AutoCloner

Multiple sequence alignment - TraesCS7B01G043800

Loading Multiple Alignment...

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	TraesCS7B01G043800	chr7B	100.000	2645	0	0	1	2645	43671563	43674207	0.000000e+00	4885.0
1	TraesCS7B01G043800	chr7B	90.732	410	28	7	2244	2645	705890731	705890324	3.000000e-149	538.0
2	TraesCS7B01G043800	chr7B	84.971	346	50	2	34	379	374982241	374982584	1.510000e-92	350.0
3	TraesCS7B01G043800	chr5B	98.422	1014	15	1	1632	2645	639763896	639762884	0.000000e+00	1783.0
4	TraesCS7B01G043800	chr5B	86.040	351	47	1	35	385	17992459	17992807	2.490000e-100	375.0
5	TraesCS7B01G043800	chr7D	87.569	1263	102	31	3	1242	91105562	91106792	0.000000e+00	1411.0
6	TraesCS7B01G043800	chr7D	93.494	415	22	2	1219	1631	91106802	91107213	1.740000e-171	612.0
7	TraesCS7B01G043800	chr3B	90.990	1010	78	9	1631	2630	774821485	774822491	0.000000e+00	1349.0
8	TraesCS7B01G043800	chr3B	90.119	1012	84	12	1632	2630	486797459	486798467	0.000000e+00	1301.0
9	TraesCS7B01G043800	chr3B	89.778	1037	63	20	1632	2645	720235505	720234489	0.000000e+00	1288.0
10	TraesCS7B01G043800	chr6A	90.396	1010	83	10	1632	2630	592275681	592276687	0.000000e+00	1315.0
11	TraesCS7B01G043800	chr2B	90.958	741	54	9	1632	2363	16305889	16306625	0.000000e+00	985.0
12	TraesCS7B01G043800	chr2B	84.553	369	49	8	34	398	798271125	798270761	2.500000e-95	359.0
13	TraesCS7B01G043800	chr7A	90.865	624	47	7	1633	2250	669871236	669871855	0.000000e+00	828.0
14	TraesCS7B01G043800	chr7A	92.099	405	28	3	2244	2645	669871925	669872328	3.820000e-158	568.0
15	TraesCS7B01G043800	chr1B	90.385	624	46	12	1634	2250	576028806	576028190	0.000000e+00	808.0
16	TraesCS7B01G043800	chr1B	87.117	326	39	3	44	367	129139258	129138934	1.500000e-97	366.0
17	TraesCS7B01G043800	chr1B	87.243	243	22	4	1002	1240	632165602	632165839	4.340000e-68	268.0
18	TraesCS7B01G043800	chr2D	89.873	632	54	8	1625	2250	292291824	292292451	0.000000e+00	804.0
19	TraesCS7B01G043800	chr2D	85.054	368	48	7	34	398	635991250	635990887	4.160000e-98	368.0
20	TraesCS7B01G043800	chr2D	83.784	370	51	9	34	398	609193744	609193379	2.520000e-90	342.0
21	TraesCS7B01G043800	chr1D	82.669	727	86	21	924	1631	460158969	460159674	2.250000e-170	608.0
22	TraesCS7B01G043800	chr1D	95.833	48	2	0	421	468	460158752	460158799	7.850000e-11	78.7
