AutoCloner

Multiple sequence alignment - TraesCS2B01G182500

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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	TraesCS2B01G182500	chr2B	100.000	3599	0	0	1	3599	157371750	157375348	0.000000e+00	6647.0
1	TraesCS2B01G182500	chr2B	92.174	115	5	3	359	469	468896582	468896696	3.720000e-35	159.0
2	TraesCS2B01G182500	chr2D	96.663	1918	40	6	702	2605	107027337	107029244	0.000000e+00	3166.0
3	TraesCS2B01G182500	chr2D	94.444	486	20	1	2419	2904	107133596	107134074	0.000000e+00	741.0
4	TraesCS2B01G182500	chr2D	89.444	360	25	7	1	357	107026369	107026718	3.300000e-120	442.0
5	TraesCS2B01G182500	chr2D	92.667	300	21	1	5	303	107135506	107135805	7.140000e-117	431.0
6	TraesCS2B01G182500	chr2D	88.955	335	28	4	3	335	107136130	107136457	4.330000e-109	405.0
7	TraesCS2B01G182500	chr2D	75.941	611	129	15	1193	1794	382380402	382381003	7.550000e-77	298.0
8	TraesCS2B01G182500	chr2D	93.525	139	9	0	702	840	107136682	107136820	1.310000e-49	207.0
9	TraesCS2B01G182500	chr2D	84.793	217	8	3	473	666	107027125	107027339	1.020000e-45	195.0
10	TraesCS2B01G182500	chr2D	82.273	220	11	4	471	666	107136469	107136684	7.990000e-37	165.0
11	TraesCS2B01G182500	chr7B	91.859	2297	107	32	589	2824	536638817	536641094	0.000000e+00	3133.0
12	TraesCS2B01G182500	chr7B	87.981	832	68	11	2799	3599	536638718	536637888	0.000000e+00	953.0
13	TraesCS2B01G182500	chr7B	84.000	350	42	12	3260	3599	536643589	536643934	1.250000e-84	324.0
14	TraesCS2B01G182500	chr7B	83.575	207	23	8	3024	3226	536642529	536642728	2.210000e-42	183.0
15	TraesCS2B01G182500	chr7B	89.516	124	7	3	347	469	624570142	624570260	6.220000e-33	152.0
16	TraesCS2B01G182500	chr7D	93.268	2050	105	11	589	2623	508334148	508332117	0.000000e+00	2990.0
17	TraesCS2B01G182500	chr7D	86.462	554	51	17	2654	3190	508327921	508327375	1.440000e-163	586.0
18	TraesCS2B01G182500	chr7D	90.000	370	32	3	3235	3599	508325415	508325046	1.170000e-129	473.0
19	TraesCS2B01G182500	chr7A	90.589	2274	130	37	589	2824	578716993	578719220	0.000000e+00	2937.0
20	TraesCS2B01G182500	chr7A	86.627	830	82	11	2799	3599	578715263	578714434	0.000000e+00	891.0
21	TraesCS2B01G182500	chr7A	83.806	247	33	6	2982	3224	578719258	578719501	1.010000e-55	228.0
22	TraesCS2B01G182500	chr2A	92.752	1904	111	12	1703	3599	103380998	103382881	0.000000e+00	2726.0
23	TraesCS2B01G182500	chr2A	94.150	906	48	4	2695	3596	103375558	103376462	0.000000e+00	1375.0
24	TraesCS2B01G182500	chr2A	96.477	369	11	2	2333	2701	103366020	103366386	3.070000e-170	608.0
25	TraesCS2B01G182500	chr2A	75.429	350	76	9	3250	3594	491559415	491559071	1.030000e-35	161.0
26	TraesCS2B01G182500	chr3D	79.062	597	113	10	1202	1792	448497005	448496415	2.010000e-107	399.0
27	TraesCS2B01G182500	chr3A	79.062	597	113	10	1202	1792	589826413	589825823	2.010000e-107	399.0
