AutoCloner

Multiple sequence alignment - TraesCS1D01G249600

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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	TraesCS1D01G249600	chr1D	100.000	3008	0	0	1	3008	342169250	342172257	0.000000e+00	5555.0
1	TraesCS1D01G249600	chr1B	92.777	2146	86	27	75	2169	458080539	458082666	0.000000e+00	3040.0
2	TraesCS1D01G249600	chr1B	90.556	1959	114	32	266	2187	458128920	458130844	0.000000e+00	2527.0
3	TraesCS1D01G249600	chr1B	91.046	1854	95	27	350	2169	458262378	458264194	0.000000e+00	2438.0
4	TraesCS1D01G249600	chr1B	90.167	1200	79	8	877	2059	458172255	458173432	0.000000e+00	1526.0
5	TraesCS1D01G249600	chr1B	88.602	851	73	5	2177	3008	458181012	458181857	0.000000e+00	1013.0
6	TraesCS1D01G249600	chr1B	86.370	741	82	2	2214	2935	458278940	458279680	0.000000e+00	791.0
7	TraesCS1D01G249600	chr1B	86.972	284	27	3	1	276	458126159	458126440	8.100000e-81	311.0
8	TraesCS1D01G249600	chr1B	86.620	284	28	5	1	276	458260772	458261053	3.770000e-79	305.0
9	TraesCS1D01G249600	chr1A	93.746	1775	58	19	593	2325	441841567	441843330	0.000000e+00	2614.0
10	TraesCS1D01G249600	chr1A	90.498	442	23	2	153	594	441841051	441841473	1.570000e-157	566.0
11	TraesCS1D01G249600	chr1A	87.273	165	12	6	2	157	441838310	441838474	2.380000e-41	180.0
12	TraesCS1D01G249600	chr1A	86.087	115	8	5	21	127	464836457	464836571	1.890000e-22	117.0
13	TraesCS1D01G249600	chr1A	82.759	116	12	5	9	116	434432185	434432070	2.470000e-16	97.1
14	TraesCS1D01G249600	chr5B	85.815	994	118	14	998	1978	585495922	585494939	0.000000e+00	1033.0
15	TraesCS1D01G249600	chr5B	77.551	245	48	3	449	686	527839298	527839542	1.120000e-29	141.0
16	TraesCS1D01G249600	chr5B	85.217	115	10	3	20	127	406538044	406537930	8.810000e-21	111.0
17	TraesCS1D01G249600	chr5A	85.758	990	126	8	998	1978	597280073	597279090	0.000000e+00	1033.0
18	TraesCS1D01G249600	chr5A	85.189	871	110	12	998	1857	597265620	597264758	0.000000e+00	876.0
19	TraesCS1D01G249600	chr5D	85.685	992	123	10	998	1978	478001037	478000054	0.000000e+00	1027.0
20	TraesCS1D01G249600	chr2D	82.968	957	131	16	1035	1972	637802135	637803078	0.000000e+00	835.0
21	TraesCS1D01G249600	chr2A	85.392	664	86	6	1310	1972	761541929	761541276	0.000000e+00	678.0
22	TraesCS1D01G249600	chr2A	84.111	579	67	18	1035	1603	14997665	14998228	1.230000e-148	536.0
23	TraesCS1D01G249600	chr7A	80.833	240	39	6	461	694	515737757	515737519	6.620000e-42	182.0
