AutoCloner

Multiple sequence alignment - TraesCS2B01G123200

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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	TraesCS2B01G123200	chr2B	100.000	2828	0	0	1	2828	90570609	90573436	0.000000e+00	5223
1	TraesCS2B01G123200	chr2D	91.568	1601	91	20	422	1985	57264292	57265885	0.000000e+00	2169
2	TraesCS2B01G123200	chr2D	82.558	774	93	28	2074	2817	469861733	469860972	0.000000e+00	643
3	TraesCS2B01G123200	chr2D	97.753	89	2	0	1972	2060	57265905	57265993	1.360000e-33	154
4	TraesCS2B01G123200	chr2D	93.333	75	4	1	1965	2038	57297804	57297878	2.980000e-20	110
5	TraesCS2B01G123200	chr2A	93.224	1402	74	9	601	1985	58460067	58461464	0.000000e+00	2043
6	TraesCS2B01G123200	chr2A	86.918	795	72	12	2058	2828	661405011	661404225	0.000000e+00	863
7	TraesCS2B01G123200	chr2A	83.002	553	58	15	58	580	58459462	58460008	4.270000e-128	468
8	TraesCS2B01G123200	chr2A	97.802	91	0	1	1972	2060	58461484	58461574	3.770000e-34	156
9	TraesCS2B01G123200	chr7A	89.003	782	61	7	2066	2828	208801889	208802664	0.000000e+00	944
10	TraesCS2B01G123200	chr7A	87.484	791	67	12	2063	2828	605180062	605179279	0.000000e+00	883
11	TraesCS2B01G123200	chr6B	88.665	794	62	14	2058	2828	609644872	609645660	0.000000e+00	942
12	TraesCS2B01G123200	chr5D	83.014	783	93	26	2067	2822	317754962	317755731	0.000000e+00	673
13	TraesCS2B01G123200	chr5D	80.198	808	98	29	2056	2828	541481925	541482705	1.480000e-152	549
14	TraesCS2B01G123200	chr3D	84.091	704	74	22	2128	2821	532767795	532767120	0.000000e+00	645
15	TraesCS2B01G123200	chr3D	81.563	499	80	8	997	1494	114082966	114082479	4.390000e-108	401
16	TraesCS2B01G123200	chr1D	81.024	801	83	36	2058	2808	465459246	465458465	8.790000e-160	573
17	TraesCS2B01G123200	chr1D	80.612	784	97	24	2066	2828	162536335	162535586	3.180000e-154	555
18	TraesCS2B01G123200	chr7D	80.247	810	110	29	2057	2828	464356738	464357535	5.290000e-157	564
19	TraesCS2B01G123200	chr7D	88.725	204	19	4	2058	2260	105649795	105649995	2.180000e-61	246
20	TraesCS2B01G123200	chr7D	87.864	206	17	6	2063	2261	180420995	180420791	4.710000e-58	235
21	TraesCS2B01G123200	chr1A	83.630	562	74	14	2262	2818	235233509	235232961	1.940000e-141	512
22	TraesCS2B01G123200	chr3B	80.055	722	100	17	997	1716	124388814	124389493	1.960000e-136	496
23	TraesCS2B01G123200	chr3B	78.795	797	99	38	2059	2808	6682894	6682121	3.300000e-129	472
