AutoCloner

Multiple sequence alignment - TraesCS3B01G507200

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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	TraesCS3B01G507200	chr3B	100.000	2555	0	0	1	2555	750902192	750899638	0.000000e+00	4719.0
1	TraesCS3B01G507200	chr3B	79.327	416	79	7	1126	1537	751014258	751013846	4.160000e-73	285.0
2	TraesCS3B01G507200	chr3D	91.489	1316	79	13	957	2265	563435242	563433953	0.000000e+00	1779.0
3	TraesCS3B01G507200	chr3D	86.914	405	41	9	1772	2167	133227445	133227044	6.490000e-121	444.0
4	TraesCS3B01G507200	chr3D	79.326	445	84	8	1126	1565	563595429	563594988	3.190000e-79	305.0
5	TraesCS3B01G507200	chr3D	88.444	225	15	8	1710	1925	563433659	563433437	7.010000e-66	261.0
6	TraesCS3B01G507200	chr3D	88.384	198	19	2	1936	2133	563433390	563433197	4.250000e-58	235.0
7	TraesCS3B01G507200	chr3D	96.053	76	3	0	2356	2431	563432370	563432295	9.600000e-25	124.0
8	TraesCS3B01G507200	chr3D	98.148	54	1	0	2499	2552	399727271	399727324	7.530000e-16	95.3
9	TraesCS3B01G507200	chr3D	94.828	58	3	0	2498	2555	523767322	523767379	9.730000e-15	91.6
10	TraesCS3B01G507200	chr3D	100.000	29	0	0	1610	1638	7597942	7597970	1.000000e-03	54.7
11	TraesCS3B01G507200	chr4D	94.819	965	44	6	1	963	408578570	408579530	0.000000e+00	1500.0
12	TraesCS3B01G507200	chr4D	94.828	58	3	0	2498	2555	123276063	123276120	9.730000e-15	91.6
13	TraesCS3B01G507200	chr4D	94.828	58	3	0	2498	2555	123319462	123319519	9.730000e-15	91.6
14	TraesCS3B01G507200	chr4D	95.000	40	2	0	1649	1688	48537943	48537904	2.120000e-06	63.9
15	TraesCS3B01G507200	chr3A	94.759	706	30	4	953	1652	698030960	698030256	0.000000e+00	1092.0
16	TraesCS3B01G507200	chr3A	79.148	446	83	9	1126	1565	698168017	698167576	1.490000e-77	300.0
17	TraesCS3B01G507200	chr3A	90.446	157	13	2	2360	2515	698029392	698029237	3.330000e-49	206.0
18	TraesCS3B01G507200	chr3A	92.857	42	1	2	1610	1651	12804486	12804447	2.750000e-05	60.2
19	TraesCS3B01G507200	chr7A	92.278	777	46	11	183	954	73944832	73945599	0.000000e+00	1090.0
20	TraesCS3B01G507200	chr7A	91.286	723	38	3	232	954	642889686	642890383	0.000000e+00	963.0
21	TraesCS3B01G507200	chr7A	84.703	353	37	12	1	342	73944577	73944923	1.130000e-88	337.0
22	TraesCS3B01G507200	chr7A	83.761	351	37	17	1	338	642889294	642889637	5.310000e-82	315.0
23	TraesCS3B01G507200	chr7A	85.714	217	25	6	129	342	642889459	642889672	9.200000e-55	224.0
