AutoCloner

Multiple sequence alignment - TraesCS3B01G099000

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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	TraesCS3B01G099000	chr3B	100.000	2555	0	0	1	2555	66472136	66469582	0.000000e+00	4719.0
1	TraesCS3B01G099000	chr3B	82.627	967	113	23	1356	2280	66478604	66477651	0.000000e+00	804.0
2	TraesCS3B01G099000	chr3B	79.200	875	138	25	1397	2245	143509976	143510832	4.520000e-158	568.0
3	TraesCS3B01G099000	chr3B	77.047	928	155	32	1359	2258	143604241	143605138	6.060000e-132	481.0
4	TraesCS3B01G099000	chr3B	100.000	210	0	0	2914	3123	66469223	66469014	3.780000e-104	388.0
5	TraesCS3B01G099000	chr3B	84.615	104	15	1	487	590	66479295	66479193	5.510000e-18	102.0
6	TraesCS3B01G099000	chr3A	94.118	1054	54	6	1329	2381	54232937	54231891	0.000000e+00	1596.0
7	TraesCS3B01G099000	chr3A	89.327	862	57	16	483	1327	54233728	54232885	0.000000e+00	1050.0
8	TraesCS3B01G099000	chr3A	82.103	894	117	24	1398	2257	54284868	54283984	0.000000e+00	725.0
9	TraesCS3B01G099000	chr3A	77.962	903	149	28	1397	2268	547182357	547183240	1.280000e-143	520.0
10	TraesCS3B01G099000	chr3A	88.636	264	21	6	943	1202	54285195	54284937	2.340000e-81	313.0
11	TraesCS3B01G099000	chr3A	87.907	215	17	7	2914	3123	54231752	54231542	8.650000e-61	244.0
12	TraesCS3B01G099000	chr3A	97.059	34	1	0	1	34	149077764	149077797	1.210000e-04	58.4
13	TraesCS3B01G099000	chr3D	92.986	1055	60	8	1328	2381	42679909	42678868	0.000000e+00	1526.0
14	TraesCS3B01G099000	chr3D	89.777	851	59	13	483	1325	42680688	42679858	0.000000e+00	1064.0
15	TraesCS3B01G099000	chr3D	84.308	701	99	9	1584	2280	42687197	42686504	0.000000e+00	675.0
16	TraesCS3B01G099000	chr3D	77.840	898	146	33	1397	2268	92896048	92895178	9.990000e-140	507.0
17	TraesCS3B01G099000	chr3D	76.700	691	116	27	1584	2257	92813676	92813014	2.980000e-90	342.0
18	TraesCS3B01G099000	chr3D	88.940	217	12	8	2915	3123	42678690	42678478	1.110000e-64	257.0
19	TraesCS3B01G099000	chr3D	89.677	155	7	7	2401	2555	42678888	42678743	4.110000e-44	189.0
20	TraesCS3B01G099000	chr3D	85.185	162	20	1	1359	1520	42687516	42687359	2.490000e-36	163.0
21	TraesCS3B01G099000	chr3D	86.538	104	13	1	487	590	42688211	42688109	2.550000e-21	113.0
22	TraesCS3B01G099000	chr2B	92.562	484	30	4	1	482	604325967	604326446	0.000000e+00	689.0
23	TraesCS3B01G099000	chr6D	92.541	429	28	3	59	485	389969846	389969420	2.060000e-171	612.0
24	TraesCS3B01G099000	chr6D	95.890	73	3	0	1	73	389969934	389969862	5.470000e-23	119.0
25	TraesCS3B01G099000	chr7B	89.938	487	26	9	1	483	135983091	135983558	9.580000e-170	606.0
26	TraesCS3B01G099000	chr7B	81.724	290	40	12	200	485	135981994	135981714	2.420000e-56	230.0
27	TraesCS3B01G099000	chr7B	87.402	127	14	2	1	127	703268765	703268641	9.030000e-31	145.0
