AutoCloner

Multiple sequence alignment - TraesCS1D01G375200

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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	TraesCS1D01G375200	chr1D	100.000	2809	0	0	1	2809	452339039	452336231	0.000000e+00	5188.0
1	TraesCS1D01G375200	chr1D	93.762	1058	62	4	1081	2138	452269994	452268941	0.000000e+00	1585.0
2	TraesCS1D01G375200	chr1D	93.182	1056	66	6	1081	2133	452262226	452261174	0.000000e+00	1546.0
3	TraesCS1D01G375200	chr1D	93.006	1058	69	5	1081	2138	452265100	452264048	0.000000e+00	1539.0
4	TraesCS1D01G375200	chr1D	100.000	550	0	0	2145	2694	452351458	452352007	0.000000e+00	1016.0
5	TraesCS1D01G375200	chr1D	90.196	153	8	2	931	1083	452262613	452262468	2.860000e-45	193.0
6	TraesCS1D01G375200	chr1D	87.838	148	6	3	931	1078	452265493	452265358	2.240000e-36	163.0
7	TraesCS1D01G375200	chr1D	98.039	51	1	0	1033	1083	452270299	452270249	3.850000e-14	89.8
8	TraesCS1D01G375200	chr1A	94.471	1049	52	3	1084	2128	547216640	547215594	0.000000e+00	1611.0
9	TraesCS1D01G375200	chr1A	94.471	1049	52	3	1084	2128	547238538	547237492	0.000000e+00	1611.0
10	TraesCS1D01G375200	chr1A	89.867	602	39	10	497	1083	547217500	547216906	0.000000e+00	754.0
11	TraesCS1D01G375200	chr1A	89.701	602	40	10	497	1083	547239396	547238802	0.000000e+00	749.0
12	TraesCS1D01G375200	chr1A	87.110	481	53	7	8	486	547218025	547217552	1.150000e-148	536.0
13	TraesCS1D01G375200	chr1A	87.110	481	53	7	8	486	547239921	547239448	1.150000e-148	536.0
14	TraesCS1D01G375200	chr1A	87.110	481	53	7	8	486	547252256	547251783	1.150000e-148	536.0
15	TraesCS1D01G375200	chrUn	94.185	1049	55	3	1084	2128	246249567	246248521	0.000000e+00	1594.0
16	TraesCS1D01G375200	chrUn	90.033	602	38	10	497	1083	362687901	362688495	0.000000e+00	760.0
17	TraesCS1D01G375200	chrUn	90.733	464	26	9	630	1083	246250285	246249829	1.110000e-168	603.0
18	TraesCS1D01G375200	chrUn	86.777	484	55	7	5	486	362687373	362687849	5.330000e-147	531.0
19	TraesCS1D01G375200	chrUn	91.204	216	17	2	5	218	1066228	1066443	2.740000e-75	292.0
20	TraesCS1D01G375200	chr1B	93.379	1027	58	5	1104	2128	622218303	622219321	0.000000e+00	1511.0
21	TraesCS1D01G375200	chr1B	92.256	1046	70	7	1086	2128	622358714	622359751	0.000000e+00	1472.0
22	TraesCS1D01G375200	chr1B	92.110	1052	69	6	1077	2128	622313063	622314100	0.000000e+00	1471.0
23	TraesCS1D01G375200	chr1B	83.874	924	105	16	26	921	622216867	622217774	0.000000e+00	841.0
24	TraesCS1D01G375200	chr1B	88.845	251	22	4	490	735	622221822	622222071	1.260000e-78	303.0
25	TraesCS1D01G375200	chr1B	88.446	251	23	2	490	735	622316572	622316821	5.880000e-77	298.0
