AutoCloner

Multiple sequence alignment - TraesCS5D01G257700

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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	TraesCS5D01G257700	chr5D	100.000	8075	0	0	1	8075	364401488	364393414	0.000000e+00	14912.0
1	TraesCS5D01G257700	chr5D	91.379	58	3	2	3647	3703	61703044	61702988	2.420000e-10	78.7
2	TraesCS5D01G257700	chr5D	95.918	49	0	2	3646	3693	527500911	527500864	2.420000e-10	78.7
3	TraesCS5D01G257700	chr5A	98.236	2834	44	4	3520	6349	465542854	465540023	0.000000e+00	4951.0
4	TraesCS5D01G257700	chr5A	97.325	2542	61	5	1	2539	465548091	465545554	0.000000e+00	4311.0
5	TraesCS5D01G257700	chr5A	89.721	895	49	19	6344	7210	465539985	465539106	0.000000e+00	1103.0
6	TraesCS5D01G257700	chr5A	89.714	700	40	16	6531	7210	465310916	465310229	0.000000e+00	865.0
7	TraesCS5D01G257700	chr5A	94.579	535	10	1	2999	3514	465543531	465542997	0.000000e+00	809.0
8	TraesCS5D01G257700	chr5A	94.395	446	23	2	5905	6349	465313861	465313417	0.000000e+00	684.0
9	TraesCS5D01G257700	chr5A	95.685	394	10	5	6344	6733	465278428	465278038	1.910000e-175	627.0
10	TraesCS5D01G257700	chr5A	95.308	341	15	1	5902	6241	465279084	465278744	2.560000e-149	540.0
11	TraesCS5D01G257700	chr5A	86.051	509	34	10	6729	7210	465277809	465277311	5.590000e-141	512.0
12	TraesCS5D01G257700	chr5A	87.980	391	34	6	7623	8001	465540602	465540213	4.440000e-122	449.0
13	TraesCS5D01G257700	chr5A	95.361	194	8	1	6344	6536	465313379	465313186	2.830000e-79	307.0
14	TraesCS5D01G257700	chr5A	98.065	155	2	1	2804	2958	465543893	465543740	1.340000e-67	268.0
15	TraesCS5D01G257700	chr5A	94.488	127	6	1	6224	6350	465278587	465278462	2.300000e-45	195.0
16	TraesCS5D01G257700	chr5A	96.104	77	3	0	7994	8070	465303442	465303366	8.510000e-25	126.0
17	TraesCS5D01G257700	chr5A	85.156	128	8	9	7301	7428	465309155	465309039	3.960000e-23	121.0
18	TraesCS5D01G257700	chr5B	96.408	2979	78	8	1	2961	430472982	430470015	0.000000e+00	4881.0
19	TraesCS5D01G257700	chr5B	96.695	2481	72	5	3873	6347	430469146	430466670	0.000000e+00	4119.0
20	TraesCS5D01G257700	chr5B	96.068	941	30	4	6344	7282	430466630	430465695	0.000000e+00	1526.0
21	TraesCS5D01G257700	chr5B	97.418	736	12	4	7284	8014	430465657	430464924	0.000000e+00	1247.0
22	TraesCS5D01G257700	chr5B	93.712	827	26	10	3120	3920	430470006	430469180	0.000000e+00	1216.0
23	TraesCS5D01G257700	chr5B	92.689	766	37	11	6359	7117	430376586	430375833	0.000000e+00	1086.0
24	TraesCS5D01G257700	chr5B	96.725	458	13	1	7620	8075	430246399	430245942	0.000000e+00	761.0
