AutoCloner

Multiple sequence alignment - TraesCS2D01G211400

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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	TraesCS2D01G211400	chr2D	100.000	4625	0	0	1	4625	168596082	168600706	0.000000e+00	8541.0
1	TraesCS2D01G211400	chr2D	96.018	653	8	3	3974	4625	159576842	159577477	0.000000e+00	1046.0
2	TraesCS2D01G211400	chr2D	86.268	619	57	10	1236	1840	69260433	69259829	0.000000e+00	647.0
3	TraesCS2D01G211400	chr2D	77.033	209	38	7	1260	1463	37609059	37609262	1.360000e-20	111.0
4	TraesCS2D01G211400	chr2A	95.420	1572	71	1	2349	3919	181847352	181845781	0.000000e+00	2503.0
5	TraesCS2D01G211400	chr2A	94.282	1609	65	12	540	2138	181849372	181847781	0.000000e+00	2436.0
6	TraesCS2D01G211400	chr2A	93.269	208	12	1	2137	2344	181847603	181847398	5.810000e-79	305.0
7	TraesCS2D01G211400	chr2A	89.778	225	19	3	109	332	181854017	181853796	7.570000e-73	285.0
8	TraesCS2D01G211400	chr2A	79.439	214	15	12	1579	1763	108245336	108245549	1.750000e-24	124.0
9	TraesCS2D01G211400	chr2A	77.512	209	37	7	1260	1463	42471046	42471249	2.920000e-22	117.0
10	TraesCS2D01G211400	chr2A	92.982	57	2	2	3728	3784	181845907	181845853	1.070000e-11	82.4
11	TraesCS2D01G211400	chr2B	92.224	1646	87	16	2289	3919	229621014	229619395	0.000000e+00	2292.0
12	TraesCS2D01G211400	chr2B	93.575	1463	47	18	531	1985	229622902	229621479	0.000000e+00	2137.0
13	TraesCS2D01G211400	chr2B	94.622	688	31	3	3940	4625	357951510	357952193	0.000000e+00	1061.0
14	TraesCS2D01G211400	chr2B	92.354	497	29	3	4	499	229623382	229622894	0.000000e+00	699.0
15	TraesCS2D01G211400	chr2B	88.114	387	34	7	1917	2293	229621479	229621095	2.540000e-122	449.0
16	TraesCS2D01G211400	chr2B	92.647	68	4	1	3728	3794	229619521	229619454	3.810000e-16	97.1
17	TraesCS2D01G211400	chr4D	87.074	1114	93	26	1195	2290	24257840	24256760	0.000000e+00	1212.0
18	TraesCS2D01G211400	chr7B	96.474	709	18	4	3919	4625	10956656	10955953	0.000000e+00	1164.0
19	TraesCS2D01G211400	chr7B	85.152	1017	108	19	1236	2226	500215027	500216026	0.000000e+00	1002.0
20	TraesCS2D01G211400	chr7B	87.169	717	75	10	3919	4624	195333797	195334507	0.000000e+00	798.0
21	TraesCS2D01G211400	chr7D	95.757	707	13	2	3920	4625	90602764	90602074	0.000000e+00	1123.0
22	TraesCS2D01G211400	chr1A	92.635	706	31	12	3920	4623	3592338	3593024	0.000000e+00	996.0
23	TraesCS2D01G211400	chr6A	91.226	718	51	5	3920	4625	101831310	101832027	0.000000e+00	966.0
24	TraesCS2D01G211400	chr5B	83.317	1019	100	27	1236	2226	466536056	466537032	0.000000e+00	876.0
25	TraesCS2D01G211400	chr5B	88.967	707	52	8	3920	4625	579042856	579042175	0.000000e+00	850.0