24	TraesCS3B01G507200	chr7A	85.185	216	27	5	129	342	73944741	73944953	1.540000e-52	217.0
25	TraesCS3B01G507200	chr7A	88.750	160	12	5	183	342	642889550	642889703	9.330000e-45	191.0
26	TraesCS3B01G507200	chr7A	83.696	184	25	5	773	954	672319760	672319580	4.370000e-38	169.0
27	TraesCS3B01G507200	chr7A	89.922	129	11	2	826	954	705140207	705140081	5.660000e-37	165.0
28	TraesCS3B01G507200	chr7A	93.333	45	3	0	1659	1703	341433544	341433500	1.640000e-07	67.6
29	TraesCS3B01G507200	chr4B	85.235	298	38	2	26	323	108343703	108343994	4.130000e-78	302.0
30	TraesCS3B01G507200	chr4B	80.097	412	76	6	545	955	108344049	108344455	4.130000e-78	302.0
31	TraesCS3B01G507200	chr4B	79.459	185	30	6	773	954	604535201	604535380	9.600000e-25	124.0
32	TraesCS3B01G507200	chr5B	81.271	299	28	15	26	323	255410094	255410365	1.540000e-52	217.0
33	TraesCS3B01G507200	chr5B	89.147	129	12	2	826	954	467174596	467174470	2.630000e-35	159.0
34	TraesCS3B01G507200	chr5B	77.186	263	55	4	197	455	255410205	255410466	5.700000e-32	148.0
35	TraesCS3B01G507200	chr2B	84.024	169	23	3	787	954	752856456	752856621	2.630000e-35	159.0
36	TraesCS3B01G507200	chr2D	96.552	58	2	0	2498	2555	39501115	39501172	2.090000e-16	97.1
37	TraesCS3B01G507200	chr2D	94.828	58	3	0	2498	2555	189930006	189930063	9.730000e-15	91.6
38	TraesCS3B01G507200	chr1B	96.552	58	2	0	2498	2555	672570110	672570053	2.090000e-16	97.1
39	TraesCS3B01G507200	chr1B	92.000	50	4	0	1647	1696	673957675	673957626	1.270000e-08	71.3
40	TraesCS3B01G507200	chr1B	100.000	36	0	0	1653	1688	93980933	93980898	1.640000e-07	67.6
41	TraesCS3B01G507200	chr1A	96.491	57	1	1	1647	1703	580941442	580941387	2.710000e-15	93.5
42	TraesCS3B01G507200	chrUn	94.828	58	3	0	2498	2555	86445468	86445525	9.730000e-15	91.6
43	TraesCS3B01G507200	chrUn	94.828	58	3	0	2498	2555	206782637	206782694	9.730000e-15	91.6
44	TraesCS3B01G507200	chr7D	93.333	45	3	0	1659	1703	312564577	312564533	1.640000e-07	67.6
45	TraesCS3B01G507200	chr7B	93.333	45	3	0	1659	1703	303156104	303156060	1.640000e-07	67.6
46	TraesCS3B01G507200	chr5A	95.238	42	0	2	1647	1687	404563318	404563278	5.900000e-07	65.8

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	TraesCS3B01G507200	chr3B	750899638	750902192	2554	True	4719.00	4719	100.000000	1	2555	1	chr3B.!!$R1	2554
1	TraesCS3B01G507200	chr3D	563432295	563435242	2947	True	599.75	1779	91.092500	957	2431	4	chr3D.!!$R3	1474
