AutoCloner

Multiple sequence alignment - TraesCS5B01G345100

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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	TraesCS5B01G345100	chr5B	100.000	3056	0	0	1	3056	527790256	527787201	0.000000e+00	5644
1	TraesCS5B01G345100	chr5B	92.879	1980	95	12	895	2839	527610458	527608490	0.000000e+00	2833
2	TraesCS5B01G345100	chr5B	86.524	794	81	15	1	789	592069356	592070128	0.000000e+00	850
3	TraesCS5B01G345100	chr5B	86.309	745	85	7	45	786	445551310	445552040	0.000000e+00	795
4	TraesCS5B01G345100	chr5B	82.647	801	94	24	1	789	477356951	477356184	0.000000e+00	667
5	TraesCS5B01G345100	chr5B	79.146	1031	130	39	1629	2617	527775065	527774078	4.300000e-178	634
6	TraesCS5B01G345100	chr5B	85.866	566	58	12	226	789	573487515	573488060	1.580000e-162	582
7	TraesCS5B01G345100	chr5B	95.580	181	8	0	2876	3056	527608495	527608315	1.070000e-74	291
8	TraesCS5B01G345100	chr5B	84.444	135	15	2	2605	2739	527495904	527495776	8.890000e-26	128
9	TraesCS5B01G345100	chr5D	95.669	2055	64	10	807	2839	434652822	434654873	0.000000e+00	3278
10	TraesCS5B01G345100	chr5D	91.046	2055	116	23	809	2839	434571953	434569943	0.000000e+00	2713
11	TraesCS5B01G345100	chr5D	81.385	693	80	21	2243	2903	434661607	434662282	1.260000e-143	520
12	TraesCS5B01G345100	chr5D	81.858	452	59	17	2317	2758	434712395	434712833	2.900000e-95	359
13	TraesCS5B01G345100	chr5D	77.833	609	97	23	1635	2229	434554036	434553452	2.920000e-90	342
14	TraesCS5B01G345100	chr5D	97.238	181	5	0	2876	3056	434654868	434655048	1.060000e-79	307
15	TraesCS5B01G345100	chr5D	94.972	179	9	0	2876	3054	434569948	434569770	6.450000e-72	281
16	TraesCS5B01G345100	chr5D	74.843	318	48	19	1973	2271	434605313	434605009	6.920000e-22	115
17	TraesCS5B01G345100	chr2B	88.197	771	78	8	1	770	775132239	775132997	0.000000e+00	907
18	TraesCS5B01G345100	chr7B	87.500	792	82	12	1	789	551894524	551895301	0.000000e+00	898
19	TraesCS5B01G345100	chr7B	85.985	792	83	15	6	779	412897100	412896319	0.000000e+00	822
20	TraesCS5B01G345100	chr7B	86.676	743	89	7	49	789	666409175	666409909	0.000000e+00	815
21	TraesCS5B01G345100	chr4B	84.868	793	104	10	1	789	622322078	622322858	0.000000e+00	785
22	TraesCS5B01G345100	chr4B	84.557	790	93	11	1	789	193560967	193560206	0.000000e+00	756
23	TraesCS5B01G345100	chr1B	82.029	818	102	18	1	789	114599222	114598421	0.000000e+00	654
24	TraesCS5B01G345100	chr2A	84.915	590	76	11	1	580	673146997	673147583	4.390000e-163	584
25	TraesCS5B01G345100	chr3B	84.672	411	41	7	380	789	11265900	11265511	1.030000e-104	390