28	TraesCS2B01G182500	chr3A	75.965	570	114	15	1994	2556	589824862	589824309	4.580000e-69	272.0
29	TraesCS2B01G182500	chr3B	78.595	598	116	10	1202	1793	588696522	588695931	5.640000e-103	385.0
30	TraesCS2B01G182500	chr3B	76.091	573	108	18	1994	2556	588694864	588694311	4.580000e-69	272.0
31	TraesCS2B01G182500	chr3B	91.453	117	6	3	359	472	761883182	761883067	1.340000e-34	158.0
32	TraesCS2B01G182500	chrUn	94.040	151	9	0	2841	2991	441827478	441827328	2.790000e-56	230.0
33	TraesCS2B01G182500	chrUn	83.516	91	15	0	1899	1989	126799514	126799604	6.400000e-13	86.1
34	TraesCS2B01G182500	chr5D	94.040	151	9	0	2838	2988	240134732	240134882	2.790000e-56	230.0
35	TraesCS2B01G182500	chr5D	94.040	151	9	0	2841	2991	449152123	449151973	2.790000e-56	230.0
36	TraesCS2B01G182500	chr1D	94.040	151	9	0	2841	2991	483917573	483917423	2.790000e-56	230.0
37	TraesCS2B01G182500	chr1D	89.474	133	8	5	348	476	118812006	118811876	2.880000e-36	163.0
38	TraesCS2B01G182500	chr1D	89.600	125	9	4	347	469	96183486	96183608	4.810000e-34	156.0
39	TraesCS2B01G182500	chr5B	91.525	118	6	3	356	472	508629538	508629652	3.720000e-35	159.0
40	TraesCS2B01G182500	chr5B	87.879	132	10	5	346	473	472118145	472118274	2.240000e-32	150.0
41	TraesCS2B01G182500	chr5A	89.062	128	10	3	347	473	544309676	544309552	4.810000e-34	156.0
42	TraesCS2B01G182500	chr4B	88.889	126	10	3	347	469	88313935	88314059	6.220000e-33	152.0
43	TraesCS2B01G182500	chr4B	76.000	225	48	6	3149	3370	509535762	509535541	1.060000e-20	111.0

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	TraesCS2B01G182500	chr2B	157371750	157375348	3598	False	6647.000000	6647	100.0000	1	3599	1	chr2B.!!$F1	3598
1	TraesCS2B01G182500	chr2D	107026369	107029244	2875	False	1267.666667	3166	90.3000	1	2605	3	chr2D.!!$F2	2604
2	TraesCS2B01G182500	chr2D	107133596	107136820	3224	False	389.800000	741	90.3728	3	2904	5	chr2D.!!$F3	2901
3	TraesCS2B01G182500	chr2D	382380402	382381003	601	False	298.000000	298	75.9410	1193	1794	1	chr2D.!!$F1	601
4	TraesCS2B01G182500	chr7B	536638817	536643934	5117	False	1213.333333	3133	86.4780	589	3599	3	chr7B.!!$F2	3010
5	TraesCS2B01G182500	chr7B	536637888	536638718	830	True	953.000000	953	87.9810	2799	3599	1	chr7B.!!$R1	800
6	TraesCS2B01G182500	chr7D	508332117	508334148	2031	True	2990.000000	2990	93.2680	589	2623	1	chr7D.!!$R1	2034
7	TraesCS2B01G182500	chr7D	508325046	508327921	2875	True	529.500000	586	88.2310	2654	3599	2	chr7D.!!$R2	945
8	TraesCS2B01G182500	chr7A	578716993	578719501	2508	False	1582.500000	2937	87.1975	589	3224	2	chr7A.!!$F1	2635
9	TraesCS2B01G182500	chr7A	578714434	578715263	829	True	891.000000	891	86.6270	2799	3599	1	chr7A.!!$R1	800
10	TraesCS2B01G182500	chr2A	103380998	103382881	1883	False	2726.000000	2726	92.7520	1703	3599	1	chr2A.!!$F3	1896
