AutoCloner

Multiple sequence alignment - TraesCS1A01G439200

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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	TraesCS1A01G439200	chr1A	100.000	3569	0	0	1	3569	588693848	588690280	0.000000e+00	6591.0
1	TraesCS1A01G439200	chr1A	96.326	626	23	0	2944	3569	394576979	394577604	0.000000e+00	1029.0
2	TraesCS1A01G439200	chr1A	82.938	844	79	31	998	1818	29155971	29155170	0.000000e+00	701.0
3	TraesCS1A01G439200	chr1A	81.766	702	79	26	957	1646	29122951	29123615	3.130000e-150	542.0
4	TraesCS1A01G439200	chr1A	80.000	310	46	7	2275	2569	14554794	14555102	7.760000e-52	215.0
5	TraesCS1A01G439200	chr1A	83.133	83	11	2	743	822	29156302	29156220	4.940000e-09	73.1
6	TraesCS1A01G439200	chr1D	92.885	2024	86	15	960	2943	490503392	490501387	0.000000e+00	2887.0
7	TraesCS1A01G439200	chr1D	80.673	1278	171	40	998	2235	28173955	28172714	0.000000e+00	922.0
8	TraesCS1A01G439200	chr1D	85.520	884	79	22	1	848	490543947	490543077	0.000000e+00	878.0
9	TraesCS1A01G439200	chr1D	86.667	90	11	1	871	960	490503540	490503452	8.150000e-17	99.0
10	TraesCS1A01G439200	chr1D	93.333	60	0	3	2818	2877	490501395	490501340	6.350000e-13	86.1
11	TraesCS1A01G439200	chr1B	91.858	1965	131	16	960	2906	683319539	683317586	0.000000e+00	2715.0
12	TraesCS1A01G439200	chr1B	90.085	1876	119	21	997	2839	683265919	683264078	0.000000e+00	2372.0
13	TraesCS1A01G439200	chr1B	97.444	626	14	1	2944	3569	3261237	3261860	0.000000e+00	1066.0
14	TraesCS1A01G439200	chr1B	97.129	627	17	1	2944	3569	458329582	458328956	0.000000e+00	1057.0
15	TraesCS1A01G439200	chr1B	80.091	1316	172	35	957	2235	45442316	45443578	0.000000e+00	896.0
16	TraesCS1A01G439200	chr1B	79.949	1172	162	39	1099	2235	45487230	45486097	0.000000e+00	795.0
17	TraesCS1A01G439200	chr1B	90.638	470	34	5	1	467	683340222	683339760	1.820000e-172	616.0
18	TraesCS1A01G439200	chr1B	86.250	480	54	8	1	478	683269339	683268870	8.840000e-141	510.0
19	TraesCS1A01G439200	chr1B	79.430	632	84	27	1099	1722	45513430	45512837	4.290000e-109	405.0
20	TraesCS1A01G439200	chr1B	77.273	682	88	32	1299	1951	45571787	45571144	4.410000e-89	339.0
21	TraesCS1A01G439200	chr1B	89.855	207	15	4	482	682	683266505	683266299	9.830000e-66	261.0
22	TraesCS1A01G439200	chr1B	78.543	247	32	6	1726	1951	45512466	45512220	3.710000e-30	143.0
23	TraesCS1A01G439200	chr1B	78.543	247	32	6	1726	1951	45721744	45721498	3.710000e-30	143.0
