AutoCloner

Multiple sequence alignment - TraesCS1D01G431100

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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	TraesCS1D01G431100	chr1D	100.000	3183	0	0	1	3183	481497292	481500474	0.000000e+00	5879.0
1	TraesCS1D01G431100	chr1D	94.205	811	34	3	994	1792	481466882	481466073	0.000000e+00	1225.0
2	TraesCS1D01G431100	chr1D	80.892	628	110	10	2561	3183	481488239	481488861	1.330000e-133	486.0
3	TraesCS1D01G431100	chr1D	84.106	453	49	13	2504	2937	481451915	481452363	1.770000e-112	416.0
4	TraesCS1D01G431100	chr1D	80.040	501	83	14	1124	1623	481476270	481475786	3.910000e-94	355.0
5	TraesCS1D01G431100	chr1D	80.040	501	83	13	1124	1623	481563983	481564467	3.910000e-94	355.0
6	TraesCS1D01G431100	chr1D	91.411	163	14	0	3019	3181	481552072	481551910	1.150000e-54	224.0
7	TraesCS1D01G431100	chr1D	87.963	108	13	0	2054	2161	481465802	481465695	9.270000e-26	128.0
8	TraesCS1D01G431100	chr1A	92.975	1452	58	7	747	2161	578196212	578197656	0.000000e+00	2076.0
9	TraesCS1D01G431100	chr1A	91.441	958	66	6	2242	3183	578206151	578207108	0.000000e+00	1301.0
10	TraesCS1D01G431100	chr1A	94.974	756	35	3	1	756	578184783	578185535	0.000000e+00	1182.0
11	TraesCS1D01G431100	chr1A	89.913	575	51	4	1	569	578038270	578038843	0.000000e+00	734.0
12	TraesCS1D01G431100	chr1A	88.318	214	18	3	668	880	578052072	578052279	1.900000e-62	250.0
13	TraesCS1D01G431100	chr1A	97.600	125	3	0	1474	1598	578052289	578052413	6.920000e-52	215.0
14	TraesCS1D01G431100	chr1A	89.697	165	17	0	3019	3183	577986851	577986687	8.950000e-51	211.0
15	TraesCS1D01G431100	chr1A	93.651	63	4	0	2159	2221	580149142	580149204	9.400000e-16	95.3
16	TraesCS1D01G431100	chr1B	84.896	1205	125	26	681	1836	670168027	670166831	0.000000e+00	1164.0
17	TraesCS1D01G431100	chr1B	85.442	1154	112	24	709	1836	670034007	670035130	0.000000e+00	1149.0
18	TraesCS1D01G431100	chr1B	92.702	507	29	5	2678	3183	670150038	670149539	0.000000e+00	725.0
19	TraesCS1D01G431100	chr1B	76.991	678	112	34	1124	1781	670025512	670026165	6.530000e-92	348.0
20	TraesCS1D01G431100	chr1B	79.802	505	77	21	1124	1623	670184385	670183901	8.450000e-91	344.0
21	TraesCS1D01G431100	chr1B	88.066	243	11	9	2452	2679	670150601	670150362	4.050000e-69	272.0
22	TraesCS1D01G431100	chr1B	93.333	165	11	0	3019	3183	670160437	670160273	8.820000e-61	244.0
23	TraesCS1D01G431100	chr1B	91.411	163	14	0	3019	3181	669924119	669923957	1.150000e-54	224.0