26	TraesCS1D01G375200	chr1B	85.774	239	25	4	497	735	622362279	622362508	7.770000e-61	244.0
27	TraesCS1D01G375200	chr1B	95.588	68	3	0	1011	1078	622312735	622312802	2.960000e-20	110.0
28	TraesCS1D01G375200	chr1B	95.588	68	3	0	1011	1078	622358375	622358442	2.960000e-20	110.0
29	TraesCS1D01G375200	chr6A	80.787	661	80	29	2153	2806	261514949	261514329	9.110000e-130	473.0
30	TraesCS1D01G375200	chr6A	83.742	326	47	3	2483	2806	261507820	261508141	1.260000e-78	303.0
31	TraesCS1D01G375200	chr6A	84.615	299	41	3	2145	2439	261507512	261507809	2.740000e-75	292.0
32	TraesCS1D01G375200	chr5A	80.775	671	70	35	2145	2806	53107620	53108240	1.180000e-128	470.0
33	TraesCS1D01G375200	chr5A	82.857	210	30	3	2430	2639	101318143	101317940	1.720000e-42	183.0
34	TraesCS1D01G375200	chr5A	76.779	267	32	17	2366	2610	650671336	650671594	3.800000e-24	122.0
35	TraesCS1D01G375200	chr4A	86.890	328	37	3	2481	2806	606728983	606729306	2.060000e-96	363.0
36	TraesCS1D01G375200	chr2B	80.755	265	34	7	2366	2613	635704608	635704344	1.030000e-44	191.0
37	TraesCS1D01G375200	chr2D	80.377	265	35	7	2366	2613	534492390	534492126	4.780000e-43	185.0
38	TraesCS1D01G375200	chr2A	80.377	265	35	7	2366	2613	678018077	678017813	4.780000e-43	185.0
39	TraesCS1D01G375200	chr5D	78.195	266	30	15	2366	2610	524481327	524481585	8.110000e-31	145.0

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	TraesCS1D01G375200	chr1D	452336231	452339039	2808	True	5188.000000	5188	100.000000	1	2809	1	chr1D.!!$R1	2808
1	TraesCS1D01G375200	chr1D	452351458	452352007	549	False	1016.000000	1016	100.000000	2145	2694	1	chr1D.!!$F1	549
2	TraesCS1D01G375200	chr1D	452261174	452270299	9125	True	852.633333	1585	92.670500	931	2138	6	chr1D.!!$R2	1207
3	TraesCS1D01G375200	chr1A	547215594	547218025	2431	True	967.000000	1611	90.482667	8	2128	3	chr1A.!!$R2	2120
4	TraesCS1D01G375200	chr1A	547237492	547239921	2429	True	965.333333	1611	90.427333	8	2128	3	chr1A.!!$R3	2120
5	TraesCS1D01G375200	chrUn	246248521	246250285	1764	True	1098.500000	1594	92.459000	630	2128	2	chrUn.!!$R1	1498
6	TraesCS1D01G375200	chrUn	362687373	362688495	1122	False	645.500000	760	88.405000	5	1083	2	chrUn.!!$F2	1078
7	TraesCS1D01G375200	chr1B	622216867	622222071	5204	False	885.000000	1511	88.699333	26	2128	3	chr1B.!!$F1	2102
8	TraesCS1D01G375200	chr1B	622312735	622316821	4086	False	626.333333	1471	92.048000	490	2128	3	chr1B.!!$F2	1638
9	TraesCS1D01G375200	chr1B	622358375	622362508	4133	False	608.666667	1472	91.206000	497	2128	3	chr1B.!!$F3	1631
10	TraesCS1D01G375200	chr6A	261514329	261514949	620	True	473.000000	473	80.787000	2153	2806	1	chr6A.!!$R1	653