24	TraesCS1D01G249600	chr2B	79.518	249	43	4	449	689	35131046	35130798	1.430000e-38	171.0
25	TraesCS1D01G249600	chr4A	78.715	249	45	4	449	689	655564353	655564601	3.100000e-35	159.0
26	TraesCS1D01G249600	chrUn	77.470	253	50	6	449	694	218391831	218391579	8.690000e-31	145.0
27	TraesCS1D01G249600	chr3A	87.850	107	8	2	10	116	49817750	49817851	1.460000e-23	121.0
28	TraesCS1D01G249600	chr6D	83.740	123	13	5	10	128	380573376	380573257	3.170000e-20	110.0
29	TraesCS1D01G249600	chr3D	82.707	133	10	9	11	134	38408403	38408275	4.100000e-19	106.0
30	TraesCS1D01G249600	chr6A	82.927	123	14	5	10	128	522059613	522059494	1.480000e-18	104.0

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	TraesCS1D01G249600	chr1D	342169250	342172257	3007	False	5555.0	5555	100.000000	1	3008	1	chr1D.!!$F1	3007
1	TraesCS1D01G249600	chr1B	458080539	458082666	2127	False	3040.0	3040	92.777000	75	2169	1	chr1B.!!$F1	2094
2	TraesCS1D01G249600	chr1B	458172255	458173432	1177	False	1526.0	1526	90.167000	877	2059	1	chr1B.!!$F2	1182
3	TraesCS1D01G249600	chr1B	458126159	458130844	4685	False	1419.0	2527	88.764000	1	2187	2	chr1B.!!$F5	2186
4	TraesCS1D01G249600	chr1B	458260772	458264194	3422	False	1371.5	2438	88.833000	1	2169	2	chr1B.!!$F6	2168
5	TraesCS1D01G249600	chr1B	458181012	458181857	845	False	1013.0	1013	88.602000	2177	3008	1	chr1B.!!$F3	831
6	TraesCS1D01G249600	chr1B	458278940	458279680	740	False	791.0	791	86.370000	2214	2935	1	chr1B.!!$F4	721
7	TraesCS1D01G249600	chr1A	441838310	441843330	5020	False	1120.0	2614	90.505667	2	2325	3	chr1A.!!$F2	2323
8	TraesCS1D01G249600	chr5B	585494939	585495922	983	True	1033.0	1033	85.815000	998	1978	1	chr5B.!!$R2	980
9	TraesCS1D01G249600	chr5A	597279090	597280073	983	True	1033.0	1033	85.758000	998	1978	1	chr5A.!!$R2	980
10	TraesCS1D01G249600	chr5A	597264758	597265620	862	True	876.0	876	85.189000	998	1857	1	chr5A.!!$R1	859
11	TraesCS1D01G249600	chr5D	478000054	478001037	983	True	1027.0	1027	85.685000	998	1978	1	chr5D.!!$R1	980
12	TraesCS1D01G249600	chr2D	637802135	637803078	943	False	835.0	835	82.968000	1035	1972	1	chr2D.!!$F1	937
13	TraesCS1D01G249600	chr2A	761541276	761541929	653	True	678.0	678	85.392000	1310	1972	1	chr2A.!!$R1	662
14	TraesCS1D01G249600	chr2A	14997665	14998228	563	False	536.0	536	84.111000	1035	1603	1	chr2A.!!$F1	568

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