23	TraesCS7B01G043800	chr1A	84.112	642	68	21	1002	1631	551641347	551641966	8.150000e-165	590.0
24	TraesCS7B01G043800	chrUn	92.462	398	26	3	2084	2478	478298924	478298528	1.370000e-157	566.0
25	TraesCS7B01G043800	chr3D	89.976	409	33	7	2244	2645	36169625	36170032	3.020000e-144	521.0
26	TraesCS7B01G043800	chr3D	83.673	392	48	13	34	414	5168712	5168326	3.240000e-94	355.0
27	TraesCS7B01G043800	chr4D	84.900	351	47	6	43	390	484939305	484939652	1.510000e-92	350.0
28	TraesCS7B01G043800	chr6D	84.857	350	48	5	33	379	23096102	23096449	5.420000e-92	348.0

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	TraesCS7B01G043800	chr7B	43671563	43674207	2644	False	4885.00	4885	100.0000	1	2645	1	chr7B.!!$F1	2644
1	TraesCS7B01G043800	chr5B	639762884	639763896	1012	True	1783.00	1783	98.4220	1632	2645	1	chr5B.!!$R1	1013
2	TraesCS7B01G043800	chr7D	91105562	91107213	1651	False	1011.50	1411	90.5315	3	1631	2	chr7D.!!$F1	1628
3	TraesCS7B01G043800	chr3B	774821485	774822491	1006	False	1349.00	1349	90.9900	1631	2630	1	chr3B.!!$F2	999
4	TraesCS7B01G043800	chr3B	486797459	486798467	1008	False	1301.00	1301	90.1190	1632	2630	1	chr3B.!!$F1	998
5	TraesCS7B01G043800	chr3B	720234489	720235505	1016	True	1288.00	1288	89.7780	1632	2645	1	chr3B.!!$R1	1013
6	TraesCS7B01G043800	chr6A	592275681	592276687	1006	False	1315.00	1315	90.3960	1632	2630	1	chr6A.!!$F1	998
7	TraesCS7B01G043800	chr2B	16305889	16306625	736	False	985.00	985	90.9580	1632	2363	1	chr2B.!!$F1	731
8	TraesCS7B01G043800	chr7A	669871236	669872328	1092	False	698.00	828	91.4820	1633	2645	2	chr7A.!!$F1	1012
9	TraesCS7B01G043800	chr1B	576028190	576028806	616	True	808.00	808	90.3850	1634	2250	1	chr1B.!!$R2	616
10	TraesCS7B01G043800	chr2D	292291824	292292451	627	False	804.00	804	89.8730	1625	2250	1	chr2D.!!$F1	625
11	TraesCS7B01G043800	chr1D	460158752	460159674	922	False	343.35	608	89.2510	421	1631	2	chr1D.!!$F1	1210
12	TraesCS7B01G043800	chr1A	551641347	551641966	619	False	590.00	590	84.1120	1002	1631	1	chr1A.!!$F1	629

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
922	952	0.102481	CGTGATCTCCGAATCCCGTT	59.898	55.0	0.0	0.0	36.31	4.44	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1777	1864	3.706373	CTGCTGTACTGGGCCGGT	61.706	66.667	23.8	23.8	0.0	5.28	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