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	TraesCS5B01G345100	chr5B	527787201	527790256	3055	True	5644.0	5644	100.0000	1	3056	1	chr5B.!!$R4	3055
1	TraesCS5B01G345100	chr5B	527608315	527610458	2143	True	1562.0	2833	94.2295	895	3056	2	chr5B.!!$R5	2161
2	TraesCS5B01G345100	chr5B	592069356	592070128	772	False	850.0	850	86.5240	1	789	1	chr5B.!!$F3	788
3	TraesCS5B01G345100	chr5B	445551310	445552040	730	False	795.0	795	86.3090	45	786	1	chr5B.!!$F1	741
4	TraesCS5B01G345100	chr5B	477356184	477356951	767	True	667.0	667	82.6470	1	789	1	chr5B.!!$R1	788
5	TraesCS5B01G345100	chr5B	527774078	527775065	987	True	634.0	634	79.1460	1629	2617	1	chr5B.!!$R3	988
6	TraesCS5B01G345100	chr5B	573487515	573488060	545	False	582.0	582	85.8660	226	789	1	chr5B.!!$F2	563
7	TraesCS5B01G345100	chr5D	434652822	434655048	2226	False	1792.5	3278	96.4535	807	3056	2	chr5D.!!$F3	2249
8	TraesCS5B01G345100	chr5D	434569770	434571953	2183	True	1497.0	2713	93.0090	809	3054	2	chr5D.!!$R3	2245
9	TraesCS5B01G345100	chr5D	434661607	434662282	675	False	520.0	520	81.3850	2243	2903	1	chr5D.!!$F1	660
10	TraesCS5B01G345100	chr5D	434553452	434554036	584	True	342.0	342	77.8330	1635	2229	1	chr5D.!!$R1	594
11	TraesCS5B01G345100	chr2B	775132239	775132997	758	False	907.0	907	88.1970	1	770	1	chr2B.!!$F1	769
12	TraesCS5B01G345100	chr7B	551894524	551895301	777	False	898.0	898	87.5000	1	789	1	chr7B.!!$F1	788
13	TraesCS5B01G345100	chr7B	412896319	412897100	781	True	822.0	822	85.9850	6	779	1	chr7B.!!$R1	773
14	TraesCS5B01G345100	chr7B	666409175	666409909	734	False	815.0	815	86.6760	49	789	1	chr7B.!!$F2	740
15	TraesCS5B01G345100	chr4B	622322078	622322858	780	False	785.0	785	84.8680	1	789	1	chr4B.!!$F1	788
16	TraesCS5B01G345100	chr4B	193560206	193560967	761	True	756.0	756	84.5570	1	789	1	chr4B.!!$R1	788
17	TraesCS5B01G345100	chr1B	114598421	114599222	801	True	654.0	654	82.0290	1	789	1	chr1B.!!$R1	788
18	TraesCS5B01G345100	chr2A	673146997	673147583	586	False	584.0	584	84.9150	1	580	1	chr2A.!!$F1	579

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
799	864	0.392595	GGGCCGAACCGAGATTCTTT	60.393	55.0	0.0	0.0	40.62	2.52	F
1016	1103	0.190069	AGTATGTATCCGCCTCCCCA	59.810	55.0	0.0	0.0	0.00	4.96	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1657	1776	1.134965	GTCGTCCATCTTCCTGGTGAG	60.135	57.143	0.0	0.0	37.57	3.51	R
2989	3217	0.533978	TCAAGCAGCAACGCCAGTAA	60.534	50.000	0.0	0.0	0.00	2.24	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
132	151	0.873312	CAGTGGAGCCATCGTCATCG	60.873	60.000	0.00	0.00	38.55	3.84
181	200	2.521958	CTTCGCCTGGTCCAACCGAT	62.522	60.000	12.67	0.00	42.58	4.18
260	281	1.374758	CGAGTCCACCCTGAAGTGC	60.375	63.158	0.00	0.00	36.38	4.40
