AutoCloner

Multiple sequence alignment - TraesCS4A01G013100

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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	TraesCS4A01G013100	chr4A	100.000	4237	0	0	1	4237	7416039	7411803	0.000000e+00	7825
1	TraesCS4A01G013100	chr4A	88.215	874	98	1	969	1842	572558205	572559073	0.000000e+00	1038
2	TraesCS4A01G013100	chr4A	95.149	268	13	0	253	520	7415907	7416174	1.410000e-114	424
3	TraesCS4A01G013100	chr4A	93.985	133	8	0	1	133	7415655	7415787	7.180000e-48	202
4	TraesCS4A01G013100	chr4A	93.382	136	9	0	1	136	643426595	643426460	7.180000e-48	202
5	TraesCS4A01G013100	chr4A	94.175	103	6	0	140	242	7415968	7415866	1.580000e-34	158
6	TraesCS4A01G013100	chr4D	96.492	3136	68	17	517	3622	460989395	460992518	0.000000e+00	5144
7	TraesCS4A01G013100	chr4D	84.656	2457	338	20	970	3404	164887534	164885095	0.000000e+00	2412
8	TraesCS4A01G013100	chr4D	95.819	598	8	4	3644	4237	460992782	460993366	0.000000e+00	950
9	TraesCS4A01G013100	chr4B	94.246	3128	98	30	517	3622	576183193	576186260	0.000000e+00	4704
10	TraesCS4A01G013100	chr4B	94.718	568	18	7	3680	4237	576190297	576190862	0.000000e+00	872
11	TraesCS4A01G013100	chr1A	88.870	2309	238	9	969	3265	157348730	157351031	0.000000e+00	2822
12	TraesCS4A01G013100	chr2D	84.963	2454	332	18	970	3404	86029277	86031712	0.000000e+00	2453
13	TraesCS4A01G013100	chr2D	94.118	136	7	1	1	136	283139312	283139446	5.550000e-49	206
14	TraesCS4A01G013100	chr6A	88.444	1350	137	9	1928	3265	202359516	202360858	0.000000e+00	1611
15	TraesCS4A01G013100	chr7B	83.854	1313	145	23	1485	2784	623752756	623754014	0.000000e+00	1188
16	TraesCS4A01G013100	chr1B	84.961	1157	152	13	2252	3397	612823754	612824899	0.000000e+00	1153
17	TraesCS4A01G013100	chr1B	84.066	1092	163	5	970	2061	612822675	612823755	0.000000e+00	1042
18	TraesCS4A01G013100	chr1B	95.636	275	11	1	249	523	653798370	653798097	1.400000e-119	440
19	TraesCS4A01G013100	chr1B	95.149	268	13	0	253	520	310921713	310921980	1.410000e-114	424
20	TraesCS4A01G013100	chr1B	93.284	134	9	0	1	134	310921845	310921712	9.290000e-47	198
21	TraesCS4A01G013100	chr2A	87.076	766	96	3	1288	2052	681513547	681512784	0.000000e+00	863
22	TraesCS4A01G013100	chr2A	96.324	272	9	1	251	521	103912964	103912693	3.010000e-121	446
23	TraesCS4A01G013100	chr5A	96.491	513	17	1	1	513	606346575	606347086	0.000000e+00	846
24	TraesCS4A01G013100	chr5A	93.985	133	8	0	1	133	606346959	606346827	7.180000e-48	202
25	TraesCS4A01G013100	chr5A	97.000	100	3	0	140	239	606346646	606346745	7.290000e-38	169
