AutoCloner

Multiple sequence alignment - TraesCS7D01G090700

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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	TraesCS7D01G090700	chr7D	100.000	2384	0	0	1	2384	54355154	54352771	0.000000e+00	4403.0
1	TraesCS7D01G090700	chr7D	90.937	1942	120	18	111	2027	54320974	54319064	0.000000e+00	2560.0
2	TraesCS7D01G090700	chr7D	87.862	1450	134	13	598	2040	54337376	54335962	0.000000e+00	1664.0
3	TraesCS7D01G090700	chr7D	88.299	1376	96	16	121	1451	54312176	54310821	0.000000e+00	1589.0
4	TraesCS7D01G090700	chr7D	86.352	381	29	12	1673	2040	54310812	54310442	6.180000e-106	394.0
5	TraesCS7D01G090700	chr7D	87.611	113	12	2	1	111	401186003	401186115	1.920000e-26	130.0
6	TraesCS7D01G090700	chr7D	94.231	52	1	2	61	111	32168731	32168781	7.070000e-11	78.7
7	TraesCS7D01G090700	chr7A	86.497	2007	157	31	108	2040	57804297	57802331	0.000000e+00	2100.0
8	TraesCS7D01G090700	chr7A	92.908	1114	51	4	377	1462	57865407	57864294	0.000000e+00	1594.0
9	TraesCS7D01G090700	chr7A	86.728	437	40	9	1608	2040	57864178	57863756	9.980000e-129	470.0
10	TraesCS7D01G090700	chr7A	100.000	32	0	0	309	340	57865510	57865479	2.560000e-05	60.2
11	TraesCS7D01G090700	chr4A	87.050	1444	135	15	113	1517	669899545	669898115	0.000000e+00	1583.0
12	TraesCS7D01G090700	chr4A	89.624	665	43	10	1608	2269	669898065	669897424	0.000000e+00	822.0
13	TraesCS7D01G090700	chr4A	86.387	191	25	1	1449	1638	137382538	137382348	8.640000e-50	207.0
14	TraesCS7D01G090700	chr4A	94.958	119	6	0	2265	2383	669897396	669897278	1.130000e-43	187.0
15	TraesCS7D01G090700	chr4A	92.683	123	9	0	2261	2383	669879756	669879634	6.770000e-41	178.0
16	TraesCS7D01G090700	chr4A	88.889	126	4	3	2144	2269	669879895	669879780	1.910000e-31	147.0
17	TraesCS7D01G090700	chrUn	91.930	855	68	1	598	1451	49140747	49139893	0.000000e+00	1195.0
18	TraesCS7D01G090700	chrUn	91.696	855	70	1	598	1451	49113908	49113054	0.000000e+00	1184.0
19	TraesCS7D01G090700	chrUn	91.608	858	71	1	595	1451	384623911	384624768	0.000000e+00	1184.0
20	TraesCS7D01G090700	chrUn	92.780	277	16	1	1645	1917	49113059	49112783	4.770000e-107	398.0
21	TraesCS7D01G090700	chrUn	92.780	277	16	1	1645	1917	49139898	49139622	4.770000e-107	398.0
22	TraesCS7D01G090700	chrUn	92.780	277	16	1	1645	1917	384624763	384625039	4.770000e-107	398.0
23	TraesCS7D01G090700	chrUn	93.277	119	8	0	2265	2383	49127364	49127246	2.440000e-40	176.0
