AutoCloner

Multiple sequence alignment - TraesCS7A01G292500

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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	TraesCS7A01G292500	chr7A	100.000	3368	0	0	1	3368	367017022	367013655	0.000000e+00	6220.0
1	TraesCS7A01G292500	chr5D	96.435	1795	58	3	548	2336	386950692	386948898	0.000000e+00	2955.0
2	TraesCS7A01G292500	chr5D	91.963	1070	37	11	2339	3368	386946262	386945202	0.000000e+00	1454.0
3	TraesCS7A01G292500	chr5D	93.299	194	8	3	555	743	386944862	386945055	7.110000e-72	281.0
4	TraesCS7A01G292500	chr6A	95.487	1795	72	3	551	2336	610232550	610230756	0.000000e+00	2857.0
5	TraesCS7A01G292500	chr6A	88.505	1070	31	13	2339	3368	610228843	610227826	0.000000e+00	1210.0
6	TraesCS7A01G292500	chr6A	85.563	284	23	9	548	825	610227479	610227750	7.110000e-72	281.0
7	TraesCS7A01G292500	chr6A	92.982	57	4	0	3238	3294	610228023	610227967	2.150000e-12	84.2
8	TraesCS7A01G292500	chr5B	89.015	1411	119	25	952	2336	327187102	327188502	0.000000e+00	1714.0
9	TraesCS7A01G292500	chr5B	93.232	591	34	5	2339	2929	327191093	327191677	0.000000e+00	865.0
10	TraesCS7A01G292500	chr5B	87.240	384	40	5	550	925	327157142	327157524	2.400000e-116	429.0
11	TraesCS7A01G292500	chr3D	91.223	1071	35	16	2338	3368	547777692	547776641	0.000000e+00	1402.0
12	TraesCS7A01G292500	chr3D	96.296	108	4	0	1252	1359	547777836	547777729	9.600000e-41	178.0
13	TraesCS7A01G292500	chr3B	92.504	667	50	0	1670	2336	819198389	819197723	0.000000e+00	955.0
14	TraesCS7A01G292500	chr3B	81.541	753	78	19	2339	3051	819195091	819194360	6.310000e-157	564.0
15	TraesCS7A01G292500	chr3B	83.729	590	80	13	958	1536	819199269	819198685	8.220000e-151	544.0
16	TraesCS7A01G292500	chr3B	84.880	291	34	6	550	832	819212438	819212150	5.500000e-73	285.0
17	TraesCS7A01G292500	chr3B	84.333	300	35	8	542	832	819192972	819193268	1.980000e-72	283.0
18	TraesCS7A01G292500	chr2A	92.204	667	50	1	1670	2336	748171972	748172636	0.000000e+00	942.0
19	TraesCS7A01G292500	chr2A	84.341	645	80	17	905	1536	748171041	748171677	2.220000e-171	612.0
20	TraesCS7A01G292500	chr2A	82.673	606	71	12	2464	3051	748175423	748176012	1.080000e-139	507.0
21	TraesCS7A01G292500	chr2A	85.417	288	34	4	550	832	748170726	748171010	3.290000e-75	292.0
22	TraesCS7A01G292500	chr2A	90.751	173	15	1	2339	2511	748175263	748175434	2.610000e-56	230.0
