AutoCloner

Multiple sequence alignment - TraesCS7B01G183400

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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	TraesCS7B01G183400	chr7B	100.000	2405	0	0	1	2405	290064844	290067248	0.000000e+00	4442
1	TraesCS7B01G183400	chr7B	85.314	749	105	2	900	1648	18886839	18886096	0.000000e+00	769
2	TraesCS7B01G183400	chr7B	83.946	735	101	15	900	1621	36427180	36426450	0.000000e+00	688
3	TraesCS7B01G183400	chr7B	82.133	722	108	13	1	717	381487467	381486762	1.230000e-167	599
4	TraesCS7B01G183400	chr7B	80.594	438	68	7	467	900	404793755	404793331	2.980000e-84	322
5	TraesCS7B01G183400	chr7A	89.178	2421	191	26	1	2405	353972527	353970162	0.000000e+00	2953
6	TraesCS7B01G183400	chr4B	88.184	914	100	4	900	1806	87612950	87613862	0.000000e+00	1083
7	TraesCS7B01G183400	chr4B	86.499	674	64	12	1	671	87544459	87545108	0.000000e+00	715
8	TraesCS7B01G183400	chr2B	86.504	904	104	12	2	902	317247161	317248049	0.000000e+00	977
9	TraesCS7B01G183400	chr2B	87.234	752	85	8	900	1643	598978572	598979320	0.000000e+00	846
10	TraesCS7B01G183400	chr2B	89.003	682	61	7	900	1572	317248110	317248786	0.000000e+00	832
11	TraesCS7B01G183400	chr7D	85.017	861	109	14	1	856	102630044	102629199	0.000000e+00	857
12	TraesCS7B01G183400	chr7D	82.201	736	112	16	900	1621	449977859	449977129	1.220000e-172	616
13	TraesCS7B01G183400	chr3B	82.648	876	125	16	1	869	252601657	252600802	0.000000e+00	750
14	TraesCS7B01G183400	chr3B	79.295	908	164	11	1	902	718831423	718830534	4.390000e-172	614
15	TraesCS7B01G183400	chr3B	78.431	765	125	26	900	1636	379919753	379920505	1.680000e-126	462
16	TraesCS7B01G183400	chr5D	81.818	880	143	10	1	869	185214594	185215467	0.000000e+00	723
17	TraesCS7B01G183400	chr5D	79.976	839	132	14	1	805	46685018	46684182	9.580000e-164	586
18	TraesCS7B01G183400	chr5B	84.626	735	95	16	900	1621	575036843	575036114	0.000000e+00	715
19	TraesCS7B01G183400	chr5B	81.658	567	88	7	340	902	575037458	575036904	7.840000e-125	457
20	TraesCS7B01G183400	chr6B	84.060	734	102	12	900	1621	567117298	567116568	0.000000e+00	693
21	TraesCS7B01G183400	chr6B	83.897	739	96	19	900	1621	717731315	717732047	0.000000e+00	684
22	TraesCS7B01G183400	chr6B	80.000	900	163	8	7	902	446289996	446289110	0.000000e+00	649
23	TraesCS7B01G183400	chr6B	81.050	438	67	7	469	902	717730829	717731254	3.830000e-88	335
24	TraesCS7B01G183400	chr5A	81.229	879	144	13	1	875	357887965	357888826	0.000000e+00	689
25	TraesCS7B01G183400	chr6D	83.607	732	108	9	899	1621	345634814	345635542	0.000000e+00	676
26	TraesCS7B01G183400	chr4D	83.537	735	104	13	900	1621	473970334	473969604	0.000000e+00	671