11	TraesCS1D01G375200	chr6A	261507512	261508141	629	False	297.500000	303	84.178500	2145	2806	2	chr6A.!!$F1	661
12	TraesCS1D01G375200	chr5A	53107620	53108240	620	False	470.000000	470	80.775000	2145	2806	1	chr5A.!!$F1	661

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
988	1158	0.386858	GAGTCACGACACTTGCGCTA	60.387	55.0	9.73	0.0	0.0	4.26	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2774	12904	0.395312	GGGAGAAAGACGTGGACCAA	59.605	55.0	0.0	0.0	0.0	3.67	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
108	110	2.818714	CCTCCTCTTGCAGCAGCG	60.819	66.667	0.00	0.00	46.23	5.18
176	179	6.214615	TCTGATTCCCCAATGACTACAAAGTA	59.785	38.462	0.00	0.00	35.56	2.24
202	205	6.560253	TGACTTATTCCTCTTCTTTGTTGC	57.440	37.500	0.00	0.00	0.00	4.17
212	215	4.724399	TCTTCTTTGTTGCCACCTTATCA	58.276	39.130	0.00	0.00	0.00	2.15
234	237	4.783621	CCTTGCCAGCCAGCGCTA	62.784	66.667	10.99	0.00	46.25	4.26
247	250	3.369381	GCGCTAGCTTCTTCATCCA	57.631	52.632	13.93	0.00	41.01	3.41
259	262	0.893270	TTCATCCACTTGCCGTTGGG	60.893	55.000	0.00	0.00	0.00	4.12
260	263	1.303236	CATCCACTTGCCGTTGGGA	60.303	57.895	0.00	0.00	34.06	4.37
264	267	0.609131	CCACTTGCCGTTGGGAGAAT	60.609	55.000	0.00	0.00	34.06	2.40
282	285	4.697756	CAACTGAAGGGCGGCCGA	62.698	66.667	33.48	5.32	0.00	5.54
285	288	1.906105	AACTGAAGGGCGGCCGATTA	61.906	55.000	33.48	11.57	0.00	1.75
327	330	1.621317	TGTAGCCAATCTTCGTGGACA	59.379	47.619	0.00	0.00	38.54	4.02
331	334	1.421485	CAATCTTCGTGGACAGCGC	59.579	57.895	0.00	0.00	0.00	5.92
350	353	0.668706	CGACAGAGAGCTTGGTGGTG	60.669	60.000	0.00	0.00	0.00	4.17
353	356	1.212935	ACAGAGAGCTTGGTGGTGTTT	59.787	47.619	0.00	0.00	0.00	2.83
386	389	2.936919	TCCTTGCCGCATTCATCTAT	57.063	45.000	0.00	0.00	0.00	1.98
388	391	2.158769	TCCTTGCCGCATTCATCTATGT	60.159	45.455	0.00	0.00	0.00	2.29
392	395	1.335324	GCCGCATTCATCTATGTTGGC	60.335	52.381	0.00	0.00	39.88	4.52
416	419	2.458969	TAACGCTGGTGGGAGGGGTA	62.459	60.000	0.00	0.00	0.00	3.69
417	420	3.006728	CGCTGGTGGGAGGGGTAA	61.007	66.667	0.00	0.00	0.00	2.85
460	463	1.584495	GTTCCATTCCCGGTGCAAC	59.416	57.895	0.00	0.00	0.00	4.17
506	549	1.977293	GAGGCGGGAAGAGGAGCAAT	61.977	60.000	0.00	0.00	0.00	3.56
528	571	8.430828	GCAATGAGAATCTTTTGCTAAAACTTC	58.569	33.333	18.51	1.67	45.22	3.01
613	661	2.289195	TGTGAGGGTTTGGTTAGCTACG	60.289	50.000	0.00	0.00	0.00	3.51
661	709	8.626526	TCCTTTAAAGAGTTAAGCGTTTTTGAT	58.373	29.630	16.98	0.00	30.92	2.57
894	945	0.449388	CGCAGATGTTGAGGCTTTCC	59.551	55.000	0.00	0.00	0.00	3.13
898	949	3.152341	CAGATGTTGAGGCTTTCCTGTT	58.848	45.455	0.00	0.00	44.46	3.16
921	972	7.284489	TGTTTAGTTCACCAGCAAAGAAAGTAT	59.716	33.333	0.00	0.00	0.00	2.12