23	TraesCS7A01G292500	chr6B	87.126	668	83	3	1670	2336	317689902	317690567	0.000000e+00	754.0
24	TraesCS7A01G292500	chr6B	87.126	668	83	3	1670	2336	317699516	317700181	0.000000e+00	754.0
25	TraesCS7A01G292500	chr6B	81.751	948	100	36	2339	3223	317702809	317703746	0.000000e+00	725.0
26	TraesCS7A01G292500	chr6B	86.888	633	80	3	1670	2301	317695653	317696283	0.000000e+00	706.0
27	TraesCS7A01G292500	chr6B	78.806	335	54	9	3	320	328499948	328500282	3.410000e-50	209.0
28	TraesCS7A01G292500	chr6B	84.343	198	30	1	124	320	154391469	154391272	3.430000e-45	193.0
29	TraesCS7A01G292500	chr7B	91.021	568	27	4	1	550	285457368	285456807	0.000000e+00	745.0
30	TraesCS7A01G292500	chr7B	86.527	668	87	3	1670	2336	97864702	97864037	0.000000e+00	732.0
31	TraesCS7A01G292500	chr7B	81.038	944	110	30	2339	3221	97859690	97858755	0.000000e+00	688.0
32	TraesCS7A01G292500	chr7B	79.217	332	52	9	6	320	304668836	304668505	7.320000e-52	215.0
33	TraesCS7A01G292500	chrUn	87.480	631	76	3	1707	2336	462354893	462355521	0.000000e+00	725.0
34	TraesCS7A01G292500	chr6D	83.156	754	69	11	2339	3051	365443819	365444555	1.320000e-178	636.0
35	TraesCS7A01G292500	chr6D	84.828	290	34	7	551	832	365445971	365445684	1.980000e-72	283.0
36	TraesCS7A01G292500	chr4B	85.859	198	27	1	124	320	318228459	318228262	3.410000e-50	209.0
37	TraesCS7A01G292500	chr4B	85.859	198	27	1	124	320	336602374	336602177	3.410000e-50	209.0
38	TraesCS7A01G292500	chr4B	85.859	198	27	1	124	320	336609420	336609223	3.410000e-50	209.0
39	TraesCS7A01G292500	chr4B	85.354	198	28	1	124	320	317639711	317639514	1.580000e-48	204.0
40	TraesCS7A01G292500	chr4B	85.354	198	28	1	124	320	318235489	318235292	1.580000e-48	204.0

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	TraesCS7A01G292500	chr7A	367013655	367017022	3367	True	6220.000000	6220	100.000000	1	3368	1	chr7A.!!$R1	3367
1	TraesCS7A01G292500	chr5D	386945202	386950692	5490	True	2204.500000	2955	94.199000	548	3368	2	chr5D.!!$R1	2820
2	TraesCS7A01G292500	chr6A	610227826	610232550	4724	True	1383.733333	2857	92.324667	551	3368	3	chr6A.!!$R1	2817
3	TraesCS7A01G292500	chr5B	327187102	327191677	4575	False	1289.500000	1714	91.123500	952	2929	2	chr5B.!!$F2	1977
4	TraesCS7A01G292500	chr3D	547776641	547777836	1195	True	790.000000	1402	93.759500	1252	3368	2	chr3D.!!$R1	2116
5	TraesCS7A01G292500	chr3B	819194360	819199269	4909	True	687.666667	955	85.924667	958	3051	3	chr3B.!!$R2	2093
