AutoCloner

Multiple sequence alignment - TraesCS1D01G079200

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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	TraesCS1D01G079200	chr1D	100.000	3196	0	0	1	3196	61945193	61941998	0.000000e+00	5903.0
1	TraesCS1D01G079200	chr1D	92.771	83	6	0	2970	3052	249135476	249135558	1.560000e-23	121.0
2	TraesCS1D01G079200	chr1A	95.868	1452	49	2	770	2218	59842563	59841120	0.000000e+00	2338.0
3	TraesCS1D01G079200	chr1A	96.812	690	14	3	1	682	59857584	59856895	0.000000e+00	1146.0
4	TraesCS1D01G079200	chr1A	85.752	379	30	15	2208	2565	59821656	59821281	2.330000e-101	379.0
5	TraesCS1D01G079200	chr1A	97.590	83	2	0	653	735	59856868	59856786	3.320000e-30	143.0
6	TraesCS1D01G079200	chr1A	100.000	30	0	0	653	682	59856896	59856867	4.450000e-04	56.5
7	TraesCS1D01G079200	chr1B	94.102	1492	59	10	862	2341	98447606	98446132	0.000000e+00	2241.0
8	TraesCS1D01G079200	chr1B	93.534	665	37	5	1	662	98722505	98721844	0.000000e+00	985.0
9	TraesCS1D01G079200	chr1B	86.696	684	51	23	2340	3008	98439682	98439024	0.000000e+00	723.0
10	TraesCS1D01G079200	chr1B	86.550	684	52	23	2340	3008	98392327	98391669	0.000000e+00	717.0
11	TraesCS1D01G079200	chr1B	78.761	226	28	12	2978	3184	444786525	444786749	2.000000e-27	134.0
12	TraesCS1D01G079200	chr1B	92.771	83	6	0	2970	3052	329380753	329380671	1.560000e-23	121.0
13	TraesCS1D01G079200	chr6B	90.467	514	41	8	2468	2978	551911202	551911710	0.000000e+00	671.0
14	TraesCS1D01G079200	chr6B	88.016	509	55	5	2473	2977	533277539	533277033	5.900000e-167	597.0
15	TraesCS1D01G079200	chr6B	84.685	222	22	5	2976	3185	702598549	702598328	8.980000e-51	211.0
16	TraesCS1D01G079200	chr7B	91.147	497	39	5	2473	2966	664608058	664607564	0.000000e+00	669.0
17	TraesCS1D01G079200	chr7B	86.555	119	15	1	3067	3185	142862799	142862916	2.590000e-26	130.0
18	TraesCS1D01G079200	chr7B	88.776	98	11	0	2970	3067	164170359	164170262	1.560000e-23	121.0
19	TraesCS1D01G079200	chr7B	100.000	29	0	0	3159	3187	677687015	677686987	2.000000e-03	54.7
20	TraesCS1D01G079200	chr7B	90.476	42	3	1	3144	3185	702467968	702467928	2.000000e-03	54.7
21	TraesCS1D01G079200	chr4A	89.764	508	47	5	2473	2977	545600948	545600443	0.000000e+00	645.0
22	TraesCS1D01G079200	chr4A	83.163	196	19	5	2970	3152	545600101	545599907	1.970000e-37	167.0
23	TraesCS1D01G079200	chr4A	89.535	86	9	0	2970	3055	563046972	563047057	3.370000e-20	110.0
24	TraesCS1D01G079200	chr2D	89.861	503	46	3	2473	2971	194648681	194649182	2.690000e-180	641.0