25	TraesCS5D01G257700	chr5B	94.878	449	19	3	5902	6349	430378761	430378316	0.000000e+00	699.0
26	TraesCS5D01G257700	chr5B	97.389	383	10	0	7620	8002	430141910	430141528	0.000000e+00	652.0
27	TraesCS5D01G257700	chr5B	86.105	439	49	6	5721	6159	430246444	430246018	5.710000e-126	462.0
28	TraesCS5D01G257700	chr5B	86.375	411	44	6	5749	6159	430141927	430141529	9.620000e-119	438.0
29	TraesCS5D01G257700	chr5B	93.548	279	12	2	7794	8067	430317929	430317652	2.100000e-110	411.0
30	TraesCS5D01G257700	chr7D	87.905	802	95	2	1	801	318251746	318252546	0.000000e+00	942.0
31	TraesCS5D01G257700	chr7D	100.000	46	0	0	3648	3693	146632787	146632742	1.440000e-12	86.1
32	TraesCS5D01G257700	chr7D	87.500	64	5	3	3648	3710	588024162	588024223	4.040000e-08	71.3
33	TraesCS5D01G257700	chr7B	86.284	802	107	3	1	801	302546510	302545711	0.000000e+00	869.0
34	TraesCS5D01G257700	chr7B	86.142	801	108	3	1	800	302513295	302512497	0.000000e+00	861.0
35	TraesCS5D01G257700	chrUn	97.149	456	13	0	7620	8075	369774184	369774639	0.000000e+00	771.0
36	TraesCS5D01G257700	chrUn	96.711	456	15	0	7620	8075	361244537	361244082	0.000000e+00	760.0
37	TraesCS5D01G257700	chrUn	97.442	391	10	0	7620	8010	399317420	399317030	0.000000e+00	667.0
38	TraesCS5D01G257700	chrUn	97.389	383	10	0	7620	8002	400072270	400071888	0.000000e+00	652.0
39	TraesCS5D01G257700	chrUn	85.973	442	50	6	5718	6159	369774136	369774565	5.710000e-126	462.0
40	TraesCS5D01G257700	chrUn	86.105	439	49	6	5721	6159	400072315	400071889	5.710000e-126	462.0
41	TraesCS5D01G257700	chrUn	85.877	439	50	6	5721	6159	361244582	361244156	2.660000e-124	457.0
42	TraesCS5D01G257700	chrUn	85.877	439	50	6	5721	6159	399317465	399317039	2.660000e-124	457.0
43	TraesCS5D01G257700	chr6D	97.826	46	1	0	3648	3693	470575093	470575048	6.720000e-11	80.5
44	TraesCS5D01G257700	chr4B	95.833	48	2	0	3646	3693	612274829	612274876	2.420000e-10	78.7
45	TraesCS5D01G257700	chr3B	95.745	47	2	0	3648	3694	663972393	663972439	8.690000e-10	76.8

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	TraesCS5D01G257700	chr5D	364393414	364401488	8074	True	14912.000000	14912	100.000000	1	8075	1	chr5D.!!$R2	8074
1	TraesCS5D01G257700	chr5A	465539106	465548091	8985	True	1981.833333	4951	94.317667	1	8001	6	chr5A.!!$R4	8000
2	TraesCS5D01G257700	chr5A	465309039	465313861	4822	True	494.250000	865	91.156500	5905	7428	4	chr5A.!!$R3	1523
3	TraesCS5D01G257700	chr5A	465277311	465279084	1773	True	468.500000	627	92.883000	5902	7210	4	chr5A.!!$R2	1308
4	TraesCS5D01G257700	chr5B	430464924	430472982	8058	True	2597.800000	4881	96.060200	1	8014	5	chr5B.!!$R5	8013