335	5557	0.465705	AGCCACCTATGACACATCGG	59.534	55.0	0.0	0.0	0.0	4.18	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2013	7306	0.966875	AATCACATGCACATGCCGGT	60.967	50.0	10.5	0.0	42.39	5.28	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
295	5517	1.373497	CTGGCGCTCGTTGAGTTCT	60.373	57.895	7.64	0.00	31.39	3.01
328	5550	1.946745	GCTTCTGAGCCACCTATGAC	58.053	55.000	0.00	0.00	43.29	3.06
329	5551	1.208052	GCTTCTGAGCCACCTATGACA	59.792	52.381	0.00	0.00	43.29	3.58
330	5552	2.898705	CTTCTGAGCCACCTATGACAC	58.101	52.381	0.00	0.00	0.00	3.67
331	5553	1.937191	TCTGAGCCACCTATGACACA	58.063	50.000	0.00	0.00	0.00	3.72
332	5554	2.470990	TCTGAGCCACCTATGACACAT	58.529	47.619	0.00	0.00	0.00	3.21
333	5555	2.432146	TCTGAGCCACCTATGACACATC	59.568	50.000	0.00	0.00	0.00	3.06
334	5556	1.136891	TGAGCCACCTATGACACATCG	59.863	52.381	0.00	0.00	0.00	3.84
335	5557	0.465705	AGCCACCTATGACACATCGG	59.534	55.000	0.00	0.00	0.00	4.18
337	5559	1.406887	GCCACCTATGACACATCGGTT	60.407	52.381	5.42	0.00	0.00	4.44
338	5560	2.550978	CCACCTATGACACATCGGTTC	58.449	52.381	5.42	0.00	0.00	3.62
339	5561	2.093711	CCACCTATGACACATCGGTTCA	60.094	50.000	5.42	0.00	0.00	3.18
340	5562	3.595173	CACCTATGACACATCGGTTCAA	58.405	45.455	5.42	0.00	0.00	2.69
341	5563	3.370978	CACCTATGACACATCGGTTCAAC	59.629	47.826	5.42	0.00	0.00	3.18
342	5564	3.007506	ACCTATGACACATCGGTTCAACA	59.992	43.478	0.00	0.00	0.00	3.33
343	5565	4.000325	CCTATGACACATCGGTTCAACAA	59.000	43.478	0.00	0.00	0.00	2.83
344	5566	4.454161	CCTATGACACATCGGTTCAACAAA	59.546	41.667	0.00	0.00	0.00	2.83
345	5567	4.909696	ATGACACATCGGTTCAACAAAA	57.090	36.364	0.00	0.00	0.00	2.44
346	5568	4.703645	TGACACATCGGTTCAACAAAAA	57.296	36.364	0.00	0.00	0.00	1.94
347	5569	5.255710	TGACACATCGGTTCAACAAAAAT	57.744	34.783	0.00	0.00	0.00	1.82
348	5570	5.277825	TGACACATCGGTTCAACAAAAATC	58.722	37.500	0.00	0.00	0.00	2.17
370	5592	8.451908	AATCCGGTTCAATAAAAATCCTCTAG	57.548	34.615	0.00	0.00	0.00	2.43
380	5602	4.657814	AAAATCCTCTAGAAACAGGGCA	57.342	40.909	0.00	0.00	0.00	5.36
383	5605	0.615331	CCTCTAGAAACAGGGCAGCA	59.385	55.000	0.00	0.00	0.00	4.41
430	5652	2.325583	TCGCAGCCCCTAATAAACTG	57.674	50.000	0.00	0.00	0.00	3.16
433	5655	2.870411	CGCAGCCCCTAATAAACTGTAC	59.130	50.000	0.00	0.00	0.00	2.90
436	5658	5.298347	GCAGCCCCTAATAAACTGTACTAG	58.702	45.833	0.00	0.00	0.00	2.57
437	5659	5.163332	GCAGCCCCTAATAAACTGTACTAGT	60.163	44.000	0.00	0.00	42.89	2.57
