AutoCloner

Multiple sequence alignment - TraesCS1D01G344700

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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	TraesCS1D01G344700	chr1D	100.000	5229	0	0	1	5229	433217844	433212616	0.000000e+00	9657.0
1	TraesCS1D01G344700	chr1A	94.606	5284	200	37	1	5228	531612625	531607371	0.000000e+00	8100.0
2	TraesCS1D01G344700	chr1A	89.583	48	5	0	3813	3860	485031909	485031862	1.570000e-05	62.1
3	TraesCS1D01G344700	chr1B	95.653	4624	141	24	640	5228	585077237	585072639	0.000000e+00	7371.0
4	TraesCS1D01G344700	chr1B	84.557	531	48	10	2	508	585078067	585077547	3.640000e-136	496.0
5	TraesCS1D01G344700	chr2D	87.639	720	80	3	2425	3141	442448970	442448257	0.000000e+00	828.0
6	TraesCS1D01G344700	chr2D	83.607	366	47	5	2776	3141	522888330	522887978	1.090000e-86	331.0
7	TraesCS1D01G344700	chr2D	84.412	340	41	4	2403	2742	522888660	522888333	1.820000e-84	324.0
8	TraesCS1D01G344700	chr2D	84.348	230	35	1	2325	2553	442449191	442448962	1.890000e-54	224.0
9	TraesCS1D01G344700	chr7D	86.631	748	86	8	2425	3165	453305289	453304549	0.000000e+00	815.0
10	TraesCS1D01G344700	chr7D	84.348	230	35	1	2325	2553	453305510	453305281	1.890000e-54	224.0
11	TraesCS1D01G344700	chr7D	80.000	190	38	0	3434	3623	473093764	473093575	1.960000e-29	141.0
12	TraesCS1D01G344700	chr3A	71.701	3145	705	135	1057	4096	506231081	506228017	0.000000e+00	706.0
13	TraesCS1D01G344700	chr3A	95.349	43	2	0	3813	3855	96682781	96682739	9.400000e-08	69.4
14	TraesCS1D01G344700	chr3D	71.531	2789	644	108	1393	4096	383113076	383110353	9.620000e-172	614.0
15	TraesCS1D01G344700	chr3D	90.054	372	25	3	3005	3376	594157710	594158069	6.130000e-129	472.0
16	TraesCS1D01G344700	chr3D	74.592	551	103	26	3087	3620	382754291	382753761	1.910000e-49	207.0
17	TraesCS1D01G344700	chr3B	74.696	1233	239	53	2906	4096	498728704	498727503	1.020000e-131	481.0
18	TraesCS1D01G344700	chr3B	71.361	1683	353	91	2473	4096	498368442	498366830	8.450000e-83	318.0
19	TraesCS1D01G344700	chr4A	83.373	421	60	6	1953	2372	435629278	435628867	1.060000e-101	381.0
20	TraesCS1D01G344700	chr6A	90.106	283	19	4	2090	2372	250073992	250074265	4.980000e-95	359.0
21	TraesCS1D01G344700	chr5D	90.588	255	23	1	3129	3383	68892324	68892577	2.330000e-88	337.0
22	TraesCS1D01G344700	chr5D	90.244	123	12	0	3005	3127	68877451	68877573	1.510000e-35	161.0
23	TraesCS1D01G344700	chr5D	93.023	43	3	0	3803	3845	368333267	368333309	4.370000e-06	63.9