922	973	8.780249	GTTTAGTTCACCAGCAAAGAAAGTATA	58.220	33.333	0.00	0.00	0.00	1.47
923	974	8.911918	TTAGTTCACCAGCAAAGAAAGTATAA	57.088	30.769	0.00	0.00	0.00	0.98
924	975	9.515226	TTAGTTCACCAGCAAAGAAAGTATAAT	57.485	29.630	0.00	0.00	0.00	1.28
926	977	9.515226	AGTTCACCAGCAAAGAAAGTATAATAA	57.485	29.630	0.00	0.00	0.00	1.40
969	1139	2.842208	TTGCCAACACTTTCTTGACG	57.158	45.000	0.00	0.00	0.00	4.35
971	1141	1.939934	TGCCAACACTTTCTTGACGAG	59.060	47.619	0.00	0.00	0.00	4.18
972	1142	1.940613	GCCAACACTTTCTTGACGAGT	59.059	47.619	0.00	0.00	0.00	4.18
974	1144	3.194861	CCAACACTTTCTTGACGAGTCA	58.805	45.455	1.24	1.24	37.91	3.41
975	1145	3.001330	CCAACACTTTCTTGACGAGTCAC	59.999	47.826	5.30	0.00	39.66	3.67
988	1158	0.386858	GAGTCACGACACTTGCGCTA	60.387	55.000	9.73	0.00	0.00	4.26
1008	1178	5.393135	CGCTACCTACTTCATCAGAGACAAA	60.393	44.000	0.00	0.00	0.00	2.83
1016	1186	9.429359	CTACTTCATCAGAGACAAATTTACTGT	57.571	33.333	0.00	0.00	0.00	3.55
1078	1252	5.894964	TCAACATGTGATCCATCATCCAATT	59.105	36.000	0.00	0.00	39.30	2.32
1142	1600	1.474320	GCAATGGCGACTACCACCATA	60.474	52.381	0.00	0.00	43.40	2.74
1267	1725	0.323178	CAGGTTTCATCAGGCAGCCT	60.323	55.000	8.70	8.70	0.00	4.58
1303	1761	2.037367	TGTGCTCTACCTCGGCCT	59.963	61.111	0.00	0.00	0.00	5.19
1334	1792	2.494918	CCCCCGAGCTACTTGACG	59.505	66.667	0.00	0.00	0.00	4.35
1337	1795	3.285371	CCGAGCTACTTGACGGGT	58.715	61.111	1.46	0.00	41.41	5.28
1414	1872	2.632602	TTTGCCAAGAACCGGGAGCA	62.633	55.000	6.32	1.96	0.00	4.26
1469	1927	3.082579	GCTCGGATGCGTCTTCCCT	62.083	63.158	6.49	0.00	0.00	4.20
1476	1934	0.326264	ATGCGTCTTCCCTGAGCTTT	59.674	50.000	0.00	0.00	0.00	3.51
1522	1980	0.252197	GAGGCCGTATGGTTCAAGGT	59.748	55.000	2.17	0.00	37.67	3.50
1587	2045	4.790962	CCAGCCTCGTGCATGCCT	62.791	66.667	16.68	0.00	44.83	4.75
1591	2049	1.070445	GCCTCGTGCATGCCTAGAT	59.930	57.895	16.68	0.00	40.77	1.98
1592	2050	0.533755	GCCTCGTGCATGCCTAGATT	60.534	55.000	16.68	0.00	40.77	2.40
1713	2171	2.757124	GGGGGCAGATTCGACCCAT	61.757	63.158	17.60	0.00	46.21	4.00
1769	2227	3.073650	AGCTGAAGGTGAAGGAAGTCAAT	59.926	43.478	0.00	0.00	0.00	2.57
1781	2239	2.344025	GAAGTCAATAACGGTCGCCTT	58.656	47.619	0.00	0.00	0.00	4.35
1805	2263	4.082026	GCCATGTTCTCTATGTTTGGCTTT	60.082	41.667	3.87	0.00	43.68	3.51
1812	2270	4.819630	TCTCTATGTTTGGCTTTTTCGTGT	59.180	37.500	0.00	0.00	0.00	4.49
1832	2290	3.799755	GCCATCGTCACCGGCAAC	61.800	66.667	0.00	0.00	45.52	4.17
2021	7387	9.469807	TTCAAATTGTAACATCATGGTGTAAAC	57.530	29.630	13.06	14.03	0.00	2.01
2031	7397	6.823689	ACATCATGGTGTAAACTACAAGGATC	59.176	38.462	10.65	0.00	40.93	3.36
2115	10357	5.163416	TGCTCCATGAGAAATGAGAACGATA	60.163	40.000	0.00	0.00	0.00	2.92
