AutoCloner

Multiple sequence alignment - TraesCS1D01G051800

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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	TraesCS1D01G051800	chr1D	100.000	3033	0	0	1	3033	32532118	32529086	0.000000e+00	5602.0
1	TraesCS1D01G051800	chr1D	76.923	663	112	19	2389	3033	112485313	112484674	3.750000e-89	339.0
2	TraesCS1D01G051800	chr1D	80.240	167	19	12	72	229	257330717	257330556	2.470000e-21	113.0
3	TraesCS1D01G051800	chr1D	95.918	49	2	0	1353	1401	395033113	395033161	2.510000e-11	80.5
4	TraesCS1D01G051800	chr1B	92.261	1822	114	8	1219	3033	50155181	50153380	0.000000e+00	2558.0
5	TraesCS1D01G051800	chr1B	91.324	876	70	5	1	872	50182434	50181561	0.000000e+00	1192.0
6	TraesCS1D01G051800	chr1B	90.821	207	15	2	969	1171	50155388	50155182	1.070000e-69	274.0
7	TraesCS1D01G051800	chr1B	85.053	281	28	7	1095	1370	94169051	94169322	1.070000e-69	274.0
8	TraesCS1D01G051800	chr1B	84.698	281	29	7	1095	1370	450460435	450460706	4.980000e-68	268.0
9	TraesCS1D01G051800	chr1A	85.244	2399	261	45	1	2369	31794432	31796767	0.000000e+00	2383.0
10	TraesCS1D01G051800	chr1A	84.091	704	74	12	2339	3033	31796771	31797445	0.000000e+00	645.0
11	TraesCS1D01G051800	chr1A	89.619	472	38	5	2564	3033	31188881	31188419	9.370000e-165	590.0
12	TraesCS1D01G051800	chr5A	82.283	762	84	25	1128	1843	496286635	496285879	2.000000e-171	612.0
13	TraesCS1D01G051800	chr5A	80.857	747	96	21	1128	1851	496571257	496570535	7.400000e-151	544.0
14	TraesCS1D01G051800	chr5A	87.342	79	7	1	890	968	622378526	622378601	1.500000e-13	87.9
15	TraesCS1D01G051800	chr5B	89.180	305	30	2	1541	1843	474318348	474318045	7.940000e-101	377.0
16	TraesCS1D01G051800	chr5B	79.092	617	76	23	1128	1717	474457014	474456424	2.850000e-100	375.0
17	TraesCS1D01G051800	chr5B	76.133	662	120	22	2389	3033	692409528	692410168	2.270000e-81	313.0
18	TraesCS1D01G051800	chr5B	83.333	318	45	4	1689	2001	480281205	480280891	1.380000e-73	287.0
19	TraesCS1D01G051800	chr5B	86.408	103	12	1	1744	1844	474456426	474456324	8.890000e-21	111.0
20	TraesCS1D01G051800	chr4D	78.330	563	94	12	2389	2945	505939344	505938804	3.750000e-89	339.0
21	TraesCS1D01G051800	chr4D	79.213	178	23	11	72	240	316801560	316801732	8.890000e-21	111.0
22	TraesCS1D01G051800	chr4D	78.756	193	20	17	50	229	33525317	33525501	3.200000e-20	110.0
23	TraesCS1D01G051800	chr3B	85.000	280	30	5	1095	1370	321761489	321761760	1.070000e-69	274.0
24	TraesCS1D01G051800	chr2D	83.478	230	33	5	1	229	481457999	481457774	3.060000e-50	209.0
25	TraesCS1D01G051800	chr2D	78.836	189	25	12	50	229	280941317	280941499	2.470000e-21	113.0