24	TraesCS1D01G344700	chr7A	81.283	187	35	0	3434	3620	522799161	522799347	9.070000e-33	152.0
25	TraesCS1D01G344700	chr7A	86.486	74	10	0	3774	3847	712180955	712181028	1.210000e-11	82.4
26	TraesCS1D01G344700	chr7B	89.091	55	5	1	1208	1262	302516522	302516469	3.380000e-07	67.6
27	TraesCS1D01G344700	chr6D	93.333	45	3	0	3813	3857	425902619	425902575	3.380000e-07	67.6
28	TraesCS1D01G344700	chr5B	93.023	43	3	0	3803	3845	436259157	436259199	4.370000e-06	63.9
29	TraesCS1D01G344700	chr5B	96.875	32	0	1	2605	2635	450610065	450610034	9.000000e-03	52.8
30	TraesCS1D01G344700	chr5A	93.023	43	3	0	3803	3845	470196293	470196335	4.370000e-06	63.9
31	TraesCS1D01G344700	chr5A	96.875	32	0	1	2605	2635	477814724	477814693	9.000000e-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	TraesCS1D01G344700	chr1D	433212616	433217844	5228	True	9657.0	9657	100.0000	1	5229	1	chr1D.!!$R1	5228
1	TraesCS1D01G344700	chr1A	531607371	531612625	5254	True	8100.0	8100	94.6060	1	5228	1	chr1A.!!$R2	5227
2	TraesCS1D01G344700	chr1B	585072639	585078067	5428	True	3933.5	7371	90.1050	2	5228	2	chr1B.!!$R1	5226
3	TraesCS1D01G344700	chr2D	442448257	442449191	934	True	526.0	828	85.9935	2325	3141	2	chr2D.!!$R1	816
4	TraesCS1D01G344700	chr2D	522887978	522888660	682	True	327.5	331	84.0095	2403	3141	2	chr2D.!!$R2	738
5	TraesCS1D01G344700	chr7D	453304549	453305510	961	True	519.5	815	85.4895	2325	3165	2	chr7D.!!$R2	840
6	TraesCS1D01G344700	chr3A	506228017	506231081	3064	True	706.0	706	71.7010	1057	4096	1	chr3A.!!$R2	3039
7	TraesCS1D01G344700	chr3D	383110353	383113076	2723	True	614.0	614	71.5310	1393	4096	1	chr3D.!!$R2	2703
8	TraesCS1D01G344700	chr3D	382753761	382754291	530	True	207.0	207	74.5920	3087	3620	1	chr3D.!!$R1	533
9	TraesCS1D01G344700	chr3B	498727503	498728704	1201	True	481.0	481	74.6960	2906	4096	1	chr3B.!!$R2	1190
10	TraesCS1D01G344700	chr3B	498366830	498368442	1612	True	318.0	318	71.3610	2473	4096	1	chr3B.!!$R1	1623

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
556	581	0.821517	TCTAAAATCTCGGCCAGCGA	59.178	50.000	2.24	0.00	4.93	F
1038	1251	0.468214	CCTATCTCCCACTCCTCGCA	60.468	60.000	0.00	0.00	5.10	F
1387	1600	0.811915	CGACCTCTCGATGAACAGGT	59.188	55.000	0.00	43.06	4.00	F
1910	2132	1.000955	CTACAACAAGCTGACCGGAGT	59.999	52.381	9.46	0.00	3.85	F
2910	3273	1.282157	GACAAGGTATCACCAGGCCTT	59.718	52.381	0.00	41.95	4.35	F
3767	4168	2.816689	CTCATATTGTTCGCCGTGGTA	58.183	47.619	0.00	0.00	3.25	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1910	2132	1.600107	CCGAACCTTTCCGGGATCA	59.400	57.895	0.00	41.89	2.92	R