5	TraesCS5D01G257700	chr5B	430375833	430378761	2928	True	892.500000	1086	93.783500	5902	7117	2	chr5B.!!$R4	1215
6	TraesCS5D01G257700	chr5B	430245942	430246444	502	True	611.500000	761	91.415000	5721	8075	2	chr5B.!!$R3	2354
7	TraesCS5D01G257700	chr7D	318251746	318252546	800	False	942.000000	942	87.905000	1	801	1	chr7D.!!$F1	800
8	TraesCS5D01G257700	chr7B	302545711	302546510	799	True	869.000000	869	86.284000	1	801	1	chr7B.!!$R2	800
9	TraesCS5D01G257700	chr7B	302512497	302513295	798	True	861.000000	861	86.142000	1	800	1	chr7B.!!$R1	799
10	TraesCS5D01G257700	chrUn	369774136	369774639	503	False	616.500000	771	91.561000	5718	8075	2	chrUn.!!$F1	2357
11	TraesCS5D01G257700	chrUn	361244082	361244582	500	True	608.500000	760	91.294000	5721	8075	2	chrUn.!!$R1	2354

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
900	902	0.178992	TTGGGGGCTCAGTGTTTCAG	60.179	55.000	0.00	0.00	0.00	3.02	F
1657	1671	0.250513	GGAATCGGACTGCAGGACTT	59.749	55.000	19.93	3.85	0.00	3.01	F
2969	4526	0.172352	GTGTTTGGGTGTGTGTGTGG	59.828	55.000	0.00	0.00	0.00	4.17	F
2971	4528	0.172352	GTTTGGGTGTGTGTGTGGTG	59.828	55.000	0.00	0.00	0.00	4.17	F
2972	4529	0.967887	TTTGGGTGTGTGTGTGGTGG	60.968	55.000	0.00	0.00	0.00	4.61	F
3902	5871	1.067974	ACGATGTGGAAGTTCGTGACA	59.932	47.619	0.00	0.43	43.80	3.58	F
4242	6211	3.219281	TCAAAGGAAAGCTAAAAGGCGT	58.781	40.909	0.00	0.00	37.29	5.68	F
5304	7276	2.036346	TCATGATGGCAATCGATCGTCT	59.964	45.455	15.94	0.69	35.37	4.18	F
6326	8475	1.477700	CACAATGTAGCATGTTGGGGG	59.522	52.381	0.00	0.00	0.00	5.40	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1723	1737	1.523758	CTTCCACAAACTTCCTCCGG	58.476	55.000	0.00	0.00	0.00	5.14	R
2991	4548	0.255890	CATGGGTTACTGGGTCAGGG	59.744	60.000	0.00	0.00	35.51	4.45	R
4189	6158	0.749091	TGATGCTGCACATAGGCACC	60.749	55.000	3.57	0.00	39.84	5.01	R
4517	6486	1.661463	AGGAAGGTCCTTCTGATGCA	58.339	50.000	27.14	0.00	46.91	3.96	R
4977	6946	1.539827	GGATTGTTTTCCACCTGGTCG	59.460	52.381	0.00	0.00	35.72	4.79	R
5304	7276	3.192422	CACCAAAACATTGGGCGAGAATA	59.808	43.478	11.92	0.00	46.23	1.75	R
6068	8040	2.030371	TGAGCAAAACCAGCATGTGAA	58.970	42.857	0.00	0.00	0.00	3.18	R
6614	12761	1.133253	CAGCATCAACGTTGGCTCG	59.867	57.895	27.02	17.49	33.60	5.03	R
7683	15079	1.215423	AGCATGGAACCCTTGGTATCC	59.785	52.381	0.00	7.24	37.57	2.59	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
222	223	2.652530	CGGAAGTCGTCGGGGAAA	59.347	61.111	0.00	0.00	0.00	3.13
573	575	2.455565	CGGGAGGGAGGCCATGAAT	61.456	63.158	5.01	0.00	0.00	2.57
900	902	0.178992	TTGGGGGCTCAGTGTTTCAG	60.179	55.000	0.00	0.00	0.00	3.02