26	TraesCS1D01G051800	chr4A	83.857	223	16	5	1150	1370	610731465	610731261	8.580000e-46	195.0
27	TraesCS1D01G051800	chr7D	76.413	407	57	14	2536	2937	486556535	486556907	1.860000e-42	183.0
28	TraesCS1D01G051800	chr6D	77.358	265	50	4	890	1148	439167178	439166918	6.770000e-32	148.0
29	TraesCS1D01G051800	chr6D	80.240	167	19	11	72	229	384049764	384049925	2.470000e-21	113.0
30	TraesCS1D01G051800	chr5D	91.346	104	7	1	1744	1845	394584649	394584546	1.130000e-29	141.0
31	TraesCS1D01G051800	chr7A	80.838	167	16	13	72	229	428408973	428409132	1.910000e-22	117.0
32	TraesCS1D01G051800	chr3D	77.021	235	28	21	7	229	114552920	114553140	8.890000e-21	111.0
33	TraesCS1D01G051800	chr3D	76.471	238	26	25	7	230	175449115	175448894	5.350000e-18	102.0
34	TraesCS1D01G051800	chr3D	93.878	49	3	0	1353	1401	468667173	468667221	1.170000e-09	75.0
35	TraesCS1D01G051800	chrUn	74.490	294	39	12	2576	2863	39502815	39502552	8.950000e-16	95.3
36	TraesCS1D01G051800	chrUn	74.490	294	39	12	2576	2863	178681787	178682050	8.950000e-16	95.3
37	TraesCS1D01G051800	chrUn	74.150	294	40	12	2576	2863	196140888	196140625	4.160000e-14	89.8
38	TraesCS1D01G051800	chrUn	92.500	40	2	1	2995	3033	92421725	92421686	4.220000e-04	56.5
39	TraesCS1D01G051800	chr3A	97.619	42	1	0	1778	1819	744614462	744614421	4.190000e-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	TraesCS1D01G051800	chr1D	32529086	32532118	3032	True	5602	5602	100.0000	1	3033	1	chr1D.!!$R1	3032
1	TraesCS1D01G051800	chr1D	112484674	112485313	639	True	339	339	76.9230	2389	3033	1	chr1D.!!$R2	644
2	TraesCS1D01G051800	chr1B	50153380	50155388	2008	True	1416	2558	91.5410	969	3033	2	chr1B.!!$R2	2064
3	TraesCS1D01G051800	chr1B	50181561	50182434	873	True	1192	1192	91.3240	1	872	1	chr1B.!!$R1	871
4	TraesCS1D01G051800	chr1A	31794432	31797445	3013	False	1514	2383	84.6675	1	3033	2	chr1A.!!$F1	3032
5	TraesCS1D01G051800	chr5A	496285879	496286635	756	True	612	612	82.2830	1128	1843	1	chr5A.!!$R1	715
6	TraesCS1D01G051800	chr5A	496570535	496571257	722	True	544	544	80.8570	1128	1851	1	chr5A.!!$R2	723
7	TraesCS1D01G051800	chr5B	692409528	692410168	640	False	313	313	76.1330	2389	3033	1	chr5B.!!$F1	644
8	TraesCS1D01G051800	chr5B	474456324	474457014	690	True	243	375	82.7500	1128	1844	2	chr5B.!!$R3	716
9	TraesCS1D01G051800	chr4D	505938804	505939344	540	True	339	339	78.3300	2389	2945	1	chr4D.!!$R1	556

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
662	679	0.106708	ACGACTCATTATGCCGCCAT	59.893	50.0	0.0	0.0	35.44	4.40	F
865	882	0.249238	CACTCCAGCTCGCATAGACC	60.249	60.0	0.0	0.0	0.00	3.85	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1832	1911	0.038744	ACAAATGTAGCCTGCAGCCT	59.961	50.0	8.66	4.98	45.47	4.58	R