2	TraesCS3B01G507200	chr4D	408578570	408579530	960	False	1500.00	1500	94.819000	1	963	1	chr4D.!!$F3	962
3	TraesCS3B01G507200	chr3A	698029237	698030960	1723	True	649.00	1092	92.602500	953	2515	2	chr3A.!!$R3	1562
4	TraesCS3B01G507200	chr7A	73944577	73945599	1022	False	548.00	1090	87.388667	1	954	3	chr7A.!!$F1	953
5	TraesCS3B01G507200	chr7A	642889294	642890383	1089	False	423.25	963	87.377750	1	954	4	chr7A.!!$F2	953
6	TraesCS3B01G507200	chr4B	108343703	108344455	752	False	302.00	302	82.666000	26	955	2	chr4B.!!$F2	929

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
370	532	0.530744	CGAGCTACCACCTGCTACAA	59.469	55.0	0.0	0.0	39.91	2.41	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2002	2186	0.472471	AACCTTCGGAGAGCAACCAA	59.528	50.0	0.0	0.0	38.43	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
17	18	3.953775	ACCAGCGTTGACAGGGGG	61.954	66.667	0.00	0.00	0.00	5.40
212	250	4.100084	TGCAGCGGCCACAGCTAT	62.100	61.111	9.71	0.00	44.06	2.97
370	532	0.530744	CGAGCTACCACCTGCTACAA	59.469	55.000	0.00	0.00	39.91	2.41
744	906	6.043938	AGGAAATTACTCAACAGGACCTAACA	59.956	38.462	0.00	0.00	0.00	2.41
801	963	1.203440	ACCTGACAATGGGACCTACCT	60.203	52.381	0.00	0.00	38.98	3.08
803	965	2.187958	CTGACAATGGGACCTACCTGA	58.812	52.381	0.00	0.00	38.98	3.86
806	968	2.505819	GACAATGGGACCTACCTGACAT	59.494	50.000	0.00	0.00	38.98	3.06
816	978	5.416271	ACCTACCTGACATATTCGTTGTT	57.584	39.130	0.00	0.00	0.00	2.83
867	1029	5.581126	TTCTGAAAACTGTCAGCACAATT	57.419	34.783	0.00	0.00	44.01	2.32
936	1101	1.329913	GGGTCCCCAATTGTGATGGC	61.330	60.000	4.43	0.00	36.58	4.40
961	1126	2.729028	TGCAATTTACTCTAGGGGGC	57.271	50.000	0.00	0.00	0.00	5.80
1038	1203	2.025418	CTACACCAACGACGGCACC	61.025	63.158	0.00	0.00	0.00	5.01
1082	1247	1.213296	GGCTGGTTCCCCAAGATCTA	58.787	55.000	0.00	0.00	41.27	1.98
1146	1311	0.184933	TCCTGGTTGAACTTGGTGGG	59.815	55.000	0.00	0.00	0.00	4.61
1155	1320	2.674380	CTTGGTGGGCAGGTGCTC	60.674	66.667	1.26	0.00	43.24	4.26
1236	1401	2.894387	GTGGAGAGCATCGGCAGC	60.894	66.667	0.00	0.00	44.61	5.25
1431	1596	0.533978	TGAAGCCGCACAAGCTGTTA	60.534	50.000	0.00	0.00	40.49	2.41
1572	1737	7.228706	TCGTTTTAATTTTCTCTCTTGCCTTCT	59.771	33.333	0.00	0.00	0.00	2.85
1587	1752	8.458573	TCTTGCCTTCTGTTCTGTTAATTTTA	57.541	30.769	0.00	0.00	0.00	1.52
1720	1889	6.069029	AGGGAGTACTATTTTGTGGGCTTAAT	60.069	38.462	0.00	0.00	0.00	1.40
1760	1929	7.618019	ATGAACCTAATGCTCCATCTACTTA	57.382	36.000	0.00	0.00	0.00	2.24
