AutoCloner

Multiple sequence alignment - TraesCS7A01G174400

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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	TraesCS7A01G174400	chr7A	100.000	1558	0	0	1	1558	128391957	128393514	0.000000e+00	2878.0
1	TraesCS7A01G174400	chr7A	100.000	1385	0	0	1762	3146	128393718	128395102	0.000000e+00	2558.0
2	TraesCS7A01G174400	chr7A	89.068	558	40	5	1	544	128227374	128227924	0.000000e+00	673.0
3	TraesCS7A01G174400	chr7A	86.842	76	10	0	1000	1075	735979855	735979780	5.590000e-13	86.1
4	TraesCS7A01G174400	chr7D	93.720	828	47	3	2323	3146	127677768	127678594	0.000000e+00	1236.0
5	TraesCS7A01G174400	chr7D	91.920	854	35	16	2321	3146	127644227	127645074	0.000000e+00	1164.0
6	TraesCS7A01G174400	chr7D	93.370	724	47	1	834	1556	127641911	127642634	0.000000e+00	1070.0
7	TraesCS7A01G174400	chr7D	93.201	706	48	0	834	1539	127676062	127676767	0.000000e+00	1038.0
8	TraesCS7A01G174400	chr7D	95.404	544	25	0	1	544	127640601	127641144	0.000000e+00	867.0
9	TraesCS7A01G174400	chr7D	94.867	487	23	2	1762	2248	127643723	127644207	0.000000e+00	760.0
10	TraesCS7A01G174400	chr7D	91.560	545	44	2	1	544	127506512	127507055	0.000000e+00	750.0
11	TraesCS7A01G174400	chr7D	92.727	495	36	0	50	544	127675249	127675743	0.000000e+00	715.0
12	TraesCS7A01G174400	chr7D	90.574	488	40	5	1762	2248	127677264	127677746	2.650000e-180	641.0
13	TraesCS7A01G174400	chr7D	93.243	222	14	1	545	766	127641270	127641490	3.030000e-85	326.0
14	TraesCS7A01G174400	chr7D	89.781	137	14	0	613	749	127675908	127676044	3.220000e-40	176.0
15	TraesCS7A01G174400	chr4D	91.988	674	45	7	2321	2989	274471775	274472444	0.000000e+00	937.0
16	TraesCS7A01G174400	chr4D	91.009	456	38	3	1795	2248	274471301	274471755	2.070000e-171	612.0
17	TraesCS7A01G174400	chr3D	90.990	677	49	10	2321	2992	37823549	37824218	0.000000e+00	902.0
18	TraesCS7A01G174400	chr3D	89.876	484	46	2	1766	2248	600494731	600494250	1.240000e-173	619.0
19	TraesCS7A01G174400	chr3D	89.855	483	46	3	1767	2248	420919502	420919022	4.460000e-173	617.0
20	TraesCS7A01G174400	chr3D	84.615	364	51	5	1	361	266560510	266560871	1.070000e-94	357.0
21	TraesCS7A01G174400	chr3D	79.641	167	30	4	371	535	100737178	100737342	1.980000e-22	117.0
22	TraesCS7A01G174400	chr1A	90.815	675	54	7	2321	2989	262295610	262296282	0.000000e+00	896.0
23	TraesCS7A01G174400	chr2D	90.828	676	51	9	2321	2990	620917966	620917296	0.000000e+00	894.0
24	TraesCS7A01G174400	chr2D	89.592	490	43	5	1762	2248	462257785	462258269	1.600000e-172	616.0