322	344	4.125695	GGCGTACGCGGAACTCCT	62.126	66.667	31.78	0.00	43.06	3.69
391	413	1.668101	GACGAGGAGGAAGATGCCGT	61.668	60.000	0.00	0.00	0.00	5.68
398	420	2.125512	GAAGATGCCGTGCCGTCT	60.126	61.111	0.00	0.00	0.00	4.18
514	549	3.741476	GGCGACGACTACACCCGT	61.741	66.667	0.00	0.00	42.17	5.28
552	587	3.845259	GTAGATGGCGGGCGGTGA	61.845	66.667	0.00	0.00	0.00	4.02
571	607	1.246056	AACGCGTGGTAGTGGCTAGA	61.246	55.000	14.98	0.00	0.00	2.43
591	629	2.415512	GAGGCGTAGTTTGGCTTTAGTG	59.584	50.000	0.00	0.00	42.99	2.74
607	645	6.381801	GCTTTAGTGTGACATAGTTTGCATT	58.618	36.000	0.00	0.00	0.00	3.56
608	646	6.863126	GCTTTAGTGTGACATAGTTTGCATTT	59.137	34.615	0.00	0.00	0.00	2.32
609	647	7.382218	GCTTTAGTGTGACATAGTTTGCATTTT	59.618	33.333	0.00	0.00	0.00	1.82
651	693	7.671827	ACAAATTTTAATAAATTTCGCCGAGC	58.328	30.769	0.00	0.00	46.03	5.03
792	857	4.760047	CCTGTGGGCCGAACCGAG	62.760	72.222	0.00	0.00	40.62	4.63
793	858	3.691342	CTGTGGGCCGAACCGAGA	61.691	66.667	0.00	0.00	40.62	4.04
794	859	3.000819	TGTGGGCCGAACCGAGAT	61.001	61.111	0.00	0.00	40.62	2.75
795	860	2.267961	GTGGGCCGAACCGAGATT	59.732	61.111	0.00	0.00	40.62	2.40
796	861	1.814169	GTGGGCCGAACCGAGATTC	60.814	63.158	0.00	0.00	40.62	2.52
797	862	1.987855	TGGGCCGAACCGAGATTCT	60.988	57.895	0.00	0.00	40.62	2.40
798	863	1.221021	GGGCCGAACCGAGATTCTT	59.779	57.895	0.00	0.00	40.62	2.52
799	864	0.392595	GGGCCGAACCGAGATTCTTT	60.393	55.000	0.00	0.00	40.62	2.52
800	865	1.134610	GGGCCGAACCGAGATTCTTTA	60.135	52.381	0.00	0.00	40.62	1.85
801	866	2.624636	GGCCGAACCGAGATTCTTTAA	58.375	47.619	0.00	0.00	0.00	1.52
802	867	3.203716	GGCCGAACCGAGATTCTTTAAT	58.796	45.455	0.00	0.00	0.00	1.40
803	868	4.374399	GGCCGAACCGAGATTCTTTAATA	58.626	43.478	0.00	0.00	0.00	0.98
804	869	4.812626	GGCCGAACCGAGATTCTTTAATAA	59.187	41.667	0.00	0.00	0.00	1.40
805	870	5.295045	GGCCGAACCGAGATTCTTTAATAAA	59.705	40.000	0.00	0.00	0.00	1.40
806	871	6.190264	GCCGAACCGAGATTCTTTAATAAAC	58.810	40.000	0.00	0.00	0.00	2.01
807	872	6.712549	CCGAACCGAGATTCTTTAATAAACC	58.287	40.000	0.00	0.00	0.00	3.27
808	873	6.314400	CCGAACCGAGATTCTTTAATAAACCA	59.686	38.462	0.00	0.00	0.00	3.67
809	874	7.148373	CCGAACCGAGATTCTTTAATAAACCAA	60.148	37.037	0.00	0.00	0.00	3.67
810	875	7.691050	CGAACCGAGATTCTTTAATAAACCAAC	59.309	37.037	0.00	0.00	0.00	3.77
811	876	8.631480	AACCGAGATTCTTTAATAAACCAACT	57.369	30.769	0.00	0.00	0.00	3.16
812	877	9.729281	AACCGAGATTCTTTAATAAACCAACTA	57.271	29.630	0.00	0.00	0.00	2.24
813	878	9.901172	ACCGAGATTCTTTAATAAACCAACTAT	57.099	29.630	0.00	0.00	0.00	2.12
829	894	4.158025	CCAACTATAGTCCGTCTTGTGTCT	59.842	45.833	5.70	0.00	0.00	3.41
