AutoCloner

Multiple sequence alignment - TraesCS3D01G084700

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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	TraesCS3D01G084700	chr3D	100.000	3793	0	0	1	3793	42789329	42793121	0.000000e+00	7005.0
1	TraesCS3D01G084700	chr3D	87.974	1871	151	39	981	2815	42787654	42785822	0.000000e+00	2141.0
2	TraesCS3D01G084700	chr3D	85.492	1930	208	47	920	2818	42847873	42845985	0.000000e+00	1947.0
3	TraesCS3D01G084700	chr3A	90.457	2515	175	30	719	3187	53416422	53413927	0.000000e+00	3254.0
4	TraesCS3D01G084700	chr3A	90.179	2515	182	27	716	3184	54804221	54806716	0.000000e+00	3216.0
5	TraesCS3D01G084700	chr3A	86.393	1558	163	32	981	2510	54876831	54875295	0.000000e+00	1657.0
6	TraesCS3D01G084700	chr3A	91.977	349	28	0	3445	3793	40296009	40296357	1.220000e-134	490.0
7	TraesCS3D01G084700	chr3A	92.593	324	22	1	1	324	54672551	54672872	7.420000e-127	464.0
8	TraesCS3D01G084700	chr3A	87.632	380	24	9	523	879	53416806	53416427	1.630000e-113	420.0
9	TraesCS3D01G084700	chr3A	87.402	381	23	7	523	879	54803840	54804219	7.580000e-112	414.0
10	TraesCS3D01G084700	chr3A	91.489	235	20	0	2564	2798	54874969	54874735	1.310000e-84	324.0
11	TraesCS3D01G084700	chr3A	91.509	212	11	4	315	526	54674409	54674613	6.200000e-73	285.0
12	TraesCS3D01G084700	chr3A	88.608	158	17	1	725	881	54804147	54804304	1.390000e-44	191.0
13	TraesCS3D01G084700	chr3A	85.629	167	22	2	719	884	53416504	53416339	1.400000e-39	174.0
14	TraesCS3D01G084700	chr3B	91.993	2323	130	24	978	3275	66613497	66611206	0.000000e+00	3208.0
15	TraesCS3D01G084700	chr3B	87.291	1857	154	43	989	2797	66714707	66712885	0.000000e+00	2047.0
16	TraesCS3D01G084700	chr3B	85.372	2003	207	58	920	2874	66711150	66709186	0.000000e+00	1997.0
17	TraesCS3D01G084700	chr3B	87.591	1515	145	25	1009	2510	66599295	66597811	0.000000e+00	1716.0
18	TraesCS3D01G084700	chr3B	95.759	448	17	2	3334	3781	66611121	66610676	0.000000e+00	721.0
19	TraesCS3D01G084700	chr3B	86.984	315	34	5	2564	2874	66597700	66597389	7.800000e-92	348.0
20	TraesCS3D01G084700	chr3B	84.122	296	31	11	594	884	66613926	66613642	4.830000e-69	272.0
21	TraesCS3D01G084700	chr3B	94.805	77	4	0	516	592	66614036	66613960	1.850000e-23	121.0
22	TraesCS3D01G084700	chr3B	82.482	137	23	1	378	513	66614376	66614240	6.660000e-23	119.0