2850	2975	0.392998	GACACCGTGGCAATGGAGAT	60.393	55.0	6.27	0.00	36.21	2.75	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
79	85	3.366374	GCACTTGCATGTCCTTACTTTCC	60.366	47.826	1.56	0.00	41.59	3.13
104	110	5.708948	CTGCCTATACTCTAGACTTGCATC	58.291	45.833	0.00	0.00	0.00	3.91
151	157	6.054860	AGCTAAGTCCAAATCTGCTAAGAA	57.945	37.500	0.00	0.00	35.59	2.52
162	168	7.761249	CCAAATCTGCTAAGAACTAAAATTGGG	59.239	37.037	0.00	0.00	35.59	4.12
218	225	4.111577	TCATCCCCCTCAAGACATACTTT	58.888	43.478	0.00	0.00	36.61	2.66
237	244	3.692791	TTCGATCCTACATCGTGTCTG	57.307	47.619	4.06	0.00	41.77	3.51
246	254	0.884259	CATCGTGTCTGTTGTGGCCA	60.884	55.000	0.00	0.00	0.00	5.36
301	309	0.464916	TAGGATCGCTCGTGCCACTA	60.465	55.000	3.52	0.00	35.36	2.74
349	357	4.202388	GGGCATTCTTGGGATTTTGCATAT	60.202	41.667	0.00	0.00	0.00	1.78
420	428	3.833070	TGAGACAACTAGGGTTTCTCTCC	59.167	47.826	11.14	0.00	38.64	3.71
421	429	3.174779	AGACAACTAGGGTTTCTCTCCC	58.825	50.000	0.00	0.00	44.90	4.30
433	444	2.116827	TCTCTCCCGTCTCACTTCTC	57.883	55.000	0.00	0.00	0.00	2.87
444	455	4.323417	GTCTCACTTCTCTGTCTCTCTCA	58.677	47.826	0.00	0.00	0.00	3.27
449	460	3.244422	ACTTCTCTGTCTCTCTCACTCGT	60.244	47.826	0.00	0.00	0.00	4.18
461	472	4.338400	TCTCTCACTCGTGTCTTTCTTTCA	59.662	41.667	0.00	0.00	0.00	2.69
478	489	1.273759	TCAATCTGCTCTCCACTGCT	58.726	50.000	0.00	0.00	0.00	4.24
518	529	2.103143	CAGCTCCGACTACCTGCG	59.897	66.667	0.00	0.00	0.00	5.18
545	562	2.816411	CCCTCTACTGGTACAAGGACA	58.184	52.381	1.45	0.00	38.70	4.02
562	579	4.115199	ACATCTGCCCCCTTCGCC	62.115	66.667	0.00	0.00	0.00	5.54
620	637	0.252513	TCAGCCAGCCACCTACCTTA	60.253	55.000	0.00	0.00	0.00	2.69
651	668	1.405821	GGAGGACGATCAACGACTCAT	59.594	52.381	1.19	0.00	44.28	2.90
662	679	0.106708	ACGACTCATTATGCCGCCAT	59.893	50.000	0.00	0.00	35.44	4.40
690	707	2.125147	CGCCGGCAAATCAGGAGA	60.125	61.111	28.98	0.00	31.98	3.71
697	714	1.079503	GCAAATCAGGAGACGTGGTC	58.920	55.000	0.00	0.00	0.00	4.02
715	732	1.449246	CTTGAAGAGGCGCTCCTGG	60.449	63.158	7.64	0.00	44.46	4.45
727	744	1.329256	GCTCCTGGAGCGAGGTAATA	58.671	55.000	31.03	0.00	45.85	0.98
762	779	2.283173	CCCAACTCAGGCCCCAAC	60.283	66.667	0.00	0.00	0.00	3.77
795	812	4.590918	TCACCTCTCTACTTCGAAGTGAT	58.409	43.478	35.24	15.58	40.07	3.06
817	834	1.296715	GTTGCTCCAGTCGGGACAT	59.703	57.895	1.17	0.00	42.15	3.06
836	853	4.118093	CATGAGGACATGTACACCGTTA	57.882	45.455	11.55	0.00	46.01	3.18
865	882	0.249238	CACTCCAGCTCGCATAGACC	60.249	60.000	0.00	0.00	0.00	3.85
869	886	3.147595	AGCTCGCATAGACCGCCA	61.148	61.111	0.00	0.00	0.00	5.69
