AutoCloner

Multiple sequence alignment - TraesCS3B01G564000

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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	TraesCS3B01G564000	chr3B	100.000	4202	0	0	873	5074	797224907	797220706	0.000000e+00	7760.0
1	TraesCS3B01G564000	chr3B	92.097	2227	122	28	2015	4225	798107629	798109817	0.000000e+00	3088.0
2	TraesCS3B01G564000	chr3B	82.335	2253	295	56	2015	4205	798122890	798125101	0.000000e+00	1860.0
3	TraesCS3B01G564000	chr3B	92.300	1026	32	9	1021	2000	798106534	798107558	0.000000e+00	1413.0
4	TraesCS3B01G564000	chr3B	83.390	1481	174	31	2036	3505	797639198	797640617	0.000000e+00	1306.0
5	TraesCS3B01G564000	chr3B	100.000	457	0	0	1	457	797225779	797225323	0.000000e+00	845.0
6	TraesCS3B01G564000	chr3B	85.514	428	55	2	1526	1946	797638704	797639131	1.680000e-119	440.0
7	TraesCS3B01G564000	chr3B	87.733	375	20	8	873	1246	797637804	797638153	1.020000e-111	414.0
8	TraesCS3B01G564000	chr3B	96.471	85	3	0	1186	1270	797224645	797224561	1.900000e-29	141.0
9	TraesCS3B01G564000	chr3B	78.788	165	32	3	3	164	747081652	747081816	1.930000e-19	108.0
10	TraesCS3B01G564000	chr3B	80.282	142	25	3	29	168	744553461	744553321	2.500000e-18	104.0
11	TraesCS3B01G564000	chr3D	94.902	3962	82	34	1186	5074	594183631	594179717	0.000000e+00	6087.0
12	TraesCS3B01G564000	chr3D	93.503	3294	126	40	1006	4225	594494471	594497750	0.000000e+00	4817.0
13	TraesCS3B01G564000	chr3D	94.875	2712	68	13	2383	5055	594363597	594366276	0.000000e+00	4172.0
14	TraesCS3B01G564000	chr3D	79.894	1323	205	34	2933	4225	594077812	594076521	0.000000e+00	913.0
15	TraesCS3B01G564000	chr3D	87.259	777	78	9	1186	1942	594362235	594363010	0.000000e+00	867.0
16	TraesCS3B01G564000	chr3D	93.884	327	16	3	873	1195	594184032	594183706	1.640000e-134	490.0
17	TraesCS3B01G564000	chr3D	83.516	455	39	14	3	457	594184933	594184515	4.760000e-105	392.0
18	TraesCS3B01G564000	chr3D	86.495	311	35	2	2015	2325	594363160	594363463	8.140000e-88	335.0
19	TraesCS3B01G564000	chr3D	92.810	153	11	0	1186	1338	594053635	594053483	6.610000e-54	222.0
20	TraesCS3B01G564000	chr3D	96.471	85	3	0	1135	1219	594494651	594494735	1.900000e-29	141.0
21	TraesCS3B01G564000	chr3D	85.714	133	14	4	4891	5023	93257495	93257368	8.860000e-28	135.0
22	TraesCS3B01G564000	chr3D	84.106	151	6	4	4888	5023	528190531	528190678	4.120000e-26	130.0
23	TraesCS3B01G564000	chr3A	95.757	1697	65	6	2294	3987	725099851	725101543	0.000000e+00	2728.0