26	TraesCS2D01G211400	chr5B	88.021	576	60	7	1655	2226	233907245	233906675	0.000000e+00	673.0
27	TraesCS2D01G211400	chr5B	94.030	268	13	2	3920	4184	540864827	540865094	2.000000e-108	403.0
28	TraesCS2D01G211400	chr4B	87.690	723	43	12	3920	4625	576198387	576199080	0.000000e+00	800.0
29	TraesCS2D01G211400	chr3D	85.605	521	57	12	1271	1775	261085446	261085964	8.810000e-147	531.0
30	TraesCS2D01G211400	chr3B	85.714	378	49	4	1852	2226	790628226	790628601	1.210000e-105	394.0
31	TraesCS2D01G211400	chr6B	82.178	202	19	8	1579	1763	670296652	670296853	1.720000e-34	158.0
32	TraesCS2D01G211400	chr1D	83.333	126	21	0	1339	1464	439022344	439022469	2.920000e-22	117.0

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	TraesCS2D01G211400	chr2D	168596082	168600706	4624	False	8541.00	8541	100.00000	1	4625	1	chr2D.!!$F3	4624
1	TraesCS2D01G211400	chr2D	159576842	159577477	635	False	1046.00	1046	96.01800	3974	4625	1	chr2D.!!$F2	651
2	TraesCS2D01G211400	chr2D	69259829	69260433	604	True	647.00	647	86.26800	1236	1840	1	chr2D.!!$R1	604
3	TraesCS2D01G211400	chr2A	181845781	181849372	3591	True	1331.60	2503	93.98825	540	3919	4	chr2A.!!$R2	3379
4	TraesCS2D01G211400	chr2B	229619395	229623382	3987	True	1134.82	2292	91.78280	4	3919	5	chr2B.!!$R1	3915
5	TraesCS2D01G211400	chr2B	357951510	357952193	683	False	1061.00	1061	94.62200	3940	4625	1	chr2B.!!$F1	685
6	TraesCS2D01G211400	chr4D	24256760	24257840	1080	True	1212.00	1212	87.07400	1195	2290	1	chr4D.!!$R1	1095
7	TraesCS2D01G211400	chr7B	10955953	10956656	703	True	1164.00	1164	96.47400	3919	4625	1	chr7B.!!$R1	706
8	TraesCS2D01G211400	chr7B	500215027	500216026	999	False	1002.00	1002	85.15200	1236	2226	1	chr7B.!!$F2	990
9	TraesCS2D01G211400	chr7B	195333797	195334507	710	False	798.00	798	87.16900	3919	4624	1	chr7B.!!$F1	705
10	TraesCS2D01G211400	chr7D	90602074	90602764	690	True	1123.00	1123	95.75700	3920	4625	1	chr7D.!!$R1	705
11	TraesCS2D01G211400	chr1A	3592338	3593024	686	False	996.00	996	92.63500	3920	4623	1	chr1A.!!$F1	703
12	TraesCS2D01G211400	chr6A	101831310	101832027	717	False	966.00	966	91.22600	3920	4625	1	chr6A.!!$F1	705
13	TraesCS2D01G211400	chr5B	466536056	466537032	976	False	876.00	876	83.31700	1236	2226	1	chr5B.!!$F1	990
14	TraesCS2D01G211400	chr5B	579042175	579042856	681	True	850.00	850	88.96700	3920	4625	1	chr5B.!!$R2	705
15	TraesCS2D01G211400	chr5B	233906675	233907245	570	True	673.00	673	88.02100	1655	2226	1	chr5B.!!$R1	571
16	TraesCS2D01G211400	chr4B	576198387	576199080	693	False	800.00	800	87.69000	3920	4625	1	chr4B.!!$F1	705