25	TraesCS1D01G079200	chr2D	87.403	516	62	3	2468	2980	612818158	612817643	9.870000e-165	590.0
26	TraesCS1D01G079200	chr2D	93.333	45	1	1	3143	3185	366062078	366062034	7.400000e-07	65.8
27	TraesCS1D01G079200	chr6A	89.237	511	48	3	2468	2971	4869753	4870263	1.620000e-177	632.0
28	TraesCS1D01G079200	chr6D	88.757	507	55	2	2473	2977	392580577	392580071	1.260000e-173	619.0
29	TraesCS1D01G079200	chr6D	89.076	119	13	0	3067	3185	392577093	392576975	7.140000e-32	148.0
30	TraesCS1D01G079200	chr3A	87.598	508	60	3	2466	2971	423534056	423534562	1.280000e-163	586.0
31	TraesCS1D01G079200	chr4D	84.649	228	21	4	2970	3184	51078768	51078994	6.940000e-52	215.0
32	TraesCS1D01G079200	chr5B	79.668	241	21	7	2970	3182	441526042	441526282	7.140000e-32	148.0
33	TraesCS1D01G079200	chr7D	88.136	118	5	5	3067	3184	615917243	615917135	7.190000e-27	132.0
34	TraesCS1D01G079200	chr5A	86.735	98	13	0	2970	3067	36390490	36390393	3.370000e-20	110.0
35	TraesCS1D01G079200	chr5A	91.304	46	4	0	3064	3109	607597656	607597701	2.660000e-06	63.9
36	TraesCS1D01G079200	chr3B	100.000	29	0	0	3159	3187	757776288	757776260	2.000000e-03	54.7
37	TraesCS1D01G079200	chr2B	100.000	29	0	0	1351	1379	76081288	76081316	2.000000e-03	54.7

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	TraesCS1D01G079200	chr1D	61941998	61945193	3195	True	5903.0	5903	100.0000	1	3196	1	chr1D.!!$R1	3195
1	TraesCS1D01G079200	chr1A	59841120	59842563	1443	True	2338.0	2338	95.8680	770	2218	1	chr1A.!!$R2	1448
2	TraesCS1D01G079200	chr1A	59856786	59857584	798	True	448.5	1146	98.1340	1	735	3	chr1A.!!$R3	734
3	TraesCS1D01G079200	chr1B	98446132	98447606	1474	True	2241.0	2241	94.1020	862	2341	1	chr1B.!!$R3	1479
4	TraesCS1D01G079200	chr1B	98721844	98722505	661	True	985.0	985	93.5340	1	662	1	chr1B.!!$R4	661
5	TraesCS1D01G079200	chr1B	98439024	98439682	658	True	723.0	723	86.6960	2340	3008	1	chr1B.!!$R2	668
6	TraesCS1D01G079200	chr1B	98391669	98392327	658	True	717.0	717	86.5500	2340	3008	1	chr1B.!!$R1	668
7	TraesCS1D01G079200	chr6B	551911202	551911710	508	False	671.0	671	90.4670	2468	2978	1	chr6B.!!$F1	510
8	TraesCS1D01G079200	chr6B	533277033	533277539	506	True	597.0	597	88.0160	2473	2977	1	chr6B.!!$R1	504
9	TraesCS1D01G079200	chr4A	545599907	545600948	1041	True	406.0	645	86.4635	2473	3152	2	chr4A.!!$R1	679
10	TraesCS1D01G079200	chr2D	194648681	194649182	501	False	641.0	641	89.8610	2473	2971	1	chr2D.!!$F1	498
11	TraesCS1D01G079200	chr2D	612817643	612818158	515	True	590.0	590	87.4030	2468	2980	1	chr2D.!!$R2	512
