16	3.46
2617	2805	9.925268	TTCTCAAAACGTAAAATTCAGAGTTAC	57.075	29.630	0.00	0.00	0.00	2.50
2618	2806	9.321562	TCTCAAAACGTAAAATTCAGAGTTACT	57.678	29.630	0.00	0.00	0.00	2.24
2619	2807	9.582223	CTCAAAACGTAAAATTCAGAGTTACTC	57.418	33.333	3.85	3.85	0.00	2.59
2620	2808	8.553696	TCAAAACGTAAAATTCAGAGTTACTCC	58.446	33.333	8.96	0.00	0.00	3.85
2621	2809	7.430992	AAACGTAAAATTCAGAGTTACTCCC	57.569	36.000	8.96	0.00	0.00	4.30
2622	2810	6.356186	ACGTAAAATTCAGAGTTACTCCCT	57.644	37.500	8.96	0.00	0.00	4.20
2623	2811	6.396450	ACGTAAAATTCAGAGTTACTCCCTC	58.604	40.000	8.96	0.00	0.00	4.30
2624	2812	5.811100	CGTAAAATTCAGAGTTACTCCCTCC	59.189	44.000	8.96	0.00	0.00	4.30
2625	2813	5.843019	AAAATTCAGAGTTACTCCCTCCA	57.157	39.130	8.96	0.00	0.00	3.86
2626	2814	6.394345	AAAATTCAGAGTTACTCCCTCCAT	57.606	37.500	8.96	0.00	0.00	3.41
2627	2815	7.510675	AAAATTCAGAGTTACTCCCTCCATA	57.489	36.000	8.96	0.00	0.00	2.74
2628	2816	7.510675	AAATTCAGAGTTACTCCCTCCATAA	57.489	36.000	8.96	0.00	0.00	1.90
2629	2817	7.510675	AATTCAGAGTTACTCCCTCCATAAA	57.489	36.000	8.96	0.00	0.00	1.40
2630	2818	5.934402	TCAGAGTTACTCCCTCCATAAAC	57.066	43.478	8.96	0.00	0.00	2.01
2631	2819	5.590818	TCAGAGTTACTCCCTCCATAAACT	58.409	41.667	8.96	0.00	0.00	2.66
2632	2820	6.738635	TCAGAGTTACTCCCTCCATAAACTA	58.261	40.000	8.96	0.00	0.00	2.24
2633	2821	7.186972	TCAGAGTTACTCCCTCCATAAACTAA	58.813	38.462	8.96	0.00	0.00	2.24
2634	2822	7.844779	TCAGAGTTACTCCCTCCATAAACTAAT	59.155	37.037	8.96	0.00	0.00	1.73
2635	2823	9.144298	CAGAGTTACTCCCTCCATAAACTAATA	57.856	37.037	8.96	0.00	0.00	0.98
2636	2824	9.900112	AGAGTTACTCCCTCCATAAACTAATAT	57.100	33.333	8.96	0.00	0.00	1.28
2642	2830	8.817876	ACTCCCTCCATAAACTAATATAAGAGC	58.182	37.037	0.00	0.00	0.00	4.09
2643	2831	8.736097	TCCCTCCATAAACTAATATAAGAGCA	57.264	34.615	0.00	0.00	0.00	4.26
2644	2832	9.338968	TCCCTCCATAAACTAATATAAGAGCAT	57.661	33.333	0.00	0.00	0.00	3.79
2645	2833	9.965902	CCCTCCATAAACTAATATAAGAGCATT	57.034	33.333	0.00	0.00	0.00	3.56
2694	2882	9.530633	AAACGCTCTTATATTAGTTTACAGAGG	57.469	33.333	0.00	0.00	31.14	3.69
2695	2883	8.461249	ACGCTCTTATATTAGTTTACAGAGGA	57.539	34.615	0.00	0.00	0.00	3.71
2696	2884	8.910944	ACGCTCTTATATTAGTTTACAGAGGAA	58.089	33.333	0.00	0.00	0.00	3.36
2697	2885	9.400638	CGCTCTTATATTAGTTTACAGAGGAAG	57.599	37.037	0.00	0.00	0.00	3.46
2761	2950	1.604593	GGCCTGGTGCATGAAGTGT	60.605	57.895	0.00	0.00	43.89	3.55

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
4	5	1.946768	TGCATTTATTAGCACTCCGCC	59.053	47.619	0.00	0.00	44.04	6.13