6	TraesCS7A01G292500	chr2A	748170726	748176012	5286	False	516.600000	942	87.077200	550	3051	5	chr2A.!!$F1	2501
7	TraesCS7A01G292500	chr6B	317689902	317690567	665	False	754.000000	754	87.126000	1670	2336	1	chr6B.!!$F1	666
8	TraesCS7A01G292500	chr6B	317695653	317703746	8093	False	728.333333	754	85.255000	1670	3223	3	chr6B.!!$F3	1553
9	TraesCS7A01G292500	chr7B	285456807	285457368	561	True	745.000000	745	91.021000	1	550	1	chr7B.!!$R3	549
10	TraesCS7A01G292500	chr7B	97864037	97864702	665	True	732.000000	732	86.527000	1670	2336	1	chr7B.!!$R2	666
11	TraesCS7A01G292500	chr7B	97858755	97859690	935	True	688.000000	688	81.038000	2339	3221	1	chr7B.!!$R1	882
12	TraesCS7A01G292500	chrUn	462354893	462355521	628	False	725.000000	725	87.480000	1707	2336	1	chrUn.!!$F1	629
13	TraesCS7A01G292500	chr6D	365443819	365444555	736	False	636.000000	636	83.156000	2339	3051	1	chr6D.!!$F1	712

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
434	451	0.533755	CACCACTATGCTAGGCCTGC	60.534	60.0	17.99	17.54	0.0	4.85	F
1086	1117	0.034337	TTCTCGACCCAACTTTCCCG	59.966	55.0	0.00	0.00	0.0	5.14	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2351	9906	2.382305	TCCTCCTACCTCTTCCACTTGA	59.618	50.0	0.0	0.0	0.0	3.02	R
2779	10415	0.644380	TCATCCCACTCATCCCCTCT	59.356	55.0	0.0	0.0	0.0	3.69	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
58	59	4.094739	CGACATGATGCAACAAGTTATGGA	59.905	41.667	6.29	0.00	0.00	3.41
65	66	7.669427	TGATGCAACAAGTTATGGAAAGAATT	58.331	30.769	0.00	0.00	0.00	2.17
66	67	8.801299	TGATGCAACAAGTTATGGAAAGAATTA	58.199	29.630	0.00	0.00	0.00	1.40
77	78	8.739972	GTTATGGAAAGAATTATGGAACTGTGT	58.260	33.333	0.00	0.00	0.00	3.72
91	92	5.178797	GGAACTGTGTGTGCAATAGTAGAT	58.821	41.667	0.00	0.00	0.00	1.98
92	93	5.063944	GGAACTGTGTGTGCAATAGTAGATG	59.936	44.000	0.00	0.00	0.00	2.90
93	94	4.507710	ACTGTGTGTGCAATAGTAGATGG	58.492	43.478	0.00	0.00	0.00	3.51
102	103	6.051717	GTGCAATAGTAGATGGTTGAGATGT	58.948	40.000	0.00	0.00	0.00	3.06
147	164	5.068329	TGTCACCAAAACATGCTTACATCAA	59.932	36.000	0.00	0.00	32.87	2.57
169	186	4.907879	AGGTGAAACTTGCTTTCTTCAG	57.092	40.909	0.00	0.00	39.36	3.02
174	191	7.285401	AGGTGAAACTTGCTTTCTTCAGAATTA	59.715	33.333	0.00	0.00	39.36	1.40
206	223	4.979943	TGCAGAACTTGTTTTGTCATGA	57.020	36.364	0.00	0.00	0.00	3.07
224	241	5.122869	GTCATGAGCTGAAAGTTGATGCTTA	59.877	40.000	0.00	0.00	38.55	3.09