12	TraesCS1D01G079200	chr6A	4869753	4870263	510	False	632.0	632	89.2370	2468	2971	1	chr6A.!!$F1	503
13	TraesCS1D01G079200	chr6D	392576975	392580577	3602	True	383.5	619	88.9165	2473	3185	2	chr6D.!!$R1	712
14	TraesCS1D01G079200	chr3A	423534056	423534562	506	False	586.0	586	87.5980	2466	2971	1	chr3A.!!$F1	505

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
760	826	0.605589	AGGAAAAGGTGTGGCTACGC	60.606	55.0	5.0	5.0	36.58	4.42	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2283	2364	0.600255	AGCTGAGGAAACAACGGTCG	60.6	55.0	0.0	0.0	0.0	4.79	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
85	92	7.327975	CCATGGTTAGTCTACAACATCAACTA	58.672	38.462	2.57	0.00	0.00	2.24
163	170	3.433740	GGACTTGAACAGAGTTGAAGGGT	60.434	47.826	12.41	0.00	0.00	4.34
315	322	2.065799	ACCCCAGGAGTTTGAGATTGT	58.934	47.619	0.00	0.00	0.00	2.71
362	369	7.017645	GCGATGACACATGTGATTATTATTCC	58.982	38.462	31.94	9.26	0.00	3.01
433	441	4.878971	CGATGTAACAAACCACCCATGATA	59.121	41.667	0.00	0.00	0.00	2.15
592	600	7.038048	TCATCACATTGTTCTGTCAGATACTC	58.962	38.462	2.68	0.00	0.00	2.59
605	613	8.370940	TCTGTCAGATACTCTCAAGTTTTTCAT	58.629	33.333	0.00	0.00	36.92	2.57
648	656	5.652014	ACTGAACAAGTTGACAAATCCTCAA	59.348	36.000	10.54	0.00	34.57	3.02
649	657	5.890334	TGAACAAGTTGACAAATCCTCAAC	58.110	37.500	10.54	3.56	45.36	3.18
650	658	4.918810	ACAAGTTGACAAATCCTCAACC	57.081	40.909	10.54	0.00	45.92	3.77
651	659	4.277476	ACAAGTTGACAAATCCTCAACCA	58.723	39.130	10.54	0.00	45.92	3.67
699	765	1.369625	CTGCCTCGTGTTTGTATCCC	58.630	55.000	0.00	0.00	0.00	3.85
710	776	3.763360	TGTTTGTATCCCAGCAAATCAGG	59.237	43.478	0.00	0.00	37.02	3.86
735	801	2.578021	AGGGCCTGCATTCTCTTAAGAA	59.422	45.455	4.50	0.00	45.36	2.52
736	802	3.010584	AGGGCCTGCATTCTCTTAAGAAA	59.989	43.478	4.50	4.81	44.49	2.52
737	803	3.763897	GGGCCTGCATTCTCTTAAGAAAA	59.236	43.478	6.63	0.00	44.49	2.29
738	804	4.220602	GGGCCTGCATTCTCTTAAGAAAAA	59.779	41.667	6.63	4.66	44.49	1.94
739	805	5.405797	GGCCTGCATTCTCTTAAGAAAAAG	58.594	41.667	6.63	0.00	44.49	2.27
740	806	5.183904	GGCCTGCATTCTCTTAAGAAAAAGA	59.816	40.000	6.63	0.00	44.49	2.52
741	807	6.294731	GGCCTGCATTCTCTTAAGAAAAAGAA	60.295	38.462	6.63	6.96	44.49	2.52
742	808	6.805760	GCCTGCATTCTCTTAAGAAAAAGAAG	59.194	38.462	6.63	0.71	44.49	2.85
743	809	7.311408	CCTGCATTCTCTTAAGAAAAAGAAGG	58.689	38.462	6.43	6.43	44.49	3.46
744	810	7.175641	CCTGCATTCTCTTAAGAAAAAGAAGGA	59.824	37.037	13.56	0.00	44.49	3.36
745	811	8.463930	TGCATTCTCTTAAGAAAAAGAAGGAA	57.536	30.769	16.49	10.18	44.49	3.36