24	TraesCS2B01G123200	chr6D	80.156	640	75	26	2058	2669	84299986	84300601	5.600000e-117	431
25	TraesCS2B01G123200	chr5A	80.885	497	52	25	2061	2528	295324110	295323628	4.480000e-93	351
26	TraesCS2B01G123200	chr4A	78.662	553	96	11	997	1549	714048894	714048364	5.800000e-92	348
27	TraesCS2B01G123200	chr4A	88.235	119	14	0	1598	1716	714048347	714048229	2.940000e-30	143

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	TraesCS2B01G123200	chr2B	90570609	90573436	2827	False	5223.0	5223	100.000000	1	2828	1	chr2B.!!$F1	2827
1	TraesCS2B01G123200	chr2D	57264292	57265993	1701	False	1161.5	2169	94.660500	422	2060	2	chr2D.!!$F2	1638
2	TraesCS2B01G123200	chr2D	469860972	469861733	761	True	643.0	643	82.558000	2074	2817	1	chr2D.!!$R1	743
3	TraesCS2B01G123200	chr2A	58459462	58461574	2112	False	889.0	2043	91.342667	58	2060	3	chr2A.!!$F1	2002
4	TraesCS2B01G123200	chr2A	661404225	661405011	786	True	863.0	863	86.918000	2058	2828	1	chr2A.!!$R1	770
5	TraesCS2B01G123200	chr7A	208801889	208802664	775	False	944.0	944	89.003000	2066	2828	1	chr7A.!!$F1	762
6	TraesCS2B01G123200	chr7A	605179279	605180062	783	True	883.0	883	87.484000	2063	2828	1	chr7A.!!$R1	765
7	TraesCS2B01G123200	chr6B	609644872	609645660	788	False	942.0	942	88.665000	2058	2828	1	chr6B.!!$F1	770
8	TraesCS2B01G123200	chr5D	317754962	317755731	769	False	673.0	673	83.014000	2067	2822	1	chr5D.!!$F1	755
9	TraesCS2B01G123200	chr5D	541481925	541482705	780	False	549.0	549	80.198000	2056	2828	1	chr5D.!!$F2	772
10	TraesCS2B01G123200	chr3D	532767120	532767795	675	True	645.0	645	84.091000	2128	2821	1	chr3D.!!$R2	693
11	TraesCS2B01G123200	chr1D	465458465	465459246	781	True	573.0	573	81.024000	2058	2808	1	chr1D.!!$R2	750
12	TraesCS2B01G123200	chr1D	162535586	162536335	749	True	555.0	555	80.612000	2066	2828	1	chr1D.!!$R1	762
13	TraesCS2B01G123200	chr7D	464356738	464357535	797	False	564.0	564	80.247000	2057	2828	1	chr7D.!!$F2	771
14	TraesCS2B01G123200	chr1A	235232961	235233509	548	True	512.0	512	83.630000	2262	2818	1	chr1A.!!$R1	556
15	TraesCS2B01G123200	chr3B	124388814	124389493	679	False	496.0	496	80.055000	997	1716	1	chr3B.!!$F1	719
16	TraesCS2B01G123200	chr3B	6682121	6682894	773	True	472.0	472	78.795000	2059	2808	1	chr3B.!!$R1	749
17	TraesCS2B01G123200	chr6D	84299986	84300601	615	False	431.0	431	80.156000	2058	2669	1	chr6D.!!$F1	611