241	258	5.435686	TGCTTATCCTCAACATTGTACCT	57.564	39.130	0.00	0.00	0.00	3.08
245	262	3.334583	TCCTCAACATTGTACCTGAGC	57.665	47.619	10.28	0.00	35.09	4.26
269	286	2.162681	GCCAGCACACAAGATTTAGGT	58.837	47.619	0.00	0.00	0.00	3.08
276	293	7.438459	CCAGCACACAAGATTTAGGTAGTATAC	59.562	40.741	0.00	0.00	42.04	1.47
325	342	0.938008	GCTAGGAGCGCATTGTAACC	59.062	55.000	11.47	0.91	0.00	2.85
339	356	5.853282	GCATTGTAACCGAGATTTATCATGC	59.147	40.000	0.00	0.00	0.00	4.06
353	370	6.493449	TTTATCATGCGAAGATGACAAACA	57.507	33.333	0.00	0.00	35.17	2.83
363	380	5.505173	AAGATGACAAACAAGGTGAACTG	57.495	39.130	0.00	0.00	0.00	3.16
368	385	1.681264	CAAACAAGGTGAACTGGGGAC	59.319	52.381	0.00	0.00	0.00	4.46
385	402	4.466370	TGGGGACGTCCTCATCATTATATC	59.534	45.833	33.50	11.43	42.76	1.63
431	448	3.369892	CCATATCACCACTATGCTAGGCC	60.370	52.174	0.00	0.00	0.00	5.19
433	450	1.123077	TCACCACTATGCTAGGCCTG	58.877	55.000	17.99	6.68	0.00	4.85
434	451	0.533755	CACCACTATGCTAGGCCTGC	60.534	60.000	17.99	17.54	0.00	4.85
435	452	0.982852	ACCACTATGCTAGGCCTGCA	60.983	55.000	25.46	25.46	44.95	4.41
457	474	2.253758	CCAAGGCACCACACGTCTG	61.254	63.158	0.00	0.00	0.00	3.51
471	488	3.594603	ACGTCTGGTGAGTTCCTATTG	57.405	47.619	0.00	0.00	0.00	1.90
472	489	2.271800	CGTCTGGTGAGTTCCTATTGC	58.728	52.381	0.00	0.00	0.00	3.56
473	490	2.353704	CGTCTGGTGAGTTCCTATTGCA	60.354	50.000	0.00	0.00	0.00	4.08
474	491	3.674997	GTCTGGTGAGTTCCTATTGCAA	58.325	45.455	0.00	0.00	0.00	4.08
475	492	3.686726	GTCTGGTGAGTTCCTATTGCAAG	59.313	47.826	4.94	0.00	0.00	4.01
476	493	3.582647	TCTGGTGAGTTCCTATTGCAAGA	59.417	43.478	4.94	0.00	0.00	3.02
477	494	4.041567	TCTGGTGAGTTCCTATTGCAAGAA	59.958	41.667	4.94	0.00	0.00	2.52
478	495	4.072131	TGGTGAGTTCCTATTGCAAGAAC	58.928	43.478	17.76	17.76	40.14	3.01
479	496	4.072131	GGTGAGTTCCTATTGCAAGAACA	58.928	43.478	23.92	8.67	41.86	3.18
480	497	4.083271	GGTGAGTTCCTATTGCAAGAACAC	60.083	45.833	23.92	19.79	41.86	3.32
481	498	4.515191	GTGAGTTCCTATTGCAAGAACACA	59.485	41.667	23.92	21.50	41.86	3.72
482	499	5.008613	GTGAGTTCCTATTGCAAGAACACAA	59.991	40.000	22.41	11.07	40.88	3.33
483	500	5.769662	TGAGTTCCTATTGCAAGAACACAAT	59.230	36.000	23.92	9.77	41.86	2.71
484	501	6.265196	TGAGTTCCTATTGCAAGAACACAATT	59.735	34.615	23.92	9.49	41.86	2.32
485	502	6.449698	AGTTCCTATTGCAAGAACACAATTG	58.550	36.000	23.92	3.24	41.86	2.32
