AutoCloner

Multiple sequence alignment - TraesCS3D01G193700

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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	TraesCS3D01G193700	chr3D	100.000	3467	0	0	1	3467	184381834	184378368	0.000000e+00	6403.0
1	TraesCS3D01G193700	chr3D	98.464	521	8	0	2947	3467	397784174	397784694	0.000000e+00	918.0
2	TraesCS3D01G193700	chr3D	97.679	517	12	0	2951	3467	181112161	181111645	0.000000e+00	889.0
3	TraesCS3D01G193700	chr3B	92.027	1317	49	21	927	2235	262902664	262901396	0.000000e+00	1799.0
4	TraesCS3D01G193700	chr3B	89.300	514	21	17	2224	2724	262878547	262878055	6.360000e-172	614.0
5	TraesCS3D01G193700	chr3B	97.826	92	2	0	2829	2920	262864420	262864329	3.580000e-35	159.0
6	TraesCS3D01G193700	chr3B	92.857	70	4	1	2766	2834	262878054	262877985	2.200000e-17	100.0
7	TraesCS3D01G193700	chr3B	100.000	34	0	0	2914	2947	262857010	262856977	2.890000e-06	63.9
8	TraesCS3D01G193700	chr4D	97.690	909	19	1	1	907	46173488	46174396	0.000000e+00	1561.0
9	TraesCS3D01G193700	chr7D	96.593	910	26	2	1	907	561529746	561528839	0.000000e+00	1504.0
10	TraesCS3D01G193700	chr7D	97.706	523	10	2	2946	3467	13323227	13322706	0.000000e+00	898.0
11	TraesCS3D01G193700	chr7D	88.106	227	16	9	1	217	54602305	54602530	3.430000e-65	259.0
12	TraesCS3D01G193700	chr3A	94.178	979	25	14	929	1902	235382382	235381431	0.000000e+00	1463.0
13	TraesCS3D01G193700	chr3A	94.654	318	11	4	2583	2895	235380701	235380385	4.020000e-134	488.0
14	TraesCS3D01G193700	chr3A	92.857	210	13	2	2389	2597	235380948	235380740	1.560000e-78	303.0
15	TraesCS3D01G193700	chr3A	90.659	182	11	4	1956	2134	235381422	235381244	1.610000e-58	237.0
16	TraesCS3D01G193700	chr3A	85.784	204	18	9	24	217	32710413	32710211	4.540000e-49	206.0
17	TraesCS3D01G193700	chr3A	94.595	74	4	0	2162	2235	235381260	235381187	7.860000e-22	115.0
18	TraesCS3D01G193700	chr3A	82.456	114	7	5	2222	2322	235381152	235381039	1.710000e-13	87.9
19	TraesCS3D01G193700	chr3A	87.692	65	8	0	477	541	53568798	53568862	3.710000e-10	76.8
20	TraesCS3D01G193700	chr2D	99.042	522	5	0	2946	3467	203045789	203046310	0.000000e+00	937.0
21	TraesCS3D01G193700	chr2D	96.983	232	7	0	385	616	5086488	5086257	1.170000e-104	390.0
22	TraesCS3D01G193700	chr6D	98.467	522	7	1	2947	3467	119965197	119965718	0.000000e+00	918.0
23	TraesCS3D01G193700	chr1D	98.084	522	10	0	2946	3467	62577880	62578401	0.000000e+00	909.0
24	TraesCS3D01G193700	chr1D	88.710	62	7	0	845	906	198265205	198265144	3.710000e-10	76.8
25	TraesCS3D01G193700	chr5D	97.897	523	9	2	2946	3467	377361184	377361705	0.000000e+00	904.0
