AutoCloner

Multiple sequence alignment - TraesCS2A01G407600

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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	TraesCS2A01G407600	chr2A	100.000	8495	0	0	1	8495	663318194	663326688	0.000000e+00	15688.0
1	TraesCS2A01G407600	chr2A	99.581	477	1	1	193	669	663303114	663302639	0.000000e+00	869.0
2	TraesCS2A01G407600	chr2A	97.619	210	3	2	1	209	663303421	663303213	8.110000e-95	359.0
3	TraesCS2A01G407600	chr2A	78.385	421	68	15	6574	6977	655053401	655052987	1.420000e-62	252.0
4	TraesCS2A01G407600	chr2D	97.542	4476	52	12	673	5119	519123554	519128000	0.000000e+00	7603.0
5	TraesCS2A01G407600	chr2D	97.196	1462	24	8	6323	7773	519129480	519130935	0.000000e+00	2457.0
6	TraesCS2A01G407600	chr2D	98.477	788	11	1	5765	6551	519128693	519129480	0.000000e+00	1387.0
7	TraesCS2A01G407600	chr2D	99.027	514	4	1	5112	5625	519128180	519128692	0.000000e+00	920.0
8	TraesCS2A01G407600	chr2D	90.524	496	18	9	8012	8495	519131232	519131710	5.600000e-176	628.0
9	TraesCS2A01G407600	chr2D	96.648	179	6	0	7781	7959	519131053	519131231	1.790000e-76	298.0
10	TraesCS2A01G407600	chr2D	77.984	377	61	13	6621	6977	511945669	511945295	5.160000e-52	217.0
11	TraesCS2A01G407600	chr2B	95.222	4542	149	33	3609	8104	611276961	611281480	0.000000e+00	7123.0
12	TraesCS2A01G407600	chr2B	95.404	2959	98	13	673	3611	611273804	611276744	0.000000e+00	4676.0
13	TraesCS2A01G407600	chr2B	91.288	264	9	5	8238	8495	611281478	611281733	1.760000e-91	348.0
14	TraesCS2A01G407600	chr5A	96.226	477	11	2	193	669	664383520	664383051	0.000000e+00	774.0
15	TraesCS2A01G407600	chr5A	97.143	210	5	1	1	209	664383827	664383618	3.770000e-93	353.0
16	TraesCS2A01G407600	chr5B	95.092	489	8	5	193	670	114443246	114442763	0.000000e+00	756.0
17	TraesCS2A01G407600	chr5B	97.619	210	4	1	1	209	114443554	114443345	8.110000e-95	359.0
18	TraesCS2A01G407600	chr3B	93.424	441	19	3	193	630	749136236	749136669	0.000000e+00	645.0
19	TraesCS2A01G407600	chr3B	98.095	210	3	1	1	209	749135928	749136137	1.740000e-96	364.0
20	TraesCS2A01G407600	chr3B	97.590	83	1	1	588	670	749133048	749132967	3.200000e-29	141.0
21	TraesCS2A01G407600	chr3B	79.487	156	26	6	6818	6969	18496505	18496658	1.170000e-18	106.0
22	TraesCS2A01G407600	chr3B	100.000	44	0	0	1845	1888	44620690	44620647	1.970000e-11	82.4
23	TraesCS2A01G407600	chr6B	81.854	755	120	10	1619	2366	504604650	504603906	3.370000e-173	619.0
24	TraesCS2A01G407600	chr6B	86.920	237	13	7	8262	8492	154906903	154907127	5.090000e-62	250.0
25	TraesCS2A01G407600	chr6D	81.638	757	122	10	1611	2360	318805039	318805785	5.640000e-171	612.0
26	TraesCS2A01G407600	chr6A	81.709	749	120	10	1619	2360	456597725	456598463	7.290000e-170	608.0