1761	1930	7.618019	TGAACCTAATGCTCCATCTACTTAT	57.382	36.000	0.00	0.00	0.00	1.73
1822	2001	6.583806	CCATTGTTTCACTTTGCAATAGTCTC	59.416	38.462	0.00	0.00	31.29	3.36
1882	2062	5.048504	TCTGAATTTAGCCTTGCAACTGAAG	60.049	40.000	0.00	0.00	0.00	3.02
1883	2063	4.584325	TGAATTTAGCCTTGCAACTGAAGT	59.416	37.500	0.00	0.00	0.00	3.01
1884	2064	5.767665	TGAATTTAGCCTTGCAACTGAAGTA	59.232	36.000	0.00	0.00	0.00	2.24
1886	2066	7.609918	TGAATTTAGCCTTGCAACTGAAGTATA	59.390	33.333	0.00	0.00	0.00	1.47
1929	2113	9.696917	AGGATTTGTTTATTTTTCAGTAGCAAG	57.303	29.630	0.00	0.00	0.00	4.01
1979	2163	2.151202	GAATCTGGTTCCGCAGTTGAA	58.849	47.619	0.00	0.00	0.00	2.69
1997	2181	4.235939	TGAACCATTGAACATTTGTCGG	57.764	40.909	0.00	0.00	0.00	4.79
2002	2186	3.756434	CCATTGAACATTTGTCGGGTAGT	59.244	43.478	0.00	0.00	0.00	2.73
2009	2193	1.310904	TTTGTCGGGTAGTTGGTTGC	58.689	50.000	0.00	0.00	0.00	4.17
2015	2199	0.391263	GGGTAGTTGGTTGCTCTCCG	60.391	60.000	0.00	0.00	0.00	4.63
2056	2240	6.313744	TGCATTTCTCATATCTGATTGCAG	57.686	37.500	5.53	0.00	43.67	4.41
2065	2249	5.826208	TCATATCTGATTGCAGCTCAACATT	59.174	36.000	0.00	0.00	42.01	2.71
2081	2265	6.690098	GCTCAACATTATGTTAAGATGTGCAG	59.310	38.462	12.09	0.00	38.77	4.41
2083	2267	7.529158	TCAACATTATGTTAAGATGTGCAGTG	58.471	34.615	10.46	0.00	38.77	3.66
2086	2270	6.095860	ACATTATGTTAAGATGTGCAGTGCAT	59.904	34.615	22.87	5.89	41.91	3.96
2088	2272	5.746307	ATGTTAAGATGTGCAGTGCATAG	57.254	39.130	22.87	0.00	41.91	2.23
2112	2296	4.201685	GCAAATTTCATGTGATTGCTGCTC	60.202	41.667	15.72	0.00	42.24	4.26
2123	2307	0.547712	TTGCTGCTCCTAGAGGGGTT	60.548	55.000	0.00	0.00	38.19	4.11
2133	2317	5.675538	CTCCTAGAGGGGTTTTGTAGATTG	58.324	45.833	0.00	0.00	35.41	2.67
2135	2319	5.788533	TCCTAGAGGGGTTTTGTAGATTGAA	59.211	40.000	0.00	0.00	35.41	2.69
2246	2430	6.375455	CAGGATATTCATGGCCAACTAATACC	59.625	42.308	10.96	15.86	0.00	2.73
2330	3368	9.302345	CATACTATTCATGGCTAACTAATACCG	57.698	37.037	0.00	0.00	0.00	4.02
2331	3369	6.698380	ACTATTCATGGCTAACTAATACCGG	58.302	40.000	0.00	0.00	0.00	5.28
2332	3370	4.345859	TTCATGGCTAACTAATACCGGG	57.654	45.455	6.32	0.00	0.00	5.73
2335	3373	3.036452	TGGCTAACTAATACCGGGTCT	57.964	47.619	6.32	0.00	0.00	3.85
2336	3374	3.377573	TGGCTAACTAATACCGGGTCTT	58.622	45.455	6.32	2.36	0.00	3.01
2337	3375	3.133362	TGGCTAACTAATACCGGGTCTTG	59.867	47.826	6.32	0.00	0.00	3.02
2339	3377	4.040095	GGCTAACTAATACCGGGTCTTGAT	59.960	45.833	6.32	0.00	0.00	2.57