26	TraesCS3D01G193700	chr5D	94.271	192	7	4	1	192	546785953	546786140	1.220000e-74	291.0
27	TraesCS3D01G193700	chr6B	97.529	526	12	1	2943	3467	142803823	142803298	0.000000e+00	898.0
28	TraesCS3D01G193700	chr6B	97.505	521	13	0	2947	3467	207153871	207153351	0.000000e+00	891.0
29	TraesCS3D01G193700	chr4A	87.591	548	60	6	369	915	323886877	323887417	2.270000e-176	628.0
30	TraesCS3D01G193700	chr5A	85.294	204	19	9	24	217	398692289	398692491	2.110000e-47	200.0
31	TraesCS3D01G193700	chr2A	85.294	204	19	9	24	217	728080158	728079956	2.110000e-47	200.0
32	TraesCS3D01G193700	chr2A	90.164	61	6	0	845	905	143025462	143025402	2.870000e-11	80.5
33	TraesCS3D01G193700	chr2A	90.164	61	6	0	845	905	751002644	751002584	2.870000e-11	80.5
34	TraesCS3D01G193700	chr7B	83.803	142	15	7	2337	2476	64976891	64976756	1.010000e-25	128.0
35	TraesCS3D01G193700	chr1A	90.323	62	6	0	845	906	571363931	571363992	7.980000e-12	82.4
36	TraesCS3D01G193700	chr4B	85.507	69	10	0	845	913	640107578	640107510	4.800000e-09	73.1
37	TraesCS3D01G193700	chr1B	85.135	74	8	3	828	901	601222771	601222841	4.800000e-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	TraesCS3D01G193700	chr3D	184378368	184381834	3466	True	6403.000000	6403	100.0000	1	3467	1	chr3D.!!$R2	3466
1	TraesCS3D01G193700	chr3D	397784174	397784694	520	False	918.000000	918	98.4640	2947	3467	1	chr3D.!!$F1	520
2	TraesCS3D01G193700	chr3D	181111645	181112161	516	True	889.000000	889	97.6790	2951	3467	1	chr3D.!!$R1	516
3	TraesCS3D01G193700	chr3B	262901396	262902664	1268	True	1799.000000	1799	92.0270	927	2235	1	chr3B.!!$R3	1308
4	TraesCS3D01G193700	chr3B	262877985	262878547	562	True	357.000000	614	91.0785	2224	2834	2	chr3B.!!$R4	610
5	TraesCS3D01G193700	chr4D	46173488	46174396	908	False	1561.000000	1561	97.6900	1	907	1	chr4D.!!$F1	906
6	TraesCS3D01G193700	chr7D	561528839	561529746	907	True	1504.000000	1504	96.5930	1	907	1	chr7D.!!$R2	906
7	TraesCS3D01G193700	chr7D	13322706	13323227	521	True	898.000000	898	97.7060	2946	3467	1	chr7D.!!$R1	521
8	TraesCS3D01G193700	chr3A	235380385	235382382	1997	True	448.983333	1463	91.5665	929	2895	6	chr3A.!!$R2	1966
9	TraesCS3D01G193700	chr2D	203045789	203046310	521	False	937.000000	937	99.0420	2946	3467	1	chr2D.!!$F1	521
10	TraesCS3D01G193700	chr6D	119965197	119965718	521	False	918.000000	918	98.4670	2947	3467	1	chr6D.!!$F1	520
11	TraesCS3D01G193700	chr1D	62577880	62578401	521	False	909.000000	909	98.0840	2946	3467	1	chr1D.!!$F1	521
12	TraesCS3D01G193700	chr5D	377361184	377361705	521	False	904.000000	904	97.8970	2946	3467	1	chr5D.!!$F1	521
13	TraesCS3D01G193700	chr6B	142803298	142803823	525	True	898.000000	898	97.5290	2943	3467	1	chr6B.!!$R1	524