24	25	4.101448	GGCCACTCCACCGCAGAT	62.101	66.667	0.00	0.00	34.01	2.90
234	255	2.433318	GCTGAGGACGGACTGCAC	60.433	66.667	0.00	0.00	0.00	4.57
278	307	3.500299	GGTGAAAAGACAAGAGCTTCCTC	59.500	47.826	0.00	0.00	38.42	3.71
336	373	0.892063	CCCAACCCATACAAAACGGG	59.108	55.000	0.00	0.00	46.22	5.28
391	428	4.095632	GGAAGAGGTTCAATCTTAAGCTGC	59.904	45.833	0.00	0.00	37.14	5.25
449	486	4.349365	TCTCTCTTTTTCTCTCCCTCTCC	58.651	47.826	0.00	0.00	0.00	3.71
451	488	5.015178	TCTCTCTCTCTTTTTCTCTCCCTCT	59.985	44.000	0.00	0.00	0.00	3.69
455	492	6.180472	TCTCTCTCTCTCTCTTTTTCTCTCC	58.820	44.000	0.00	0.00	0.00	3.71
456	493	7.106239	TCTCTCTCTCTCTCTCTTTTTCTCTC	58.894	42.308	0.00	0.00	0.00	3.20
457	494	7.020827	TCTCTCTCTCTCTCTCTTTTTCTCT	57.979	40.000	0.00	0.00	0.00	3.10
458	495	7.106239	TCTCTCTCTCTCTCTCTCTTTTTCTC	58.894	42.308	0.00	0.00	0.00	2.87
460	497	7.106239	TCTCTCTCTCTCTCTCTCTCTTTTTC	58.894	42.308	0.00	0.00	0.00	2.29
461	498	7.020827	TCTCTCTCTCTCTCTCTCTCTTTTT	57.979	40.000	0.00	0.00	0.00	1.94
462	499	6.441924	TCTCTCTCTCTCTCTCTCTCTCTTTT	59.558	42.308	0.00	0.00	0.00	2.27
463	500	5.960811	TCTCTCTCTCTCTCTCTCTCTCTTT	59.039	44.000	0.00	0.00	0.00	2.52
536	573	4.072131	GGCAAACACCACTCTGATTAAGA	58.928	43.478	0.00	0.00	0.00	2.10
537	574	3.820467	TGGCAAACACCACTCTGATTAAG	59.180	43.478	0.00	0.00	33.75	1.85
538	575	3.820467	CTGGCAAACACCACTCTGATTAA	59.180	43.478	0.00	0.00	35.33	1.40
539	576	3.181445	ACTGGCAAACACCACTCTGATTA	60.181	43.478	0.00	0.00	35.33	1.75
540	577	2.233271	CTGGCAAACACCACTCTGATT	58.767	47.619	0.00	0.00	35.33	2.57
599	636	0.813184	CGATGCTGCCATCAACCTTT	59.187	50.000	0.00	0.00	46.59	3.11
632	679	3.564053	TTTTAGGGGACGTGTTTCTGT	57.436	42.857	0.00	0.00	0.00	3.41
653	700	4.083696	AGTCACGTTCGTGTTTCTGTTTTT	60.084	37.500	21.61	0.00	37.40	1.94
654	701	3.434299	AGTCACGTTCGTGTTTCTGTTTT	59.566	39.130	21.61	0.43	37.40	2.43
655	702	2.997986	AGTCACGTTCGTGTTTCTGTTT	59.002	40.909	21.61	1.68	37.40	2.83
656	703	2.613691	AGTCACGTTCGTGTTTCTGTT	58.386	42.857	21.61	2.52	37.40	3.16
860	925	1.278127	TGGAGAAAGTGGGGATCGAAC	59.722	52.381	0.00	0.00	0.00	3.95
950	1039	6.407202	GGGTGTGCTTAATCTCTAGAGAAAA	58.593	40.000	25.77	20.06	41.36	2.29
988	1084	2.102749	CGCCATTTGGATGCGTGG	59.897	61.111	0.00	0.00	37.39	4.94
1108	1213	7.170998	GCATGTGTGGTTATACTACATACCTTC	59.829	40.741	0.00	0.00	41.57	3.46
1119	1241	2.160615	TGCGTTGCATGTGTGGTTATAC	59.839	45.455	0.00	0.00	31.71	1.47
1120	1242	2.427506	TGCGTTGCATGTGTGGTTATA	58.572	42.857	0.00	0.00	31.71	0.98