746	812	8.912988	TGCATTCTCTTAAGAAAAAGAAGGAAA	58.087	29.630	16.49	5.38	44.49	3.13
747	813	9.750125	GCATTCTCTTAAGAAAAAGAAGGAAAA	57.250	29.630	16.49	0.00	44.49	2.29
750	816	9.475620	TTCTCTTAAGAAAAAGAAGGAAAAGGT	57.524	29.630	6.63	0.00	38.58	3.50
751	817	8.903820	TCTCTTAAGAAAAAGAAGGAAAAGGTG	58.096	33.333	6.63	0.00	35.14	4.00
752	818	8.589701	TCTTAAGAAAAAGAAGGAAAAGGTGT	57.410	30.769	1.68	0.00	32.59	4.16
753	819	8.466798	TCTTAAGAAAAAGAAGGAAAAGGTGTG	58.533	33.333	1.68	0.00	32.59	3.82
754	820	5.598416	AGAAAAAGAAGGAAAAGGTGTGG	57.402	39.130	0.00	0.00	0.00	4.17
755	821	3.819564	AAAAGAAGGAAAAGGTGTGGC	57.180	42.857	0.00	0.00	0.00	5.01
756	822	2.755952	AAGAAGGAAAAGGTGTGGCT	57.244	45.000	0.00	0.00	0.00	4.75
757	823	3.876309	AAGAAGGAAAAGGTGTGGCTA	57.124	42.857	0.00	0.00	0.00	3.93
758	824	3.141767	AGAAGGAAAAGGTGTGGCTAC	57.858	47.619	0.00	0.00	0.00	3.58
759	825	1.804748	GAAGGAAAAGGTGTGGCTACG	59.195	52.381	0.00	0.00	0.00	3.51
760	826	0.605589	AGGAAAAGGTGTGGCTACGC	60.606	55.000	5.00	5.00	36.58	4.42
778	844	2.427245	CCCAGGGGTACTCGCTCAG	61.427	68.421	0.00	0.00	36.43	3.35
797	863	3.014807	TCAGTCCCCTTATCCTTACCCTT	59.985	47.826	0.00	0.00	0.00	3.95
798	864	3.136626	CAGTCCCCTTATCCTTACCCTTG	59.863	52.174	0.00	0.00	0.00	3.61
807	873	1.638589	TCCTTACCCTTGGGTTCCATG	59.361	52.381	17.30	1.74	31.53	3.66
834	900	5.582689	TCGATGAAGACATAGCAAGAAGA	57.417	39.130	0.00	0.00	36.82	2.87
851	917	8.810041	AGCAAGAAGATCAATGAAACCTTTATT	58.190	29.630	0.00	0.00	0.00	1.40
852	918	9.428097	GCAAGAAGATCAATGAAACCTTTATTT	57.572	29.630	0.00	0.00	0.00	1.40
1128	1209	0.318784	GCGACTCAAACTCCGACACT	60.319	55.000	0.00	0.00	0.00	3.55
1265	1346	1.883926	GTACCTTGCGTCCAAACCATT	59.116	47.619	0.00	0.00	0.00	3.16
1282	1363	3.689649	ACCATTGCTCGTTTAGTTCCATC	59.310	43.478	0.00	0.00	0.00	3.51
1296	1377	1.210538	TCCATCCAAGCAGAGCTCAT	58.789	50.000	17.77	0.00	38.25	2.90
1298	1379	1.134189	CCATCCAAGCAGAGCTCATCA	60.134	52.381	17.77	0.00	38.25	3.07
1299	1380	2.214347	CATCCAAGCAGAGCTCATCAG	58.786	52.381	17.77	3.79	38.25	2.90
1315	1396	0.030773	TCAGCTACGTGCCATCGATC	59.969	55.000	0.00	0.00	44.23	3.69
1336	1417	3.939939	TGCCTGTGCAGCCGAGAA	61.940	61.111	0.00	0.00	44.23	2.87
1380	1461	1.377725	TACCTGGAGTCGTCGGGTC	60.378	63.158	0.00	0.00	33.34	4.46
1538	1619	3.550431	GGGCAGGGCTCGATGCTA	61.550	66.667	8.50	0.00	42.19	3.49
2213	2294	1.663695	AAGAACACGACCACTTGTGG	58.336	50.000	17.34	17.34	40.39	4.17
2237	2318	5.633830	TTTGGTCGAGGTGTAAGTACTAG	57.366	43.478	0.00	0.00	0.00	2.57