486	503	5.389859	TCCTATTGCAAGAACACAATTGG	57.610	39.130	10.83	9.10	45.05	3.16
487	504	4.832266	TCCTATTGCAAGAACACAATTGGT	59.168	37.500	10.83	2.02	44.44	3.67
488	505	6.007076	TCCTATTGCAAGAACACAATTGGTA	58.993	36.000	10.83	2.13	44.44	3.25
489	506	6.491745	TCCTATTGCAAGAACACAATTGGTAA	59.508	34.615	10.83	0.00	44.44	2.85
490	507	6.808212	CCTATTGCAAGAACACAATTGGTAAG	59.192	38.462	10.83	0.00	41.39	2.34
491	508	3.976169	TGCAAGAACACAATTGGTAAGC	58.024	40.909	10.83	5.13	0.00	3.09
492	509	3.382865	TGCAAGAACACAATTGGTAAGCA	59.617	39.130	10.83	7.59	0.00	3.91
493	510	3.735746	GCAAGAACACAATTGGTAAGCAC	59.264	43.478	10.83	0.00	0.00	4.40
494	511	4.499696	GCAAGAACACAATTGGTAAGCACT	60.500	41.667	10.83	0.00	0.00	4.40
495	512	5.278266	GCAAGAACACAATTGGTAAGCACTA	60.278	40.000	10.83	0.00	0.00	2.74
496	513	6.570378	GCAAGAACACAATTGGTAAGCACTAT	60.570	38.462	10.83	0.00	0.00	2.12
497	514	7.361713	GCAAGAACACAATTGGTAAGCACTATA	60.362	37.037	10.83	0.00	0.00	1.31
498	515	8.677300	CAAGAACACAATTGGTAAGCACTATAT	58.323	33.333	10.83	0.00	0.00	0.86
499	516	9.899661	AAGAACACAATTGGTAAGCACTATATA	57.100	29.630	10.83	0.00	0.00	0.86
696	713	1.929836	GTCTACGGATTTGCTGCTGAG	59.070	52.381	0.00	0.00	0.00	3.35
708	725	0.535780	CTGCTGAGTGGGCTTGACAA	60.536	55.000	0.00	0.00	0.00	3.18
800	822	4.003648	CCTTGGACTAATGTTTCTCGCTT	58.996	43.478	0.00	0.00	0.00	4.68
832	854	3.996124	CTCGGCGGGATAGGGCAG	61.996	72.222	0.00	0.00	0.00	4.85
860	882	5.048083	GCACAACTTTTTCCATATCACCTCA	60.048	40.000	0.00	0.00	0.00	3.86
898	920	2.094752	GCAAATCGGTACATGCCTGTTT	60.095	45.455	0.00	0.00	36.79	2.83
946	973	1.107114	TCTCTCCCTTCTGATCGTGC	58.893	55.000	0.00	0.00	0.00	5.34
1078	1109	1.292223	CTCGCCTTTCTCGACCCAA	59.708	57.895	0.00	0.00	32.08	4.12
1086	1117	0.034337	TTCTCGACCCAACTTTCCCG	59.966	55.000	0.00	0.00	0.00	5.14
1092	1123	0.256464	ACCCAACTTTCCCGTGTTCA	59.744	50.000	0.00	0.00	0.00	3.18
1110	1141	3.255969	TCACGGTAGGGTTAAGATTGC	57.744	47.619	0.00	0.00	0.00	3.56
1528	1563	9.855021	AATGCTACATACTGTTGGAAATAAAAC	57.145	29.630	0.00	0.00	27.30	2.43
1585	1772	3.068873	GGCAAGTACCCAAACAACATTGA	59.931	43.478	0.00	0.00	31.84	2.57
2202	6279	3.856747	AAGAGGAGGTCTAGGAGGTTT	57.143	47.619	0.00	0.00	32.65	3.27
2336	6413	2.682594	AGAAGATGGGGATGACGATCA	58.317	47.619	0.00	0.00	0.00	2.92
2351	9906	2.094700	ACGATCACGACAACTGCTATGT	60.095	45.455	0.00	0.00	42.66	2.29