2260	2485	2.815647	CACCTCGCCGGAAAGCTC	60.816	66.667	5.05	36.31	4.09	R
3267	3645	0.238289	GCTTGACGATGTTGGTGTGG	59.762	55.000	0.00	0.00	4.17	R
3689	4082	0.179000	ATCAAGGTGAGGTGATCGGC	59.821	55.000	0.00	27.99	5.54	R
3985	4386	0.318699	CGAGCTTGAACACGACCTCA	60.319	55.000	0.00	0.00	3.86	R
5004	5442	0.616395	TGGACGGTGGGCTCTATGAA	60.616	55.000	0.00	0.00	2.57	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
26	27	2.865119	AGGATATCATGATGGCGCAA	57.135	45.000	18.72	0.00	0.00	4.85
77	78	7.142021	ACAACTCGATACAAGTAGCATATGAG	58.858	38.462	6.97	0.00	0.00	2.90
78	79	6.260870	ACTCGATACAAGTAGCATATGAGG	57.739	41.667	6.97	0.00	0.00	3.86
81	83	6.914259	TCGATACAAGTAGCATATGAGGAAG	58.086	40.000	6.97	0.00	0.00	3.46
111	113	6.482641	TCACATTTTGGTGACATTTCAATTGG	59.517	34.615	5.42	0.00	42.56	3.16
155	157	8.846943	TTGTAGTTGACATTGACTTCACATAT	57.153	30.769	0.00	0.00	38.07	1.78
165	167	7.613022	ACATTGACTTCACATATCCACAATTCT	59.387	33.333	0.00	0.00	0.00	2.40
203	205	5.473039	TCCATGCACATATGAATAGTCGAG	58.527	41.667	10.38	0.00	0.00	4.04
205	207	6.208599	TCCATGCACATATGAATAGTCGAGTA	59.791	38.462	10.38	1.68	0.00	2.59
207	209	5.449304	TGCACATATGAATAGTCGAGTACG	58.551	41.667	10.38	0.00	41.26	3.67
208	210	5.237779	TGCACATATGAATAGTCGAGTACGA	59.762	40.000	10.38	0.00	46.56	3.43
248	250	7.337480	ACATTCACATATGCACATACACATT	57.663	32.000	1.58	0.00	0.00	2.71
335	355	8.781067	TCTACAAGATCAATTTGTGAAAAACG	57.219	30.769	8.63	0.00	40.50	3.60
473	498	3.821600	GCATAGAGTATGGAGGAGTCGAA	59.178	47.826	0.00	0.00	36.68	3.71
487	512	0.974383	GTCGAAGAAGGGGAGGTCAA	59.026	55.000	0.00	0.00	39.69	3.18
556	581	0.821517	TCTAAAATCTCGGCCAGCGA	59.178	50.000	2.24	0.00	0.00	4.93
557	582	1.412710	TCTAAAATCTCGGCCAGCGAT	59.587	47.619	2.24	0.00	0.00	4.58
576	601	4.148825	CAGGGCGGGAAGACGAGG	62.149	72.222	0.00	0.00	35.47	4.63
607	638	2.269241	GGTGGGGAAAGAGAGGCG	59.731	66.667	0.00	0.00	0.00	5.52
610	641	2.291043	TGGGGAAAGAGAGGCGTCC	61.291	63.158	2.06	0.00	0.00	4.79
613	644	2.881352	GAAAGAGAGGCGTCCGCG	60.881	66.667	0.00	0.00	43.06	6.46
673	876	2.906354	CGTCCCCTTCAGTCCAATTAG	58.094	52.381	0.00	0.00	0.00	1.73
740	943	6.731164	ACACGAATTAAACAACCAAGTAAGG	58.269	36.000	0.00	0.00	0.00	2.69
802	1005	2.097466	CCCAACGAGCACAATATCCAAC	59.903	50.000	0.00	0.00	0.00	3.77
803	1006	2.746904	CCAACGAGCACAATATCCAACA	59.253	45.455	0.00	0.00	0.00	3.33