17	TraesCS2D01G211400	chr3D	261085446	261085964	518	False	531.00	531	85.60500	1271	1775	1	chr3D.!!$F1	504

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
502	504	0.108585	TTCCGCTGCTCCTCAGTTTT	59.891	50.000	44.66	2.43	F
692	694	0.179032	TGCTTTCTTCGCCACCAAGA	60.179	50.000	0.00	3.02	F
1564	1598	0.537188	TCGGGAGATGCTCTGTTTCC	59.463	55.000	0.00	3.13	F
2592	3053	1.081840	GACGCAACAAAGCAGCCTC	60.082	57.895	0.00	4.70	F
3327	3788	0.251698	TGGGCAAACTGATGGATGCA	60.252	50.000	40.51	3.96	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1734	1799	0.670546	ACAGACCACAATTCCGCTCG	60.671	55.000	0.00	0.00	5.03	R
2464	2925	1.247567	ACCTTGCGAAAACCCTGATG	58.752	50.000	0.00	0.00	3.07	R
2868	3329	0.247736	CGGAATCGATCCCATCCCTC	59.752	60.000	0.18	46.39	4.30	R
3501	3969	0.527817	GAGCAGGGTCACCGATAACG	60.528	60.000	0.00	43.47	3.18	R
4581	5098	4.087892	GCTGAGCTCCCTCGCCAA	62.088	66.667	12.15	41.13	4.52	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
43	44	8.915871	ACAATAACAAATGCTCACATACATTC	57.084	30.769	0.00	0.00	35.49	2.67
48	49	6.792326	ACAAATGCTCACATACATTCATGAG	58.208	36.000	0.00	0.00	41.29	2.90
71	72	1.993370	CTTACTCTTAGGCACACACGC	59.007	52.381	0.00	0.00	0.00	5.34
76	77	0.443869	CTTAGGCACACACGCACATC	59.556	55.000	0.00	0.00	0.00	3.06
88	89	3.809832	ACACGCACATCCTATCTTTATGC	59.190	43.478	0.00	0.00	0.00	3.14
95	96	3.284323	TCCTATCTTTATGCGCGTCTC	57.716	47.619	4.79	0.00	0.00	3.36
97	98	2.983136	CCTATCTTTATGCGCGTCTCTG	59.017	50.000	4.79	0.00	0.00	3.35
105	106	1.949465	TGCGCGTCTCTGAGATACTA	58.051	50.000	11.07	0.00	0.00	1.82
107	108	2.288186	TGCGCGTCTCTGAGATACTAAG	59.712	50.000	11.07	1.62	0.00	2.18
120	121	7.014326	TCTGAGATACTAAGCCGACATAACATT	59.986	37.037	0.00	0.00	0.00	2.71
160	161	8.350722	AGTCATCATAAATACGTCGTAGTTGAT	58.649	33.333	24.02	17.71	29.28	2.57
177	178	2.439409	TGATGAAACACATGCTCCCAG	58.561	47.619	0.00	0.00	39.56	4.45
190	191	1.909376	CTCCCAGTACACGAACATCG	58.091	55.000	0.00	0.00	46.93	3.84
241	242	6.210078	TGTTAAAAACTTAAACCCTGATGCG	58.790	36.000	0.00	0.00	0.00	4.73
273	274	6.183360	CCACCACAAGAAAACCTAAACATCTT	60.183	38.462	0.00	0.00	0.00	2.40
275	276	7.860872	CACCACAAGAAAACCTAAACATCTTAC	59.139	37.037	0.00	0.00	0.00	2.34
280	281	8.557029	CAAGAAAACCTAAACATCTTACGAGTT	58.443	33.333	0.00	0.00	0.00	3.01
281	282	9.768662	AAGAAAACCTAAACATCTTACGAGTTA	57.231	29.630	0.00	0.00	0.00	2.24
285	286	5.097529	CCTAAACATCTTACGAGTTACGCA	58.902	41.667	0.00	0.00	46.94	5.24
362	364	1.713297	TACCGAATAGAGGGGAAGGC	58.287	55.000	0.00	0.00	0.00	4.35
388	390	5.662211	TGCGTGTTCTAGAAAAAGTAACC	57.338	39.130	6.78	0.00	0.00	2.85
499	501	2.654079	CCTTCCGCTGCTCCTCAGT	61.654	63.158	0.00	0.00	44.66	3.41