25	TraesCS7A01G174400	chr6D	90.746	670	54	6	2326	2989	438695921	438696588	0.000000e+00	887.0
26	TraesCS7A01G174400	chr6D	80.120	166	31	2	371	535	254641258	254641094	4.260000e-24	122.0
27	TraesCS7A01G174400	chr5D	90.370	675	52	10	2321	2991	247754821	247755486	0.000000e+00	874.0
28	TraesCS7A01G174400	chr5D	90.289	484	38	4	1766	2248	247754326	247754801	2.660000e-175	625.0
29	TraesCS7A01G174400	chr2A	89.353	695	58	15	2321	3007	741022044	741021358	0.000000e+00	859.0
30	TraesCS7A01G174400	chr2A	94.805	77	3	1	2249	2325	738119949	738120024	5.510000e-23	119.0
31	TraesCS7A01G174400	chr2A	93.671	79	3	2	2249	2326	754446741	754446818	1.980000e-22	117.0
32	TraesCS7A01G174400	chr4A	89.344	488	44	5	1765	2248	260508168	260508651	9.650000e-170	606.0
33	TraesCS7A01G174400	chr4B	88.636	484	48	6	1766	2248	449341276	449340799	1.630000e-162	582.0
34	TraesCS7A01G174400	chr4B	84.267	375	47	8	1	369	93519281	93519649	3.860000e-94	355.0
35	TraesCS7A01G174400	chr4B	93.750	80	4	1	2249	2328	115550328	115550250	5.510000e-23	119.0
36	TraesCS7A01G174400	chr4B	94.805	77	3	1	2249	2325	167393844	167393919	5.510000e-23	119.0
37	TraesCS7A01G174400	chr4B	79.012	162	30	4	376	535	327852461	327852620	1.190000e-19	108.0
38	TraesCS7A01G174400	chr5B	85.531	546	71	4	1	540	111250666	111251209	5.890000e-157	564.0
39	TraesCS7A01G174400	chr5B	94.872	78	2	2	2249	2325	36189321	36189245	1.530000e-23	121.0
40	TraesCS7A01G174400	chr2B	83.551	383	53	10	1	378	415028612	415028989	1.800000e-92	350.0
41	TraesCS7A01G174400	chr2B	81.871	171	28	3	371	540	288477946	288478114	1.180000e-29	141.0
42	TraesCS7A01G174400	chr6B	84.110	365	52	6	1	362	44248733	44249094	6.460000e-92	348.0
43	TraesCS7A01G174400	chr6A	94.595	74	4	0	2249	2322	142247642	142247715	7.130000e-22	115.0
44	TraesCS7A01G174400	chr6A	94.595	74	4	0	2249	2322	142276784	142276857	7.130000e-22	115.0
45	TraesCS7A01G174400	chr6A	89.362	94	6	4	2249	2340	238303167	238303076	7.130000e-22	115.0
46	TraesCS7A01G174400	chr6A	88.298	94	7	4	2249	2340	238333383	238333292	3.320000e-20	110.0
47	TraesCS7A01G174400	chr3A	74.892	231	52	5	1000	1227	702488227	702488000	2.000000e-17	100.0

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	TraesCS7A01G174400	chr7A	128391957	128395102	3145	False	2718.0	2878	100.0000	1	3146	2	chr7A.!!$F2	3145
1	TraesCS7A01G174400	chr7A	128227374	128227924	550	False	673.0	673	89.0680	1	544	1	chr7A.!!$F1	543
2	TraesCS7A01G174400	chr7D	127640601	127645074	4473	False	837.4	1164	93.7608	1	3146	5	chr7D.!!$F2	3145