28	TraesCS3B01G099000	chr2A	91.705	434	29	6	57	487	181844832	181845261	2.070000e-166	595.0
29	TraesCS3B01G099000	chr2A	97.183	71	2	0	1	71	181837431	181837501	1.520000e-23	121.0
30	TraesCS3B01G099000	chr2D	90.736	421	27	3	57	477	498319573	498319981	4.550000e-153	551.0
31	TraesCS3B01G099000	chr2D	95.890	73	3	0	1	73	498319482	498319554	5.470000e-23	119.0
32	TraesCS3B01G099000	chr5A	84.562	434	58	8	57	485	469134530	469134959	3.720000e-114	422.0
33	TraesCS3B01G099000	chr4D	78.899	327	58	9	158	479	340093579	340093259	8.770000e-51	211.0
34	TraesCS3B01G099000	chr5D	78.659	328	52	14	165	482	25302292	25301973	5.280000e-48	202.0
35	TraesCS3B01G099000	chr6B	100.000	31	0	0	4	34	720008308	720008338	1.210000e-04	58.4
36	TraesCS3B01G099000	chr7D	96.774	31	1	0	1	31	45762388	45762418	6.000000e-03	52.8

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	TraesCS3B01G099000	chr3B	66469014	66472136	3122	True	2553.500000	4719	100.000000	1	3123	2	chr3B.!!$R1	3122
1	TraesCS3B01G099000	chr3B	143509976	143510832	856	False	568.000000	568	79.200000	1397	2245	1	chr3B.!!$F1	848
2	TraesCS3B01G099000	chr3B	143604241	143605138	897	False	481.000000	481	77.047000	1359	2258	1	chr3B.!!$F2	899
3	TraesCS3B01G099000	chr3B	66477651	66479295	1644	True	453.000000	804	83.621000	487	2280	2	chr3B.!!$R2	1793
4	TraesCS3B01G099000	chr3A	54231542	54233728	2186	True	963.333333	1596	90.450667	483	3123	3	chr3A.!!$R1	2640
5	TraesCS3B01G099000	chr3A	547182357	547183240	883	False	520.000000	520	77.962000	1397	2268	1	chr3A.!!$F2	871
6	TraesCS3B01G099000	chr3A	54283984	54285195	1211	True	519.000000	725	85.369500	943	2257	2	chr3A.!!$R2	1314
7	TraesCS3B01G099000	chr3D	42678478	42680688	2210	True	759.000000	1526	90.345000	483	3123	4	chr3D.!!$R3	2640
8	TraesCS3B01G099000	chr3D	92895178	92896048	870	True	507.000000	507	77.840000	1397	2268	1	chr3D.!!$R2	871
9	TraesCS3B01G099000	chr3D	92813014	92813676	662	True	342.000000	342	76.700000	1584	2257	1	chr3D.!!$R1	673
10	TraesCS3B01G099000	chr3D	42686504	42688211	1707	True	317.000000	675	85.343667	487	2280	3	chr3D.!!$R4	1793
11	TraesCS3B01G099000	chr6D	389969420	389969934	514	True	365.500000	612	94.215500	1	485	2	chr6D.!!$R1	484

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	Hairpin	End Stability	Orientation
259	290	0.248012	TATGGCGCTCGGTCTTTTCA	59.752	50.0	7.64	0.00	2.69	F
309	342	0.378257	AAATATGCGTTGGCTGAGCG	59.622	50.0	0.00	40.82	5.03	F
1790	2008	0.175073	CCCCTACCAGCTCGTGTAAC	59.825	60.0	0.00	0.00	2.50	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1431	1544	0.037590	TTTGGATCCACCCTGAACCG	59.962	55.0	15.91	0.00	38.0	4.44	R
1863	2088	0.804364	GCGATCAATCAAGGTGCACA	59.196	50.0	20.43	0.00	0.0	4.57	R
2917	3178	0.532115	GTGGAAGGATGCGGCAAATT	59.468	50.0	6.82	1.69	0.0	1.82	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