23	TraesCS3D01G084700	chr3B	100.000	40	0	0	3296	3335	66611208	66611169	1.460000e-09	75.0
24	TraesCS3D01G084700	chr2D	83.947	1875	205	56	981	2801	507434669	507432837	0.000000e+00	1707.0
25	TraesCS3D01G084700	chr2B	83.253	1863	219	52	980	2787	596075963	596074139	0.000000e+00	1626.0
26	TraesCS3D01G084700	chr2B	85.294	68	10	0	667	734	461132081	461132014	1.890000e-08	71.3
27	TraesCS3D01G084700	chr6B	91.213	239	14	1	3555	3793	632561011	632561242	6.110000e-83	318.0
28	TraesCS3D01G084700	chr6B	89.474	76	8	0	2887	2962	663097599	663097674	3.120000e-16	97.1
29	TraesCS3D01G084700	chr1D	79.482	463	59	17	2880	3333	468440011	468440446	2.860000e-76	296.0
30	TraesCS3D01G084700	chr1D	90.667	75	3	2	3337	3407	468440499	468440573	3.120000e-16	97.1
31	TraesCS3D01G084700	chr7A	78.851	383	54	14	2880	3255	634916838	634916476	2.280000e-57	233.0
32	TraesCS3D01G084700	chr7A	90.789	76	3	2	3336	3407	634916362	634916287	8.670000e-17	99.0
33	TraesCS3D01G084700	chr6A	84.028	144	23	0	135	278	20742452	20742595	5.110000e-29	139.0
34	TraesCS3D01G084700	chr2A	85.000	80	9	3	667	744	526103729	526103651	1.130000e-10	78.7
35	TraesCS3D01G084700	chr7B	85.507	69	10	0	3340	3408	134223498	134223566	5.260000e-09	73.1

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	TraesCS3D01G084700	chr3D	42789329	42793121	3792	False	7005.000000	7005	100.000000	1	3793	1	chr3D.!!$F1	3792
1	TraesCS3D01G084700	chr3D	42785822	42787654	1832	True	2141.000000	2141	87.974000	981	2815	1	chr3D.!!$R1	1834
2	TraesCS3D01G084700	chr3D	42845985	42847873	1888	True	1947.000000	1947	85.492000	920	2818	1	chr3D.!!$R2	1898
3	TraesCS3D01G084700	chr3A	53413927	53416806	2879	True	1282.666667	3254	87.906000	523	3187	3	chr3A.!!$R1	2664
4	TraesCS3D01G084700	chr3A	54803840	54806716	2876	False	1273.666667	3216	88.729667	523	3184	3	chr3A.!!$F3	2661
5	TraesCS3D01G084700	chr3A	54874735	54876831	2096	True	990.500000	1657	88.941000	981	2798	2	chr3A.!!$R2	1817
6	TraesCS3D01G084700	chr3A	54672551	54674613	2062	False	374.500000	464	92.051000	1	526	2	chr3A.!!$F2	525
7	TraesCS3D01G084700	chr3B	66709186	66714707	5521	True	2022.000000	2047	86.331500	920	2874	2	chr3B.!!$R3	1954
8	TraesCS3D01G084700	chr3B	66597389	66599295	1906	True	1032.000000	1716	87.287500	1009	2874	2	chr3B.!!$R1	1865
9	TraesCS3D01G084700	chr3B	66610676	66614376	3700	True	752.666667	3208	91.526833	378	3781	6	chr3B.!!$R2	3403