438	5660	6.041296	GCAGCCCCTAATAAACTGTACTAGTA	59.959	42.308	0.00	0.00	39.18	1.82
441	5663	9.531158	AGCCCCTAATAAACTGTACTAGTATAG	57.469	37.037	21.36	21.36	46.50	1.31
455	5677	5.440207	CTAGTATAGTACTCCCTCCCTCC	57.560	52.174	0.00	0.00	40.14	4.30
458	5680	2.004408	TAGTACTCCCTCCCTCCGGC	62.004	65.000	0.00	0.00	0.00	6.13
459	5681	3.028098	TACTCCCTCCCTCCGGCT	61.028	66.667	0.00	0.00	0.00	5.52
460	5682	3.070987	TACTCCCTCCCTCCGGCTC	62.071	68.421	0.00	0.00	0.00	4.70
469	5691	1.553704	TCCCTCCGGCTCTTTTTAGTC	59.446	52.381	0.00	0.00	0.00	2.59
470	5692	1.555533	CCCTCCGGCTCTTTTTAGTCT	59.444	52.381	0.00	0.00	0.00	3.24
472	5694	2.003301	CTCCGGCTCTTTTTAGTCTGC	58.997	52.381	0.00	0.00	0.00	4.26
473	5695	1.346395	TCCGGCTCTTTTTAGTCTGCA	59.654	47.619	0.00	0.00	0.00	4.41
479	5701	6.292919	CCGGCTCTTTTTAGTCTGCATATAAC	60.293	42.308	0.00	0.00	0.00	1.89
493	5715	8.827677	GTCTGCATATAACTTTTATCCGAAGTT	58.172	33.333	7.32	7.32	46.09	2.66
554	5776	5.106197	GCATCAACACAATACCAGATCAACA	60.106	40.000	0.00	0.00	0.00	3.33
555	5777	6.405065	GCATCAACACAATACCAGATCAACAT	60.405	38.462	0.00	0.00	0.00	2.71
556	5778	7.541162	CATCAACACAATACCAGATCAACATT	58.459	34.615	0.00	0.00	0.00	2.71
676	5900	9.848710	TTGGTTTGACATAAATATAATACGGGA	57.151	29.630	0.00	0.00	0.00	5.14
691	5915	6.812879	AATACGGGAAGTAAAAAGAACCAG	57.187	37.500	0.00	0.00	39.04	4.00
692	5916	4.426736	ACGGGAAGTAAAAAGAACCAGA	57.573	40.909	0.00	0.00	0.00	3.86
694	5918	3.188667	CGGGAAGTAAAAAGAACCAGAGC	59.811	47.826	0.00	0.00	0.00	4.09
695	5919	3.188667	GGGAAGTAAAAAGAACCAGAGCG	59.811	47.826	0.00	0.00	0.00	5.03
945	6193	2.027561	TCGTCGATTGACCCCAGAATTT	60.028	45.455	7.54	0.00	42.37	1.82
946	6194	2.747446	CGTCGATTGACCCCAGAATTTT	59.253	45.455	7.54	0.00	42.37	1.82
947	6195	3.190535	CGTCGATTGACCCCAGAATTTTT	59.809	43.478	7.54	0.00	42.37	1.94
948	6196	4.485163	GTCGATTGACCCCAGAATTTTTG	58.515	43.478	1.10	0.00	39.30	2.44
949	6197	4.022329	GTCGATTGACCCCAGAATTTTTGT	60.022	41.667	1.10	0.00	39.30	2.83
981	6229	1.887242	GGCACATCGCGCCTTATCA	60.887	57.895	0.00	0.00	46.56	2.15
1031	6279	1.101049	AGAGCTGCTCCGAGTCTAGC	61.101	60.000	25.09	11.26	39.25	3.42
2011	7303	3.911155	CTCGCGGCGCAGTGAAAAC	62.911	63.158	32.61	0.00	0.00	2.43
2013	7306	3.959975	GCGGCGCAGTGAAAACCA	61.960	61.111	29.21	0.00	0.00	3.67
2049	7352	6.348621	TGTGATTCATGTATGTGTGATTCG	57.651	37.500	0.00	0.00	31.00	3.34
2064	7367	4.156922	TGTGATTCGAGGAGTTCTCTTCTC	59.843	45.833	9.57	4.01	41.61	2.87