31	32	4.825546	CAGTATCTGCAGCCCATTTAAG	57.174	45.455	9.47	0.00	0.00	1.85
98	129	2.513204	CACGAGCTCAGCATGGGG	60.513	66.667	15.40	0.00	36.76	4.96
121	152	2.648059	GAGTGGCTGTAATGGCTGAAT	58.352	47.619	0.00	0.00	0.00	2.57
179	210	5.983118	CCTTTTTGGCGTTAATTTTCTCAGT	59.017	36.000	0.00	0.00	0.00	3.41
183	214	5.600908	TGGCGTTAATTTTCTCAGTGTAC	57.399	39.130	0.00	0.00	0.00	2.90
184	215	4.150980	TGGCGTTAATTTTCTCAGTGTACG	59.849	41.667	0.00	0.00	0.00	3.67
198	229	4.810491	TCAGTGTACGGTGGTTAGTTTTTC	59.190	41.667	0.00	0.00	0.00	2.29
200	231	4.812626	AGTGTACGGTGGTTAGTTTTTCTG	59.187	41.667	0.00	0.00	0.00	3.02
208	239	6.362283	CGGTGGTTAGTTTTTCTGCAAATAAG	59.638	38.462	0.00	0.00	0.00	1.73
258	289	1.062148	GTTATGGCGCTCGGTCTTTTC	59.938	52.381	7.64	0.00	0.00	2.29
259	290	0.248012	TATGGCGCTCGGTCTTTTCA	59.752	50.000	7.64	0.00	0.00	2.69
309	342	0.378257	AAATATGCGTTGGCTGAGCG	59.622	50.000	0.00	0.00	40.82	5.03
339	372	0.762418	TTGATAGGTGGGCCCATACG	59.238	55.000	31.45	0.00	34.66	3.06
362	395	3.120321	TGGATACACCCGCAACATATC	57.880	47.619	0.00	0.00	46.17	1.63
366	399	4.578928	GGATACACCCGCAACATATCTTTT	59.421	41.667	0.00	0.00	0.00	2.27
367	400	3.848272	ACACCCGCAACATATCTTTTG	57.152	42.857	0.00	0.00	0.00	2.44
368	401	2.491693	ACACCCGCAACATATCTTTTGG	59.508	45.455	0.00	0.00	0.00	3.28
412	445	6.494842	GTCAAGTTAAGTGACTGCAATTTCA	58.505	36.000	10.62	0.00	41.80	2.69
413	446	6.634436	GTCAAGTTAAGTGACTGCAATTTCAG	59.366	38.462	3.36	3.36	41.80	3.02
419	452	8.482429	GTTAAGTGACTGCAATTTCAGATTTTG	58.518	33.333	12.25	0.00	37.51	2.44
446	479	6.296026	AGTTCTAGCACCAAACTGAACATTA	58.704	36.000	0.00	0.00	37.03	1.90
450	483	3.636300	AGCACCAAACTGAACATTAAGCA	59.364	39.130	0.00	0.00	0.00	3.91
457	490	6.198966	CCAAACTGAACATTAAGCACAAGTTC	59.801	38.462	0.00	0.00	39.11	3.01
463	496	8.565896	TGAACATTAAGCACAAGTTCTATGAT	57.434	30.769	0.00	0.00	39.33	2.45
469	502	5.339008	AGCACAAGTTCTATGATTACCGA	57.661	39.130	0.00	0.00	0.00	4.69
552	585	9.739276	TGGTCCAGATATTAAAATTATAGGCAG	57.261	33.333	0.00	0.00	0.00	4.85
692	733	2.662520	GCGTGCCAAAAATGCAATGTTC	60.663	45.455	0.00	0.00	41.06	3.18
780	821	4.201637	GCAATTAACCGTTTTAAATGCCCG	60.202	41.667	12.56	0.00	35.73	6.13
788	829	4.327627	CCGTTTTAAATGCCCGGTAATTTG	59.672	41.667	17.52	4.82	34.10	2.32
795	836	3.409026	TGCCCGGTAATTTGCATTTTT	57.591	38.095	0.00	0.00	0.00	1.94
799	840	2.093467	CCGGTAATTTGCATTTTTGCCG	59.907	45.455	19.34	19.34	36.82	5.69
801	842	3.060628	CGGTAATTTGCATTTTTGCCGAG	59.939	43.478	20.74	1.43	39.05	4.63
862	947	8.781067	TTCAAAATAGCGTACAAATATGCATC	57.219	30.769	0.19	0.00	44.58	3.91
873	962	1.527034	ATATGCATCCATGGCGTGAC	58.473	50.000	17.93	10.94	32.85	3.67
874	963	0.879839	TATGCATCCATGGCGTGACG	60.880	55.000	17.93	0.00	32.85	4.35