27	TraesCS2A01G407600	chr6A	87.500	240	12	8	8262	8495	390131386	390131613	2.350000e-65	261.0
28	TraesCS2A01G407600	chr3D	89.218	473	44	2	198	670	355432424	355431959	1.230000e-162	584.0
29	TraesCS2A01G407600	chr3D	86.469	473	51	6	200	669	221076026	221076488	2.740000e-139	507.0
30	TraesCS2A01G407600	chr3D	85.835	473	53	7	200	669	106553309	106552848	2.760000e-134	490.0
31	TraesCS2A01G407600	chr3D	95.714	210	8	1	1	209	106553623	106553414	3.800000e-88	337.0
32	TraesCS2A01G407600	chr3D	95.714	210	8	1	1	209	221075712	221075921	3.800000e-88	337.0
33	TraesCS2A01G407600	chr3D	97.917	96	2	0	4623	4718	121666967	121666872	5.270000e-37	167.0
34	TraesCS2A01G407600	chr3D	83.439	157	21	3	6818	6971	58555548	58555394	3.200000e-29	141.0
35	TraesCS2A01G407600	chr7D	89.171	434	28	4	194	614	145829392	145829819	2.720000e-144	523.0
36	TraesCS2A01G407600	chr7D	85.865	474	50	7	200	670	586793527	586793986	9.910000e-134	488.0
37	TraesCS2A01G407600	chr7D	95.238	210	9	1	1	209	145829083	145829292	1.770000e-86	331.0
38	TraesCS2A01G407600	chr7D	95.238	210	9	1	1	209	586793213	586793422	1.770000e-86	331.0
39	TraesCS2A01G407600	chr4B	92.958	213	11	3	1	212	208180839	208180630	2.980000e-79	307.0
40	TraesCS2A01G407600	chr7A	86.667	240	14	8	8262	8495	431482916	431483143	5.090000e-62	250.0
41	TraesCS2A01G407600	chr1A	85.833	240	12	10	8262	8495	380359640	380359417	1.430000e-57	235.0
42	TraesCS2A01G407600	chr1A	88.889	72	8	0	6818	6889	14485889	14485818	1.170000e-13	89.8
43	TraesCS2A01G407600	chr5D	76.852	432	68	18	6574	6977	552785568	552785141	1.860000e-51	215.0
44	TraesCS2A01G407600	chr5D	82.803	157	18	5	6818	6971	216147539	216147689	1.920000e-26	132.0
45	TraesCS2A01G407600	chr4A	95.420	131	5	1	7931	8060	389306587	389306717	3.110000e-49	207.0
46	TraesCS2A01G407600	chr4A	100.000	44	0	0	1845	1888	583528374	583528331	1.970000e-11	82.4
47	TraesCS2A01G407600	chr3A	76.952	269	44	10	6709	6971	67773688	67773432	4.140000e-28	137.0
48	TraesCS2A01G407600	chr7B	97.872	47	1	0	1842	1888	77317717	77317763	1.970000e-11	82.4
49	TraesCS2A01G407600	chr1B	97.872	47	1	0	1842	1888	155719959	155720005	1.970000e-11	82.4

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	TraesCS2A01G407600	chr2A	663318194	663326688	8494	False	15688.0	15688	100.000000	1	8495	1	chr2A.!!$F1	8494
1	TraesCS2A01G407600	chr2A	663302639	663303421	782	True	614.0	869	98.600000	1	669	2	chr2A.!!$R2	668
2	TraesCS2A01G407600	chr2D	519123554	519131710	8156	False	2215.5	7603	96.569000	673	8495	6	chr2D.!!$F1	7822
3	TraesCS2A01G407600	chr2B	611273804	611281733	7929	False	4049.0	7123	93.971333	673	8495	3	chr2B.!!$F1	7822
4	TraesCS2A01G407600	chr5A	664383051	664383827	776	True	563.5	774	96.684500	1	669	2	chr5A.!!$R1	668