26	TraesCS4A01G013100	chr3B	83.250	800	131	1	970	1769	446711143	446711939	0.000000e+00	732
27	TraesCS4A01G013100	chr3B	95.273	275	13	0	253	527	800267215	800266941	1.810000e-118	436
28	TraesCS4A01G013100	chrUn	87.346	569	72	0	969	1537	281064901	281064333	0.000000e+00	652
29	TraesCS4A01G013100	chrUn	87.346	569	72	0	969	1537	291669002	291668434	0.000000e+00	652
30	TraesCS4A01G013100	chr5B	97.015	268	8	0	253	520	465251660	465251927	6.460000e-123	451
31	TraesCS4A01G013100	chr5B	94.118	136	8	0	1	136	465251792	465251657	1.540000e-49	207
32	TraesCS4A01G013100	chr6B	95.956	272	11	0	253	524	48355644	48355373	3.890000e-120	442
33	TraesCS4A01G013100	chr6B	95.588	136	6	0	1	136	3807885	3808020	7.130000e-53	219
34	TraesCS4A01G013100	chr6B	93.284	134	9	0	1	134	48355512	48355645	9.290000e-47	198
35	TraesCS4A01G013100	chr7A	95.896	268	11	0	253	520	338089740	338090007	6.510000e-118	435
36	TraesCS4A01G013100	chr6D	81.955	266	36	8	3045	3307	430315810	430316066	9.230000e-52	215
37	TraesCS4A01G013100	chr6D	98.507	67	1	0	140	206	54662868	54662802	7.440000e-23	119
38	TraesCS4A01G013100	chr6D	98.507	67	1	0	140	206	426993287	426993353	7.440000e-23	119
39	TraesCS4A01G013100	chr5D	98.507	67	1	0	140	206	58020494	58020560	7.440000e-23	119
40	TraesCS4A01G013100	chr5D	98.507	67	1	0	140	206	373566975	373567041	7.440000e-23	119
41	TraesCS4A01G013100	chr3D	98.507	67	1	0	140	206	544407341	544407275	7.440000e-23	119
42	TraesCS4A01G013100	chr1D	98.507	67	1	0	140	206	364839953	364839887	7.440000e-23	119

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	TraesCS4A01G013100	chr4A	7411803	7416039	4236	True	3991.5	7825	97.0875	1	4237	2	chr4A.!!$R2	4236
1	TraesCS4A01G013100	chr4A	572558205	572559073	868	False	1038.0	1038	88.2150	969	1842	1	chr4A.!!$F1	873
2	TraesCS4A01G013100	chr4A	7415655	7416174	519	False	313.0	424	94.5670	1	520	2	chr4A.!!$F2	519
3	TraesCS4A01G013100	chr4D	460989395	460993366	3971	False	3047.0	5144	96.1555	517	4237	2	chr4D.!!$F1	3720
4	TraesCS4A01G013100	chr4D	164885095	164887534	2439	True	2412.0	2412	84.6560	970	3404	1	chr4D.!!$R1	2434
5	TraesCS4A01G013100	chr4B	576183193	576186260	3067	False	4704.0	4704	94.2460	517	3622	1	chr4B.!!$F1	3105
6	TraesCS4A01G013100	chr4B	576190297	576190862	565	False	872.0	872	94.7180	3680	4237	1	chr4B.!!$F2	557
7	TraesCS4A01G013100	chr1A	157348730	157351031	2301	False	2822.0	2822	88.8700	969	3265	1	chr1A.!!$F1	2296
8	TraesCS4A01G013100	chr2D	86029277	86031712	2435	False	2453.0	2453	84.9630	970	3404	1	chr2D.!!$F1	2434