500	502	1.294780	CTTCCGCTGCTCCTCAGTT	59.705	57.895	0.00	0.00	44.66	3.16
501	503	0.321122	CTTCCGCTGCTCCTCAGTTT	60.321	55.000	0.00	0.00	44.66	2.66
502	504	0.108585	TTCCGCTGCTCCTCAGTTTT	59.891	50.000	0.00	0.00	44.66	2.43
503	505	0.603707	TCCGCTGCTCCTCAGTTTTG	60.604	55.000	0.00	0.00	44.66	2.44
504	506	0.886490	CCGCTGCTCCTCAGTTTTGT	60.886	55.000	0.00	0.00	44.66	2.83
505	507	0.947244	CGCTGCTCCTCAGTTTTGTT	59.053	50.000	0.00	0.00	44.66	2.83
506	508	1.334869	CGCTGCTCCTCAGTTTTGTTT	59.665	47.619	0.00	0.00	44.66	2.83
507	509	2.223572	CGCTGCTCCTCAGTTTTGTTTT	60.224	45.455	0.00	0.00	44.66	2.43
508	510	3.734902	CGCTGCTCCTCAGTTTTGTTTTT	60.735	43.478	0.00	0.00	44.66	1.94
509	511	3.553105	GCTGCTCCTCAGTTTTGTTTTTG	59.447	43.478	0.00	0.00	44.66	2.44
510	512	4.747810	CTGCTCCTCAGTTTTGTTTTTGT	58.252	39.130	0.00	0.00	38.02	2.83
511	513	5.146010	TGCTCCTCAGTTTTGTTTTTGTT	57.854	34.783	0.00	0.00	0.00	2.83
512	514	5.546526	TGCTCCTCAGTTTTGTTTTTGTTT	58.453	33.333	0.00	0.00	0.00	2.83
513	515	5.994668	TGCTCCTCAGTTTTGTTTTTGTTTT	59.005	32.000	0.00	0.00	0.00	2.43
514	516	6.484977	TGCTCCTCAGTTTTGTTTTTGTTTTT	59.515	30.769	0.00	0.00	0.00	1.94
535	537	6.530019	TTTTGTTTTTGAGAAAGAGCTCCT	57.470	33.333	10.93	0.00	33.95	3.69
536	538	5.757850	TTGTTTTTGAGAAAGAGCTCCTC	57.242	39.130	10.93	10.70	33.95	3.71
537	539	4.780815	TGTTTTTGAGAAAGAGCTCCTCA	58.219	39.130	10.93	13.33	35.38	3.86
538	540	4.818546	TGTTTTTGAGAAAGAGCTCCTCAG	59.181	41.667	17.21	0.00	38.08	3.35
692	694	0.179032	TGCTTTCTTCGCCACCAAGA	60.179	50.000	0.00	0.00	0.00	3.02
710	712	3.223589	AAAAAGCCCGCGCCTTGT	61.224	55.556	0.00	0.00	34.57	3.16
1367	1388	3.660111	GCCGGCAACAGCTTCGTT	61.660	61.111	24.80	0.00	36.91	3.85
1554	1588	1.739049	GTCCTCTGCTCGGGAGATG	59.261	63.158	0.00	0.00	38.80	2.90
1564	1598	0.537188	TCGGGAGATGCTCTGTTTCC	59.463	55.000	0.00	0.00	0.00	3.13
1681	1743	9.780186	ATATATTCTTTGTACTACTTCCCTTGC	57.220	33.333	0.00	0.00	0.00	4.01
1734	1799	3.251917	CCAATTTGGCGTTTCTTTTGC	57.748	42.857	1.71	0.00	0.00	3.68
2022	2154	1.760192	GTGGCCATGCATTCTTCTCT	58.240	50.000	9.72	0.00	0.00	3.10
2135	2267	8.396272	AGACTTTAGCACTGTGTATTTCAAAT	57.604	30.769	9.86	0.00	0.00	2.32
2183	2495	7.768120	ACTGCAGATTTCTTCTAAGATAACTGG	59.232	37.037	23.35	7.98	37.36	4.00
2279	2598	5.136828	TGGAGCAATTTGGTTCAGTCTTTA	58.863	37.500	5.46	0.00	28.72	1.85
2303	2710	5.339008	TCAGTTATAGGTGGCAACTACTG	57.661	43.478	22.32	22.32	31.46	2.74
2352	2800	6.089551	CGAGTGACACTAAAAATACCACTGAG	59.910	42.308	8.41	0.00	34.06	3.35
2380	2828	7.315142	TGGCATTTTGACTGAGTTTATGATTC	58.685	34.615	0.00	0.00	0.00	2.52
2404	2852	9.725019	TTCTACTGTTGTGAAGAATTATGATGT	57.275	29.630	0.00	0.00	0.00	3.06