24	TraesCS1D01G431100	chr3B	84.500	200	27	4	2234	2429	370152132	370151933	9.010000e-46	195.0
25	TraesCS1D01G431100	chr7B	83.000	200	27	5	2235	2431	15558617	15558422	1.170000e-39	174.0
26	TraesCS1D01G431100	chr6D	81.116	233	25	16	2207	2430	96654605	96654383	5.460000e-38	169.0
27	TraesCS1D01G431100	chr6D	90.278	72	5	2	2160	2230	468870363	468870433	3.380000e-15	93.5
28	TraesCS1D01G431100	chr5A	74.877	406	85	12	1230	1628	546237949	546237554	5.460000e-38	169.0
29	TraesCS1D01G431100	chr5A	91.071	56	5	0	2374	2429	332920433	332920488	3.400000e-10	76.8
30	TraesCS1D01G431100	chr2B	82.955	176	28	2	2256	2429	418952145	418951970	1.180000e-34	158.0
31	TraesCS1D01G431100	chr2B	89.474	76	4	3	2161	2233	170418260	170418334	3.380000e-15	93.5
32	TraesCS1D01G431100	chr4D	81.006	179	28	5	2258	2432	157351967	157351791	1.540000e-28	137.0
33	TraesCS1D01G431100	chr4D	89.796	49	3	2	1334	1381	502425858	502425811	9.530000e-06	62.1
34	TraesCS1D01G431100	chr4A	79.330	179	22	7	2257	2432	691201071	691200905	9.330000e-21	111.0
35	TraesCS1D01G431100	chr4A	96.667	60	2	0	2159	2218	741985066	741985007	2.020000e-17	100.0
36	TraesCS1D01G431100	chr7A	96.610	59	2	0	2159	2217	34752756	34752814	7.270000e-17	99.0
37	TraesCS1D01G431100	chr7A	90.141	71	5	2	2161	2230	6840465	6840396	1.220000e-14	91.6
38	TraesCS1D01G431100	chr4B	95.161	62	3	0	2159	2220	437405152	437405213	7.270000e-17	99.0
39	TraesCS1D01G431100	chr4B	89.796	49	3	2	1334	1381	646818753	646818706	9.530000e-06	62.1
40	TraesCS1D01G431100	chr7D	92.647	68	3	2	2155	2221	1420480	1420546	2.610000e-16	97.1
41	TraesCS1D01G431100	chr3D	95.082	61	3	0	2161	2221	613625396	613625336	2.610000e-16	97.1
42	TraesCS1D01G431100	chr2A	87.273	55	6	1	2376	2429	654555883	654555829	9.530000e-06	62.1

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	TraesCS1D01G431100	chr1D	481497292	481500474	3182	False	5879.0	5879	100.000	1	3183	1	chr1D.!!$F3	3182
1	TraesCS1D01G431100	chr1D	481465695	481466882	1187	True	676.5	1225	91.084	994	2161	2	chr1D.!!$R3	1167
2	TraesCS1D01G431100	chr1D	481488239	481488861	622	False	486.0	486	80.892	2561	3183	1	chr1D.!!$F2	622
3	TraesCS1D01G431100	chr1A	578196212	578197656	1444	False	2076.0	2076	92.975	747	2161	1	chr1A.!!$F3	1414
4	TraesCS1D01G431100	chr1A	578206151	578207108	957	False	1301.0	1301	91.441	2242	3183	1	chr1A.!!$F4	941
5	TraesCS1D01G431100	chr1A	578184783	578185535	752	False	1182.0	1182	94.974	1	756	1	chr1A.!!$F2	755