24	TraesCS3B01G564000	chr3A	93.438	1585	57	12	1186	2723	724947541	724949125	0.000000e+00	2307.0
25	TraesCS3B01G564000	chr3A	83.231	1634	219	34	2605	4207	725119762	725121371	0.000000e+00	1448.0
26	TraesCS3B01G564000	chr3A	84.038	1491	180	30	2036	3505	724895869	724897322	0.000000e+00	1382.0
27	TraesCS3B01G564000	chr3A	92.100	519	41	0	1006	1524	725098072	725098590	0.000000e+00	732.0
28	TraesCS3B01G564000	chr3A	82.601	546	64	13	2015	2559	725099344	725099859	2.150000e-123	453.0
29	TraesCS3B01G564000	chr3A	90.265	339	33	0	1186	1524	724797948	724797610	1.300000e-120	444.0
30	TraesCS3B01G564000	chr3A	85.023	434	50	7	1526	1946	725119178	725119609	1.310000e-115	427.0
31	TraesCS3B01G564000	chr3A	87.397	365	46	0	1572	1936	725098817	725099181	2.180000e-113	420.0
32	TraesCS3B01G564000	chr3A	94.757	267	13	1	873	1138	724945959	724946225	1.020000e-111	414.0
33	TraesCS3B01G564000	chr3A	94.757	267	13	1	873	1138	724947122	724947388	1.020000e-111	414.0
34	TraesCS3B01G564000	chr3A	94.382	267	14	1	873	1138	724935307	724935573	4.730000e-110	409.0
35	TraesCS3B01G564000	chr3A	93.633	267	15	2	873	1138	724937696	724937961	1.020000e-106	398.0
36	TraesCS3B01G564000	chr3A	88.855	332	21	6	127	457	724940937	724941253	1.320000e-105	394.0
37	TraesCS3B01G564000	chr3A	85.788	387	35	13	3	383	724934846	724935218	4.760000e-105	392.0
38	TraesCS3B01G564000	chr3A	88.485	330	22	9	127	455	724939662	724939976	7.970000e-103	385.0
39	TraesCS3B01G564000	chr3A	90.909	264	15	6	127	383	724946772	724947033	3.760000e-91	346.0
40	TraesCS3B01G564000	chr3A	90.152	264	17	7	127	383	724938509	724938770	8.140000e-88	335.0
41	TraesCS3B01G564000	chr3A	89.773	264	18	7	127	383	724937346	724937607	3.790000e-86	329.0
42	TraesCS3B01G564000	chr3A	91.093	247	16	4	127	369	724944446	724944690	3.790000e-86	329.0
43	TraesCS3B01G564000	chr3A	85.600	250	29	2	2076	2325	724949136	724949378	6.520000e-64	255.0
44	TraesCS3B01G564000	chr3A	91.011	89	7	1	3	90	724893743	724893831	8.920000e-23	119.0
45	TraesCS3B01G564000	chr3A	77.439	164	33	4	3	163	739123127	739122965	1.500000e-15	95.3
46	TraesCS3B01G564000	chr7A	81.847	2242	314	54	2015	4205	92363067	92360868	0.000000e+00	1799.0
47	TraesCS3B01G564000	chr7A	93.182	44	3	0	4707	4750	699839056	699839099	1.180000e-06	65.8
48	TraesCS3B01G564000	chrUn	83.268	1542	211	31	2605	4118	33329830	33331352	0.000000e+00	1375.0
49	TraesCS3B01G564000	chrUn	84.954	432	52	5	1526	1944	33329239	33329670	4.700000e-115	425.0