2405	2853	9.154847	TCTACTGTTGTGAAGAATTATGATGTG	57.845	33.333	0.00	0.00	0.00	3.21
2426	2874	5.008613	TGTGTATTCAGTTTCACCTTCTTGC	59.991	40.000	0.00	0.00	0.00	4.01
2456	2917	9.394477	GGTCATTGTTAGTTTGTAACATCTTTC	57.606	33.333	0.00	0.00	37.29	2.62
2541	3002	1.181741	TGCGGGGCAGCAAACATTTA	61.182	50.000	4.39	0.00	45.06	1.40
2592	3053	1.081840	GACGCAACAAAGCAGCCTC	60.082	57.895	0.00	0.00	0.00	4.70
2650	3111	2.548920	GGTTCTTCTGGTGAGTCCACTG	60.549	54.545	0.00	0.00	41.93	3.66
2661	3122	4.215370	TCCACTGTGGACCCTGAG	57.785	61.111	25.12	0.00	42.67	3.35
2838	3299	2.880167	GCTCCTTCAGAACCCGGATTTT	60.880	50.000	0.73	0.00	0.00	1.82
2868	3329	0.907486	TCAAGATGCACAGGGAGAGG	59.093	55.000	0.00	0.00	0.00	3.69
2874	3335	1.383803	GCACAGGGAGAGGAGGGAT	60.384	63.158	0.00	0.00	0.00	3.85
2997	3458	0.678048	GTTCCCCTGCACATCCAGTC	60.678	60.000	0.00	0.00	0.00	3.51
3064	3525	1.138859	CGGACCTTAGTGATGGCATGA	59.861	52.381	3.81	0.00	0.00	3.07
3081	3542	0.963355	TGATGCCGGGTAACTTTGGC	60.963	55.000	2.18	2.77	45.47	4.52
3209	3670	0.964358	GCTGCTCATTGCCAAGACCT	60.964	55.000	0.00	0.00	42.00	3.85
3213	3674	1.883638	GCTCATTGCCAAGACCTCACA	60.884	52.381	0.00	0.00	35.15	3.58
3214	3675	2.082231	CTCATTGCCAAGACCTCACAG	58.918	52.381	0.00	0.00	0.00	3.66
3267	3728	2.511600	GGAGGAACGGATGGCACG	60.512	66.667	0.00	0.00	37.36	5.34
3327	3788	0.251698	TGGGCAAACTGATGGATGCA	60.252	50.000	0.00	0.00	40.51	3.96
3357	3818	1.388837	AAATTTGGGGCGCCGATACC	61.389	55.000	22.54	16.79	0.00	2.73
3437	3898	0.464036	ATAGCGATTCCCGACAAGCA	59.536	50.000	0.00	0.00	41.76	3.91
3443	3904	2.632377	GATTCCCGACAAGCATGAGAA	58.368	47.619	0.00	0.00	0.00	2.87
3454	3915	4.461781	ACAAGCATGAGAAATTCTGGGAAG	59.538	41.667	0.00	0.00	0.00	3.46
3510	3978	0.319083	TGGACAAGTGCGTTATCGGT	59.681	50.000	0.00	0.00	37.56	4.69
3534	4002	0.873054	CTGCTCTTGAGCAACACAGG	59.127	55.000	23.12	9.27	44.88	4.00
3883	4353	2.044946	AAGTGCTCCGGCCAATCC	60.045	61.111	2.24	0.00	37.74	3.01
4074	4548	6.251255	TGATCATGATTATGACAGTTGGGA	57.749	37.500	10.14	0.00	45.54	4.37

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
14	15	8.787852	TGTATGTGAGCATTTGTTATTGTACAA	58.212	29.630	11.41	11.41	36.58	2.41
43	44	3.868077	GTGCCTAAGAGTAAGTGCTCATG	59.132	47.826	0.00	0.00	37.94	3.07
48	49	2.737252	GTGTGTGCCTAAGAGTAAGTGC	59.263	50.000	0.00	0.00	0.00	4.40
71	72	3.059884	ACGCGCATAAAGATAGGATGTG	58.940	45.455	5.73	0.00	34.83	3.21
76	77	2.983136	CAGAGACGCGCATAAAGATAGG	59.017	50.000	5.73	0.00	0.00	2.57
88	89	2.350007	GGCTTAGTATCTCAGAGACGCG	60.350	54.545	3.53	3.53	0.00	6.01
95	96	6.073327	TGTTATGTCGGCTTAGTATCTCAG	57.927	41.667	0.00	0.00	0.00	3.35