6	TraesCS1D01G431100	chr1A	578038270	578038843	573	False	734.0	734	89.913	1	569	1	chr1A.!!$F1	568
7	TraesCS1D01G431100	chr1B	670166831	670168027	1196	True	1164.0	1164	84.896	681	1836	1	chr1B.!!$R3	1155
8	TraesCS1D01G431100	chr1B	670034007	670035130	1123	False	1149.0	1149	85.442	709	1836	1	chr1B.!!$F2	1127
9	TraesCS1D01G431100	chr1B	670149539	670150601	1062	True	498.5	725	90.384	2452	3183	2	chr1B.!!$R5	731
10	TraesCS1D01G431100	chr1B	670025512	670026165	653	False	348.0	348	76.991	1124	1781	1	chr1B.!!$F1	657

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
629	637	1.929836	GCAACAGCGAGATAGTGAAGG	59.070	52.381	0.0	0.0	0.00	3.46	F
2038	2167	0.881796	TGTCTGCTACACTCGTCTGG	59.118	55.000	0.0	0.0	31.43	3.86	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2166	2295	2.833794	GCAATTACATGCGGACTAGGA	58.166	47.619	0.0	0.0	36.45	2.94	R
3008	3505	2.119801	CCATCAGGTGAGTCCTTTGG	57.880	55.000	0.0	0.0	45.67	3.28	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
88	89	4.486125	ACAATTGAATTATTGGGGTGGC	57.514	40.909	13.59	0.00	39.33	5.01
184	187	8.202137	GCCTCGGTAGCCTTTATATTATTATGA	58.798	37.037	0.00	0.00	0.00	2.15
272	275	6.485313	TCGATCACCTTATTGTGTCACTTTTT	59.515	34.615	4.27	0.00	37.51	1.94
284	287	7.867305	TGTGTCACTTTTTCTATTGGTTACA	57.133	32.000	4.27	0.00	0.00	2.41
387	390	8.488651	TGATAGCTATGTCATGAAATATGCAG	57.511	34.615	11.94	8.72	0.00	4.41
397	404	8.192774	TGTCATGAAATATGCAGAAGAATTTCC	58.807	33.333	0.00	4.80	37.48	3.13
453	460	2.776312	TGTCGAGCGGAATAGTCATC	57.224	50.000	0.00	0.00	0.00	2.92
467	474	7.147932	CGGAATAGTCATCAGATCTACCATCAT	60.148	40.741	0.00	0.00	0.00	2.45
613	621	7.095187	CCTCCTACTGAAATATTAATCCGCAAC	60.095	40.741	0.00	0.00	0.00	4.17
629	637	1.929836	GCAACAGCGAGATAGTGAAGG	59.070	52.381	0.00	0.00	0.00	3.46
652	660	5.010282	GGTCAAATGTAGGGTTTGATCACT	58.990	41.667	0.00	0.00	44.56	3.41
710	718	6.267496	TGACGGACGATAATCATGTGATAT	57.733	37.500	0.00	0.00	33.73	1.63
888	896	3.060363	CGGCTACATGTAAACGTTGAGAC	59.940	47.826	16.48	1.10	0.00	3.36
954	992	7.264947	ACTTCCAATTGCTATTAATTTTCCCG	58.735	34.615	0.00	0.00	0.00	5.14
1008	1053	2.124819	CTCTGCTCAATGGCGGCT	60.125	61.111	11.43	0.00	38.38	5.52
1205	1250	2.742372	CAACCTCTTCGCCACCGG	60.742	66.667	0.00	0.00	34.56	5.28
1381	1426	1.753078	ATGCTCCGCTACTCCGACA	60.753	57.895	0.00	0.00	0.00	4.35
1620	1665	4.394712	CAGTGCACCCCCGACCTC	62.395	72.222	14.63	0.00	0.00	3.85
1747	1803	2.136229	GCCCTTCATCAATGGCCCC	61.136	63.158	0.00	0.00	37.34	5.80