2065	7368	4.398044	GTGATTCGAGGAGTTCTCTTCTCT	59.602	45.833	9.57	0.00	42.56	3.10
2066	7369	5.587043	GTGATTCGAGGAGTTCTCTTCTCTA	59.413	44.000	9.57	0.00	42.56	2.43
2164	7467	5.093849	TGCTAAGGCTTAATAAACTCGGT	57.906	39.130	8.54	0.00	39.59	4.69
2282	7586	2.524394	AGTCACGGGAGCTGGTGT	60.524	61.111	0.00	0.00	35.67	4.16
2283	7587	2.100879	GAGTCACGGGAGCTGGTGTT	62.101	60.000	0.00	0.00	35.67	3.32
2336	7649	6.349300	ACGGAGTGAATAGCATCAAATTACT	58.651	36.000	0.00	0.00	42.51	2.24
2400	7713	8.564509	AAGGACTCCACTATATATCTTACGTC	57.435	38.462	0.00	0.00	0.00	4.34
2404	7717	9.386010	GACTCCACTATATATCTTACGTCAGAT	57.614	37.037	16.05	16.05	37.31	2.90
2405	7718	9.742144	ACTCCACTATATATCTTACGTCAGATT	57.258	33.333	16.91	8.20	35.08	2.40
2458	7791	4.394920	GTCGAGGATGGCAAATTTAGTTGA	59.605	41.667	0.00	0.00	0.00	3.18
2529	7862	4.704833	AGCGCCCGCAACATCAGT	62.705	61.111	15.50	0.00	44.88	3.41
2570	7903	2.997315	CCTGCGGGTGGAGACTGA	60.997	66.667	2.29	0.00	35.14	3.41
2619	7952	1.302192	GGGTGTAGAACAGGCGCAA	60.302	57.895	10.83	0.00	0.00	4.85
2620	7953	0.887387	GGGTGTAGAACAGGCGCAAA	60.887	55.000	10.83	0.00	0.00	3.68
2632	7965	2.390288	CGCAAACGATCGTGGACG	59.610	61.111	23.51	20.40	43.93	4.79
2698	8031	0.827089	CCACAACAACCATGAGGCCA	60.827	55.000	5.01	0.00	39.06	5.36
2700	8033	0.185901	ACAACAACCATGAGGCCAGT	59.814	50.000	5.01	0.00	39.06	4.00
2729	8062	1.339610	CTCGATCATGGACCTCACCTC	59.660	57.143	0.00	0.00	0.00	3.85
2753	8086	4.007940	CAACGTCCACGCAACGGG	62.008	66.667	9.22	0.00	44.21	5.28
2784	8118	4.056050	ACAAAGAATAGGACGTGTGACAC	58.944	43.478	5.47	5.47	0.00	3.67
2834	8168	1.975680	ACCGTGTCCCATGTTCTACTT	59.024	47.619	0.00	0.00	0.00	2.24
2837	8171	3.818773	CCGTGTCCCATGTTCTACTTTTT	59.181	43.478	0.00	0.00	0.00	1.94
2838	8172	4.083484	CCGTGTCCCATGTTCTACTTTTTC	60.083	45.833	0.00	0.00	0.00	2.29
2869	8203	1.531578	GACCCGCAACTTCACTTCTTC	59.468	52.381	0.00	0.00	0.00	2.87
2877	8211	3.735237	ACTTCACTTCTTCGAGCTCAA	57.265	42.857	15.40	6.48	0.00	3.02
2887	8221	2.342910	TCGAGCTCAAGACCGTTAAC	57.657	50.000	15.40	0.00	0.00	2.01
2910	8244	6.133356	ACCTTTCTGTACATGGGAAGAAAAA	58.867	36.000	15.45	1.40	37.98	1.94
2911	8245	6.265422	ACCTTTCTGTACATGGGAAGAAAAAG	59.735	38.462	15.45	12.98	37.98	2.27
2915	8249	3.500680	TGTACATGGGAAGAAAAAGCGTC	59.499	43.478	0.00	0.00	0.00	5.19
2921	8255	3.434299	TGGGAAGAAAAAGCGTCGAATAC	59.566	43.478	0.00	0.00	0.00	1.89