2126	10368	8.893727	AGAAATGAGAACGATAAATACTTTGGG	58.106	33.333	0.00	0.00	0.00	4.12
2127	10369	6.619801	ATGAGAACGATAAATACTTTGGGC	57.380	37.500	0.00	0.00	0.00	5.36
2129	10371	6.880484	TGAGAACGATAAATACTTTGGGCTA	58.120	36.000	0.00	0.00	0.00	3.93
2130	10372	7.506114	TGAGAACGATAAATACTTTGGGCTAT	58.494	34.615	0.00	0.00	0.00	2.97
2133	10375	8.621286	AGAACGATAAATACTTTGGGCTATTTG	58.379	33.333	0.00	0.00	0.00	2.32
2134	10376	7.875327	ACGATAAATACTTTGGGCTATTTGT	57.125	32.000	0.00	0.00	0.00	2.83
2135	10377	8.288689	ACGATAAATACTTTGGGCTATTTGTT	57.711	30.769	0.00	0.00	0.00	2.83
2137	10379	9.581099	CGATAAATACTTTGGGCTATTTGTTTT	57.419	29.630	0.45	0.00	0.00	2.43
2139	10381	9.884636	ATAAATACTTTGGGCTATTTGTTTTCC	57.115	29.630	0.45	0.00	0.00	3.13
2140	10382	7.553504	AATACTTTGGGCTATTTGTTTTCCT	57.446	32.000	0.00	0.00	0.00	3.36
2142	10384	6.987403	ACTTTGGGCTATTTGTTTTCCTAA	57.013	33.333	0.00	0.00	0.00	2.69
2143	10385	7.368198	ACTTTGGGCTATTTGTTTTCCTAAA	57.632	32.000	0.00	0.00	0.00	1.85
2756	12886	3.550431	CATCCGGGATGGCCTCGT	61.550	66.667	26.20	0.00	36.51	4.18
2774	12904	1.305633	TCCTCCTGCTGCTAGCTGT	60.306	57.895	21.03	0.00	42.97	4.40
2779	12909	1.023513	CCTGCTGCTAGCTGTTGGTC	61.024	60.000	21.03	6.38	42.97	4.02
2783	12913	1.005037	TGCTAGCTGTTGGTCCACG	60.005	57.895	17.23	0.00	0.00	4.94
2786	12916	0.603569	CTAGCTGTTGGTCCACGTCT	59.396	55.000	0.00	0.00	0.00	4.18
2798	12928	2.561858	GTCCACGTCTTTCTCCCTACTT	59.438	50.000	0.00	0.00	0.00	2.24
2806	12936	6.059484	CGTCTTTCTCCCTACTTCTATCTCT	58.941	44.000	0.00	0.00	0.00	3.10
2807	12937	6.544564	CGTCTTTCTCCCTACTTCTATCTCTT	59.455	42.308	0.00	0.00	0.00	2.85

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
108	110	1.526917	CTCCATCCCAATCGCCCAC	60.527	63.158	0.00	0.00	0.00	4.61
231	234	2.354199	GCAAGTGGATGAAGAAGCTAGC	59.646	50.000	6.62	6.62	0.00	3.42
233	236	2.677902	CGGCAAGTGGATGAAGAAGCTA	60.678	50.000	0.00	0.00	0.00	3.32
234	237	1.831580	GGCAAGTGGATGAAGAAGCT	58.168	50.000	0.00	0.00	0.00	3.74
247	250	0.400213	TGATTCTCCCAACGGCAAGT	59.600	50.000	0.00	0.00	0.00	3.16
259	262	1.373570	CCGCCCTTCAGTTGATTCTC	58.626	55.000	0.00	0.00	0.00	2.87
260	263	0.678048	GCCGCCCTTCAGTTGATTCT	60.678	55.000	0.00	0.00	0.00	2.40
264	267	4.697756	CGGCCGCCCTTCAGTTGA	62.698	66.667	14.67	0.00	0.00	3.18
282	285	3.454375	CCACGCCGTCTACAAAGATAAT	58.546	45.455	0.00	0.00	33.30	1.28
285	288	0.739813	GCCACGCCGTCTACAAAGAT	60.740	55.000	0.00	0.00	33.30	2.40
309	312	1.405526	GCTGTCCACGAAGATTGGCTA	60.406	52.381	0.00	0.00	33.71	3.93
310	313	0.674895	GCTGTCCACGAAGATTGGCT	60.675	55.000	0.00	0.00	33.71	4.75