9	TraesCS4A01G013100	chr6A	202359516	202360858	1342	False	1611.0	1611	88.4440	1928	3265	1	chr6A.!!$F1	1337
10	TraesCS4A01G013100	chr7B	623752756	623754014	1258	False	1188.0	1188	83.8540	1485	2784	1	chr7B.!!$F1	1299
11	TraesCS4A01G013100	chr1B	612822675	612824899	2224	False	1097.5	1153	84.5135	970	3397	2	chr1B.!!$F2	2427
12	TraesCS4A01G013100	chr2A	681512784	681513547	763	True	863.0	863	87.0760	1288	2052	1	chr2A.!!$R2	764
13	TraesCS4A01G013100	chr5A	606346575	606347086	511	False	507.5	846	96.7455	1	513	2	chr5A.!!$F1	512
14	TraesCS4A01G013100	chr3B	446711143	446711939	796	False	732.0	732	83.2500	970	1769	1	chr3B.!!$F1	799
15	TraesCS4A01G013100	chrUn	281064333	281064901	568	True	652.0	652	87.3460	969	1537	1	chrUn.!!$R1	568
16	TraesCS4A01G013100	chrUn	291668434	291669002	568	True	652.0	652	87.3460	969	1537	1	chrUn.!!$R2	568

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	Hairpin	End Stability	Orientation
657	736	0.169009	GCACCGAATTCCAGCAGTTC	59.831	55.0	0.00	3.01	F
1392	1497	0.316204	TCTCTCGTCGTGGGGAAAAC	59.684	55.0	0.00	2.43	F
1864	1971	0.591170	GCTCGCTACTTTTGTTGGCA	59.409	50.0	32.85	4.92	F

Position	MSA Position	Penalty	Sequence	TM	GC	Hairpin	End Stability	Orientation
1959	2066	2.819019	TGGTGGTTTGCATGACATACAG	59.181	45.455	32.37	2.74	R
2211	2329	3.814005	AATCCAGCAAGCCATTCATTC	57.186	42.857	0.00	2.67	R
3637	3762	0.044855	AGAGGAGGGGGCAGTGTAAT	59.955	55.000	0.00	1.89	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
42	43	1.020437	TGCAAACAACGATGCAGTGA	58.980	45.000	0.00	0.00	46.87	3.41
215	216	1.770294	TTGGTCTGGTGTTGAAACCC	58.230	50.000	0.00	0.00	39.70	4.11
241	242	6.811253	AAAATAAAGAACTGCGGATACACA	57.189	33.333	0.00	0.00	0.00	3.72
242	243	5.796350	AATAAAGAACTGCGGATACACAC	57.204	39.130	0.00	0.00	0.00	3.82
243	244	3.402628	AAAGAACTGCGGATACACACT	57.597	42.857	0.00	0.00	0.00	3.55
244	245	2.370281	AGAACTGCGGATACACACTG	57.630	50.000	0.00	0.00	0.00	3.66
245	246	1.618837	AGAACTGCGGATACACACTGT	59.381	47.619	0.00	0.00	0.00	3.55
249	250	0.676736	TGCGGATACACACTGTCACA	59.323	50.000	0.00	0.00	0.00	3.58
251	252	2.289382	TGCGGATACACACTGTCACAAT	60.289	45.455	0.00	0.00	0.00	2.71
256	257	5.428253	GGATACACACTGTCACAATACCAT	58.572	41.667	0.00	0.00	0.00	3.55
299	368	6.536582	GCTCATGAGTATCTGCAGTTCTTTAA	59.463	38.462	23.38	0.00	34.92	1.52
342	411	7.487829	TGTTCAAATAAAACTGAGTTCAAGTGC	59.512	33.333	0.00	0.00	0.00	4.40
368	437	2.726066	GCATCGTTGTTTGCAGCTAGTC	60.726	50.000	0.00	0.00	38.72	2.59
412	481	4.397730	TGCTGAAAACTGCTAAGTGTTGAA	59.602	37.500	0.00	0.00	33.75	2.69