2939	8273	2.357517	GGACACCGACACTGCCTG	60.358	66.667	0.00	0.00	0.00	4.85
2975	8309	8.812972	AGACTAGGTTAAAACATGTCATGTCTA	58.187	33.333	18.66	12.73	44.07	2.59
2998	8332	9.959749	TCTACTTTTGGTTAATTGAAATGTGTC	57.040	29.630	0.00	0.00	0.00	3.67
2999	8333	9.743057	CTACTTTTGGTTAATTGAAATGTGTCA	57.257	29.630	0.00	0.00	0.00	3.58

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
280	5502	1.950098	GAGCAGAACTCAACGAGCGC	61.950	60.000	0.00	0.00	45.49	5.92
318	5540	2.093711	TGAACCGATGTGTCATAGGTGG	60.094	50.000	13.46	2.94	35.08	4.61
319	5541	3.245518	TGAACCGATGTGTCATAGGTG	57.754	47.619	13.46	0.00	35.08	4.00
320	5542	3.007506	TGTTGAACCGATGTGTCATAGGT	59.992	43.478	8.33	8.33	36.66	3.08
322	5544	5.605564	TTTGTTGAACCGATGTGTCATAG	57.394	39.130	0.00	0.00	0.00	2.23
323	5545	6.378710	TTTTTGTTGAACCGATGTGTCATA	57.621	33.333	0.00	0.00	0.00	2.15
324	5546	4.909696	TTTTGTTGAACCGATGTGTCAT	57.090	36.364	0.00	0.00	0.00	3.06
326	5548	4.679654	GGATTTTTGTTGAACCGATGTGTC	59.320	41.667	0.00	0.00	0.00	3.67
327	5549	4.616953	GGATTTTTGTTGAACCGATGTGT	58.383	39.130	0.00	0.00	0.00	3.72
328	5550	3.668191	CGGATTTTTGTTGAACCGATGTG	59.332	43.478	0.00	0.00	42.40	3.21
329	5551	3.305064	CCGGATTTTTGTTGAACCGATGT	60.305	43.478	0.00	0.00	42.40	3.06
330	5552	3.241701	CCGGATTTTTGTTGAACCGATG	58.758	45.455	0.00	0.00	42.40	3.84
331	5553	2.888414	ACCGGATTTTTGTTGAACCGAT	59.112	40.909	9.46	0.00	42.40	4.18
332	5554	2.299521	ACCGGATTTTTGTTGAACCGA	58.700	42.857	9.46	0.00	42.40	4.69
333	5555	2.785713	ACCGGATTTTTGTTGAACCG	57.214	45.000	9.46	0.00	40.03	4.44
334	5556	4.048241	TGAACCGGATTTTTGTTGAACC	57.952	40.909	9.46	0.00	0.00	3.62
335	5557	7.701809	TTATTGAACCGGATTTTTGTTGAAC	57.298	32.000	9.46	0.00	0.00	3.18
337	5559	8.718102	TTTTTATTGAACCGGATTTTTGTTGA	57.282	26.923	9.46	0.00	0.00	3.18
338	5560	9.592720	GATTTTTATTGAACCGGATTTTTGTTG	57.407	29.630	9.46	0.00	0.00	3.33
339	5561	8.779303	GGATTTTTATTGAACCGGATTTTTGTT	58.221	29.630	9.46	0.00	0.00	2.83
340	5562	8.154203	AGGATTTTTATTGAACCGGATTTTTGT	58.846	29.630	9.46	0.00	0.00	2.83
341	5563	8.546597	AGGATTTTTATTGAACCGGATTTTTG	57.453	30.769	9.46	0.00	0.00	2.44
342	5564	8.593679	AGAGGATTTTTATTGAACCGGATTTTT	58.406	29.630	9.46	0.00	0.00	1.94
343	5565	8.134202	AGAGGATTTTTATTGAACCGGATTTT	57.866	30.769	9.46	0.00	0.00	1.82
344	5566	7.718334	AGAGGATTTTTATTGAACCGGATTT	57.282	32.000	9.46	0.00	0.00	2.17
345	5567	8.272173	TCTAGAGGATTTTTATTGAACCGGATT	58.728	33.333	9.46	0.00	0.00	3.01