327	330	2.126149	CAAGCTCTCTGTCGCGCT	60.126	61.111	5.56	0.00	0.00	5.92
331	334	0.668706	CACCACCAAGCTCTCTGTCG	60.669	60.000	0.00	0.00	0.00	4.35
342	345	1.384525	CTCGGAACAAACACCACCAA	58.615	50.000	0.00	0.00	0.00	3.67
350	353	2.919228	AGGATATGGCTCGGAACAAAC	58.081	47.619	0.00	0.00	0.00	2.93
353	356	1.475034	GCAAGGATATGGCTCGGAACA	60.475	52.381	0.00	0.00	0.00	3.18
392	395	2.740826	CCCACCAGCGTTACACCG	60.741	66.667	0.00	0.00	0.00	4.94
406	409	2.608368	CACCGGTTACCCCTCCCA	60.608	66.667	2.97	0.00	0.00	4.37
441	444	1.969064	TTGCACCGGGAATGGAACG	60.969	57.895	6.32	0.00	0.00	3.95
480	502	4.785453	CTTCCCGCCTCTGCCACC	62.785	72.222	0.00	0.00	0.00	4.61
486	508	2.762043	GCTCCTCTTCCCGCCTCT	60.762	66.667	0.00	0.00	0.00	3.69
492	514	3.136260	AGATTCTCATTGCTCCTCTTCCC	59.864	47.826	0.00	0.00	0.00	3.97
506	549	7.307989	CCTCGAAGTTTTAGCAAAAGATTCTCA	60.308	37.037	0.00	0.00	30.66	3.27
519	562	1.710013	TGAGCGCCTCGAAGTTTTAG	58.290	50.000	2.29	0.00	32.35	1.85
521	564	1.305201	TTTGAGCGCCTCGAAGTTTT	58.695	45.000	2.29	0.00	31.11	2.43
528	571	1.331756	AGCATAAATTTGAGCGCCTCG	59.668	47.619	2.29	0.00	32.35	4.63
563	606	9.744468	GTTAACTCAAAAATTTAAGAAGCCTCA	57.256	29.630	0.00	0.00	0.00	3.86
593	641	2.344025	CGTAGCTAACCAAACCCTCAC	58.656	52.381	0.00	0.00	0.00	3.51
613	661	6.153510	AGGATTTCATTTTGAGGAGTTAAGCC	59.846	38.462	0.00	0.00	0.00	4.35
641	689	9.959749	TGAATTATCAAAAACGCTTAACTCTTT	57.040	25.926	0.00	0.00	30.99	2.52
876	927	1.471684	CAGGAAAGCCTCAACATCTGC	59.528	52.381	0.00	0.00	44.80	4.26
894	945	5.499139	TTCTTTGCTGGTGAACTAAACAG	57.501	39.130	0.00	0.00	0.00	3.16
898	949	8.911918	TTATACTTTCTTTGCTGGTGAACTAA	57.088	30.769	0.00	0.00	0.00	2.24
927	978	7.224557	GCAATTTTAGGCCATACGATGATTTTT	59.775	33.333	5.01	0.00	0.00	1.94
928	979	6.701400	GCAATTTTAGGCCATACGATGATTTT	59.299	34.615	5.01	0.00	0.00	1.82
929	980	6.215845	GCAATTTTAGGCCATACGATGATTT	58.784	36.000	5.01	0.00	0.00	2.17
969	1139	0.386858	TAGCGCAAGTGTCGTGACTC	60.387	55.000	11.47	0.00	41.68	3.36
971	1141	1.615107	GGTAGCGCAAGTGTCGTGAC	61.615	60.000	11.47	0.00	41.68	3.67
972	1142	1.372499	GGTAGCGCAAGTGTCGTGA	60.372	57.895	11.47	0.00	41.68	4.35
974	1144	0.109412	GTAGGTAGCGCAAGTGTCGT	60.109	55.000	11.47	0.00	41.68	4.34
975	1145	0.170561	AGTAGGTAGCGCAAGTGTCG	59.829	55.000	11.47	0.00	41.68	4.35
988	1158	8.598041	AGTAAATTTGTCTCTGATGAAGTAGGT	58.402	33.333	0.00	0.00	0.00	3.08
1008	1178	2.551887	TGCATGCAACGTGACAGTAAAT	59.448	40.909	20.30	0.00	0.00	1.40
1016	1186	2.316867	CGGTCTGCATGCAACGTGA	61.317	57.895	22.88	12.61	0.00	4.35
1078	1252	4.209307	TGTGTGTTCTCCAAACAGTGTA	57.791	40.909	0.00	0.00	36.33	2.90
1142	1600	0.466555	CGAAGGTCGAGGAGAGGGAT	60.467	60.000	0.00	0.00	43.74	3.85