10	TraesCS3D01G084700	chr2D	507432837	507434669	1832	True	1707.000000	1707	83.947000	981	2801	1	chr2D.!!$R1	1820
11	TraesCS3D01G084700	chr2B	596074139	596075963	1824	True	1626.000000	1626	83.253000	980	2787	1	chr2B.!!$R2	1807

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
68	69	0.029300	GTGCGCGGCATGAATGTATT	59.971	50.0	8.83	0.0	41.91	1.89	F
1527	3539	0.396435	AGAACCTGTTCATGCGGTCA	59.604	50.0	12.21	0.0	41.84	4.02	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1930	7622	1.021968	ACTTGTTGTCGAAGCAACCC	58.978	50.0	14.28	0.0	45.8	4.11	R
3468	9614	0.302890	GAATCCACTGCGCATTCGAG	59.697	55.0	12.24	0.0	38.1	4.04	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
26	27	1.678300	AGGTCGACGAAGGGAGGTC	60.678	63.158	9.92	0.00	0.00	3.85
67	68	1.648720	GTGCGCGGCATGAATGTAT	59.351	52.632	8.83	0.00	41.91	2.29
68	69	0.029300	GTGCGCGGCATGAATGTATT	59.971	50.000	8.83	0.00	41.91	1.89
131	132	2.985896	TGTTAAGAAAGGCAGGGATCG	58.014	47.619	0.00	0.00	0.00	3.69
156	157	7.007995	CGCGTTAGGAAAATTAGGATTTGAAAC	59.992	37.037	0.00	0.00	35.69	2.78
167	168	9.840427	AATTAGGATTTGAAACTGATTGTAACG	57.160	29.630	0.00	0.00	0.00	3.18
216	217	2.103601	GCTATAGGTTCCTGCCCGTTTA	59.896	50.000	1.04	0.00	0.00	2.01
235	236	2.413310	ATAACGTGGCTGGTTAAGGG	57.587	50.000	0.00	0.00	33.92	3.95
246	247	5.303333	TGGCTGGTTAAGGGAGTTTAAAAAG	59.697	40.000	0.00	0.00	0.00	2.27
247	248	5.227908	GCTGGTTAAGGGAGTTTAAAAAGC	58.772	41.667	0.00	0.00	31.63	3.51
312	313	1.004918	GGTGGTGGAAGGTGAGACG	60.005	63.158	0.00	0.00	0.00	4.18
324	325	5.334646	GGAAGGTGAGACGAAATAAAACCAC	60.335	44.000	0.00	0.00	0.00	4.16
325	326	4.710324	AGGTGAGACGAAATAAAACCACA	58.290	39.130	0.00	0.00	0.00	4.17
326	327	4.514066	AGGTGAGACGAAATAAAACCACAC	59.486	41.667	0.00	0.00	0.00	3.82
327	328	4.273969	GGTGAGACGAAATAAAACCACACA	59.726	41.667	0.00	0.00	0.00	3.72
356	1900	2.180276	TGAAGGAGAGGCTACCAAGTC	58.820	52.381	11.80	7.11	0.00	3.01
736	2519	3.374058	ACACTTACCAAATATGAGTGCGC	59.626	43.478	0.00	0.00	40.95	6.09
843	2798	6.380190	GTGACCTCATAGATGACGTATTACC	58.620	44.000	0.00	0.00	32.50	2.85
868	2823	5.652452	TCGTTCAATCTAGACTCTTGGATCA	59.348	40.000	0.00	0.00	0.00	2.92
898	2853	2.693591	GGACGGTCCATGATAGTTCTGA	59.306	50.000	22.10	0.00	36.28	3.27
947	2908	2.158900	CGACAACCATATGCCTTCCTCT	60.159	50.000	0.00	0.00	0.00	3.69
948	2909	3.471680	GACAACCATATGCCTTCCTCTC	58.528	50.000	0.00	0.00	0.00	3.20