872	889	4.201679	TCGCATAGACCGCCACCG	62.202	66.667	0.00	0.00	0.00	4.94
874	891	2.585247	GCATAGACCGCCACCGTC	60.585	66.667	0.00	0.00	0.00	4.79
875	892	2.106332	CATAGACCGCCACCGTCC	59.894	66.667	0.00	0.00	0.00	4.79
876	893	2.043248	ATAGACCGCCACCGTCCT	60.043	61.111	0.00	0.00	0.00	3.85
877	894	2.423898	ATAGACCGCCACCGTCCTG	61.424	63.158	0.00	0.00	0.00	3.86
918	938	0.250209	AGCCTGCCATATCTCGCTTG	60.250	55.000	0.00	0.00	0.00	4.01
936	957	3.185391	GCTTGTCTTTGTTTCTCTCTCGG	59.815	47.826	0.00	0.00	0.00	4.63
941	962	3.637229	TCTTTGTTTCTCTCTCGGTCTGT	59.363	43.478	0.00	0.00	0.00	3.41
951	972	0.596577	CTCGGTCTGTTCGGTTCTGA	59.403	55.000	0.00	0.00	0.00	3.27
955	976	1.270358	GGTCTGTTCGGTTCTGAGCTT	60.270	52.381	0.00	0.00	0.00	3.74
965	986	1.742268	GTTCTGAGCTTTGCATCCTCC	59.258	52.381	0.00	0.00	0.00	4.30
1000	1024	1.353358	TCCTCTACTGTCTTGTCGGGA	59.647	52.381	0.00	0.00	0.00	5.14
1060	1084	2.884207	CGCGGCTCTTCGTTACCC	60.884	66.667	0.00	0.00	0.00	3.69
1090	1116	2.274920	CTCGAACTTTCCCGAGGTAC	57.725	55.000	0.00	0.00	45.93	3.34
1117	1143	3.787785	TGTACCCTATGTTGTATGCGTG	58.212	45.455	0.00	0.00	0.00	5.34
1215	1245	1.110442	AGAGAGCTCCTTGGTCATCG	58.890	55.000	10.93	0.00	44.98	3.84
1312	1344	4.632538	AATTAACTGTATTCAAGCCGCC	57.367	40.909	0.00	0.00	0.00	6.13
1335	1390	4.074970	AGACATCACTTTTGCTGTTAGGG	58.925	43.478	0.00	0.00	32.13	3.53
1338	1393	5.570320	ACATCACTTTTGCTGTTAGGGTAT	58.430	37.500	0.00	0.00	27.11	2.73
1401	1456	7.090808	GTCCCAAAGTTGAATTTCAAGATACC	58.909	38.462	12.02	0.86	37.00	2.73
1468	1525	2.287427	TGCTAGTATTACGCGAGGAAGC	60.287	50.000	15.93	12.43	37.35	3.86
1488	1545	0.249322	CGTGTATCATCGGGGTGGTC	60.249	60.000	0.00	0.00	0.00	4.02
1668	1738	5.697067	TGTAAAGAACCTTTAAAGCAGGGA	58.303	37.500	9.86	0.00	35.46	4.20
1680	1750	6.481434	TTAAAGCAGGGAGATTACCTAGAC	57.519	41.667	0.00	0.00	36.32	2.59
1692	1762	6.226787	AGATTACCTAGACATTATGCTGCAC	58.773	40.000	3.57	0.00	0.00	4.57
1698	1768	5.066893	CCTAGACATTATGCTGCACATTGTT	59.933	40.000	3.57	0.84	40.38	2.83
1700	1770	4.219070	AGACATTATGCTGCACATTGTTGT	59.781	37.500	3.57	3.37	40.38	3.32
1832	1911	5.782893	AGCTTTTTATAGTTGTGGTGCAA	57.217	34.783	0.00	0.00	34.16	4.08
1855	1935	2.153645	CTGCAGGCTACATTTGTGACA	58.846	47.619	5.57	0.00	0.00	3.58
1878	1958	4.432741	GGCAAGACTGGGGAGGCC	62.433	72.222	0.00	0.00	0.00	5.19
1918	1998	1.589630	CCATGACGTCGAGGTGGAA	59.410	57.895	16.63	1.38	31.59	3.53
1935	2015	1.505477	GAAGGAGCCATGATCGCTGC	61.505	60.000	5.94	5.94	44.31	5.25
1998	2081	0.109551	TCTCGCTTCTCTTGCAGTCG	60.110	55.000	0.00	0.00	0.00	4.18
2055	2138	1.141053	AGGTTTCATATGGACGAGGGC	59.859	52.381	2.13	0.00	0.00	5.19