3	TraesCS7A01G174400	chr7D	127675249	127678594	3345	False	761.2	1236	92.0006	50	3146	5	chr7D.!!$F3	3096
4	TraesCS7A01G174400	chr7D	127506512	127507055	543	False	750.0	750	91.5600	1	544	1	chr7D.!!$F1	543
5	TraesCS7A01G174400	chr4D	274471301	274472444	1143	False	774.5	937	91.4985	1795	2989	2	chr4D.!!$F1	1194
6	TraesCS7A01G174400	chr3D	37823549	37824218	669	False	902.0	902	90.9900	2321	2992	1	chr3D.!!$F1	671
7	TraesCS7A01G174400	chr1A	262295610	262296282	672	False	896.0	896	90.8150	2321	2989	1	chr1A.!!$F1	668
8	TraesCS7A01G174400	chr2D	620917296	620917966	670	True	894.0	894	90.8280	2321	2990	1	chr2D.!!$R1	669
9	TraesCS7A01G174400	chr6D	438695921	438696588	667	False	887.0	887	90.7460	2326	2989	1	chr6D.!!$F1	663
10	TraesCS7A01G174400	chr5D	247754326	247755486	1160	False	749.5	874	90.3295	1766	2991	2	chr5D.!!$F1	1225
11	TraesCS7A01G174400	chr2A	741021358	741022044	686	True	859.0	859	89.3530	2321	3007	1	chr2A.!!$R1	686
12	TraesCS7A01G174400	chr5B	111250666	111251209	543	False	564.0	564	85.5310	1	540	1	chr5B.!!$F1	539

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
141	143	0.686789	TGCACTGCTAGGTGTCATGT	59.313	50.0	1.98	0.0	39.21	3.21	F
1226	1766	0.323629	CCTCGGTAAGCTCCCAACAA	59.676	55.0	3.53	0.0	0.00	2.83	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1259	1799	0.036164	ATGCCTGTAGCCGTGTTTCA	59.964	50.000	0.0	0.0	42.71	2.69	R
3010	4479	1.199789	TGGCATTCACAATTCGTCAGC	59.800	47.619	0.0	0.0	0.00	4.26	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
141	143	0.686789	TGCACTGCTAGGTGTCATGT	59.313	50.000	1.98	0.00	39.21	3.21
198	200	6.933521	GCTTATCTGCCTTCTCTTCATTATCA	59.066	38.462	0.00	0.00	0.00	2.15
209	211	4.512484	TCTTCATTATCATGACACGCCAA	58.488	39.130	0.00	0.00	39.28	4.52
240	242	6.037172	CGGGTGTCAATAAAGTTAATCTCCTG	59.963	42.308	0.00	0.00	0.00	3.86
241	243	7.110155	GGGTGTCAATAAAGTTAATCTCCTGA	58.890	38.462	0.00	0.00	0.00	3.86
243	245	7.606456	GGTGTCAATAAAGTTAATCTCCTGACA	59.394	37.037	0.00	0.00	0.00	3.58
246	248	9.220767	GTCAATAAAGTTAATCTCCTGACAAGT	57.779	33.333	0.00	0.00	0.00	3.16
285	291	4.942944	TCTGAGATCCACCTAACCACTTA	58.057	43.478	0.00	0.00	0.00	2.24
298	304	1.178276	CCACTTAGGAGCTCGACACT	58.822	55.000	7.83	1.25	41.22	3.55
548	693	1.656652	GTCATGTCTTGATGACCCGG	58.343	55.000	0.00	0.00	44.44	5.73
731	876	2.224079	CCATTAATCCACGCAGATTCGG	59.776	50.000	3.95	1.57	37.62	4.30
769	1309	3.062466	CGGCCTGGACTCAGACGA	61.062	66.667	0.00	0.00	43.49	4.20
775	1315	1.607801	CTGGACTCAGACGATGGCCA	61.608	60.000	8.56	8.56	43.49	5.36