2340	3378	5.454329	GGCTAACTAATACCGGGTCTTGATT	60.454	44.000	6.32	0.00	0.00	2.57
2342	3380	5.431179	AACTAATACCGGGTCTTGATTGT	57.569	39.130	6.32	0.00	0.00	2.71
2344	3382	6.742559	ACTAATACCGGGTCTTGATTGTAT	57.257	37.500	6.32	0.00	0.00	2.29
2345	3383	6.756221	ACTAATACCGGGTCTTGATTGTATC	58.244	40.000	6.32	0.00	0.00	2.24
2346	3384	5.623956	AATACCGGGTCTTGATTGTATCA	57.376	39.130	6.32	0.00	37.55	2.15
2347	3385	5.825593	ATACCGGGTCTTGATTGTATCAT	57.174	39.130	6.32	0.00	39.39	2.45
2349	3387	4.451900	ACCGGGTCTTGATTGTATCATTC	58.548	43.478	6.32	0.00	39.39	2.67
2350	3388	4.164221	ACCGGGTCTTGATTGTATCATTCT	59.836	41.667	6.32	0.00	39.39	2.40
2351	3389	4.752101	CCGGGTCTTGATTGTATCATTCTC	59.248	45.833	0.00	0.00	39.39	2.87
2352	3390	4.445718	CGGGTCTTGATTGTATCATTCTCG	59.554	45.833	0.00	0.00	39.39	4.04
2354	3392	5.360591	GGTCTTGATTGTATCATTCTCGGT	58.639	41.667	0.00	0.00	39.39	4.69
2358	4050	6.978659	TCTTGATTGTATCATTCTCGGTGTAC	59.021	38.462	0.00	0.00	39.39	2.90
2418	4110	8.736244	CCTAAGTTGCTAGATAGGAGTAGATTC	58.264	40.741	0.00	0.00	37.67	2.52
2431	4123	4.154918	GGAGTAGATTCCAACTGTTTGCTG	59.845	45.833	0.00	0.00	37.20	4.41
2464	4156	9.639601	CATGAGTAGTTTCAGACTATTTGTGTA	57.360	33.333	0.00	0.00	42.57	2.90
2511	4203	7.987750	TTTTTCCTTTTATACCCCAAAATGC	57.012	32.000	0.00	0.00	0.00	3.56
2512	4204	6.943899	TTTCCTTTTATACCCCAAAATGCT	57.056	33.333	0.00	0.00	0.00	3.79
2513	4205	6.538945	TTCCTTTTATACCCCAAAATGCTC	57.461	37.500	0.00	0.00	0.00	4.26
2515	4207	4.962362	CCTTTTATACCCCAAAATGCTCCT	59.038	41.667	0.00	0.00	0.00	3.69
2516	4208	6.068735	TCCTTTTATACCCCAAAATGCTCCTA	60.069	38.462	0.00	0.00	0.00	2.94
2517	4209	6.265422	CCTTTTATACCCCAAAATGCTCCTAG	59.735	42.308	0.00	0.00	0.00	3.02
2518	4210	2.729028	TACCCCAAAATGCTCCTAGC	57.271	50.000	0.00	0.00	42.82	3.42
2544	4236	3.891049	GAGCCTATGGTTCCATTCTTGT	58.109	45.455	9.70	0.00	0.00	3.16
2545	4237	4.273318	GAGCCTATGGTTCCATTCTTGTT	58.727	43.478	9.70	0.00	0.00	2.83
2546	4238	5.437060	GAGCCTATGGTTCCATTCTTGTTA	58.563	41.667	9.70	0.00	0.00	2.41
2547	4239	5.193679	AGCCTATGGTTCCATTCTTGTTAC	58.806	41.667	9.70	0.00	0.00	2.50
2548	4240	5.044846	AGCCTATGGTTCCATTCTTGTTACT	60.045	40.000	9.70	0.00	0.00	2.24
2549	4241	5.066505	GCCTATGGTTCCATTCTTGTTACTG	59.933	44.000	9.70	0.00	0.00	2.74
2550	4242	5.066505	CCTATGGTTCCATTCTTGTTACTGC	59.933	44.000	9.70	0.00	0.00	4.40
2551	4243	4.098914	TGGTTCCATTCTTGTTACTGCT	57.901	40.909	0.00	0.00	0.00	4.24