804	1007	3.378112	CCAACGAGCACAATATCCAACAT	59.622	43.478	0.00	0.00	0.00	2.71
805	1008	4.345288	CAACGAGCACAATATCCAACATG	58.655	43.478	0.00	0.00	0.00	3.21
806	1009	3.872696	ACGAGCACAATATCCAACATGA	58.127	40.909	0.00	0.00	0.00	3.07
807	1010	3.623060	ACGAGCACAATATCCAACATGAC	59.377	43.478	0.00	0.00	0.00	3.06
808	1011	3.622612	CGAGCACAATATCCAACATGACA	59.377	43.478	0.00	0.00	0.00	3.58
809	1012	4.494690	CGAGCACAATATCCAACATGACAC	60.495	45.833	0.00	0.00	0.00	3.67
810	1013	4.334552	AGCACAATATCCAACATGACACA	58.665	39.130	0.00	0.00	0.00	3.72
811	1014	4.156556	AGCACAATATCCAACATGACACAC	59.843	41.667	0.00	0.00	0.00	3.82
812	1015	4.082841	GCACAATATCCAACATGACACACA	60.083	41.667	0.00	0.00	0.00	3.72
813	1016	5.393352	GCACAATATCCAACATGACACACAT	60.393	40.000	0.00	0.00	40.17	3.21
959	1172	2.051345	CCAAACTGAACGCACGCC	60.051	61.111	0.00	0.00	0.00	5.68
1038	1251	0.468214	CCTATCTCCCACTCCTCGCA	60.468	60.000	0.00	0.00	0.00	5.10
1387	1600	0.811915	CGACCTCTCGATGAACAGGT	59.188	55.000	0.00	0.00	43.06	4.00
1523	1739	3.878519	GACGGTCCTCGCTCTCGG	61.879	72.222	0.00	0.00	43.89	4.63
1526	1742	4.500116	GGTCCTCGCTCTCGGCAC	62.500	72.222	0.00	0.00	41.91	5.01
1910	2132	1.000955	CTACAACAAGCTGACCGGAGT	59.999	52.381	9.46	0.00	0.00	3.85
2260	2485	1.572085	CCTGCAGCTCCAAGACAACG	61.572	60.000	8.66	0.00	0.00	4.10
2910	3273	1.282157	GACAAGGTATCACCAGGCCTT	59.718	52.381	0.00	0.00	41.95	4.35
3767	4168	2.816689	CTCATATTGTTCGCCGTGGTA	58.183	47.619	0.00	0.00	0.00	3.25
4098	4505	4.700365	GCAGGCGCACCGGAAAAC	62.700	66.667	9.46	0.00	42.76	2.43
4183	4590	1.860078	CAGTCGCCGGAAACAACTC	59.140	57.895	5.05	0.00	0.00	3.01
4216	4623	1.144057	CGGCAAGGGTAGCTTCGAT	59.856	57.895	0.00	0.00	0.00	3.59
4248	4674	9.577110	CGTCTGACAAAATATAGTTGTAAGGTA	57.423	33.333	8.73	0.00	39.29	3.08
4273	4699	7.380431	CAGTAGTACTGTAACTAGCAAGACT	57.620	40.000	20.29	0.00	41.19	3.24
4277	4703	4.258702	ACTGTAACTAGCAAGACTGTGG	57.741	45.455	0.00	0.00	0.00	4.17
4285	4711	3.498774	AGCAAGACTGTGGAGTTTCAT	57.501	42.857	0.00	0.00	30.16	2.57
4297	4723	3.118847	TGGAGTTTCATAGCAGAGCAGAG	60.119	47.826	0.00	0.00	0.00	3.35
4298	4724	2.865551	GAGTTTCATAGCAGAGCAGAGC	59.134	50.000	0.00	0.00	0.00	4.09
4299	4725	2.235650	AGTTTCATAGCAGAGCAGAGCA	59.764	45.455	0.00	0.00	0.00	4.26
4300	4726	2.598686	TTCATAGCAGAGCAGAGCAG	57.401	50.000	0.00	0.00	0.00	4.24
4301	4727	1.772836	TCATAGCAGAGCAGAGCAGA	58.227	50.000	0.00	0.00	0.00	4.26
4302	4728	2.317973	TCATAGCAGAGCAGAGCAGAT	58.682	47.619	0.00	0.00	0.00	2.90