11	TraesCS2B01G182500	chr2A	103375558	103376462	904	False	1375.000000	1375	94.1500	2695	3596	1	chr2A.!!$F2	901
12	TraesCS2B01G182500	chr3D	448496415	448497005	590	True	399.000000	399	79.0620	1202	1792	1	chr3D.!!$R1	590
13	TraesCS2B01G182500	chr3A	589824309	589826413	2104	True	335.500000	399	77.5135	1202	2556	2	chr3A.!!$R1	1354
14	TraesCS2B01G182500	chr3B	588694311	588696522	2211	True	328.500000	385	77.3430	1202	2556	2	chr3B.!!$R2	1354

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	Hairpin	End Stability	Orientation
26	27	0.388649	CACCACCGTTCCGAAGAGAG	60.389	60.000	0.00	0.00	3.20	F
710	1038	0.395311	AGGGTGCATCTCATGGCAAG	60.395	55.000	0.00	42.45	4.01	F
858	1209	1.810151	CCACCTACCATTGTCAAACCG	59.190	52.381	0.00	0.00	4.44	F
1962	2535	2.126071	ACGCCGGAGAACGTCATG	60.126	61.111	13.83	42.24	3.07	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1140	1515	0.613777	CAAGTTTACCTCCCGCTCCT	59.386	55.000	0.00	0.00	0.00	3.69	R
2112	3368	0.675837	GCTTGCTGATGCTGGACTCA	60.676	55.000	0.00	0.00	40.48	3.41	R
2278	3534	2.203422	CTCCGGGTTGTTGGCCAA	60.203	61.111	16.05	16.05	0.00	4.52	R
3293	10102	0.028902	AAACGGAAAGCGTTGCACTC	59.971	50.000	4.63	0.00	0.00	3.51	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	0.388649	CACCACCGTTCCGAAGAGAG	60.389	60.000	0.00	0.00	0.00	3.20
29	30	0.596577	CACCGTTCCGAAGAGAGACA	59.403	55.000	0.00	0.00	0.00	3.41
32	33	1.202313	CCGTTCCGAAGAGAGACATCC	60.202	57.143	0.00	0.00	0.00	3.51
43	44	3.071023	AGAGAGACATCCGTTTGGTCAAA	59.929	43.478	0.00	0.00	36.30	2.69
44	45	4.003648	GAGAGACATCCGTTTGGTCAAAT	58.996	43.478	0.00	0.00	36.30	2.32
45	46	4.003648	AGAGACATCCGTTTGGTCAAATC	58.996	43.478	0.00	0.00	36.30	2.17
47	48	3.081804	GACATCCGTTTGGTCAAATCCT	58.918	45.455	0.00	0.00	36.30	3.24
51	52	1.546773	CCGTTTGGTCAAATCCTCCCA	60.547	52.381	0.00	0.00	32.36	4.37
52	53	1.539827	CGTTTGGTCAAATCCTCCCAC	59.460	52.381	0.00	0.00	32.36	4.61
53	54	1.539827	GTTTGGTCAAATCCTCCCACG	59.460	52.381	0.00	0.00	32.36	4.94
96	98	2.126850	GTCGCGGCTCTTTTTGCC	60.127	61.111	1.90	0.00	46.42	4.52
102	104	4.256813	GCTCTTTTTGCCAGCTGC	57.743	55.556	8.66	4.57	41.77	5.25
103	105	1.731969	GCTCTTTTTGCCAGCTGCG	60.732	57.895	8.66	2.70	45.60	5.18
104	106	1.951510	CTCTTTTTGCCAGCTGCGA	59.048	52.632	8.66	0.64	45.60	5.10
153	155	1.591703	GGTGATCGGAGACACTGCA	59.408	57.895	14.47	0.00	42.51	4.41
184	186	2.087646	GACTTGGATGAAGGCCAGTTC	58.912	52.381	5.01	0.68	32.79	3.01
194	196	2.270527	GCCAGTTCCAGCCTCCTC	59.729	66.667	0.00	0.00	0.00	3.71
196	198	2.581354	CAGTTCCAGCCTCCTCGG	59.419	66.667	0.00	0.00	0.00	4.63
240	243	8.179509	TCTCCCTTATAGAATTTAGGAGTTCG	57.820	38.462	0.00	0.00	40.28	3.95
261	264	3.006110	CGGTTAGGTGTGGTGTAGAGAAA	59.994	47.826	0.00	0.00	0.00	2.52
285	288	9.715121	AAATACACTCGAAATTTTACTCCACTA	57.285	29.630	0.00	0.00	0.00	2.74