27	TraesCS7B01G183400	chr4D	79.803	203	33	3	1834	2030	287210934	287210734	8.960000e-30	141
28	TraesCS7B01G183400	chr1D	83.089	615	82	11	1	606	460641256	460640655	7.560000e-150	540
29	TraesCS7B01G183400	chr1A	84.095	547	79	7	1	543	551800820	551800278	2.740000e-144	521

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	TraesCS7B01G183400	chr7B	290064844	290067248	2404	False	4442.0	4442	100.0000	1	2405	1	chr7B.!!$F1	2404
1	TraesCS7B01G183400	chr7B	18886096	18886839	743	True	769.0	769	85.3140	900	1648	1	chr7B.!!$R1	748
2	TraesCS7B01G183400	chr7B	36426450	36427180	730	True	688.0	688	83.9460	900	1621	1	chr7B.!!$R2	721
3	TraesCS7B01G183400	chr7B	381486762	381487467	705	True	599.0	599	82.1330	1	717	1	chr7B.!!$R3	716
4	TraesCS7B01G183400	chr7A	353970162	353972527	2365	True	2953.0	2953	89.1780	1	2405	1	chr7A.!!$R1	2404
5	TraesCS7B01G183400	chr4B	87612950	87613862	912	False	1083.0	1083	88.1840	900	1806	1	chr4B.!!$F2	906
6	TraesCS7B01G183400	chr4B	87544459	87545108	649	False	715.0	715	86.4990	1	671	1	chr4B.!!$F1	670
7	TraesCS7B01G183400	chr2B	317247161	317248786	1625	False	904.5	977	87.7535	2	1572	2	chr2B.!!$F2	1570
8	TraesCS7B01G183400	chr2B	598978572	598979320	748	False	846.0	846	87.2340	900	1643	1	chr2B.!!$F1	743
9	TraesCS7B01G183400	chr7D	102629199	102630044	845	True	857.0	857	85.0170	1	856	1	chr7D.!!$R1	855
10	TraesCS7B01G183400	chr7D	449977129	449977859	730	True	616.0	616	82.2010	900	1621	1	chr7D.!!$R2	721
11	TraesCS7B01G183400	chr3B	252600802	252601657	855	True	750.0	750	82.6480	1	869	1	chr3B.!!$R1	868
12	TraesCS7B01G183400	chr3B	718830534	718831423	889	True	614.0	614	79.2950	1	902	1	chr3B.!!$R2	901
13	TraesCS7B01G183400	chr3B	379919753	379920505	752	False	462.0	462	78.4310	900	1636	1	chr3B.!!$F1	736
14	TraesCS7B01G183400	chr5D	185214594	185215467	873	False	723.0	723	81.8180	1	869	1	chr5D.!!$F1	868
15	TraesCS7B01G183400	chr5D	46684182	46685018	836	True	586.0	586	79.9760	1	805	1	chr5D.!!$R1	804
16	TraesCS7B01G183400	chr5B	575036114	575037458	1344	True	586.0	715	83.1420	340	1621	2	chr5B.!!$R1	1281
17	TraesCS7B01G183400	chr6B	567116568	567117298	730	True	693.0	693	84.0600	900	1621	1	chr6B.!!$R2	721
18	TraesCS7B01G183400	chr6B	446289110	446289996	886	True	649.0	649	80.0000	7	902	1	chr6B.!!$R1	895
19	TraesCS7B01G183400	chr6B	717730829	717732047	1218	False	509.5	684	82.4735	469	1621	2	chr6B.!!$F1	1152
20	TraesCS7B01G183400	chr5A	357887965	357888826	861	False	689.0	689	81.2290	1	875	1	chr5A.!!$F1	874
21	TraesCS7B01G183400	chr6D	345634814	345635542	728	False	676.0	676	83.6070	899	1621	1	chr6D.!!$F1	722
22	TraesCS7B01G183400	chr4D	473969604	473970334	730	True	671.0	671	83.5370	900	1621	1	chr4D.!!$R2	721