932	934	2.965147	GCGCACGAACCTTGATGCA	61.965	57.895	0.30	0.00	37.97	3.96
1333	1347	2.880629	ATCTCACCCCTAGCACCGCT	62.881	60.000	0.00	0.00	43.41	5.52
1495	1509	4.499633	CCCATACCCGCACCCACC	62.500	72.222	0.00	0.00	0.00	4.61
1657	1671	0.250513	GGAATCGGACTGCAGGACTT	59.749	55.000	19.93	3.85	0.00	3.01
1702	1716	2.425143	TCATGAATGAGTTGGAGGGC	57.575	50.000	0.00	0.00	32.11	5.19
1866	1880	5.220416	GGTTTGTTCTGCTCGATGTGTATAC	60.220	44.000	0.00	0.00	0.00	1.47
1869	1883	5.102313	TGTTCTGCTCGATGTGTATACTTG	58.898	41.667	4.17	0.00	0.00	3.16
1870	1884	4.983671	TCTGCTCGATGTGTATACTTGT	57.016	40.909	4.17	0.00	0.00	3.16
1909	1923	2.489329	GTGGATGATGGTTGACACTTGG	59.511	50.000	0.00	0.00	0.00	3.61
1942	1956	2.684881	ACCTTCTAGGCGCAAATGATTG	59.315	45.455	10.83	0.00	39.63	2.67
1977	1991	3.055675	CCAAATGTGATGCCCTGTGAATT	60.056	43.478	0.00	0.00	0.00	2.17
1978	1992	4.563993	CCAAATGTGATGCCCTGTGAATTT	60.564	41.667	0.00	0.00	0.00	1.82
2464	2481	4.585955	AGCGAGTGTTAACTGAAAGAGA	57.414	40.909	7.22	0.00	36.52	3.10
2529	4082	5.069383	CCAATTTCCATGTCTGGCATATTCA	59.931	40.000	0.00	0.00	42.80	2.57
2540	4093	5.349817	GTCTGGCATATTCATGATACTTCCG	59.650	44.000	0.00	0.00	33.67	4.30
2578	4131	9.408648	GTCCTGATAAGGATTTTAGGATTTTCA	57.591	33.333	0.79	0.00	40.51	2.69
2639	4195	3.185880	AGTTCTAGGGTTCAGGCACTA	57.814	47.619	0.00	0.00	36.02	2.74
2694	4250	5.586155	TGTAAAACCAAAGACCCCTCATA	57.414	39.130	0.00	0.00	0.00	2.15
2696	4252	3.451402	AAACCAAAGACCCCTCATACC	57.549	47.619	0.00	0.00	0.00	2.73
2708	4264	8.171337	AGACCCCTCATACCTACTTTATTTTT	57.829	34.615	0.00	0.00	0.00	1.94
2745	4301	4.335594	GTGTTCTGGGTATATGAACCTTGC	59.664	45.833	0.00	0.00	39.24	4.01
2747	4303	4.853468	TCTGGGTATATGAACCTTGCAA	57.147	40.909	0.00	0.00	39.65	4.08
2810	4366	6.076981	TCAACAGCTCCTCAAATTTCTTTC	57.923	37.500	0.00	0.00	0.00	2.62
2910	4467	6.354130	AGTCCTGTGTTAAGACTGCTAAAAA	58.646	36.000	4.21	0.00	39.36	1.94
2961	4518	3.312736	AATCCAAGAGTGTTTGGGTGT	57.687	42.857	5.06	0.00	46.16	4.16
2963	4520	1.283613	TCCAAGAGTGTTTGGGTGTGT	59.716	47.619	5.06	0.00	46.16	3.72
2965	4522	2.091541	CAAGAGTGTTTGGGTGTGTGT	58.908	47.619	0.00	0.00	0.00	3.72
2966	4523	1.750193	AGAGTGTTTGGGTGTGTGTG	58.250	50.000	0.00	0.00	0.00	3.82
2967	4524	1.004277	AGAGTGTTTGGGTGTGTGTGT	59.996	47.619	0.00	0.00	0.00	3.72
2969	4526	0.172352	GTGTTTGGGTGTGTGTGTGG	59.828	55.000	0.00	0.00	0.00	4.17
2970	4527	0.251386	TGTTTGGGTGTGTGTGTGGT	60.251	50.000	0.00	0.00	0.00	4.16
2971	4528	0.172352	GTTTGGGTGTGTGTGTGGTG	59.828	55.000	0.00	0.00	0.00	4.17