2552	4244	3.820467	TGGTTCCATTCTTGTTACTGCTG	59.180	43.478	0.00	0.00	0.00	4.41
2553	4245	3.191371	GGTTCCATTCTTGTTACTGCTGG	59.809	47.826	0.00	0.00	0.00	4.85
2554	4246	4.072131	GTTCCATTCTTGTTACTGCTGGA	58.928	43.478	0.00	0.00	0.00	3.86

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
17	18	2.349817	CGGATGCAGGCGTGATTATTTC	60.350	50.000	11.29	0.00	0.00	2.17
744	906	2.223803	AACAGAGTGAGGAGACGGAT	57.776	50.000	0.00	0.00	0.00	4.18
816	978	3.823281	TCGATCAATTAGGGCCGTTTA	57.177	42.857	1.81	0.00	0.00	2.01
824	986	7.278646	TCAGAAAACACTGATCGATCAATTAGG	59.721	37.037	27.09	17.78	41.21	2.69
830	992	6.859420	TTTTCAGAAAACACTGATCGATCA	57.141	33.333	25.80	25.80	44.67	2.92
961	1126	0.322546	GGGTACTCCTTGGCCTTGTG	60.323	60.000	3.32	0.00	0.00	3.33
1038	1203	3.847542	TGATTTTGCAATGAATCCCGTG	58.152	40.909	17.26	0.00	32.57	4.94
1082	1247	5.163374	TGAGGATTGACATGAATCAGATCGT	60.163	40.000	0.00	2.35	34.50	3.73
1146	1311	1.520342	GACGAGGATGAGCACCTGC	60.520	63.158	0.00	0.00	37.93	4.85
1236	1401	1.153369	ACCGACGAAGATGGCATGG	60.153	57.895	3.81	0.00	0.00	3.66
1306	1471	5.980116	GTCGATCAATGTAGTAGATGCAGTT	59.020	40.000	0.00	0.00	0.00	3.16
1452	1617	1.066573	AGAAGCTGGATGACGGTGAAG	60.067	52.381	0.00	0.00	0.00	3.02
1547	1712	7.324616	CAGAAGGCAAGAGAGAAAATTAAAACG	59.675	37.037	0.00	0.00	0.00	3.60
1565	1730	6.490040	AGCTAAAATTAACAGAACAGAAGGCA	59.510	34.615	0.00	0.00	0.00	4.75
1587	1752	3.837731	AGCCTCTTCTCAAGTTCTTAGCT	59.162	43.478	0.00	0.00	0.00	3.32
1686	1855	4.405756	AATAGTACTCCCTCCGATCCAT	57.594	45.455	0.00	0.00	0.00	3.41
1743	1912	7.580302	GCATCAGGATAAGTAGATGGAGCATTA	60.580	40.741	0.00	0.00	38.57	1.90
1760	1929	5.104610	ACACAAACAGAGATAGCATCAGGAT	60.105	40.000	0.00	0.00	0.00	3.24
1761	1930	4.223700	ACACAAACAGAGATAGCATCAGGA	59.776	41.667	0.00	0.00	0.00	3.86
1822	2001	0.865769	AACCGACTTTTGCTAGCACG	59.134	50.000	19.17	16.97	0.00	5.34
1882	2062	4.627467	CCTGCAGAGAACCGCATAATATAC	59.373	45.833	17.39	0.00	37.54	1.47
1883	2063	4.526650	TCCTGCAGAGAACCGCATAATATA	59.473	41.667	17.39	0.00	37.54	0.86
1884	2064	3.324846	TCCTGCAGAGAACCGCATAATAT	59.675	43.478	17.39	0.00	37.54	1.28
1886	2066	1.486310	TCCTGCAGAGAACCGCATAAT	59.514	47.619	17.39	0.00	37.54	1.28
1946	2130	2.158325	ACCAGATTCAGAAAGGGGCAAA	60.158	45.455	5.06	0.00	0.00	3.68
1947	2131	1.428912	ACCAGATTCAGAAAGGGGCAA	59.571	47.619	5.06	0.00	0.00	4.52
1951	2135	2.359900	CGGAACCAGATTCAGAAAGGG	58.640	52.381	5.06	1.77	39.30	3.95