18	TraesCS2B01G123200	chr4A	714048229	714048894	665	True	245.5	348	83.448500	997	1716	2	chr4A.!!$R1	719

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
817	914	0.105964	CCACGTCCAAAGTCTCCACA	59.894	55.0	0.0	0.0	0.00	4.17	F
1777	1879	0.325933	CTGCATGGACCTCTTCACCA	59.674	55.0	0.0	0.0	38.09	4.17	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1812	1914	0.093026	GCGGTCAAACAGTCGAATCG	59.907	55.000	0.00	0.00	0.00	3.34	R
2679	2910	7.112984	GGAACACGTGTTGAAAATTCATAAGAC	59.887	37.037	36.74	16.35	38.56	3.01	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
20	21	2.225348	CGACAAGTGACGCACATGT	58.775	52.632	16.67	16.67	46.56	3.21
21	22	1.414378	CGACAAGTGACGCACATGTA	58.586	50.000	16.68	0.00	44.47	2.29
22	23	1.386748	CGACAAGTGACGCACATGTAG	59.613	52.381	16.68	13.95	44.47	2.74
23	24	2.404215	GACAAGTGACGCACATGTAGT	58.596	47.619	16.68	1.26	44.47	2.73
24	25	2.155732	GACAAGTGACGCACATGTAGTG	59.844	50.000	16.68	8.63	44.47	2.74
25	26	4.344864	GACAAGTGACGCACATGTAGTGT	61.345	47.826	16.68	11.44	44.47	3.55
36	37	3.381045	ACATGTAGTGTGTCACTTGTCG	58.619	45.455	7.70	0.00	42.59	4.35
37	38	1.847818	TGTAGTGTGTCACTTGTCGC	58.152	50.000	7.70	0.00	42.59	5.19
38	39	1.407618	TGTAGTGTGTCACTTGTCGCT	59.592	47.619	7.70	0.00	42.59	4.93
39	40	2.619646	TGTAGTGTGTCACTTGTCGCTA	59.380	45.455	7.70	0.00	42.59	4.26
40	41	2.135664	AGTGTGTCACTTGTCGCTAC	57.864	50.000	4.27	0.00	42.59	3.58
41	42	1.137513	GTGTGTCACTTGTCGCTACC	58.862	55.000	4.27	0.00	0.00	3.18
42	43	1.037493	TGTGTCACTTGTCGCTACCT	58.963	50.000	4.27	0.00	0.00	3.08
43	44	1.269569	TGTGTCACTTGTCGCTACCTG	60.270	52.381	4.27	0.00	0.00	4.00
44	45	0.317160	TGTCACTTGTCGCTACCTGG	59.683	55.000	0.00	0.00	0.00	4.45
45	46	0.389948	GTCACTTGTCGCTACCTGGG	60.390	60.000	0.00	0.00	0.00	4.45
46	47	0.541063	TCACTTGTCGCTACCTGGGA	60.541	55.000	0.00	0.00	35.14	4.37
47	48	0.108615	CACTTGTCGCTACCTGGGAG	60.109	60.000	0.00	0.00	38.33	4.30
48	49	1.258445	ACTTGTCGCTACCTGGGAGG	61.258	60.000	8.30	0.00	42.49	4.30
80	81	4.077108	CCTTTGGAAGGGGTACTGTTTAC	58.923	47.826	0.00	0.00	45.27	2.01
90	91	7.325725	AGGGGTACTGTTTACTTAGTGATTT	57.674	36.000	0.00	0.00	0.00	2.17
108	109	7.267857	AGTGATTTTGGGTTTTCTTCTCTTTG	58.732	34.615	0.00	0.00	0.00	2.77
110	111	7.222805	GTGATTTTGGGTTTTCTTCTCTTTGTC	59.777	37.037	0.00	0.00	0.00	3.18
111	112	6.850752	TTTTGGGTTTTCTTCTCTTTGTCT	57.149	33.333	0.00	0.00	0.00	3.41
112	113	7.948034	TTTTGGGTTTTCTTCTCTTTGTCTA	57.052	32.000	0.00	0.00	0.00	2.59