14	TraesCS3D01G193700	chr6B	207153351	207153871	520	True	891.000000	891	97.5050	2947	3467	1	chr6B.!!$R2	520
15	TraesCS3D01G193700	chr4A	323886877	323887417	540	False	628.000000	628	87.5910	369	915	1	chr4A.!!$F1	546

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
374	377	0.179032	ACGGCACCACAAACAGATCA	60.179	50.0	0.0	0.0	0.00	2.92	F
993	997	0.667487	CTGTATGGGTATGCCGCTCG	60.667	60.0	0.0	0.0	34.97	5.03	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1860	1960	0.032117	TCACATCGGGATCAGGAGGT	60.032	55.0	0.0	0.0	0.0	3.85	R
2657	2940	0.548031	AATCTGTGATGGTCCGGCAT	59.452	50.0	0.0	0.0	0.0	4.40	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
238	241	1.840635	GAGATGTAGCCTTGGGGTCTT	59.159	52.381	0.00	0.00	34.28	3.01
366	369	3.542676	ACTCGGACGGCACCACAA	61.543	61.111	0.00	0.00	0.00	3.33
374	377	0.179032	ACGGCACCACAAACAGATCA	60.179	50.000	0.00	0.00	0.00	2.92
561	565	4.666253	GTTGGGGGCTGCTGCTCA	62.666	66.667	17.93	9.76	42.67	4.26
735	739	2.159085	GGTTAGTGGATGAGGAAGGTCG	60.159	54.545	0.00	0.00	0.00	4.79
754	758	2.148052	TGGGGTGCGGTAGTGGAAA	61.148	57.895	0.00	0.00	0.00	3.13
907	911	9.543018	CGTAAGCACTTTTTAGATTTTAGGAAG	57.457	33.333	0.00	0.00	0.00	3.46
910	914	9.574516	AAGCACTTTTTAGATTTTAGGAAGAGA	57.425	29.630	0.00	0.00	0.00	3.10
911	915	9.574516	AGCACTTTTTAGATTTTAGGAAGAGAA	57.425	29.630	0.00	0.00	0.00	2.87
937	941	2.442502	AGTATACTCCTACTCCGCTGGT	59.557	50.000	0.00	0.00	0.00	4.00
979	983	2.111878	GCCAGCGCCATCCTGTAT	59.888	61.111	2.29	0.00	0.00	2.29
993	997	0.667487	CTGTATGGGTATGCCGCTCG	60.667	60.000	0.00	0.00	34.97	5.03
997	1001	4.221422	GGGTATGCCGCTCGCTCA	62.221	66.667	0.00	0.00	38.78	4.26
1115	1124	4.457496	CGCCAGCCTCGACACCAT	62.457	66.667	0.00	0.00	0.00	3.55
1613	1628	1.376466	GCTTCTTGCTGGACCAGGA	59.624	57.895	23.09	18.18	38.95	3.86
1748	1843	4.864334	GGAGGCCATGGTGAGCGG	62.864	72.222	14.67	0.00	0.00	5.52
1801	1896	1.132462	AGAGCTGGGGGATGATCTGAT	60.132	52.381	0.00	0.00	0.00	2.90
1860	1960	2.400399	CGCTTTTAGTGTCTTGTCGGA	58.600	47.619	0.00	0.00	0.00	4.55
1866	1966	0.178958	AGTGTCTTGTCGGACCTCCT	60.179	55.000	5.55	0.00	35.54	3.69
1870	1970	1.135333	GTCTTGTCGGACCTCCTGATC	59.865	57.143	5.55	0.00	0.00	2.92
1871	1971	0.461961	CTTGTCGGACCTCCTGATCC	59.538	60.000	5.55	0.00	0.00	3.36
1872	1972	0.976073	TTGTCGGACCTCCTGATCCC	60.976	60.000	5.55	0.00	0.00	3.85
1873	1973	2.123854	TCGGACCTCCTGATCCCG	60.124	66.667	0.00	0.00	41.36	5.14
1874	1974	2.123854	CGGACCTCCTGATCCCGA	60.124	66.667	0.00	0.00	42.49	5.14
1875	1975	1.531840	CGGACCTCCTGATCCCGAT	60.532	63.158	0.00	0.00	42.49	4.18