4303	4729	2.036089	TCATAGCAGAGCAGAGCAGATG	59.964	50.000	0.00	0.00	0.00	2.90
4315	4741	2.508716	AGAGCAGATGACAATGGTGGAT	59.491	45.455	0.92	0.00	0.00	3.41
4317	4743	3.698040	GAGCAGATGACAATGGTGGATTT	59.302	43.478	0.92	0.00	0.00	2.17
4326	4752	5.596361	TGACAATGGTGGATTTTTGTACACT	59.404	36.000	0.00	0.00	32.73	3.55
4370	4805	5.479375	AGCAGTTGGATCAAATTCAGACAAT	59.521	36.000	0.00	0.00	0.00	2.71
4371	4806	5.575606	GCAGTTGGATCAAATTCAGACAATG	59.424	40.000	0.00	0.00	0.00	2.82
4402	4837	3.865011	TCTGAAGACAGAGATGAGCAC	57.135	47.619	0.00	0.00	46.55	4.40
4553	4989	5.163499	GGATTACAAAACACCACCAGACAAA	60.163	40.000	0.00	0.00	0.00	2.83
4754	5190	0.252197	ACCACCAGGCGATTAGGAAC	59.748	55.000	0.00	0.00	39.06	3.62
4775	5211	4.916870	ACGTTCGAAGGGAAAAGAAAAAG	58.083	39.130	20.83	0.00	36.14	2.27
4824	5262	2.025887	ACTCTGGGTTCAATCCATCCAC	60.026	50.000	0.00	0.00	33.29	4.02
4971	5409	4.805956	CCCCGAGGAGATCTGAAAGAGTC	61.806	56.522	0.00	0.00	41.28	3.36
5001	5439	2.549754	GCAGCTGCTGAACTTCTTGTAA	59.450	45.455	32.30	0.00	38.21	2.41
5004	5442	4.214971	CAGCTGCTGAACTTCTTGTAATGT	59.785	41.667	24.88	0.00	32.44	2.71
5228	5666	4.398988	TCAGCATGTTAATCAATGGTCACC	59.601	41.667	0.00	0.00	37.40	4.02

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
26	27	5.064558	GCACATGATGGAAGAGATCATTCT	58.935	41.667	0.00	0.00	38.28	2.40
77	78	3.005684	TCACCAAAATGTGACATGCTTCC	59.994	43.478	0.00	0.00	40.22	3.46
78	79	4.241590	TCACCAAAATGTGACATGCTTC	57.758	40.909	0.00	0.00	40.22	3.86
111	113	2.830772	ATGTATGTGCACGTCAATGC	57.169	45.000	16.44	5.41	46.32	3.56
181	183	5.233225	ACTCGACTATTCATATGTGCATGG	58.767	41.667	1.90	0.00	0.00	3.66
207	209	8.851960	TGTGAATGTACGAATAGTGACTATTC	57.148	34.615	27.36	27.36	45.03	1.75
212	214	7.169140	TGCATATGTGAATGTACGAATAGTGAC	59.831	37.037	4.29	0.00	0.00	3.67
217	219	7.961325	ATGTGCATATGTGAATGTACGAATA	57.039	32.000	4.29	0.00	43.11	1.75
222	224	7.245419	TGTGTATGTGCATATGTGAATGTAC	57.755	36.000	6.16	0.00	41.30	2.90
248	250	8.161699	CATGTGAATCTTGACATGGATGATTA	57.838	34.615	12.83	0.00	45.20	1.75
332	352	1.463444	GCTACCGCATCAAGTTTCGTT	59.537	47.619	0.00	0.00	35.78	3.85
334	354	1.061131	CTGCTACCGCATCAAGTTTCG	59.939	52.381	0.00	0.00	46.74	3.46
335	355	2.076863	ACTGCTACCGCATCAAGTTTC	58.923	47.619	0.00	0.00	46.74	2.78
454	479	5.369409	TTCTTCGACTCCTCCATACTCTA	57.631	43.478	0.00	0.00	0.00	2.43
457	482	3.292460	CCTTCTTCGACTCCTCCATACT	58.708	50.000	0.00	0.00	0.00	2.12
473	498	1.068121	CACCTTTGACCTCCCCTTCT	58.932	55.000	0.00	0.00	0.00	2.85