97	98	7.948278	AAATGTTATGTCGGCTTAGTATCTC	57.052	36.000	0.00	0.00	0.00	2.75
105	106	7.116233	GTCAATTTCAAAATGTTATGTCGGCTT	59.884	33.333	0.00	0.00	0.00	4.35
107	108	6.452350	CGTCAATTTCAAAATGTTATGTCGGC	60.452	38.462	0.00	0.00	0.00	5.54
151	152	4.436050	GGAGCATGTGTTTCATCAACTACG	60.436	45.833	0.00	0.00	36.21	3.51
160	161	2.105649	TGTACTGGGAGCATGTGTTTCA	59.894	45.455	0.00	0.00	0.00	2.69
177	178	3.781341	TTTTCTGCGATGTTCGTGTAC	57.219	42.857	0.00	0.00	42.81	2.90
217	218	6.210078	CGCATCAGGGTTTAAGTTTTTAACA	58.790	36.000	0.00	0.00	0.00	2.41
220	221	4.521256	AGCGCATCAGGGTTTAAGTTTTTA	59.479	37.500	11.47	0.00	0.00	1.52
241	242	1.305201	TTTCTTGTGGTGGAACGAGC	58.695	50.000	0.00	0.00	38.12	5.03
273	274	0.452618	CGAACCGTGCGTAACTCGTA	60.453	55.000	0.00	0.00	42.13	3.43
275	276	3.051171	GCGAACCGTGCGTAACTCG	62.051	63.158	0.00	0.00	43.12	4.18
280	281	4.424566	GGGAGCGAACCGTGCGTA	62.425	66.667	0.00	0.00	37.44	4.42
285	286	3.459063	GCTAGGGGAGCGAACCGT	61.459	66.667	0.00	0.00	42.62	4.83
362	364	2.873170	TTTTCTAGAACACGCATGCG	57.127	45.000	36.79	36.79	46.03	4.73
423	425	4.143333	CTACCGTCCCCACGCAGG	62.143	72.222	0.00	0.00	45.29	4.85
424	426	1.105167	TATCTACCGTCCCCACGCAG	61.105	60.000	0.00	0.00	45.29	5.18
425	427	1.076850	TATCTACCGTCCCCACGCA	60.077	57.895	0.00	0.00	45.29	5.24
426	428	1.361632	GTATCTACCGTCCCCACGC	59.638	63.158	0.00	0.00	45.29	5.34
468	470	1.078918	GGAAGGAAACGGGTACGGG	60.079	63.158	0.00	0.00	46.48	5.28
473	475	2.032071	CAGCGGAAGGAAACGGGT	59.968	61.111	0.00	0.00	0.00	5.28
511	513	6.935167	AGGAGCTCTTTCTCAAAAACAAAAA	58.065	32.000	14.64	0.00	34.84	1.94
512	514	6.152661	TGAGGAGCTCTTTCTCAAAAACAAAA	59.847	34.615	14.64	0.00	34.97	2.44
513	515	5.652014	TGAGGAGCTCTTTCTCAAAAACAAA	59.348	36.000	14.64	0.00	34.97	2.83
514	516	5.192927	TGAGGAGCTCTTTCTCAAAAACAA	58.807	37.500	14.64	0.00	34.97	2.83
515	517	4.780815	TGAGGAGCTCTTTCTCAAAAACA	58.219	39.130	14.64	0.00	34.97	2.83
516	518	5.059833	TCTGAGGAGCTCTTTCTCAAAAAC	58.940	41.667	18.15	0.00	37.13	2.43
517	519	5.296151	TCTGAGGAGCTCTTTCTCAAAAA	57.704	39.130	18.15	7.72	37.13	1.94
518	520	4.963318	TCTGAGGAGCTCTTTCTCAAAA	57.037	40.909	18.15	9.60	37.13	2.44
519	521	4.529769	TGATCTGAGGAGCTCTTTCTCAAA	59.470	41.667	18.15	9.14	37.13	2.69
520	522	4.092279	TGATCTGAGGAGCTCTTTCTCAA	58.908	43.478	18.15	11.64	37.13	3.02
521	523	3.706183	TGATCTGAGGAGCTCTTTCTCA	58.294	45.455	14.64	16.11	36.30	3.27
522	524	4.341806	TGATGATCTGAGGAGCTCTTTCTC	59.658	45.833	14.64	12.25	0.00	2.87
523	525	4.288398	TGATGATCTGAGGAGCTCTTTCT	58.712	43.478	14.64	1.61	0.00	2.52
524	526	4.669206	TGATGATCTGAGGAGCTCTTTC	57.331	45.455	14.64	12.23	0.00	2.62