1837	1920	3.999663	CAGAGGGTGAGCTCTTAACTTTG	59.000	47.826	16.19	9.35	0.00	2.77
1899	2007	8.854237	TGCTTCCCTCTATATATATTTAGGCA	57.146	34.615	13.83	7.52	0.00	4.75
1970	2099	2.983192	TCAACCAGTGTCCATTTCCCTA	59.017	45.455	0.00	0.00	0.00	3.53
1971	2100	3.591527	TCAACCAGTGTCCATTTCCCTAT	59.408	43.478	0.00	0.00	0.00	2.57
2038	2167	0.881796	TGTCTGCTACACTCGTCTGG	59.118	55.000	0.00	0.00	31.43	3.86
2083	2212	2.841442	ACAGGGAGAAAGTACAGTGC	57.159	50.000	0.00	0.00	0.00	4.40
2087	2216	1.623811	GGGAGAAAGTACAGTGCTCCA	59.376	52.381	20.12	0.00	45.39	3.86
2125	2254	3.550437	ACTCTTGCCTACAATAGCAGG	57.450	47.619	0.00	0.00	40.73	4.85
2161	2290	3.524095	TTGGCTCTTTTCATGGAGGAA	57.476	42.857	0.00	0.00	0.00	3.36
2162	2291	3.524095	TGGCTCTTTTCATGGAGGAAA	57.476	42.857	0.00	0.00	35.11	3.13
2163	2292	3.424703	TGGCTCTTTTCATGGAGGAAAG	58.575	45.455	0.00	0.00	37.98	2.62
2164	2293	3.074390	TGGCTCTTTTCATGGAGGAAAGA	59.926	43.478	11.31	11.31	37.98	2.52
2165	2294	4.082125	GGCTCTTTTCATGGAGGAAAGAA	58.918	43.478	12.27	0.00	37.98	2.52
2166	2295	4.708909	GGCTCTTTTCATGGAGGAAAGAAT	59.291	41.667	12.27	0.00	37.98	2.40
2167	2296	5.163571	GGCTCTTTTCATGGAGGAAAGAATC	60.164	44.000	12.27	8.81	37.98	2.52
2177	2306	2.981859	GGAAAGAATCCTAGTCCGCA	57.018	50.000	0.00	0.00	45.56	5.69
2178	2307	3.477210	GGAAAGAATCCTAGTCCGCAT	57.523	47.619	0.00	0.00	45.56	4.73
2179	2308	3.134458	GGAAAGAATCCTAGTCCGCATG	58.866	50.000	0.00	0.00	45.56	4.06
2180	2309	3.432326	GGAAAGAATCCTAGTCCGCATGT	60.432	47.826	0.00	0.00	45.56	3.21
2181	2310	4.202223	GGAAAGAATCCTAGTCCGCATGTA	60.202	45.833	0.00	0.00	45.56	2.29
2182	2311	5.353394	AAAGAATCCTAGTCCGCATGTAA	57.647	39.130	0.00	0.00	0.00	2.41
2183	2312	5.552870	AAGAATCCTAGTCCGCATGTAAT	57.447	39.130	0.00	0.00	0.00	1.89
2184	2313	5.552870	AGAATCCTAGTCCGCATGTAATT	57.447	39.130	0.00	0.00	0.00	1.40
2185	2314	5.300752	AGAATCCTAGTCCGCATGTAATTG	58.699	41.667	0.00	0.00	0.00	2.32
2186	2315	2.833794	TCCTAGTCCGCATGTAATTGC	58.166	47.619	0.00	0.00	39.29	3.56
2196	2325	4.600012	GCATGTAATTGCGTGTAACTCT	57.400	40.909	15.87	0.00	32.06	3.24
2197	2326	4.969816	GCATGTAATTGCGTGTAACTCTT	58.030	39.130	15.87	0.00	32.06	2.85
2198	2327	5.390613	GCATGTAATTGCGTGTAACTCTTT	58.609	37.500	15.87	0.00	32.06	2.52
2199	2328	5.283717	GCATGTAATTGCGTGTAACTCTTTG	59.716	40.000	15.87	0.00	32.06	2.77
2200	2329	5.994887	TGTAATTGCGTGTAACTCTTTGT	57.005	34.783	0.00	0.00	31.75	2.83
2201	2330	7.514805	CATGTAATTGCGTGTAACTCTTTGTA	58.485	34.615	7.52	0.00	31.75	2.41