5	TraesCS2A01G407600	chr5B	114442763	114443554	791	True	557.5	756	96.355500	1	670	2	chr5B.!!$R1	669
6	TraesCS2A01G407600	chr3B	749135928	749136669	741	False	504.5	645	95.759500	1	630	2	chr3B.!!$F2	629
7	TraesCS2A01G407600	chr6B	504603906	504604650	744	True	619.0	619	81.854000	1619	2366	1	chr6B.!!$R1	747
8	TraesCS2A01G407600	chr6D	318805039	318805785	746	False	612.0	612	81.638000	1611	2360	1	chr6D.!!$F1	749
9	TraesCS2A01G407600	chr6A	456597725	456598463	738	False	608.0	608	81.709000	1619	2360	1	chr6A.!!$F2	741
10	TraesCS2A01G407600	chr3D	221075712	221076488	776	False	422.0	507	91.091500	1	669	2	chr3D.!!$F1	668
11	TraesCS2A01G407600	chr3D	106552848	106553623	775	True	413.5	490	90.774500	1	669	2	chr3D.!!$R4	668
12	TraesCS2A01G407600	chr7D	145829083	145829819	736	False	427.0	523	92.204500	1	614	2	chr7D.!!$F1	613
13	TraesCS2A01G407600	chr7D	586793213	586793986	773	False	409.5	488	90.551500	1	670	2	chr7D.!!$F2	669

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
684	822	0.999712	TCCCCTTTTGCCCTAAGGAG	59.000	55.000	9.48	44.01	3.69	F
2323	2466	0.036388	GGAAGCTGATTGGTCGTGGA	60.036	55.000	0.00	0.00	4.02	F
3207	3368	2.896685	CAATGCCCACCTTAAAGGAACA	59.103	45.455	0.00	37.67	3.18	F
3288	3449	3.615110	CGCGCCTAGTGGATATGATTCTT	60.615	47.826	0.00	34.57	2.52	F
3289	3450	4.380550	CGCGCCTAGTGGATATGATTCTTA	60.381	45.833	0.00	34.57	2.10	F
5492	6098	1.667724	CTTCTGCCAGATAACAAGCCG	59.332	52.381	0.00	0.00	5.52	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2439	2582	0.320771	AGTTACGCAAGCACCTCAGG	60.321	55.000	0.00	0.00	45.62	3.86	R
3423	3584	3.315191	ACCATATCATGCTTTAACACGCC	59.685	43.478	0.00	0.00	0.00	5.68	R
4571	4957	7.984050	CCATATATATGCAACCAAAACAAACCA	59.016	33.333	16.08	0.00	32.40	3.67	R
5237	5840	3.119919	GCAGGAAGCAGAAAGTCAATCTG	60.120	47.826	0.00	0.00	45.65	2.90	R
5709	6316	8.637986	TGTGGACAAAATTATATTTATCTGCCC	58.362	33.333	0.00	0.00	0.00	5.36	R
7904	8863	0.732571	ATGTAATTGAACGCAGGCGG	59.267	50.000	18.63	0.14	44.69	6.13	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
670	808	3.117625	GGGGTTAAAATCGATTCTCCCCT	60.118	47.826	30.43	10.49	46.96	4.79
671	809	4.533815	GGGTTAAAATCGATTCTCCCCTT	58.466	43.478	11.83	3.44	0.00	3.95
684	822	0.999712	TCCCCTTTTGCCCTAAGGAG	59.000	55.000	9.48	0.00	44.01	3.69
689	827	1.815003	CTTTTGCCCTAAGGAGTGCTG	59.185	52.381	0.00	0.00	33.47	4.41
695	833	1.021390	CCTAAGGAGTGCTGTTGGCG	61.021	60.000	0.00	0.00	45.43	5.69
773	911	8.995220	TGTGTTAGACTTTAATGTGTATGGAAC	58.005	33.333	0.00	0.00	0.00	3.62
779	917	7.942341	AGACTTTAATGTGTATGGAACTGGAAA	59.058	33.333	0.00	0.00	0.00	3.13
813	951	4.111577	TGGAATCTTACTCCATCTTGGGT	58.888	43.478	0.00	0.00	38.07	4.51
832	970	4.837860	TGGGTTCTTGGTTTTGCAGATATT	59.162	37.500	0.00	0.00	0.00	1.28
849	987	1.448985	ATTGTTCCATTGTCGGTCCG	58.551	50.000	4.39	4.39	0.00	4.79