24	TraesCS7D01G090700	chrUn	88.889	126	4	3	2144	2269	49127507	49127392	1.910000e-31	147.0
25	TraesCS7D01G090700	chrUn	88.889	126	4	3	2144	2269	261595118	261595003	1.910000e-31	147.0
26	TraesCS7D01G090700	chrUn	90.625	64	6	0	2265	2328	261594975	261594912	4.220000e-13	86.1
27	TraesCS7D01G090700	chr2A	85.864	191	26	1	1449	1638	249493231	249493041	4.020000e-48	202.0
28	TraesCS7D01G090700	chr2B	85.492	193	27	1	1449	1640	58515224	58515032	1.450000e-47	200.0
29	TraesCS7D01G090700	chr6A	84.135	208	30	3	1449	1654	316928075	316927869	5.200000e-47	198.0
30	TraesCS7D01G090700	chr5A	85.340	191	27	1	1449	1638	432109086	432109276	1.870000e-46	196.0
31	TraesCS7D01G090700	chr5A	94.231	52	2	1	61	111	546810570	546810621	7.070000e-11	78.7
32	TraesCS7D01G090700	chr3A	85.340	191	27	1	1449	1638	739091554	739091744	1.870000e-46	196.0
33	TraesCS7D01G090700	chr3A	84.343	198	29	2	1443	1638	25213366	25213563	2.420000e-45	193.0
34	TraesCS7D01G090700	chr6B	84.956	113	15	2	1	111	29421270	29421158	1.940000e-21	113.0
35	TraesCS7D01G090700	chr6B	93.243	74	4	1	39	111	11705505	11705432	9.010000e-20	108.0
36	TraesCS7D01G090700	chr3D	88.372	86	9	1	27	111	553900312	553900397	4.190000e-18	102.0
37	TraesCS7D01G090700	chr2D	88.462	78	4	2	39	111	107868507	107868584	3.260000e-14	89.8
38	TraesCS7D01G090700	chr2D	94.340	53	2	1	61	112	599002356	599002408	1.960000e-11	80.5
39	TraesCS7D01G090700	chr1D	92.857	56	3	1	134	189	402837773	402837827	1.960000e-11	80.5
40	TraesCS7D01G090700	chr7B	91.071	56	3	2	62	115	714055805	714055860	9.140000e-10	75.0

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	TraesCS7D01G090700	chr7D	54352771	54355154	2383	True	4403.000000	4403	100.0000	1	2384	1	chr7D.!!$R3	2383
1	TraesCS7D01G090700	chr7D	54319064	54320974	1910	True	2560.000000	2560	90.9370	111	2027	1	chr7D.!!$R1	1916
2	TraesCS7D01G090700	chr7D	54335962	54337376	1414	True	1664.000000	1664	87.8620	598	2040	1	chr7D.!!$R2	1442
3	TraesCS7D01G090700	chr7D	54310442	54312176	1734	True	991.500000	1589	87.3255	121	2040	2	chr7D.!!$R4	1919
4	TraesCS7D01G090700	chr7A	57802331	57804297	1966	True	2100.000000	2100	86.4970	108	2040	1	chr7A.!!$R1	1932
5	TraesCS7D01G090700	chr7A	57863756	57865510	1754	True	708.066667	1594	93.2120	309	2040	3	chr7A.!!$R2	1731
6	TraesCS7D01G090700	chr4A	669897278	669899545	2267	True	864.000000	1583	90.5440	113	2383	3	chr4A.!!$R3	2270