513	538	1.445942	CCCGCCGATATCCAACTGT	59.554	57.895	0.00	0.00	0.00	3.55
514	539	1.961277	GCCCGCCGATATCCAACTG	60.961	63.158	0.00	0.00	0.00	3.16
556	581	4.473520	CGTCTTCCCGCCCTGCAT	62.474	66.667	0.00	0.00	0.00	3.96
581	606	2.821679	CTTTCCCCACCCTTCTCGGC	62.822	65.000	0.00	0.00	0.00	5.54
582	607	1.198759	TCTTTCCCCACCCTTCTCGG	61.199	60.000	0.00	0.00	0.00	4.63
583	608	0.250513	CTCTTTCCCCACCCTTCTCG	59.749	60.000	0.00	0.00	0.00	4.04
584	609	1.557371	CTCTCTTTCCCCACCCTTCTC	59.443	57.143	0.00	0.00	0.00	2.87
585	610	1.662686	CTCTCTTTCCCCACCCTTCT	58.337	55.000	0.00	0.00	0.00	2.85
586	611	0.621082	CCTCTCTTTCCCCACCCTTC	59.379	60.000	0.00	0.00	0.00	3.46
587	612	1.501654	GCCTCTCTTTCCCCACCCTT	61.502	60.000	0.00	0.00	0.00	3.95
636	837	2.117910	GACGCGTTCTAGATGGTTAGC	58.882	52.381	15.53	0.00	0.00	3.09
673	876	1.254026	GGGTTTAGGCAGGGTCAAAC	58.746	55.000	0.00	0.00	0.00	2.93
802	1005	6.584942	CCTTTTTCATTCTGATGTGTGTCATG	59.415	38.462	0.00	0.00	36.83	3.07
803	1006	6.491062	TCCTTTTTCATTCTGATGTGTGTCAT	59.509	34.615	0.00	0.00	39.77	3.06
804	1007	5.827267	TCCTTTTTCATTCTGATGTGTGTCA	59.173	36.000	0.00	0.00	34.77	3.58
805	1008	6.317789	TCCTTTTTCATTCTGATGTGTGTC	57.682	37.500	0.00	0.00	34.77	3.67
806	1009	6.713762	TTCCTTTTTCATTCTGATGTGTGT	57.286	33.333	0.00	0.00	34.77	3.72
807	1010	9.695526	TTAATTCCTTTTTCATTCTGATGTGTG	57.304	29.630	0.00	0.00	34.77	3.82
1038	1251	2.601666	TGCAGGACGAGGCAGAGT	60.602	61.111	0.00	0.00	34.58	3.24
1337	1550	1.972198	CCCGTGCAGTTGTAGAGGA	59.028	57.895	0.00	0.00	0.00	3.71
1385	1598	4.144703	GGAGGTCGCCGGAGAACC	62.145	72.222	20.52	17.58	0.00	3.62
1523	1739	3.357079	CGGTGAGCTGGTTGGTGC	61.357	66.667	0.00	0.00	0.00	5.01
1526	1742	4.641645	TGCCGGTGAGCTGGTTGG	62.642	66.667	1.90	0.00	43.16	3.77
1572	1788	3.997064	CTTGAGCGTCTGGAGGCCG	62.997	68.421	10.97	0.00	42.66	6.13
1910	2132	1.600107	CCGAACCTTTCCGGGATCA	59.400	57.895	0.00	0.00	41.89	2.92
2007	2229	4.003788	AGGAACACCAGCGACGGG	62.004	66.667	0.00	0.00	0.00	5.28
2260	2485	2.815647	CACCTCGCCGGAAAGCTC	60.816	66.667	5.05	0.00	36.31	4.09
2987	3353	4.803908	GCCCCTTCCGCCTCTTGG	62.804	72.222	0.00	0.00	0.00	3.61
3267	3645	0.238289	GCTTGACGATGTTGGTGTGG	59.762	55.000	0.00	0.00	0.00	4.17
3324	3708	1.108776	TGCCCATGTACTCGTAGACC	58.891	55.000	0.00	0.00	0.00	3.85
3601	3994	4.933064	GGCCTCGACGAGCATCCG	62.933	72.222	19.55	6.52	0.00	4.18
3689	4082	0.179000	ATCAAGGTGAGGTGATCGGC	59.821	55.000	0.00	0.00	27.99	5.54