1876	1976	1.810606	CGGACCTCCTGATCCCGATG	61.811	65.000	0.00	0.00	42.49	3.84
1877	1977	0.760945	GGACCTCCTGATCCCGATGT	60.761	60.000	0.00	0.00	0.00	3.06
1878	1978	0.390860	GACCTCCTGATCCCGATGTG	59.609	60.000	0.00	0.00	0.00	3.21
1879	1979	0.032117	ACCTCCTGATCCCGATGTGA	60.032	55.000	0.00	0.00	0.00	3.58
1915	2015	2.674796	AGTGGTCGATGGTTTAGCTC	57.325	50.000	0.00	0.00	0.00	4.09
1934	2034	0.605589	CGATCATGGAGGGAGTAGCC	59.394	60.000	0.00	0.00	0.00	3.93
1954	2054	1.066303	CTAGATGCTGTCGTGGGAGAC	59.934	57.143	0.00	0.00	41.30	3.36
1975	2075	3.751698	ACCCTTTTTGTTGAGATCGTAGC	59.248	43.478	0.00	0.00	0.00	3.58
1976	2076	4.003648	CCCTTTTTGTTGAGATCGTAGCT	58.996	43.478	0.00	0.00	0.00	3.32
1977	2077	4.455877	CCCTTTTTGTTGAGATCGTAGCTT	59.544	41.667	0.00	0.00	0.00	3.74
1978	2078	5.390991	CCCTTTTTGTTGAGATCGTAGCTTC	60.391	44.000	0.00	0.00	0.00	3.86
2034	2134	7.699391	GGTCAATGATGATGTTAATCACTTGTG	59.301	37.037	0.00	0.00	45.51	3.33
2044	2144	5.872617	TGTTAATCACTTGTGGTCTAATCCG	59.127	40.000	0.64	0.00	0.00	4.18
2045	2145	4.553330	AATCACTTGTGGTCTAATCCGT	57.447	40.909	0.64	0.00	0.00	4.69
2046	2146	3.587797	TCACTTGTGGTCTAATCCGTC	57.412	47.619	0.64	0.00	0.00	4.79
2047	2147	2.232941	TCACTTGTGGTCTAATCCGTCC	59.767	50.000	0.64	0.00	0.00	4.79
2053	2154	2.019249	TGGTCTAATCCGTCCGTAGTG	58.981	52.381	0.00	0.00	0.00	2.74
2076	2177	8.634444	AGTGGTACTGCATTACAATTTACAAAA	58.366	29.630	15.24	0.00	0.00	2.44
2078	2179	9.632807	TGGTACTGCATTACAATTTACAAAATC	57.367	29.630	15.24	0.00	0.00	2.17
2098	2199	1.812571	CTTGTGCTGGTGTTATGGTCC	59.187	52.381	0.00	0.00	0.00	4.46
2131	2232	1.471153	GCCTTTCAGCTACTCCGTACC	60.471	57.143	0.00	0.00	0.00	3.34
2132	2233	1.202268	CCTTTCAGCTACTCCGTACCG	60.202	57.143	0.00	0.00	0.00	4.02
2329	2492	1.490490	TGGAGTGAAAAGTCAGCTGGT	59.510	47.619	15.13	0.00	33.27	4.00
2340	2503	4.899352	AGTCAGCTGGTATTCAGAGTTT	57.101	40.909	15.13	0.00	46.18	2.66
2342	2505	6.360370	AGTCAGCTGGTATTCAGAGTTTAA	57.640	37.500	15.13	0.00	46.18	1.52
2343	2506	6.166982	AGTCAGCTGGTATTCAGAGTTTAAC	58.833	40.000	15.13	0.00	46.18	2.01
2347	2510	4.567159	GCTGGTATTCAGAGTTTAACGGAG	59.433	45.833	0.00	0.00	46.18	4.63
2348	2511	5.623824	GCTGGTATTCAGAGTTTAACGGAGA	60.624	44.000	0.00	0.00	46.18	3.71
2349	2512	5.962433	TGGTATTCAGAGTTTAACGGAGAG	58.038	41.667	0.00	0.00	0.00	3.20
2350	2513	5.479375	TGGTATTCAGAGTTTAACGGAGAGT	59.521	40.000	0.00	0.00	0.00	3.24
2361	2524	3.963428	AACGGAGAGTTAACAGCAGAT	57.037	42.857	8.61	0.00	42.14	2.90
2380	2543	3.775316	AGATGACGGAAAGTACCCAGAAT	59.225	43.478	0.00	0.00	0.00	2.40
2407	2623	7.606456	ACAAGTTGTAGAACCGATTTATGTCAT	59.394	33.333	6.75	0.00	31.81	3.06