23	TraesCS7B01G183400	chr1D	460640655	460641256	601	True	540.0	540	83.0890	1	606	1	chr1D.!!$R1	605
24	TraesCS7B01G183400	chr1A	551800278	551800820	542	True	521.0	521	84.0950	1	543	1	chr1A.!!$R1	542

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
716	752	0.031616	AACCAAAAGGCCAAGGACCA	60.032	50.0	5.01	0.0	0.0	4.02	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2159	2338	0.105349	TTAGGCTACCCTACCGCCAT	60.105	55.0	0.0	0.0	46.14	4.4	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
37	39	1.808531	TTGCCAGTGACTGCCATTGC	61.809	55.000	7.16	5.44	31.85	3.56
117	119	7.264947	CGCCAAAAGGATAGGTGAAAATAAAT	58.735	34.615	0.00	0.00	34.93	1.40
273	279	1.657094	CGTACGCTGGTGTTTCATACC	59.343	52.381	0.52	0.00	38.71	2.73
283	289	0.802494	GTTTCATACCAGGTGCACCG	59.198	55.000	29.68	22.83	42.08	4.94
297	303	0.237498	GCACCGCAAGAACCAGTAAC	59.763	55.000	0.00	0.00	43.02	2.50
330	340	3.391296	GAGGCCTCATAAGTACCATTGGA	59.609	47.826	28.43	0.00	0.00	3.53
488	499	5.838521	TCAGTCACAATGGCCTGAGTATATA	59.161	40.000	3.32	0.00	30.80	0.86
510	521	3.837146	AGGCCACATATCATTCTCGATCT	59.163	43.478	5.01	0.00	0.00	2.75
534	545	0.034896	CTCACGGTGCCTACAAAGGT	59.965	55.000	2.51	0.00	45.64	3.50
558	569	9.719355	GGTAAGAAGAAGAAGAAGAAGAAGAAT	57.281	33.333	0.00	0.00	0.00	2.40
580	615	9.268282	AGAATAAAGAGGTTTAGGAGTGACATA	57.732	33.333	0.00	0.00	31.56	2.29
631	666	4.864704	ACAATTTGGTAGCGGTCATTTT	57.135	36.364	0.78	0.00	0.00	1.82
662	698	4.037803	CACCAGACATCAACAATTGTGGAA	59.962	41.667	19.43	5.10	30.68	3.53
716	752	0.031616	AACCAAAAGGCCAAGGACCA	60.032	50.000	5.01	0.00	0.00	4.02
784	826	2.356992	TGGCACACGATGAGGTACA	58.643	52.632	0.00	0.00	0.00	2.90
881	926	1.000486	AGTCTTAGAGGAGCCGGCA	60.000	57.895	31.54	2.66	0.00	5.69
1019	1159	1.131126	CATGGCTTCATCGTGTTCCAC	59.869	52.381	0.00	0.00	0.00	4.02
1034	1174	3.776781	CACGACATGGCCCCCGTA	61.777	66.667	0.00	0.00	33.62	4.02
1083	1223	1.303317	GGGTGACGCCAAGTTGGAT	60.303	57.895	26.52	12.49	40.96	3.41
1099	1240	7.256296	CCAAGTTGGATAAGGTGAAGGAAAAAT	60.256	37.037	17.60	0.00	40.96	1.82
1133	1274	3.613030	CATCATGTTGGTGTGGAGATGA	58.387	45.455	0.00	0.00	34.79	2.92
1268	1418	0.391927	CCGCCGGTATGTTCAAAGGA	60.392	55.000	1.90	0.00	0.00	3.36
1384	1550	4.077300	TGGATAGATCAAGATGTGCCAC	57.923	45.455	0.00	0.00	0.00	5.01
1402	1568	4.344679	TGCCACAAGATGTCAAAAAGGATT	59.655	37.500	0.00	0.00	0.00	3.01
1417	1583	9.443323	TCAAAAAGGATTAACATCGAGATTGTA	57.557	29.630	0.00	0.00	0.00	2.41
1456	1622	5.245531	TGTTTGAAGAAGCATACCGAAGAT	58.754	37.500	0.00	0.00	0.00	2.40
1528	1694	0.329596	GGAGGAGAGGGCACACAAAT	59.670	55.000	0.00	0.00	0.00	2.32
1594	1760	2.586792	GCGATGCCCAAGAGGAGT	59.413	61.111	0.00	0.00	38.24	3.85