2064	2147	1.814169	GGACGAGGGCGGTGATTTC	60.814	63.158	0.00	0.00	43.17	2.17
2068	2151	1.693083	CGAGGGCGGTGATTTCGAAC	61.693	60.000	0.00	0.00	33.38	3.95
2114	2197	2.427410	GTTCGGCGTTGCTTGCAG	60.427	61.111	6.85	0.00	0.00	4.41
2345	2428	1.986631	TCCCCGACAAAGGATGGTAAA	59.013	47.619	0.00	0.00	0.00	2.01
2398	2517	3.943381	TCGTAATACTCGACTGTGACCAT	59.057	43.478	0.00	0.00	32.30	3.55
2417	2536	4.041938	ACCATTGCATGTTTCCTTTTCCAT	59.958	37.500	0.00	0.00	0.00	3.41
2425	2544	7.154656	GCATGTTTCCTTTTCCATTACTTCTT	58.845	34.615	0.00	0.00	0.00	2.52
2436	2555	8.519799	TTTCCATTACTTCTTCTGTCACTTTT	57.480	30.769	0.00	0.00	0.00	2.27
2495	2616	6.342338	TGAGGACATGATGATCATACTCAG	57.658	41.667	22.03	9.32	36.89	3.35
2496	2617	5.837438	TGAGGACATGATGATCATACTCAGT	59.163	40.000	22.03	11.80	36.89	3.41
2791	2916	3.627395	TGGAGTTAATCGACAAGGCAT	57.373	42.857	0.00	0.00	0.00	4.40
2794	2919	4.394920	TGGAGTTAATCGACAAGGCATTTC	59.605	41.667	0.00	0.00	0.00	2.17
2850	2975	9.391006	CCTAACTATGGCTTTGTAGTTTTATCA	57.609	33.333	3.47	0.00	40.53	2.15
2878	3003	1.227823	CCACGGTGTCTGGCTTTGA	60.228	57.895	7.45	0.00	0.00	2.69
2906	3031	5.958987	ACCTATGTTCCTGCTCTTACTACTT	59.041	40.000	0.00	0.00	0.00	2.24
2945	3070	8.512138	GCTATTTAGCTTTTGTAACCTCTTGAA	58.488	33.333	0.00	0.00	45.62	2.69
2952	3086	4.345859	TTGTAACCTCTTGAACGGATGT	57.654	40.909	0.00	0.00	0.00	3.06
2962	3096	1.001487	TGAACGGATGTTGCTTGCTTG	60.001	47.619	0.00	0.00	38.78	4.01
2973	3107	4.156556	TGTTGCTTGCTTGTTGGATAGATC	59.843	41.667	0.00	0.00	0.00	2.75
3022	3158	3.194329	ACTCGATGATGTCTTGCTTCTGA	59.806	43.478	0.00	0.00	0.00	3.27

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
38	39	8.290325	GCAAGTGCAAGTAAAGTAGAAAGTAAT	58.710	33.333	0.00	0.00	41.59	1.89
79	85	3.610585	GCAAGTCTAGAGTATAGGCAGCG	60.611	52.174	0.00	0.00	0.00	5.18
104	110	2.348666	GCAATACAAGAGCACCGTACAG	59.651	50.000	0.00	0.00	0.00	2.74
218	225	2.640184	ACAGACACGATGTAGGATCGA	58.360	47.619	10.83	0.00	43.59	3.59
237	244	1.555075	TCTCCTAGTCATGGCCACAAC	59.445	52.381	8.16	9.78	0.00	3.32
246	254	1.395826	GCGGGCACTCTCCTAGTCAT	61.396	60.000	0.00	0.00	35.76	3.06
420	428	2.418628	GAGAGACAGAGAAGTGAGACGG	59.581	54.545	0.00	0.00	0.00	4.79
421	429	3.334691	AGAGAGACAGAGAAGTGAGACG	58.665	50.000	0.00	0.00	0.00	4.18
422	430	4.154195	GTGAGAGAGACAGAGAAGTGAGAC	59.846	50.000	0.00	0.00	0.00	3.36
433	444	2.422597	AGACACGAGTGAGAGAGACAG	58.577	52.381	10.50	0.00	0.00	3.51
444	455	4.212214	GCAGATTGAAAGAAAGACACGAGT	59.788	41.667	0.00	0.00	0.00	4.18
449	460	4.999950	GGAGAGCAGATTGAAAGAAAGACA	59.000	41.667	0.00	0.00	0.00	3.41