925	1018	0.867746	GCGTGAGTGAAGCATTGTGA	59.132	50.000	0.00	0.00	0.00	3.58
929	1022	3.120752	CGTGAGTGAAGCATTGTGAGAAG	60.121	47.826	0.00	0.00	0.00	2.85
968	1064	2.094659	CAGGAAGCACGCACGTAGG	61.095	63.158	0.00	0.00	0.00	3.18
975	1071	0.928908	GCACGCACGTAGGTAGATCG	60.929	60.000	0.00	0.00	0.00	3.69
976	1072	0.654160	CACGCACGTAGGTAGATCGA	59.346	55.000	0.00	0.00	0.00	3.59
977	1073	1.263484	CACGCACGTAGGTAGATCGAT	59.737	52.381	0.00	0.00	0.00	3.59
978	1074	1.530293	ACGCACGTAGGTAGATCGATC	59.470	52.381	17.91	17.91	0.00	3.69
988	1084	3.634448	AGGTAGATCGATCTGTTGTCCAG	59.366	47.826	33.22	0.00	42.97	3.86
1184	1280	2.091499	TCTTGGATAGGAGCTCCGGTAA	60.091	50.000	26.95	16.64	42.08	2.85
1209	1309	7.275920	AGTATCATCTTTTTCTCCTACGCATT	58.724	34.615	0.00	0.00	0.00	3.56
1213	1313	4.637276	TCTTTTTCTCCTACGCATTGACA	58.363	39.130	0.00	0.00	0.00	3.58
1238	1338	9.011095	CAATCAGGAGATTATGCTAATCATGTT	57.989	33.333	14.38	0.00	42.46	2.71
1269	1373	6.786122	AGTAGACTAAATTAAGTGGCCCAAA	58.214	36.000	0.00	0.00	0.00	3.28
1270	1374	7.235804	AGTAGACTAAATTAAGTGGCCCAAAA	58.764	34.615	0.00	0.00	0.00	2.44
1274	1378	9.095700	AGACTAAATTAAGTGGCCCAAAAATAA	57.904	29.630	0.00	0.00	0.00	1.40
1279	1383	6.809630	TTAAGTGGCCCAAAAATAAATTGC	57.190	33.333	0.00	0.00	0.00	3.56
1280	1384	3.333804	AGTGGCCCAAAAATAAATTGCG	58.666	40.909	0.00	0.00	0.00	4.85
1281	1385	3.007398	AGTGGCCCAAAAATAAATTGCGA	59.993	39.130	0.00	0.00	0.00	5.10
1283	1387	3.937706	TGGCCCAAAAATAAATTGCGATG	59.062	39.130	0.00	0.00	0.00	3.84
1284	1388	3.938334	GGCCCAAAAATAAATTGCGATGT	59.062	39.130	0.00	0.00	0.00	3.06
1286	1390	5.006261	GGCCCAAAAATAAATTGCGATGTAC	59.994	40.000	0.00	0.00	0.00	2.90
1287	1391	5.276161	GCCCAAAAATAAATTGCGATGTACG	60.276	40.000	0.00	0.00	45.66	3.67
1288	1392	5.231147	CCCAAAAATAAATTGCGATGTACGG	59.769	40.000	0.00	0.00	42.83	4.02
1289	1393	6.030849	CCAAAAATAAATTGCGATGTACGGA	58.969	36.000	0.00	0.00	42.83	4.69
1297	1401	2.756829	TGCGATGTACGGAAAAGTTCA	58.243	42.857	0.00	0.00	39.76	3.18
1298	1402	3.331150	TGCGATGTACGGAAAAGTTCAT	58.669	40.909	0.00	0.00	39.76	2.57
1299	1403	3.124466	TGCGATGTACGGAAAAGTTCATG	59.876	43.478	0.00	0.00	39.76	3.07
1300	1404	3.670203	CGATGTACGGAAAAGTTCATGC	58.330	45.455	0.00	0.00	33.32	4.06
1301	1405	3.124466	CGATGTACGGAAAAGTTCATGCA	59.876	43.478	0.00	0.00	33.32	3.96
1302	1406	4.651994	GATGTACGGAAAAGTTCATGCAG	58.348	43.478	0.00	0.00	33.32	4.41
1303	1407	3.472652	TGTACGGAAAAGTTCATGCAGT	58.527	40.909	0.00	0.00	0.00	4.40
1304	1408	3.880490	TGTACGGAAAAGTTCATGCAGTT	59.120	39.130	0.00	0.00	0.00	3.16
1305	1409	3.626028	ACGGAAAAGTTCATGCAGTTC	57.374	42.857	0.00	0.00	0.00	3.01
1315	1419	6.017400	AGTTCATGCAGTTCGATTGAATTT	57.983	33.333	0.00	0.00	36.29	1.82
1319	1423	4.159377	TGCAGTTCGATTGAATTTGACC	57.841	40.909	12.10	0.00	36.29	4.02