2564	2780	2.863809	AGTGTGGCTTTTCTTACCAGG	58.136	47.619	0.00	0.00	33.12	4.45
2570	2786	2.504367	GCTTTTCTTACCAGGCAGACA	58.496	47.619	0.00	0.00	0.00	3.41
2855	3138	0.038892	GACAACCTTGCAGGCACATG	60.039	55.000	0.00	0.00	39.63	3.21
2865	3148	2.229543	TGCAGGCACATGAATTTCACTC	59.770	45.455	0.00	0.00	0.00	3.51
2895	3178	4.067896	ACACAAGCTCTCAACAATACAGG	58.932	43.478	0.00	0.00	0.00	4.00
2896	3179	3.077359	ACAAGCTCTCAACAATACAGGC	58.923	45.455	0.00	0.00	0.00	4.85
2897	3180	3.244700	ACAAGCTCTCAACAATACAGGCT	60.245	43.478	0.00	0.00	0.00	4.58
2898	3181	4.020218	ACAAGCTCTCAACAATACAGGCTA	60.020	41.667	0.00	0.00	0.00	3.93
2899	3182	4.130286	AGCTCTCAACAATACAGGCTAC	57.870	45.455	0.00	0.00	0.00	3.58
2900	3183	3.118592	AGCTCTCAACAATACAGGCTACC	60.119	47.826	0.00	0.00	0.00	3.18
2901	3184	3.798202	CTCTCAACAATACAGGCTACCC	58.202	50.000	0.00	0.00	0.00	3.69
2902	3185	2.167693	TCTCAACAATACAGGCTACCCG	59.832	50.000	0.00	0.00	35.76	5.28
2903	3186	2.167693	CTCAACAATACAGGCTACCCGA	59.832	50.000	0.00	0.00	35.76	5.14
2904	3187	2.568062	TCAACAATACAGGCTACCCGAA	59.432	45.455	0.00	0.00	35.76	4.30
2905	3188	2.936498	CAACAATACAGGCTACCCGAAG	59.064	50.000	0.00	0.00	35.76	3.79
2906	3189	1.134491	ACAATACAGGCTACCCGAAGC	60.134	52.381	0.00	0.00	41.99	3.86
2912	3195	4.858680	GCTACCCGAAGCCCAGGC	62.859	72.222	0.00	0.00	42.33	4.85
2913	3196	4.176752	CTACCCGAAGCCCAGGCC	62.177	72.222	4.70	0.00	43.17	5.19
2927	3210	3.503099	GGCCAACCTTCCTACCCA	58.497	61.111	0.00	0.00	0.00	4.51
2928	3211	1.001269	GGCCAACCTTCCTACCCAC	60.001	63.158	0.00	0.00	0.00	4.61
2929	3212	1.001269	GCCAACCTTCCTACCCACC	60.001	63.158	0.00	0.00	0.00	4.61
2930	3213	1.785353	GCCAACCTTCCTACCCACCA	61.785	60.000	0.00	0.00	0.00	4.17
2931	3214	0.999712	CCAACCTTCCTACCCACCAT	59.000	55.000	0.00	0.00	0.00	3.55
2932	3215	1.357761	CCAACCTTCCTACCCACCATT	59.642	52.381	0.00	0.00	0.00	3.16
2933	3216	2.620627	CCAACCTTCCTACCCACCATTC	60.621	54.545	0.00	0.00	0.00	2.67
2934	3217	2.308866	CAACCTTCCTACCCACCATTCT	59.691	50.000	0.00	0.00	0.00	2.40
2935	3218	1.916181	ACCTTCCTACCCACCATTCTG	59.084	52.381	0.00	0.00	0.00	3.02
2936	3219	1.916181	CCTTCCTACCCACCATTCTGT	59.084	52.381	0.00	0.00	0.00	3.41
2937	3220	2.092914	CCTTCCTACCCACCATTCTGTC	60.093	54.545	0.00	0.00	0.00	3.51
2938	3221	2.642171	TCCTACCCACCATTCTGTCT	57.358	50.000	0.00	0.00	0.00	3.41
2939	3222	2.187958	TCCTACCCACCATTCTGTCTG	58.812	52.381	0.00	0.00	0.00	3.51
2940	3223	1.909302	CCTACCCACCATTCTGTCTGT	59.091	52.381	0.00	0.00	0.00	3.41
2941	3224	3.104512	CCTACCCACCATTCTGTCTGTA	58.895	50.000	0.00	0.00	0.00	2.74
2942	3225	3.118738	CCTACCCACCATTCTGTCTGTAC	60.119	52.174	0.00	0.00	0.00	2.90