40	41	3.002038	ACTAACCTCTACCGAGAGTGG	57.998	52.381	1.54	2.50	46.93	4.00
42	43	1.313812	AACCTCTACCGAGAGTGGCG	61.314	60.000	1.54	0.00	46.93	5.69
57	58	3.587933	GCGTTTTGGCACACCGGA	61.588	61.111	9.46	0.00	39.29	5.14
60	61	3.283684	TTTTGGCACACCGGAGCG	61.284	61.111	9.46	0.00	39.29	5.03
93	94	8.507249	CCTGGTTTTCAAAATGTGTTTTAAACA	58.493	29.630	6.41	6.41	37.42	2.83
133	134	8.518151	AAAAAGCTTCAAACAAAAATTTGGTG	57.482	26.923	0.00	7.84	42.34	4.17
134	135	5.233957	AGCTTCAAACAAAAATTTGGTGC	57.766	34.783	10.38	3.81	42.34	5.01
159	160	7.112287	GCGTACATCTCGATATTATACATGCTC	59.888	40.741	0.00	0.00	0.00	4.26
161	162	9.958234	GTACATCTCGATATTATACATGCTCAT	57.042	33.333	0.00	0.00	0.00	2.90
183	184	7.708051	TCATAAAGTCATTTCACGAAAAACCA	58.292	30.769	0.00	0.00	33.56	3.67
197	198	6.020995	CACGAAAAACCAACAACTTATGTGTC	60.021	38.462	0.00	0.00	42.99	3.67
203	204	0.511221	ACAACTTATGTGTCGCGTGC	59.489	50.000	5.77	0.57	41.93	5.34
218	219	2.215363	CGCGTGCGAAAAAGACAAAATT	59.785	40.909	8.89	0.00	42.83	1.82
219	220	3.301515	CGCGTGCGAAAAAGACAAAATTT	60.302	39.130	8.89	0.00	42.83	1.82
221	222	4.259610	GCGTGCGAAAAAGACAAAATTTGA	60.260	37.500	13.19	0.00	0.00	2.69
224	225	5.616785	GTGCGAAAAAGACAAAATTTGATGC	59.383	36.000	13.19	1.72	0.00	3.91
225	226	5.523188	TGCGAAAAAGACAAAATTTGATGCT	59.477	32.000	13.19	3.98	0.00	3.79
226	227	6.699204	TGCGAAAAAGACAAAATTTGATGCTA	59.301	30.769	13.19	0.00	0.00	3.49
234	235	8.947055	AGACAAAATTTGATGCTAAAAAGTGT	57.053	26.923	13.19	0.00	0.00	3.55
255	256	6.457676	GTGTTTTTCACACGACATCTTTTTG	58.542	36.000	0.00	0.00	46.51	2.44
257	258	6.306837	TGTTTTTCACACGACATCTTTTTGTC	59.693	34.615	0.00	0.00	42.10	3.18
259	260	5.403897	TTCACACGACATCTTTTTGTCTC	57.596	39.130	0.00	0.00	43.10	3.36
274	275	8.234546	TCTTTTTGTCTCTTTTACACAAGTCAC	58.765	33.333	0.00	0.00	31.81	3.67
275	276	7.441890	TTTTGTCTCTTTTACACAAGTCACA	57.558	32.000	0.00	0.00	31.81	3.58
310	311	5.940192	TTTATCTGAAACTTGACGTGCAT	57.060	34.783	0.00	0.00	0.00	3.96
312	313	4.928661	ATCTGAAACTTGACGTGCATAC	57.071	40.909	0.00	0.00	0.00	2.39
321	322	7.786178	AACTTGACGTGCATACATATAATGT	57.214	32.000	0.00	0.00	46.92	2.71
325	326	6.386654	TGACGTGCATACATATAATGTCGAT	58.613	36.000	0.00	0.00	43.67	3.59
326	327	6.866248	TGACGTGCATACATATAATGTCGATT	59.134	34.615	0.00	0.00	43.67	3.34
336	337	2.704725	AATGTCGATTTGTGTGTGCC	57.295	45.000	0.00	0.00	0.00	5.01