859	997	2.049802	TCGGTCCGTCGTGAAAGC	60.050	61.111	11.88	0.00	0.00	3.51
861	999	3.110178	GGTCCGTCGTGAAAGCCG	61.110	66.667	0.00	0.00	0.00	5.52
960	1100	2.226330	GGTAACATTGTGGTGACTGCA	58.774	47.619	0.00	0.00	0.00	4.41
962	1102	1.761449	AACATTGTGGTGACTGCACA	58.239	45.000	0.00	0.00	46.96	4.57
965	1105	1.174712	ATTGTGGTGACTGCACAGCC	61.175	55.000	4.29	0.00	46.96	4.85
989	1129	6.014499	CCGGTTAGATATACCACAGATCCTTT	60.014	42.308	0.00	0.00	35.31	3.11
1131	1271	3.978855	GCACAAAATCAAAACGGAGGTAC	59.021	43.478	0.00	0.00	0.00	3.34
1311	1451	0.801251	GCACTGCTTCTGATGTCACC	59.199	55.000	0.00	0.00	0.00	4.02
1413	1553	5.809001	AGGTCAGAAATAGTGATTGCTTCA	58.191	37.500	0.00	0.00	26.96	3.02
1660	1800	3.555956	GTGCTATCACCACCAAGAATACG	59.444	47.826	0.00	0.00	37.24	3.06
1840	1980	4.956700	AGAAGTCCGAGAAGAATATGTCCA	59.043	41.667	0.00	0.00	0.00	4.02
2323	2466	0.036388	GGAAGCTGATTGGTCGTGGA	60.036	55.000	0.00	0.00	0.00	4.02
3207	3368	2.896685	CAATGCCCACCTTAAAGGAACA	59.103	45.455	0.00	0.00	37.67	3.18
3288	3449	3.615110	CGCGCCTAGTGGATATGATTCTT	60.615	47.826	0.00	0.00	34.57	2.52
3289	3450	4.380550	CGCGCCTAGTGGATATGATTCTTA	60.381	45.833	0.00	0.00	34.57	2.10
3290	3451	4.865365	GCGCCTAGTGGATATGATTCTTAC	59.135	45.833	0.00	0.00	34.57	2.34
3291	3452	5.336849	GCGCCTAGTGGATATGATTCTTACT	60.337	44.000	0.00	0.00	34.57	2.24
3292	3453	6.692486	CGCCTAGTGGATATGATTCTTACTT	58.308	40.000	0.00	0.00	34.57	2.24
3293	3454	7.155328	CGCCTAGTGGATATGATTCTTACTTT	58.845	38.462	0.00	0.00	34.57	2.66
3294	3455	7.329717	CGCCTAGTGGATATGATTCTTACTTTC	59.670	40.741	0.00	0.00	34.57	2.62
3295	3456	8.371699	GCCTAGTGGATATGATTCTTACTTTCT	58.628	37.037	0.00	0.00	34.57	2.52
3423	3584	9.823647	AGTCACTGAATTCTAGTTACCATATTG	57.176	33.333	7.05	0.00	0.00	1.90
3787	4170	6.925610	TTATTCAGTGGCATCACATAGTTC	57.074	37.500	0.00	0.00	45.91	3.01
4571	4957	7.380423	AGAATACAGTCCATAGGTAGCATTT	57.620	36.000	0.00	0.00	0.00	2.32
4572	4958	7.220030	AGAATACAGTCCATAGGTAGCATTTG	58.780	38.462	0.00	0.00	0.00	2.32
4730	5122	7.255139	GCTAAACATGTAAGTTTTCTGGTCACT	60.255	37.037	0.00	0.00	41.58	3.41
5237	5840	6.792726	GTCGATTAAACTTTGAGTTCAGCTTC	59.207	38.462	0.00	0.00	37.47	3.86
5492	6098	1.667724	CTTCTGCCAGATAACAAGCCG	59.332	52.381	0.00	0.00	0.00	5.52
5712	6319	5.757808	TGCTGAAAAAGAAAATAAACTGGGC	59.242	36.000	0.00	0.00	0.00	5.36
5714	6321	6.073602	GCTGAAAAAGAAAATAAACTGGGCAG	60.074	38.462	0.00	0.00	0.00	4.85
5716	6323	7.734942	TGAAAAAGAAAATAAACTGGGCAGAT	58.265	30.769	0.00	0.00	0.00	2.90
6172	6780	6.860080	TGTAGACCGAATTCTAAGGTAACAG	58.140	40.000	3.52	0.00	38.57	3.16
6331	6939	3.264450	AGGGTCAGACAATTTACCAGAGG	59.736	47.826	2.17	0.00	33.46	3.69
6419	7255	1.338294	ACACACACTGTCGTCCAAACA	60.338	47.619	0.00	0.00	0.00	2.83