800	1340	3.369400	CCCAATTTCCGCACGCCA	61.369	61.111	0.00	0.00	0.00	5.69
802	1342	2.625823	CCAATTTCCGCACGCCACT	61.626	57.895	0.00	0.00	0.00	4.00
811	1351	4.015406	CACGCCACTGCCCACCTA	62.015	66.667	0.00	0.00	0.00	3.08
861	1401	2.029964	CGCCCGCCATTATACCGT	59.970	61.111	0.00	0.00	0.00	4.83
873	1413	4.587684	CCATTATACCGTCTTCCACCTACT	59.412	45.833	0.00	0.00	0.00	2.57
875	1415	2.592102	TACCGTCTTCCACCTACTGT	57.408	50.000	0.00	0.00	0.00	3.55
929	1469	1.621317	TCCTCACCTCACGCACATTAA	59.379	47.619	0.00	0.00	0.00	1.40
936	1476	1.394917	CTCACGCACATTAACCTCTGC	59.605	52.381	0.00	0.00	0.00	4.26
998	1538	4.008933	GCCACTCTGCTCACCGGT	62.009	66.667	0.00	0.00	0.00	5.28
1022	1562	2.203070	GCGCCCGAACCTCATGAT	60.203	61.111	0.00	0.00	0.00	2.45
1156	1696	3.216292	GCACCCACGGCTTTGTGT	61.216	61.111	0.00	0.00	38.20	3.72
1169	1709	3.816367	TTGTGTGCGCCATCGGTCA	62.816	57.895	4.18	0.00	35.95	4.02
1170	1710	3.490759	GTGTGCGCCATCGGTCAG	61.491	66.667	4.18	0.00	35.95	3.51
1175	1715	1.033202	TGCGCCATCGGTCAGTACTA	61.033	55.000	4.18	0.00	35.95	1.82
1184	1724	1.226603	GTCAGTACTAGGCACGGCG	60.227	63.158	4.80	4.80	0.00	6.46
1226	1766	0.323629	CCTCGGTAAGCTCCCAACAA	59.676	55.000	3.53	0.00	0.00	2.83
1235	1775	1.305219	GCTCCCAACAATGCGCACTA	61.305	55.000	14.90	0.00	0.00	2.74
1236	1776	1.164411	CTCCCAACAATGCGCACTAA	58.836	50.000	14.90	0.00	0.00	2.24
1277	1817	0.036164	ATGAAACACGGCTACAGGCA	59.964	50.000	3.53	0.00	44.01	4.75
1316	1856	2.688507	CTGGTGAAGCACAATAGTCGT	58.311	47.619	0.00	0.00	35.86	4.34
1340	1880	3.733960	CACGACCTCGGACGAGCA	61.734	66.667	15.78	0.00	44.95	4.26
1353	1893	0.387929	ACGAGCACACCTTCGAAGAA	59.612	50.000	26.61	0.00	45.90	2.52
1871	3297	5.801531	ACCCGCAGTAGATATCAAATGTA	57.198	39.130	5.32	0.00	0.00	2.29
2094	3521	2.424956	GGATGAACACCTCAGCAAATCC	59.575	50.000	0.00	0.00	42.55	3.01
2101	3528	1.281867	ACCTCAGCAAATCCGGATTGA	59.718	47.619	29.84	21.30	0.00	2.57
2118	3545	6.308766	CCGGATTGAACACAAAATTGAAGATC	59.691	38.462	0.00	0.00	0.00	2.75
2157	3584	4.261572	CCCAATAAATAAGGACGTGCATGG	60.262	45.833	10.52	4.31	0.00	3.66
2171	3598	3.613737	CGTGCATGGCAAGAAATAAAAGG	59.386	43.478	0.00	0.00	41.47	3.11
2248	3677	9.827198	AATAGAGGAGATCTGATAAAGATGAGT	57.173	33.333	0.00	0.00	46.12	3.41
2249	3678	7.765695	AGAGGAGATCTGATAAAGATGAGTC	57.234	40.000	0.00	0.00	46.12	3.36
2250	3679	6.721208	AGAGGAGATCTGATAAAGATGAGTCC	59.279	42.308	0.00	0.00	46.12	3.85
2251	3680	6.380414	AGGAGATCTGATAAAGATGAGTCCA	58.620	40.000	0.00	0.00	46.12	4.02
2252	3681	6.843333	AGGAGATCTGATAAAGATGAGTCCAA	59.157	38.462	0.00	0.00	46.12	3.53