113	114	6.937436	TTGGGTTTTCTTCTCTTTGTCTAC	57.063	37.500	0.00	0.00	0.00	2.59
114	115	6.248569	TGGGTTTTCTTCTCTTTGTCTACT	57.751	37.500	0.00	0.00	0.00	2.57
117	118	7.067008	TGGGTTTTCTTCTCTTTGTCTACTTTG	59.933	37.037	0.00	0.00	0.00	2.77
118	119	7.067129	GGGTTTTCTTCTCTTTGTCTACTTTGT	59.933	37.037	0.00	0.00	0.00	2.83
121	122	8.964476	TTTCTTCTCTTTGTCTACTTTGTGAT	57.036	30.769	0.00	0.00	0.00	3.06
122	123	8.964476	TTCTTCTCTTTGTCTACTTTGTGATT	57.036	30.769	0.00	0.00	0.00	2.57
123	124	8.964476	TCTTCTCTTTGTCTACTTTGTGATTT	57.036	30.769	0.00	0.00	0.00	2.17
124	125	9.396022	TCTTCTCTTTGTCTACTTTGTGATTTT	57.604	29.630	0.00	0.00	0.00	1.82
125	126	9.657121	CTTCTCTTTGTCTACTTTGTGATTTTC	57.343	33.333	0.00	0.00	0.00	2.29
127	128	9.396022	TCTCTTTGTCTACTTTGTGATTTTCTT	57.604	29.630	0.00	0.00	0.00	2.52
130	131	9.787532	CTTTGTCTACTTTGTGATTTTCTTTCA	57.212	29.630	0.00	0.00	0.00	2.69
132	133	9.734620	TTGTCTACTTTGTGATTTTCTTTCATG	57.265	29.630	0.00	0.00	0.00	3.07
134	135	9.173939	GTCTACTTTGTGATTTTCTTTCATGTG	57.826	33.333	0.00	0.00	0.00	3.21
135	136	8.902806	TCTACTTTGTGATTTTCTTTCATGTGT	58.097	29.630	0.00	0.00	0.00	3.72
136	137	9.520204	CTACTTTGTGATTTTCTTTCATGTGTT	57.480	29.630	0.00	0.00	0.00	3.32
137	138	8.776376	ACTTTGTGATTTTCTTTCATGTGTTT	57.224	26.923	0.00	0.00	0.00	2.83
138	139	9.218440	ACTTTGTGATTTTCTTTCATGTGTTTT	57.782	25.926	0.00	0.00	0.00	2.43
257	272	9.987272	AAATTTCTCTTTCCTTCCACTTTTATG	57.013	29.630	0.00	0.00	0.00	1.90
264	279	9.635404	TCTTTCCTTCCACTTTTATGAAAACTA	57.365	29.630	0.00	0.00	0.00	2.24
286	301	2.808543	AGATTATTCGGCCGCTCATTTC	59.191	45.455	23.51	12.68	0.00	2.17
289	304	1.392589	ATTCGGCCGCTCATTTCAAT	58.607	45.000	23.51	9.64	0.00	2.57
290	305	0.451383	TTCGGCCGCTCATTTCAATG	59.549	50.000	23.51	0.00	37.75	2.82
297	312	1.137479	CGCTCATTTCAATGGCCCAAT	59.863	47.619	0.00	0.00	37.03	3.16
332	347	9.398170	CTGTATTGAACACGATTCAAAGATTTT	57.602	29.630	18.69	8.04	41.16	1.82
360	375	0.467290	TTGGAAGACCTTGTGCCACC	60.467	55.000	0.00	0.00	37.04	4.61
364	379	0.178990	AAGACCTTGTGCCACCCTTC	60.179	55.000	0.00	0.00	0.00	3.46
400	415	2.599578	GCCATGCCCCCTATGCTG	60.600	66.667	0.00	0.00	0.00	4.41
420	435	4.380550	GCTGTCAAACTAATTTGCCCCTAC	60.381	45.833	0.00	0.00	44.22	3.18
442	457	8.603181	CCTACAGGAACAAAGAAAAACATTTTG	58.397	33.333	0.00	0.00	36.32	2.44
472	509	7.807907	TGAAGAAAAGAACAAAGAAGAACACAC	59.192	33.333	0.00	0.00	0.00	3.82