426	495	2.434336	GTGTTGAAAGCCTTTCCCCTTT	59.566	45.455	14.35	0.00	38.90	3.11
439	508	1.354368	TCCCCTTTTGTGATCTGGACC	59.646	52.381	0.00	0.00	0.00	4.46
612	686	1.454111	CTCTCGATCCCGACCTGGT	60.454	63.158	0.00	0.00	40.30	4.00
615	689	1.304630	TCGATCCCGACCTGGTTCA	60.305	57.895	0.00	0.00	40.30	3.18
616	690	1.153628	CGATCCCGACCTGGTTCAC	60.154	63.158	0.00	0.00	38.22	3.18
617	691	1.884075	CGATCCCGACCTGGTTCACA	61.884	60.000	0.00	0.00	38.22	3.58
649	728	4.796495	AGGCCGGCACCGAATTCC	62.796	66.667	30.85	7.16	42.83	3.01
651	730	3.508840	GCCGGCACCGAATTCCAG	61.509	66.667	24.80	0.00	42.83	3.86
652	731	3.508840	CCGGCACCGAATTCCAGC	61.509	66.667	11.42	1.46	42.83	4.85
653	732	2.745884	CGGCACCGAATTCCAGCA	60.746	61.111	2.01	0.00	42.83	4.41
654	733	2.753966	CGGCACCGAATTCCAGCAG	61.754	63.158	2.01	5.73	42.83	4.24
655	734	1.675641	GGCACCGAATTCCAGCAGT	60.676	57.895	11.88	0.00	0.00	4.40
656	735	1.244019	GGCACCGAATTCCAGCAGTT	61.244	55.000	11.88	0.00	0.00	3.16
657	736	0.169009	GCACCGAATTCCAGCAGTTC	59.831	55.000	0.00	0.00	0.00	3.01
658	737	0.804989	CACCGAATTCCAGCAGTTCC	59.195	55.000	0.00	0.00	0.00	3.62
659	738	0.693049	ACCGAATTCCAGCAGTTCCT	59.307	50.000	0.00	0.00	0.00	3.36
660	739	1.339151	ACCGAATTCCAGCAGTTCCTC	60.339	52.381	0.00	0.00	0.00	3.71
795	886	0.679002	CAGCAGCAGCACCAAGGTAT	60.679	55.000	3.17	0.00	45.49	2.73
796	887	0.679002	AGCAGCAGCACCAAGGTATG	60.679	55.000	3.17	0.00	45.49	2.39
922	1013	0.539986	CTCAACCTAGGGCGCCTTTA	59.460	55.000	28.56	17.85	34.61	1.85
931	1022	0.735978	GGGCGCCTTTATGTTTGTGC	60.736	55.000	28.56	0.00	0.00	4.57
948	1039	5.459536	TTGTGCAGCCATGTTACAATTTA	57.540	34.783	0.00	0.00	33.60	1.40
949	1040	5.058149	TGTGCAGCCATGTTACAATTTAG	57.942	39.130	0.00	0.00	0.00	1.85
950	1041	4.764308	TGTGCAGCCATGTTACAATTTAGA	59.236	37.500	0.00	0.00	0.00	2.10
951	1042	5.106197	TGTGCAGCCATGTTACAATTTAGAG	60.106	40.000	0.00	0.00	0.00	2.43
1326	1431	5.928839	TCAGTACTCAGCAAAGAACTCATTC	59.071	40.000	0.00	0.00	34.78	2.67
1365	1470	1.113788	GGATGCAATGCCCAGCTAAA	58.886	50.000	1.53	0.00	0.00	1.85
1392	1497	0.316204	TCTCTCGTCGTGGGGAAAAC	59.684	55.000	0.00	0.00	0.00	2.43
1567	1672	1.211457	CTCCTGTTATGGAAGCTGGCT	59.789	52.381	0.00	0.00	35.43	4.75
1659	1765	1.751544	TGCTGGAGATGCACATGCC	60.752	57.895	0.49	0.00	41.18	4.40
1668	1774	3.220110	AGATGCACATGCCCTTTATCAG	58.780	45.455	0.49	0.00	41.18	2.90
1864	1971	0.591170	GCTCGCTACTTTTGTTGGCA	59.409	50.000	0.00	0.00	32.85	4.92
1959	2066	4.142182	TGGCTGTTTAAATCTTGGCTATGC	60.142	41.667	0.00	0.00	0.00	3.14
2062	2169	2.862536	CAAGCTCGTCATAGATGGTGTG	59.137	50.000	0.00	0.00	0.00	3.82