1650	1816	1.818674	GTGACCCAATAAGGCCTTGTG	59.181	52.381	28.77	23.27	35.39	3.33
1660	1826	5.630415	ATAAGGCCTTGTGAAGCACTATA	57.370	39.130	28.77	2.92	35.11	1.31
1678	1844	6.614580	GCACTATATCTTTCATTCGCGAACTC	60.615	42.308	26.00	0.00	0.00	3.01
1702	1868	7.096551	TCGTGATGAAGTATGTCTTTCATTCA	58.903	34.615	1.74	0.00	37.91	2.57
1720	1886	3.378911	TCACGCACTTGTCATGAACTA	57.621	42.857	0.00	0.00	0.00	2.24
1751	1917	0.451628	CGCGCACTTGTCATGAACTG	60.452	55.000	8.75	0.00	0.00	3.16
1814	1980	8.790718	TCGTAGACCTATATTTTCCATGACTAC	58.209	37.037	0.00	0.00	0.00	2.73
1825	1991	3.000041	TCCATGACTACGATGTTGTTGC	59.000	45.455	0.00	0.00	0.00	4.17
1828	1994	3.106242	TGACTACGATGTTGTTGCTGT	57.894	42.857	0.00	0.00	0.00	4.40
1830	1996	3.247411	TGACTACGATGTTGTTGCTGTTG	59.753	43.478	0.00	0.00	0.00	3.33
1851	2017	4.869215	TGTGCATGATGTTAACAACAAGG	58.131	39.130	20.61	16.43	45.86	3.61
1885	2051	6.580788	GGATACTCTGTTTTCTACCCTTACC	58.419	44.000	0.00	0.00	0.00	2.85
1888	2054	2.901839	TCTGTTTTCTACCCTTACCGCT	59.098	45.455	0.00	0.00	0.00	5.52
1900	2066	2.169769	CCTTACCGCTACAGGATTTGGA	59.830	50.000	0.00	0.00	34.73	3.53
1920	2086	3.710165	GGAGGTAGGTGTAACAAGCCTAT	59.290	47.826	0.00	0.00	39.98	2.57
1935	2101	1.179174	CCTATCGCCATGGACCTCGA	61.179	60.000	18.40	15.47	35.34	4.04
1936	2102	0.039074	CTATCGCCATGGACCTCGAC	60.039	60.000	18.40	0.00	33.59	4.20
1974	2140	0.036952	CAGTGGAACCGTGCTGAGAT	60.037	55.000	0.00	0.00	37.80	2.75
1975	2141	0.687354	AGTGGAACCGTGCTGAGATT	59.313	50.000	0.00	0.00	37.80	2.40
1977	2143	0.321564	TGGAACCGTGCTGAGATTGG	60.322	55.000	0.00	0.00	0.00	3.16
1982	2148	1.004745	ACCGTGCTGAGATTGGGAAAT	59.995	47.619	0.00	0.00	0.00	2.17
1984	2150	3.278574	CCGTGCTGAGATTGGGAAATTA	58.721	45.455	0.00	0.00	0.00	1.40
2030	2196	2.088104	CCATAGGCCTCTGTGGTAGA	57.912	55.000	9.68	0.00	44.33	2.59
2068	2234	3.078836	TGGTAGGGTAGGCACCGC	61.079	66.667	0.00	0.00	46.86	5.68
2070	2236	3.455469	GTAGGGTAGGCACCGCGT	61.455	66.667	4.92	0.00	46.86	6.01
2078	2244	0.466543	TAGGCACCGCGTAATGGAAT	59.533	50.000	4.92	0.00	0.00	3.01
2089	2255	3.243177	GCGTAATGGAATCGTTCTGAGAC	59.757	47.826	0.00	0.00	0.00	3.36
2097	2263	4.152580	GGAATCGTTCTGAGACAGGAAAAC	59.847	45.833	0.00	0.00	31.51	2.43
2112	2291	5.217400	CAGGAAAACTAGGGGTATCCTACT	58.783	45.833	0.00	0.00	45.98	2.57
2141	2320	3.463585	CGGCGGTAGGGTTGCCTA	61.464	66.667	0.00	0.00	46.67	3.93
2142	2321	2.992164	GGCGGTAGGGTTGCCTAA	59.008	61.111	0.00	0.00	45.40	2.69
2143	2322	1.530283	GGCGGTAGGGTTGCCTAAT	59.470	57.895	0.00	0.00	45.40	1.73
2144	2323	0.534427	GGCGGTAGGGTTGCCTAATC	60.534	60.000	0.00	0.00	45.40	1.75
2145	2324	0.468648	GCGGTAGGGTTGCCTAATCT	59.531	55.000	0.00	0.00	0.00	2.40