294	297	9.704098	CGAAATTTTACTCCACTATAGCTTTTC	57.296	33.333	0.00	0.00	0.00	2.29
308	311	2.014068	GCTTTTCAGGGGATCGACCAG	61.014	57.143	7.69	0.19	41.20	4.00
367	543	4.672899	AGATGCTCTAATCTACTCCCTCC	58.327	47.826	0.00	0.00	35.09	4.30
368	544	2.865079	TGCTCTAATCTACTCCCTCCG	58.135	52.381	0.00	0.00	0.00	4.63
369	545	2.175069	TGCTCTAATCTACTCCCTCCGT	59.825	50.000	0.00	0.00	0.00	4.69
371	547	3.414269	CTCTAATCTACTCCCTCCGTCC	58.586	54.545	0.00	0.00	0.00	4.79
374	550	0.635009	ATCTACTCCCTCCGTCCCAA	59.365	55.000	0.00	0.00	0.00	4.12
375	551	0.410663	TCTACTCCCTCCGTCCCAAA	59.589	55.000	0.00	0.00	0.00	3.28
376	552	1.203212	TCTACTCCCTCCGTCCCAAAA	60.203	52.381	0.00	0.00	0.00	2.44
377	553	1.838077	CTACTCCCTCCGTCCCAAAAT	59.162	52.381	0.00	0.00	0.00	1.82
386	562	3.821033	CTCCGTCCCAAAATTCTTGTCTT	59.179	43.478	0.00	0.00	0.00	3.01
387	563	4.975631	TCCGTCCCAAAATTCTTGTCTTA	58.024	39.130	0.00	0.00	0.00	2.10
389	565	5.001232	CCGTCCCAAAATTCTTGTCTTAGA	58.999	41.667	0.00	0.00	0.00	2.10
393	569	7.538678	CGTCCCAAAATTCTTGTCTTAGATTTG	59.461	37.037	0.00	0.00	29.84	2.32
404	580	8.622157	TCTTGTCTTAGATTTGTCTAGATACGG	58.378	37.037	0.00	0.00	0.00	4.02
405	581	8.515695	TTGTCTTAGATTTGTCTAGATACGGA	57.484	34.615	0.00	0.00	0.00	4.69
406	582	8.693120	TGTCTTAGATTTGTCTAGATACGGAT	57.307	34.615	0.00	0.00	0.00	4.18
407	583	8.568794	TGTCTTAGATTTGTCTAGATACGGATG	58.431	37.037	0.00	0.00	0.00	3.51
408	584	8.569641	GTCTTAGATTTGTCTAGATACGGATGT	58.430	37.037	0.00	0.00	0.00	3.06
409	585	9.788889	TCTTAGATTTGTCTAGATACGGATGTA	57.211	33.333	0.00	0.00	34.45	2.29
426	602	7.556844	ACGGATGTATCTAAACATGGATATCC	58.443	38.462	15.39	15.39	40.17	2.59
427	603	6.697455	CGGATGTATCTAAACATGGATATCCG	59.303	42.308	17.04	14.27	40.71	4.18
428	604	7.556844	GGATGTATCTAAACATGGATATCCGT	58.443	38.462	17.04	14.13	40.17	4.69
429	605	8.692710	GGATGTATCTAAACATGGATATCCGTA	58.307	37.037	16.31	0.00	40.17	4.02
435	611	9.922477	ATCTAAACATGGATATCCGTATCTAGA	57.078	33.333	16.31	18.76	37.46	2.43
437	613	7.776618	AAACATGGATATCCGTATCTAGACA	57.223	36.000	16.31	0.00	37.46	3.41
439	615	7.776618	ACATGGATATCCGTATCTAGACAAA	57.223	36.000	16.31	0.00	37.46	2.83
440	616	8.367660	ACATGGATATCCGTATCTAGACAAAT	57.632	34.615	16.31	0.00	37.46	2.32
441	617	8.470805	ACATGGATATCCGTATCTAGACAAATC	58.529	37.037	16.31	0.00	37.46	2.17
442	618	8.690884	CATGGATATCCGTATCTAGACAAATCT	58.309	37.037	16.31	0.00	37.46	2.40
443	619	9.922477	ATGGATATCCGTATCTAGACAAATCTA	57.078	33.333	15.20	0.00	37.46	1.98
444	620	9.749340	TGGATATCCGTATCTAGACAAATCTAA	57.251	33.333	17.04	0.00	36.49	2.10
448	624	8.693120	ATCCGTATCTAGACAAATCTAAGACA	57.307	34.615	0.00	0.00	36.98	3.41
449	625	8.515695	TCCGTATCTAGACAAATCTAAGACAA	57.484	34.615	0.00	0.00	36.98	3.18
450	626	8.622157	TCCGTATCTAGACAAATCTAAGACAAG	58.378	37.037	0.00	0.00	36.98	3.16