1320	1424	3.057596	TGCAGTTCGATTGAATTTGACCC	60.058	43.478	12.10	0.00	36.29	4.46
1325	1429	6.646240	CAGTTCGATTGAATTTGACCCAAAAT	59.354	34.615	0.00	0.00	36.90	1.82
1326	1430	7.171337	CAGTTCGATTGAATTTGACCCAAAATT	59.829	33.333	0.00	0.00	41.34	1.82
1431	1544	2.460757	TTAGTTCCAAGGTGGCGTAC	57.539	50.000	0.00	0.00	37.47	3.67
1654	1872	3.172106	TTGGGCAACGTGGAGGGA	61.172	61.111	0.00	0.00	37.60	4.20
1684	1902	2.613977	CGCTCTCCAGACCAACATCTTT	60.614	50.000	0.00	0.00	0.00	2.52
1790	2008	0.175073	CCCCTACCAGCTCGTGTAAC	59.825	60.000	0.00	0.00	0.00	2.50
1852	2077	4.835678	TGCGGATCAATGCATATATCTGT	58.164	39.130	21.97	0.00	35.90	3.41
1929	2154	0.036010	CGGGTGCTCAAGAACCTCAT	60.036	55.000	7.12	0.00	43.60	2.90
2062	2299	1.167781	CCGCCGTGTTACAGGGTTTT	61.168	55.000	22.65	0.00	40.97	2.43
2122	2359	1.959848	CTCACTGAGCCTGTCGTGA	59.040	57.895	0.00	0.00	36.79	4.35
2143	2380	4.593864	GCGATCCGGAGCCTGACC	62.594	72.222	15.35	0.00	0.00	4.02
2346	2587	9.799106	AAAGAAGGTCTGAATTCATAAGAAAGA	57.201	29.630	8.96	0.00	37.29	2.52
2381	2623	7.343316	TCTTTTTGTGGGAAAGAGGAAAACATA	59.657	33.333	0.00	0.00	38.00	2.29
2382	2624	7.425224	TTTTGTGGGAAAGAGGAAAACATAA	57.575	32.000	0.00	0.00	0.00	1.90
2383	2625	6.648879	TTGTGGGAAAGAGGAAAACATAAG	57.351	37.500	0.00	0.00	0.00	1.73
2384	2626	5.947663	TGTGGGAAAGAGGAAAACATAAGA	58.052	37.500	0.00	0.00	0.00	2.10
2385	2627	6.369629	TGTGGGAAAGAGGAAAACATAAGAA	58.630	36.000	0.00	0.00	0.00	2.52
2386	2628	6.836527	TGTGGGAAAGAGGAAAACATAAGAAA	59.163	34.615	0.00	0.00	0.00	2.52
2387	2629	7.014230	TGTGGGAAAGAGGAAAACATAAGAAAG	59.986	37.037	0.00	0.00	0.00	2.62
2388	2630	7.230712	GTGGGAAAGAGGAAAACATAAGAAAGA	59.769	37.037	0.00	0.00	0.00	2.52
2389	2631	7.782644	TGGGAAAGAGGAAAACATAAGAAAGAA	59.217	33.333	0.00	0.00	0.00	2.52
2390	2632	8.300286	GGGAAAGAGGAAAACATAAGAAAGAAG	58.700	37.037	0.00	0.00	0.00	2.85
2391	2633	9.067986	GGAAAGAGGAAAACATAAGAAAGAAGA	57.932	33.333	0.00	0.00	0.00	2.87
2416	2658	4.681074	AAAAATTGCGGGAAAGAGGAAA	57.319	36.364	0.00	0.00	0.00	3.13
2417	2659	4.681074	AAAATTGCGGGAAAGAGGAAAA	57.319	36.364	0.00	0.00	0.00	2.29
2418	2660	3.660501	AATTGCGGGAAAGAGGAAAAC	57.339	42.857	0.00	0.00	0.00	2.43
2419	2661	2.060050	TTGCGGGAAAGAGGAAAACA	57.940	45.000	0.00	0.00	0.00	2.83
2420	2662	2.286365	TGCGGGAAAGAGGAAAACAT	57.714	45.000	0.00	0.00	0.00	2.71
2518	2779	1.804326	CGTACGACCGGCTTTCCAG	60.804	63.158	10.44	0.00	0.00	3.86
2549	2810	5.389411	GCTGTGCCCGTCAAAATTTTATTTC	60.389	40.000	2.44	0.00	0.00	2.17
3064	3332	7.174599	GGAAATCAACCTCTAATCATCATCAGG	59.825	40.741	0.00	0.00	0.00	3.86
3072	3341	6.149640	CCTCTAATCATCATCAGGCAATCTTG	59.850	42.308	0.00	0.00	0.00	3.02
3121	3390	8.831715	ACAAATTTATGGAAAGAATTGACCAC	57.168	30.769	0.00	0.00	37.97	4.16
3122	3391	7.598493	ACAAATTTATGGAAAGAATTGACCACG	59.402	33.333	0.00	0.00	37.97	4.94