1979	2163	2.593026	ACCCGACAAATGTTCAATGGT	58.407	42.857	0.00	0.00	0.00	3.55
1982	2166	4.217550	CCAACTACCCGACAAATGTTCAAT	59.782	41.667	0.00	0.00	0.00	2.57
1997	2181	0.606604	TCGGAGAGCAACCAACTACC	59.393	55.000	0.00	0.00	0.00	3.18
2002	2186	0.472471	AACCTTCGGAGAGCAACCAA	59.528	50.000	0.00	0.00	38.43	3.67
2009	2193	4.335594	ACAAGAAACAAAACCTTCGGAGAG	59.664	41.667	0.00	0.00	38.43	3.20
2015	2199	6.421377	AATGCAACAAGAAACAAAACCTTC	57.579	33.333	0.00	0.00	0.00	3.46
2056	2240	6.554419	TGCACATCTTAACATAATGTTGAGC	58.446	36.000	0.00	0.00	41.85	4.26
2065	2249	5.759763	CCTATGCACTGCACATCTTAACATA	59.240	40.000	5.67	0.00	43.04	2.29
2083	2267	5.277154	GCAATCACATGAAATTTGCCTATGC	60.277	40.000	0.00	0.00	37.34	3.14
2086	2270	5.412640	CAGCAATCACATGAAATTTGCCTA	58.587	37.500	17.34	0.00	42.73	3.93
2088	2272	3.181514	GCAGCAATCACATGAAATTTGCC	60.182	43.478	17.34	6.13	42.73	4.52
2098	2282	2.104451	CCTCTAGGAGCAGCAATCACAT	59.896	50.000	0.00	0.00	37.39	3.21
2112	2296	5.693769	TCAATCTACAAAACCCCTCTAGG	57.306	43.478	0.00	0.00	0.00	3.02
2133	2317	7.412891	GCCTGGCATAAACATGTAAAACATTTC	60.413	37.037	15.17	0.00	36.53	2.17
2135	2319	5.874261	GCCTGGCATAAACATGTAAAACATT	59.126	36.000	15.17	0.00	36.53	2.71
2151	2335	8.828417	ATACAATCAGTACACATGCCTGGCAT	62.828	42.308	27.95	27.95	42.13	4.40
2199	2383	1.142060	CCCGTTGCCATCCCTATTACA	59.858	52.381	0.00	0.00	0.00	2.41
2222	2406	6.045459	TGGTATTAGTTGGCCATGAATATCCT	59.955	38.462	6.09	0.00	0.00	3.24
2305	2489	8.475639	CCGGTATTAGTTAGCCATGAATAGTAT	58.524	37.037	0.00	0.00	0.00	2.12
2311	3349	3.712733	ACCCGGTATTAGTTAGCCATGAA	59.287	43.478	0.00	0.00	0.00	2.57
2325	3363	5.825593	ATGATACAATCAAGACCCGGTAT	57.174	39.130	0.00	0.00	43.50	2.73
2329	3367	4.445718	CGAGAATGATACAATCAAGACCCG	59.554	45.833	0.00	0.00	43.50	5.28
2330	3368	4.752101	CCGAGAATGATACAATCAAGACCC	59.248	45.833	0.00	0.00	43.50	4.46
2331	3369	5.235186	CACCGAGAATGATACAATCAAGACC	59.765	44.000	0.00	0.00	43.50	3.85
2332	3370	5.812642	ACACCGAGAATGATACAATCAAGAC	59.187	40.000	0.00	0.00	43.50	3.01
2335	3373	6.873997	AGTACACCGAGAATGATACAATCAA	58.126	36.000	0.00	0.00	43.50	2.57
2336	3374	6.465439	AGTACACCGAGAATGATACAATCA	57.535	37.500	0.00	0.00	44.55	2.57
2337	3375	8.297426	TCATAGTACACCGAGAATGATACAATC	58.703	37.037	0.00	0.00	0.00	2.67
2339	3377	7.576861	TCATAGTACACCGAGAATGATACAA	57.423	36.000	0.00	0.00	0.00	2.41
2340	3378	7.284716	AGTTCATAGTACACCGAGAATGATACA	59.715	37.037	0.00	0.00	0.00	2.29