24	TraesCS1A01G439200	chr1B	84.559	136	14	3	957	1092	45559650	45559778	1.040000e-25	128.0
25	TraesCS1A01G439200	chr1B	83.784	148	7	9	2741	2877	683264078	683263937	1.350000e-24	124.0
26	TraesCS1A01G439200	chr1B	90.000	60	2	3	2818	2877	683317541	683317486	1.370000e-09	75.0
27	TraesCS1A01G439200	chr1B	97.619	42	1	0	2902	2943	683317574	683317533	4.940000e-09	73.1
28	TraesCS1A01G439200	chr5B	97.923	626	12	1	2944	3569	332423096	332423720	0.000000e+00	1083.0
29	TraesCS1A01G439200	chr5B	97.444	626	16	0	2944	3569	537597629	537597004	0.000000e+00	1068.0
30	TraesCS1A01G439200	chr4A	97.444	626	16	0	2944	3569	668946659	668947284	0.000000e+00	1068.0
31	TraesCS1A01G439200	chr4A	97.289	627	16	1	2943	3569	714738750	714739375	0.000000e+00	1062.0
32	TraesCS1A01G439200	chrUn	97.289	627	16	1	2943	3569	353400247	353400872	0.000000e+00	1062.0
33	TraesCS1A01G439200	chrUn	78.104	749	94	33	1232	1951	436831933	436832640	9.220000e-111	411.0
34	TraesCS1A01G439200	chrUn	89.908	109	8	2	998	1103	243509025	243508917	1.730000e-28	137.0
35	TraesCS1A01G439200	chr7A	97.129	627	17	1	2944	3569	507815882	507816508	0.000000e+00	1057.0

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	TraesCS1A01G439200	chr1A	588690280	588693848	3568	True	6591.000000	6591	100.000000	1	3569	1	chr1A.!!$R1	3568
1	TraesCS1A01G439200	chr1A	394576979	394577604	625	False	1029.000000	1029	96.326000	2944	3569	1	chr1A.!!$F3	625
2	TraesCS1A01G439200	chr1A	29122951	29123615	664	False	542.000000	542	81.766000	957	1646	1	chr1A.!!$F2	689
3	TraesCS1A01G439200	chr1A	29155170	29156302	1132	True	387.050000	701	83.035500	743	1818	2	chr1A.!!$R2	1075
4	TraesCS1A01G439200	chr1D	490501340	490503540	2200	True	1024.033333	2887	90.961667	871	2943	3	chr1D.!!$R3	2072
5	TraesCS1A01G439200	chr1D	28172714	28173955	1241	True	922.000000	922	80.673000	998	2235	1	chr1D.!!$R1	1237
6	TraesCS1A01G439200	chr1D	490543077	490543947	870	True	878.000000	878	85.520000	1	848	1	chr1D.!!$R2	847
7	TraesCS1A01G439200	chr1B	3261237	3261860	623	False	1066.000000	1066	97.444000	2944	3569	1	chr1B.!!$F1	625
8	TraesCS1A01G439200	chr1B	458328956	458329582	626	True	1057.000000	1057	97.129000	2944	3569	1	chr1B.!!$R4	625
9	TraesCS1A01G439200	chr1B	683317486	683319539	2053	True	954.366667	2715	93.159000	960	2943	3	chr1B.!!$R8	1983