2238	2319	4.292186	TGGTCGAGGTGTAAGTACTAGT	57.708	45.455	0.00	0.00	0.00	2.57
2241	2322	4.272261	GGTCGAGGTGTAAGTACTAGTAGC	59.728	50.000	1.87	0.00	0.00	3.58
2242	2323	4.872691	GTCGAGGTGTAAGTACTAGTAGCA	59.127	45.833	1.87	0.00	0.00	3.49
2243	2324	5.526846	GTCGAGGTGTAAGTACTAGTAGCAT	59.473	44.000	1.87	0.00	0.00	3.79
2244	2325	6.038050	GTCGAGGTGTAAGTACTAGTAGCATT	59.962	42.308	1.87	1.80	0.00	3.56
2245	2326	6.600822	TCGAGGTGTAAGTACTAGTAGCATTT	59.399	38.462	1.87	0.00	0.00	2.32
2246	2327	7.770433	TCGAGGTGTAAGTACTAGTAGCATTTA	59.230	37.037	1.87	0.00	0.00	1.40
2247	2328	8.566260	CGAGGTGTAAGTACTAGTAGCATTTAT	58.434	37.037	1.87	0.00	0.00	1.40
2259	2340	9.032420	ACTAGTAGCATTTATTAAAGCGAAGAC	57.968	33.333	0.00	0.29	0.00	3.01
2260	2341	7.843490	AGTAGCATTTATTAAAGCGAAGACA	57.157	32.000	0.00	0.00	0.00	3.41
2283	2364	3.983044	AAACTGGATCAGGTACACCTC	57.017	47.619	0.00	0.00	46.65	3.85
2354	2435	5.782893	TTACTGGAATTGTTGGGAACTTG	57.217	39.130	0.00	0.00	0.00	3.16
2375	2456	8.574251	ACTTGCTCAGGACTATATAGAGTATG	57.426	38.462	16.79	9.11	0.00	2.39
2376	2457	7.122055	ACTTGCTCAGGACTATATAGAGTATGC	59.878	40.741	16.79	12.31	0.00	3.14
2377	2458	6.726379	TGCTCAGGACTATATAGAGTATGCT	58.274	40.000	16.79	1.73	0.00	3.79
2430	2519	2.475200	CTCGCATGAGTATGTCACGA	57.525	50.000	0.00	0.00	38.28	4.35
2436	2527	5.098211	CGCATGAGTATGTCACGATATCAT	58.902	41.667	3.12	0.00	38.28	2.45
2438	2529	6.328507	CATGAGTATGTCACGATATCATGC	57.671	41.667	3.12	0.00	38.28	4.06
2446	2537	4.508861	TGTCACGATATCATGCATTCACTG	59.491	41.667	0.00	0.00	0.00	3.66
2455	2546	1.351076	TGCATTCACTGGGACTGAGA	58.649	50.000	0.95	0.00	0.00	3.27
2466	2557	5.026121	ACTGGGACTGAGAATAGATGTTCA	58.974	41.667	0.00	0.00	0.00	3.18
2500	2591	3.889538	TCTAGCAGACCACGTATAATGCT	59.110	43.478	17.87	17.87	45.35	3.79
2505	2596	2.891580	AGACCACGTATAATGCTCCGAT	59.108	45.455	0.00	0.00	0.00	4.18
2518	2609	1.332904	GCTCCGATCCGCAAAATAACG	60.333	52.381	0.00	0.00	0.00	3.18
2519	2610	1.931172	CTCCGATCCGCAAAATAACGT	59.069	47.619	0.00	0.00	0.00	3.99
2535	2629	2.773993	ACGTCAAAATATGGGTCCGT	57.226	45.000	0.00	0.00	0.00	4.69
2573	2667	4.745125	CCGATCAGACACTATAAATGCGTT	59.255	41.667	0.00	0.00	0.00	4.84
2621	2715	2.290705	CGGTAAAATCCCACCTCCAACT	60.291	50.000	0.00	0.00	32.29	3.16
2622	2716	3.774734	GGTAAAATCCCACCTCCAACTT	58.225	45.455	0.00	0.00	0.00	2.66
3065	6036	1.329599	GCATAGCGGAACCCTAAAACG	59.670	52.381	0.00	0.00	0.00	3.60
3089	6087	3.094062	GCTATGCGGGGTCTGCTCA	62.094	63.158	0.30	0.00	0.00	4.26