6543	7379	8.562949	TTTCTACTGCCTATATCCTAAAAGGT	57.437	34.615	0.00	0.00	36.53	3.50
6751	7593	4.317980	CCACACAAAAATGACAATTGCGAC	60.318	41.667	5.05	0.00	0.00	5.19
6815	7659	7.149973	AGAAATCACCATTTTGACATTCTGTG	58.850	34.615	0.00	0.00	35.35	3.66
6981	7828	3.086282	TCCAAAAATCCGCTTTCCCTAC	58.914	45.455	0.00	0.00	0.00	3.18
7006	7853	3.248602	GTGGACTATTCATTAAGCAGGCG	59.751	47.826	0.00	0.00	0.00	5.52
7015	7862	1.550130	TTAAGCAGGCGCCTAGGTGT	61.550	55.000	32.30	19.15	39.83	4.16
7326	8173	0.252284	CTACTCCCCTGTCTGGTGGT	60.252	60.000	0.00	0.00	0.00	4.16
7370	8217	4.646945	TCATTCAAAGCAACCAACCTACAA	59.353	37.500	0.00	0.00	0.00	2.41
7480	8328	1.003580	GCATCAAGTCTCACAGGGGAA	59.996	52.381	0.00	0.00	0.00	3.97
7699	8547	3.778954	ACTATCAAGGATAGGCCAAGC	57.221	47.619	5.01	0.00	44.33	4.01
7773	8621	4.012374	CCAGTCAGTGGCTTGAATTGTAT	58.988	43.478	0.00	0.00	40.39	2.29
7774	8622	4.095483	CCAGTCAGTGGCTTGAATTGTATC	59.905	45.833	0.00	0.00	40.39	2.24
7775	8623	4.696877	CAGTCAGTGGCTTGAATTGTATCA	59.303	41.667	0.00	0.00	0.00	2.15
7776	8624	5.356190	CAGTCAGTGGCTTGAATTGTATCAT	59.644	40.000	0.00	0.00	0.00	2.45
7777	8625	6.539826	CAGTCAGTGGCTTGAATTGTATCATA	59.460	38.462	0.00	0.00	0.00	2.15
7778	8626	7.066163	CAGTCAGTGGCTTGAATTGTATCATAA	59.934	37.037	0.00	0.00	0.00	1.90
7779	8627	7.776969	AGTCAGTGGCTTGAATTGTATCATAAT	59.223	33.333	0.00	0.00	0.00	1.28
7904	8863	8.002665	GTCACGATCTTACAGTTTTTAGTTGAC	58.997	37.037	0.00	0.00	0.00	3.18
7961	8920	0.667993	ACCTTCAATGTTGTGTGCCG	59.332	50.000	0.00	0.00	0.00	5.69
7963	8922	0.030504	CTTCAATGTTGTGTGCCGCA	59.969	50.000	0.00	0.00	0.00	5.69
7976	8935	1.086696	TGCCGCATTTTCTAGCACTC	58.913	50.000	0.00	0.00	0.00	3.51
7977	8936	1.086696	GCCGCATTTTCTAGCACTCA	58.913	50.000	0.00	0.00	0.00	3.41
8054	9014	4.276678	TCAAAATGTTCTCCTGAGCTTGTG	59.723	41.667	0.00	0.00	0.00	3.33
8073	9033	6.926272	GCTTGTGGAACTATAGAGTTAGGATG	59.074	42.308	6.78	0.00	46.23	3.51
8074	9034	6.406692	TGTGGAACTATAGAGTTAGGATGC	57.593	41.667	6.78	0.00	46.23	3.91
8075	9035	5.897250	TGTGGAACTATAGAGTTAGGATGCA	59.103	40.000	6.78	0.00	46.23	3.96
8076	9036	6.183360	TGTGGAACTATAGAGTTAGGATGCAC	60.183	42.308	6.78	3.46	46.23	4.57
8077	9037	5.009710	TGGAACTATAGAGTTAGGATGCACG	59.990	44.000	6.78	0.00	46.23	5.34
8079	9039	6.071840	GGAACTATAGAGTTAGGATGCACGAT	60.072	42.308	6.78	0.00	46.23	3.73
8080	9040	6.260870	ACTATAGAGTTAGGATGCACGATG	57.739	41.667	6.78	0.00	28.61	3.84
8087	9053	2.996249	AGGATGCACGATGAAGACAT	57.004	45.000	0.00	0.00	39.67	3.06
8139	9105	2.116869	TATGAGATGCCAGCCCCTAA	57.883	50.000	0.00	0.00	0.00	2.69
8166	9132	1.600023	TGACTTGTTTTAGTGCCCCG	58.400	50.000	0.00	0.00	0.00	5.73
8169	9135	1.134037	ACTTGTTTTAGTGCCCCGTCA	60.134	47.619	0.00	0.00	0.00	4.35