10	TraesCS1A01G439200	chr1B	45442316	45443578	1262	False	896.000000	896	80.091000	957	2235	1	chr1B.!!$F2	1278
11	TraesCS1A01G439200	chr1B	683263937	683269339	5402	True	816.750000	2372	87.493500	1	2877	4	chr1B.!!$R7	2876
12	TraesCS1A01G439200	chr1B	45486097	45487230	1133	True	795.000000	795	79.949000	1099	2235	1	chr1B.!!$R1	1136
13	TraesCS1A01G439200	chr1B	45571144	45571787	643	True	339.000000	339	77.273000	1299	1951	1	chr1B.!!$R2	652
14	TraesCS1A01G439200	chr1B	45512220	45513430	1210	True	274.000000	405	78.986500	1099	1951	2	chr1B.!!$R6	852
15	TraesCS1A01G439200	chr5B	332423096	332423720	624	False	1083.000000	1083	97.923000	2944	3569	1	chr5B.!!$F1	625
16	TraesCS1A01G439200	chr5B	537597004	537597629	625	True	1068.000000	1068	97.444000	2944	3569	1	chr5B.!!$R1	625
17	TraesCS1A01G439200	chr4A	668946659	668947284	625	False	1068.000000	1068	97.444000	2944	3569	1	chr4A.!!$F1	625
18	TraesCS1A01G439200	chr4A	714738750	714739375	625	False	1062.000000	1062	97.289000	2943	3569	1	chr4A.!!$F2	626
19	TraesCS1A01G439200	chrUn	353400247	353400872	625	False	1062.000000	1062	97.289000	2943	3569	1	chrUn.!!$F1	626
20	TraesCS1A01G439200	chrUn	436831933	436832640	707	False	411.000000	411	78.104000	1232	1951	1	chrUn.!!$F2	719
21	TraesCS1A01G439200	chr7A	507815882	507816508	626	False	1057.000000	1057	97.129000	2944	3569	1	chr7A.!!$F1	625

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
150	151	1.019805	GTAGGACGAAGCAAGGCCAC	61.020	60.0	5.01	0.0	39.93	5.01	F
1407	4017	0.255318	AGTCCCTCTCCGTGTACGAT	59.745	55.0	5.91	0.0	43.02	3.73	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2066	5121	0.035458	AAACTTGTCCTGGAGGCTCG	59.965	55.0	8.69	0.0	34.44	5.03	R
2934	6204	2.111972	TCCTTCCTTGTCTACAGGGTCT	59.888	50.0	10.67	0.0	42.97	3.85	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
53	54	5.048573	ACACGAGGAGTAGAAGAAGAAGAAC	60.049	44.000	0.00	0.00	0.00	3.01
150	151	1.019805	GTAGGACGAAGCAAGGCCAC	61.020	60.000	5.01	0.00	39.93	5.01
152	153	2.357034	GACGAAGCAAGGCCACGA	60.357	61.111	5.01	0.00	33.57	4.35
168	169	2.710902	CGAGCCACGGACTCCATGA	61.711	63.158	0.00	0.00	38.46	3.07
205	206	4.157120	CCACGTAGAAGGCCCCCG	62.157	72.222	0.00	0.00	0.00	5.73
206	207	4.832608	CACGTAGAAGGCCCCCGC	62.833	72.222	0.00	0.00	0.00	6.13
271	273	3.570212	CCCTAGGGATTGGGCCGG	61.570	72.222	24.99	0.00	36.61	6.13
286	288	2.032071	CGGGTTCGGGCTCAAGTT	59.968	61.111	0.00	0.00	0.00	2.66