7	TraesCS7D01G090700	chrUn	49139622	49140747	1125	True	796.500000	1195	92.3550	598	1917	2	chrUn.!!$R3	1319
8	TraesCS7D01G090700	chrUn	49112783	49113908	1125	True	791.000000	1184	92.2380	598	1917	2	chrUn.!!$R1	1319
9	TraesCS7D01G090700	chrUn	384623911	384625039	1128	False	791.000000	1184	92.1940	595	1917	2	chrUn.!!$F1	1322

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
60	61	0.179062	GTGCATAGCCAGACTGGGAG	60.179	60.0	23.09	0.0	38.19	4.3	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1955	2109	0.106708	CCGACCCACCGATCAATCAT	59.893	55.0	0.0	0.0	0.0	2.45	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
25	26	8.096400	CATGAGCTAATTTCACATACAAAACG	57.904	34.615	0.00	0.00	0.00	3.60
26	27	6.083630	TGAGCTAATTTCACATACAAAACGC	58.916	36.000	0.00	0.00	0.00	4.84
27	28	6.007936	AGCTAATTTCACATACAAAACGCA	57.992	33.333	0.00	0.00	0.00	5.24
28	29	6.086222	AGCTAATTTCACATACAAAACGCAG	58.914	36.000	0.00	0.00	0.00	5.18
30	31	6.183359	GCTAATTTCACATACAAAACGCAGTG	60.183	38.462	0.00	0.00	45.00	3.66
31	32	3.617540	TTCACATACAAAACGCAGTGG	57.382	42.857	0.00	0.00	45.00	4.00
32	33	1.265635	TCACATACAAAACGCAGTGGC	59.734	47.619	0.00	0.00	45.00	5.01
33	34	0.596082	ACATACAAAACGCAGTGGCC	59.404	50.000	0.00	0.00	45.00	5.36
34	35	0.595588	CATACAAAACGCAGTGGCCA	59.404	50.000	0.00	0.00	45.00	5.36
35	36	1.000827	CATACAAAACGCAGTGGCCAA	60.001	47.619	7.24	0.00	45.00	4.52
36	37	1.103803	TACAAAACGCAGTGGCCAAA	58.896	45.000	7.24	0.00	45.00	3.28
37	38	0.459411	ACAAAACGCAGTGGCCAAAC	60.459	50.000	7.24	0.00	45.00	2.93
38	39	1.142965	AAAACGCAGTGGCCAAACC	59.857	52.632	7.24	0.00	45.00	3.27
46	47	4.211893	TGGCCAAACCATGTGCAT	57.788	50.000	0.61	0.00	46.36	3.96
47	48	3.370798	TGGCCAAACCATGTGCATA	57.629	47.368	0.61	0.00	46.36	3.14
48	49	1.184431	TGGCCAAACCATGTGCATAG	58.816	50.000	0.61	0.00	46.36	2.23
49	50	0.179103	GGCCAAACCATGTGCATAGC	60.179	55.000	0.00	0.00	38.86	2.97
50	51	0.179103	GCCAAACCATGTGCATAGCC	60.179	55.000	0.00	0.00	0.00	3.93
51	52	1.184431	CCAAACCATGTGCATAGCCA	58.816	50.000	0.00	0.00	0.00	4.75
52	53	1.135527	CCAAACCATGTGCATAGCCAG	59.864	52.381	0.00	0.00	0.00	4.85
53	54	2.093890	CAAACCATGTGCATAGCCAGA	58.906	47.619	0.00	0.00	0.00	3.86
54	55	1.755179	AACCATGTGCATAGCCAGAC	58.245	50.000	0.00	0.00	0.00	3.51
55	56	0.914644	ACCATGTGCATAGCCAGACT	59.085	50.000	0.00	0.00	0.00	3.24
56	57	1.306148	CCATGTGCATAGCCAGACTG	58.694	55.000	0.00	0.00	0.00	3.51
57	58	1.306148	CATGTGCATAGCCAGACTGG	58.694	55.000	17.83	17.83	41.55	4.00