344	345	5.460419	GTCGATTTGTGTGTGCCAAATTTTA	59.540	36.000	0.00	0.00	41.34	1.52
345	346	6.145371	GTCGATTTGTGTGTGCCAAATTTTAT	59.855	34.615	0.00	0.00	41.34	1.40
348	349	7.320797	CGATTTGTGTGTGCCAAATTTTATTTG	59.679	33.333	5.39	5.39	41.34	2.32
392	393	2.714259	TTTTTCCAGTGACAGGGCG	58.286	52.632	0.00	0.00	0.00	6.13
393	394	1.452145	TTTTTCCAGTGACAGGGCGC	61.452	55.000	0.00	0.00	0.00	6.53
394	395	4.680237	TTCCAGTGACAGGGCGCG	62.680	66.667	0.00	0.00	0.00	6.86
419	427	1.273048	TGCCAAAGCGAATTTCTGCAT	59.727	42.857	13.12	2.01	44.31	3.96
435	443	0.598065	GCATGGATCCCCGCAATAAC	59.402	55.000	9.90	0.00	34.29	1.89
487	495	8.310382	CAGATCCTAGGAAACAAATCTATCGAT	58.690	37.037	17.30	2.16	0.00	3.59
561	569	4.479786	AGAATAGGAAGCACAACCTCTC	57.520	45.455	0.00	0.00	37.68	3.20
565	573	1.546476	AGGAAGCACAACCTCTCTACG	59.454	52.381	0.00	0.00	0.00	3.51
566	574	1.272769	GGAAGCACAACCTCTCTACGT	59.727	52.381	0.00	0.00	0.00	3.57
567	575	2.490903	GGAAGCACAACCTCTCTACGTA	59.509	50.000	0.00	0.00	0.00	3.57
568	576	3.130693	GGAAGCACAACCTCTCTACGTAT	59.869	47.826	0.00	0.00	0.00	3.06
569	577	4.337555	GGAAGCACAACCTCTCTACGTATA	59.662	45.833	0.00	0.00	0.00	1.47
570	578	5.502153	AAGCACAACCTCTCTACGTATAG	57.498	43.478	0.00	0.00	0.00	1.31
571	579	4.778579	AGCACAACCTCTCTACGTATAGA	58.221	43.478	9.97	9.97	36.01	1.98
572	580	4.575645	AGCACAACCTCTCTACGTATAGAC	59.424	45.833	6.58	0.00	33.66	2.59
627	638	3.008594	TGGCCGATTCCTTTTCAAGTCTA	59.991	43.478	0.00	0.00	0.00	2.59
629	640	3.623510	GCCGATTCCTTTTCAAGTCTAGG	59.376	47.826	0.00	0.00	0.00	3.02
630	641	3.623510	CCGATTCCTTTTCAAGTCTAGGC	59.376	47.826	0.00	0.00	0.00	3.93
631	642	4.508662	CGATTCCTTTTCAAGTCTAGGCT	58.491	43.478	0.00	0.00	0.00	4.58
632	643	4.938226	CGATTCCTTTTCAAGTCTAGGCTT	59.062	41.667	3.04	3.04	0.00	4.35
633	644	5.412904	CGATTCCTTTTCAAGTCTAGGCTTT	59.587	40.000	6.92	0.00	0.00	3.51
734	752	3.451178	AGGGAACACTGATGCGTATACTT	59.549	43.478	0.56	0.00	0.00	2.24
735	753	3.555956	GGGAACACTGATGCGTATACTTG	59.444	47.826	0.56	0.00	0.00	3.16
736	754	3.001330	GGAACACTGATGCGTATACTTGC	59.999	47.826	0.56	0.00	0.00	4.01
737	755	3.526931	ACACTGATGCGTATACTTGCT	57.473	42.857	0.56	0.00	0.00	3.91
738	756	3.190079	ACACTGATGCGTATACTTGCTG	58.810	45.455	0.56	0.00	0.00	4.41
740	758	4.142249	ACACTGATGCGTATACTTGCTGTA	60.142	41.667	0.56	0.00	35.37	2.74
741	759	4.207224	CACTGATGCGTATACTTGCTGTAC	59.793	45.833	0.56	0.00	33.45	2.90