2943	3226	1.628846	ACCCACCATTCTGTCTGTACC	59.371	52.381	0.00	0.00	0.00	3.34
2944	3227	1.628340	CCCACCATTCTGTCTGTACCA	59.372	52.381	0.00	0.00	0.00	3.25
3147	3430	3.272334	GAATAGGCGGTGGCGCAG	61.272	66.667	10.83	0.00	41.24	5.18
3312	3596	2.677836	CAATCGGGAATGTTGACGTGAT	59.322	45.455	0.00	0.00	0.00	3.06

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
238	241	6.127619	ACTCATCGATCACATGACAACTTCTA	60.128	38.462	0.00	0.00	0.00	2.10
366	369	9.376075	CGCATCTATAAATAGGATTGATCTGTT	57.624	33.333	0.00	0.00	0.00	3.16
374	377	7.332926	CAGCAGTTCGCATCTATAAATAGGATT	59.667	37.037	0.00	0.00	46.13	3.01
713	717	2.838202	GACCTTCCTCATCCACTAACCA	59.162	50.000	0.00	0.00	0.00	3.67
735	739	2.400269	TTTCCACTACCGCACCCCAC	62.400	60.000	0.00	0.00	0.00	4.61
754	758	7.760340	GGTTCATCTCTATCTACTTTTGTCGTT	59.240	37.037	0.00	0.00	0.00	3.85
825	829	3.770040	CCGATCACGTCCTGGCCA	61.770	66.667	4.71	4.71	37.88	5.36
916	920	2.442502	ACCAGCGGAGTAGGAGTATACT	59.557	50.000	4.68	4.68	38.72	2.12
917	921	2.861274	ACCAGCGGAGTAGGAGTATAC	58.139	52.381	0.00	0.00	0.00	1.47
918	922	3.137913	AGAACCAGCGGAGTAGGAGTATA	59.862	47.826	1.50	0.00	0.00	1.47
919	923	2.091775	AGAACCAGCGGAGTAGGAGTAT	60.092	50.000	1.50	0.00	0.00	2.12
920	924	1.284198	AGAACCAGCGGAGTAGGAGTA	59.716	52.381	1.50	0.00	0.00	2.59
921	925	0.039911	AGAACCAGCGGAGTAGGAGT	59.960	55.000	1.50	0.00	0.00	3.85
922	926	0.457851	CAGAACCAGCGGAGTAGGAG	59.542	60.000	1.50	0.00	0.00	3.69
923	927	0.970937	CCAGAACCAGCGGAGTAGGA	60.971	60.000	1.50	0.00	0.00	2.94
924	928	1.517832	CCAGAACCAGCGGAGTAGG	59.482	63.158	1.50	0.00	0.00	3.18
925	929	1.258445	ACCCAGAACCAGCGGAGTAG	61.258	60.000	1.50	0.00	0.00	2.57
937	941	1.276989	GAATGGTGGACGTACCCAGAA	59.723	52.381	12.70	0.00	40.09	3.02
993	997	2.613223	GCGGGGGATTTATAGAGTGAGC	60.613	54.545	0.00	0.00	0.00	4.26
997	1001	0.974383	CGGCGGGGGATTTATAGAGT	59.026	55.000	0.00	0.00	0.00	3.24
1115	1124	4.715130	CGGGGAGGTGGGACCAGA	62.715	72.222	0.00	0.00	41.95	3.86
1254	1269	3.082055	GAGGAAGGGGTCGGGGAC	61.082	72.222	0.00	0.00	0.00	4.46
1801	1896	7.518188	AGGAAAAAGACTAATCCTTGAGAACA	58.482	34.615	0.00	0.00	39.23	3.18
1860	1960	0.032117	TCACATCGGGATCAGGAGGT	60.032	55.000	0.00	0.00	0.00	3.85
1870	1970	1.001746	CCATCTGATCCTCACATCGGG	59.998	57.143	0.00	0.00	30.92	5.14
1871	1971	1.690893	ACCATCTGATCCTCACATCGG	59.309	52.381	0.00	0.00	0.00	4.18
1872	1972	2.606551	CGACCATCTGATCCTCACATCG	60.607	54.545	0.00	0.00	0.00	3.84
1873	1973	2.288702	CCGACCATCTGATCCTCACATC	60.289	54.545	0.00	0.00	0.00	3.06
1874	1974	1.690893	CCGACCATCTGATCCTCACAT	59.309	52.381	0.00	0.00	0.00	3.21
1875	1975	1.114627	CCGACCATCTGATCCTCACA	58.885	55.000	0.00	0.00	0.00	3.58