949	2910	2.173569	ACAACCATATGCCTTCCTCTCC	59.826	50.000	0.00	0.00	0.00	3.71
950	2911	2.441001	CAACCATATGCCTTCCTCTCCT	59.559	50.000	0.00	0.00	0.00	3.69
953	2914	2.707791	CCATATGCCTTCCTCTCCTCAA	59.292	50.000	0.00	0.00	0.00	3.02
954	2915	3.330110	CCATATGCCTTCCTCTCCTCAAT	59.670	47.826	0.00	0.00	0.00	2.57
956	2917	2.260639	TGCCTTCCTCTCCTCAATCT	57.739	50.000	0.00	0.00	0.00	2.40
957	2918	2.114616	TGCCTTCCTCTCCTCAATCTC	58.885	52.381	0.00	0.00	0.00	2.75
1213	3218	2.270205	CCTTCCGCATGCTCACCT	59.730	61.111	17.13	0.00	0.00	4.00
1228	3239	2.149383	ACCTTGACCTGCAGCTCCA	61.149	57.895	8.66	2.31	0.00	3.86
1451	3463	2.742372	GTTCCGCGACATGGCTGT	60.742	61.111	8.23	0.00	38.67	4.40
1527	3539	0.396435	AGAACCTGTTCATGCGGTCA	59.604	50.000	12.21	0.00	41.84	4.02
1560	3574	3.190535	CGATTTTCAAGATTGGGTTCGGT	59.809	43.478	0.00	0.00	0.00	4.69
1593	3613	2.261671	CTGTCCCGGTCCAACTCG	59.738	66.667	0.00	0.00	0.00	4.18
1668	7354	1.914764	GTACCGGTTCCTGGACCCA	60.915	63.158	15.04	0.00	36.28	4.51
1671	7357	1.611261	CCGGTTCCTGGACCCACTA	60.611	63.158	11.15	0.00	36.28	2.74
1764	7450	1.933041	CGTGTACGCCGTCATCGAG	60.933	63.158	0.00	0.00	39.71	4.04
1791	7477	1.780503	TCGATCAGATGGGCAGAGAA	58.219	50.000	0.00	0.00	0.00	2.87
1794	7480	1.072015	GATCAGATGGGCAGAGAAGGG	59.928	57.143	0.00	0.00	0.00	3.95
1828	7515	4.514401	ACGTGAGCTTTAATTCCCCTTAG	58.486	43.478	0.00	0.00	0.00	2.18
1831	7518	5.646360	CGTGAGCTTTAATTCCCCTTAGAAA	59.354	40.000	0.00	0.00	0.00	2.52
1912	7604	4.207955	ACATACTGTCGAGATTCCTGCTA	58.792	43.478	0.00	0.00	0.00	3.49
1918	7610	3.118223	TGTCGAGATTCCTGCTAGAGAGA	60.118	47.826	0.00	0.00	0.00	3.10
1930	7622	2.616842	GCTAGAGAGAGAGAAAGACCCG	59.383	54.545	0.00	0.00	0.00	5.28
1933	7625	0.410270	AGAGAGAGAAAGACCCGGGT	59.590	55.000	30.81	30.81	0.00	5.28
1987	7679	0.249120	TCAACTTCATGATCGCCGGT	59.751	50.000	1.90	0.00	0.00	5.28
2032	7724	0.456312	CGTGGTTCCTCTACGTGCTC	60.456	60.000	0.00	0.00	44.07	4.26
2065	7757	1.162800	GCATCCAGGACAAGATCGCC	61.163	60.000	0.00	0.00	0.00	5.54
2067	7759	0.911769	ATCCAGGACAAGATCGCCAA	59.088	50.000	0.00	0.00	0.00	4.52
2423	8179	0.759436	AGTTCCTATGGGGCGACGAT	60.759	55.000	0.00	0.00	34.39	3.73
2513	8549	2.178912	TCACCGCTTTCCAGGTAAAG	57.821	50.000	6.91	6.91	39.00	1.85
2819	8898	4.826274	TTGTGCTGCTATAAGAAGTCCT	57.174	40.909	0.00	0.00	0.00	3.85