451	627	8.622157	CCGTATCTAGACAAATCTAAGACAAGA	58.378	37.037	0.00	0.00	36.98	3.02
466	642	8.840321	TCTAAGACAAGAATTTTGAAACTGAGG	58.160	33.333	7.18	0.00	0.00	3.86
467	643	6.396829	AGACAAGAATTTTGAAACTGAGGG	57.603	37.500	7.18	0.00	0.00	4.30
469	645	6.607198	AGACAAGAATTTTGAAACTGAGGGAA	59.393	34.615	7.18	0.00	0.00	3.97
471	647	8.477419	ACAAGAATTTTGAAACTGAGGGAATA	57.523	30.769	7.18	0.00	0.00	1.75
541	835	5.066593	ACAGGGTGAAGAGCTTAAAAGAAG	58.933	41.667	0.00	0.00	0.00	2.85
542	836	5.163195	ACAGGGTGAAGAGCTTAAAAGAAGA	60.163	40.000	0.00	0.00	0.00	2.87
543	837	5.765182	CAGGGTGAAGAGCTTAAAAGAAGAA	59.235	40.000	0.00	0.00	0.00	2.52
544	838	6.263168	CAGGGTGAAGAGCTTAAAAGAAGAAA	59.737	38.462	0.00	0.00	0.00	2.52
566	860	4.756084	AAAAATCTTTCTGGTCGAGCAG	57.244	40.909	33.38	33.38	0.00	4.24
580	874	2.552315	TCGAGCAGGGTTGATGAAAAAC	59.448	45.455	0.00	0.00	0.00	2.43
581	875	2.293122	CGAGCAGGGTTGATGAAAAACA	59.707	45.455	0.00	0.00	0.00	2.83
677	1001	1.728971	GCAGTCTCAATTCTGACCACG	59.271	52.381	4.32	0.00	34.02	4.94
682	1006	0.955428	TCAATTCTGACCACGCAGGC	60.955	55.000	0.00	0.00	43.14	4.85
710	1038	0.395311	AGGGTGCATCTCATGGCAAG	60.395	55.000	0.00	0.00	42.45	4.01
858	1209	1.810151	CCACCTACCATTGTCAAACCG	59.190	52.381	0.00	0.00	0.00	4.44
859	1210	2.551287	CCACCTACCATTGTCAAACCGA	60.551	50.000	0.00	0.00	0.00	4.69
860	1211	3.343617	CACCTACCATTGTCAAACCGAT	58.656	45.455	0.00	0.00	0.00	4.18
861	1212	4.509616	CACCTACCATTGTCAAACCGATA	58.490	43.478	0.00	0.00	0.00	2.92
862	1213	4.331717	CACCTACCATTGTCAAACCGATAC	59.668	45.833	0.00	0.00	0.00	2.24
863	1214	3.875134	CCTACCATTGTCAAACCGATACC	59.125	47.826	0.00	0.00	0.00	2.73
866	1217	3.287222	CCATTGTCAAACCGATACCCAT	58.713	45.455	0.00	0.00	0.00	4.00
960	1322	4.389992	CACCAGCTCAAACACACATACTAG	59.610	45.833	0.00	0.00	0.00	2.57
1155	1530	2.496942	CGTAGGAGCGGGAGGTAAA	58.503	57.895	0.00	0.00	43.00	2.01
1166	1541	2.359478	AGGTAAACTTGGCGGCGG	60.359	61.111	9.78	1.94	0.00	6.13
1896	2469	2.149578	CCAGGAGACAAAGACAAGCTG	58.850	52.381	0.00	0.00	0.00	4.24
1962	2535	2.126071	ACGCCGGAGAACGTCATG	60.126	61.111	13.83	0.00	42.24	3.07
2112	3368	2.885861	GACGACGAGCCCATCACT	59.114	61.111	0.00	0.00	0.00	3.41
2278	3534	3.542676	TCGTCAACGCCTGGTGGT	61.543	61.111	12.58	0.87	39.60	4.16
2400	3659	1.373812	CTTCCGGTTCCTCCCGTTT	59.626	57.895	0.00	0.00	46.66	3.60
2569	3828	0.391528	GCACATTGCCAACCATTCCC	60.392	55.000	0.00	0.00	37.42	3.97
2740	4022	2.692368	GGAGGATCACCCCTGGCA	60.692	66.667	0.00	0.00	36.49	4.92
2907	4279	1.214673	TCCGGGCTATATATCCTCGCT	59.785	52.381	0.00	0.00	0.00	4.93
2923	4752	1.081892	CGCTGAACTCTGGTCATTGG	58.918	55.000	0.00	0.00	0.00	3.16
2939	4771	8.292444	TGGTCATTGGATCAAATTAACCTTAG	57.708	34.615	18.69	0.00	29.14	2.18
3040	7217	3.120991	CGTTGTTAGCGTCCTTCTGAAAG	60.121	47.826	0.00	0.00	0.00	2.62