3123	6121	1.664649	GGCCTGCAAAGCCGTTTTC	60.665	57.895	11.41	0.00	41.41	2.29
3153	6151	2.608546	TGTAAACGAGTTTTGTGGGTCG	59.391	45.455	6.53	0.00	38.40	4.79
3154	6152	1.018910	AAACGAGTTTTGTGGGTCGG	58.981	50.000	0.00	0.00	36.74	4.79
3157	6155	2.593436	AGTTTTGTGGGTCGGCGG	60.593	61.111	7.21	0.00	0.00	6.13
3185	6183	3.430453	GGGTCTGCTAGAGATGCTCTAT	58.570	50.000	4.77	0.00	41.49	1.98
3186	6184	3.193267	GGGTCTGCTAGAGATGCTCTATG	59.807	52.174	4.77	1.93	41.49	2.23
3187	6185	4.078537	GGTCTGCTAGAGATGCTCTATGA	58.921	47.826	4.77	2.50	41.49	2.15
3188	6186	4.522405	GGTCTGCTAGAGATGCTCTATGAA	59.478	45.833	4.77	0.00	41.49	2.57
3189	6187	5.460646	GTCTGCTAGAGATGCTCTATGAAC	58.539	45.833	4.77	0.00	41.49	3.18
3190	6188	5.009510	GTCTGCTAGAGATGCTCTATGAACA	59.990	44.000	4.77	2.05	41.49	3.18
3191	6189	5.595952	TCTGCTAGAGATGCTCTATGAACAA	59.404	40.000	4.77	0.00	41.49	2.83
3192	6190	6.267242	TCTGCTAGAGATGCTCTATGAACAAT	59.733	38.462	4.77	0.00	41.49	2.71
3193	6191	6.221659	TGCTAGAGATGCTCTATGAACAATG	58.778	40.000	4.77	0.00	41.49	2.82
3194	6192	5.120519	GCTAGAGATGCTCTATGAACAATGC	59.879	44.000	4.77	0.00	41.49	3.56
3195	6193	5.293319	AGAGATGCTCTATGAACAATGCT	57.707	39.130	0.00	0.00	39.28	3.79

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
85	92	3.338249	ACATTTGATTAGTGCGAGTGCT	58.662	40.909	0.00	0.00	43.34	4.40
163	170	1.221566	CAGGATGTCCATCGGCACA	59.778	57.895	1.30	0.00	38.69	4.57
240	247	0.886490	AACTTCAAGCAGCCGTCTGG	60.886	55.000	0.00	0.00	40.65	3.86
283	290	3.077088	ACTCCTGGGGTTTCTAGTAGACA	59.923	47.826	0.00	0.00	0.00	3.41
315	322	1.337384	ATATCCCGTGTGGCTGCAGA	61.337	55.000	20.43	0.00	0.00	4.26
386	393	4.718961	CAGTAGGGGGAAAGAATACATGG	58.281	47.826	0.00	0.00	0.00	3.66
433	441	7.040617	TCGAAACACTTCTCATCTACTTACAGT	60.041	37.037	0.00	0.00	0.00	3.55
592	600	8.706035	CCAGATAGCAAAAATGAAAAACTTGAG	58.294	33.333	0.00	0.00	0.00	3.02
605	613	7.067615	TGTTCAGTTTGTACCAGATAGCAAAAA	59.932	33.333	0.00	0.00	33.43	1.94
710	776	1.823041	GAGAATGCAGGCCCTCAGC	60.823	63.158	0.00	0.00	42.60	4.26
735	801	3.374764	AGCCACACCTTTTCCTTCTTTT	58.625	40.909	0.00	0.00	0.00	2.27
736	802	3.032265	AGCCACACCTTTTCCTTCTTT	57.968	42.857	0.00	0.00	0.00	2.52
737	803	2.755952	AGCCACACCTTTTCCTTCTT	57.244	45.000	0.00	0.00	0.00	2.52
738	804	2.550208	CGTAGCCACACCTTTTCCTTCT	60.550	50.000	0.00	0.00	0.00	2.85
739	805	1.804748	CGTAGCCACACCTTTTCCTTC	59.195	52.381	0.00	0.00	0.00	3.46
740	806	1.892209	CGTAGCCACACCTTTTCCTT	58.108	50.000	0.00	0.00	0.00	3.36
741	807	3.625745	CGTAGCCACACCTTTTCCT	57.374	52.632	0.00	0.00	0.00	3.36