461	472	1.350351	ACAAGCAGTGGAGAGCAGATT	59.650	47.619	0.00	0.00	0.00	2.40
478	489	1.477685	GGGGTCGGTGGAGAGAACAA	61.478	60.000	0.00	0.00	0.00	2.83
528	539	4.462834	CAGATGTGTCCTTGTACCAGTAGA	59.537	45.833	0.00	0.00	0.00	2.59
545	562	4.115199	GGCGAAGGGGGCAGATGT	62.115	66.667	0.00	0.00	0.00	3.06
595	612	3.058160	GTGGCTGGCTGATTGCGT	61.058	61.111	2.00	0.00	44.05	5.24
620	637	1.305381	CGTCCTCCACCTCCTCCTT	60.305	63.158	0.00	0.00	0.00	3.36
651	668	2.203139	CACGGGATGGCGGCATAA	60.203	61.111	25.86	0.00	0.00	1.90
690	707	1.006102	CGCCTCTTCAAGACCACGT	60.006	57.895	0.00	0.00	0.00	4.49
697	714	1.449246	CCAGGAGCGCCTCTTCAAG	60.449	63.158	5.80	0.00	44.80	3.02
715	732	7.036829	GGATAAGAAAGGATATTACCTCGCTC	58.963	42.308	0.00	0.00	39.62	5.03
727	744	2.020037	TGGGGAGGGGATAAGAAAGGAT	60.020	50.000	0.00	0.00	0.00	3.24
762	779	1.002274	AGAGGTGAGGGGTAGCAGG	59.998	63.158	0.00	0.00	0.00	4.85
795	812	4.680237	CCGACTGGAGCAACGCCA	62.680	66.667	0.00	0.00	37.49	5.69
817	834	4.221041	TCAATAACGGTGTACATGTCCTCA	59.779	41.667	0.00	0.00	0.00	3.86
830	847	1.207329	GAGTGGCCTCTCAATAACGGT	59.793	52.381	26.29	0.00	34.69	4.83
836	853	0.913451	AGCTGGAGTGGCCTCTCAAT	60.913	55.000	30.51	13.87	37.86	2.57
869	886	1.608627	GGTGTACCTCCAGGACGGT	60.609	63.158	13.40	13.40	38.94	4.83
872	889	1.980844	GGTGGTGTACCTCCAGGAC	59.019	63.158	15.41	0.00	46.30	3.85
881	901	2.670592	GGTTGGCGGGTGGTGTAC	60.671	66.667	0.00	0.00	0.00	2.90
891	911	3.993614	TATGGCAGGCTGGTTGGCG	62.994	63.158	17.64	0.00	46.88	5.69
896	916	1.750930	CGAGATATGGCAGGCTGGT	59.249	57.895	17.64	0.00	0.00	4.00
902	922	2.522836	AGACAAGCGAGATATGGCAG	57.477	50.000	0.00	0.00	0.00	4.85
918	938	3.984633	CAGACCGAGAGAGAAACAAAGAC	59.015	47.826	0.00	0.00	0.00	3.01
936	957	2.156343	AAGCTCAGAACCGAACAGAC	57.844	50.000	0.00	0.00	0.00	3.51
941	962	1.806542	GATGCAAAGCTCAGAACCGAA	59.193	47.619	0.00	0.00	0.00	4.30
951	972	0.403271	ACACAGGAGGATGCAAAGCT	59.597	50.000	0.00	0.00	0.00	3.74
955	976	1.608055	CAACACACAGGAGGATGCAA	58.392	50.000	0.00	0.00	0.00	4.08
1000	1024	0.392998	GACATTGGCGACCTCACCAT	60.393	55.000	0.00	0.00	35.42	3.55
1089	1115	4.699925	ACAACATAGGGTACAACACTGT	57.300	40.909	0.00	0.00	39.75	3.55
1090	1116	5.064707	GCATACAACATAGGGTACAACACTG	59.935	44.000	0.00	0.00	31.80	3.66
1117	1143	2.307049	GTATGCACGCAACAAGAACAC	58.693	47.619	0.00	0.00	0.00	3.32
1215	1245	1.327690	TACCTCGTGATGGACCAGCC	61.328	60.000	7.40	0.00	37.10	4.85
1338	1393	7.110043	TGTTATAATCATCCTTGCATTGCAA	57.890	32.000	21.97	21.97	46.80	4.08
1357	1412	6.430864	TGGGACAACAACATCCATATGTTAT	58.569	36.000	1.24	0.00	45.11	1.89
1401	1456	0.826062	GTGGGAAATTCCTGCCATGG	59.174	55.000	12.28	7.63	39.24	3.66