2253	3682	7.346698	AGGAGATCTGATAAAGATGAGTCCAAA	59.653	37.037	0.00	0.00	46.12	3.28
2254	3683	7.989741	GGAGATCTGATAAAGATGAGTCCAAAA	59.010	37.037	0.00	0.00	46.12	2.44
2255	3684	9.558396	GAGATCTGATAAAGATGAGTCCAAAAT	57.442	33.333	0.00	0.00	46.12	1.82
2271	3700	8.103948	AGTCCAAAATAGATGACTCAACTTTG	57.896	34.615	0.00	0.00	32.85	2.77
2272	3701	7.721399	AGTCCAAAATAGATGACTCAACTTTGT	59.279	33.333	0.00	0.00	32.85	2.83
2273	3702	8.999431	GTCCAAAATAGATGACTCAACTTTGTA	58.001	33.333	0.00	0.00	0.00	2.41
2274	3703	9.739276	TCCAAAATAGATGACTCAACTTTGTAT	57.261	29.630	0.00	0.00	0.00	2.29
2312	3741	9.140286	TGAAGTTGAGTCATCTATTTTAGAACG	57.860	33.333	4.14	0.00	38.50	3.95
2313	3742	8.480643	AAGTTGAGTCATCTATTTTAGAACGG	57.519	34.615	4.14	0.00	38.50	4.44
2314	3743	7.837863	AGTTGAGTCATCTATTTTAGAACGGA	58.162	34.615	1.70	0.00	38.50	4.69
2315	3744	7.976734	AGTTGAGTCATCTATTTTAGAACGGAG	59.023	37.037	1.70	0.00	38.50	4.63
2316	3745	6.806751	TGAGTCATCTATTTTAGAACGGAGG	58.193	40.000	0.00	0.00	38.50	4.30
2317	3746	6.163135	AGTCATCTATTTTAGAACGGAGGG	57.837	41.667	0.00	0.00	38.50	4.30
2318	3747	5.897824	AGTCATCTATTTTAGAACGGAGGGA	59.102	40.000	0.00	0.00	38.50	4.20
2319	3748	6.041069	AGTCATCTATTTTAGAACGGAGGGAG	59.959	42.308	0.00	0.00	38.50	4.30
2457	3886	7.679881	AGGGATCAATACCTATGACATGTATGA	59.320	37.037	0.00	0.84	40.12	2.15
2667	4104	4.468153	TGCTTAAACTGAAAACCACCCTTT	59.532	37.500	0.00	0.00	0.00	3.11
2911	4350	5.114081	GGCCGTAGCTACAAATTCTTAGAA	58.886	41.667	23.21	0.00	39.73	2.10
3105	4574	1.214175	TCAAGTTTCTCCAGGCCACAA	59.786	47.619	5.01	0.00	0.00	3.33

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
35	37	3.320541	CCCAAATGACTGTTTTGCCACTA	59.679	43.478	0.48	0.00	33.66	2.74
198	200	1.667830	CGTCCAGTTGGCGTGTCAT	60.668	57.895	6.77	0.00	34.44	3.06
209	211	2.370849	ACTTTATTGACACCCGTCCAGT	59.629	45.455	0.00	0.00	41.85	4.00
240	242	0.177141	TACATGGCGGCCTACTTGTC	59.823	55.000	21.46	0.00	0.00	3.18
241	243	0.107848	GTACATGGCGGCCTACTTGT	60.108	55.000	21.46	18.74	0.00	3.16
243	245	0.464452	GAGTACATGGCGGCCTACTT	59.536	55.000	21.46	4.45	0.00	2.24
246	248	0.106167	AGAGAGTACATGGCGGCCTA	60.106	55.000	21.46	7.11	0.00	3.93
285	291	2.653702	GTGCAGTGTCGAGCTCCT	59.346	61.111	8.47	0.00	0.00	3.69
298	304	1.438651	GCAAGTCACTAATCGGTGCA	58.561	50.000	0.00	0.00	37.16	4.57
434	454	0.991920	CCCTAGAAAAGCCTCCCACA	59.008	55.000	0.00	0.00	0.00	4.17
507	527	2.168313	CCAAGACAAGCCAACAAAACCT	59.832	45.455	0.00	0.00	0.00	3.50
513	533	0.257328	TGACCCAAGACAAGCCAACA	59.743	50.000	0.00	0.00	0.00	3.33