346	5568	7.802117	TCTAGAGGATTTTTATTGAACCGGAT	58.198	34.615	9.46	0.00	0.00	4.18
347	5569	7.190335	TCTAGAGGATTTTTATTGAACCGGA	57.810	36.000	9.46	0.00	0.00	5.14
348	5570	7.859325	TTCTAGAGGATTTTTATTGAACCGG	57.141	36.000	0.00	0.00	0.00	5.28
370	5592	3.005791	AGTTAACAATGCTGCCCTGTTTC	59.994	43.478	17.90	12.82	35.09	2.78
399	5621	3.197790	CTGCGATCCGGTTGCCTG	61.198	66.667	0.00	0.00	36.30	4.85
408	5630	2.152016	GTTTATTAGGGGCTGCGATCC	58.848	52.381	0.00	0.00	0.00	3.36
433	5655	4.080975	CGGAGGGAGGGAGTACTATACTAG	60.081	54.167	0.00	0.00	39.59	2.57
436	5658	3.070476	CGGAGGGAGGGAGTACTATAC	57.930	57.143	0.00	0.00	0.00	1.47
453	5675	1.346395	TGCAGACTAAAAAGAGCCGGA	59.654	47.619	5.05	0.00	0.00	5.14
455	5677	6.480320	AGTTATATGCAGACTAAAAAGAGCCG	59.520	38.462	0.00	0.00	0.00	5.52
530	5752	5.106197	TGTTGATCTGGTATTGTGTTGATGC	60.106	40.000	0.00	0.00	0.00	3.91
531	5753	6.499234	TGTTGATCTGGTATTGTGTTGATG	57.501	37.500	0.00	0.00	0.00	3.07
673	5897	3.188667	CGCTCTGGTTCTTTTTACTTCCC	59.811	47.826	0.00	0.00	0.00	3.97
674	5898	3.813724	ACGCTCTGGTTCTTTTTACTTCC	59.186	43.478	0.00	0.00	0.00	3.46
676	5900	5.235831	GTGTACGCTCTGGTTCTTTTTACTT	59.764	40.000	0.00	0.00	0.00	2.24
687	5911	1.268899	GTGTACTGTGTACGCTCTGGT	59.731	52.381	8.10	4.43	0.00	4.00
689	5913	2.991434	AGTGTACTGTGTACGCTCTG	57.009	50.000	15.50	0.95	33.47	3.35
690	5914	5.668471	TCTATAGTGTACTGTGTACGCTCT	58.332	41.667	22.01	16.61	38.91	4.09
691	5915	5.980698	TCTATAGTGTACTGTGTACGCTC	57.019	43.478	22.01	7.84	38.91	5.03
692	5916	6.018098	GTGATCTATAGTGTACTGTGTACGCT	60.018	42.308	22.02	22.02	40.80	5.07
694	5918	6.259387	TGGTGATCTATAGTGTACTGTGTACG	59.741	42.308	0.00	0.00	0.00	3.67
695	5919	7.282675	ACTGGTGATCTATAGTGTACTGTGTAC	59.717	40.741	0.00	1.33	0.00	2.90
945	6193	4.098044	TGTGCCGTCCTTTTATTGAACAAA	59.902	37.500	0.00	0.00	0.00	2.83
946	6194	3.632604	TGTGCCGTCCTTTTATTGAACAA	59.367	39.130	0.00	0.00	0.00	2.83
947	6195	3.215151	TGTGCCGTCCTTTTATTGAACA	58.785	40.909	0.00	0.00	0.00	3.18
948	6196	3.907894	TGTGCCGTCCTTTTATTGAAC	57.092	42.857	0.00	0.00	0.00	3.18
949	6197	3.126171	CGATGTGCCGTCCTTTTATTGAA	59.874	43.478	0.00	0.00	0.00	2.69
981	6229	0.975040	TGGTTTGGTGTTTGCTGCCT	60.975	50.000	0.00	0.00	0.00	4.75
2011	7303	3.063704	ACATGCACATGCCGGTGG	61.064	61.111	10.50	0.00	42.39	4.61
2013	7306	0.966875	AATCACATGCACATGCCGGT	60.967	50.000	10.50	0.00	42.39	5.28