1121	1243	1.242989	TGCGTTGCATGTGTGGTTAT	58.757	45.000	0.00	0.00	31.71	1.89
1545	1683	5.065859	GTGGAAAAACAAAAACATCCCCTTG	59.934	40.000	0.00	0.00	0.00	3.61
1562	1700	4.479158	AGTGAATTAGCCCTTGTGGAAAA	58.521	39.130	0.00	0.00	35.39	2.29
1669	1807	0.758310	TGGCTTGGATGCAAACACCA	60.758	50.000	10.71	10.71	34.04	4.17
1695	1833	5.601313	AGGCTTTGGCAATGATATCATCTTT	59.399	36.000	18.44	1.37	40.87	2.52
1696	1834	5.145564	AGGCTTTGGCAATGATATCATCTT	58.854	37.500	18.44	2.12	40.87	2.40
1938	2084	0.321671	CGGTGGGCGGATGAGATTAT	59.678	55.000	0.00	0.00	0.00	1.28
1940	2086	1.910580	AACGGTGGGCGGATGAGATT	61.911	55.000	0.00	0.00	0.00	2.40
1956	2102	0.964358	ACACTAGGGTCCCGAGAACG	60.964	60.000	23.79	13.54	39.43	3.95
1967	2113	4.442472	CCAGAATACGGGTAAACACTAGGG	60.442	50.000	0.00	0.00	0.00	3.53
2018	2165	1.144503	AGGCAGGCCCATCTTAGAATG	59.855	52.381	6.70	0.00	36.58	2.67
2068	2215	1.887088	CGACCTCCTCCTGTACTGTGT	60.887	57.143	0.00	0.00	0.00	3.72
2072	2219	0.927767	ATCCGACCTCCTCCTGTACT	59.072	55.000	0.00	0.00	0.00	2.73
2200	2353	3.579709	GACCACTGTATCGCTCATATGG	58.420	50.000	2.13	0.00	0.00	2.74
2366	2546	6.170506	TGTCACTGAACTTGACTGTAAACTT	58.829	36.000	4.27	0.00	43.30	2.66
2515	2703	9.204570	AGTGTAAACTAGCTGTATTTGTAACTG	57.795	33.333	0.00	0.00	0.00	3.16
2617	2805	8.816894	TGCTCTTATATTAGTTTATGGAGGGAG	58.183	37.037	0.00	0.00	0.00	4.30
2618	2806	8.736097	TGCTCTTATATTAGTTTATGGAGGGA	57.264	34.615	0.00	0.00	0.00	4.20
2619	2807	9.965902	AATGCTCTTATATTAGTTTATGGAGGG	57.034	33.333	0.00	0.00	0.00	4.30
2668	2856	9.530633	CCTCTGTAAACTAATATAAGAGCGTTT	57.469	33.333	0.00	0.00	0.00	3.60
2669	2857	8.910944	TCCTCTGTAAACTAATATAAGAGCGTT	58.089	33.333	0.00	0.00	0.00	4.84
2670	2858	8.461249	TCCTCTGTAAACTAATATAAGAGCGT	57.539	34.615	0.00	0.00	0.00	5.07
2671	2859	9.400638	CTTCCTCTGTAAACTAATATAAGAGCG	57.599	37.037	0.00	0.00	0.00	5.03
2683	2871	8.982723	ACATGTATGATACTTCCTCTGTAAACT	58.017	33.333	0.00	0.00	0.00	2.66
2684	2872	9.601217	AACATGTATGATACTTCCTCTGTAAAC	57.399	33.333	0.00	0.00	0.00	2.01
2686	2874	9.817809	GAAACATGTATGATACTTCCTCTGTAA	57.182	33.333	0.00	0.00	0.00	2.41
2687	2875	9.201989	AGAAACATGTATGATACTTCCTCTGTA	57.798	33.333	0.00	0.00	0.00	2.74
2688	2876	8.083828	AGAAACATGTATGATACTTCCTCTGT	57.916	34.615	0.00	0.00	0.00	3.41
2689	2877	8.420222	AGAGAAACATGTATGATACTTCCTCTG	58.580	37.037	0.00	0.00	0.00	3.35
2690	2878	8.546083	AGAGAAACATGTATGATACTTCCTCT	57.454	34.615	0.00	4.92	0.00	3.69

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.