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
10	11	3.004106	GCTTAAATGGGCTGCAGATACTG	59.996	47.826	20.43	0.00	34.12	2.74
31	32	4.424061	TGAACAGTAATGCATGTCAAGC	57.576	40.909	0.00	0.00	0.00	4.01
80	111	2.267006	CCCATGCTGAGCTCGTGT	59.733	61.111	9.64	0.00	0.00	4.49
98	129	0.035056	AGCCATTACAGCCACTCCAC	60.035	55.000	0.00	0.00	0.00	4.02
121	152	2.112928	ACACGCCATGTTCAGCCA	59.887	55.556	0.00	0.00	38.98	4.75
179	210	3.560896	GCAGAAAAACTAACCACCGTACA	59.439	43.478	0.00	0.00	0.00	2.90
183	214	3.701532	TTGCAGAAAAACTAACCACCG	57.298	42.857	0.00	0.00	0.00	4.94
184	215	7.207383	ACTTATTTGCAGAAAAACTAACCACC	58.793	34.615	0.00	0.00	0.00	4.61
198	229	7.865706	ACCTCCTTGTATTACTTATTTGCAG	57.134	36.000	0.00	0.00	0.00	4.41
247	278	4.921470	TTTATTCGCTGAAAAGACCGAG	57.079	40.909	0.00	0.00	0.00	4.63
309	342	3.144506	CCACCTATCAATGACTGATGGC	58.855	50.000	0.00	0.00	44.84	4.40
324	357	1.344065	CATACGTATGGGCCCACCTA	58.656	55.000	31.51	14.94	41.11	3.08
339	372	2.319136	TGTTGCGGGTGTATCCATAC	57.681	50.000	0.00	0.00	38.11	2.39
362	395	1.136085	CGTGCACATACGGTCCAAAAG	60.136	52.381	18.64	0.00	40.22	2.27
366	399	2.433491	GCGTGCACATACGGTCCA	60.433	61.111	18.64	0.00	43.87	4.02
410	443	6.061441	TGGTGCTAGAACTTTCAAAATCTGA	58.939	36.000	0.00	0.00	0.00	3.27
412	445	6.959639	TTGGTGCTAGAACTTTCAAAATCT	57.040	33.333	0.00	0.00	0.00	2.40
413	446	7.168135	CAGTTTGGTGCTAGAACTTTCAAAATC	59.832	37.037	0.00	0.00	31.63	2.17
419	452	5.065988	TGTTCAGTTTGGTGCTAGAACTTTC	59.934	40.000	0.00	0.00	37.03	2.62
432	465	5.591099	ACTTGTGCTTAATGTTCAGTTTGG	58.409	37.500	0.00	0.00	0.00	3.28
446	479	5.730550	TCGGTAATCATAGAACTTGTGCTT	58.269	37.500	0.00	0.00	0.00	3.91
653	690	6.585702	TGGCACGCAATAAATTAATGATATGC	59.414	34.615	0.00	0.00	0.00	3.14
780	821	3.993736	ACTCGGCAAAAATGCAAATTACC	59.006	39.130	2.97	0.00	36.33	2.85
788	829	8.628882	AGTAAATAAATACTCGGCAAAAATGC	57.371	30.769	0.00	0.00	30.26	3.56
795	836	8.967664	AAATGGTAGTAAATAAATACTCGGCA	57.032	30.769	0.00	0.00	37.34	5.69
834	911	9.579768	TGCATATTTGTACGCTATTTTGAAATT	57.420	25.926	0.00	0.00	0.00	1.82
835	912	9.748708	ATGCATATTTGTACGCTATTTTGAAAT	57.251	25.926	0.00	0.00	0.00	2.17
855	940	0.879839	CGTCACGCCATGGATGCATA	60.880	55.000	18.40	0.00	0.00	3.14
873	962	0.828022	TAAGGGTAGATGTGCCACCG	59.172	55.000	0.00	0.00	32.84	4.94
874	963	4.910458	ATATAAGGGTAGATGTGCCACC	57.090	45.455	0.00	0.00	0.00	4.61
925	1018	1.274712	CCAGGTTCTGAGCTCCTTCT	58.725	55.000	12.15	0.00	32.44	2.85
929	1022	2.937433	GCTTAACCAGGTTCTGAGCTCC	60.937	54.545	20.34	0.00	32.44	4.70
988	1084	1.135286	GGAAGCCATTGTTAGCTGCAC	60.135	52.381	1.02	0.00	39.87	4.57
1029	1125	1.669927	GGAGGGGGAGGATGAGGAGA	61.670	65.000	0.00	0.00	0.00	3.71
1184	1280	6.222038	TGCGTAGGAGAAAAAGATGATACT	57.778	37.500	0.00	0.00	0.00	2.12