1016	1103	0.190069	AGTATGTATCCGCCTCCCCA	59.810	55.000	0.00	0.00	0.00	4.96
1019	1106	1.122019	ATGTATCCGCCTCCCCACTC	61.122	60.000	0.00	0.00	0.00	3.51
1034	1121	0.888619	CACTCCTTCTGCAGTACGGA	59.111	55.000	14.67	15.82	0.00	4.69
1064	1157	0.602638	GCCATGTCCGACACTGAACA	60.603	55.000	2.57	0.00	0.00	3.18
1083	1177	2.110420	GGTAAATCCCCTCCGCCG	59.890	66.667	0.00	0.00	0.00	6.46
1293	1410	0.877071	CTGAAACAGCAGCGGACATT	59.123	50.000	0.00	0.00	0.00	2.71
1311	1428	5.134725	ACATTTTTGGGAGCTGGATATCT	57.865	39.130	2.05	0.00	0.00	1.98
1517	1636	2.158813	ACCACAATCGTGTTCTCAAGGT	60.159	45.455	0.00	0.00	41.93	3.50
1608	1727	1.068541	CGTTGTCTCTCCGATGACACA	60.069	52.381	0.00	0.00	42.06	3.72
1657	1776	4.202151	ACTTCCTTGTCAAATTCAGCAACC	60.202	41.667	0.00	0.00	0.00	3.77
1974	2111	3.287222	CTTCAAGGACCACAGGAAAACA	58.713	45.455	0.00	0.00	0.00	2.83
2011	2148	1.375908	GAGCACATTGACCTCGCCA	60.376	57.895	0.00	0.00	0.00	5.69
2013	2150	0.322816	AGCACATTGACCTCGCCAAT	60.323	50.000	0.00	0.00	34.83	3.16
2052	2189	3.458163	CCTACCGGCCGAGCAGAA	61.458	66.667	30.73	3.68	0.00	3.02
2153	2302	5.297527	CCTTATGTAGTTTGCTGCATCATCA	59.702	40.000	1.84	0.44	43.03	3.07
2375	2532	4.180817	TGTCGTTCTGTATTACATGCCTG	58.819	43.478	0.00	0.00	0.00	4.85
2645	2822	2.511373	TGCCGACTGCCTAATGCG	60.511	61.111	0.00	0.00	45.60	4.73
2716	2893	8.970691	ACGTTGATGATTTCCATTTTAAGAAG	57.029	30.769	0.00	0.00	35.17	2.85
2735	2912	5.109662	GAAGAAAACCTTCCTTACACTGC	57.890	43.478	0.00	0.00	44.27	4.40
2739	2916	6.543735	AGAAAACCTTCCTTACACTGCTAAT	58.456	36.000	0.00	0.00	31.28	1.73
2802	2979	6.731467	TGCTTATTTCTTATCCCAAAGTCCT	58.269	36.000	0.00	0.00	0.00	3.85
2828	3005	4.413520	TGGCCCTTTAATAGCTTCTCTCAT	59.586	41.667	0.00	0.00	0.00	2.90
2829	3006	5.103940	TGGCCCTTTAATAGCTTCTCTCATT	60.104	40.000	0.00	0.00	0.00	2.57
2830	3007	5.830457	GGCCCTTTAATAGCTTCTCTCATTT	59.170	40.000	0.00	0.00	0.00	2.32
2831	3008	6.016693	GGCCCTTTAATAGCTTCTCTCATTTC	60.017	42.308	0.00	0.00	0.00	2.17
2832	3009	6.543831	GCCCTTTAATAGCTTCTCTCATTTCA	59.456	38.462	0.00	0.00	0.00	2.69
2839	3016	8.975663	AATAGCTTCTCTCATTTCATCATTCA	57.024	30.769	0.00	0.00	0.00	2.57
2840	3017	8.975663	ATAGCTTCTCTCATTTCATCATTCAA	57.024	30.769	0.00	0.00	0.00	2.69
2841	3018	7.698506	AGCTTCTCTCATTTCATCATTCAAA	57.301	32.000	0.00	0.00	0.00	2.69
2842	3019	8.118976	AGCTTCTCTCATTTCATCATTCAAAA	57.881	30.769	0.00	0.00	0.00	2.44
2843	3020	8.582437	AGCTTCTCTCATTTCATCATTCAAAAA	58.418	29.630	0.00	0.00	0.00	1.94
2844	3021	9.367444	GCTTCTCTCATTTCATCATTCAAAAAT	57.633	29.630	0.00	0.00	0.00	1.82
2846	3023	8.697846	TCTCTCATTTCATCATTCAAAAATGC	57.302	30.769	0.00	0.00	41.76	3.56
2847	3024	8.528643	TCTCTCATTTCATCATTCAAAAATGCT	58.471	29.630	0.00	0.00	41.76	3.79