3048	7225	4.056050	GCGTCCTTCTGAAAGTAGAAACA	58.944	43.478	0.00	0.00	36.34	2.83
3097	7274	5.581085	GGTCGGCACATCATATTATAGAACC	59.419	44.000	0.00	0.00	0.00	3.62
3158	7341	5.885912	AGCTTCAGGTTTTCAAGTAAGTTGA	59.114	36.000	0.00	0.00	43.82	3.18
3293	10102	6.528321	TCTTGGCCTAATGATCAGATACAAG	58.472	40.000	3.32	15.64	34.51	3.16
3359	10172	3.565764	TCACCTGGCAATGATTAGAGG	57.434	47.619	0.00	0.00	0.00	3.69
3437	10253	6.253746	GCAGACATGAAACAAGTGATCATAC	58.746	40.000	0.00	0.00	32.73	2.39
3440	10256	7.332678	CAGACATGAAACAAGTGATCATACTCA	59.667	37.037	0.00	0.00	32.73	3.41
3444	10260	6.758254	TGAAACAAGTGATCATACTCAGTCA	58.242	36.000	0.00	0.00	0.00	3.41
3480	10296	4.414337	ACCTAGAAGTGATTGCCATCTC	57.586	45.455	0.00	0.00	0.00	2.75

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
26	27	3.081804	AGGATTTGACCAAACGGATGTC	58.918	45.455	0.00	0.00	32.51	3.06
29	30	2.620627	GGGAGGATTTGACCAAACGGAT	60.621	50.000	0.00	0.00	32.51	4.18
32	33	1.539827	GTGGGAGGATTTGACCAAACG	59.460	52.381	0.00	0.00	34.26	3.60
43	44	1.000993	AGCTCACTCGTGGGAGGAT	59.999	57.895	17.81	0.00	44.93	3.24
44	45	1.679305	GAGCTCACTCGTGGGAGGA	60.679	63.158	17.81	0.00	44.93	3.71
45	46	2.888863	GAGCTCACTCGTGGGAGG	59.111	66.667	17.81	0.93	44.93	4.30
53	54	4.381505	CCAAGTCCTAGAAAGAGCTCACTC	60.382	50.000	17.77	11.60	43.82	3.51
87	89	1.654220	GTCGCAGCTGGCAAAAAGA	59.346	52.632	17.12	0.00	45.17	2.52
116	118	1.883084	CTACGACCATTGCTCCGGC	60.883	63.158	0.00	0.00	39.26	6.13
129	131	0.253894	TGTCTCCGATCACCCTACGA	59.746	55.000	0.00	0.00	0.00	3.43
153	155	4.379243	CCAAGTCCTGCGCCTCGT	62.379	66.667	4.18	0.00	0.00	4.18
163	165	0.329596	ACTGGCCTTCATCCAAGTCC	59.670	55.000	3.32	0.00	29.89	3.85
194	196	1.804601	AACTTTTTACTCCTCGGCCG	58.195	50.000	22.12	22.12	0.00	6.13
196	198	4.083431	GGAGAAAACTTTTTACTCCTCGGC	60.083	45.833	17.17	0.00	39.14	5.54
197	199	4.454847	GGGAGAAAACTTTTTACTCCTCGG	59.545	45.833	20.45	0.00	40.43	4.63
198	200	5.306394	AGGGAGAAAACTTTTTACTCCTCG	58.694	41.667	20.45	0.00	40.43	4.63
236	239	2.297033	TCTACACCACACCTAACCGAAC	59.703	50.000	0.00	0.00	0.00	3.95
240	243	4.612264	TTTCTCTACACCACACCTAACC	57.388	45.455	0.00	0.00	0.00	2.85
280	283	4.646572	GATCCCCTGAAAAGCTATAGTGG	58.353	47.826	0.84	0.00	0.00	4.00
285	288	2.104963	GGTCGATCCCCTGAAAAGCTAT	59.895	50.000	0.00	0.00	0.00	2.97
294	297	1.889829	GTATCTCTGGTCGATCCCCTG	59.110	57.143	0.00	0.00	34.77	4.45
353	357	1.854939	TGGGACGGAGGGAGTAGATTA	59.145	52.381	0.00	0.00	0.00	1.75
355	359	0.635009	TTGGGACGGAGGGAGTAGAT	59.365	55.000	0.00	0.00	0.00	1.98
356	360	0.410663	TTTGGGACGGAGGGAGTAGA	59.589	55.000	0.00	0.00	0.00	2.59
357	361	1.272807	TTTTGGGACGGAGGGAGTAG	58.727	55.000	0.00	0.00	0.00	2.57
359	535	1.004394	GAATTTTGGGACGGAGGGAGT	59.996	52.381	0.00	0.00	0.00	3.85