289	291	1.896660	GGTTCGGGCTCAAGTTGCA	60.897	57.895	0.00	0.00	0.00	4.08
296	298	2.180017	CTCAAGTTGCATGGGCGC	59.820	61.111	0.00	0.00	45.35	6.53
469	472	6.585416	TGATCCATATCCACAATATCATCGG	58.415	40.000	0.00	0.00	0.00	4.18
479	482	5.351458	CACAATATCATCGGAGAAGACACA	58.649	41.667	0.00	0.00	43.58	3.72
626	2995	7.305474	ACCAAACAAAATCATCGACTATTGTC	58.695	34.615	0.00	0.00	39.70	3.18
703	3099	6.425417	TCGATTAGCATACAAACTTGTTGACA	59.575	34.615	0.00	0.00	42.35	3.58
705	3101	8.387354	CGATTAGCATACAAACTTGTTGACATA	58.613	33.333	0.00	0.00	42.35	2.29
799	3200	1.215647	CCACCGAAGACGAGGGAAG	59.784	63.158	0.00	0.00	42.66	3.46
800	3201	1.533469	CCACCGAAGACGAGGGAAGT	61.533	60.000	0.00	0.00	42.66	3.01
862	3338	5.581085	ACACAAGTGATAGCTTATTTCCGTC	59.419	40.000	7.28	0.00	0.00	4.79
865	3341	2.475487	GTGATAGCTTATTTCCGTCGGC	59.525	50.000	6.34	0.00	0.00	5.54
885	3361	1.465689	CGCAGCCCGATTAAACAAGTG	60.466	52.381	0.00	0.00	40.02	3.16
1024	3625	2.203308	CGTCGGAGGCTAGCCCTA	60.203	66.667	30.42	10.46	46.60	3.53
1218	3822	2.990479	GGCCTCTTCGTCACCCAT	59.010	61.111	0.00	0.00	0.00	4.00
1252	3856	1.619363	CTCCCCATCTTCCACCCCA	60.619	63.158	0.00	0.00	0.00	4.96
1407	4017	0.255318	AGTCCCTCTCCGTGTACGAT	59.745	55.000	5.91	0.00	43.02	3.73
1478	4118	3.465403	CCTCCCCGAGCCTGAGTG	61.465	72.222	0.00	0.00	0.00	3.51
1557	4197	3.865929	CTGCTTCCGCGTGGTCACT	62.866	63.158	16.01	0.00	39.65	3.41
1728	4753	0.749454	CCGGGCTCATCTTTTGGAGG	60.749	60.000	0.00	0.00	0.00	4.30
1798	4829	1.838073	AATCGTCCCGCTCCCAGTTT	61.838	55.000	0.00	0.00	0.00	2.66
1864	4916	4.377943	CGTGTTGCCTTTTGAATATCGTCA	60.378	41.667	0.00	0.00	0.00	4.35
1906	4958	0.607489	GCTGCTCAAGAAGAAGGGCA	60.607	55.000	0.00	0.00	30.16	5.36
1932	4987	3.056328	GGGCTTGCGTGGGAGTTC	61.056	66.667	0.00	0.00	0.00	3.01
2016	5071	0.729116	CTGCCGGACTAGCAATTGTG	59.271	55.000	5.05	0.77	40.35	3.33
2074	5129	2.683933	TCAAGGACCCGAGCCTCC	60.684	66.667	0.00	0.00	33.76	4.30
2134	5191	0.687098	CCAAATGCCATGGCCACCTA	60.687	55.000	33.44	15.55	41.09	3.08
2200	5266	0.868406	GTATGCTTGCCGAGGTATGC	59.132	55.000	10.33	10.33	0.00	3.14
2295	5392	1.729586	ACTTCAGTGCTTCCCTACCA	58.270	50.000	0.00	0.00	0.00	3.25
2312	5409	3.091633	ACCAAACTGAGCTGCCAATAT	57.908	42.857	0.00	0.00	0.00	1.28
2316	5413	3.641434	AACTGAGCTGCCAATATCACT	57.359	42.857	0.00	0.00	0.00	3.41
2326	5423	3.314913	TGCCAATATCACTATTTGGCACG	59.685	43.478	21.12	0.00	41.43	5.34