8173	9139	2.554893	TGTTTTAGTGCCCCGTCATTTC	59.445	45.455	0.00	0.00	0.00	2.17
8178	9144	3.140814	GCCCCGTCATTTCCCAGC	61.141	66.667	0.00	0.00	0.00	4.85
8197	9163	4.180817	CAGCGTTATGTGGTAAGTCATGA	58.819	43.478	0.00	0.00	0.00	3.07
8246	9212	3.740115	TCCACACTTGAGCCTTTACTTC	58.260	45.455	0.00	0.00	0.00	3.01
8263	9229	3.664107	ACTTCTTCAAGCATCGCACTTA	58.336	40.909	0.00	0.00	32.09	2.24
8321	9293	7.865707	ACTAATTTTGCTCTTTATATCGCAGG	58.134	34.615	0.00	0.00	33.48	4.85
8322	9294	4.552166	TTTTGCTCTTTATATCGCAGGC	57.448	40.909	0.00	0.00	33.48	4.85
8323	9295	2.169832	TGCTCTTTATATCGCAGGCC	57.830	50.000	0.00	0.00	0.00	5.19
8324	9296	1.416030	TGCTCTTTATATCGCAGGCCA	59.584	47.619	5.01	0.00	0.00	5.36
8325	9297	2.038952	TGCTCTTTATATCGCAGGCCAT	59.961	45.455	5.01	0.00	0.00	4.40
8326	9298	2.675348	GCTCTTTATATCGCAGGCCATC	59.325	50.000	5.01	0.00	0.00	3.51
8327	9299	3.265791	CTCTTTATATCGCAGGCCATCC	58.734	50.000	5.01	0.00	0.00	3.51
8328	9300	2.637382	TCTTTATATCGCAGGCCATCCA	59.363	45.455	5.01	0.00	33.74	3.41
8329	9301	3.264193	TCTTTATATCGCAGGCCATCCAT	59.736	43.478	5.01	0.00	33.74	3.41

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
8	9	1.474330	GATGGGGATGAAAAACCGCT	58.526	50.000	0.00	0.00	39.38	5.52
689	827	2.422127	ACAGTATTAACCATGCGCCAAC	59.578	45.455	4.18	0.00	0.00	3.77
695	833	6.021596	CAGTTCGAAACAGTATTAACCATGC	58.978	40.000	0.00	0.00	0.00	4.06
779	917	5.810095	AGTAAGATTCCAGCTAGCACTTTT	58.190	37.500	18.83	4.47	0.00	2.27
813	951	6.041409	TGGAACAATATCTGCAAAACCAAGAA	59.959	34.615	0.00	0.00	31.92	2.52
849	987	2.027625	CACCCTCGGCTTTCACGAC	61.028	63.158	0.00	0.00	36.25	4.34
859	997	3.443045	GGCATGCAACACCCTCGG	61.443	66.667	21.36	0.00	0.00	4.63
861	999	1.134946	GTTATGGCATGCAACACCCTC	59.865	52.381	21.36	0.00	0.00	4.30
929	1069	5.596361	ACCACAATGTTACCAAAACTGATCA	59.404	36.000	0.00	0.00	0.00	2.92
956	1096	2.533266	ATATCTAACCGGCTGTGCAG	57.467	50.000	0.00	0.00	0.00	4.41
960	1100	3.302161	TGTGGTATATCTAACCGGCTGT	58.698	45.455	0.00	0.00	40.08	4.40
962	1102	3.840991	TCTGTGGTATATCTAACCGGCT	58.159	45.455	0.00	0.00	40.08	5.52
965	1105	6.591750	AAGGATCTGTGGTATATCTAACCG	57.408	41.667	0.00	0.00	40.08	4.44
989	1129	5.818857	CACCATGATGGCATATCGAATATGA	59.181	40.000	12.25	1.21	42.67	2.15
1029	1169	5.096443	TGGTGGTTTTCTTTGCATCTTTT	57.904	34.783	0.00	0.00	0.00	2.27
1131	1271	1.588404	GTTGTATCATCGCCACGTCTG	59.412	52.381	0.00	0.00	0.00	3.51
1243	1383	1.092348	GGAAGCGGTTGGGAATGTAC	58.908	55.000	3.70	0.00	0.00	2.90
1311	1451	6.633500	TTTTCTAATATGGGCCTTGATTCG	57.367	37.500	4.53	0.00	0.00	3.34
1660	1800	1.742268	GCTGTCTTTGCCATCTCCTTC	59.258	52.381	0.00	0.00	0.00	3.46
1840	1980	3.525199	AGGCTGAAGTTGGAATATGGTCT	59.475	43.478	0.00	0.00	0.00	3.85
2323	2466	5.916318	CCAACATATACATGGCCAAATGTT	58.084	37.500	16.89	18.56	41.09	2.71