525	527	4.383989	GGTTGATGATCTGAGGAGCTCTTT	60.384	45.833	14.64	1.93	0.00	2.52
526	528	3.134442	GGTTGATGATCTGAGGAGCTCTT	59.866	47.826	14.64	5.66	0.00	2.85
527	529	2.699846	GGTTGATGATCTGAGGAGCTCT	59.300	50.000	14.64	0.00	0.00	4.09
528	530	2.699846	AGGTTGATGATCTGAGGAGCTC	59.300	50.000	4.71	4.71	0.00	4.09
529	531	2.435069	CAGGTTGATGATCTGAGGAGCT	59.565	50.000	0.00	0.00	0.00	4.09
530	532	2.433604	TCAGGTTGATGATCTGAGGAGC	59.566	50.000	0.00	0.00	33.21	4.70
531	533	4.750021	TTCAGGTTGATGATCTGAGGAG	57.250	45.455	0.00	0.00	38.55	3.69
532	534	4.202192	CGATTCAGGTTGATGATCTGAGGA	60.202	45.833	0.00	0.00	38.55	3.71
533	535	4.056740	CGATTCAGGTTGATGATCTGAGG	58.943	47.826	0.00	0.00	38.55	3.86
534	536	4.744137	GTCGATTCAGGTTGATGATCTGAG	59.256	45.833	0.00	0.00	38.55	3.35
535	537	4.442052	GGTCGATTCAGGTTGATGATCTGA	60.442	45.833	0.00	0.00	35.95	3.27
536	538	3.806521	GGTCGATTCAGGTTGATGATCTG	59.193	47.826	0.00	0.00	0.00	2.90
537	539	3.491619	CGGTCGATTCAGGTTGATGATCT	60.492	47.826	0.00	0.00	0.00	2.75
538	540	2.797156	CGGTCGATTCAGGTTGATGATC	59.203	50.000	0.00	0.00	0.00	2.92
587	589	0.879400	CCGATGAGCTGGTCTGATGC	60.879	60.000	8.47	0.00	0.00	3.91
1331	1339	3.866582	GGGCCCCAGGAGATGACG	61.867	72.222	12.23	0.00	0.00	4.35
1554	1588	4.113354	CAGATACCTAACGGAAACAGAGC	58.887	47.826	0.00	0.00	0.00	4.09
1564	1598	2.427453	ACAGAGTGCCAGATACCTAACG	59.573	50.000	0.00	0.00	0.00	3.18
1671	1733	4.021981	GCTCACAAAATAAGCAAGGGAAGT	60.022	41.667	0.00	0.00	36.06	3.01
1673	1735	3.057596	CGCTCACAAAATAAGCAAGGGAA	60.058	43.478	0.00	0.00	35.76	3.97
1675	1737	2.415893	CCGCTCACAAAATAAGCAAGGG	60.416	50.000	0.00	0.00	35.76	3.95
1676	1738	2.487762	TCCGCTCACAAAATAAGCAAGG	59.512	45.455	0.00	0.00	35.76	3.61
1677	1739	3.189287	ACTCCGCTCACAAAATAAGCAAG	59.811	43.478	0.00	0.00	35.76	4.01
1678	1740	3.146066	ACTCCGCTCACAAAATAAGCAA	58.854	40.909	0.00	0.00	35.76	3.91
1679	1741	2.778299	ACTCCGCTCACAAAATAAGCA	58.222	42.857	0.00	0.00	35.76	3.91
1680	1742	3.058224	ACAACTCCGCTCACAAAATAAGC	60.058	43.478	0.00	0.00	0.00	3.09
1681	1743	4.466828	CACAACTCCGCTCACAAAATAAG	58.533	43.478	0.00	0.00	0.00	1.73
1734	1799	0.670546	ACAGACCACAATTCCGCTCG	60.671	55.000	0.00	0.00	0.00	5.03
1775	1840	8.396390	CAGTGATCAAGATAATCCAGTTCTTTG	58.604	37.037	0.00	0.00	0.00	2.77
2022	2154	1.381872	GGAGGCAGGCTGAGGAGTA	60.382	63.158	20.86	0.00	0.00	2.59
2176	2488	5.716703	CCCACCAAAGAATTTCTCCAGTTAT	59.283	40.000	0.00	0.00	35.03	1.89
2178	2490	3.897505	CCCACCAAAGAATTTCTCCAGTT	59.102	43.478	0.00	0.00	35.03	3.16
2183	2495	5.535030	AGTGTTACCCACCAAAGAATTTCTC	59.465	40.000	0.00	0.00	45.74	2.87