2094	2201	9.947669	CATATCATGAAGAAGATTCCTGAAAAC	57.052	33.333	0.00	0.00	29.43	2.43
2389	2507	6.369615	GCAATTTGTGGAGCAGTATGAAAATT	59.630	34.615	0.00	0.00	39.69	1.82
2390	2508	7.095102	GCAATTTGTGGAGCAGTATGAAAATTT	60.095	33.333	0.00	0.00	39.69	1.82
3129	3254	2.463752	TCCCTATTCGCAGTGTAGGTT	58.536	47.619	4.36	0.00	35.23	3.50
3481	3606	4.201841	GCATACCACACGGTTAATGGTTAC	60.202	45.833	12.32	2.03	46.31	2.50
3622	3747	2.072298	CTTGTACCTCTTCAGCACAGC	58.928	52.381	0.00	0.00	0.00	4.40
3624	3749	0.391793	GTACCTCTTCAGCACAGCCC	60.392	60.000	0.00	0.00	0.00	5.19
3626	3751	2.600729	CCTCTTCAGCACAGCCCCT	61.601	63.158	0.00	0.00	0.00	4.79
3627	3752	1.267574	CCTCTTCAGCACAGCCCCTA	61.268	60.000	0.00	0.00	0.00	3.53
3628	3753	0.835941	CTCTTCAGCACAGCCCCTAT	59.164	55.000	0.00	0.00	0.00	2.57
3629	3754	1.211457	CTCTTCAGCACAGCCCCTATT	59.789	52.381	0.00	0.00	0.00	1.73
3631	3756	0.698238	TTCAGCACAGCCCCTATTGT	59.302	50.000	0.00	0.00	0.00	2.71
3632	3757	0.698238	TCAGCACAGCCCCTATTGTT	59.302	50.000	0.00	0.00	0.00	2.83
3633	3758	0.813184	CAGCACAGCCCCTATTGTTG	59.187	55.000	0.00	0.00	0.00	3.33
3634	3759	0.405585	AGCACAGCCCCTATTGTTGT	59.594	50.000	0.00	0.00	0.00	3.32
3635	3760	0.527565	GCACAGCCCCTATTGTTGTG	59.472	55.000	3.32	3.32	41.45	3.33
3636	3761	1.886222	GCACAGCCCCTATTGTTGTGA	60.886	52.381	10.74	0.00	41.12	3.58
3637	3762	2.513753	CACAGCCCCTATTGTTGTGAA	58.486	47.619	1.64	0.00	41.12	3.18
3638	3763	3.091545	CACAGCCCCTATTGTTGTGAAT	58.908	45.455	1.64	0.00	41.12	2.57
3639	3764	3.511146	CACAGCCCCTATTGTTGTGAATT	59.489	43.478	1.64	0.00	41.12	2.17
3640	3765	4.704540	CACAGCCCCTATTGTTGTGAATTA	59.295	41.667	1.64	0.00	41.12	1.40
3641	3766	4.705023	ACAGCCCCTATTGTTGTGAATTAC	59.295	41.667	0.00	0.00	0.00	1.89
3642	3767	4.704540	CAGCCCCTATTGTTGTGAATTACA	59.295	41.667	0.00	0.00	37.56	2.41
3661	4028	4.095400	TGCCCCCTCCTCTCCCTC	62.095	72.222	0.00	0.00	0.00	4.30
3713	4081	1.486726	GGGTCTCCCACTATTCCACTG	59.513	57.143	0.00	0.00	44.65	3.66
3794	4168	6.712998	TCCTCCTTTTGTTGTGATTCGATTTA	59.287	34.615	0.00	0.00	0.00	1.40
3796	4170	6.378582	TCCTTTTGTTGTGATTCGATTTAGC	58.621	36.000	0.00	0.00	0.00	3.09
3797	4171	6.206634	TCCTTTTGTTGTGATTCGATTTAGCT	59.793	34.615	0.00	0.00	0.00	3.32
3798	4172	6.863126	CCTTTTGTTGTGATTCGATTTAGCTT	59.137	34.615	0.00	0.00	0.00	3.74
4121	4498	2.234414	CAACCCAACCAATCCCAATCAG	59.766	50.000	0.00	0.00	0.00	2.90

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
42	43	8.519526	TGTTCAAATAAAACTGAGTTCAAGTGT	58.480	29.630	0.00	0.00	0.00	3.55
233	234	4.827692	TGGTATTGTGACAGTGTGTATCC	58.172	43.478	0.00	0.00	0.00	2.59