548	693	1.201987	CCCATTTTACGCTGTGTACGC	60.202	52.381	0.00	0.00	31.20	4.42
635	780	2.737180	CAGCCGACACAGTGAGGT	59.263	61.111	7.81	0.00	0.00	3.85
748	893	2.435586	CTGAGTCCAGGCCGCTTG	60.436	66.667	0.00	0.00	36.77	4.01
754	899	1.142748	CCATCGTCTGAGTCCAGGC	59.857	63.158	0.00	0.00	41.47	4.85
775	1315	0.532115	GCGGAAATTGGGCAGTCAAT	59.468	50.000	0.00	0.00	38.84	2.57
800	1340	3.706373	CTGCGGTAGGTGGGCAGT	61.706	66.667	4.20	0.00	46.82	4.40
838	1378	2.495366	TATAATGGCGGGCGGTAGCG	62.495	60.000	10.57	10.57	46.35	4.26
861	1401	2.653366	AGGTAGGACAGTAGGTGGAAGA	59.347	50.000	0.00	0.00	0.00	2.87
873	1413	2.750141	ATAGGCGAAGAGGTAGGACA	57.250	50.000	0.00	0.00	0.00	4.02
875	1415	4.343239	GGTTTTATAGGCGAAGAGGTAGGA	59.657	45.833	0.00	0.00	0.00	2.94
929	1469	1.306568	GGAGAGAAGGGGCAGAGGT	60.307	63.158	0.00	0.00	0.00	3.85
936	1476	2.266055	GCGTGTGGAGAGAAGGGG	59.734	66.667	0.00	0.00	0.00	4.79
1022	1562	0.975040	GAGCTCCTCTGCCTTCTCCA	60.975	60.000	0.87	0.00	0.00	3.86
1068	1608	2.646175	CCCCGACATCCACACGTCT	61.646	63.158	0.00	0.00	0.00	4.18
1075	1615	3.860605	CCATCGCCCCGACATCCA	61.861	66.667	0.00	0.00	39.18	3.41
1138	1678	2.906897	CACAAAGCCGTGGGTGCT	60.907	61.111	0.00	0.00	41.89	4.40
1156	1696	1.033202	TAGTACTGACCGATGGCGCA	61.033	55.000	10.83	0.00	35.83	6.09
1169	1709	2.362120	ACCGCCGTGCCTAGTACT	60.362	61.111	0.00	0.00	0.00	2.73
1170	1710	2.103736	GACCGCCGTGCCTAGTAC	59.896	66.667	0.00	0.00	0.00	2.73
1226	1766	1.097547	GGATGCCTGTTAGTGCGCAT	61.098	55.000	15.91	5.37	44.36	4.73
1235	1775	2.206635	CTCCTCGAGGATGCCTGTT	58.793	57.895	33.66	0.00	44.46	3.16
1236	1776	3.947173	CTCCTCGAGGATGCCTGT	58.053	61.111	33.66	0.00	44.46	4.00
1259	1799	0.036164	ATGCCTGTAGCCGTGTTTCA	59.964	50.000	0.00	0.00	42.71	2.69
1277	1817	1.153901	CAGCCGTTGTCCGTCGTAT	60.154	57.895	0.00	0.00	33.66	3.06
1337	1877	1.541233	CCACTTCTTCGAAGGTGTGCT	60.541	52.381	29.09	8.56	32.49	4.40
1340	1880	1.269621	CGACCACTTCTTCGAAGGTGT	60.270	52.381	24.37	19.01	37.43	4.16
1374	1914	3.746949	GATGCCGCTAGCTGCCTGT	62.747	63.158	25.73	13.38	44.23	4.00
1830	3255	7.662897	TGCGGGTTTAATGTTAGAAAAATCTT	58.337	30.769	0.00	0.00	0.00	2.40
1841	3266	6.588204	TGATATCTACTGCGGGTTTAATGTT	58.412	36.000	3.98	0.00	0.00	2.71
2037	3463	5.874810	CACTACCGGAATGAAAGAAAGATGA	59.125	40.000	9.46	0.00	0.00	2.92
2039	3465	6.049955	TCACTACCGGAATGAAAGAAAGAT	57.950	37.500	9.46	0.00	0.00	2.40
2094	3521	6.862608	TGATCTTCAATTTTGTGTTCAATCCG	59.137	34.615	0.00	0.00	33.32	4.18
2118	3545	6.757897	TTATTGGGTGTCTCTAGCAAATTG	57.242	37.500	0.00	0.00	0.00	2.32