363	539	2.488153	GACAAGAATTTTGGGACGGAGG	59.512	50.000	0.00	0.00	0.00	4.30
367	543	6.743575	ATCTAAGACAAGAATTTTGGGACG	57.256	37.500	5.68	0.00	0.00	4.79
368	544	8.360390	ACAAATCTAAGACAAGAATTTTGGGAC	58.640	33.333	0.00	0.00	33.04	4.46
369	545	8.477419	ACAAATCTAAGACAAGAATTTTGGGA	57.523	30.769	0.00	0.00	33.04	4.37
400	576	8.692710	GGATATCCATGTTTAGATACATCCGTA	58.307	37.037	17.34	0.00	36.64	4.02
401	577	7.556844	GGATATCCATGTTTAGATACATCCGT	58.443	38.462	17.34	0.00	36.64	4.69
402	578	6.697455	CGGATATCCATGTTTAGATACATCCG	59.303	42.308	21.70	14.27	39.42	4.18
403	579	7.556844	ACGGATATCCATGTTTAGATACATCC	58.443	38.462	21.70	0.00	36.64	3.51
406	582	9.475620	AGATACGGATATCCATGTTTAGATACA	57.524	33.333	21.70	0.00	38.43	2.29
409	585	9.922477	TCTAGATACGGATATCCATGTTTAGAT	57.078	33.333	21.70	3.00	38.43	1.98
410	586	9.175312	GTCTAGATACGGATATCCATGTTTAGA	57.825	37.037	21.70	15.11	38.43	2.10
411	587	8.957466	TGTCTAGATACGGATATCCATGTTTAG	58.043	37.037	21.70	13.14	38.43	1.85
412	588	8.873186	TGTCTAGATACGGATATCCATGTTTA	57.127	34.615	21.70	3.75	38.43	2.01
413	589	7.776618	TGTCTAGATACGGATATCCATGTTT	57.223	36.000	21.70	7.42	38.43	2.83
414	590	7.776618	TTGTCTAGATACGGATATCCATGTT	57.223	36.000	21.70	5.12	38.43	2.71
415	591	7.776618	TTTGTCTAGATACGGATATCCATGT	57.223	36.000	21.70	14.06	38.43	3.21
416	592	8.690884	AGATTTGTCTAGATACGGATATCCATG	58.309	37.037	21.70	8.72	38.43	3.66
417	593	8.830915	AGATTTGTCTAGATACGGATATCCAT	57.169	34.615	21.70	9.28	38.43	3.41
423	599	8.693120	TGTCTTAGATTTGTCTAGATACGGAT	57.307	34.615	0.00	0.00	0.00	4.18
440	616	8.840321	CCTCAGTTTCAAAATTCTTGTCTTAGA	58.160	33.333	0.00	0.00	0.00	2.10
441	617	8.078596	CCCTCAGTTTCAAAATTCTTGTCTTAG	58.921	37.037	0.00	0.00	0.00	2.18
442	618	7.777910	TCCCTCAGTTTCAAAATTCTTGTCTTA	59.222	33.333	0.00	0.00	0.00	2.10
443	619	6.607198	TCCCTCAGTTTCAAAATTCTTGTCTT	59.393	34.615	0.00	0.00	0.00	3.01
444	620	6.129179	TCCCTCAGTTTCAAAATTCTTGTCT	58.871	36.000	0.00	0.00	0.00	3.41
445	621	6.391227	TCCCTCAGTTTCAAAATTCTTGTC	57.609	37.500	0.00	0.00	0.00	3.18
446	622	6.790232	TTCCCTCAGTTTCAAAATTCTTGT	57.210	33.333	0.00	0.00	0.00	3.16
456	632	8.429641	GGAGTACATTATATTCCCTCAGTTTCA	58.570	37.037	0.00	0.00	0.00	2.69
457	633	7.878644	GGGAGTACATTATATTCCCTCAGTTTC	59.121	40.741	6.81	0.00	43.39	2.78
458	634	7.746703	GGGAGTACATTATATTCCCTCAGTTT	58.253	38.462	6.81	0.00	43.39	2.66
459	635	7.317722	GGGAGTACATTATATTCCCTCAGTT	57.682	40.000	6.81	0.00	43.39	3.16
465	641	4.536489	AGCCAGGGAGTACATTATATTCCC	59.464	45.833	6.07	6.07	46.41	3.97
466	642	5.485708	AGAGCCAGGGAGTACATTATATTCC	59.514	44.000	0.00	0.00	0.00	3.01
467	643	6.439058	AGAGAGCCAGGGAGTACATTATATTC	59.561	42.308	0.00	0.00	0.00	1.75
469	645	5.719085	CAGAGAGCCAGGGAGTACATTATAT	59.281	44.000	0.00	0.00	0.00	0.86
471	647	3.900601	CAGAGAGCCAGGGAGTACATTAT	59.099	47.826	0.00	0.00	0.00	1.28