58	59	0.182061	ATGTGCATAGCCAGACTGGG	59.818	55.000	23.09	7.35	38.19	4.45
59	60	0.909133	TGTGCATAGCCAGACTGGGA	60.909	55.000	23.09	0.00	38.19	4.37
60	61	0.179062	GTGCATAGCCAGACTGGGAG	60.179	60.000	23.09	0.00	38.19	4.30
61	62	1.227793	GCATAGCCAGACTGGGAGC	60.228	63.158	23.09	8.78	38.19	4.70
62	63	1.068753	CATAGCCAGACTGGGAGCG	59.931	63.158	23.09	0.00	38.19	5.03
63	64	2.801631	ATAGCCAGACTGGGAGCGC	61.802	63.158	23.09	0.00	38.19	5.92
66	67	4.007644	CCAGACTGGGAGCGCACA	62.008	66.667	14.26	4.52	32.67	4.57
67	68	2.740055	CAGACTGGGAGCGCACAC	60.740	66.667	11.47	4.64	0.00	3.82
68	69	4.008933	AGACTGGGAGCGCACACC	62.009	66.667	11.47	9.35	0.00	4.16
384	422	5.630264	TCATGTTCGAAGATGCAAAATGTTG	59.370	36.000	25.97	4.87	35.04	3.33
490	528	6.414732	TGACGAGAATTGAACCAAGGAATAT	58.585	36.000	0.00	0.00	0.00	1.28
549	613	3.810941	CCAAACTTTACAGCGGTAACTCA	59.189	43.478	9.06	0.00	39.14	3.41
556	620	1.225855	CAGCGGTAACTCACTTGCAA	58.774	50.000	0.00	0.00	32.90	4.08
743	833	1.586028	GCATGTTGGCGTTGTCCAT	59.414	52.632	0.00	0.00	35.77	3.41
756	846	1.264045	TGTCCATCACCATCCTCGCA	61.264	55.000	0.00	0.00	0.00	5.10
1191	1281	4.113815	CCCCCGCTGAGGATGCAA	62.114	66.667	0.00	0.00	45.00	4.08
1356	1446	2.995574	CTGAACGGGGTCGGGTCT	60.996	66.667	0.00	0.00	41.39	3.85
1377	1467	1.733399	GAGGACCGAAGCGTCACAC	60.733	63.158	0.00	0.00	34.24	3.82
1454	1554	9.486497	ACATGCATGTTTTCATTGTAATTGTTA	57.514	25.926	26.61	0.00	37.90	2.41
1457	1557	9.755804	TGCATGTTTTCATTGTAATTGTTAAGA	57.244	25.926	0.00	0.00	38.64	2.10
1475	1575	9.569122	TTGTTAAGAAAATCTTTAGCTGGTAGT	57.431	29.630	0.00	0.00	37.89	2.73
1489	1589	1.547372	TGGTAGTTACTCGGTTGGCTC	59.453	52.381	0.00	0.00	0.00	4.70
1490	1590	1.547372	GGTAGTTACTCGGTTGGCTCA	59.453	52.381	0.00	0.00	0.00	4.26
1535	1639	6.543430	AATCAGCAAGTTAATTGGCCATTA	57.457	33.333	6.09	4.83	39.47	1.90
1584	1689	0.242825	TCGGCTACTCGGTGACTTTG	59.757	55.000	0.00	0.00	0.00	2.77
1591	1696	1.338973	ACTCGGTGACTTTGCGAGTAA	59.661	47.619	11.82	0.00	39.19	2.24
1602	1736	6.876789	TGACTTTGCGAGTAAGGATTAATCAA	59.123	34.615	17.07	0.00	45.20	2.57
1643	1777	9.994432	AATCGAATAAATTCTTGAACAAGCTAG	57.006	29.630	9.38	0.00	38.28	3.42
1658	1792	9.019656	TGAACAAGCTAGGCAATTTATTTCTTA	57.980	29.630	0.00	0.00	0.00	2.10
1769	1903	2.100631	CATGACGCCCTTGACGACC	61.101	63.158	0.00	0.00	0.00	4.79
1936	2084	3.677424	GCTCGAGTGCCTGACTAAGATTT	60.677	47.826	15.13	0.00	33.83	2.17
1955	2109	5.486775	AGATTTGAAGATGAGAAGTGGGAGA	59.513	40.000	0.00	0.00	0.00	3.71