2848	3025	8.697846	TCTCATTTCATCATTCAAAAATGCTC	57.302	30.769	0.00	0.00	41.76	4.26
2849	3026	8.528643	TCTCATTTCATCATTCAAAAATGCTCT	58.471	29.630	0.00	0.00	41.76	4.09
2850	3027	9.151471	CTCATTTCATCATTCAAAAATGCTCTT	57.849	29.630	0.00	0.00	41.76	2.85
2851	3028	8.931775	TCATTTCATCATTCAAAAATGCTCTTG	58.068	29.630	0.00	0.00	41.76	3.02
2852	3029	8.717821	CATTTCATCATTCAAAAATGCTCTTGT	58.282	29.630	0.00	0.00	41.76	3.16
2853	3030	9.932207	ATTTCATCATTCAAAAATGCTCTTGTA	57.068	25.926	0.00	0.00	41.76	2.41
2854	3031	9.932207	TTTCATCATTCAAAAATGCTCTTGTAT	57.068	25.926	0.00	0.00	41.76	2.29
2855	3032	9.577110	TTCATCATTCAAAAATGCTCTTGTATC	57.423	29.630	0.00	0.00	41.76	2.24
2856	3033	8.741841	TCATCATTCAAAAATGCTCTTGTATCA	58.258	29.630	0.00	0.00	41.76	2.15
2857	3034	8.804743	CATCATTCAAAAATGCTCTTGTATCAC	58.195	33.333	0.00	0.00	41.76	3.06
2858	3035	7.315142	TCATTCAAAAATGCTCTTGTATCACC	58.685	34.615	0.00	0.00	41.76	4.02
2859	3036	6.899393	TTCAAAAATGCTCTTGTATCACCT	57.101	33.333	0.00	0.00	0.00	4.00
2860	3037	6.258230	TCAAAAATGCTCTTGTATCACCTG	57.742	37.500	0.00	0.00	0.00	4.00
2861	3038	5.183713	TCAAAAATGCTCTTGTATCACCTGG	59.816	40.000	0.00	0.00	0.00	4.45
2862	3039	4.307032	AAATGCTCTTGTATCACCTGGT	57.693	40.909	0.00	0.00	0.00	4.00
2863	3040	3.550437	ATGCTCTTGTATCACCTGGTC	57.450	47.619	0.00	0.00	0.00	4.02
2864	3041	2.256306	TGCTCTTGTATCACCTGGTCA	58.744	47.619	0.00	0.00	0.00	4.02
2865	3042	2.840038	TGCTCTTGTATCACCTGGTCAT	59.160	45.455	0.00	0.00	0.00	3.06
2866	3043	3.201290	GCTCTTGTATCACCTGGTCATG	58.799	50.000	0.00	0.00	0.00	3.07
2867	3044	3.801698	CTCTTGTATCACCTGGTCATGG	58.198	50.000	0.00	0.00	0.00	3.66
2868	3045	2.092968	TCTTGTATCACCTGGTCATGGC	60.093	50.000	0.00	0.00	0.00	4.40
2869	3046	1.284313	TGTATCACCTGGTCATGGCA	58.716	50.000	0.00	0.00	0.00	4.92
2870	3047	1.065491	TGTATCACCTGGTCATGGCAC	60.065	52.381	0.00	0.00	0.00	5.01
2871	3048	1.210478	GTATCACCTGGTCATGGCACT	59.790	52.381	0.00	0.00	0.00	4.40
2872	3049	0.700564	ATCACCTGGTCATGGCACTT	59.299	50.000	0.00	0.00	0.00	3.16
2873	3050	1.357137	TCACCTGGTCATGGCACTTA	58.643	50.000	0.00	0.00	0.00	2.24
2874	3051	1.915489	TCACCTGGTCATGGCACTTAT	59.085	47.619	0.00	0.00	0.00	1.73
2929	3157	6.038161	TGGAACTATTGGCATCTAAATGAACG	59.962	38.462	0.00	0.00	34.61	3.95
2934	3162	3.417101	TGGCATCTAAATGAACGGTTGT	58.583	40.909	0.00	0.00	34.61	3.32
2989	3217	1.375551	ACGAGAAAAACAACTGCGGT	58.624	45.000	0.00	0.00	0.00	5.68

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
69	88	2.739996	CCTCCGGCTCTGGCTTGAT	61.740	63.158	0.00	0.00	38.73	2.57
260	281	1.299468	GACATAGTCCTCCTGCGCG	60.299	63.158	0.00	0.00	0.00	6.86