1209	1309	7.738847	TGATTAGCATAATCTCCTGATTGTCA	58.261	34.615	10.09	0.00	42.34	3.58
1213	1313	9.011095	CAACATGATTAGCATAATCTCCTGATT	57.989	33.333	0.00	0.00	44.32	2.57
1262	1366	3.938334	ACATCGCAATTTATTTTTGGGCC	59.062	39.130	0.00	0.00	37.06	5.80
1269	1373	7.309920	ACTTTTCCGTACATCGCAATTTATTT	58.690	30.769	0.00	0.00	38.35	1.40
1270	1374	6.848451	ACTTTTCCGTACATCGCAATTTATT	58.152	32.000	0.00	0.00	38.35	1.40
1274	1378	4.214545	TGAACTTTTCCGTACATCGCAATT	59.785	37.500	0.00	0.00	38.35	2.32
1279	1383	3.124466	TGCATGAACTTTTCCGTACATCG	59.876	43.478	0.00	0.00	39.52	3.84
1280	1384	4.154195	ACTGCATGAACTTTTCCGTACATC	59.846	41.667	0.00	0.00	0.00	3.06
1281	1385	4.072131	ACTGCATGAACTTTTCCGTACAT	58.928	39.130	0.00	0.00	0.00	2.29
1283	1387	4.464112	GAACTGCATGAACTTTTCCGTAC	58.536	43.478	0.00	0.00	0.00	3.67
1284	1388	3.185594	CGAACTGCATGAACTTTTCCGTA	59.814	43.478	0.00	0.00	0.00	4.02
1286	1390	2.223144	TCGAACTGCATGAACTTTTCCG	59.777	45.455	0.00	0.00	0.00	4.30
1287	1391	3.896648	TCGAACTGCATGAACTTTTCC	57.103	42.857	0.00	0.00	0.00	3.13
1288	1392	5.451908	TCAATCGAACTGCATGAACTTTTC	58.548	37.500	0.00	0.00	0.00	2.29
1289	1393	5.437289	TCAATCGAACTGCATGAACTTTT	57.563	34.783	0.00	0.00	0.00	2.27
1290	1394	5.437289	TTCAATCGAACTGCATGAACTTT	57.563	34.783	0.00	0.00	0.00	2.66
1291	1395	5.633830	ATTCAATCGAACTGCATGAACTT	57.366	34.783	0.00	0.00	33.29	2.66
1292	1396	5.633830	AATTCAATCGAACTGCATGAACT	57.366	34.783	0.00	0.00	33.29	3.01
1293	1397	5.858049	TCAAATTCAATCGAACTGCATGAAC	59.142	36.000	0.00	0.00	33.29	3.18
1294	1398	5.858049	GTCAAATTCAATCGAACTGCATGAA	59.142	36.000	0.00	0.00	32.81	2.57
1295	1399	5.393124	GTCAAATTCAATCGAACTGCATGA	58.607	37.500	0.00	0.00	32.81	3.07
1296	1400	4.560035	GGTCAAATTCAATCGAACTGCATG	59.440	41.667	0.00	0.00	32.81	4.06
1297	1401	4.380867	GGGTCAAATTCAATCGAACTGCAT	60.381	41.667	0.00	0.00	32.81	3.96
1298	1402	3.057596	GGGTCAAATTCAATCGAACTGCA	60.058	43.478	0.00	0.00	32.81	4.41
1299	1403	3.057596	TGGGTCAAATTCAATCGAACTGC	60.058	43.478	0.00	0.00	32.81	4.40
1300	1404	4.764679	TGGGTCAAATTCAATCGAACTG	57.235	40.909	0.00	0.00	32.81	3.16
1301	1405	5.782893	TTTGGGTCAAATTCAATCGAACT	57.217	34.783	0.00	0.00	32.81	3.01
1302	1406	7.420184	AATTTTGGGTCAAATTCAATCGAAC	57.580	32.000	0.00	0.00	33.19	3.95
1303	1407	9.547753	TTTAATTTTGGGTCAAATTCAATCGAA	57.452	25.926	0.00	0.00	33.19	3.71
1304	1408	9.717942	ATTTAATTTTGGGTCAAATTCAATCGA	57.282	25.926	0.00	0.00	33.19	3.59
1315	1419	5.788450	ACATCGCAATTTAATTTTGGGTCA	58.212	33.333	12.46	0.41	38.00	4.02
1319	1423	8.417780	TTCCATACATCGCAATTTAATTTTGG	57.582	30.769	0.00	0.00	0.00	3.28
1325	1429	8.300286	TCAACTTTTCCATACATCGCAATTTAA	58.700	29.630	0.00	0.00	0.00	1.52
1326	1430	7.821652	TCAACTTTTCCATACATCGCAATTTA	58.178	30.769	0.00	0.00	0.00	1.40