742	760	4.098044	ACTGATGCGTATACTTGCTGTACT	59.902	41.667	0.56	0.00	33.45	2.73
744	762	5.516996	TGATGCGTATACTTGCTGTACTAC	58.483	41.667	0.56	0.00	33.45	2.73
747	765	6.872628	TGCGTATACTTGCTGTACTACTAT	57.127	37.500	0.56	0.00	33.45	2.12
748	766	6.665465	TGCGTATACTTGCTGTACTACTATG	58.335	40.000	0.56	0.00	33.45	2.23
751	769	7.859377	GCGTATACTTGCTGTACTACTATGAAA	59.141	37.037	0.56	0.00	33.45	2.69
752	770	9.726232	CGTATACTTGCTGTACTACTATGAAAA	57.274	33.333	0.56	0.00	33.45	2.29
806	836	4.617959	TCCTAGCGCTGATGTGTATTTAC	58.382	43.478	22.90	0.00	0.00	2.01
816	846	6.037830	GCTGATGTGTATTTACGGTTACCAAT	59.962	38.462	1.13	0.00	0.00	3.16
820	850	5.642919	TGTGTATTTACGGTTACCAATCACC	59.357	40.000	1.13	0.00	0.00	4.02
847	877	4.142838	CGCGTACCTATGGTGATTATACGA	60.143	45.833	0.00	0.00	33.65	3.43
871	901	1.678627	CCTATCCAGGAGTGTCTCACG	59.321	57.143	0.00	0.00	45.91	4.35
903	933	4.188462	TGTGTGCACTATACCATAACTGC	58.812	43.478	19.41	0.00	0.00	4.40
912	942	2.604046	ACCATAACTGCGTGATCTCC	57.396	50.000	0.00	0.00	0.00	3.71
913	943	1.202417	ACCATAACTGCGTGATCTCCG	60.202	52.381	0.00	0.00	0.00	4.63
915	945	2.481276	CCATAACTGCGTGATCTCCGAA	60.481	50.000	9.14	0.00	0.00	4.30
916	946	3.384668	CATAACTGCGTGATCTCCGAAT	58.615	45.455	9.14	0.00	0.00	3.34
917	947	1.927895	AACTGCGTGATCTCCGAATC	58.072	50.000	9.14	0.00	0.00	2.52
919	949	0.598680	CTGCGTGATCTCCGAATCCC	60.599	60.000	9.14	0.00	0.00	3.85
920	950	1.661821	GCGTGATCTCCGAATCCCG	60.662	63.158	9.14	0.00	38.18	5.14
921	951	1.734137	CGTGATCTCCGAATCCCGT	59.266	57.895	0.00	0.00	36.31	5.28
922	952	0.102481	CGTGATCTCCGAATCCCGTT	59.898	55.000	0.00	0.00	36.31	4.44
946	976	5.006649	TGCAAATCTGTCATGCTTCGTATAC	59.993	40.000	0.00	0.00	40.66	1.47
986	1019	4.452114	TCGATGCACATGCCATAGTTAATC	59.548	41.667	0.49	0.00	41.18	1.75
1040	1076	2.360350	AGGTGTGCCATTGCCTCG	60.360	61.111	0.00	0.00	37.19	4.63
1056	1092	2.464865	CCTCGGATCGTGCTTCTAAAG	58.535	52.381	0.00	0.00	0.00	1.85
1149	1185	3.737559	TCATTGGGTGCCTTCTTATGT	57.262	42.857	0.00	0.00	0.00	2.29
1420	1493	2.140065	GCATATGCTGCGTCACTCTA	57.860	50.000	20.64	0.00	41.97	2.43
1479	1552	3.129287	CACAGGAATTGCCCAAGTATGAC	59.871	47.826	0.00	0.00	37.37	3.06
1480	1553	2.355756	CAGGAATTGCCCAAGTATGACG	59.644	50.000	0.00	0.00	37.37	4.35
1481	1554	2.238646	AGGAATTGCCCAAGTATGACGA	59.761	45.455	0.00	0.00	37.37	4.20