1991	2148	2.192187	GGGAATGCCTGCTAGCTGC	61.192	63.158	17.23	18.29	43.25	5.25
2003	2160	5.788450	CCTGCTAGCTGCTGTATATAGTTT	58.212	41.667	17.23	0.00	43.37	2.66
2051	2211	3.065233	GGCATTCGAAGCATATGTTGTCA	59.935	43.478	17.39	0.00	0.00	3.58
2059	2219	4.220693	AGCATATGTTGTCAACTAGCCA	57.779	40.909	16.45	0.00	0.00	4.75
2062	2222	4.790766	GCATATGTTGTCAACTAGCCATGC	60.791	45.833	16.45	16.70	0.00	4.06
2088	2248	2.842485	CGTTGGAACGTTACTAGCTACG	59.158	50.000	12.67	13.75	46.63	3.51
2168	2328	1.068741	AGAGGGCGTCGGTAATGAATC	59.931	52.381	0.96	0.00	0.00	2.52
2191	2351	6.454795	TCATATGATACACAAATAGCGAGCA	58.545	36.000	0.00	0.00	0.00	4.26
2192	2352	7.099120	TCATATGATACACAAATAGCGAGCAT	58.901	34.615	0.00	0.00	0.00	3.79
2193	2353	7.603784	TCATATGATACACAAATAGCGAGCATT	59.396	33.333	0.00	0.00	0.00	3.56
2194	2354	8.872845	CATATGATACACAAATAGCGAGCATTA	58.127	33.333	0.00	0.00	0.00	1.90
2195	2355	6.769608	TGATACACAAATAGCGAGCATTAG	57.230	37.500	0.00	0.00	0.00	1.73
2196	2356	6.280643	TGATACACAAATAGCGAGCATTAGT	58.719	36.000	0.00	0.00	0.00	2.24
2197	2357	6.761242	TGATACACAAATAGCGAGCATTAGTT	59.239	34.615	0.00	0.00	0.00	2.24
2198	2358	5.470845	ACACAAATAGCGAGCATTAGTTC	57.529	39.130	0.00	0.00	0.00	3.01
2199	2359	4.332819	ACACAAATAGCGAGCATTAGTTCC	59.667	41.667	0.00	0.00	0.00	3.62
2200	2360	4.572389	CACAAATAGCGAGCATTAGTTCCT	59.428	41.667	0.00	0.00	0.00	3.36
2206	2366	2.612672	GCGAGCATTAGTTCCTTAACCC	59.387	50.000	0.00	0.00	36.15	4.11
2207	2367	3.203716	CGAGCATTAGTTCCTTAACCCC	58.796	50.000	0.00	0.00	36.15	4.95
2225	2385	4.833390	ACCCCGAGTTTTTAGAAGATGAG	58.167	43.478	0.00	0.00	0.00	2.90
2232	2392	6.811170	CGAGTTTTTAGAAGATGAGAGCTCTT	59.189	38.462	19.36	1.78	35.69	2.85
2271	2463	1.074951	GGGGTTGACTTGACTGGGG	59.925	63.158	0.00	0.00	0.00	4.96
2282	2474	4.037927	ACTTGACTGGGGCTAGCTATTTA	58.962	43.478	15.72	0.00	0.00	1.40
2288	2480	5.961897	ACTGGGGCTAGCTATTTAGTACTA	58.038	41.667	15.72	0.00	0.00	1.82
2291	2483	7.038941	ACTGGGGCTAGCTATTTAGTACTAATG	60.039	40.741	15.92	10.38	0.00	1.90
2359	2551	0.893727	GGGACGCATGTTTTCCTGGT	60.894	55.000	8.67	0.00	0.00	4.00
2376	2568	2.632996	CTGGTTGTTGAGAGGTCAGGTA	59.367	50.000	0.00	0.00	32.98	3.08
2383	2575	6.097915	TGTTGAGAGGTCAGGTAAGTTAAG	57.902	41.667	0.00	0.00	32.98	1.85

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
1	2	6.747280	GCGTTTTGTATGTGAAATTAGCTCAT	59.253	34.615	0.00	0.00	0.00	2.90