478	503	4.707840	TCGTCGTCGTCGTCGCAC	62.708	66.667	15.28	5.87	44.86	5.34
479	504	4.707840	GTCGTCGTCGTCGTCGCA	62.708	66.667	15.28	3.94	44.86	5.10
514	549	0.973632	TGCCGAGAAGCCTGTAGAAA	59.026	50.000	0.00	0.00	0.00	2.52
552	587	1.214589	CTAGCCACTACCACGCGTT	59.785	57.895	10.22	0.00	0.00	4.84
558	593	0.256752	TACGCCTCTAGCCACTACCA	59.743	55.000	0.00	0.00	38.78	3.25
571	607	2.224450	ACACTAAAGCCAAACTACGCCT	60.224	45.455	0.00	0.00	0.00	5.52
641	682	2.180017	GGTACGAGCTCGGCGAAA	59.820	61.111	36.93	15.86	44.95	3.46
651	693	5.844914	CGAAATTACGTAGATCTGGTACGAG	59.155	44.000	20.39	0.00	44.90	4.18
779	844	1.550130	AAGAATCTCGGTTCGGCCCA	61.550	55.000	0.00	0.00	33.36	5.36
795	860	9.807649	GACGGACTATAGTTGGTTTATTAAAGA	57.192	33.333	6.88	0.00	0.00	2.52
796	861	9.813446	AGACGGACTATAGTTGGTTTATTAAAG	57.187	33.333	6.88	0.00	0.00	1.85
798	863	9.590451	CAAGACGGACTATAGTTGGTTTATTAA	57.410	33.333	6.88	0.00	0.00	1.40
799	864	8.752187	ACAAGACGGACTATAGTTGGTTTATTA	58.248	33.333	6.88	0.00	0.00	0.98
800	865	7.548075	CACAAGACGGACTATAGTTGGTTTATT	59.452	37.037	6.88	3.11	0.00	1.40
801	866	7.039882	CACAAGACGGACTATAGTTGGTTTAT	58.960	38.462	6.88	0.00	0.00	1.40
802	867	6.015180	ACACAAGACGGACTATAGTTGGTTTA	60.015	38.462	6.88	0.00	0.00	2.01
803	868	5.221581	ACACAAGACGGACTATAGTTGGTTT	60.222	40.000	6.88	1.04	0.00	3.27
804	869	4.282703	ACACAAGACGGACTATAGTTGGTT	59.717	41.667	6.88	0.00	0.00	3.67
805	870	3.830755	ACACAAGACGGACTATAGTTGGT	59.169	43.478	6.88	8.08	0.00	3.67
806	871	4.158025	AGACACAAGACGGACTATAGTTGG	59.842	45.833	6.88	4.80	0.00	3.77
807	872	5.312120	AGACACAAGACGGACTATAGTTG	57.688	43.478	6.88	5.72	0.00	3.16
808	873	5.979288	AAGACACAAGACGGACTATAGTT	57.021	39.130	6.88	0.00	0.00	2.24
809	874	5.979288	AAAGACACAAGACGGACTATAGT	57.021	39.130	4.68	4.68	0.00	2.12
810	875	5.577164	CCAAAAGACACAAGACGGACTATAG	59.423	44.000	0.00	0.00	0.00	1.31
811	876	5.011329	ACCAAAAGACACAAGACGGACTATA	59.989	40.000	0.00	0.00	0.00	1.31
812	877	4.202326	ACCAAAAGACACAAGACGGACTAT	60.202	41.667	0.00	0.00	0.00	2.12
813	878	3.133362	ACCAAAAGACACAAGACGGACTA	59.867	43.478	0.00	0.00	0.00	2.59
814	879	2.093128	ACCAAAAGACACAAGACGGACT	60.093	45.455	0.00	0.00	0.00	3.85
815	880	2.031683	CACCAAAAGACACAAGACGGAC	59.968	50.000	0.00	0.00	0.00	4.79
816	881	2.285083	CACCAAAAGACACAAGACGGA	58.715	47.619	0.00	0.00	0.00	4.69
817	882	2.014128	ACACCAAAAGACACAAGACGG	58.986	47.619	0.00	0.00	0.00	4.79
818	883	2.418628	ACACACCAAAAGACACAAGACG	59.581	45.455	0.00	0.00	0.00	4.18
819	884	4.165779	CAACACACCAAAAGACACAAGAC	58.834	43.478	0.00	0.00	0.00	3.01
829	894	1.251527	ACCCGCACAACACACCAAAA	61.252	50.000	0.00	0.00	0.00	2.44