2146	2325	1.690352	GCGGTAGGGTTGCCTAATCTA	59.310	52.381	0.00	0.00	0.00	1.98
2147	2326	2.547430	GCGGTAGGGTTGCCTAATCTAC	60.547	54.545	0.00	0.00	0.00	2.59
2148	2327	2.036862	CGGTAGGGTTGCCTAATCTACC	59.963	54.545	0.00	0.00	43.77	3.18
2149	2328	2.036862	GGTAGGGTTGCCTAATCTACCG	59.963	54.545	0.00	0.00	40.06	4.02
2150	2329	0.468648	AGGGTTGCCTAATCTACCGC	59.531	55.000	0.00	0.00	33.56	5.68
2151	2330	0.534427	GGGTTGCCTAATCTACCGCC	60.534	60.000	0.00	0.00	33.56	6.13
2152	2331	0.468648	GGTTGCCTAATCTACCGCCT	59.531	55.000	0.00	0.00	0.00	5.52
2153	2332	1.690352	GGTTGCCTAATCTACCGCCTA	59.310	52.381	0.00	0.00	0.00	3.93
2154	2333	2.547430	GGTTGCCTAATCTACCGCCTAC	60.547	54.545	0.00	0.00	0.00	3.18
2155	2334	2.076207	TGCCTAATCTACCGCCTACA	57.924	50.000	0.00	0.00	0.00	2.74
2156	2335	2.605257	TGCCTAATCTACCGCCTACAT	58.395	47.619	0.00	0.00	0.00	2.29
2157	2336	2.561419	TGCCTAATCTACCGCCTACATC	59.439	50.000	0.00	0.00	0.00	3.06
2158	2337	2.094130	GCCTAATCTACCGCCTACATCC	60.094	54.545	0.00	0.00	0.00	3.51
2159	2338	3.162666	CCTAATCTACCGCCTACATCCA	58.837	50.000	0.00	0.00	0.00	3.41
2160	2339	3.769844	CCTAATCTACCGCCTACATCCAT	59.230	47.826	0.00	0.00	0.00	3.41
2161	2340	3.685139	AATCTACCGCCTACATCCATG	57.315	47.619	0.00	0.00	0.00	3.66
2162	2341	1.338107	TCTACCGCCTACATCCATGG	58.662	55.000	4.97	4.97	0.00	3.66
2163	2342	0.320771	CTACCGCCTACATCCATGGC	60.321	60.000	6.96	0.00	42.94	4.40
2166	2345	2.510906	GCCTACATCCATGGCGGT	59.489	61.111	6.96	10.11	37.11	5.68
2167	2346	1.752198	GCCTACATCCATGGCGGTA	59.248	57.895	6.96	10.76	37.11	4.02
2168	2347	0.320771	GCCTACATCCATGGCGGTAG	60.321	60.000	24.65	24.65	37.11	3.18
2169	2348	0.321671	CCTACATCCATGGCGGTAGG	59.678	60.000	30.85	30.85	44.79	3.18
2170	2349	0.321671	CTACATCCATGGCGGTAGGG	59.678	60.000	24.21	9.67	35.57	3.53
2171	2350	0.399376	TACATCCATGGCGGTAGGGT	60.399	55.000	6.96	0.00	35.57	4.34
2172	2351	0.399376	ACATCCATGGCGGTAGGGTA	60.399	55.000	6.96	0.00	35.57	3.69
2173	2352	0.321671	CATCCATGGCGGTAGGGTAG	59.678	60.000	6.96	0.00	35.57	3.18
2193	2372	0.665298	CCTAACCTACCGCCTACGTC	59.335	60.000	0.00	0.00	37.70	4.34
2195	2374	0.034574	TAACCTACCGCCTACGTCCA	60.035	55.000	0.00	0.00	37.70	4.02
2209	2388	1.746517	GTCCATGGCGGTAGGGTAG	59.253	63.158	6.96	0.00	35.57	3.18
2237	2416	0.510359	CAGCGCAACTGTTCTGAGAC	59.490	55.000	11.47	0.00	41.86	3.36
2239	2418	1.891060	GCGCAACTGTTCTGAGACGG	61.891	60.000	0.30	0.00	0.00	4.79
2250	2429	0.753262	CTGAGACGGGATTACTGGGG	59.247	60.000	0.00	0.00	0.00	4.96
2251	2430	0.042131	TGAGACGGGATTACTGGGGT	59.958	55.000	0.00	0.00	0.00	4.95
2288	2467	3.973425	GTAGACTACCCTACCACCAAGA	58.027	50.000	0.72	0.00	34.43	3.02