1876	1976	1.115467	ACCGACCATCTGATCCTCAC	58.885	55.000	0.00	0.00	0.00	3.51
1877	1977	2.091830	ACTACCGACCATCTGATCCTCA	60.092	50.000	0.00	0.00	0.00	3.86
1878	1978	2.294791	CACTACCGACCATCTGATCCTC	59.705	54.545	0.00	0.00	0.00	3.71
1879	1979	2.311463	CACTACCGACCATCTGATCCT	58.689	52.381	0.00	0.00	0.00	3.24
1915	2015	0.605589	GGCTACTCCCTCCATGATCG	59.394	60.000	0.00	0.00	0.00	3.69
1934	2034	1.066303	GTCTCCCACGACAGCATCTAG	59.934	57.143	0.00	0.00	34.11	2.43
1954	2054	4.003648	AGCTACGATCTCAACAAAAAGGG	58.996	43.478	0.00	0.00	0.00	3.95
1975	2075	5.987347	TCCACTTTACAAAACTCCTACGAAG	59.013	40.000	0.00	0.00	0.00	3.79
1976	2076	5.916318	TCCACTTTACAAAACTCCTACGAA	58.084	37.500	0.00	0.00	0.00	3.85
1977	2077	5.534207	TCCACTTTACAAAACTCCTACGA	57.466	39.130	0.00	0.00	0.00	3.43
1978	2078	6.796705	AATCCACTTTACAAAACTCCTACG	57.203	37.500	0.00	0.00	0.00	3.51
2034	2134	1.336125	CCACTACGGACGGATTAGACC	59.664	57.143	0.00	0.00	36.56	3.85
2044	2144	2.667473	AATGCAGTACCACTACGGAC	57.333	50.000	0.00	0.00	38.63	4.79
2045	2145	3.090790	TGTAATGCAGTACCACTACGGA	58.909	45.455	20.63	0.00	38.63	4.69
2046	2146	3.513680	TGTAATGCAGTACCACTACGG	57.486	47.619	20.63	0.00	42.50	4.02
2047	2147	6.417191	AAATTGTAATGCAGTACCACTACG	57.583	37.500	20.63	0.00	0.00	3.51
2053	2154	9.855021	AGATTTTGTAAATTGTAATGCAGTACC	57.145	29.630	20.63	5.56	0.00	3.34
2076	2177	3.347216	GACCATAACACCAGCACAAGAT	58.653	45.455	0.00	0.00	0.00	2.40
2078	2179	1.812571	GGACCATAACACCAGCACAAG	59.187	52.381	0.00	0.00	0.00	3.16
2098	2199	2.143122	TGAAAGGCAGAGCACGTTTAG	58.857	47.619	0.00	0.00	0.00	1.85
2131	2232	2.484264	GACCATCCCTCTGTCAAAAACG	59.516	50.000	0.00	0.00	0.00	3.60
2132	2233	3.486383	TGACCATCCCTCTGTCAAAAAC	58.514	45.455	0.00	0.00	36.16	2.43
2329	2492	8.579006	TGTTAACTCTCCGTTAAACTCTGAATA	58.421	33.333	7.22	0.00	46.48	1.75
2340	2503	4.461431	TCATCTGCTGTTAACTCTCCGTTA	59.539	41.667	7.22	0.00	37.05	3.18
2342	2505	2.826128	TCATCTGCTGTTAACTCTCCGT	59.174	45.455	7.22	0.00	0.00	4.69
2343	2506	3.182967	GTCATCTGCTGTTAACTCTCCG	58.817	50.000	7.22	0.00	0.00	4.63
2347	2510	3.232213	TCCGTCATCTGCTGTTAACTC	57.768	47.619	7.22	0.00	0.00	3.01
2348	2511	3.678056	TTCCGTCATCTGCTGTTAACT	57.322	42.857	7.22	0.00	0.00	2.24
2349	2512	3.746492	ACTTTCCGTCATCTGCTGTTAAC	59.254	43.478	0.00	0.00	0.00	2.01
2350	2513	4.002906	ACTTTCCGTCATCTGCTGTTAA	57.997	40.909	0.00	0.00	0.00	2.01
2353	2516	2.353803	GGTACTTTCCGTCATCTGCTGT	60.354	50.000	0.00	0.00	0.00	4.40
2361	2524	3.833650	TGTATTCTGGGTACTTTCCGTCA	59.166	43.478	0.00	0.00	0.00	4.35
2380	2543	8.089597	TGACATAAATCGGTTCTACAACTTGTA	58.910	33.333	1.67	1.67	32.50	2.41