2202	2331	7.661127	TGTAATTGCGTGTAACTCTTTGTAT	57.339	32.000	0.00	0.00	31.75	2.29
2203	2332	7.514805	TGTAATTGCGTGTAACTCTTTGTATG	58.485	34.615	0.00	0.00	31.75	2.39
2204	2333	6.554334	AATTGCGTGTAACTCTTTGTATGT	57.446	33.333	0.00	0.00	31.75	2.29
2205	2334	5.994887	TTGCGTGTAACTCTTTGTATGTT	57.005	34.783	0.00	0.00	31.75	2.71
2206	2335	5.994887	TGCGTGTAACTCTTTGTATGTTT	57.005	34.783	0.00	0.00	31.75	2.83
2207	2336	7.479897	TTGCGTGTAACTCTTTGTATGTTTA	57.520	32.000	0.00	0.00	31.75	2.01
2208	2337	7.112528	TGCGTGTAACTCTTTGTATGTTTAG	57.887	36.000	0.00	0.00	31.75	1.85
2209	2338	6.013689	GCGTGTAACTCTTTGTATGTTTAGC	58.986	40.000	0.00	0.00	31.75	3.09
2210	2339	6.347079	GCGTGTAACTCTTTGTATGTTTAGCA	60.347	38.462	0.00	0.00	31.75	3.49
2211	2340	7.623506	GCGTGTAACTCTTTGTATGTTTAGCAT	60.624	37.037	0.00	0.00	36.70	3.79
2212	2341	8.227791	CGTGTAACTCTTTGTATGTTTAGCATT	58.772	33.333	0.00	0.00	35.02	3.56
2231	2360	7.664082	AGCATTATTGTATAGTCACTCATGC	57.336	36.000	0.00	0.00	0.00	4.06
2232	2361	7.219322	AGCATTATTGTATAGTCACTCATGCA	58.781	34.615	0.00	0.00	0.00	3.96
2233	2362	7.716560	AGCATTATTGTATAGTCACTCATGCAA	59.283	33.333	0.00	0.00	32.48	4.08
2234	2363	8.509690	GCATTATTGTATAGTCACTCATGCAAT	58.490	33.333	12.02	12.02	39.67	3.56
2238	2367	8.613060	ATTGTATAGTCACTCATGCAATAAGG	57.387	34.615	0.00	0.00	36.22	2.69
2239	2368	7.124573	TGTATAGTCACTCATGCAATAAGGT	57.875	36.000	0.00	0.00	0.00	3.50
2240	2369	7.564793	TGTATAGTCACTCATGCAATAAGGTT	58.435	34.615	0.00	0.00	0.00	3.50
2251	2380	9.494271	CTCATGCAATAAGGTTAGCTATAAGAA	57.506	33.333	0.00	0.00	0.00	2.52
2318	2451	4.453819	GCAATTGCCTAGGAGTAAGCATAG	59.546	45.833	20.06	0.00	34.72	2.23
2368	2501	4.399303	CCCACTATTTTTCCACATCACTCC	59.601	45.833	0.00	0.00	0.00	3.85
2369	2502	5.256474	CCACTATTTTTCCACATCACTCCT	58.744	41.667	0.00	0.00	0.00	3.69
2389	2522	5.136828	TCCTTTTCACATAGGCAAAAGTGA	58.863	37.500	9.87	0.00	39.06	3.41
2390	2523	5.009610	TCCTTTTCACATAGGCAAAAGTGAC	59.990	40.000	9.87	0.00	40.37	3.67
2392	2525	4.829064	TTCACATAGGCAAAAGTGACAC	57.171	40.909	0.00	0.00	40.37	3.67
2399	2532	1.671845	GGCAAAAGTGACACGTAACCA	59.328	47.619	0.00	0.00	30.49	3.67
2400	2533	2.286772	GGCAAAAGTGACACGTAACCAG	60.287	50.000	0.00	0.00	30.49	4.00
2445	2578	4.612932	GCTCTAAGCACCTGATGAAAAG	57.387	45.455	0.00	0.00	41.89	2.27
2450	2583	1.203994	AGCACCTGATGAAAAGCATGC	59.796	47.619	10.51	10.51	37.34	4.06
2633	2792	5.563751	CGAAATCACCATTAACAAACAGACG	59.436	40.000	0.00	0.00	0.00	4.18