515	556	1.676014	CGTCGCTCTGGGGAAGAAAAT	60.676	52.381	0.00	0.00	36.37	1.82
522	564	5.567423	CGCTCTGGGGAAGAAAATTTTCAAT	60.567	40.000	28.00	18.28	39.61	2.57
558	600	0.515127	TTGATGCTTTGCACGTACCG	59.485	50.000	0.00	0.00	43.04	4.02
583	628	1.333177	CGCCTCCTCCTAGCATTACT	58.667	55.000	0.00	0.00	0.00	2.24
584	629	1.271102	CGCCTCCTCCTAGCATTACTC	59.729	57.143	0.00	0.00	0.00	2.59
585	630	2.604139	GCCTCCTCCTAGCATTACTCT	58.396	52.381	0.00	0.00	0.00	3.24
586	631	3.768878	GCCTCCTCCTAGCATTACTCTA	58.231	50.000	0.00	0.00	0.00	2.43
587	632	3.761752	GCCTCCTCCTAGCATTACTCTAG	59.238	52.174	0.00	0.00	34.70	2.43
588	633	3.761752	CCTCCTCCTAGCATTACTCTAGC	59.238	52.174	0.00	0.00	33.83	3.42
661	750	3.816994	AGTCTTCATATTAAACCCCGCC	58.183	45.455	0.00	0.00	0.00	6.13
663	752	1.877443	CTTCATATTAAACCCCGCCGG	59.123	52.381	0.00	0.00	37.81	6.13
686	775	6.425114	CGGAGATCGTGAATCCAAATATTTCT	59.575	38.462	0.00	0.00	34.67	2.52
747	836	2.167693	CGCCACCTGTAATTCCAGACTA	59.832	50.000	0.00	0.00	34.23	2.59
775	872	0.770499	TCATGTCCTCCCACTTTGCA	59.230	50.000	0.00	0.00	0.00	4.08
784	881	2.249309	CACTTTGCACACCTCGCG	59.751	61.111	0.00	0.00	0.00	5.87
785	882	2.108157	ACTTTGCACACCTCGCGA	59.892	55.556	9.26	9.26	0.00	5.87
816	913	0.106149	ACCACGTCCAAAGTCTCCAC	59.894	55.000	0.00	0.00	0.00	4.02
817	914	0.105964	CCACGTCCAAAGTCTCCACA	59.894	55.000	0.00	0.00	0.00	4.17
834	931	2.368439	CACACATCACCACCCATAAGG	58.632	52.381	0.00	0.00	43.78	2.69
865	962	3.017048	TCAATCATCCATCAACACCCC	57.983	47.619	0.00	0.00	0.00	4.95
867	964	1.212375	ATCATCCATCAACACCCCGA	58.788	50.000	0.00	0.00	0.00	5.14
885	982	1.135546	CGAATCGATCCTGGATCCTCG	60.136	57.143	26.73	25.23	35.83	4.63
894	991	1.137872	CCTGGATCCTCGAAGACCTTG	59.862	57.143	14.23	0.00	0.00	3.61
899	996	0.970937	TCCTCGAAGACCTTGGCGAT	60.971	55.000	0.00	0.00	31.87	4.58
933	1030	2.607892	GCAATCATCGTAGCCGGCC	61.608	63.158	26.15	7.92	33.95	6.13
972	1070	1.014564	CCAAGAAGAGACGGCGGAAC	61.015	60.000	13.24	1.98	0.00	3.62
1350	1452	3.257561	CGGTTGCTCGCGATCCAG	61.258	66.667	10.36	0.00	0.00	3.86
1668	1770	3.023735	GAGGCCAAGGTGGGGGAT	61.024	66.667	5.01	0.00	38.19	3.85
1774	1876	0.907486	CCTCTGCATGGACCTCTTCA	59.093	55.000	0.00	0.00	0.00	3.02
1777	1879	0.325933	CTGCATGGACCTCTTCACCA	59.674	55.000	0.00	0.00	38.09	4.17
1812	1914	1.062206	GTCATCCGAGTCGTCCGAC	59.938	63.158	12.31	11.70	44.86	4.79
1864	1967	4.792068	TCTCATGAGGGTTTCAGTTTGTT	58.208	39.130	22.42	0.00	39.68	2.83