2	3	6.083630	GCGTTTTGTATGTGAAATTAGCTCA	58.916	36.000	0.00	0.00	0.00	4.26
3	4	6.083630	TGCGTTTTGTATGTGAAATTAGCTC	58.916	36.000	0.00	0.00	0.00	4.09
4	5	6.007936	TGCGTTTTGTATGTGAAATTAGCT	57.992	33.333	0.00	0.00	0.00	3.32
5	6	5.856455	ACTGCGTTTTGTATGTGAAATTAGC	59.144	36.000	0.00	0.00	0.00	3.09
6	7	6.305399	CCACTGCGTTTTGTATGTGAAATTAG	59.695	38.462	0.00	0.00	0.00	1.73
7	8	6.146216	CCACTGCGTTTTGTATGTGAAATTA	58.854	36.000	0.00	0.00	0.00	1.40
8	9	4.981674	CCACTGCGTTTTGTATGTGAAATT	59.018	37.500	0.00	0.00	0.00	1.82
9	10	4.545610	CCACTGCGTTTTGTATGTGAAAT	58.454	39.130	0.00	0.00	0.00	2.17
10	11	3.793801	GCCACTGCGTTTTGTATGTGAAA	60.794	43.478	0.00	0.00	0.00	2.69
11	12	2.287308	GCCACTGCGTTTTGTATGTGAA	60.287	45.455	0.00	0.00	0.00	3.18
12	13	1.265635	GCCACTGCGTTTTGTATGTGA	59.734	47.619	0.00	0.00	0.00	3.58
13	14	1.665735	GGCCACTGCGTTTTGTATGTG	60.666	52.381	0.00	0.00	38.85	3.21
14	15	0.596082	GGCCACTGCGTTTTGTATGT	59.404	50.000	0.00	0.00	38.85	2.29
15	16	0.595588	TGGCCACTGCGTTTTGTATG	59.404	50.000	0.00	0.00	38.85	2.39
16	17	1.323412	TTGGCCACTGCGTTTTGTAT	58.677	45.000	3.88	0.00	38.85	2.29
17	18	1.103803	TTTGGCCACTGCGTTTTGTA	58.896	45.000	3.88	0.00	38.85	2.41
18	19	0.459411	GTTTGGCCACTGCGTTTTGT	60.459	50.000	3.88	0.00	38.85	2.83
19	20	1.151172	GGTTTGGCCACTGCGTTTTG	61.151	55.000	3.88	0.00	38.85	2.44
20	21	1.142965	GGTTTGGCCACTGCGTTTT	59.857	52.632	3.88	0.00	38.85	2.43
21	22	2.055042	TGGTTTGGCCACTGCGTTT	61.055	52.632	3.88	0.00	43.61	3.60
22	23	2.441164	TGGTTTGGCCACTGCGTT	60.441	55.556	3.88	0.00	43.61	4.84
30	31	0.179103	GCTATGCACATGGTTTGGCC	60.179	55.000	0.00	0.00	37.90	5.36
31	32	0.179103	GGCTATGCACATGGTTTGGC	60.179	55.000	0.00	0.00	0.00	4.52
32	33	1.135527	CTGGCTATGCACATGGTTTGG	59.864	52.381	0.00	0.00	0.00	3.28
33	34	2.093890	TCTGGCTATGCACATGGTTTG	58.906	47.619	0.00	0.00	0.00	2.93
34	35	2.094675	GTCTGGCTATGCACATGGTTT	58.905	47.619	0.00	0.00	0.00	3.27
35	36	1.283029	AGTCTGGCTATGCACATGGTT	59.717	47.619	0.00	0.00	0.00	3.67
36	37	0.914644	AGTCTGGCTATGCACATGGT	59.085	50.000	0.00	0.00	0.00	3.55
37	38	1.306148	CAGTCTGGCTATGCACATGG	58.694	55.000	0.00	0.00	0.00	3.66
38	39	1.306148	CCAGTCTGGCTATGCACATG	58.694	55.000	5.79	0.00	0.00	3.21
39	40	0.182061	CCCAGTCTGGCTATGCACAT	59.818	55.000	13.99	0.00	35.79	3.21
40	41	0.909133	TCCCAGTCTGGCTATGCACA	60.909	55.000	13.99	0.00	35.79	4.57
41	42	0.179062	CTCCCAGTCTGGCTATGCAC	60.179	60.000	13.99	0.00	35.79	4.57