2294	2473	1.604378	CCTACCACCAAGAGCCCTG	59.396	63.158	0.00	0.00	0.00	4.45
2295	2474	1.604378	CTACCACCAAGAGCCCTGG	59.396	63.158	0.00	0.00	0.00	4.45
2315	2494	2.314246	GCGGTAGGGTAGTGGTTATCT	58.686	52.381	0.00	0.00	0.00	1.98

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
37	39	4.149922	TGAGCTTGAAGAACGTACATTTCG	59.850	41.667	0.00	0.00	0.00	3.46
117	119	5.546499	AGTCATCAACCTTGAAGGGTTAGTA	59.454	40.000	16.78	0.00	46.58	1.82
122	124	2.224867	CCAGTCATCAACCTTGAAGGGT	60.225	50.000	16.78	5.93	40.58	4.34
162	165	8.939929	TCTAATGATTTGTTGATGTGAAGACTC	58.060	33.333	0.00	0.00	0.00	3.36
273	279	2.639286	GTTCTTGCGGTGCACCTG	59.361	61.111	32.28	25.18	38.71	4.00
283	289	2.221055	CACTGACGTTACTGGTTCTTGC	59.779	50.000	0.00	0.00	0.00	4.01
297	303	3.691744	GAGGCCTCTCGCACTGACG	62.692	68.421	26.25	0.00	40.31	4.35
330	340	2.485426	CGGTCATGAAATGTGAGCAAGT	59.515	45.455	0.00	0.00	46.80	3.16
488	499	3.837146	AGATCGAGAATGATATGTGGCCT	59.163	43.478	3.32	0.00	0.00	5.19
510	521	1.174078	TGTAGGCACCGTGAGTTCGA	61.174	55.000	1.65	0.00	0.00	3.71
519	530	2.754946	TCTTACCTTTGTAGGCACCG	57.245	50.000	0.00	0.00	46.22	4.94
558	569	8.696374	CATCTATGTCACTCCTAAACCTCTTTA	58.304	37.037	0.00	0.00	0.00	1.85
580	615	3.761218	CGGTGTATCCAGCTAGATCATCT	59.239	47.826	0.00	0.00	36.93	2.90
631	666	1.878211	TGATGTCTGGTGGCTCCATA	58.122	50.000	9.01	0.00	46.12	2.74
662	698	2.174639	TCTGTCCCAGGTTGTCACATTT	59.825	45.455	0.00	0.00	31.51	2.32
682	718	6.813649	GCCTTTTGGTTCAATTCCTAGAATTC	59.186	38.462	0.00	0.00	42.99	2.17
686	722	4.086457	GGCCTTTTGGTTCAATTCCTAGA	58.914	43.478	0.00	0.00	42.99	2.43
697	733	0.031616	TGGTCCTTGGCCTTTTGGTT	60.032	50.000	3.32	0.00	42.99	3.67
716	752	2.269940	ACTAGTGGGAGTCTTGGCATT	58.730	47.619	0.00	0.00	0.00	3.56
784	826	1.852157	TCCTCCATGGCCACCACTT	60.852	57.895	8.16	0.00	35.80	3.16
881	926	1.366366	CGGAACCACGACAACCTCT	59.634	57.895	0.00	0.00	35.47	3.69
985	1125	3.004752	AGCCATGCCTACGAAGAAAAT	57.995	42.857	0.00	0.00	0.00	1.82
1019	1159	2.280797	CATACGGGGGCCATGTCG	60.281	66.667	4.39	6.05	0.00	4.35
1034	1174	3.262420	GACATGTCTTCACGGTTAGCAT	58.738	45.455	18.83	0.00	0.00	3.79
1083	1223	9.974980	GTTTTCATGTATTTTTCCTTCACCTTA	57.025	29.630	0.00	0.00	0.00	2.69
1133	1274	3.763897	GGTGGATACCTTCACTTTGCAAT	59.236	43.478	0.00	0.00	43.97	3.56
1384	1550	8.236586	TCGATGTTAATCCTTTTTGACATCTTG	58.763	33.333	15.53	5.94	44.31	3.02
1402	1568	6.266786	TGCCTCCTAATACAATCTCGATGTTA	59.733	38.462	0.00	0.00	32.27	2.41
1417	1583	4.479158	TCAAACAACCTTTGCCTCCTAAT	58.521	39.130	0.00	0.00	0.00	1.73
1456	1622	1.715862	CGACGCTCTTCATCCTCGGA	61.716	60.000	0.00	0.00	0.00	4.55
1528	1694	4.096681	TCCTCTTCATGAGCAACCTTCTA	58.903	43.478	0.00	0.00	41.35	2.10