2394	9949	5.367060	GGAGGGGTGTTACTGAAGATATTCT	59.633	44.000	1.19	0.00	0.00	2.40
2437	9992	5.182950	CAGCCACCAAACAAGTGATAATACA	59.817	40.000	0.00	0.00	37.42	2.29
2779	10415	3.464907	CCAATCACACAAAATGCACCAA	58.535	40.909	0.00	0.00	0.00	3.67
2827	10463	1.212441	TGCACATGTAGATGCCCATCA	59.788	47.619	10.58	0.00	41.33	3.07
2998	10676	7.620880	TCAGTATGTTTTATAGCTCCAGTGTT	58.379	34.615	0.00	0.00	37.40	3.32
2999	10677	8.755028	TCAGTATGTTTTATAGCTCCAGTGTTA	58.245	33.333	0.00	0.00	37.40	2.41
3000	10678	9.547753	CAGTATGTTTTATAGCTCCAGTGTTAT	57.452	33.333	0.00	0.00	0.00	1.89
3001	10679	9.547753	AGTATGTTTTATAGCTCCAGTGTTATG	57.452	33.333	0.00	0.00	0.00	1.90
3002	10680	9.326413	GTATGTTTTATAGCTCCAGTGTTATGT	57.674	33.333	0.00	0.00	0.00	2.29
3094	10789	5.508200	TTCTTGCCGTTAAAATTCAGTGT	57.492	34.783	0.00	0.00	0.00	3.55
3358	11055	2.300152	TGCAAGTCTTGTGCTAGTAGCT	59.700	45.455	22.34	0.00	42.97	3.32

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
58	59	5.301551	TGCACACACAGTTCCATAATTCTTT	59.698	36.000	0.00	0.00	0.00	2.52
65	66	4.905429	ACTATTGCACACACAGTTCCATA	58.095	39.130	0.00	0.00	0.00	2.74
66	67	3.754965	ACTATTGCACACACAGTTCCAT	58.245	40.909	0.00	0.00	0.00	3.41
77	78	5.675684	TCTCAACCATCTACTATTGCACA	57.324	39.130	0.00	0.00	0.00	4.57
91	92	5.164620	TGAATAGCAAGACATCTCAACCA	57.835	39.130	0.00	0.00	0.00	3.67
92	93	6.203723	GGTATGAATAGCAAGACATCTCAACC	59.796	42.308	0.00	0.00	0.00	3.77
93	94	6.989169	AGGTATGAATAGCAAGACATCTCAAC	59.011	38.462	2.63	0.00	33.40	3.18
102	103	6.070824	TGACACTTCAGGTATGAATAGCAAGA	60.071	38.462	2.63	0.00	44.32	3.02
147	164	4.949856	TCTGAAGAAAGCAAGTTTCACCTT	59.050	37.500	0.68	0.00	46.29	3.50
206	223	4.853007	AGGATAAGCATCAACTTTCAGCT	58.147	39.130	0.00	0.00	37.08	4.24
224	241	3.264193	TGCTCAGGTACAATGTTGAGGAT	59.736	43.478	13.48	0.00	37.97	3.24
241	258	1.036481	TTGTGTGCTGGCTTTGCTCA	61.036	50.000	0.00	0.00	0.00	4.26
245	262	2.806608	AATCTTGTGTGCTGGCTTTG	57.193	45.000	0.00	0.00	0.00	2.77
325	342	5.403466	TGTCATCTTCGCATGATAAATCTCG	59.597	40.000	0.00	0.00	35.23	4.04
339	356	4.273480	AGTTCACCTTGTTTGTCATCTTCG	59.727	41.667	0.00	0.00	0.00	3.79
353	370	1.752833	GACGTCCCCAGTTCACCTT	59.247	57.895	3.51	0.00	0.00	3.50
363	380	4.712337	AGATATAATGATGAGGACGTCCCC	59.288	45.833	30.82	20.98	36.42	4.81
368	385	6.128145	ACGAGACAGATATAATGATGAGGACG	60.128	42.308	0.00	0.00	0.00	4.79
431	448	2.263540	GGTGCCTTGGCAATGCAG	59.736	61.111	26.94	3.61	35.33	4.41