50	TraesCS3B01G564000	chrUn	93.633	267	16	1	873	1138	341820658	341820924	1.020000e-106	398.0
51	TraesCS3B01G564000	chrUn	88.855	332	21	6	127	457	341821472	341821788	1.320000e-105	394.0
52	TraesCS3B01G564000	chrUn	88.485	330	22	9	127	455	341820197	341820511	7.970000e-103	385.0
53	TraesCS3B01G564000	chr1D	82.390	159	24	4	3	158	464817928	464817771	8.860000e-28	135.0
54	TraesCS3B01G564000	chr1D	94.444	36	2	0	4715	4750	10540226	10540191	7.100000e-04	56.5
55	TraesCS3B01G564000	chr7D	82.353	170	10	9	4888	5040	406904247	406904413	4.120000e-26	130.0
56	TraesCS3B01G564000	chr7D	90.909	44	4	0	4707	4750	607611811	607611854	5.490000e-05	60.2
57	TraesCS3B01G564000	chr4A	83.444	151	8	2	4888	5023	329838524	329838376	1.920000e-24	124.0
58	TraesCS3B01G564000	chr4A	83.088	136	20	2	4891	5023	288641642	288641507	2.480000e-23	121.0
59	TraesCS3B01G564000	chr6D	83.108	148	8	2	4891	5023	422936554	422936409	8.920000e-23	119.0
60	TraesCS3B01G564000	chr6D	93.590	78	3	1	4946	5023	42565296	42565371	1.150000e-21	115.0
61	TraesCS3B01G564000	chr5A	92.593	81	4	1	4943	5023	698500717	698500795	1.150000e-21	115.0
62	TraesCS3B01G564000	chr7B	81.955	133	22	2	34	164	673124978	673125110	1.490000e-20	111.0
63	TraesCS3B01G564000	chr7B	80.921	152	13	6	4888	5025	689198725	689198874	6.950000e-19	106.0
64	TraesCS3B01G564000	chr7B	80.132	151	13	4	4888	5023	597147033	597147181	4.180000e-16	97.1
65	TraesCS3B01G564000	chr7B	93.182	44	3	0	4707	4750	696896021	696896064	1.180000e-06	65.8
66	TraesCS3B01G564000	chr1A	81.507	146	14	10	4891	5023	255753779	255753634	1.930000e-19	108.0
67	TraesCS3B01G564000	chr5D	80.000	150	14	12	4891	5025	365349785	365349637	4.180000e-16	97.1
68	TraesCS3B01G564000	chr1B	93.333	60	2	2	4888	4946	618008323	618008381	2.520000e-13	87.9
69	TraesCS3B01G564000	chr2D	97.727	44	1	0	4707	4750	520521670	520521627	5.450000e-10	76.8
70	TraesCS3B01G564000	chr2A	94.286	35	2	0	4716	4750	539973500	539973534	3.000000e-03	54.7

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	TraesCS3B01G564000	chr3B	797220706	797225779	5073	True	2915.333333	7760	98.823667	1	5074	3	chr3B.!!$R2	5073
1	TraesCS3B01G564000	chr3B	798106534	798109817	3283	False	2250.500000	3088	92.198500	1021	4225	2	chr3B.!!$F4	3204
2	TraesCS3B01G564000	chr3B	798122890	798125101	2211	False	1860.000000	1860	82.335000	2015	4205	1	chr3B.!!$F2	2190
3	TraesCS3B01G564000	chr3B	797637804	797640617	2813	False	720.000000	1306	85.545667	873	3505	3	chr3B.!!$F3	2632