2972	4529	0.967887	TTTGGGTGTGTGTGTGGTGG	60.968	55.000	0.00	0.00	0.00	4.61
2973	4530	2.143575	TTGGGTGTGTGTGTGGTGGT	62.144	55.000	0.00	0.00	0.00	4.16
2974	4531	2.118404	GGGTGTGTGTGTGGTGGTG	61.118	63.158	0.00	0.00	0.00	4.17
2975	4532	2.118404	GGTGTGTGTGTGGTGGTGG	61.118	63.158	0.00	0.00	0.00	4.61
2976	4533	1.377987	GTGTGTGTGTGGTGGTGGT	60.378	57.895	0.00	0.00	0.00	4.16
2977	4534	1.377856	TGTGTGTGTGGTGGTGGTG	60.378	57.895	0.00	0.00	0.00	4.17
2978	4535	2.118404	GTGTGTGTGGTGGTGGTGG	61.118	63.158	0.00	0.00	0.00	4.61
2979	4536	2.518349	GTGTGTGGTGGTGGTGGG	60.518	66.667	0.00	0.00	0.00	4.61
2980	4537	3.814906	TGTGTGGTGGTGGTGGGG	61.815	66.667	0.00	0.00	0.00	4.96
2981	4538	4.596585	GTGTGGTGGTGGTGGGGG	62.597	72.222	0.00	0.00	0.00	5.40
2983	4540	4.596585	GTGGTGGTGGTGGGGGTG	62.597	72.222	0.00	0.00	0.00	4.61
3005	4730	1.602771	GGAGCCCTGACCCAGTAAC	59.397	63.158	0.00	0.00	0.00	2.50
3107	4832	5.734498	CGAACTAATTTGCTTCCAATCTTCG	59.266	40.000	0.00	0.00	0.00	3.79
3490	5241	7.156876	TGCATAAGTTATGGTTTTGGAGAAG	57.843	36.000	21.56	0.00	36.68	2.85
3509	5260	8.274322	TGGAGAAGAAGATCCATGCTAAATTTA	58.726	33.333	0.00	0.00	40.70	1.40
3615	5503	2.047655	TCCGTTGGGCTTGCTACG	60.048	61.111	0.00	0.00	0.00	3.51
3753	5641	4.704540	TGATTTCCCATTATCACGTTTGCT	59.295	37.500	0.00	0.00	0.00	3.91
3902	5871	1.067974	ACGATGTGGAAGTTCGTGACA	59.932	47.619	0.00	0.43	43.80	3.58
4189	6158	4.797275	GCAATTTGACTTTTGAGGACCAGG	60.797	45.833	0.00	0.00	0.00	4.45
4242	6211	3.219281	TCAAAGGAAAGCTAAAAGGCGT	58.781	40.909	0.00	0.00	37.29	5.68
4977	6946	6.459670	TTTCCTGGAGAAACTGGTTTTAAC	57.540	37.500	0.00	0.00	39.60	2.01
5304	7276	2.036346	TCATGATGGCAATCGATCGTCT	59.964	45.455	15.94	0.69	35.37	4.18
5392	7364	8.675705	TGTCAATCAGAACAATGTTTCTAAGA	57.324	30.769	0.00	0.00	33.89	2.10
6068	8040	6.636454	TCAGGTAAATTTGACTGGGTATCT	57.364	37.500	18.18	0.00	0.00	1.98
6095	8067	3.456280	TGCTGGTTTTGCTCAACAATTC	58.544	40.909	1.71	0.00	38.31	2.17
6110	8082	7.518848	GCTCAACAATTCTTTGGAAATTTCACC	60.519	37.037	19.49	4.79	37.15	4.02
6172	8146	7.403312	TGGGTATTTATTCTTTCCACACATG	57.597	36.000	0.00	0.00	0.00	3.21
6221	8195	5.833406	TTTGAACTTCAATCAGCAGTCAA	57.167	34.783	5.03	0.00	36.11	3.18
6326	8475	1.477700	CACAATGTAGCATGTTGGGGG	59.522	52.381	0.00	0.00	0.00	5.40
6333	8482	2.801077	AGCATGTTGGGGGTAACTAC	57.199	50.000	0.00	0.00	0.00	2.73
6355	8547	5.982356	ACTGCAATAGCTGAACATTCTCTA	58.018	37.500	0.00	0.00	41.71	2.43
6400	10271	7.441157	CACACCGTTATCCATTATGTGTTCTAT	59.559	37.037	0.00	0.00	33.54	1.98
6614	12761	2.906354	CCAACACTGATGCTAGGGTAC	58.094	52.381	0.00	0.00	31.86	3.34