237	238	7.230510	ACAAAATATGGTATTGTGACAGTGTGT	59.769	33.333	0.00	0.00	36.03	3.72
238	239	7.592938	ACAAAATATGGTATTGTGACAGTGTG	58.407	34.615	0.00	0.00	36.03	3.82
239	240	7.759489	ACAAAATATGGTATTGTGACAGTGT	57.241	32.000	0.00	0.00	36.03	3.55
240	241	9.474920	AAAACAAAATATGGTATTGTGACAGTG	57.525	29.630	6.83	0.00	37.36	3.66
299	368	8.750515	ATTTGAACAGATTGAAACCCAAAAAT	57.249	26.923	0.00	0.00	38.43	1.82
342	411	0.030504	TGCAAACAACGATGCAGTGG	59.969	50.000	0.00	0.00	46.87	4.00
362	431	5.728898	GCAGCAAACATCAATACAGACTAGC	60.729	44.000	0.00	0.00	0.00	3.42
368	437	4.974275	GCATAGCAGCAAACATCAATACAG	59.026	41.667	0.00	0.00	0.00	2.74
412	481	2.470057	TCACAAAAGGGGAAAGGCTT	57.530	45.000	0.00	0.00	0.00	4.35
426	495	2.225382	TCCTACGGTCCAGATCACAA	57.775	50.000	0.00	0.00	0.00	3.33
439	508	4.060900	CTCCATCCAATTCACATCCTACG	58.939	47.826	0.00	0.00	0.00	3.51
450	519	7.465900	TTACCCTTCTAATCTCCATCCAATT	57.534	36.000	0.00	0.00	0.00	2.32
506	575	2.328295	CGCAAACGGACTGAGATCCAG	61.328	57.143	9.01	9.01	41.40	3.86
640	719	0.693049	AGGAACTGCTGGAATTCGGT	59.307	50.000	0.00	0.00	37.18	4.69
641	720	1.339055	TGAGGAACTGCTGGAATTCGG	60.339	52.381	0.00	0.00	41.55	4.30
647	726	0.681733	GTCTGTGAGGAACTGCTGGA	59.318	55.000	0.00	0.00	41.55	3.86
649	728	1.793258	CAGTCTGTGAGGAACTGCTG	58.207	55.000	0.00	0.00	41.55	4.41
651	730	2.537863	GCAGTCTGTGAGGAACTGC	58.462	57.895	10.54	10.54	45.24	4.40
652	731	0.321122	GGGCAGTCTGTGAGGAACTG	60.321	60.000	0.93	0.00	41.55	3.16
654	733	1.374758	CGGGCAGTCTGTGAGGAAC	60.375	63.158	0.93	0.00	0.00	3.62
655	734	2.583441	CCGGGCAGTCTGTGAGGAA	61.583	63.158	0.93	0.00	0.00	3.36
656	735	2.997315	CCGGGCAGTCTGTGAGGA	60.997	66.667	0.93	0.00	0.00	3.71
657	736	4.767255	GCCGGGCAGTCTGTGAGG	62.767	72.222	15.62	3.74	0.00	3.86
658	737	3.655810	GAGCCGGGCAGTCTGTGAG	62.656	68.421	23.09	0.00	0.00	3.51
659	738	3.695606	GAGCCGGGCAGTCTGTGA	61.696	66.667	23.09	0.00	0.00	3.58
660	739	4.767255	GGAGCCGGGCAGTCTGTG	62.767	72.222	23.09	0.00	0.00	3.66
785	876	2.173669	CCGAGCGCATACCTTGGTG	61.174	63.158	11.47	0.00	0.00	4.17
795	886	3.064987	GAGTTAGAGGCCGAGCGCA	62.065	63.158	11.47	0.00	40.31	6.09
796	887	2.278923	GAGTTAGAGGCCGAGCGC	60.279	66.667	0.00	0.00	0.00	5.92
861	952	5.599656	AGAGGATCAGAGGAGATGAGAAAAG	59.400	44.000	0.00	0.00	37.82	2.27
922	1013	2.627221	TGTAACATGGCTGCACAAACAT	59.373	40.909	0.50	0.00	0.00	2.71
931	1022	9.643693	ATTTTTCTCTAAATTGTAACATGGCTG	57.356	29.630	0.00	0.00	0.00	4.85
948	1039	7.570607	AGATCAGTAGGGGATACATTTTTCTCT	59.429	37.037	0.00	0.00	36.79	3.10