2420	2636	9.476202	TTGCACTAGATGTACATATTCATACAC	57.524	33.333	8.71	0.00	34.24	2.90
2517	2733	7.224753	ACAAATAGCATTAACACGTCATCCTAG	59.775	37.037	0.00	0.00	0.00	3.02
2564	2780	1.598130	GTGGTGTGTCCCTGTCTGC	60.598	63.158	0.00	0.00	34.77	4.26
2570	2786	1.807814	AAAGAGAGTGGTGTGTCCCT	58.192	50.000	0.00	0.00	34.77	4.20
2657	2940	0.548031	AATCTGTGATGGTCCGGCAT	59.452	50.000	0.00	0.00	0.00	4.40
2855	3138	5.929697	TGTGTCATGTCAGAGTGAAATTC	57.070	39.130	0.00	0.00	0.00	2.17
2865	3148	3.036075	TGAGAGCTTGTGTCATGTCAG	57.964	47.619	0.00	0.00	0.00	3.51
2895	3178	4.858680	GCCTGGGCTTCGGGTAGC	62.859	72.222	4.12	0.00	43.94	3.58
2896	3179	4.176752	GGCCTGGGCTTCGGGTAG	62.177	72.222	13.80	0.00	43.94	3.18
2901	3184	3.868200	AAGGTTGGCCTGGGCTTCG	62.868	63.158	21.72	0.00	46.33	3.79
2902	3185	1.979155	GAAGGTTGGCCTGGGCTTC	60.979	63.158	21.72	12.46	46.33	3.86
2903	3186	2.118294	GAAGGTTGGCCTGGGCTT	59.882	61.111	21.72	7.00	46.33	4.35
2904	3187	3.984732	GGAAGGTTGGCCTGGGCT	61.985	66.667	21.72	0.00	46.33	5.19
2905	3188	2.612493	TAGGAAGGTTGGCCTGGGC	61.612	63.158	14.23	14.23	46.33	5.36
2906	3189	1.303282	GTAGGAAGGTTGGCCTGGG	59.697	63.158	3.32	0.00	46.33	4.45
2907	3190	1.303282	GGTAGGAAGGTTGGCCTGG	59.697	63.158	3.32	0.00	46.33	4.45
2908	3191	1.303282	GGGTAGGAAGGTTGGCCTG	59.697	63.158	3.32	0.00	46.33	4.85
2910	3193	1.001269	GTGGGTAGGAAGGTTGGCC	60.001	63.158	0.00	0.00	0.00	5.36
2911	3194	1.001269	GGTGGGTAGGAAGGTTGGC	60.001	63.158	0.00	0.00	0.00	4.52
2912	3195	0.999712	ATGGTGGGTAGGAAGGTTGG	59.000	55.000	0.00	0.00	0.00	3.77
2913	3196	2.308866	AGAATGGTGGGTAGGAAGGTTG	59.691	50.000	0.00	0.00	0.00	3.77
2914	3197	2.308866	CAGAATGGTGGGTAGGAAGGTT	59.691	50.000	0.00	0.00	0.00	3.50
2915	3198	1.916181	CAGAATGGTGGGTAGGAAGGT	59.084	52.381	0.00	0.00	0.00	3.50
2916	3199	1.916181	ACAGAATGGTGGGTAGGAAGG	59.084	52.381	0.00	0.00	43.62	3.46
2917	3200	2.840651	AGACAGAATGGTGGGTAGGAAG	59.159	50.000	0.00	0.00	43.62	3.46
2918	3201	2.571653	CAGACAGAATGGTGGGTAGGAA	59.428	50.000	0.00	0.00	43.62	3.36
2919	3202	2.187958	CAGACAGAATGGTGGGTAGGA	58.812	52.381	0.00	0.00	43.62	2.94
2920	3203	1.909302	ACAGACAGAATGGTGGGTAGG	59.091	52.381	0.00	0.00	43.62	3.18
2921	3204	3.118738	GGTACAGACAGAATGGTGGGTAG	60.119	52.174	0.00	0.00	43.62	3.18
2922	3205	2.835764	GGTACAGACAGAATGGTGGGTA	59.164	50.000	0.00	0.00	43.62	3.69
2923	3206	1.628846	GGTACAGACAGAATGGTGGGT	59.371	52.381	0.00	0.00	43.62	4.51
2924	3207	1.628340	TGGTACAGACAGAATGGTGGG	59.372	52.381	0.00	0.00	43.62	4.61
3147	3430	4.097286	TGCTAGGGTATTTCGGCAAAAATC	59.903	41.667	0.00	0.00	31.50	2.17

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.