2645	2804	2.309898	AACAGACGCGTACATTTTGC	57.690	45.000	13.97	0.00	0.00	3.68
2985	3471	0.175989	GGCTGGCCACTAGTGTAGAC	59.824	60.000	21.18	14.25	35.81	2.59
3008	3505	4.115516	TGTAGAGTGGATAGTCGTCGTAC	58.884	47.826	0.00	0.00	0.00	3.67
3009	3506	2.559440	AGAGTGGATAGTCGTCGTACC	58.441	52.381	0.00	0.00	0.00	3.34
3010	3507	2.093288	AGAGTGGATAGTCGTCGTACCA	60.093	50.000	0.00	0.00	0.00	3.25
3103	3600	2.490903	GCCGTTCTTCTGGTAGTAGTCA	59.509	50.000	0.00	0.00	0.00	3.41
3144	3641	2.031674	GCAAGCTTGGTGTTGGGCTT	62.032	55.000	27.10	0.00	44.43	4.35

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
21	22	9.921637	TTGGATTACAATTAGGATTTGAACAAC	57.078	29.630	0.00	0.00	33.18	3.32
48	49	8.970020	TCAATTGTTTCCATACTAGATTTGCAT	58.030	29.630	5.13	0.00	0.00	3.96
88	89	3.891366	ACCATGTGAAACCTCTTTCTTGG	59.109	43.478	0.00	0.00	37.30	3.61
136	139	3.565482	CGATGCACAAACCCATAATAGCT	59.435	43.478	0.00	0.00	0.00	3.32
208	211	3.365264	CGGATTTGCCATGGTATCAATCG	60.365	47.826	14.67	8.64	35.94	3.34
272	275	4.693566	CAGCCGAAAACTGTAACCAATAGA	59.306	41.667	0.00	0.00	0.00	1.98
284	287	6.053650	AGTAACTAAACTTCAGCCGAAAACT	58.946	36.000	0.00	0.00	0.00	2.66
387	390	6.908870	AGCAACAAAAGTTGGAAATTCTTC	57.091	33.333	10.02	0.00	35.07	2.87
613	621	1.751351	TGACCCTTCACTATCTCGCTG	59.249	52.381	0.00	0.00	0.00	5.18
617	625	6.284459	CCTACATTTGACCCTTCACTATCTC	58.716	44.000	0.00	0.00	0.00	2.75
629	637	5.010282	AGTGATCAAACCCTACATTTGACC	58.990	41.667	0.00	0.00	46.05	4.02
710	718	7.041107	GCCAGTTTTTGCCTCATTTAATGATA	58.959	34.615	8.17	0.00	38.85	2.15
775	783	9.515226	ACTTAACTCAAACTATTCCATTTAGCA	57.485	29.630	0.00	0.00	0.00	3.49
867	875	3.991773	TGTCTCAACGTTTACATGTAGCC	59.008	43.478	5.56	0.03	0.00	3.93
888	896	2.781681	AGGGAGGGTCGTGTTTAATG	57.218	50.000	0.00	0.00	0.00	1.90
954	992	3.069586	AGCAAAGGTAGCTTTTGGAAACC	59.930	43.478	17.04	1.84	39.87	3.27
1008	1053	0.320683	CAGACAAGGCGACATGGTGA	60.321	55.000	0.00	0.00	32.07	4.02
1381	1426	2.427245	CGGCGGAGAGGAACTGGAT	61.427	63.158	0.00	0.00	41.55	3.41
1747	1803	3.807538	GGCAGCTGCACCATCACG	61.808	66.667	37.63	0.00	44.36	4.35
1956	2085	8.463930	TGAAATGATTATAGGGAAATGGACAC	57.536	34.615	0.00	0.00	0.00	3.67
1970	2099	6.819649	CACCCTGCACAATTTGAAATGATTAT	59.180	34.615	2.79	0.00	0.00	1.28
1971	2100	6.164876	CACCCTGCACAATTTGAAATGATTA	58.835	36.000	2.79	0.00	0.00	1.75
2083	2212	3.565764	TTATGAGAACCATGCCTGGAG	57.434	47.619	15.66	0.00	46.37	3.86
2087	2216	6.294473	CAAGAGTATTATGAGAACCATGCCT	58.706	40.000	0.00	0.00	36.71	4.75