4	TraesCS3B01G564000	chr3D	594494471	594497750	3279	False	2479.000000	4817	94.987000	1006	4225	2	chr3D.!!$F3	3219
5	TraesCS3B01G564000	chr3D	594179717	594184933	5216	True	2323.000000	6087	90.767333	3	5074	3	chr3D.!!$R4	5071
6	TraesCS3B01G564000	chr3D	594362235	594366276	4041	False	1791.333333	4172	89.543000	1186	5055	3	chr3D.!!$F2	3869
7	TraesCS3B01G564000	chr3D	594076521	594077812	1291	True	913.000000	913	79.894000	2933	4225	1	chr3D.!!$R3	1292
8	TraesCS3B01G564000	chr3A	725098072	725101543	3471	False	1083.250000	2728	89.463750	1006	3987	4	chr3A.!!$F3	2981
9	TraesCS3B01G564000	chr3A	725119178	725121371	2193	False	937.500000	1448	84.127000	1526	4207	2	chr3A.!!$F4	2681
10	TraesCS3B01G564000	chr3A	724893743	724897322	3579	False	750.500000	1382	87.524500	3	3505	2	chr3A.!!$F1	3502
11	TraesCS3B01G564000	chr3A	724934846	724949378	14532	False	515.923077	2307	90.894000	3	2723	13	chr3A.!!$F2	2720
12	TraesCS3B01G564000	chr7A	92360868	92363067	2199	True	1799.000000	1799	81.847000	2015	4205	1	chr7A.!!$R1	2190
13	TraesCS3B01G564000	chrUn	33329239	33331352	2113	False	900.000000	1375	84.111000	1526	4118	2	chrUn.!!$F1	2592
14	TraesCS3B01G564000	chrUn	341820197	341821788	1591	False	392.333333	398	90.324333	127	1138	3	chrUn.!!$F2	1011

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
275	3858	0.181114	AGTGCTCAGTGCCTCAAACA	59.819	50.0	42.00	2.83	F
955	6116	0.472925	TCCCCTACACCAGCAGAACA	60.473	55.0	0.00	3.18	F
2458	15533	0.535335	GTCGGTGCCTCAGTGGATTA	59.465	55.0	38.35	1.75	F

Position	MSA Position	Penalty	Sequence	TM	GC	Hairpin	End Stability	Orientation
1443	13849	0.027324	GCGCTTCTATCTTGCTGTGC	59.973	55.0	0.00	4.57	R
2603	15693	1.156736	CGTCCGAAAAGGCACAGAAT	58.843	50.0	40.77	2.40	R
4319	17453	1.760192	AAAGACCTGCTCATCATGCC	58.240	50.0	0.00	4.40	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
71	72	3.637273	GTCCTCGGTTGGCTGGGT	61.637	66.667	0.00	0.00	0.00	4.51
102	103	3.486263	CTGTTTCGGACGGCATCC	58.514	61.111	0.00	0.00	45.20	3.51
141	166	6.403964	CCGATCGATCTAACCGGTTTATCATA	60.404	42.308	27.64	17.88	35.83	2.15
206	232	9.624373	ATTTGTGCTAGAGATGAAACATATTCT	57.376	29.630	0.00	0.00	0.00	2.40
231	257	2.238521	AGAAAGCCCTTCGATTTGCAA	58.761	42.857	0.00	0.00	39.22	4.08
245	271	5.744345	TCGATTTGCAACAAATTTACGTTGT	59.256	32.000	17.73	0.00	43.52	3.32
252	3828	2.295070	ACAAATTTACGTTGTCCTGCCC	59.705	45.455	0.00	0.00	34.02	5.36