6947	13331	3.039252	AGGGTAGACTGGAATCTGAGG	57.961	52.381	0.00	0.00	0.00	3.86
6952	13336	2.028130	AGACTGGAATCTGAGGTAGCG	58.972	52.381	0.00	0.00	0.00	4.26
6988	13386	2.992543	TGCGGTGGTTACGTATGTTTAC	59.007	45.455	0.00	0.00	0.00	2.01
7025	13423	3.063997	GGTCGTTGACTGATTTGGCTATG	59.936	47.826	0.00	0.00	32.47	2.23
7282	14064	6.044404	AGGATTCGGTGGACCATATTCTTATT	59.956	38.462	0.00	0.00	35.14	1.40
7295	14113	6.431234	CCATATTCTTATTAGGCGCCTTTTCT	59.569	38.462	37.74	18.80	0.00	2.52
7322	14714	2.575532	AGGATCAAATGTACCATGCCG	58.424	47.619	0.00	0.00	0.00	5.69
7486	14882	0.179163	TAGACTGCAGTGCACGATCG	60.179	55.000	27.27	14.88	33.79	3.69
7527	14923	2.219080	TTGCAGAATGGCAGGAATGA	57.781	45.000	0.00	0.00	45.88	2.57
7683	15079	7.073265	GCAATGAACCAAATGAACTTGATTTG	58.927	34.615	6.70	6.70	39.52	2.32
7794	15190	2.203394	CCTGTGGCTGGCACAAGT	60.203	61.111	32.33	0.00	38.70	3.16
7810	15206	2.093973	ACAAGTGGGAGTGTCGATGATC	60.094	50.000	0.00	0.00	0.00	2.92
7871	15267	2.547855	GGTTTGTTCCATTGAAGGTGGC	60.548	50.000	0.00	0.00	36.66	5.01
8045	15446	1.746727	GCACTGCATCGACTACTGCG	61.747	60.000	4.42	2.54	41.32	5.18
8048	15449	0.179163	CTGCATCGACTACTGCGTCA	60.179	55.000	4.42	0.00	41.32	4.35

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
900	902	0.166814	GTGCGCTCCACTGATCAAAC	59.833	55.000	9.73	0.00	41.35	2.93
932	934	2.125106	GATCGAACGGCTGCCCTT	60.125	61.111	14.12	7.99	0.00	3.95
1307	1321	1.879575	CTAGGGGTGAGATTGTGGGA	58.120	55.000	0.00	0.00	0.00	4.37
1358	1372	0.755698	TTCTCGGAATCCTCCTCGGG	60.756	60.000	0.00	0.00	39.93	5.14
1702	1716	3.077556	CTCCGACTCCCCCACTGG	61.078	72.222	0.00	0.00	0.00	4.00
1723	1737	1.523758	CTTCCACAAACTTCCTCCGG	58.476	55.000	0.00	0.00	0.00	5.14
1866	1880	6.035435	CCACGATCACTAGAATCAGAAACAAG	59.965	42.308	0.00	0.00	0.00	3.16
1869	1883	5.651530	TCCACGATCACTAGAATCAGAAAC	58.348	41.667	0.00	0.00	0.00	2.78
1870	1884	5.914898	TCCACGATCACTAGAATCAGAAA	57.085	39.130	0.00	0.00	0.00	2.52
1887	1901	2.099141	AGTGTCAACCATCATCCACG	57.901	50.000	0.00	0.00	0.00	4.94
1929	1943	2.368655	AAACCTCAATCATTTGCGCC	57.631	45.000	4.18	0.00	32.61	6.53
1942	1956	6.698766	GCATCACATTTGGATCATAAAACCTC	59.301	38.462	0.00	0.00	0.00	3.85
2401	2418	7.078249	ACCTGGATTGAGCATTATATACACA	57.922	36.000	0.00	0.00	0.00	3.72
2464	2481	2.028203	GCCAAACATGTGGTTAGGCATT	60.028	45.455	17.26	0.00	39.29	3.56
2681	4237	7.766736	AATAAAGTAGGTATGAGGGGTCTTT	57.233	36.000	0.00	0.00	0.00	2.52
2708	4264	4.578516	CCCAGAACACAGTAATGTCAAACA	59.421	41.667	0.00	0.00	30.55	2.83
2745	4301	3.387699	ACTGGAAAAGGATTTGTGGGTTG	59.612	43.478	0.00	0.00	39.02	3.77