2342	3380	7.818997	AGTTCATAGTACACCGAGAATGATA	57.181	36.000	0.00	0.00	0.00	2.15
2344	3382	7.634671	TTAGTTCATAGTACACCGAGAATGA	57.365	36.000	0.00	0.00	0.00	2.57
2345	3383	7.921214	ACATTAGTTCATAGTACACCGAGAATG	59.079	37.037	0.00	0.00	0.00	2.67
2346	3384	8.008513	ACATTAGTTCATAGTACACCGAGAAT	57.991	34.615	0.00	0.00	0.00	2.40
2347	3385	7.400599	ACATTAGTTCATAGTACACCGAGAA	57.599	36.000	0.00	0.00	0.00	2.87
2349	3387	6.475727	CCAACATTAGTTCATAGTACACCGAG	59.524	42.308	0.00	0.00	35.28	4.63
2350	3388	6.071221	ACCAACATTAGTTCATAGTACACCGA	60.071	38.462	0.00	0.00	35.28	4.69
2351	3389	6.103997	ACCAACATTAGTTCATAGTACACCG	58.896	40.000	0.00	0.00	35.28	4.94
2352	3390	7.916914	AACCAACATTAGTTCATAGTACACC	57.083	36.000	0.00	0.00	35.28	4.16
2354	3392	9.733556	ATCAAACCAACATTAGTTCATAGTACA	57.266	29.630	0.00	0.00	35.28	2.90
2431	4123	5.126384	AGTCTGAAACTACTCATGCTAGGAC	59.874	44.000	0.00	0.00	36.07	3.85
2464	4156	9.783081	AAAAATGACCAGCAAGAAAAATAGAAT	57.217	25.926	0.00	0.00	0.00	2.40
2489	4181	6.070481	GGAGCATTTTGGGGTATAAAAGGAAA	60.070	38.462	0.00	0.00	32.34	3.13
2492	4184	4.962362	AGGAGCATTTTGGGGTATAAAAGG	59.038	41.667	0.00	0.00	33.40	3.11
2519	4211	4.507342	AGAATGGAACCATAGGCTCCTAT	58.493	43.478	6.77	2.65	38.66	2.57
2520	4212	3.941629	AGAATGGAACCATAGGCTCCTA	58.058	45.455	6.77	0.00	38.66	2.94
2521	4213	2.781667	AGAATGGAACCATAGGCTCCT	58.218	47.619	6.77	0.00	38.66	3.69
2522	4214	3.217626	CAAGAATGGAACCATAGGCTCC	58.782	50.000	6.77	0.00	38.37	4.70
2523	4215	3.891049	ACAAGAATGGAACCATAGGCTC	58.109	45.455	6.77	1.44	35.31	4.70
2524	4216	4.322057	AACAAGAATGGAACCATAGGCT	57.678	40.909	6.77	0.00	35.31	4.58
2525	4217	5.066505	CAGTAACAAGAATGGAACCATAGGC	59.933	44.000	6.77	0.80	35.31	3.93
2526	4218	5.066505	GCAGTAACAAGAATGGAACCATAGG	59.933	44.000	6.77	0.65	35.31	2.57
2527	4219	5.882557	AGCAGTAACAAGAATGGAACCATAG	59.117	40.000	6.77	1.32	35.31	2.23
2528	4220	5.647658	CAGCAGTAACAAGAATGGAACCATA	59.352	40.000	6.77	0.00	35.31	2.74
2529	4221	4.460382	CAGCAGTAACAAGAATGGAACCAT	59.540	41.667	0.00	0.00	38.46	3.55
2530	4222	3.820467	CAGCAGTAACAAGAATGGAACCA	59.180	43.478	0.00	0.00	0.00	3.67
2531	4223	3.191371	CCAGCAGTAACAAGAATGGAACC	59.809	47.826	0.00	0.00	0.00	3.62
2532	4224	4.072131	TCCAGCAGTAACAAGAATGGAAC	58.928	43.478	0.00	0.00	32.62	3.62
2533	4225	4.365514	TCCAGCAGTAACAAGAATGGAA	57.634	40.909	0.00	0.00	32.62	3.53

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.