2453	5550	4.005650	TCCTCTAGTAGAAAGCGAACGAA	58.994	43.478	0.64	0.00	0.00	3.85
2464	5561	3.729526	AGCGAACGAACAATGATGAAG	57.270	42.857	0.00	0.00	0.00	3.02
2659	5785	2.849880	ACTTGTCATTGCACACACAC	57.150	45.000	0.00	0.00	0.00	3.82
2660	5786	2.090760	ACTTGTCATTGCACACACACA	58.909	42.857	0.00	0.00	0.00	3.72
2865	6135	9.362151	TCTCTTGTTTCCATTTGGTATTTAAGT	57.638	29.630	0.00	0.00	36.34	2.24
2933	6203	7.549615	TTGCACAATAGATCAAGAGATGAAG	57.450	36.000	0.00	0.00	42.54	3.02
2934	6204	6.881570	TGCACAATAGATCAAGAGATGAAGA	58.118	36.000	0.00	0.00	42.54	2.87
2935	6205	6.985059	TGCACAATAGATCAAGAGATGAAGAG	59.015	38.462	0.00	0.00	42.54	2.85
2936	6206	7.147776	TGCACAATAGATCAAGAGATGAAGAGA	60.148	37.037	0.00	0.00	42.54	3.10
2937	6207	7.169645	GCACAATAGATCAAGAGATGAAGAGAC	59.830	40.741	0.00	0.00	42.54	3.36
2938	6208	7.652909	CACAATAGATCAAGAGATGAAGAGACC	59.347	40.741	0.00	0.00	42.54	3.85
2939	6209	6.916360	ATAGATCAAGAGATGAAGAGACCC	57.084	41.667	0.00	0.00	42.54	4.46
2940	6210	4.882559	AGATCAAGAGATGAAGAGACCCT	58.117	43.478	0.00	0.00	42.54	4.34
2941	6211	4.650588	AGATCAAGAGATGAAGAGACCCTG	59.349	45.833	0.00	0.00	42.54	4.45
2983	6253	2.978156	ATTCATGTGTGTCCAAGGGT	57.022	45.000	0.00	0.00	0.00	4.34
3013	6283	0.824109	TCACACCTCCTATTCGCAGG	59.176	55.000	0.00	0.00	37.00	4.85
3014	6284	0.824109	CACACCTCCTATTCGCAGGA	59.176	55.000	0.00	1.09	42.62	3.86
3114	6384	4.006989	CACAGGACAATTCATTAACCCGA	58.993	43.478	0.00	0.00	0.00	5.14
3120	6390	5.038247	ACAATTCATTAACCCGACGAAAC	57.962	39.130	0.00	0.00	0.00	2.78
3299	6571	7.318141	AGCAACTTACTAAGCGTATCTTACAA	58.682	34.615	0.00	0.00	36.25	2.41

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
12	13	1.229529	GTGGTTCTCCTCCCCCTCA	60.230	63.158	0.00	0.00	34.23	3.86
53	54	2.111878	CTGGATGGCGCCCTAAGG	59.888	66.667	26.77	7.75	0.00	2.69
75	76	3.624777	CAGGCCATCTCTGGTACATTTT	58.375	45.455	5.01	0.00	45.10	1.82
108	109	2.184830	CACATCGGCTCCCATGCAG	61.185	63.158	0.00	0.00	34.04	4.41
132	133	1.295423	GTGGCCTTGCTTCGTCCTA	59.705	57.895	3.32	0.00	0.00	2.94
150	151	2.202797	CATGGAGTCCGTGGCTCG	60.203	66.667	22.00	1.28	36.92	5.03
152	153	2.660064	GGTCATGGAGTCCGTGGCT	61.660	63.158	30.21	0.00	43.91	4.75
159	160	1.340114	GGTTCCTTGGGTCATGGAGTC	60.340	57.143	0.00	0.00	38.58	3.36
168	169	3.190349	CCCCATGGTTCCTTGGGT	58.810	61.111	29.06	0.00	44.96	4.51