1873	1976	4.825085	GGGTTTCAGTTTGTTCCTATGACA	59.175	41.667	0.00	0.00	0.00	3.58
1962	2067	0.314935	ATGCTTTTGTCCAAGGCGTG	59.685	50.000	0.00	0.00	0.00	5.34
2142	2293	6.455113	CGCCGAAAAGATTTTTCTATTCGAGA	60.455	38.462	11.25	0.00	28.93	4.04

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
1	2	1.831389	ACATGTGCGTCACTTGTCGC	61.831	55.000	18.71	12.93	45.26	5.19
2	3	1.386748	CTACATGTGCGTCACTTGTCG	59.613	52.381	24.00	18.01	45.26	4.35
3	4	2.155732	CACTACATGTGCGTCACTTGTC	59.844	50.000	24.00	0.00	45.26	3.18
5	6	2.861763	CACTACATGTGCGTCACTTG	57.138	50.000	9.11	17.79	42.61	3.16
15	16	3.381045	CGACAAGTGACACACTACATGT	58.619	45.455	8.59	2.69	44.62	3.21
16	17	2.155732	GCGACAAGTGACACACTACATG	59.844	50.000	8.59	0.00	44.62	3.21
17	18	2.035961	AGCGACAAGTGACACACTACAT	59.964	45.455	8.59	0.00	44.62	2.29
18	19	1.407618	AGCGACAAGTGACACACTACA	59.592	47.619	8.59	0.00	44.62	2.74
19	20	2.135664	AGCGACAAGTGACACACTAC	57.864	50.000	8.59	0.00	44.62	2.73
20	21	2.030540	GGTAGCGACAAGTGACACACTA	60.031	50.000	8.59	0.00	44.62	2.74
22	23	1.137513	GGTAGCGACAAGTGACACAC	58.862	55.000	8.59	0.00	34.10	3.82
23	24	1.037493	AGGTAGCGACAAGTGACACA	58.963	50.000	8.59	0.00	0.00	3.72
24	25	1.419374	CAGGTAGCGACAAGTGACAC	58.581	55.000	0.00	0.00	0.00	3.67
25	26	0.317160	CCAGGTAGCGACAAGTGACA	59.683	55.000	0.00	0.00	0.00	3.58
26	27	0.389948	CCCAGGTAGCGACAAGTGAC	60.390	60.000	0.00	0.00	0.00	3.67
27	28	0.541063	TCCCAGGTAGCGACAAGTGA	60.541	55.000	0.00	0.00	0.00	3.41
28	29	0.108615	CTCCCAGGTAGCGACAAGTG	60.109	60.000	0.00	0.00	0.00	3.16
29	30	1.258445	CCTCCCAGGTAGCGACAAGT	61.258	60.000	0.00	0.00	0.00	3.16
30	31	1.517832	CCTCCCAGGTAGCGACAAG	59.482	63.158	0.00	0.00	0.00	3.16
31	32	3.708210	CCTCCCAGGTAGCGACAA	58.292	61.111	0.00	0.00	0.00	3.18
40	41	1.679898	GTCACTTCCACCTCCCAGG	59.320	63.158	0.00	0.00	42.49	4.45
41	42	0.838122	AGGTCACTTCCACCTCCCAG	60.838	60.000	0.00	0.00	40.54	4.45
42	43	0.401395	AAGGTCACTTCCACCTCCCA	60.401	55.000	0.00	0.00	44.03	4.37
43	44	0.771755	AAAGGTCACTTCCACCTCCC	59.228	55.000	0.00	0.00	44.03	4.30
44	45	1.545651	CCAAAGGTCACTTCCACCTCC	60.546	57.143	0.00	0.00	44.03	4.30
45	46	1.420138	TCCAAAGGTCACTTCCACCTC	59.580	52.381	0.00	0.00	44.03	3.85
47	48	2.230660	CTTCCAAAGGTCACTTCCACC	58.769	52.381	0.00	0.00	35.41	4.61
48	49	2.230660	CCTTCCAAAGGTCACTTCCAC	58.769	52.381	0.00	0.00	43.95	4.02