1431	1544	0.037590	TTTGGATCCACCCTGAACCG	59.962	55.000	15.91	0.00	38.00	4.44
1482	1595	1.131928	AGAAGGCCGTTACAACCCCT	61.132	55.000	0.00	0.00	0.00	4.79
1573	1788	2.222976	CGACGTGAGCTACAAGATACGT	60.223	50.000	0.00	0.00	45.92	3.57
1575	1790	2.353889	TCCGACGTGAGCTACAAGATAC	59.646	50.000	0.00	0.00	0.00	2.24
1577	1792	1.402259	CTCCGACGTGAGCTACAAGAT	59.598	52.381	0.00	0.00	0.00	2.40
1684	1902	1.667830	CTCGCCTTTGCCGTTCAGA	60.668	57.895	0.00	0.00	0.00	3.27
1790	2008	2.911636	AGCTAGGGGATGATTGATGGAG	59.088	50.000	0.00	0.00	0.00	3.86
1863	2088	0.804364	GCGATCAATCAAGGTGCACA	59.196	50.000	20.43	0.00	0.00	4.57
2062	2299	2.731571	GGGGCAGCCATAGACGTCA	61.732	63.158	19.50	4.13	0.00	4.35
2122	2359	3.771160	AGGCTCCGGATCGCGTTT	61.771	61.111	3.57	0.00	0.00	3.60
2395	2637	4.681074	TTTCCTCTTTCCCGCAATTTTT	57.319	36.364	0.00	0.00	0.00	1.94
2396	2638	4.141824	TGTTTTCCTCTTTCCCGCAATTTT	60.142	37.500	0.00	0.00	0.00	1.82
2397	2639	3.386402	TGTTTTCCTCTTTCCCGCAATTT	59.614	39.130	0.00	0.00	0.00	1.82
2398	2640	2.962421	TGTTTTCCTCTTTCCCGCAATT	59.038	40.909	0.00	0.00	0.00	2.32
2399	2641	2.593026	TGTTTTCCTCTTTCCCGCAAT	58.407	42.857	0.00	0.00	0.00	3.56
2400	2642	2.060050	TGTTTTCCTCTTTCCCGCAA	57.940	45.000	0.00	0.00	0.00	4.85
2401	2643	2.286365	ATGTTTTCCTCTTTCCCGCA	57.714	45.000	0.00	0.00	0.00	5.69
2402	2644	3.317150	CAAATGTTTTCCTCTTTCCCGC	58.683	45.455	0.00	0.00	0.00	6.13
2403	2645	3.320826	ACCAAATGTTTTCCTCTTTCCCG	59.679	43.478	0.00	0.00	0.00	5.14
2404	2646	4.955811	ACCAAATGTTTTCCTCTTTCCC	57.044	40.909	0.00	0.00	0.00	3.97
2405	2647	6.264518	TCACTACCAAATGTTTTCCTCTTTCC	59.735	38.462	0.00	0.00	0.00	3.13
2406	2648	7.272037	TCACTACCAAATGTTTTCCTCTTTC	57.728	36.000	0.00	0.00	0.00	2.62
2407	2649	7.039714	GGATCACTACCAAATGTTTTCCTCTTT	60.040	37.037	0.00	0.00	0.00	2.52
2408	2650	6.434340	GGATCACTACCAAATGTTTTCCTCTT	59.566	38.462	0.00	0.00	0.00	2.85
2409	2651	5.946377	GGATCACTACCAAATGTTTTCCTCT	59.054	40.000	0.00	0.00	0.00	3.69
2410	2652	5.125578	GGGATCACTACCAAATGTTTTCCTC	59.874	44.000	0.00	0.00	0.00	3.71
2411	2653	5.016831	GGGATCACTACCAAATGTTTTCCT	58.983	41.667	0.00	0.00	0.00	3.36
2412	2654	4.770010	TGGGATCACTACCAAATGTTTTCC	59.230	41.667	0.00	0.00	32.89	3.13
2413	2655	5.975693	TGGGATCACTACCAAATGTTTTC	57.024	39.130	0.00	0.00	32.89	2.29
2472	2714	6.293462	GGAGAACGAACAAATAAGCTGAAACT	60.293	38.462	0.00	0.00	0.00	2.66
2917	3178	0.532115	GTGGAAGGATGCGGCAAATT	59.468	50.000	6.82	1.69	0.00	1.82
2962	3228	2.363306	TTGGTCTGATTTGGCAGTGT	57.637	45.000	0.00	0.00	37.20	3.55
2963	3229	3.087031	AGATTGGTCTGATTTGGCAGTG	58.913	45.455	0.00	0.00	37.20	3.66
3030	3296	2.025887	AGAGGTTGATTTCCGGCTGATT	60.026	45.455	0.00	0.00	0.00	2.57
3095	3364	9.271828	GTGGTCAATTCTTTCCATAAATTTGTT	57.728	29.630	0.00	0.00	32.45	2.83

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.