1283	1741	2.697761	GCCGAGGTAGAGCACACGA	61.698	63.158	0.00	0.00	32.70	4.35
1337	1795	2.036098	TAGTCGCCGGGGAACTCA	59.964	61.111	24.36	5.65	0.00	3.41
1414	1872	2.982130	GGCAGTGGATCACCTCGT	59.018	61.111	0.00	0.00	34.49	4.18
1469	1927	0.865218	CGTTGCGTGCAAAAAGCTCA	60.865	50.000	9.13	0.00	45.94	4.26
1586	2044	5.188555	TGCCCAGATAGCAAGGATAATCTAG	59.811	44.000	0.00	0.00	37.28	2.43
1587	2045	5.093677	TGCCCAGATAGCAAGGATAATCTA	58.906	41.667	0.00	0.00	37.28	1.98
1591	2049	3.811810	GCATGCCCAGATAGCAAGGATAA	60.812	47.826	6.36	0.00	44.83	1.75
1592	2050	2.290514	GCATGCCCAGATAGCAAGGATA	60.291	50.000	6.36	0.00	44.83	2.59
1703	2161	0.684153	CCAAGCCCAATGGGTCGAAT	60.684	55.000	21.02	0.00	46.51	3.34
1751	2209	4.392138	CCGTTATTGACTTCCTTCACCTTC	59.608	45.833	0.00	0.00	0.00	3.46
1769	2227	1.743623	CATGGCAAGGCGACCGTTA	60.744	57.895	0.00	0.00	0.00	3.18
1805	2263	0.604073	TGACGATGGCCTACACGAAA	59.396	50.000	3.32	0.00	0.00	3.46
1832	2290	3.358076	GAGGTTCTCGAGTGGGCCG	62.358	68.421	13.13	0.00	0.00	6.13
1969	7327	3.485394	ACATTATGTGTGCAGTTCACCA	58.515	40.909	0.00	0.00	45.03	4.17
2021	7387	4.316025	TTTCCCCAAAGGATCCTTGTAG	57.684	45.455	27.71	18.97	46.94	2.74
2031	7397	3.840078	AGATCAAACCATTTCCCCAAAGG	59.160	43.478	0.00	0.00	0.00	3.11
2115	10357	7.973402	AGGAAAACAAATAGCCCAAAGTATTT	58.027	30.769	0.00	0.00	40.26	1.40
2123	10365	8.887264	TCTAATTTAGGAAAACAAATAGCCCA	57.113	30.769	3.66	0.00	0.00	5.36
2130	10372	9.635404	TCAAGACCTCTAATTTAGGAAAACAAA	57.365	29.630	12.26	0.00	37.57	2.83
2133	10375	7.390718	TGCTCAAGACCTCTAATTTAGGAAAAC	59.609	37.037	12.26	3.14	37.57	2.43
2134	10376	7.390718	GTGCTCAAGACCTCTAATTTAGGAAAA	59.609	37.037	12.26	0.00	37.57	2.29
2135	10377	6.879458	GTGCTCAAGACCTCTAATTTAGGAAA	59.121	38.462	12.26	0.00	37.57	3.13
2137	10379	5.483937	TGTGCTCAAGACCTCTAATTTAGGA	59.516	40.000	12.26	0.00	37.57	2.94
2138	10380	5.582665	GTGTGCTCAAGACCTCTAATTTAGG	59.417	44.000	3.66	5.25	40.20	2.69
2139	10381	6.091441	GTGTGTGCTCAAGACCTCTAATTTAG	59.909	42.308	0.00	0.00	0.00	1.85
2140	10382	5.932303	GTGTGTGCTCAAGACCTCTAATTTA	59.068	40.000	0.00	0.00	0.00	1.40
2142	10384	4.319177	GTGTGTGCTCAAGACCTCTAATT	58.681	43.478	0.00	0.00	0.00	1.40
2143	10385	3.307059	GGTGTGTGCTCAAGACCTCTAAT	60.307	47.826	9.84	0.00	0.00	1.73
2756	12886	0.906756	AACAGCTAGCAGCAGGAGGA	60.907	55.000	18.83	0.00	45.56	3.71
2774	12904	0.395312	GGGAGAAAGACGTGGACCAA	59.605	55.000	0.00	0.00	0.00	3.67
2779	12909	2.826725	AGAAGTAGGGAGAAAGACGTGG	59.173	50.000	0.00	0.00	0.00	4.94
2783	12913	7.712797	CAAGAGATAGAAGTAGGGAGAAAGAC	58.287	42.308	0.00	0.00	0.00	3.01

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.