3721	4116	2.226437	TGAGCTGCAAGAAATTTCGTCC	59.774	45.455	12.42	0.04	34.07	4.79
3767	4168	0.460109	TACGCGCACTCTGCAATCAT	60.460	50.000	5.73	0.00	45.36	2.45
3985	4386	0.318699	CGAGCTTGAACACGACCTCA	60.319	55.000	0.00	0.00	0.00	3.86
4100	4507	2.202453	GGCCGTCTTCTCGTCGAC	60.202	66.667	5.18	5.18	0.00	4.20
4179	4586	4.421479	CAGCGGCGTCGGAGAGTT	62.421	66.667	13.05	0.00	36.95	3.01
4257	4683	4.021894	ACTCCACAGTCTTGCTAGTTACAG	60.022	45.833	0.00	0.00	0.00	2.74
4258	4684	3.895656	ACTCCACAGTCTTGCTAGTTACA	59.104	43.478	0.00	0.00	0.00	2.41
4259	4685	4.522722	ACTCCACAGTCTTGCTAGTTAC	57.477	45.455	0.00	0.00	0.00	2.50
4263	4689	3.995199	TGAAACTCCACAGTCTTGCTAG	58.005	45.455	0.00	0.00	29.93	3.42
4267	4693	4.318332	TGCTATGAAACTCCACAGTCTTG	58.682	43.478	0.00	0.00	29.93	3.02
4273	4699	2.302733	TGCTCTGCTATGAAACTCCACA	59.697	45.455	0.00	0.00	0.00	4.17
4277	4703	2.865551	GCTCTGCTCTGCTATGAAACTC	59.134	50.000	0.00	0.00	0.00	3.01
4285	4711	1.408340	GTCATCTGCTCTGCTCTGCTA	59.592	52.381	0.00	0.00	0.00	3.49
4297	4723	4.460948	AAAATCCACCATTGTCATCTGC	57.539	40.909	0.00	0.00	0.00	4.26
4298	4724	5.786311	ACAAAAATCCACCATTGTCATCTG	58.214	37.500	0.00	0.00	30.58	2.90
4299	4725	6.493115	TGTACAAAAATCCACCATTGTCATCT	59.507	34.615	0.00	0.00	37.25	2.90
4300	4726	6.586082	GTGTACAAAAATCCACCATTGTCATC	59.414	38.462	0.00	0.00	37.25	2.92
4301	4727	6.267471	AGTGTACAAAAATCCACCATTGTCAT	59.733	34.615	0.00	0.00	37.25	3.06
4302	4728	5.596361	AGTGTACAAAAATCCACCATTGTCA	59.404	36.000	0.00	0.00	37.25	3.58
4303	4729	5.920273	CAGTGTACAAAAATCCACCATTGTC	59.080	40.000	0.00	0.00	37.25	3.18
4315	4741	3.773860	CTGGCACACAGTGTACAAAAA	57.226	42.857	5.69	0.00	42.42	1.94
4326	4752	0.607217	CATCTCAAGGCTGGCACACA	60.607	55.000	3.38	0.00	0.00	3.72
4553	4989	1.354368	TCTGCCGATTCTTTTTCCCCT	59.646	47.619	0.00	0.00	0.00	4.79
4754	5190	5.164606	TCTTTTTCTTTTCCCTTCGAACG	57.835	39.130	0.00	0.00	0.00	3.95
4795	5233	3.788227	TTGAACCCAGAGTGTAGCAAT	57.212	42.857	0.00	0.00	0.00	3.56
4796	5234	3.559171	GGATTGAACCCAGAGTGTAGCAA	60.559	47.826	0.00	0.00	0.00	3.91
5001	5439	1.139058	GACGGTGGGCTCTATGAACAT	59.861	52.381	0.00	0.00	0.00	2.71
5004	5442	0.616395	TGGACGGTGGGCTCTATGAA	60.616	55.000	0.00	0.00	0.00	2.57
5058	5496	2.672996	CGGGACAAGGTGCCAAGG	60.673	66.667	7.68	0.00	44.45	3.61
5059	5497	2.672996	CCGGGACAAGGTGCCAAG	60.673	66.667	7.68	0.00	44.45	3.61
5187	5625	3.691118	GCTGATCTCATGTTTAGGTTGCA	59.309	43.478	0.00	0.00	0.00	4.08

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.