755	821	2.487532	CGAGTACCCCTGGGCGTAG	61.488	68.421	7.39	0.00	39.32	3.51
756	822	2.440796	CGAGTACCCCTGGGCGTA	60.441	66.667	7.39	8.55	39.32	4.42
759	825	3.851128	GAGCGAGTACCCCTGGGC	61.851	72.222	7.39	0.00	39.32	5.36
760	826	2.363795	TGAGCGAGTACCCCTGGG	60.364	66.667	5.50	5.50	42.03	4.45
761	827	1.668101	GACTGAGCGAGTACCCCTGG	61.668	65.000	0.00	0.00	33.83	4.45
762	828	1.668101	GGACTGAGCGAGTACCCCTG	61.668	65.000	0.00	0.00	33.83	4.45
763	829	1.380112	GGACTGAGCGAGTACCCCT	60.380	63.158	0.00	0.00	33.83	4.79
764	830	3.208335	GGACTGAGCGAGTACCCC	58.792	66.667	0.00	0.00	33.83	4.95
767	833	1.760192	TAAGGGGACTGAGCGAGTAC	58.240	55.000	0.00	0.00	42.68	2.73
768	834	2.584236	GATAAGGGGACTGAGCGAGTA	58.416	52.381	0.00	0.00	42.68	2.59
778	844	2.442126	CCAAGGGTAAGGATAAGGGGAC	59.558	54.545	0.00	0.00	0.00	4.46
797	863	1.417517	CATCGATCTCCATGGAACCCA	59.582	52.381	17.00	0.08	38.19	4.51
798	864	1.694150	TCATCGATCTCCATGGAACCC	59.306	52.381	17.00	6.39	0.00	4.11
807	873	4.511617	TGCTATGTCTTCATCGATCTCC	57.488	45.455	0.00	0.00	35.70	3.71
851	917	7.315066	TGACCAGCTGGATATAATCATACAA	57.685	36.000	39.19	5.74	38.94	2.41
852	918	6.933514	TGACCAGCTGGATATAATCATACA	57.066	37.500	39.19	15.78	38.94	2.29
853	919	8.097038	TCTTTGACCAGCTGGATATAATCATAC	58.903	37.037	39.19	13.72	38.94	2.39
854	920	8.206126	TCTTTGACCAGCTGGATATAATCATA	57.794	34.615	39.19	22.22	38.94	2.15
855	921	7.083062	TCTTTGACCAGCTGGATATAATCAT	57.917	36.000	39.19	13.54	38.94	2.45
856	922	6.499106	TCTTTGACCAGCTGGATATAATCA	57.501	37.500	39.19	26.28	38.94	2.57
857	923	7.148507	CGATTCTTTGACCAGCTGGATATAATC	60.149	40.741	39.19	29.45	38.94	1.75
858	924	6.652481	CGATTCTTTGACCAGCTGGATATAAT	59.348	38.462	39.19	25.59	38.94	1.28
1050	1131	2.537863	GAGTTCACAGCACTCCAGC	58.462	57.895	0.00	0.00	35.53	4.85
1054	1135	0.946221	CGTGGGAGTTCACAGCACTC	60.946	60.000	0.00	0.00	40.12	3.51
1065	1146	4.988716	TCCGTCCTGCGTGGGAGT	62.989	66.667	0.00	0.00	39.32	3.85
1265	1346	3.334691	CTTGGATGGAACTAAACGAGCA	58.665	45.455	0.00	0.00	0.00	4.26
1282	1363	2.395651	GCTGATGAGCTCTGCTTGG	58.604	57.895	16.19	1.79	43.43	3.61
1296	1377	0.030773	GATCGATGGCACGTAGCTGA	59.969	55.000	0.54	4.46	44.79	4.26
1298	1379	1.008424	CGATCGATGGCACGTAGCT	60.008	57.895	10.26	0.00	44.79	3.32
1299	1380	2.649257	GCGATCGATGGCACGTAGC	61.649	63.158	25.21	0.00	44.65	3.58
1301	1382	0.939106	CATGCGATCGATGGCACGTA	60.939	55.000	33.09	16.27	44.13	3.57
1380	1461	0.324943	ACTCCATCGGTGAAGTTGGG	59.675	55.000	0.00	0.00	33.08	4.12