2099	2228	7.332926	CCTGCTATTGTAGGCAAGAGTATTATG	59.667	40.741	0.00	0.00	43.63	1.90
2102	2231	5.615289	CCTGCTATTGTAGGCAAGAGTATT	58.385	41.667	0.00	0.00	43.63	1.89
2105	2234	3.550437	CCTGCTATTGTAGGCAAGAGT	57.450	47.619	0.00	0.00	43.63	3.24
2125	2254	4.082026	AGAGCCAAACAATGAGGTTTATGC	60.082	41.667	0.00	0.00	38.86	3.14
2161	2290	5.552870	ATTACATGCGGACTAGGATTCTT	57.447	39.130	0.00	0.00	0.00	2.52
2162	2291	5.300752	CAATTACATGCGGACTAGGATTCT	58.699	41.667	0.00	0.00	0.00	2.40
2163	2292	4.083802	GCAATTACATGCGGACTAGGATTC	60.084	45.833	0.00	0.00	36.45	2.52
2164	2293	3.815401	GCAATTACATGCGGACTAGGATT	59.185	43.478	0.00	0.00	36.45	3.01
2165	2294	3.403038	GCAATTACATGCGGACTAGGAT	58.597	45.455	0.00	0.00	36.45	3.24
2166	2295	2.833794	GCAATTACATGCGGACTAGGA	58.166	47.619	0.00	0.00	36.45	2.94
2175	2304	4.600012	AGAGTTACACGCAATTACATGC	57.400	40.909	0.00	0.00	42.94	4.06
2176	2305	6.370593	ACAAAGAGTTACACGCAATTACATG	58.629	36.000	0.00	0.00	0.00	3.21
2177	2306	6.554334	ACAAAGAGTTACACGCAATTACAT	57.446	33.333	0.00	0.00	0.00	2.29
2178	2307	5.994887	ACAAAGAGTTACACGCAATTACA	57.005	34.783	0.00	0.00	0.00	2.41
2179	2308	7.515643	ACATACAAAGAGTTACACGCAATTAC	58.484	34.615	0.00	0.00	0.00	1.89
2180	2309	7.661127	ACATACAAAGAGTTACACGCAATTA	57.339	32.000	0.00	0.00	0.00	1.40
2181	2310	6.554334	ACATACAAAGAGTTACACGCAATT	57.446	33.333	0.00	0.00	0.00	2.32
2182	2311	6.554334	AACATACAAAGAGTTACACGCAAT	57.446	33.333	0.00	0.00	0.00	3.56
2183	2312	5.994887	AACATACAAAGAGTTACACGCAA	57.005	34.783	0.00	0.00	0.00	4.85
2184	2313	5.994887	AAACATACAAAGAGTTACACGCA	57.005	34.783	0.00	0.00	0.00	5.24
2185	2314	6.013689	GCTAAACATACAAAGAGTTACACGC	58.986	40.000	0.00	0.00	0.00	5.34
2186	2315	7.112528	TGCTAAACATACAAAGAGTTACACG	57.887	36.000	0.00	0.00	0.00	4.49
2205	2334	9.208022	GCATGAGTGACTATACAATAATGCTAA	57.792	33.333	10.05	0.00	44.39	3.09
2206	2335	8.367156	TGCATGAGTGACTATACAATAATGCTA	58.633	33.333	15.83	4.31	46.47	3.49
2207	2336	7.219322	TGCATGAGTGACTATACAATAATGCT	58.781	34.615	15.83	0.00	46.47	3.79
2208	2337	7.425577	TGCATGAGTGACTATACAATAATGC	57.574	36.000	10.31	10.31	46.49	3.56
2212	2341	9.710900	CCTTATTGCATGAGTGACTATACAATA	57.289	33.333	0.00	6.01	0.00	1.90
2213	2342	8.213679	ACCTTATTGCATGAGTGACTATACAAT	58.786	33.333	0.00	7.46	0.00	2.71
2214	2343	7.564793	ACCTTATTGCATGAGTGACTATACAA	58.435	34.615	0.00	0.00	0.00	2.41
2215	2344	7.124573	ACCTTATTGCATGAGTGACTATACA	57.875	36.000	0.00	0.00	0.00	2.29