1594	1760	3.325870	CTTTCTTGTCACGTGCCTCATA	58.674	45.455	11.67	0.00	0.00	2.15
1650	1816	5.402568	TCGCGAATGAAAGATATAGTGCTTC	59.597	40.000	6.20	0.00	0.00	3.86
1660	1826	2.345641	CACGAGTTCGCGAATGAAAGAT	59.654	45.455	26.23	4.50	44.43	2.40
1678	1844	7.176075	GTGAATGAAAGACATACTTCATCACG	58.824	38.462	0.00	0.00	38.38	4.35
1681	1847	6.183360	TGCGTGAATGAAAGACATACTTCATC	60.183	38.462	0.00	0.00	38.38	2.92
1687	1853	4.928661	AGTGCGTGAATGAAAGACATAC	57.071	40.909	0.00	0.00	38.38	2.39
1702	1868	3.664107	ACATAGTTCATGACAAGTGCGT	58.336	40.909	0.00	0.00	38.10	5.24
1720	1886	1.442769	AGTGCGCGAATGAAAGACAT	58.557	45.000	12.10	0.00	41.45	3.06
1768	1934	8.135529	TCTACGACATAGTTCATGATTCGAAAT	58.864	33.333	0.00	0.00	36.89	2.17
1814	1980	1.122849	GCACAACAGCAACAACATCG	58.877	50.000	0.00	0.00	0.00	3.84
1825	1991	5.811018	GTTGTTAACATCATGCACAACAG	57.189	39.130	17.45	0.00	44.35	3.16
1828	1994	5.068329	TCCTTGTTGTTAACATCATGCACAA	59.932	36.000	17.74	17.00	41.79	3.33
1830	1996	5.119931	TCCTTGTTGTTAACATCATGCAC	57.880	39.130	17.74	9.08	41.79	4.57
1866	2032	3.056035	AGCGGTAAGGGTAGAAAACAGAG	60.056	47.826	0.00	0.00	0.00	3.35
1885	2051	2.224066	CCTACCTCCAAATCCTGTAGCG	60.224	54.545	0.00	0.00	0.00	4.26
1888	2054	3.798515	ACACCTACCTCCAAATCCTGTA	58.201	45.455	0.00	0.00	0.00	2.74
1900	2066	3.383825	CGATAGGCTTGTTACACCTACCT	59.616	47.826	4.20	2.67	38.83	3.08
1920	2086	3.822192	CGTCGAGGTCCATGGCGA	61.822	66.667	6.96	7.55	0.00	5.54
1949	2115	4.619227	ACGGTTCCACTGCACGGG	62.619	66.667	0.00	0.00	0.00	5.28
1952	2118	2.591715	AGCACGGTTCCACTGCAC	60.592	61.111	10.00	0.00	33.06	4.57
1995	2161	3.858225	GGCGGTAGGGTGGCTACC	61.858	72.222	11.52	11.52	46.76	3.18
2030	2196	1.905512	GAGGTCAATGGCGGTAGGT	59.094	57.895	0.00	0.00	0.00	3.08
2051	2217	3.078836	GCGGTGCCTACCCTACCA	61.079	66.667	0.00	0.00	44.53	3.25
2068	2234	4.421058	TGTCTCAGAACGATTCCATTACG	58.579	43.478	0.00	0.00	0.00	3.18
2070	2236	4.709886	TCCTGTCTCAGAACGATTCCATTA	59.290	41.667	0.00	0.00	32.44	1.90
2078	2244	4.022242	CCTAGTTTTCCTGTCTCAGAACGA	60.022	45.833	0.00	0.00	32.44	3.85
2089	2255	5.070580	CAGTAGGATACCCCTAGTTTTCCTG	59.929	48.000	0.00	0.00	46.62	3.86
2138	2317	3.162666	TGGATGTAGGCGGTAGATTAGG	58.837	50.000	0.00	0.00	0.00	2.69
2139	2318	4.382040	CCATGGATGTAGGCGGTAGATTAG	60.382	50.000	5.56	0.00	0.00	1.73
2140	2319	3.513912	CCATGGATGTAGGCGGTAGATTA	59.486	47.826	5.56	0.00	0.00	1.75
2141	2320	2.303022	CCATGGATGTAGGCGGTAGATT	59.697	50.000	5.56	0.00	0.00	2.40
2142	2321	1.902508	CCATGGATGTAGGCGGTAGAT	59.097	52.381	5.56	0.00	0.00	1.98
2143	2322	1.338107	CCATGGATGTAGGCGGTAGA	58.662	55.000	5.56	0.00	0.00	2.59
2144	2323	0.320771	GCCATGGATGTAGGCGGTAG	60.321	60.000	18.40	0.00	38.86	3.18