1499	1572	1.077501	ACGCAGCCCATACTTGCAT	60.078	52.632	0.00	0.00	37.69	3.96
1518	1591	2.810870	TACACGGGTGGGCATTAATT	57.189	45.000	0.00	0.00	34.19	1.40
1562	1640	4.746115	GTGTGTTGATTGATGCACATGTTT	59.254	37.500	0.00	0.00	42.66	2.83
1622	1704	0.101219	GTTGAAATCTGATGCGGCCC	59.899	55.000	0.00	0.00	0.00	5.80
1777	1864	5.066375	CGTAATCAGGATTTGCTGAATTGGA	59.934	40.000	5.86	0.00	32.98	3.53
2588	2773	7.700611	AGAAAGAAATAATTTTTACGTCGCG	57.299	32.000	0.00	0.00	0.00	5.87

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
31	32	2.966309	GCCAAAACGCCACTCTCGG	61.966	63.158	0.00	0.00	0.00	4.63
40	41	3.536498	CTCCGGTGTGCCAAAACGC	62.536	63.158	0.00	0.00	34.09	4.84
42	43	2.335011	GCTCCGGTGTGCCAAAAC	59.665	61.111	0.00	0.00	34.09	2.43
60	61	0.383949	TTTGAAAACCAGGAGCGTGC	59.616	50.000	0.00	0.00	0.00	5.34
62	63	2.693074	ACATTTTGAAAACCAGGAGCGT	59.307	40.909	0.00	0.00	0.00	5.07
63	64	3.052036	CACATTTTGAAAACCAGGAGCG	58.948	45.455	0.00	0.00	0.00	5.03
64	65	4.058721	ACACATTTTGAAAACCAGGAGC	57.941	40.909	0.00	0.00	0.00	4.70
65	66	6.983474	AAAACACATTTTGAAAACCAGGAG	57.017	33.333	0.00	0.00	36.64	3.69
66	67	8.722394	GTTTAAAACACATTTTGAAAACCAGGA	58.278	29.630	0.00	0.00	38.50	3.86
67	68	8.507249	TGTTTAAAACACATTTTGAAAACCAGG	58.493	29.630	0.00	0.00	36.38	4.45
113	114	4.027724	CGCACCAAATTTTTGTTTGAAGC	58.972	39.130	2.63	4.16	40.64	3.86
114	115	5.215239	ACGCACCAAATTTTTGTTTGAAG	57.785	34.783	2.63	1.38	40.64	3.02
115	116	5.637810	TGTACGCACCAAATTTTTGTTTGAA	59.362	32.000	2.63	0.00	40.64	2.69
123	124	3.749088	TCGAGATGTACGCACCAAATTTT	59.251	39.130	0.00	0.00	0.00	1.82
132	133	6.691388	GCATGTATAATATCGAGATGTACGCA	59.309	38.462	0.00	0.00	0.00	5.24
133	134	6.913132	AGCATGTATAATATCGAGATGTACGC	59.087	38.462	0.00	1.40	0.00	4.42
134	135	8.122952	TGAGCATGTATAATATCGAGATGTACG	58.877	37.037	0.00	0.00	0.00	3.67
159	160	7.922505	TGGTTTTTCGTGAAATGACTTTATG	57.077	32.000	0.00	0.00	0.00	1.90
161	162	7.313646	TGTTGGTTTTTCGTGAAATGACTTTA	58.686	30.769	0.00	0.00	0.00	1.85
183	184	1.070175	GCACGCGACACATAAGTTGTT	60.070	47.619	15.93	0.00	36.00	2.83
197	198	1.184349	TTTTGTCTTTTTCGCACGCG	58.816	45.000	3.53	3.53	41.35	6.01
203	204	9.913451	TTTTAGCATCAAATTTTGTCTTTTTCG	57.087	25.926	8.89	0.00	0.00	3.46
234	235	6.862944	GACAAAAAGATGTCGTGTGAAAAA	57.137	33.333	0.00	0.00	40.23	1.94