266	3849	4.767255	GCCCCCGAGTGCTCAGTG	62.767	72.222	0.00	0.00	0.00	3.66
268	3851	4.767255	CCCCGAGTGCTCAGTGCC	62.767	72.222	0.00	0.00	42.00	5.01
269	3852	3.699894	CCCGAGTGCTCAGTGCCT	61.700	66.667	0.00	0.00	42.00	4.75
270	3853	2.125753	CCGAGTGCTCAGTGCCTC	60.126	66.667	0.00	0.00	42.00	4.70
271	3854	2.653115	CGAGTGCTCAGTGCCTCA	59.347	61.111	11.26	0.00	42.00	3.86
272	3855	1.005748	CGAGTGCTCAGTGCCTCAA	60.006	57.895	11.26	0.00	42.00	3.02
273	3856	0.601046	CGAGTGCTCAGTGCCTCAAA	60.601	55.000	11.26	0.00	42.00	2.69
274	3857	0.871057	GAGTGCTCAGTGCCTCAAAC	59.129	55.000	7.63	0.00	42.00	2.93
275	3858	0.181114	AGTGCTCAGTGCCTCAAACA	59.819	50.000	0.00	0.00	42.00	2.83
315	3899	2.503356	TCTGCTTCTCCCTTCAATCTCC	59.497	50.000	0.00	0.00	0.00	3.71
955	6116	0.472925	TCCCCTACACCAGCAGAACA	60.473	55.000	0.00	0.00	0.00	3.18
959	6120	1.540363	CCTACACCAGCAGAACAACGT	60.540	52.381	0.00	0.00	0.00	3.99
962	6123	0.732571	CACCAGCAGAACAACGTTGT	59.267	50.000	27.70	27.70	44.72	3.32
1053	6214	3.765381	TGATGGAGATGAGGCAAACAAA	58.235	40.909	0.00	0.00	0.00	2.83
1172	6360	1.928567	AAGGGGGCCAAGATCCGAA	60.929	57.895	4.39	0.00	0.00	4.30
1295	13701	0.949397	CTGCTGCTGAAAACAGAGCA	59.051	50.000	16.56	16.56	42.94	4.26
1436	13842	2.890945	ACCTGCCACTTTATTTGACACC	59.109	45.455	0.00	0.00	0.00	4.16
1563	14037	4.713553	TCAGTCTTCTGGTTTGTTATGCA	58.286	39.130	0.00	0.00	41.59	3.96
1584	14201	4.733523	GCATGGTGATTTTATCCCGTGTTC	60.734	45.833	0.00	0.00	38.15	3.18
1643	14272	1.066573	CGTGAGCTCAAGGAACCAGAT	60.067	52.381	20.19	0.00	0.00	2.90
1936	14571	2.637382	TCATTGACTCCAACCACAGCTA	59.363	45.455	0.00	0.00	34.72	3.32
2117	14839	1.533753	TTTGGGCAAGCCTTCCTGG	60.534	57.895	11.40	0.00	39.35	4.45
2304	15270	7.798596	AAACTAGCATGATTTCTATGACTGG	57.201	36.000	0.00	0.00	0.00	4.00
2446	15521	6.619446	GCTTCTGAATTATATCATGTCGGTGC	60.619	42.308	0.00	0.00	0.00	5.01
2458	15533	0.535335	GTCGGTGCCTCAGTGGATTA	59.465	55.000	0.00	0.00	38.35	1.75
2603	15693	5.353956	CACTGTAGCCATTAAGTATGTGCAA	59.646	40.000	0.00	0.00	34.67	4.08
2670	15760	1.879575	TTGTAGCTGCCTGGTAGGAT	58.120	50.000	13.86	0.00	37.67	3.24
3138	16232	8.448615	GTTAATTACTGGTTGTACTCACAATCC	58.551	37.037	0.00	1.58	46.03	3.01
3614	16715	0.548926	TGTCCTGGAGGGTGGCATTA	60.549	55.000	0.00	0.00	36.25	1.90
3883	16996	6.183360	CGATCTCTTGTTTCAGCATAAACCAT	60.183	38.462	10.36	0.00	38.35	3.55
4066	17188	5.862678	TTTGTTCCTTTTAGACCCTTTGG	57.137	39.130	0.00	0.00	37.80	3.28
4099	17226	5.982890	GGAAAGAGATTTGTCCCATTTGA	57.017	39.130	0.00	0.00	0.00	2.69