880	951	6.273071	GTGCGAATCTGGCCTTATAAATTTT	58.727	36.000	3.32	0.00	0.00	1.82
884	955	3.211045	GGTGCGAATCTGGCCTTATAAA	58.789	45.455	3.32	0.00	0.00	1.40
1019	1106	1.218316	GGGTCCGTACTGCAGAAGG	59.782	63.158	23.35	19.24	0.00	3.46
1034	1121	3.675619	GACATGGCGGCGTTAGGGT	62.676	63.158	9.37	0.00	0.00	4.34
1064	1157	2.738938	GGCGGAGGGGATTTACCGT	61.739	63.158	0.00	0.00	45.91	4.83
1083	1177	3.756117	CTTAGGGTTCAATGGGGATAGC	58.244	50.000	0.00	0.00	0.00	2.97
1164	1279	5.248248	CCCTTGAAATATCCCAAAACTGGTT	59.752	40.000	0.00	0.00	0.00	3.67
1293	1410	4.044308	TGGTAGATATCCAGCTCCCAAAA	58.956	43.478	0.00	0.00	0.00	2.44
1311	1428	6.767524	ATTCAGGTTGCGAAAATTATGGTA	57.232	33.333	0.00	0.00	0.00	3.25
1484	1603	7.536855	AACACGATTGTGGTTTGTAAAAAGTA	58.463	30.769	17.50	0.00	46.11	2.24
1517	1636	3.948719	GGTTGGTGTCCCGAGCCA	61.949	66.667	0.00	0.00	36.74	4.75
1581	1700	1.300931	GGAGAGACAACGCAGCACA	60.301	57.895	0.00	0.00	0.00	4.57
1608	1727	3.133721	CCATCCTCCTTCTGAACGAATCT	59.866	47.826	0.00	0.00	0.00	2.40
1657	1776	1.134965	GTCGTCCATCTTCCTGGTGAG	60.135	57.143	0.00	0.00	37.57	3.51
1751	1882	4.662179	AGAGATCATCTCCATAAAGGCCAA	59.338	41.667	11.33	0.00	44.42	4.52
1974	2111	3.748568	GCTCTTGAACGAACTTCTCCAAT	59.251	43.478	0.00	0.00	0.00	3.16
2011	2148	2.282391	TGAAGTGGCAGCGGCATT	60.282	55.556	11.88	1.78	43.71	3.56
2013	2150	3.848301	ATGTGAAGTGGCAGCGGCA	62.848	57.895	11.88	5.90	43.71	5.69
2052	2189	8.082242	GGTTAATAATGGCAATCGAGCTTTTAT	58.918	33.333	0.00	0.00	34.17	1.40
2153	2302	2.851195	AGTTGTTCTTGGCTCGACAAT	58.149	42.857	0.00	0.00	34.86	2.71
2645	2822	3.005791	CACCCCTGAATCCAAACAACTTC	59.994	47.826	0.00	0.00	0.00	3.01
2716	2893	6.819397	ATTAGCAGTGTAAGGAAGGTTTTC	57.181	37.500	0.00	0.00	0.00	2.29
2802	2979	4.413520	AGAGAAGCTATTAAAGGGCCATCA	59.586	41.667	6.18	0.00	0.00	3.07
2828	3005	9.932207	ATACAAGAGCATTTTTGAATGATGAAA	57.068	25.926	3.47	0.00	31.98	2.69
2829	3006	9.577110	GATACAAGAGCATTTTTGAATGATGAA	57.423	29.630	3.47	0.00	31.98	2.57
2830	3007	8.741841	TGATACAAGAGCATTTTTGAATGATGA	58.258	29.630	3.47	0.00	31.98	2.92
2831	3008	8.804743	GTGATACAAGAGCATTTTTGAATGATG	58.195	33.333	3.47	0.13	31.98	3.07
2832	3009	7.977853	GGTGATACAAGAGCATTTTTGAATGAT	59.022	33.333	3.47	0.00	31.98	2.45
2836	3013	6.294675	CCAGGTGATACAAGAGCATTTTTGAA	60.295	38.462	0.00	0.00	0.00	2.69
2837	3014	5.183713	CCAGGTGATACAAGAGCATTTTTGA	59.816	40.000	0.00	0.00	0.00	2.69
2838	3015	5.047802	ACCAGGTGATACAAGAGCATTTTTG	60.048	40.000	0.00	0.00	0.00	2.44
2839	3016	5.079643	ACCAGGTGATACAAGAGCATTTTT	58.920	37.500	0.00	0.00	0.00	1.94
2840	3017	4.666512	ACCAGGTGATACAAGAGCATTTT	58.333	39.130	0.00	0.00	0.00	1.82