2747	4303	3.230976	GACTGGAAAAGGATTTGTGGGT	58.769	45.455	0.00	0.00	39.02	4.51
2910	4467	5.128991	GGTTATGTTAACCTGGCTAGAGTCT	59.871	44.000	2.48	0.00	37.34	3.24
2961	4518	2.273776	CCACCACCACCACACACA	59.726	61.111	0.00	0.00	0.00	3.72
2963	4520	3.814906	CCCCACCACCACCACACA	61.815	66.667	0.00	0.00	0.00	3.72
2966	4523	4.596585	CACCCCCACCACCACCAC	62.597	72.222	0.00	0.00	0.00	4.16
2985	4542	3.635869	TACTGGGTCAGGGCTCCCC	62.636	68.421	0.32	0.00	45.90	4.81
2986	4543	1.615424	TTACTGGGTCAGGGCTCCC	60.615	63.158	0.00	0.00	43.67	4.30
2987	4544	1.602771	GTTACTGGGTCAGGGCTCC	59.397	63.158	0.00	0.00	35.51	4.70
2988	4545	1.602771	GGTTACTGGGTCAGGGCTC	59.397	63.158	0.00	0.00	35.51	4.70
2989	4546	1.923909	GGGTTACTGGGTCAGGGCT	60.924	63.158	0.00	0.00	35.51	5.19
2990	4547	1.571773	ATGGGTTACTGGGTCAGGGC	61.572	60.000	0.00	0.00	35.51	5.19
2991	4548	0.255890	CATGGGTTACTGGGTCAGGG	59.744	60.000	0.00	0.00	35.51	4.45
2992	4549	0.991920	ACATGGGTTACTGGGTCAGG	59.008	55.000	0.00	0.00	35.51	3.86
2993	4550	1.909302	AGACATGGGTTACTGGGTCAG	59.091	52.381	0.00	0.00	37.52	3.51
2994	4551	2.038863	AGACATGGGTTACTGGGTCA	57.961	50.000	0.00	0.00	0.00	4.02
2995	4552	4.259356	GTTAAGACATGGGTTACTGGGTC	58.741	47.826	0.00	0.00	0.00	4.46
2996	4553	3.009805	GGTTAAGACATGGGTTACTGGGT	59.990	47.826	0.00	0.00	0.00	4.51
2997	4554	3.617284	GGTTAAGACATGGGTTACTGGG	58.383	50.000	0.00	0.00	0.00	4.45
3005	4730	2.565391	GGTTTTGGGGTTAAGACATGGG	59.435	50.000	0.00	0.00	0.00	4.00
3107	4832	9.903682	TTATGTACAAGACACTGTAAGAACTAC	57.096	33.333	0.00	0.00	42.17	2.73
3284	5029	7.337942	AGAAAAAGTGGAATCGCTTAAGATGAT	59.662	33.333	6.67	5.76	42.30	2.45
3615	5503	6.042143	AGATGAAACAAACATCACAAACCAC	58.958	36.000	0.00	0.00	44.29	4.16
3753	5641	8.746052	AAGTATGGTATGCACAATTAGCTAAA	57.254	30.769	10.85	0.00	0.00	1.85
3902	5871	3.413846	ACTCACATTCACAGCACTCAT	57.586	42.857	0.00	0.00	0.00	2.90
4189	6158	0.749091	TGATGCTGCACATAGGCACC	60.749	55.000	3.57	0.00	39.84	5.01
4242	6211	5.652014	CAGGCCAACAGATTTATCAACCTTA	59.348	40.000	5.01	0.00	0.00	2.69
4517	6486	1.661463	AGGAAGGTCCTTCTGATGCA	58.339	50.000	27.14	0.00	46.91	3.96
4977	6946	1.539827	GGATTGTTTTCCACCTGGTCG	59.460	52.381	0.00	0.00	35.72	4.79
5304	7276	3.192422	CACCAAAACATTGGGCGAGAATA	59.808	43.478	11.92	0.00	46.23	1.75
5392	7364	5.239306	TGCTCTGATTGACGAAAATTTCAGT	59.761	36.000	6.53	4.92	0.00	3.41
5577	7549	6.385649	TCAAAACCTGGTTCATTACTTGAC	57.614	37.500	13.36	0.00	32.84	3.18
6068	8040	2.030371	TGAGCAAAACCAGCATGTGAA	58.970	42.857	0.00	0.00	0.00	3.18
6095	8067	7.632721	CAATTGACTTGGTGAAATTTCCAAAG	58.367	34.615	15.48	15.98	42.14	2.77