286	287	5.507077	TGCACGTCAAGTTTCAGATAAAAC	58.493	37.500	0.00	0.00	39.03	2.43
291	292	4.314961	TGTATGCACGTCAAGTTTCAGAT	58.685	39.130	0.00	0.00	0.00	2.90
310	311	7.254624	GGCACACACAAATCGACATTATATGTA	60.255	37.037	0.00	0.00	45.03	2.29
312	313	5.909054	GGCACACACAAATCGACATTATATG	59.091	40.000	0.00	0.00	0.00	1.78
321	322	3.724508	AATTTGGCACACACAAATCGA	57.275	38.095	4.14	0.00	45.07	3.59
325	326	6.599244	TCCAAATAAAATTTGGCACACACAAA	59.401	30.769	21.41	3.84	46.40	2.83
326	327	6.115446	TCCAAATAAAATTTGGCACACACAA	58.885	32.000	21.41	4.43	46.40	3.33
393	394	3.593551	ATTCGCTTTGGCACGCACG	62.594	57.895	8.45	1.04	38.60	5.34
394	395	0.939106	AAATTCGCTTTGGCACGCAC	60.939	50.000	8.45	0.00	38.60	5.34
395	396	0.662970	GAAATTCGCTTTGGCACGCA	60.663	50.000	8.45	0.00	38.60	5.24
396	397	0.387239	AGAAATTCGCTTTGGCACGC	60.387	50.000	0.00	0.00	38.60	5.34
419	427	1.525077	GCGTTATTGCGGGGATCCA	60.525	57.895	15.23	0.00	0.00	3.41
435	443	6.398621	CGAGATTAGAAACCACAATATACGCG	60.399	42.308	3.53	3.53	0.00	6.01
565	573	2.649614	GCCGGGAGCCGTCTATAC	59.350	66.667	2.18	0.00	46.80	1.47
566	574	2.981909	CGCCGGGAGCCGTCTATA	60.982	66.667	2.18	0.00	46.80	1.31
627	638	9.821765	CCTAAGAAGGAAAGGAAAGGAAAGCCT	62.822	44.444	0.00	0.00	46.69	4.58
629	640	6.260870	CTAAGAAGGAAAGGAAAGGAAAGC	57.739	41.667	0.00	0.00	0.00	3.51
751	769	9.793259	AGGGAAGTTTTTCTTTTCTTTTCTTTT	57.207	25.926	0.00	0.00	36.40	2.27
752	770	9.436957	GAGGGAAGTTTTTCTTTTCTTTTCTTT	57.563	29.630	0.00	0.00	36.40	2.52
753	771	7.759886	CGAGGGAAGTTTTTCTTTTCTTTTCTT	59.240	33.333	0.00	0.00	36.40	2.52
754	772	7.258441	CGAGGGAAGTTTTTCTTTTCTTTTCT	58.742	34.615	0.00	0.00	36.40	2.52
756	774	5.810587	GCGAGGGAAGTTTTTCTTTTCTTTT	59.189	36.000	0.00	0.00	36.40	2.27
757	775	5.105513	TGCGAGGGAAGTTTTTCTTTTCTTT	60.106	36.000	0.00	0.00	36.40	2.52
758	776	4.401202	TGCGAGGGAAGTTTTTCTTTTCTT	59.599	37.500	0.00	0.00	36.40	2.52
760	778	4.036380	TCTGCGAGGGAAGTTTTTCTTTTC	59.964	41.667	0.00	0.00	36.40	2.29
761	779	3.951680	TCTGCGAGGGAAGTTTTTCTTTT	59.048	39.130	0.00	0.00	36.40	2.27
762	780	3.551846	TCTGCGAGGGAAGTTTTTCTTT	58.448	40.909	0.00	0.00	36.40	2.52
763	781	3.208747	TCTGCGAGGGAAGTTTTTCTT	57.791	42.857	0.00	0.00	39.32	2.52
766	784	2.040412	AGGATCTGCGAGGGAAGTTTTT	59.960	45.455	0.00	0.00	0.00	1.94
767	785	1.630878	AGGATCTGCGAGGGAAGTTTT	59.369	47.619	0.00	0.00	0.00	2.43