205	206	3.040763	GCATCCTCGAGCGATGGC	61.041	66.667	29.26	22.04	38.05	4.40
206	207	1.664017	CAGCATCCTCGAGCGATGG	60.664	63.158	29.26	18.12	38.05	3.51
208	209	2.733301	CCAGCATCCTCGAGCGAT	59.267	61.111	6.99	8.69	35.48	4.58
209	210	4.212913	GCCAGCATCCTCGAGCGA	62.213	66.667	6.99	6.49	35.48	4.93
269	271	2.032071	AACTTGAGCCCGAACCCG	59.968	61.111	0.00	0.00	0.00	5.28
270	272	2.626780	GCAACTTGAGCCCGAACCC	61.627	63.158	0.00	0.00	0.00	4.11
271	273	1.244019	ATGCAACTTGAGCCCGAACC	61.244	55.000	0.00	0.00	0.00	3.62
276	278	3.010413	GCCCATGCAACTTGAGCCC	62.010	63.158	0.00	0.00	37.47	5.19
277	279	2.575461	GCCCATGCAACTTGAGCC	59.425	61.111	0.00	0.00	37.47	4.70
278	280	2.180017	CGCCCATGCAACTTGAGC	59.820	61.111	0.00	0.00	37.32	4.26
296	298	1.980772	ACTCCCTCCCACGTTACCG	60.981	63.158	0.00	0.00	40.83	4.02
299	301	0.613853	CCTCACTCCCTCCCACGTTA	60.614	60.000	0.00	0.00	0.00	3.18
304	306	2.788230	ATTGCCCTCACTCCCTCCCA	62.788	60.000	0.00	0.00	0.00	4.37
380	383	7.982371	ACGAAATAGTTGTTACCTATTCGAG	57.018	36.000	10.99	0.51	34.77	4.04
479	482	8.794553	TGTACTTCTTTATCTCGAGACTCTTTT	58.205	33.333	19.30	2.87	0.00	2.27
595	2961	3.361644	CGATGATTTTGTTTGGTTCTGCG	59.638	43.478	0.00	0.00	0.00	5.18
652	3023	0.603569	ACTCGATCGCAAGGACAACT	59.396	50.000	11.09	0.00	38.47	3.16
739	3137	7.148154	CGTGAAACCCATGGATCAAAAGTTATA	60.148	37.037	15.22	0.00	0.00	0.98
740	3138	6.350110	CGTGAAACCCATGGATCAAAAGTTAT	60.350	38.462	15.22	0.00	0.00	1.89
741	3139	5.048364	CGTGAAACCCATGGATCAAAAGTTA	60.048	40.000	15.22	0.00	0.00	2.24
754	3152	1.302192	CACCGGTCGTGAAACCCAT	60.302	57.895	2.59	0.00	46.20	4.00
799	3200	2.535934	TGTCACTTGCGTTTGTTGAC	57.464	45.000	0.00	0.00	0.00	3.18
800	3201	3.560902	TTTGTCACTTGCGTTTGTTGA	57.439	38.095	0.00	0.00	0.00	3.18
836	3279	6.128282	ACGGAAATAAGCTATCACTTGTGTTG	60.128	38.462	0.46	0.00	0.00	3.33
865	3341	0.802494	ACTTGTTTAATCGGGCTGCG	59.198	50.000	0.00	0.00	0.00	5.18
983	3584	3.765257	ATCAGGGGAGGAGCGGGAG	62.765	68.421	0.00	0.00	0.00	4.30
1024	3625	1.755393	GAGTCAAGGGTGGTGACCGT	61.755	60.000	0.00	0.00	45.39	4.83
1269	3873	2.360475	GCTGCAAGGTCTGGGTCC	60.360	66.667	0.00	0.00	0.00	4.46
1389	3999	0.662085	GATCGTACACGGAGAGGGAC	59.338	60.000	1.39	0.00	40.29	4.46
1478	4118	0.864455	GAGCAAGCAGTCCGATATGC	59.136	55.000	0.00	1.29	42.87	3.14
1647	4290	3.832492	TCGATGCCGATGCCGTCA	61.832	61.111	0.00	0.00	40.30	4.35
1728	4753	1.751924	AGCGAGGAGTTCAGGTCATAC	59.248	52.381	0.00	0.00	0.00	2.39