2841	3018	4.263462	TGACCAGGTGATACAAGAGCATTT	60.263	41.667	0.00	0.00	0.00	2.32
2842	3019	3.264193	TGACCAGGTGATACAAGAGCATT	59.736	43.478	0.00	0.00	0.00	3.56
2843	3020	2.840038	TGACCAGGTGATACAAGAGCAT	59.160	45.455	0.00	0.00	0.00	3.79
2844	3021	2.256306	TGACCAGGTGATACAAGAGCA	58.744	47.619	0.00	0.00	0.00	4.26
2845	3022	3.201290	CATGACCAGGTGATACAAGAGC	58.799	50.000	0.00	0.00	0.00	4.09
2846	3023	3.801698	CCATGACCAGGTGATACAAGAG	58.198	50.000	0.00	0.00	0.00	2.85
2847	3024	2.092968	GCCATGACCAGGTGATACAAGA	60.093	50.000	0.00	0.00	0.00	3.02
2848	3025	2.292267	GCCATGACCAGGTGATACAAG	58.708	52.381	0.00	0.00	0.00	3.16
2849	3026	1.632920	TGCCATGACCAGGTGATACAA	59.367	47.619	0.00	0.00	0.00	2.41
2850	3027	1.065491	GTGCCATGACCAGGTGATACA	60.065	52.381	0.00	0.00	0.00	2.29
2851	3028	1.210478	AGTGCCATGACCAGGTGATAC	59.790	52.381	0.00	0.00	0.00	2.24
2852	3029	1.583556	AGTGCCATGACCAGGTGATA	58.416	50.000	0.00	0.00	0.00	2.15
2853	3030	0.700564	AAGTGCCATGACCAGGTGAT	59.299	50.000	0.00	0.00	0.00	3.06
2854	3031	1.357137	TAAGTGCCATGACCAGGTGA	58.643	50.000	0.00	0.00	0.00	4.02
2855	3032	2.425143	ATAAGTGCCATGACCAGGTG	57.575	50.000	0.00	0.00	0.00	4.00
2856	3033	2.308570	TGAATAAGTGCCATGACCAGGT	59.691	45.455	0.00	0.00	0.00	4.00
2857	3034	3.003394	TGAATAAGTGCCATGACCAGG	57.997	47.619	0.00	0.00	0.00	4.45
2858	3035	4.885907	AGAATGAATAAGTGCCATGACCAG	59.114	41.667	0.00	0.00	0.00	4.00
2859	3036	4.858850	AGAATGAATAAGTGCCATGACCA	58.141	39.130	0.00	0.00	0.00	4.02
2860	3037	5.841957	AAGAATGAATAAGTGCCATGACC	57.158	39.130	0.00	0.00	0.00	4.02
2861	3038	6.753744	GGAAAAGAATGAATAAGTGCCATGAC	59.246	38.462	0.00	0.00	0.00	3.06
2862	3039	6.127366	GGGAAAAGAATGAATAAGTGCCATGA	60.127	38.462	0.00	0.00	0.00	3.07
2863	3040	6.044682	GGGAAAAGAATGAATAAGTGCCATG	58.955	40.000	0.00	0.00	0.00	3.66
2864	3041	5.129320	GGGGAAAAGAATGAATAAGTGCCAT	59.871	40.000	0.00	0.00	0.00	4.40
2865	3042	4.466015	GGGGAAAAGAATGAATAAGTGCCA	59.534	41.667	0.00	0.00	0.00	4.92
2866	3043	4.141937	GGGGGAAAAGAATGAATAAGTGCC	60.142	45.833	0.00	0.00	0.00	5.01
2867	3044	4.711846	AGGGGGAAAAGAATGAATAAGTGC	59.288	41.667	0.00	0.00	0.00	4.40
2868	3045	7.954666	TTAGGGGGAAAAGAATGAATAAGTG	57.045	36.000	0.00	0.00	0.00	3.16
2871	3048	9.429109	GGTTATTAGGGGGAAAAGAATGAATAA	57.571	33.333	0.00	0.00	0.00	1.40
2872	3049	8.797674	AGGTTATTAGGGGGAAAAGAATGAATA	58.202	33.333	0.00	0.00	0.00	1.75
2873	3050	7.565029	CAGGTTATTAGGGGGAAAAGAATGAAT	59.435	37.037	0.00	0.00	0.00	2.57
2874	3051	6.895204	CAGGTTATTAGGGGGAAAAGAATGAA	59.105	38.462	0.00	0.00	0.00	2.57
2989	3217	0.533978	TCAAGCAGCAACGCCAGTAA	60.534	50.000	0.00	0.00	0.00	2.24

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.