2900	8995	0.173255	GATGTGCCCGTCCATTTTGG	59.827	55.000	0.00	0.00	39.43	3.28
3019	9115	6.183360	TGTGTTTTGGCATCTGATATTCATCC	60.183	38.462	0.00	0.00	0.00	3.51
3135	9233	9.841295	ACGAATATGTTATGTGGTAATAAGGTT	57.159	29.630	0.00	0.00	0.00	3.50
3141	9239	7.340256	TGTTATGTGGTAATAAGGTTGGTAGG	58.660	38.462	0.00	0.00	0.00	3.18
3209	9307	4.748892	CGAAGGACAGAAAGCAAGATAGA	58.251	43.478	0.00	0.00	0.00	1.98
3216	9314	3.870419	CAGAAAGCAAGATAGAGAGGCAC	59.130	47.826	0.00	0.00	0.00	5.01
3217	9315	2.593346	AAGCAAGATAGAGAGGCACG	57.407	50.000	0.00	0.00	0.00	5.34
3218	9316	1.769026	AGCAAGATAGAGAGGCACGA	58.231	50.000	0.00	0.00	0.00	4.35
3232	9330	0.657840	GCACGACATAAGATGGGCAC	59.342	55.000	0.00	0.00	33.60	5.01
3272	9370	9.803507	GGGTAAATAACTAAATATAAGGGCTGT	57.196	33.333	0.00	0.00	0.00	4.40
3275	9373	8.760980	AAATAACTAAATATAAGGGCTGTGCA	57.239	30.769	0.00	0.00	0.00	4.57
3276	9374	7.986085	ATAACTAAATATAAGGGCTGTGCAG	57.014	36.000	0.00	0.00	0.00	4.41
3288	9386	2.943843	CTGTGCAGCATATCACGATG	57.056	50.000	0.00	0.00	36.06	3.84
3289	9387	1.529865	CTGTGCAGCATATCACGATGG	59.470	52.381	0.00	0.00	36.06	3.51
3290	9388	0.236711	GTGCAGCATATCACGATGGC	59.763	55.000	0.00	0.00	0.00	4.40
3291	9389	1.223417	TGCAGCATATCACGATGGCG	61.223	55.000	0.00	0.00	44.79	5.69
3292	9390	1.494628	CAGCATATCACGATGGCGC	59.505	57.895	0.00	0.00	42.48	6.53
3293	9391	2.023771	AGCATATCACGATGGCGCG	61.024	57.895	0.00	0.00	42.48	6.86
3294	9392	2.310233	GCATATCACGATGGCGCGT	61.310	57.895	8.43	0.00	46.88	6.01
3421	9567	0.105224	TTCTCGGAGAAAACACGCCA	59.895	50.000	17.70	0.00	34.09	5.69
3452	9598	1.302033	GCTCCCGCAGATACCATGG	60.302	63.158	11.19	11.19	35.78	3.66
3468	9614	5.116069	ACCATGGAACGTATGTTTTTCAC	57.884	39.130	21.47	0.00	38.78	3.18
3476	9622	4.708601	ACGTATGTTTTTCACTCGAATGC	58.291	39.130	0.00	0.00	32.79	3.56
3488	9634	4.983090	GAATGCGCAGTGGATTCG	57.017	55.556	18.12	0.00	44.06	3.34
3552	9698	6.640518	AGTGTTTTTCAGAGAACTCACACTA	58.359	36.000	16.20	0.00	41.35	2.74
3636	9782	6.865205	TCATCTTCATCATGTTACAGCGATAG	59.135	38.462	0.00	0.00	0.00	2.08
3661	9807	2.014128	AGTGGGAAAACACAAGACACG	58.986	47.619	0.00	0.00	43.72	4.49
3664	9810	0.030235	GGAAAACACAAGACACGGGC	59.970	55.000	0.00	0.00	0.00	6.13
3681	9827	1.226974	GCGCGCTGATCTGGTTCTA	60.227	57.895	26.67	0.00	0.00	2.10
3691	9837	5.564651	GCTGATCTGGTTCTAGCTCTCATAC	60.565	48.000	0.00	0.00	0.00	2.39