433	450	2.047939	GTGGTGCCTTGGCAATGC	60.048	61.111	18.93	18.93	0.00	3.56
434	451	1.005867	GTGTGGTGCCTTGGCAATG	60.006	57.895	16.55	0.00	0.00	2.82
435	452	2.563798	CGTGTGGTGCCTTGGCAAT	61.564	57.895	16.55	0.00	0.00	3.56
436	453	3.215568	CGTGTGGTGCCTTGGCAA	61.216	61.111	16.55	0.00	0.00	4.52
437	454	4.497984	ACGTGTGGTGCCTTGGCA	62.498	61.111	10.65	10.65	0.00	4.92
438	455	3.660111	GACGTGTGGTGCCTTGGC	61.660	66.667	4.43	4.43	0.00	4.52
439	456	2.111043	AGACGTGTGGTGCCTTGG	59.889	61.111	0.00	0.00	0.00	3.61
440	457	2.253758	CCAGACGTGTGGTGCCTTG	61.254	63.158	23.08	0.00	32.32	3.61
441	458	2.111043	CCAGACGTGTGGTGCCTT	59.889	61.111	23.08	0.00	32.32	4.35
457	474	4.072131	TGTTCTTGCAATAGGAACTCACC	58.928	43.478	22.90	5.14	43.60	4.02
460	477	5.689383	TTGTGTTCTTGCAATAGGAACTC	57.311	39.130	22.90	20.43	43.60	3.01
461	478	6.449698	CAATTGTGTTCTTGCAATAGGAACT	58.550	36.000	22.90	7.36	43.60	3.01
462	479	5.634859	CCAATTGTGTTCTTGCAATAGGAAC	59.365	40.000	18.33	18.33	43.53	3.62
463	480	5.304101	ACCAATTGTGTTCTTGCAATAGGAA	59.696	36.000	0.00	0.00	34.61	3.36
464	481	4.832266	ACCAATTGTGTTCTTGCAATAGGA	59.168	37.500	0.00	0.00	34.61	2.94
465	482	5.138125	ACCAATTGTGTTCTTGCAATAGG	57.862	39.130	0.00	0.00	34.61	2.57
466	483	6.308766	GCTTACCAATTGTGTTCTTGCAATAG	59.691	38.462	0.00	0.00	34.61	1.73
467	484	6.155827	GCTTACCAATTGTGTTCTTGCAATA	58.844	36.000	0.00	0.00	34.61	1.90
468	485	4.990426	GCTTACCAATTGTGTTCTTGCAAT	59.010	37.500	0.00	0.00	36.95	3.56
469	486	4.142071	TGCTTACCAATTGTGTTCTTGCAA	60.142	37.500	4.43	0.00	0.00	4.08
470	487	3.382865	TGCTTACCAATTGTGTTCTTGCA	59.617	39.130	4.43	7.84	0.00	4.08
471	488	3.735746	GTGCTTACCAATTGTGTTCTTGC	59.264	43.478	4.43	5.80	0.00	4.01
472	489	5.186996	AGTGCTTACCAATTGTGTTCTTG	57.813	39.130	4.43	0.00	0.00	3.02
473	490	8.807948	ATATAGTGCTTACCAATTGTGTTCTT	57.192	30.769	4.43	0.00	0.00	2.52
542	559	8.753133	CCACCAGTGATATTAGCTCATTATCTA	58.247	37.037	0.00	0.00	0.00	1.98
543	560	7.236432	ACCACCAGTGATATTAGCTCATTATCT	59.764	37.037	0.00	0.00	0.00	1.98
544	561	7.390027	ACCACCAGTGATATTAGCTCATTATC	58.610	38.462	0.00	0.00	0.00	1.75
545	562	7.321717	ACCACCAGTGATATTAGCTCATTAT	57.678	36.000	0.00	0.00	0.00	1.28
546	563	6.747414	ACCACCAGTGATATTAGCTCATTA	57.253	37.500	0.00	0.00	0.00	1.90
547	564	5.636903	ACCACCAGTGATATTAGCTCATT	57.363	39.130	0.00	0.00	0.00	2.57
696	713	3.030652	CCACGTTGTCAAGCCCAC	58.969	61.111	0.00	0.00	0.00	4.61