42	43	1.976132	GCTCCCAGTCTGGCTATGCA	61.976	60.000	13.99	0.00	35.79	3.96
43	44	1.227793	GCTCCCAGTCTGGCTATGC	60.228	63.158	13.99	10.08	35.79	3.14
44	45	1.068753	CGCTCCCAGTCTGGCTATG	59.931	63.158	13.99	0.00	35.79	2.23
45	46	2.801631	GCGCTCCCAGTCTGGCTAT	61.802	63.158	13.99	0.00	35.79	2.97
46	47	3.461773	GCGCTCCCAGTCTGGCTA	61.462	66.667	13.99	2.71	35.79	3.93
49	50	4.007644	TGTGCGCTCCCAGTCTGG	62.008	66.667	12.40	12.40	37.25	3.86
50	51	2.740055	GTGTGCGCTCCCAGTCTG	60.740	66.667	9.73	0.00	0.00	3.51
51	52	4.008933	GGTGTGCGCTCCCAGTCT	62.009	66.667	9.73	0.00	0.00	3.24
63	64	4.704833	CACCTGAGGCGGGGTGTG	62.705	72.222	15.00	1.74	45.52	3.82
94	95	4.537433	CACTAGAGGCTGGGGCGC	62.537	72.222	0.00	0.00	39.81	6.53
95	96	3.854669	CCACTAGAGGCTGGGGCG	61.855	72.222	0.00	0.00	39.81	6.13
96	97	2.365635	TCCACTAGAGGCTGGGGC	60.366	66.667	0.53	0.00	37.82	5.80
97	98	3.962557	CTCCACTAGAGGCTGGGG	58.037	66.667	0.53	0.00	39.13	4.96
105	106	5.242393	GGTAGTTGTTGTGTACTCCACTAGA	59.758	44.000	0.00	0.00	44.81	2.43
106	107	5.467705	GGTAGTTGTTGTGTACTCCACTAG	58.532	45.833	0.00	0.00	44.81	2.57
384	422	7.307160	GGGAAAATAAAGTTACACTTTTGCTGC	60.307	37.037	7.17	0.00	45.38	5.25
490	528	8.634335	TCCATCATTGTTGTCTTATCTTTTGA	57.366	30.769	0.00	0.00	0.00	2.69
498	537	7.936496	TTTAGCATCCATCATTGTTGTCTTA	57.064	32.000	0.00	0.00	0.00	2.10
549	613	4.389890	TGTTTGCTTTCATCTTGCAAGT	57.610	36.364	25.19	10.69	45.52	3.16
556	620	5.105473	CCATCTCCATTGTTTGCTTTCATCT	60.105	40.000	0.00	0.00	0.00	2.90
726	816	0.880441	TGATGGACAACGCCAACATG	59.120	50.000	0.00	0.00	42.16	3.21
743	833	1.323271	GGAGACTGCGAGGATGGTGA	61.323	60.000	0.00	0.00	0.00	4.02
905	995	2.807107	TTCCTGCGTGACCAGTGCT	61.807	57.895	1.49	0.00	0.00	4.40
953	1043	4.351938	CCGACCGCCTCAACGTCA	62.352	66.667	0.00	0.00	0.00	4.35
1217	1307	4.193334	TCTCCTGCGCCGACATCG	62.193	66.667	4.18	0.00	39.44	3.84
1356	1446	1.001764	TGACGCTTCGGTCCTCCTA	60.002	57.895	0.00	0.00	36.07	2.94
1454	1554	9.438228	GAGTAACTACCAGCTAAAGATTTTCTT	57.562	33.333	0.00	0.00	38.59	2.52
1457	1557	6.817140	CCGAGTAACTACCAGCTAAAGATTTT	59.183	38.462	0.00	0.00	0.00	1.82
1463	1563	4.322198	CCAACCGAGTAACTACCAGCTAAA	60.322	45.833	0.00	0.00	0.00	1.85
1467	1567	2.005560	GCCAACCGAGTAACTACCAGC	61.006	57.143	0.00	0.00	0.00	4.85
1475	1575	3.627395	ATTCATGAGCCAACCGAGTAA	57.373	42.857	0.00	0.00	0.00	2.24
1489	1589	7.496346	TTAGCCTACTAATCCCCTATTCATG	57.504	40.000	0.00	0.00	33.35	3.07