2157	3584	4.086457	TGGGTCCTCCTTTTATTTCTTGC	58.914	43.478	0.00	0.00	36.20	4.01
2248	3677	9.739276	ATACAAAGTTGAGTCATCTATTTTGGA	57.261	29.630	14.35	9.09	40.00	3.53
2286	3715	9.140286	CGTTCTAAAATAGATGACTCAACTTCA	57.860	33.333	0.00	0.00	34.22	3.02
2287	3716	8.596380	CCGTTCTAAAATAGATGACTCAACTTC	58.404	37.037	0.00	0.00	34.22	3.01
2288	3717	8.311836	TCCGTTCTAAAATAGATGACTCAACTT	58.688	33.333	0.00	0.00	34.22	2.66
2289	3718	7.837863	TCCGTTCTAAAATAGATGACTCAACT	58.162	34.615	0.00	0.00	34.22	3.16
2290	3719	7.222999	CCTCCGTTCTAAAATAGATGACTCAAC	59.777	40.741	0.00	0.00	34.22	3.18
2291	3720	7.265673	CCTCCGTTCTAAAATAGATGACTCAA	58.734	38.462	0.00	0.00	34.22	3.02
2292	3721	6.183360	CCCTCCGTTCTAAAATAGATGACTCA	60.183	42.308	0.00	0.00	34.22	3.41
2293	3722	6.040616	TCCCTCCGTTCTAAAATAGATGACTC	59.959	42.308	0.00	0.00	34.22	3.36
2294	3723	5.897824	TCCCTCCGTTCTAAAATAGATGACT	59.102	40.000	0.00	0.00	34.22	3.41
2295	3724	6.158023	TCCCTCCGTTCTAAAATAGATGAC	57.842	41.667	0.00	0.00	34.22	3.06
2296	3725	5.897824	ACTCCCTCCGTTCTAAAATAGATGA	59.102	40.000	0.00	0.00	34.22	2.92
2297	3726	6.163135	ACTCCCTCCGTTCTAAAATAGATG	57.837	41.667	0.00	0.00	34.22	2.90
2298	3727	9.771140	ATATACTCCCTCCGTTCTAAAATAGAT	57.229	33.333	0.00	0.00	34.22	1.98
2302	3731	9.597681	TCTTATATACTCCCTCCGTTCTAAAAT	57.402	33.333	0.00	0.00	0.00	1.82
2303	3732	9.425248	TTCTTATATACTCCCTCCGTTCTAAAA	57.575	33.333	0.00	0.00	0.00	1.52
2304	3733	9.075678	CTTCTTATATACTCCCTCCGTTCTAAA	57.924	37.037	0.00	0.00	0.00	1.85
2305	3734	8.443176	TCTTCTTATATACTCCCTCCGTTCTAA	58.557	37.037	0.00	0.00	0.00	2.10
2306	3735	7.982252	TCTTCTTATATACTCCCTCCGTTCTA	58.018	38.462	0.00	0.00	0.00	2.10
2307	3736	6.850234	TCTTCTTATATACTCCCTCCGTTCT	58.150	40.000	0.00	0.00	0.00	3.01
2308	3737	7.447853	TCTTCTTCTTATATACTCCCTCCGTTC	59.552	40.741	0.00	0.00	0.00	3.95
2309	3738	7.296098	TCTTCTTCTTATATACTCCCTCCGTT	58.704	38.462	0.00	0.00	0.00	4.44
2310	3739	6.850234	TCTTCTTCTTATATACTCCCTCCGT	58.150	40.000	0.00	0.00	0.00	4.69
2311	3740	7.762588	TTCTTCTTCTTATATACTCCCTCCG	57.237	40.000	0.00	0.00	0.00	4.63
2312	3741	9.369672	TCTTTCTTCTTCTTATATACTCCCTCC	57.630	37.037	0.00	0.00	0.00	4.30
2457	3886	7.382488	CGTCCATATTTCATCACTATTTCTCGT	59.618	37.037	0.00	0.00	0.00	4.18
2622	4058	6.611642	AGCATCACCAACTTAGGATAACTCTA	59.388	38.462	0.00	0.00	0.00	2.43
2667	4104	3.679502	CACTTCGAAGACATGTGTGCATA	59.320	43.478	31.08	0.00	34.32	3.14
3010	4479	1.199789	TGGCATTCACAATTCGTCAGC	59.800	47.619	0.00	0.00	0.00	4.26

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.