3744	9890	7.609146	TGCTGATCTGTTTCTGATTCAACTATT	59.391	33.333	1.27	0.00	0.00	1.73
3750	9896	9.383519	TCTGTTTCTGATTCAACTATTATGACC	57.616	33.333	0.00	0.00	0.00	4.02
3782	9928	9.832445	TTCAGACTAAAGAAAGTTGTATTGTCT	57.168	29.630	0.00	0.00	0.00	3.41
3783	9929	9.261180	TCAGACTAAAGAAAGTTGTATTGTCTG	57.739	33.333	0.00	0.00	44.95	3.51
3784	9930	8.012241	CAGACTAAAGAAAGTTGTATTGTCTGC	58.988	37.037	0.00	0.00	40.34	4.26
3785	9931	7.934120	AGACTAAAGAAAGTTGTATTGTCTGCT	59.066	33.333	0.00	0.00	31.09	4.24
3786	9932	8.089115	ACTAAAGAAAGTTGTATTGTCTGCTC	57.911	34.615	0.00	0.00	0.00	4.26
3787	9933	7.934120	ACTAAAGAAAGTTGTATTGTCTGCTCT	59.066	33.333	0.00	0.00	0.00	4.09
3788	9934	6.551385	AAGAAAGTTGTATTGTCTGCTCTG	57.449	37.500	0.00	0.00	0.00	3.35
3789	9935	5.858381	AGAAAGTTGTATTGTCTGCTCTGA	58.142	37.500	0.00	0.00	0.00	3.27
3790	9936	5.931146	AGAAAGTTGTATTGTCTGCTCTGAG	59.069	40.000	0.00	0.00	0.00	3.35
3791	9937	5.474578	AAGTTGTATTGTCTGCTCTGAGA	57.525	39.130	9.28	0.00	0.00	3.27
3792	9938	5.474578	AGTTGTATTGTCTGCTCTGAGAA	57.525	39.130	9.28	0.00	0.00	2.87

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
8	9	1.678300	GACCTCCCTTCGTCGACCT	60.678	63.158	10.58	0.00	0.00	3.85
16	17	1.740664	GTTTCGGCGACCTCCCTTC	60.741	63.158	10.16	0.00	0.00	3.46
131	132	8.027189	AGTTTCAAATCCTAATTTTCCTAACGC	58.973	33.333	0.00	0.00	32.69	4.84
216	217	1.910671	TCCCTTAACCAGCCACGTTAT	59.089	47.619	0.00	0.00	0.00	1.89
223	224	5.779922	CTTTTTAAACTCCCTTAACCAGCC	58.220	41.667	0.00	0.00	0.00	4.85
227	228	8.400184	TCTAAGCTTTTTAAACTCCCTTAACC	57.600	34.615	3.20	0.00	0.00	2.85
282	283	0.926293	CCACCACCACCCCTTCATAT	59.074	55.000	0.00	0.00	0.00	1.78
283	284	0.178858	TCCACCACCACCCCTTCATA	60.179	55.000	0.00	0.00	0.00	2.15
292	293	0.250338	GTCTCACCTTCCACCACCAC	60.250	60.000	0.00	0.00	0.00	4.16
334	1878	3.961408	GACTTGGTAGCCTCTCCTTCATA	59.039	47.826	0.00	0.00	0.00	2.15
342	1886	1.307084	GGGGGACTTGGTAGCCTCT	60.307	63.158	0.00	0.00	0.00	3.69
350	1894	4.101856	TCTACTTCTAAAGGGGGACTTGG	58.898	47.826	0.00	0.00	39.96	3.61
351	1895	5.024118	TCTCTACTTCTAAAGGGGGACTTG	58.976	45.833	0.00	0.00	39.96	3.16
356	1900	6.374588	TGTCTATCTCTACTTCTAAAGGGGG	58.625	44.000	0.00	0.00	0.00	5.40
433	1977	7.462571	TTGCACATATATGGTCGACTATAGT	57.537	36.000	23.49	14.83	0.00	2.12
496	2041	8.166706	CGTGACACTACATAAAATAAGAACACC	58.833	37.037	3.68	0.00	0.00	4.16