49	50	2.656947	CCTTCCAAAGGTCACTTCCA	57.343	50.000	0.00	0.00	43.95	3.53
74	75	8.973182	AGAAAACCCAAAATCACTAAGTAAACA	58.027	29.630	0.00	0.00	0.00	2.83
80	81	8.171164	AGAGAAGAAAACCCAAAATCACTAAG	57.829	34.615	0.00	0.00	0.00	2.18
90	91	6.659824	AGTAGACAAAGAGAAGAAAACCCAA	58.340	36.000	0.00	0.00	0.00	4.12
108	109	9.173939	CACATGAAAGAAAATCACAAAGTAGAC	57.826	33.333	0.00	0.00	0.00	2.59
110	111	9.520204	AACACATGAAAGAAAATCACAAAGTAG	57.480	29.630	0.00	0.00	0.00	2.57
111	112	9.868277	AAACACATGAAAGAAAATCACAAAGTA	57.132	25.926	0.00	0.00	0.00	2.24
112	113	8.776376	AAACACATGAAAGAAAATCACAAAGT	57.224	26.923	0.00	0.00	0.00	2.66
222	237	8.585018	GGAAGGAAAGAGAAATTTTGGACATTA	58.415	33.333	0.00	0.00	0.00	1.90
233	248	8.940397	TCATAAAAGTGGAAGGAAAGAGAAAT	57.060	30.769	0.00	0.00	0.00	2.17
234	249	8.760980	TTCATAAAAGTGGAAGGAAAGAGAAA	57.239	30.769	0.00	0.00	0.00	2.52
257	272	4.272748	AGCGGCCGAATAATCTTAGTTTTC	59.727	41.667	33.48	4.03	0.00	2.29
264	279	2.550830	ATGAGCGGCCGAATAATCTT	57.449	45.000	33.48	12.69	0.00	2.40
273	288	1.064621	CCATTGAAATGAGCGGCCG	59.935	57.895	24.05	24.05	38.70	6.13
276	291	1.321805	TGGGCCATTGAAATGAGCGG	61.322	55.000	0.00	0.00	38.70	5.52
286	301	4.124238	CAGAAATGCTTATTGGGCCATTG	58.876	43.478	7.26	0.00	0.00	2.82
289	304	2.818921	ACAGAAATGCTTATTGGGCCA	58.181	42.857	0.00	0.00	0.00	5.36
290	305	5.068987	TCAATACAGAAATGCTTATTGGGCC	59.931	40.000	0.00	0.00	33.38	5.80
297	312	7.609760	ATCGTGTTCAATACAGAAATGCTTA	57.390	32.000	0.00	0.00	37.45	3.09
332	347	5.719173	CACAAGGTCTTCCAAAAGTGAAAA	58.281	37.500	0.00	0.00	35.89	2.29
336	351	2.223805	GGCACAAGGTCTTCCAAAAGTG	60.224	50.000	0.00	0.00	35.89	3.16
344	359	0.178990	AAGGGTGGCACAAGGTCTTC	60.179	55.000	20.82	0.00	44.16	2.87
372	387	1.095807	GGGCATGGCGTAAGGTCTTC	61.096	60.000	13.76	0.00	38.28	2.87
381	396	4.586235	GCATAGGGGGCATGGCGT	62.586	66.667	13.76	2.88	0.00	5.68
445	460	8.356657	TGTGTTCTTCTTTGTTCTTTTCTTCAA	58.643	29.630	0.00	0.00	0.00	2.69
446	461	7.807907	GTGTGTTCTTCTTTGTTCTTTTCTTCA	59.192	33.333	0.00	0.00	0.00	3.02
447	462	7.273598	GGTGTGTTCTTCTTTGTTCTTTTCTTC	59.726	37.037	0.00	0.00	0.00	2.87
455	470	5.102313	CCTTTGGTGTGTTCTTCTTTGTTC	58.898	41.667	0.00	0.00	0.00	3.18
472	509	4.292186	TCTGACCTGAGAATTCCTTTGG	57.708	45.455	0.65	2.55	0.00	3.28
558	600	1.811645	GCTAGGAGGAGGCGTCCATC	61.812	65.000	26.40	18.96	46.80	3.51
583	628	7.831691	AGAAATGAGCTAGAGTAATGCTAGA	57.168	36.000	0.00	0.00	38.03	2.43