1488	1545	4.752101	CCTTTGACTTGTAGTTCACTCAGG	59.248	45.833	0.00	0.00	0.00	3.86
1668	1738	6.183361	TGTGCAGCATAATGTCTAGGTAATCT	60.183	38.462	0.00	0.00	0.00	2.40
1680	1750	8.533965	GTTATAACAACAATGTGCAGCATAATG	58.466	33.333	10.81	5.69	40.46	1.90
1698	1768	9.391006	CTTTGGCAACCTATAAGAGTTATAACA	57.609	33.333	17.65	0.00	0.00	2.41
1700	1770	9.391006	CACTTTGGCAACCTATAAGAGTTATAA	57.609	33.333	0.00	0.00	0.00	0.98
1832	1911	0.038744	ACAAATGTAGCCTGCAGCCT	59.961	50.000	8.66	4.98	45.47	4.58
1855	1935	1.614824	CCCCAGTCTTGCCCTCTCT	60.615	63.158	0.00	0.00	0.00	3.10
1878	1958	0.465460	CTCTGGTCTCCTCCTCCTCG	60.465	65.000	0.00	0.00	0.00	4.63
1918	1998	1.117749	TAGCAGCGATCATGGCTCCT	61.118	55.000	5.39	0.00	39.08	3.69
1935	2015	4.690748	ACAAAGTGACCATGTTGTCGATAG	59.309	41.667	0.00	0.00	38.11	2.08
1998	2081	2.836360	CATGCCCTGGGGATGCAC	60.836	66.667	30.70	6.56	43.96	4.57
2055	2138	4.174009	ACTATGACAGTTCGAAATCACCG	58.826	43.478	0.00	2.41	31.59	4.94
2064	2147	2.631418	ACACCGACTATGACAGTTCG	57.369	50.000	0.00	0.00	37.72	3.95
2068	2151	2.417379	CCTCCAACACCGACTATGACAG	60.417	54.545	0.00	0.00	0.00	3.51
2211	2294	3.575965	GGAAATGTCCAATTCGCTTGT	57.424	42.857	0.00	0.00	44.26	3.16
2273	2356	8.353423	ACATATAATAATTGATGGCAGGGTTC	57.647	34.615	0.00	0.00	0.00	3.62
2385	2504	1.441738	CATGCAATGGTCACAGTCGA	58.558	50.000	0.00	0.00	41.79	4.20
2398	2517	6.418057	AGTAATGGAAAAGGAAACATGCAA	57.582	33.333	0.00	0.00	0.00	4.08
2417	2536	6.017109	GGCATGAAAAGTGACAGAAGAAGTAA	60.017	38.462	0.00	0.00	0.00	2.24
2425	2544	5.945191	TGATATTGGCATGAAAAGTGACAGA	59.055	36.000	0.00	0.00	35.70	3.41
2436	2555	3.949586	TGGTCCTTGATATTGGCATGA	57.050	42.857	0.00	0.00	0.00	3.07
2495	2616	5.648960	ACTTGTCTCTTAGCACCTCTAGTAC	59.351	44.000	0.00	0.00	0.00	2.73
2496	2617	5.817784	ACTTGTCTCTTAGCACCTCTAGTA	58.182	41.667	0.00	0.00	0.00	1.82
2573	2694	0.526211	CCCTACCGCCTTGAAAAAGC	59.474	55.000	0.00	0.00	0.00	3.51
2670	2794	7.151999	TGCACTTGTAATTTTGTACCATAGG	57.848	36.000	0.00	0.00	0.00	2.57
2697	2821	7.984050	TGAAAACTGAATGGTTTTTGCATAGAA	59.016	29.630	6.75	0.00	45.62	2.10
2791	2916	6.811253	ATATAACTTGGTTCAACTGCGAAA	57.189	33.333	0.00	0.00	0.00	3.46
2850	2975	0.392998	GACACCGTGGCAATGGAGAT	60.393	55.000	6.27	0.00	36.21	2.75
2878	3003	2.826488	AGAGCAGGAACATAGGTGAGT	58.174	47.619	0.00	0.00	0.00	3.41
2945	3070	1.032014	AACAAGCAAGCAACATCCGT	58.968	45.000	0.00	0.00	0.00	4.69
2952	3086	3.374988	CGATCTATCCAACAAGCAAGCAA	59.625	43.478	0.00	0.00	0.00	3.91
2962	3096	7.807680	GGATTGTAAAATCCGATCTATCCAAC	58.192	38.462	8.98	0.00	39.33	3.77

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.