4232	17366	6.503589	TGTTTTAAATTAGTGGACATCCCG	57.496	37.500	0.00	0.00	37.93	5.14
4319	17453	7.042925	GCCGTAAAACATAGTAAGATAGTGGTG	60.043	40.741	0.00	0.00	0.00	4.17
4412	17546	5.125578	GGTGGAGTTGGAAGACCATAATTTC	59.874	44.000	0.00	0.00	46.34	2.17
4464	17598	4.287720	CAAACATGATTGATGATGCTCGG	58.712	43.478	9.99	0.00	35.80	4.63
4530	17664	7.325694	ACCAAAATTCCATGCTTGATCTAAAG	58.674	34.615	0.22	0.00	0.00	1.85
4606	17740	1.523154	TTTGAACACTCCATGCCCGC	61.523	55.000	0.00	0.00	0.00	6.13
4607	17741	3.134127	GAACACTCCATGCCCGCC	61.134	66.667	0.00	0.00	0.00	6.13
4608	17742	4.740822	AACACTCCATGCCCGCCC	62.741	66.667	0.00	0.00	0.00	6.13
4787	17927	1.201181	CAGAGCTCAGCGACAGTAACT	59.799	52.381	17.77	0.00	0.00	2.24
4788	17928	2.420372	CAGAGCTCAGCGACAGTAACTA	59.580	50.000	17.77	0.00	0.00	2.24
4789	17929	3.082548	AGAGCTCAGCGACAGTAACTAA	58.917	45.455	17.77	0.00	0.00	2.24
4790	17930	3.119779	AGAGCTCAGCGACAGTAACTAAC	60.120	47.826	17.77	0.00	0.00	2.34
4791	17931	2.094649	AGCTCAGCGACAGTAACTAACC	60.095	50.000	0.00	0.00	0.00	2.85
4792	17932	2.352421	GCTCAGCGACAGTAACTAACCA	60.352	50.000	0.00	0.00	0.00	3.67
4793	17933	3.502920	CTCAGCGACAGTAACTAACCAG	58.497	50.000	0.00	0.00	0.00	4.00
4794	17934	2.230508	TCAGCGACAGTAACTAACCAGG	59.769	50.000	0.00	0.00	0.00	4.45
4795	17935	2.029290	CAGCGACAGTAACTAACCAGGT	60.029	50.000	0.00	0.00	0.00	4.00
4908	18068	7.502226	TGTGGCCATTCCTAAATATAAGTCTTG	59.498	37.037	9.72	0.00	35.26	3.02
5025	18201	7.634718	AGACTTAAATTTAGGAAAGGAGGAGG	58.365	38.462	13.73	0.00	0.00	4.30
5026	18202	7.461363	AGACTTAAATTTAGGAAAGGAGGAGGA	59.539	37.037	13.73	0.00	0.00	3.71
5027	18203	7.634718	ACTTAAATTTAGGAAAGGAGGAGGAG	58.365	38.462	13.73	0.00	0.00	3.69

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
19	20	0.166814	CTTGTTGCGCTTGAGGCTAC	59.833	55.000	9.73	0.00	39.13	3.58
71	72	0.250124	AAACAGCGTCCGATCAACCA	60.250	50.000	0.00	0.00	0.00	3.67
98	99	3.704381	GCTCGGTAGCTATCGGATG	57.296	57.895	25.35	16.35	45.85	3.51
119	120	7.265673	CCATATGATAAACCGGTTAGATCGAT	58.734	38.462	22.60	20.29	0.00	3.59
120	121	6.627243	CCATATGATAAACCGGTTAGATCGA	58.373	40.000	22.60	17.03	0.00	3.59
206	232	4.320935	GCAAATCGAAGGGCTTTCTAAACA	60.321	41.667	7.79	0.00	33.44	2.83
216	242	2.147436	TTTGTTGCAAATCGAAGGGC	57.853	45.000	0.00	0.00	0.00	5.19
231	257	2.295070	GGGCAGGACAACGTAAATTTGT	59.705	45.455	0.00	0.00	39.94	2.83
263	3846	6.470570	GGCTCTTGTTTTGTTTGAGGCACT	62.471	45.833	9.43	0.00	45.61	4.40