949	1040	7.740805	AGATCAGTAGGGGATACATTTTTCTC	58.259	38.462	0.00	0.00	36.79	2.87
950	1041	7.698163	AGATCAGTAGGGGATACATTTTTCT	57.302	36.000	0.00	0.00	36.79	2.52
951	1042	8.753497	AAAGATCAGTAGGGGATACATTTTTC	57.247	34.615	0.00	0.00	36.79	2.29
1132	1237	1.956802	CCTTCTTGGGTTCCAACGC	59.043	57.895	0.00	0.00	38.75	4.84
1224	1329	3.512680	GTGTCTGGTCGTCCTTCTTATG	58.487	50.000	0.00	0.00	34.23	1.90
1326	1431	1.927174	CTTGTCGACGGATTAGGCTTG	59.073	52.381	11.62	0.00	0.00	4.01
1365	1470	3.368116	CCCCACGACGAGAGAAATTACTT	60.368	47.826	0.00	0.00	0.00	2.24
1392	1497	4.384846	AGCGTAACAGTCGTGATACAAAAG	59.615	41.667	0.00	0.00	32.73	2.27
1567	1672	5.476599	CACCAAACTCAAGATTTCCATACCA	59.523	40.000	0.00	0.00	0.00	3.25
1659	1765	9.288576	TGCATATGGAGAAAATACTGATAAAGG	57.711	33.333	4.56	0.00	0.00	3.11
1668	1774	8.677300	TCTTTTGACTGCATATGGAGAAAATAC	58.323	33.333	28.65	12.98	36.93	1.89
1959	2066	2.819019	TGGTGGTTTGCATGACATACAG	59.181	45.455	0.00	0.00	32.37	2.74
2062	2169	7.390996	AGGAATCTTCTTCATGATATGACATGC	59.609	37.037	0.00	0.00	44.79	4.06
2211	2329	3.814005	AATCCAGCAAGCCATTCATTC	57.186	42.857	0.00	0.00	0.00	2.67
2389	2507	9.584008	TTCTTTCTCTACCTTGTCTCTTAGTAA	57.416	33.333	0.00	0.00	0.00	2.24
2390	2508	9.584008	TTTCTTTCTCTACCTTGTCTCTTAGTA	57.416	33.333	0.00	0.00	0.00	1.82
3129	3254	3.973973	TCCTTTCTCTTTGAAGGAGGACA	59.026	43.478	4.42	0.00	36.99	4.02
3633	3758	1.682087	GGAGGGGGCAGTGTAATTCAC	60.682	57.143	0.00	0.00	46.46	3.18
3634	3759	0.623723	GGAGGGGGCAGTGTAATTCA	59.376	55.000	0.00	0.00	0.00	2.57
3635	3760	0.919710	AGGAGGGGGCAGTGTAATTC	59.080	55.000	0.00	0.00	0.00	2.17
3636	3761	0.919710	GAGGAGGGGGCAGTGTAATT	59.080	55.000	0.00	0.00	0.00	1.40
3637	3762	0.044855	AGAGGAGGGGGCAGTGTAAT	59.955	55.000	0.00	0.00	0.00	1.89
3638	3763	0.617820	GAGAGGAGGGGGCAGTGTAA	60.618	60.000	0.00	0.00	0.00	2.41
3639	3764	1.001760	GAGAGGAGGGGGCAGTGTA	59.998	63.158	0.00	0.00	0.00	2.90
3640	3765	2.284995	GAGAGGAGGGGGCAGTGT	60.285	66.667	0.00	0.00	0.00	3.55
3641	3766	3.086600	GGAGAGGAGGGGGCAGTG	61.087	72.222	0.00	0.00	0.00	3.66
3642	3767	4.423209	GGGAGAGGAGGGGGCAGT	62.423	72.222	0.00	0.00	0.00	4.40
3644	3769	4.095400	GAGGGAGAGGAGGGGGCA	62.095	72.222	0.00	0.00	0.00	5.36
3645	3770	4.890306	GGAGGGAGAGGAGGGGGC	62.890	77.778	0.00	0.00	0.00	5.80
3702	4070	8.088365	GCTAAAATTCAAAACCAGTGGAATAGT	58.912	33.333	18.40	0.00	30.29	2.12
3713	4081	5.047731	AGGAGCAGAGCTAAAATTCAAAACC	60.048	40.000	0.00	0.00	39.88	3.27
3821	4195	5.180304	TCCATGACAAATCGAAACGAAATCA	59.820	36.000	0.00	0.00	39.99	2.57

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.