736	2519	5.713792	AATAGGTCATCTATGAGGTCACG	57.286	43.478	0.00	0.00	38.60	4.35
795	2578	4.876107	CCGCACTCATATTGGTAACTCTTT	59.124	41.667	0.00	0.00	37.61	2.52
843	2798	5.568685	TCCAAGAGTCTAGATTGAACGAG	57.431	43.478	6.20	0.00	0.00	4.18
933	2894	4.286549	AGATTGAGGAGAGGAAGGCATATG	59.713	45.833	0.00	0.00	0.00	1.78
947	2908	1.596934	GCCGTGTGGAGATTGAGGA	59.403	57.895	0.00	0.00	37.49	3.71
948	2909	1.811266	CGCCGTGTGGAGATTGAGG	60.811	63.158	0.00	0.00	37.19	3.86
949	2910	2.456119	GCGCCGTGTGGAGATTGAG	61.456	63.158	0.00	0.00	37.19	3.02
950	2911	2.434185	GCGCCGTGTGGAGATTGA	60.434	61.111	0.00	0.00	37.19	2.57
953	2914	3.649277	GAGTGCGCCGTGTGGAGAT	62.649	63.158	4.18	0.00	37.19	2.75
954	2915	4.357947	GAGTGCGCCGTGTGGAGA	62.358	66.667	4.18	0.00	37.19	3.71
956	2917	2.986979	TAGAGTGCGCCGTGTGGA	60.987	61.111	4.18	0.00	37.49	4.02
957	2918	2.507102	CTAGAGTGCGCCGTGTGG	60.507	66.667	4.18	0.00	38.77	4.17
1100	3105	4.143333	CCACGGGTGGGTAGCTCG	62.143	72.222	10.05	0.00	46.81	5.03
1213	3218	1.300963	GGATGGAGCTGCAGGTCAA	59.699	57.895	38.37	32.26	43.82	3.18
1228	3239	3.755628	CGGGTCGACGGTGTGGAT	61.756	66.667	9.92	0.00	0.00	3.41
1374	3385	3.591254	GAAGCTGGCGACCTTCCGT	62.591	63.158	0.00	0.00	33.13	4.69
1500	3512	3.871463	GCATGAACAGGTTCTCCATGTCT	60.871	47.826	12.86	0.00	40.14	3.41
1527	3539	2.163818	TGAAAATCGAGTCCAGCGTT	57.836	45.000	0.00	0.00	0.00	4.84
1764	7450	3.244009	TGCCCATCTGATCGATCTTCTTC	60.244	47.826	25.02	9.59	0.00	2.87
1776	7462	1.630126	GCCCTTCTCTGCCCATCTGA	61.630	60.000	0.00	0.00	0.00	3.27
1791	7477	1.274167	TCACGTACGAATTCTTGCCCT	59.726	47.619	24.41	0.00	0.00	5.19
1794	7480	1.993370	AGCTCACGTACGAATTCTTGC	59.007	47.619	24.41	14.61	0.00	4.01
1912	7604	1.341581	CCCGGGTCTTTCTCTCTCTCT	60.342	57.143	14.18	0.00	0.00	3.10
1918	7610	1.128188	AGCAACCCGGGTCTTTCTCT	61.128	55.000	30.40	14.43	0.00	3.10
1930	7622	1.021968	ACTTGTTGTCGAAGCAACCC	58.978	50.000	14.28	0.00	45.80	4.11
1933	7625	2.869801	CAGGTACTTGTTGTCGAAGCAA	59.130	45.455	0.00	0.00	34.60	3.91
2032	7724	2.125229	ATGCGCTGGTCTCTGCAG	60.125	61.111	7.63	7.63	41.19	4.41
2065	7757	4.785453	GCCTCCCGCACCTCCTTG	62.785	72.222	0.00	0.00	37.47	3.61
2114	7806	2.434884	CGCCGTGAACTCCTGCAT	60.435	61.111	0.00	0.00	0.00	3.96
2119	7811	4.681978	AGGCACGCCGTGAACTCC	62.682	66.667	23.33	12.55	41.95	3.85
2398	8154	1.417890	CGCCCCATAGGAACTTCATCT	59.582	52.381	0.00	0.00	41.75	2.90