2216	2345	9.197694	CTAACCTTATTGCATGAGTGACTATAC	57.802	37.037	0.00	0.00	0.00	1.47
2217	2346	7.872993	GCTAACCTTATTGCATGAGTGACTATA	59.127	37.037	0.00	0.00	0.00	1.31
2218	2347	6.708054	GCTAACCTTATTGCATGAGTGACTAT	59.292	38.462	0.00	0.00	0.00	2.12
2219	2348	6.049149	GCTAACCTTATTGCATGAGTGACTA	58.951	40.000	0.00	0.00	0.00	2.59
2220	2349	4.878397	GCTAACCTTATTGCATGAGTGACT	59.122	41.667	0.00	0.00	0.00	3.41
2221	2350	4.878397	AGCTAACCTTATTGCATGAGTGAC	59.122	41.667	0.00	0.00	0.00	3.67
2222	2351	5.102953	AGCTAACCTTATTGCATGAGTGA	57.897	39.130	0.00	0.00	0.00	3.41
2223	2352	8.607441	TTATAGCTAACCTTATTGCATGAGTG	57.393	34.615	0.00	0.00	0.00	3.51
2224	2353	8.651389	TCTTATAGCTAACCTTATTGCATGAGT	58.349	33.333	0.00	0.00	0.00	3.41
2225	2354	9.494271	TTCTTATAGCTAACCTTATTGCATGAG	57.506	33.333	0.00	0.00	0.00	2.90
2277	2409	9.101655	GGCAATTGCAATAAATATGAAGAAAGT	57.898	29.630	30.32	0.00	44.36	2.66
2285	2417	7.889469	ACTCCTAGGCAATTGCAATAAATATG	58.111	34.615	30.32	8.03	44.36	1.78
2346	2479	5.256474	AGGAGTGATGTGGAAAAATAGTGG	58.744	41.667	0.00	0.00	0.00	4.00
2368	2501	5.687285	GTGTCACTTTTGCCTATGTGAAAAG	59.313	40.000	0.00	0.00	40.47	2.27
2369	2502	5.587289	GTGTCACTTTTGCCTATGTGAAAA	58.413	37.500	0.00	0.00	40.47	2.29
2389	2522	3.175109	GCTTATAGCCTGGTTACGTGT	57.825	47.619	0.00	0.00	34.48	4.49
2424	2557	3.181502	GCTTTTCATCAGGTGCTTAGAGC	60.182	47.826	0.00	0.00	42.82	4.09
2491	2636	9.167311	GATTAAGCAATAATCCCGACAGATTAT	57.833	33.333	9.85	8.59	46.57	1.28
2633	2792	2.587612	TCACGAAGCAAAATGTACGC	57.412	45.000	0.00	0.00	0.00	4.42
2645	2804	6.692232	ATTTCTCGTTCTAGTTTCACGAAG	57.308	37.500	0.00	5.72	42.10	3.79
2743	3229	2.436542	ACTATTACCAGCGCCATAACCA	59.563	45.455	2.29	0.00	0.00	3.67
2746	3232	4.617253	ATGACTATTACCAGCGCCATAA	57.383	40.909	2.29	0.13	0.00	1.90
2850	3336	2.494918	GACTACGCCTGCGGTCAT	59.505	61.111	16.63	0.00	44.69	3.06
2853	3339	3.760035	CTGGACTACGCCTGCGGT	61.760	66.667	16.63	4.78	44.69	5.68
2901	3387	4.874977	TGGTGTGTCGCGAACGCA	62.875	61.111	25.19	21.49	45.93	5.24
2928	3414	4.452733	GTAGGCCGCTGCGACCTT	62.453	66.667	33.58	18.07	36.00	3.50
2974	3460	5.758790	TCCACTCTACAGTCTACACTAGT	57.241	43.478	0.00	0.00	0.00	2.57
2976	3462	7.434927	ACTATCCACTCTACAGTCTACACTA	57.565	40.000	0.00	0.00	0.00	2.74
2985	3471	3.196463	ACGACGACTATCCACTCTACAG	58.804	50.000	0.00	0.00	0.00	2.74
3008	3505	2.119801	CCATCAGGTGAGTCCTTTGG	57.880	55.000	0.00	0.00	45.67	3.28

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.