1613	1694	4.680237	TCCGGCAGCGTGAGGTTG	62.680	66.667	0.00	0.00	41.81	3.77
2213	2294	4.625028	AGTACTTACACCTCGACCAAAAC	58.375	43.478	0.00	0.00	0.00	2.43
2237	2318	8.889849	TTTGTCTTCGCTTTAATAAATGCTAC	57.110	30.769	5.93	0.00	34.46	3.58
2238	2319	9.900710	TTTTTGTCTTCGCTTTAATAAATGCTA	57.099	25.926	5.93	0.00	34.46	3.49
2283	2364	0.600255	AGCTGAGGAAACAACGGTCG	60.600	55.000	0.00	0.00	0.00	4.79
2324	2405	6.265876	TCCCAACAATTCCAGTAAAAACTACC	59.734	38.462	0.00	0.00	0.00	3.18
2354	2435	7.639113	AAGCATACTCTATATAGTCCTGAGC	57.361	40.000	9.58	8.23	0.00	4.26
2388	2477	9.685828	CGAGTATAATCTTTTTGTTTGGGAAAA	57.314	29.630	0.00	0.00	0.00	2.29
2429	2518	4.454847	CAGTCCCAGTGAATGCATGATATC	59.545	45.833	0.00	0.00	31.53	1.63
2430	2519	4.103627	TCAGTCCCAGTGAATGCATGATAT	59.896	41.667	0.00	0.00	38.91	1.63
2436	2527	1.351076	TCTCAGTCCCAGTGAATGCA	58.649	50.000	0.00	0.00	38.91	3.96
2438	2529	5.604758	TCTATTCTCAGTCCCAGTGAATG	57.395	43.478	0.00	0.00	40.39	2.67
2446	2537	5.606348	AGTGAACATCTATTCTCAGTCCC	57.394	43.478	0.00	0.00	0.00	4.46
2466	2557	4.467795	TGGTCTGCTAGAGATGCTTTTAGT	59.532	41.667	0.00	0.00	31.63	2.24
2500	2591	1.928503	GACGTTATTTTGCGGATCGGA	59.071	47.619	4.16	0.00	0.00	4.55
2505	2596	6.030849	CCATATTTTGACGTTATTTTGCGGA	58.969	36.000	0.00	0.00	0.00	5.54
2518	2609	3.340034	TCACACGGACCCATATTTTGAC	58.660	45.455	0.00	0.00	0.00	3.18
2519	2610	3.704800	TCACACGGACCCATATTTTGA	57.295	42.857	0.00	0.00	0.00	2.69
2547	2641	4.686554	GCATTTATAGTGTCTGATCGGACC	59.313	45.833	27.92	19.75	35.54	4.46
2597	2691	1.078001	AGGTGGGATTTTACCGCGG	60.078	57.895	26.86	26.86	41.85	6.46
2922	3032	1.004918	GCACAAGTACTCACCGGCT	60.005	57.895	0.00	0.00	0.00	5.52
2966	3076	7.228308	TCTGAATTTGACACATATGACACAACA	59.772	33.333	10.38	6.09	29.93	3.33
3031	4647	3.379865	TATGCGGGGTCTGTTCGGC	62.380	63.158	0.00	0.00	0.00	5.54
3057	6028	1.329599	GCATAGCGGAACCGTTTTAGG	59.670	52.381	14.63	8.07	42.09	2.69
3058	6029	2.732001	GCATAGCGGAACCGTTTTAG	57.268	50.000	14.63	3.96	42.09	1.85
3109	6107	2.725008	CGGGAAAACGGCTTTGCA	59.275	55.556	6.20	0.00	37.10	4.08
3123	6121	0.665369	ACTCGTTTACAGTTCGCGGG	60.665	55.000	6.13	0.00	0.00	6.13
3153	6151	2.732658	CAGACCCCGTATACCGCC	59.267	66.667	0.00	0.00	34.38	6.13
3154	6152	1.174712	TAGCAGACCCCGTATACCGC	61.175	60.000	0.00	0.00	34.38	5.68
3157	6155	3.137446	TCTCTAGCAGACCCCGTATAC	57.863	52.381	0.00	0.00	0.00	1.47
3163	6161	0.678950	GAGCATCTCTAGCAGACCCC	59.321	60.000	0.00	0.00	32.26	4.95

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.