265	3848	2.159114	GGCTCTTGTTTTGTTTGAGGCA	60.159	45.455	9.43	0.00	45.61	4.75
266	3849	2.473816	GGCTCTTGTTTTGTTTGAGGC	58.526	47.619	0.00	0.00	41.65	4.70
268	3851	2.731217	CGGGCTCTTGTTTTGTTTGAG	58.269	47.619	0.00	0.00	0.00	3.02
269	3852	1.202359	GCGGGCTCTTGTTTTGTTTGA	60.202	47.619	0.00	0.00	0.00	2.69
270	3853	1.208259	GCGGGCTCTTGTTTTGTTTG	58.792	50.000	0.00	0.00	0.00	2.93
271	3854	0.820871	TGCGGGCTCTTGTTTTGTTT	59.179	45.000	0.00	0.00	0.00	2.83
272	3855	0.102300	GTGCGGGCTCTTGTTTTGTT	59.898	50.000	0.00	0.00	0.00	2.83
273	3856	1.733526	GTGCGGGCTCTTGTTTTGT	59.266	52.632	0.00	0.00	0.00	2.83
274	3857	1.370414	CGTGCGGGCTCTTGTTTTG	60.370	57.895	0.00	0.00	0.00	2.44
275	3858	3.030652	CGTGCGGGCTCTTGTTTT	58.969	55.556	0.00	0.00	0.00	2.43
315	3899	0.460311	CCTAGGTAGCCACTTGTCGG	59.540	60.000	0.00	0.00	0.00	4.79
431	5247	2.675423	CAGAGGACGTGGTCGGGA	60.675	66.667	0.00	0.00	41.85	5.14
902	5786	2.283604	TGTAGCCGGCAGAGGACA	60.284	61.111	31.54	20.18	0.00	4.02
935	6095	0.690762	GTTCTGCTGGTGTAGGGGAA	59.309	55.000	0.00	0.00	0.00	3.97
955	6116	2.665185	GAGCTGGGCGACAACGTT	60.665	61.111	0.00	0.00	41.98	3.99
1053	6214	2.203788	TTCTCCCCTGTCCACGCT	60.204	61.111	0.00	0.00	0.00	5.07
1172	6360	1.202615	CCATGTCTGTCGCATGAGGAT	60.203	52.381	0.00	0.00	44.60	3.24
1208	13479	0.179045	AGAAATCGGATCTTGGCCCG	60.179	55.000	0.00	0.00	46.57	6.13
1295	13701	1.268079	GCTCGCTTTCTTCTTTTGCCT	59.732	47.619	0.00	0.00	0.00	4.75
1436	13842	0.461548	TATCTTGCTGTGCTCCTCCG	59.538	55.000	0.00	0.00	0.00	4.63
1443	13849	0.027324	GCGCTTCTATCTTGCTGTGC	59.973	55.000	0.00	0.00	0.00	4.57
1563	14037	4.855340	AGAACACGGGATAAAATCACCAT	58.145	39.130	0.00	0.00	0.00	3.55
1584	14201	9.770097	ATTCACAACCTACACATAGATGATAAG	57.230	33.333	0.00	0.00	0.00	1.73
1643	14272	4.100035	AGAAGCTCATCATCGGTGTATTCA	59.900	41.667	0.00	0.00	0.00	2.57
1936	14571	6.704310	ACTCATACCATAAACCTAACGTTGT	58.296	36.000	11.99	0.00	33.93	3.32
2304	15270	2.250741	GAGCCTTGGACTGCTCCCTC	62.251	65.000	0.08	0.00	46.50	4.30
2446	15521	6.715264	ACCTTTAACAACTTAATCCACTGAGG	59.285	38.462	0.00	0.00	39.47	3.86
2603	15693	1.156736	CGTCCGAAAAGGCACAGAAT	58.843	50.000	0.00	0.00	40.77	2.40
2670	15760	2.568062	TGATAGCGGTACAGGTTTCCAA	59.432	45.455	2.37	0.00	0.00	3.53
3138	16232	2.991250	ACTCCTGAATCAAATGGACCG	58.009	47.619	0.00	0.00	0.00	4.79
3614	16715	9.176460	GTAGAGTATCCTACTTACAGTCAGTTT	57.824	37.037	0.00	0.00	39.59	2.66