2191	2503	3.283751	TGAACAGTGTTACCCACCAAAG	58.716	45.455	8.88	0.00	45.74	2.77
2279	2598	6.349300	CAGTAGTTGCCACCTATAACTGAAT	58.651	40.000	0.00	0.00	36.13	2.57
2324	2731	7.544566	CAGTGGTATTTTTAGTGTCACTCGTAT	59.455	37.037	9.26	2.33	32.51	3.06
2326	2733	5.694910	CAGTGGTATTTTTAGTGTCACTCGT	59.305	40.000	9.26	0.00	32.51	4.18
2327	2734	5.924254	TCAGTGGTATTTTTAGTGTCACTCG	59.076	40.000	9.26	0.00	32.51	4.18
2345	2752	1.614903	TCAAAATGCCAAGCTCAGTGG	59.385	47.619	0.00	0.00	39.33	4.00
2352	2800	3.375782	AACTCAGTCAAAATGCCAAGC	57.624	42.857	0.00	0.00	0.00	4.01
2380	2828	8.939929	ACACATCATAATTCTTCACAACAGTAG	58.060	33.333	0.00	0.00	0.00	2.57
2404	2852	4.518970	GGCAAGAAGGTGAAACTGAATACA	59.481	41.667	0.00	0.00	36.74	2.29
2405	2853	4.082733	GGGCAAGAAGGTGAAACTGAATAC	60.083	45.833	0.00	0.00	36.74	1.89
2426	2874	5.533154	TGTTACAAACTAACAATGACCAGGG	59.467	40.000	0.00	0.00	34.84	4.45
2456	2917	4.576053	TGCGAAAACCCTGATGAATATGAG	59.424	41.667	0.00	0.00	0.00	2.90
2464	2925	1.247567	ACCTTGCGAAAACCCTGATG	58.752	50.000	0.00	0.00	0.00	3.07
2541	3002	2.002586	CGCCTGACAATCGTCTTCAAT	58.997	47.619	0.00	0.00	43.06	2.57
2592	3053	3.135348	TGAAGATAGATGAACCAGGCTGG	59.865	47.826	31.62	31.62	45.02	4.85
2628	3089	2.103153	TGGACTCACCAGAAGAACCT	57.897	50.000	0.00	0.00	44.64	3.50
2868	3329	0.247736	CGGAATCGATCCCATCCCTC	59.752	60.000	0.18	0.00	46.39	4.30
2874	3335	1.748329	CTCTGGCGGAATCGATCCCA	61.748	60.000	0.18	4.38	46.39	4.37
3064	3525	1.680989	GGCCAAAGTTACCCGGCAT	60.681	57.895	0.00	0.00	46.75	4.40
3081	3542	1.949847	ATGCTTCGACTCCGTCCAGG	61.950	60.000	0.00	0.00	42.97	4.45
3209	3670	3.654021	TGGACCTGCCAACTGTGA	58.346	55.556	0.00	0.00	45.87	3.58
3327	3788	2.181975	CCCCAAATTTGCTCACCATCT	58.818	47.619	12.92	0.00	0.00	2.90
3420	3881	1.091771	CATGCTTGTCGGGAATCGCT	61.092	55.000	0.00	0.00	39.05	4.93
3422	3883	0.933097	CTCATGCTTGTCGGGAATCG	59.067	55.000	0.00	0.00	40.90	3.34
3437	3898	4.826274	TCGACTTCCCAGAATTTCTCAT	57.174	40.909	0.00	0.00	0.00	2.90
3443	3904	4.702131	CCTCAAAATCGACTTCCCAGAATT	59.298	41.667	0.00	0.00	0.00	2.17
3454	3915	1.808411	TCCAGTGCCTCAAAATCGAC	58.192	50.000	0.00	0.00	0.00	4.20
3501	3969	0.527817	GAGCAGGGTCACCGATAACG	60.528	60.000	0.00	0.00	43.47	3.18
3534	4002	4.464008	TGATCTATGGCTTCATGTTTCCC	58.536	43.478	0.00	0.00	32.59	3.97
3907	4377	3.736759	GCTATTTACTCGCTTCTAGTGGC	59.263	47.826	0.00	0.00	0.00	5.01
4036	4510	1.067706	TGATCAATTGCAAAGCACCGG	60.068	47.619	1.71	0.00	38.71	5.28
4074	4548	7.016153	TCTATCAGTTTTCTTACATGTGGGT	57.984	36.000	9.11	0.00	0.00	4.51
4581	5098	4.087892	GCTGAGCTCCCTCGCCAA	62.088	66.667	12.15	0.00	41.13	4.52

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.