1919	4974	0.319555	CTTCTCGAACTCCCACGCAA	60.320	55.000	0.00	0.00	0.00	4.85
1932	4987	3.411415	CCTATTTGGCTTTGCTTCTCG	57.589	47.619	0.00	0.00	0.00	4.04
2016	5071	6.622549	AGAATACTTGCTACTCACACAGTAC	58.377	40.000	0.00	0.00	36.43	2.73
2066	5121	0.035458	AAACTTGTCCTGGAGGCTCG	59.965	55.000	8.69	0.00	34.44	5.03
2074	5129	4.590400	GATGACATCGAAACTTGTCCTG	57.410	45.455	12.95	0.00	41.22	3.86
2099	5154	2.397044	TTGGAAAGGGAAAGCCATGT	57.603	45.000	0.00	0.00	35.15	3.21
2134	5191	0.400594	GAAGTAGCCACCAACCCAGT	59.599	55.000	0.00	0.00	0.00	4.00
2200	5266	3.798337	AGCAAAGAAACTGCAAATTCACG	59.202	39.130	12.23	3.26	42.48	4.35
2295	5392	3.960571	AGTGATATTGGCAGCTCAGTTT	58.039	40.909	0.00	0.00	0.00	2.66
2330	5427	5.242069	AGATTCAGTCTATCACGACAGTG	57.758	43.478	0.00	0.00	41.76	3.66
2453	5550	2.559668	CCACTTGCCACTTCATCATTGT	59.440	45.455	0.00	0.00	0.00	2.71
2464	5561	4.379339	TTGTTTCTTTACCACTTGCCAC	57.621	40.909	0.00	0.00	0.00	5.01
2659	5785	6.036470	TGACGTATCTTCTAGTTGAGCAATG	58.964	40.000	0.00	0.00	0.00	2.82
2660	5786	6.208988	TGACGTATCTTCTAGTTGAGCAAT	57.791	37.500	0.00	0.00	0.00	3.56
2750	5876	6.287525	TGAATCAGTTGTATCTGAACACACA	58.712	36.000	0.62	0.00	45.65	3.72
2904	6174	9.702494	CATCTCTTGATCTATTGTGCAATAGTA	57.298	33.333	23.33	14.66	46.37	1.82
2905	6175	8.427276	TCATCTCTTGATCTATTGTGCAATAGT	58.573	33.333	23.33	14.86	46.37	2.12
2907	6177	9.269453	CTTCATCTCTTGATCTATTGTGCAATA	57.731	33.333	4.78	4.78	33.34	1.90
2908	6178	7.991460	TCTTCATCTCTTGATCTATTGTGCAAT	59.009	33.333	2.83	2.83	33.34	3.56
2909	6179	7.333323	TCTTCATCTCTTGATCTATTGTGCAA	58.667	34.615	0.00	0.00	33.34	4.08
2910	6180	6.881570	TCTTCATCTCTTGATCTATTGTGCA	58.118	36.000	0.00	0.00	33.34	4.57
2911	6181	7.169645	GTCTCTTCATCTCTTGATCTATTGTGC	59.830	40.741	0.00	0.00	33.34	4.57
2912	6182	7.652909	GGTCTCTTCATCTCTTGATCTATTGTG	59.347	40.741	0.00	0.00	33.34	3.33
2913	6183	7.201992	GGGTCTCTTCATCTCTTGATCTATTGT	60.202	40.741	0.00	0.00	33.34	2.71
2914	6184	7.015487	AGGGTCTCTTCATCTCTTGATCTATTG	59.985	40.741	0.00	0.00	33.34	1.90
2915	6185	7.015487	CAGGGTCTCTTCATCTCTTGATCTATT	59.985	40.741	0.00	0.00	33.34	1.73
2916	6186	6.494491	CAGGGTCTCTTCATCTCTTGATCTAT	59.506	42.308	0.00	0.00	33.34	1.98
2917	6187	5.832595	CAGGGTCTCTTCATCTCTTGATCTA	59.167	44.000	0.00	0.00	33.34	1.98
2918	6188	4.650588	CAGGGTCTCTTCATCTCTTGATCT	59.349	45.833	0.00	0.00	33.34	2.75