825	847	4.715523	GTTGTGCGGGCTGCCCTA	62.716	66.667	33.39	20.42	45.60	3.53
832	854	0.033366	ATGGAAAAAGTTGTGCGGGC	59.967	50.000	0.00	0.00	0.00	6.13
884	906	1.200020	GCAGACAAACAGGCATGTACC	59.800	52.381	3.57	0.00	39.29	3.34
898	920	4.121669	GAGCGCTCGAGGCAGACA	62.122	66.667	23.61	0.00	41.91	3.41
1086	1117	3.665745	TCTTAACCCTACCGTGAACAC	57.334	47.619	0.00	0.00	0.00	3.32
1092	1123	3.994931	AAGCAATCTTAACCCTACCGT	57.005	42.857	0.00	0.00	0.00	4.83
1110	1141	3.565516	GGCTTTTAACAGAAGGCGAAAG	58.434	45.455	0.00	0.00	39.42	2.62
1439	1473	6.921486	TCCACATGTTCAGTTAAGGTACTA	57.079	37.500	0.00	0.00	38.49	1.82
1654	1845	8.641155	CAACAATACATTTTCAACAGTATGCAG	58.359	33.333	0.00	0.00	42.53	4.41
1999	6076	4.137116	TCTTGTGCTCTGTAGTTGTTGT	57.863	40.909	0.00	0.00	0.00	3.32
2002	6079	4.408182	AGTTCTTGTGCTCTGTAGTTGT	57.592	40.909	0.00	0.00	0.00	3.32
2336	6413	3.059884	CACTTGACATAGCAGTTGTCGT	58.940	45.455	8.54	0.84	45.14	4.34
2351	9906	2.382305	TCCTCCTACCTCTTCCACTTGA	59.618	50.000	0.00	0.00	0.00	3.02
2437	9992	0.773644	TTGCCTCTTCCTGCCTCTTT	59.226	50.000	0.00	0.00	0.00	2.52
2700	10336	3.254166	CAGGTCCAAACATCAAGTTCCAG	59.746	47.826	0.00	0.00	40.26	3.86
2779	10415	0.644380	TCATCCCACTCATCCCCTCT	59.356	55.000	0.00	0.00	0.00	3.69
2827	10463	3.945921	CAGTCATGAACTTCTGCATCCAT	59.054	43.478	0.00	0.00	35.45	3.41
2999	10677	9.155975	GACTAGAATTTGACAGTACATGAACAT	57.844	33.333	0.00	0.00	0.00	2.71
3000	10678	8.367911	AGACTAGAATTTGACAGTACATGAACA	58.632	33.333	0.00	0.00	0.00	3.18
3001	10679	8.764524	AGACTAGAATTTGACAGTACATGAAC	57.235	34.615	0.00	0.00	0.00	3.18
3002	10680	9.208022	CAAGACTAGAATTTGACAGTACATGAA	57.792	33.333	0.00	0.00	0.00	2.57
3038	10726	3.690139	AGCAAGAATGACAGCAGATTCAG	59.310	43.478	0.00	0.00	31.98	3.02
3153	10848	5.316167	ACAGCATCATAAACTGTTCTCCAA	58.684	37.500	0.00	0.00	41.78	3.53
3226	10923	1.338105	TGACAGCATCGGAAGAACTGG	60.338	52.381	0.00	0.00	46.59	4.00
3234	10931	4.081697	TCACTAGAATTTGACAGCATCGGA	60.082	41.667	0.00	0.00	0.00	4.55
3235	10932	4.183865	TCACTAGAATTTGACAGCATCGG	58.816	43.478	0.00	0.00	0.00	4.18
3236	10933	5.980698	ATCACTAGAATTTGACAGCATCG	57.019	39.130	0.00	0.00	0.00	3.84
3310	11007	2.047830	GGTCCTGGGTTCGAATCCTAT	58.952	52.381	27.18	0.00	0.00	2.57
3312	11009	0.252742	AGGTCCTGGGTTCGAATCCT	60.253	55.000	27.18	3.80	0.00	3.24

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.