768	786	1.280457	AGGATCTGCGAGGGAAGTTT	58.720	50.000	0.00	0.00	0.00	2.66
772	801	2.431023	GCTAGGATCTGCGAGGGAA	58.569	57.895	0.00	0.00	0.00	3.97
821	851	3.327754	CACCATAGGTACGCGCGC	61.328	66.667	32.58	23.91	32.11	6.86
822	852	0.596600	AATCACCATAGGTACGCGCG	60.597	55.000	30.96	30.96	32.11	6.86
823	853	2.427232	TAATCACCATAGGTACGCGC	57.573	50.000	5.73	0.00	32.11	6.86
831	861	8.361139	GGATAGGGATTCGTATAATCACCATAG	58.639	40.741	0.00	0.00	30.48	2.23
847	877	3.051803	TGAGACACTCCTGGATAGGGATT	60.052	47.826	0.00	0.00	44.70	3.01
903	933	0.102481	AACGGGATTCGGAGATCACG	59.898	55.000	17.31	17.31	43.07	4.35
912	942	1.468520	ACAGATTTGCAACGGGATTCG	59.531	47.619	0.00	0.00	45.88	3.34
913	943	2.487762	TGACAGATTTGCAACGGGATTC	59.512	45.455	0.00	0.00	0.00	2.52
915	945	2.198827	TGACAGATTTGCAACGGGAT	57.801	45.000	0.00	0.00	0.00	3.85
916	946	1.811965	CATGACAGATTTGCAACGGGA	59.188	47.619	0.00	0.00	0.00	5.14
917	947	1.733389	GCATGACAGATTTGCAACGGG	60.733	52.381	0.00	0.00	36.40	5.28
919	949	2.624316	AGCATGACAGATTTGCAACG	57.376	45.000	0.00	0.00	38.84	4.10
920	950	2.912967	CGAAGCATGACAGATTTGCAAC	59.087	45.455	0.00	0.00	38.84	4.17
921	951	2.553602	ACGAAGCATGACAGATTTGCAA	59.446	40.909	0.00	0.00	38.84	4.08
922	952	2.153645	ACGAAGCATGACAGATTTGCA	58.846	42.857	0.00	0.00	38.84	4.08
962	995	1.875009	ACTATGGCATGTGCATCGAG	58.125	50.000	10.98	0.00	44.36	4.04
986	1019	0.116541	ATATAGGGGGTCCGGGTCTG	59.883	60.000	0.00	0.00	38.33	3.51
1056	1092	3.053455	GTGTGCGAGATTATGAGGTAGC	58.947	50.000	0.00	0.00	0.00	3.58
1149	1185	8.151596	TGATGTGTACTTACATTGTACTCCAAA	58.848	33.333	0.00	0.00	41.15	3.28
1479	1552	2.813179	GCAAGTATGGGCTGCGTCG	61.813	63.158	0.00	0.00	0.00	5.12
1480	1553	1.097547	ATGCAAGTATGGGCTGCGTC	61.098	55.000	0.00	0.00	0.00	5.19
1481	1554	0.180171	TATGCAAGTATGGGCTGCGT	59.820	50.000	0.00	0.00	0.00	5.24
1499	1572	2.026169	TCAATTAATGCCCACCCGTGTA	60.026	45.455	0.00	0.00	0.00	2.90
1518	1591	7.868922	ACACACTATTTTACAGTCGTGTATTCA	59.131	33.333	0.00	0.00	38.98	2.57
1597	1679	3.484229	CCGCATCAGATTTCAACTCGTTC	60.484	47.826	0.00	0.00	0.00	3.95
1646	1728	6.636562	TTTCGCCTACAAATTGAAGGTTTA	57.363	33.333	0.00	0.00	32.67	2.01
1777	1864	3.706373	CTGCTGTACTGGGCCGGT	61.706	66.667	23.80	23.80	0.00	5.28
2114	2213	7.727186	AGAATATATGTGGCATGTCCTTGAAAT	59.273	33.333	0.00	0.00	35.26	2.17

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.