2919	6189	4.405358	ACAGGGTCTCTTCATCTCTTGATC	59.595	45.833	0.00	0.00	33.34	2.92
2920	6190	4.360889	ACAGGGTCTCTTCATCTCTTGAT	58.639	43.478	0.00	0.00	33.34	2.57
2921	6191	3.784178	ACAGGGTCTCTTCATCTCTTGA	58.216	45.455	0.00	0.00	0.00	3.02
2922	6192	4.952957	TCTACAGGGTCTCTTCATCTCTTG	59.047	45.833	0.00	0.00	0.00	3.02
2923	6193	4.953579	GTCTACAGGGTCTCTTCATCTCTT	59.046	45.833	0.00	0.00	0.00	2.85
2924	6194	4.017958	TGTCTACAGGGTCTCTTCATCTCT	60.018	45.833	0.00	0.00	0.00	3.10
2925	6195	4.274147	TGTCTACAGGGTCTCTTCATCTC	58.726	47.826	0.00	0.00	0.00	2.75
2926	6196	4.323569	TGTCTACAGGGTCTCTTCATCT	57.676	45.455	0.00	0.00	0.00	2.90
2927	6197	4.142049	CCTTGTCTACAGGGTCTCTTCATC	60.142	50.000	3.19	0.00	38.21	2.92
2928	6198	3.772025	CCTTGTCTACAGGGTCTCTTCAT	59.228	47.826	3.19	0.00	38.21	2.57
2929	6199	3.165875	CCTTGTCTACAGGGTCTCTTCA	58.834	50.000	3.19	0.00	38.21	3.02
2930	6200	3.432378	TCCTTGTCTACAGGGTCTCTTC	58.568	50.000	10.67	0.00	42.97	2.87
2931	6201	3.544698	TCCTTGTCTACAGGGTCTCTT	57.455	47.619	10.67	0.00	42.97	2.85
2932	6202	3.436243	CTTCCTTGTCTACAGGGTCTCT	58.564	50.000	10.67	0.00	42.97	3.10
2933	6203	2.498078	CCTTCCTTGTCTACAGGGTCTC	59.502	54.545	10.67	0.00	42.97	3.36
2934	6204	2.111972	TCCTTCCTTGTCTACAGGGTCT	59.888	50.000	10.67	0.00	42.97	3.85
2935	6205	2.537143	TCCTTCCTTGTCTACAGGGTC	58.463	52.381	10.67	0.00	42.97	4.46
2936	6206	2.715763	TCCTTCCTTGTCTACAGGGT	57.284	50.000	10.67	0.00	42.97	4.34
2937	6207	4.226168	AGAAATCCTTCCTTGTCTACAGGG	59.774	45.833	4.94	4.94	43.72	4.45
2938	6208	5.423886	GAGAAATCCTTCCTTGTCTACAGG	58.576	45.833	0.00	0.00	31.28	4.00
2939	6209	5.188751	AGGAGAAATCCTTCCTTGTCTACAG	59.811	44.000	0.00	0.00	36.56	2.74
2940	6210	5.094387	AGGAGAAATCCTTCCTTGTCTACA	58.906	41.667	0.00	0.00	36.56	2.74
2941	6211	5.685520	AGGAGAAATCCTTCCTTGTCTAC	57.314	43.478	0.00	0.00	36.56	2.59
2983	6253	3.399234	AGGTGTGAGATACCTGGCA	57.601	52.632	0.00	0.00	46.48	4.92
3013	6283	5.671329	GCACGGAAGAACATTAATGTGTCTC	60.671	44.000	21.46	14.94	41.61	3.36
3014	6284	4.154195	GCACGGAAGAACATTAATGTGTCT	59.846	41.667	21.46	20.06	41.61	3.41
3114	6384	6.088173	GGCCAAATAAAATAGAACGTTTCGT	58.912	36.000	0.46	0.00	43.97	3.85
3120	6390	5.901552	ACATGGGCCAAATAAAATAGAACG	58.098	37.500	11.89	0.00	0.00	3.95
3299	6571	4.162690	GACGCCGCTTCTCCCCAT	62.163	66.667	0.00	0.00	0.00	4.00

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.