6172	8146	7.756272	TGAAACATCATTTGTCTATTGCATGAC	59.244	33.333	0.00	7.73	37.68	3.06
6221	8195	7.047891	TCTTCCTTCGATAGTTGCACATTTAT	58.952	34.615	0.00	0.00	37.40	1.40
6326	8475	6.910536	ATGTTCAGCTATTGCAGTAGTTAC	57.089	37.500	16.62	8.22	42.74	2.50
6333	8482	7.493743	AATAGAGAATGTTCAGCTATTGCAG	57.506	36.000	14.56	0.00	42.74	4.41
6355	8547	6.423905	CGGTGTGTACTGCTGCTATATTTAAT	59.576	38.462	0.00	0.00	0.00	1.40
6400	10271	3.688694	ACACGCAGATGGGTAAAAGTA	57.311	42.857	1.90	0.00	39.30	2.24
6614	12761	1.133253	CAGCATCAACGTTGGCTCG	59.867	57.895	27.02	17.49	33.60	5.03
6903	13285	3.780804	TGATCCCCACGAGAAGAAAAA	57.219	42.857	0.00	0.00	0.00	1.94
6904	13286	3.009033	ACATGATCCCCACGAGAAGAAAA	59.991	43.478	0.00	0.00	0.00	2.29
6905	13287	2.571653	ACATGATCCCCACGAGAAGAAA	59.428	45.455	0.00	0.00	0.00	2.52
6906	13288	2.187958	ACATGATCCCCACGAGAAGAA	58.812	47.619	0.00	0.00	0.00	2.52
6907	13289	1.866015	ACATGATCCCCACGAGAAGA	58.134	50.000	0.00	0.00	0.00	2.87
6908	13290	2.036475	CCTACATGATCCCCACGAGAAG	59.964	54.545	0.00	0.00	0.00	2.85
6947	13331	3.060895	GCACACACACTAGAATTCGCTAC	59.939	47.826	0.00	0.00	0.00	3.58
6952	13336	2.157668	CACCGCACACACACTAGAATTC	59.842	50.000	0.00	0.00	0.00	2.17
6988	13386	1.864711	ACGACCGAAAACAGTGTCATG	59.135	47.619	0.00	0.00	0.00	3.07
7025	13423	3.884169	TGTCACAAATTTCGCTTGCTAC	58.116	40.909	0.00	0.00	0.00	3.58
7032	13430	7.798052	AGCATTTAAAAATGTCACAAATTTCGC	59.202	29.630	14.98	0.00	45.77	4.70
7064	13462	1.829849	CACCTCTCAGGCTCAATCTGA	59.170	52.381	0.00	0.00	39.63	3.27
7268	14050	4.833390	AGGCGCCTAATAAGAATATGGTC	58.167	43.478	31.86	0.00	0.00	4.02
7282	14064	3.596214	CTTAACTCAGAAAAGGCGCCTA	58.404	45.455	33.07	12.47	0.00	3.93
7322	14714	4.966965	TCAGAGGAATCAGTTACGTCTC	57.033	45.455	0.00	0.00	0.00	3.36
7486	14882	8.301720	TGCAAATATCAATTCCAGCATTCTATC	58.698	33.333	0.00	0.00	0.00	2.08
7527	14923	2.263741	CGCCAGCTCCAGCAAGTTT	61.264	57.895	0.48	0.00	45.16	2.66
7683	15079	1.215423	AGCATGGAACCCTTGGTATCC	59.785	52.381	0.00	7.24	37.57	2.59
7794	15190	3.960755	ACATAAGATCATCGACACTCCCA	59.039	43.478	0.00	0.00	0.00	4.37
7810	15206	5.352016	CCAAAATTGGTTGCATGGACATAAG	59.648	40.000	3.95	0.00	43.43	1.73
7871	15267	7.487484	TGATCTTGACTAAGTCTGCTCATTAG	58.513	38.462	0.00	0.00	35.38	1.73
7993	15394	4.449376	CCAGCCGAGGGGTCCTATATATAT	60.449	50.000	0.00	0.00	31.76	0.86
7994	15395	3.117246	CCAGCCGAGGGGTCCTATATATA	60.117	52.174	0.00	0.00	31.76	0.86
8045	15446	2.171725	GCCGAAGTATGGGCGTGAC	61.172	63.158	0.00	0.00	40.82	3.67

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.