1516	1620	6.945218	TGATTTAATGGCCAATTAACTTGCT	58.055	32.000	10.96	0.00	39.84	3.91
1584	1689	6.619801	ATTGGTTGATTAATCCTTACTCGC	57.380	37.500	12.90	0.00	0.00	5.03
1625	1759	5.789643	TTGCCTAGCTTGTTCAAGAATTT	57.210	34.783	15.52	1.90	0.00	1.82
1640	1774	9.167311	ACTCACTGTAAGAAATAAATTGCCTAG	57.833	33.333	0.00	0.00	37.43	3.02
1642	1776	9.167311	CTACTCACTGTAAGAAATAAATTGCCT	57.833	33.333	0.00	0.00	37.43	4.75
1643	1777	8.947115	ACTACTCACTGTAAGAAATAAATTGCC	58.053	33.333	0.00	0.00	37.43	4.52
1658	1792	3.056536	TCGAGGTACGTACTACTCACTGT	60.057	47.826	24.07	0.00	43.13	3.55
1936	2084	4.356436	TCATCTCCCACTTCTCATCTTCA	58.644	43.478	0.00	0.00	0.00	3.02
1955	2109	0.106708	CCGACCCACCGATCAATCAT	59.893	55.000	0.00	0.00	0.00	2.45
2087	2247	4.774881	TAACGGCCGGTGTACGCG	62.775	66.667	29.82	3.53	42.52	6.01
2088	2248	2.882301	CTAACGGCCGGTGTACGC	60.882	66.667	29.82	0.00	42.52	4.42
2102	2262	1.001068	TCGACGATTGGTGGCAACTAA	59.999	47.619	3.27	0.00	37.61	2.24
2168	2328	6.710692	TGCTCGCTATTTGTGTATCATATG	57.289	37.500	0.00	0.00	0.00	1.78
2191	2351	5.509832	AAACTCGGGGTTAAGGAACTAAT	57.490	39.130	0.00	0.00	35.20	1.73
2192	2352	4.980339	AAACTCGGGGTTAAGGAACTAA	57.020	40.909	0.00	0.00	35.20	2.24
2193	2353	4.980339	AAAACTCGGGGTTAAGGAACTA	57.020	40.909	0.00	0.00	35.20	2.24
2194	2354	3.870538	AAAACTCGGGGTTAAGGAACT	57.129	42.857	0.00	0.00	37.48	3.01
2195	2355	5.308014	TCTAAAAACTCGGGGTTAAGGAAC	58.692	41.667	0.00	0.00	37.12	3.62
2196	2356	5.565455	TCTAAAAACTCGGGGTTAAGGAA	57.435	39.130	0.00	0.00	37.12	3.36
2197	2357	5.307716	TCTTCTAAAAACTCGGGGTTAAGGA	59.692	40.000	0.00	0.00	37.12	3.36
2198	2358	5.554070	TCTTCTAAAAACTCGGGGTTAAGG	58.446	41.667	0.00	0.00	37.12	2.69
2199	2359	6.877322	TCATCTTCTAAAAACTCGGGGTTAAG	59.123	38.462	0.00	0.00	37.12	1.85
2200	2360	6.771573	TCATCTTCTAAAAACTCGGGGTTAA	58.228	36.000	0.00	0.00	37.12	2.01
2206	2366	5.415221	AGCTCTCATCTTCTAAAAACTCGG	58.585	41.667	0.00	0.00	0.00	4.63
2207	2367	6.329496	AGAGCTCTCATCTTCTAAAAACTCG	58.671	40.000	11.45	0.00	0.00	4.18
2225	2385	4.329462	CCATCAGGGTTAGTAAGAGCTC	57.671	50.000	5.27	5.27	0.00	4.09
2282	2474	7.229106	GCTTGGTCTAGCTACTACATTAGTACT	59.771	40.741	0.00	0.00	40.14	2.73
2288	2480	4.442192	GCTGCTTGGTCTAGCTACTACATT	60.442	45.833	6.05	0.00	41.76	2.71
2291	2483	2.691011	AGCTGCTTGGTCTAGCTACTAC	59.309	50.000	0.00	0.00	45.30	2.73
2359	2551	6.488769	TTAACTTACCTGACCTCTCAACAA	57.511	37.500	0.00	0.00	0.00	2.83

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.