2049	7352	6.315393	CACAGTAGTAGAGAAGAGAACTCCTC	59.685	46.154	0.00	0.04	42.28	3.71
2064	7367	5.683302	CGCTCATCACATTACACAGTAGTAG	59.317	44.000	0.00	0.00	0.00	2.57
2065	7368	5.124936	ACGCTCATCACATTACACAGTAGTA	59.875	40.000	0.00	0.00	0.00	1.82
2066	7369	4.082190	ACGCTCATCACATTACACAGTAGT	60.082	41.667	0.00	0.00	0.00	2.73
2282	7586	2.796483	AAGCCATCGTAGCGGTGCAA	62.796	55.000	3.09	0.00	36.57	4.08
2283	7587	2.796483	AAAGCCATCGTAGCGGTGCA	62.796	55.000	3.09	0.00	36.57	4.57
2290	7603	2.743938	ACTATCGCAAAGCCATCGTAG	58.256	47.619	0.00	0.00	0.00	3.51
2336	7649	8.480133	TTTTTGAAACCCTAACCTATAAAGCA	57.520	30.769	0.00	0.00	0.00	3.91
2458	7791	2.026449	CCAGAAAGGCCAGATTCTCTGT	60.026	50.000	5.01	0.00	42.80	3.41
2475	7808	3.157252	GCCCGCTCCTCATCCAGA	61.157	66.667	0.00	0.00	0.00	3.86
2496	7829	1.372582	CGCTGCACATGGACTTGTAT	58.627	50.000	0.00	0.00	0.00	2.29
2561	7894	0.037326	GAACATGGCGTCAGTCTCCA	60.037	55.000	0.00	0.00	35.25	3.86
2570	7903	0.460284	GATCTCCGTGAACATGGCGT	60.460	55.000	8.06	0.00	37.40	5.68
2610	7943	2.357034	ACGATCGTTTGCGCCTGT	60.357	55.556	16.60	0.00	38.14	4.00
2619	7952	1.129998	CTACTGACGTCCACGATCGTT	59.870	52.381	20.14	2.95	43.02	3.85
2620	7953	0.725686	CTACTGACGTCCACGATCGT	59.274	55.000	16.60	16.60	43.02	3.73
2698	8031	2.566279	CCATGATCGAGATGGATGGACT	59.434	50.000	17.67	0.00	42.81	3.85
2700	8033	2.893424	TCCATGATCGAGATGGATGGA	58.107	47.619	20.13	14.30	43.71	3.41
2729	8062	3.541831	CGTGGACGTTGCCGATCG	61.542	66.667	8.51	8.51	37.88	3.69
2753	8086	1.475213	CCTATTCTTTGTCCCCGGAGC	60.475	57.143	0.73	0.00	0.00	4.70
2758	8092	2.027469	ACACGTCCTATTCTTTGTCCCC	60.027	50.000	0.00	0.00	0.00	4.81
2796	8130	0.460284	GTCCACATAGACACCAGGCG	60.460	60.000	0.00	0.00	36.73	5.52
2869	8203	1.067776	AGGTTAACGGTCTTGAGCTCG	60.068	52.381	9.64	0.00	0.00	5.03
2877	8211	4.942761	TGTACAGAAAGGTTAACGGTCT	57.057	40.909	0.00	0.00	0.00	3.85
2887	8221	6.648879	TTTTTCTTCCCATGTACAGAAAGG	57.351	37.500	0.33	0.60	36.77	3.11
2930	8264	2.028112	TCTAAATCTTCGCAGGCAGTGT	60.028	45.455	0.00	0.00	0.00	3.55
2939	8273	8.248117	TGTTTTAACCTAGTCTAAATCTTCGC	57.752	34.615	0.00	0.00	0.00	4.70
2970	8304	9.743057	CACATTTCAATTAACCAAAAGTAGACA	57.257	29.630	0.00	0.00	0.00	3.41
2971	8305	9.744468	ACACATTTCAATTAACCAAAAGTAGAC	57.256	29.630	0.00	0.00	0.00	2.59
2975	8309	9.442047	TTTGACACATTTCAATTAACCAAAAGT	57.558	25.926	0.00	0.00	35.42	2.66

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.