2439	2582	0.320771	AGTTACGCAAGCACCTCAGG	60.321	55.000	0.00	0.00	45.62	3.86
2690	2839	7.208080	TCCTTTGACAAACAGAAGTAGTAGTC	58.792	38.462	0.00	0.00	0.00	2.59
2913	3065	0.865218	TTCTGTTTGCAAAGCGCGTG	60.865	50.000	13.26	5.65	46.97	5.34
3288	3449	5.970640	AGGGATGTCCAATCCTAAGAAAGTA	59.029	40.000	4.46	0.00	38.26	2.24
3289	3450	4.790790	AGGGATGTCCAATCCTAAGAAAGT	59.209	41.667	4.46	0.00	38.26	2.66
3290	3451	5.379706	AGGGATGTCCAATCCTAAGAAAG	57.620	43.478	4.46	0.00	38.26	2.62
3291	3452	5.163195	GCTAGGGATGTCCAATCCTAAGAAA	60.163	44.000	4.46	0.00	38.26	2.52
3292	3453	4.348168	GCTAGGGATGTCCAATCCTAAGAA	59.652	45.833	4.46	0.00	38.26	2.52
3293	3454	3.904339	GCTAGGGATGTCCAATCCTAAGA	59.096	47.826	4.46	0.00	38.26	2.10
3294	3455	3.648067	TGCTAGGGATGTCCAATCCTAAG	59.352	47.826	4.46	3.93	38.26	2.18
3295	3456	3.391296	GTGCTAGGGATGTCCAATCCTAA	59.609	47.826	4.46	0.00	38.26	2.69
3423	3584	3.315191	ACCATATCATGCTTTAACACGCC	59.685	43.478	0.00	0.00	0.00	5.68
3787	4170	6.404844	CGGTCATCATATAGTACTAGCAAGGG	60.405	46.154	8.85	0.00	0.00	3.95
4571	4957	7.984050	CCATATATATGCAACCAAAACAAACCA	59.016	33.333	16.08	0.00	32.40	3.67
4572	4958	8.200792	TCCATATATATGCAACCAAAACAAACC	58.799	33.333	16.08	0.00	32.40	3.27
4730	5122	8.654485	TTATTACCGTATAAGAGAGGCCATTA	57.346	34.615	5.01	0.00	0.00	1.90
5224	5827	4.965814	AGTCAATCTGAAGCTGAACTCAA	58.034	39.130	0.00	0.00	0.00	3.02
5237	5840	3.119919	GCAGGAAGCAGAAAGTCAATCTG	60.120	47.826	0.00	0.00	45.65	2.90
5709	6316	8.637986	TGTGGACAAAATTATATTTATCTGCCC	58.362	33.333	0.00	0.00	0.00	5.36
5724	6331	5.539574	TCCATTCATCTGTTGTGGACAAAAT	59.460	36.000	0.00	0.00	37.93	1.82
5855	6462	4.202315	ACCAACCAAAAATGGAAGCCTTAC	60.202	41.667	1.10	0.00	39.12	2.34
6027	6635	1.696832	GCCGTTGAGAAGGATCACGC	61.697	60.000	0.00	0.00	0.00	5.34
6172	6780	7.222224	CCCGATATGTCAGTTACAAAGAAGTAC	59.778	40.741	0.00	0.00	42.70	2.73
6331	6939	3.945285	TCGAAGAATATTTTGCACCCCTC	59.055	43.478	0.00	0.00	0.00	4.30
6419	7255	4.021456	GGGTTACTGGCTTACTGCAAAAAT	60.021	41.667	0.00	0.00	45.15	1.82
6529	7365	8.745149	TGCCACCTATAACCTTTTAGGATATA	57.255	34.615	8.16	1.64	37.67	0.86
6543	7379	0.978667	TGCGACCCTGCCACCTATAA	60.979	55.000	0.00	0.00	0.00	0.98
6706	7548	6.094881	GTGGCTAGCATGGTTACTTATTTCAA	59.905	38.462	18.24	0.00	0.00	2.69
6751	7593	2.892852	TGCCCTGTTCATCTTTCCAAAG	59.107	45.455	0.00	0.00	37.36	2.77
6811	7653	8.882736	TGATGAAATAAGTAAGCATGTACACAG	58.117	33.333	0.00	0.00	0.00	3.66
6815	7659	8.208718	TGGTGATGAAATAAGTAAGCATGTAC	57.791	34.615	0.00	0.00	0.00	2.90
6981	7828	5.278169	GCCTGCTTAATGAATAGTCCACATG	60.278	44.000	0.00	0.00	0.00	3.21
7006	7853	1.078848	CTGTCCAGCACACCTAGGC	60.079	63.158	9.30	0.00	0.00	3.93
7015	7862	1.915266	CCCTCCTGTCTGTCCAGCA	60.915	63.158	0.00	0.00	0.00	4.41