2145	2324	1.752198	GCCATGGATGTAGGCGGTA	59.248	57.895	18.40	0.00	38.86	4.02
2146	2325	2.510906	GCCATGGATGTAGGCGGT	59.489	61.111	18.40	0.00	38.86	5.68
2149	2328	0.320771	CTACCGCCATGGATGTAGGC	60.321	60.000	23.62	5.72	44.89	3.93
2150	2329	0.321671	CCTACCGCCATGGATGTAGG	59.678	60.000	30.42	30.42	43.04	3.18
2151	2330	0.321671	CCCTACCGCCATGGATGTAG	59.678	60.000	24.07	24.07	42.00	2.74
2152	2331	0.399376	ACCCTACCGCCATGGATGTA	60.399	55.000	18.40	14.28	42.00	2.29
2153	2332	0.399376	TACCCTACCGCCATGGATGT	60.399	55.000	18.40	13.87	42.00	3.06
2154	2333	0.321671	CTACCCTACCGCCATGGATG	59.678	60.000	18.40	7.75	42.00	3.51
2155	2334	1.481056	GCTACCCTACCGCCATGGAT	61.481	60.000	18.40	1.87	42.00	3.41
2156	2335	2.138179	GCTACCCTACCGCCATGGA	61.138	63.158	18.40	0.00	42.00	3.41
2157	2336	2.426023	GCTACCCTACCGCCATGG	59.574	66.667	7.63	7.63	46.41	3.66
2158	2337	0.830444	TAGGCTACCCTACCGCCATG	60.830	60.000	2.12	0.00	46.14	3.66
2159	2338	0.105349	TTAGGCTACCCTACCGCCAT	60.105	55.000	0.00	0.00	46.14	4.40
2160	2339	1.044790	GTTAGGCTACCCTACCGCCA	61.045	60.000	0.00	0.00	46.14	5.69
2161	2340	1.744639	GTTAGGCTACCCTACCGCC	59.255	63.158	0.00	0.00	43.38	6.13
2162	2341	0.758310	AGGTTAGGCTACCCTACCGC	60.758	60.000	9.14	0.00	43.38	5.68
2163	2342	2.234143	GTAGGTTAGGCTACCCTACCG	58.766	57.143	28.72	0.00	43.38	4.02
2165	2344	2.234143	CGGTAGGTTAGGCTACCCTAC	58.766	57.143	30.18	30.18	46.56	3.18
2166	2345	1.479389	GCGGTAGGTTAGGCTACCCTA	60.479	57.143	13.35	13.35	42.87	3.53
2167	2346	0.758310	GCGGTAGGTTAGGCTACCCT	60.758	60.000	15.49	15.49	45.61	4.34
2168	2347	1.744639	GCGGTAGGTTAGGCTACCC	59.255	63.158	0.00	0.00	41.78	3.69
2169	2348	0.758310	AGGCGGTAGGTTAGGCTACC	60.758	60.000	0.00	0.00	41.48	3.18
2170	2349	1.986882	TAGGCGGTAGGTTAGGCTAC	58.013	55.000	0.00	0.00	41.18	3.58
2171	2350	1.815408	CGTAGGCGGTAGGTTAGGCTA	60.815	57.143	0.00	0.00	41.18	3.93
2172	2351	1.105759	CGTAGGCGGTAGGTTAGGCT	61.106	60.000	0.00	0.00	43.35	4.58
2173	2352	1.361632	CGTAGGCGGTAGGTTAGGC	59.638	63.158	0.00	0.00	0.00	3.93
2185	2364	2.694829	CTACCGCCATGGACGTAGGC	62.695	65.000	18.40	9.91	44.89	3.93
2186	2365	1.362717	CTACCGCCATGGACGTAGG	59.637	63.158	18.40	12.14	42.00	3.18
2193	2372	1.746517	GACTACCCTACCGCCATGG	59.253	63.158	7.63	7.63	46.41	3.66
2195	2374	4.290023	GGACTACCCTACCGCCAT	57.710	61.111	0.00	0.00	0.00	4.40
2221	2400	1.284982	CCCGTCTCAGAACAGTTGCG	61.285	60.000	0.00	0.00	0.00	4.85
2227	2406	2.496070	CCAGTAATCCCGTCTCAGAACA	59.504	50.000	0.00	0.00	0.00	3.18
2294	2473	1.342496	GATAACCACTACCCTACCGCC	59.658	57.143	0.00	0.00	0.00	6.13
2295	2474	2.314246	AGATAACCACTACCCTACCGC	58.686	52.381	0.00	0.00	0.00	5.68

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.