475	769	0.704664	TCAGAGAGCCAGGGAGTACA	59.295	55.000	0.00	0.00	0.00	2.90
566	860	4.048504	CCGAAACTGTTTTTCATCAACCC	58.951	43.478	7.28	0.00	0.00	4.11
580	874	0.041312	CTTCAACCGTGCCGAAACTG	60.041	55.000	0.00	0.00	0.00	3.16
581	875	1.164041	CCTTCAACCGTGCCGAAACT	61.164	55.000	0.00	0.00	0.00	2.66
622	939	3.303066	GCAAAACAAAATTTGACCGCTCC	60.303	43.478	13.19	0.00	41.73	4.70
682	1006	4.457496	ATGCACCCTCTCGCCACG	62.457	66.667	0.00	0.00	0.00	4.94
684	1008	2.685017	AGATGCACCCTCTCGCCA	60.685	61.111	0.00	0.00	0.00	5.69
862	1213	1.966901	TATATAGCGCCGGCCATGGG	61.967	60.000	23.46	7.50	41.24	4.00
863	1214	0.107897	TTATATAGCGCCGGCCATGG	60.108	55.000	23.46	7.63	41.24	3.66
866	1217	1.079405	GCTTATATAGCGCCGGCCA	60.079	57.895	23.46	6.69	40.71	5.36
887	1238	2.668212	CGTGCCATGTTCCGTGGT	60.668	61.111	4.52	0.00	42.15	4.16
960	1322	2.128035	CTAGCTTGGCGTGCTATGTAC	58.872	52.381	10.82	0.00	41.45	2.90
1140	1515	0.613777	CAAGTTTACCTCCCGCTCCT	59.386	55.000	0.00	0.00	0.00	3.69
1962	2535	4.740185	GTTGATGTTCTCGACGATGTAC	57.260	45.455	0.00	0.00	0.00	2.90
2112	3368	0.675837	GCTTGCTGATGCTGGACTCA	60.676	55.000	0.00	0.00	40.48	3.41
2278	3534	2.203422	CTCCGGGTTGTTGGCCAA	60.203	61.111	16.05	16.05	0.00	4.52
2569	3828	4.452733	GGGGTGGAAGGCGACGAG	62.453	72.222	0.00	0.00	0.00	4.18
2673	3955	9.762381	AAACCCCTTATAAATCAACTGACATTA	57.238	29.630	0.00	0.00	0.00	1.90
2674	3956	8.664669	AAACCCCTTATAAATCAACTGACATT	57.335	30.769	0.00	0.00	0.00	2.71
2715	3997	4.510205	CCAGGGGTGATCCTCCTTTTAAAA	60.510	45.833	0.00	0.00	33.94	1.52
2740	4022	6.110033	TCGTATGTAAACCACTTATGCACAT	58.890	36.000	0.00	0.00	0.00	3.21
2824	4169	6.856757	AGAGGGGCTAATGAATGACAATAAT	58.143	36.000	0.00	0.00	0.00	1.28
2907	4279	4.639078	TTGATCCAATGACCAGAGTTCA	57.361	40.909	0.00	0.00	0.00	3.18
2923	4752	8.803397	AGTTACCCACTAAGGTTAATTTGATC	57.197	34.615	0.00	0.00	41.58	2.92
2957	5600	5.897250	AGAAAAAGGGTGGCTAAAAGAAGAA	59.103	36.000	0.00	0.00	0.00	2.52
3048	7225	7.311486	CCAAAGTAAACTTAGGTATGTACCCCT	60.311	40.741	5.60	0.00	40.23	4.79
3097	7274	7.170320	GGTTCATCATTAAAATATGCAAGCCAG	59.830	37.037	0.00	0.00	0.00	4.85
3158	7341	4.680708	CGTATGAACTAGTGAGGGTGCATT	60.681	45.833	0.00	0.00	34.05	3.56
3293	10102	0.028902	AAACGGAAAGCGTTGCACTC	59.971	50.000	4.63	0.00	0.00	3.51
3341	10154	3.181436	CCATCCTCTAATCATTGCCAGGT	60.181	47.826	0.00	0.00	0.00	4.00
3359	10172	8.804912	ATCTCAGCATAATTTTAGATCCCATC	57.195	34.615	0.00	0.00	0.00	3.51
3393	10206	6.905609	GTCTGCGCTATTTTAACTAATCAACC	59.094	38.462	9.73	0.00	0.00	3.77
3437	10253	5.282510	GTTAACCCGAGATACATGACTGAG	58.717	45.833	0.00	0.00	0.00	3.35
3440	10256	4.287552	AGGTTAACCCGAGATACATGACT	58.712	43.478	21.30	0.00	38.74	3.41
3444	10260	6.040616	CACTTCTAGGTTAACCCGAGATACAT	59.959	42.308	21.30	1.71	43.56	2.29

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.