7326	8173	9.077885	GAATGATTAAAGGGAATAGCACCATTA	57.922	33.333	0.00	0.00	31.12	1.90
7480	8328	5.951747	GCTTCAGATACTATCCTCTCCTGAT	59.048	44.000	0.00	0.00	0.00	2.90
7883	8841	6.304882	GCGGTCAACTAAAAACTGTAAGATC	58.695	40.000	0.00	0.00	37.43	2.75
7904	8863	0.732571	ATGTAATTGAACGCAGGCGG	59.267	50.000	18.63	0.14	44.69	6.13
7961	8920	4.756084	AGTTGTGAGTGCTAGAAAATGC	57.244	40.909	0.00	0.00	0.00	3.56
7963	8922	7.040478	TGCATTTAGTTGTGAGTGCTAGAAAAT	60.040	33.333	0.00	0.00	33.95	1.82
7976	8935	4.305989	ACCAGTTGTGCATTTAGTTGTG	57.694	40.909	0.00	0.00	0.00	3.33
7977	8936	5.337578	AAACCAGTTGTGCATTTAGTTGT	57.662	34.783	0.00	0.00	0.00	3.32
8054	9014	5.241064	TCGTGCATCCTAACTCTATAGTTCC	59.759	44.000	0.00	0.00	42.42	3.62
8073	9033	6.344572	TGTGTATTTATGTCTTCATCGTGC	57.655	37.500	0.00	0.00	35.70	5.34
8074	9034	9.773328	AAATTGTGTATTTATGTCTTCATCGTG	57.227	29.630	0.00	0.00	34.69	4.35
8075	9035	9.988350	GAAATTGTGTATTTATGTCTTCATCGT	57.012	29.630	0.00	0.00	36.59	3.73
8076	9036	9.438291	GGAAATTGTGTATTTATGTCTTCATCG	57.562	33.333	0.00	0.00	36.59	3.84
8079	9039	9.739276	AGAGGAAATTGTGTATTTATGTCTTCA	57.261	29.630	0.00	0.00	36.59	3.02
8123	9089	0.767375	TCATTAGGGGCTGGCATCTC	59.233	55.000	2.88	0.00	0.00	2.75
8124	9090	1.453633	ATCATTAGGGGCTGGCATCT	58.546	50.000	2.88	2.59	0.00	2.90
8139	9105	7.363793	GGGGCACTAAAACAAGTCATTAATCAT	60.364	37.037	0.00	0.00	0.00	2.45
8166	9132	2.097466	CCACATAACGCTGGGAAATGAC	59.903	50.000	14.31	0.00	0.00	3.06
8169	9135	2.507407	ACCACATAACGCTGGGAAAT	57.493	45.000	0.00	0.00	0.00	2.17
8173	9139	2.277084	GACTTACCACATAACGCTGGG	58.723	52.381	0.00	0.00	0.00	4.45
8178	9144	4.180817	TGCTCATGACTTACCACATAACG	58.819	43.478	0.00	0.00	0.00	3.18
8197	9163	7.004555	TCCAGTTCATATATTTACGGATGCT	57.995	36.000	0.00	0.00	0.00	3.79
8246	9212	4.398247	GAAAGTAAGTGCGATGCTTGAAG	58.602	43.478	0.00	0.00	0.00	3.02
8263	9229	0.759346	AGCTTCAGTGTCCCGAAAGT	59.241	50.000	0.00	0.00	0.00	2.66
8310	9282	2.092968	GGATGGATGGCCTGCGATATAA	60.093	50.000	3.32	0.00	34.31	0.98
8321	9293	0.406750	TGGATGGATGGATGGATGGC	59.593	55.000	0.00	0.00	0.00	4.40
8322	9294	2.357881	GGATGGATGGATGGATGGATGG	60.358	54.545	0.00	0.00	0.00	3.51
8323	9295	2.357881	GGGATGGATGGATGGATGGATG	60.358	54.545	0.00	0.00	0.00	3.51
8324	9296	1.928077	GGGATGGATGGATGGATGGAT	59.072	52.381	0.00	0.00	0.00	3.41
8325	9297	1.131970	AGGGATGGATGGATGGATGGA	60.132	52.381	0.00	0.00	0.00	3.41
8326	9298	1.005569	CAGGGATGGATGGATGGATGG	59.994	57.143	0.00	0.00	0.00	3.51
8327	9299	1.709115	ACAGGGATGGATGGATGGATG	59.291	52.381	0.00	0.00	0.00	3.51
8328	9300	2.144800	ACAGGGATGGATGGATGGAT	57.855	50.000	0.00	0.00	0.00	3.41
8329	9301	1.911454	AACAGGGATGGATGGATGGA	58.089	50.000	0.00	0.00	0.00	3.41

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.