584	629	9.973450	TTAAGAAATGAGCTAGAGTAATGCTAG	57.027	33.333	0.00	0.00	37.16	3.42
586	631	9.487790	GATTAAGAAATGAGCTAGAGTAATGCT	57.512	33.333	0.00	0.00	40.02	3.79
587	632	9.265901	TGATTAAGAAATGAGCTAGAGTAATGC	57.734	33.333	0.00	0.00	0.00	3.56
661	750	6.425114	AGAAATATTTGGATTCACGATCTCCG	59.575	38.462	5.17	0.00	45.44	4.63
663	752	7.074502	GCAGAAATATTTGGATTCACGATCTC	58.925	38.462	5.17	0.00	35.02	2.75
747	836	1.698532	GGGAGGACATGATCAGCTGAT	59.301	52.381	29.09	29.09	37.51	2.90
775	872	3.349006	ACGTACGTCGCGAGGTGT	61.349	61.111	36.70	26.42	44.19	4.16
816	913	3.480470	GATCCTTATGGGTGGTGATGTG	58.520	50.000	0.00	0.00	36.25	3.21
817	914	2.443255	GGATCCTTATGGGTGGTGATGT	59.557	50.000	3.84	0.00	36.25	3.06
834	931	5.537295	TGATGGATGATTGAAATGTGGGATC	59.463	40.000	0.00	0.00	0.00	3.36
865	962	1.135546	CGAGGATCCAGGATCGATTCG	60.136	57.143	23.85	23.85	39.72	3.34
867	964	2.294449	TCGAGGATCCAGGATCGATT	57.706	50.000	21.35	10.74	39.72	3.34
885	982	1.808411	TGTTGATCGCCAAGGTCTTC	58.192	50.000	0.00	0.00	35.03	2.87
894	991	3.115892	TCGCGGTTGTTGATCGCC	61.116	61.111	6.13	0.00	45.74	5.54
899	996	1.440145	TTGCATGTCGCGGTTGTTGA	61.440	50.000	6.13	0.00	46.97	3.18
933	1030	1.335142	GCGCCGGAGTAGATTAGAGTG	60.335	57.143	5.05	0.00	0.00	3.51
972	1070	1.140407	GGCGATCGAGTTCTTGACCG	61.140	60.000	21.57	0.00	0.00	4.79
1179	1281	1.377202	GGACATGAGCGGCCAGAAA	60.377	57.895	2.24	0.00	0.00	2.52
1348	1450	1.883544	CGCTGATCTGAGCCTGCTG	60.884	63.158	3.42	0.00	35.36	4.41
1349	1451	2.018727	CTCGCTGATCTGAGCCTGCT	62.019	60.000	3.42	0.00	35.36	4.24
1350	1452	1.592131	CTCGCTGATCTGAGCCTGC	60.592	63.158	3.42	0.00	35.36	4.85
1668	1770	1.377366	GCTCCTCGACGTCCATGAGA	61.377	60.000	17.15	5.00	31.31	3.27
1774	1876	1.211969	CGTCGTCATCGAGGTTGGT	59.788	57.895	0.00	0.00	46.96	3.67
1812	1914	0.093026	GCGGTCAAACAGTCGAATCG	59.907	55.000	0.00	0.00	0.00	3.34
1815	1917	2.591311	GCGCGGTCAAACAGTCGAA	61.591	57.895	8.83	0.00	0.00	3.71
1849	1952	5.070685	GTCATAGGAACAAACTGAAACCCT	58.929	41.667	0.00	0.00	0.00	4.34
1873	1976	0.830648	CATCACATACGGGTCCACCT	59.169	55.000	0.00	0.00	36.97	4.00
1962	2067	7.278868	CAGACAGGAAAAAGAGATGTACATACC	59.721	40.741	8.71	3.61	0.00	2.73
2114	2259	6.455913	CGAATAGAAAAATCTTTTCGGCGGTA	60.456	38.462	17.76	0.00	42.85	4.02
2679	2910	7.112984	GGAACACGTGTTGAAAATTCATAAGAC	59.887	37.037	36.74	16.35	38.56	3.01

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.