2423	8179	3.706373	GGCCTGAACTCCTCGGCA	61.706	66.667	0.00	0.00	42.22	5.69
2513	8549	7.645058	TTGGTCCCTGAAAATAGATGATTTC	57.355	36.000	0.00	0.00	36.71	2.17
2530	8568	3.196254	TCAGGTCGTAGTTTATTGGTCCC	59.804	47.826	0.00	0.00	0.00	4.46
2819	8898	2.942376	ACATGTGAACGCTTTTGAGACA	59.058	40.909	0.00	0.00	0.00	3.41
2882	8977	1.887344	GCCAAAATGGACGGGCACAT	61.887	55.000	0.00	0.00	45.70	3.21
3122	9220	6.716173	TCAAAACCTACCAACCTTATTACCAC	59.284	38.462	0.00	0.00	0.00	4.16
3152	9250	8.548877	AGAACCCTTGCTATTCTTCTTATACAA	58.451	33.333	0.00	0.00	28.03	2.41
3209	9307	1.414181	CCCATCTTATGTCGTGCCTCT	59.586	52.381	0.00	0.00	0.00	3.69
3216	9314	2.602257	TGAGTGCCCATCTTATGTCG	57.398	50.000	0.00	0.00	0.00	4.35
3217	9315	6.058183	AGTATTTGAGTGCCCATCTTATGTC	58.942	40.000	0.00	0.00	0.00	3.06
3218	9316	6.006275	AGTATTTGAGTGCCCATCTTATGT	57.994	37.500	0.00	0.00	0.00	2.29
3272	9370	1.223417	CGCCATCGTGATATGCTGCA	61.223	55.000	4.13	4.13	0.00	4.41
3273	9371	1.494628	CGCCATCGTGATATGCTGC	59.505	57.895	0.00	0.00	0.00	5.25
3274	9372	1.494628	GCGCCATCGTGATATGCTG	59.505	57.895	0.00	0.00	38.14	4.41
3275	9373	3.957260	GCGCCATCGTGATATGCT	58.043	55.556	0.00	0.00	38.14	3.79
3292	9390	1.144969	AATAGACGTGTGTGGCAACG	58.855	50.000	8.54	8.54	42.51	4.10
3293	9391	3.002862	TCAAAATAGACGTGTGTGGCAAC	59.997	43.478	0.00	0.00	0.00	4.17
3294	9392	3.002862	GTCAAAATAGACGTGTGTGGCAA	59.997	43.478	0.00	0.00	0.00	4.52
3342	9440	9.332502	TCAAGTTTTAGCACATCTTAGTGTTAA	57.667	29.630	0.00	0.00	41.40	2.01
3386	9532	3.326747	CGAGAAACTTCTACCCACTTGG	58.673	50.000	0.00	0.00	37.73	3.61
3452	9598	5.280678	GCATTCGAGTGAAAAACATACGTTC	59.719	40.000	12.67	0.00	37.71	3.95
3468	9614	0.302890	GAATCCACTGCGCATTCGAG	59.697	55.000	12.24	0.00	38.10	4.04
3502	9648	8.792830	ACACAAAATAGACACAATACTGCTAT	57.207	30.769	0.00	0.00	0.00	2.97
3627	9773	0.391661	CCCACTGTTGCTATCGCTGT	60.392	55.000	0.00	0.00	36.97	4.40
3636	9782	2.165437	TCTTGTGTTTTCCCACTGTTGC	59.835	45.455	0.00	0.00	36.30	4.17
3664	9810	1.211818	GCTAGAACCAGATCAGCGCG	61.212	60.000	0.00	0.00	0.00	6.86
3744	9890	7.718334	TCTTTAGTCTGAATGTCAGGTCATA	57.282	36.000	5.46	0.00	44.39	2.15
3749	9895	7.227512	ACAACTTTCTTTAGTCTGAATGTCAGG	59.772	37.037	5.46	0.00	44.39	3.86
3750	9896	8.147642	ACAACTTTCTTTAGTCTGAATGTCAG	57.852	34.615	0.00	0.00	45.59	3.51

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.