3883	16996	3.273434	GAGCATACTGAGCCATGTTCAA	58.727	45.455	6.61	0.00	33.88	2.69
4066	17188	5.536538	ACAAATCTCTTTCCCTTTCAGAACC	59.463	40.000	0.00	0.00	0.00	3.62
4099	17226	8.985315	TGAGATAATAATGCCTCATTTCAAGT	57.015	30.769	0.00	0.00	35.54	3.16
4232	17366	7.521509	ACTCTAGTGAATAACATTACAACGC	57.478	36.000	0.00	0.00	0.00	4.84
4319	17453	1.760192	AAAGACCTGCTCATCATGCC	58.240	50.000	0.00	0.00	0.00	4.40
4464	17598	2.682856	TGTTTGGTTCACTCTGTCAAGC	59.317	45.455	0.00	0.00	0.00	4.01
4530	17664	7.434927	ACTCCCTCTCTAAACTAATAAACCC	57.565	40.000	0.00	0.00	0.00	4.11
4606	17740	3.890147	AGAGGTACTATTTGCTACTCGGG	59.110	47.826	0.00	0.00	41.55	5.14
4607	17741	4.579340	TCAGAGGTACTATTTGCTACTCGG	59.421	45.833	0.00	0.00	41.55	4.63
4608	17742	5.752892	TCAGAGGTACTATTTGCTACTCG	57.247	43.478	0.00	0.00	41.55	4.18
4609	17743	6.752815	GTGTTCAGAGGTACTATTTGCTACTC	59.247	42.308	0.00	0.00	41.55	2.59
4650	17787	8.905660	AGTCTACACACATATACCACTACTAG	57.094	38.462	0.00	0.00	0.00	2.57
4658	17795	7.140048	GCTGTCTAAGTCTACACACATATACC	58.860	42.308	0.00	0.00	0.00	2.73
4659	17796	7.704271	TGCTGTCTAAGTCTACACACATATAC	58.296	38.462	0.00	0.00	0.00	1.47
4660	17797	7.773690	TCTGCTGTCTAAGTCTACACACATATA	59.226	37.037	0.00	0.00	0.00	0.86
4760	17897	1.135141	GTCGCTGAGCTCTGATGAAGT	60.135	52.381	23.35	0.00	0.00	3.01
4790	17930	3.315880	AAGAGCTACCTACCTACCTGG	57.684	52.381	0.00	0.00	42.93	4.45
4791	17931	4.218852	GCATAAGAGCTACCTACCTACCTG	59.781	50.000	0.00	0.00	0.00	4.00
4792	17932	4.106663	AGCATAAGAGCTACCTACCTACCT	59.893	45.833	0.00	0.00	44.50	3.08
4793	17933	4.218852	CAGCATAAGAGCTACCTACCTACC	59.781	50.000	0.00	0.00	44.54	3.18
4794	17934	5.071370	TCAGCATAAGAGCTACCTACCTAC	58.929	45.833	0.00	0.00	44.54	3.18
4795	17935	5.320488	TCAGCATAAGAGCTACCTACCTA	57.680	43.478	0.00	0.00	44.54	3.08
4908	18068	5.071788	TGTGGTCCATAGTGAAATCCCTATC	59.928	44.000	0.00	0.00	0.00	2.08
4913	18073	4.750098	CGTATGTGGTCCATAGTGAAATCC	59.250	45.833	0.00	0.00	36.71	3.01
5007	18183	3.788708	CCCTCCTCCTCCTTTCCTAAATT	59.211	47.826	0.00	0.00	0.00	1.82
5017	18193	1.928480	TGATACTCCCTCCTCCTCCT	58.072	55.000	0.00	0.00	0.00	3.69
5018	18194	2.815158	GATGATACTCCCTCCTCCTCC	58.185	57.143	0.00	0.00	0.00	4.30
5025	18201	4.580995	TCACTCTTTCGATGATACTCCCTC	59.419	45.833	0.00	0.00	0.00	4.30
5026	18202	4.537751	TCACTCTTTCGATGATACTCCCT	58.462	43.478	0.00	0.00	0.00	4.20
5027	18203	4.794655	GCTCACTCTTTCGATGATACTCCC	60.795	50.000	0.00	0.00	0.00	4.30

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.