AutoCloner

Multiple sequence alignment - TraesCS4D01G165200

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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	TraesCS4D01G165200	chr4D	100.000	2810	0	0	1	2810	272996458	272993649	0.000000e+00	5190.0
1	TraesCS4D01G165200	chr4A	92.063	1575	70	26	540	2065	307087768	307089336	0.000000e+00	2165.0
2	TraesCS4D01G165200	chr4A	89.362	423	44	1	100	521	307086766	307087188	5.330000e-147	531.0
3	TraesCS4D01G165200	chr4B	95.048	1151	40	8	924	2058	276360998	276362147	0.000000e+00	1794.0
4	TraesCS4D01G165200	chr4B	92.235	425	31	2	100	523	276359963	276360386	4.010000e-168	601.0
5	TraesCS4D01G165200	chr4B	93.220	413	16	6	534	937	276360570	276360979	5.180000e-167	597.0
6	TraesCS4D01G165200	chr4B	87.850	107	11	2	2	107	580537206	580537101	1.060000e-24	124.0
7	TraesCS4D01G165200	chr4B	97.222	72	2	0	2063	2134	650680781	650680710	3.800000e-24	122.0
8	TraesCS4D01G165200	chr5D	97.794	680	14	1	2132	2810	114362388	114363067	0.000000e+00	1171.0
9	TraesCS4D01G165200	chr5D	90.361	83	8	0	352	434	332515407	332515489	2.960000e-20	110.0
10	TraesCS4D01G165200	chr2A	97.794	680	14	1	2132	2810	649507110	649506431	0.000000e+00	1171.0
11	TraesCS4D01G165200	chr2A	97.500	680	16	1	2132	2810	760300231	760300910	0.000000e+00	1160.0
12	TraesCS4D01G165200	chr3D	97.500	680	16	1	2132	2810	93488206	93487527	0.000000e+00	1160.0
13	TraesCS4D01G165200	chr3D	96.350	685	19	2	2132	2810	548509030	548508346	0.000000e+00	1122.0
14	TraesCS4D01G165200	chr3D	91.919	99	6	2	2	99	249768063	249768160	1.360000e-28	137.0
15	TraesCS4D01G165200	chr3D	95.238	84	2	2	2063	2145	93488326	93488244	6.320000e-27	132.0
16	TraesCS4D01G165200	chr7A	97.353	680	17	1	2132	2810	81792377	81791698	0.000000e+00	1155.0
17	TraesCS4D01G165200	chr7A	95.890	73	3	0	2063	2135	81792497	81792425	4.920000e-23	119.0
18	TraesCS4D01G165200	chr1A	96.912	680	19	2	2132	2810	500968448	500969126	0.000000e+00	1138.0
19	TraesCS4D01G165200	chr3A	96.296	675	25	0	2136	2810	124550494	124549820	0.000000e+00	1109.0
20	TraesCS4D01G165200	chr6A	95.735	680	28	1	2132	2810	224094175	224093496	0.000000e+00	1094.0
21	TraesCS4D01G165200	chr6A	95.890	73	3	0	2063	2135	224094295	224094223	4.920000e-23	119.0
22	TraesCS4D01G165200	chr7D	90.909	99	7	2	2	99	89828852	89828949	6.320000e-27	132.0
23	TraesCS4D01G165200	chr3B	97.403	77	1	1	2059	2135	689161606	689161681	2.270000e-26	130.0
24	TraesCS4D01G165200	chr2B	90.722	97	7	2	2	97	250269071	250268976	8.170000e-26	128.0
25	TraesCS4D01G165200	chr2B	90.000	100	8	2	2	101	665661075	665661172	8.170000e-26	128.0
26	TraesCS4D01G165200	chr2B	89.109	101	9	1	2	100	665658074	665657974	1.060000e-24	124.0
27	TraesCS4D01G165200	chr2B	95.890	73	3	0	2063	2135	143188998	143188926	4.920000e-23	119.0
28	TraesCS4D01G165200	chr5B	89.320	103	8	3	2	101	661838856	661838958	2.940000e-25	126.0
29	TraesCS4D01G165200	chr7B	88.462	104	11	1	2	104	707660458	707660355	1.060000e-24	124.0
30	TraesCS4D01G165200	chr6D	97.222	72	2	0	2064	2135	436077605	436077676	3.800000e-24	122.0
31	TraesCS4D01G165200	chr1D	88.073	109	6	4	2	103	249744438	249744546	3.800000e-24	122.0
32	TraesCS4D01G165200	chr6B	95.946	74	2	1	2063	2135	7170726	7170653	4.920000e-23	119.0
33	TraesCS4D01G165200	chr6B	95.946	74	2	1	2063	2135	7207595	7207522	4.920000e-23	119.0
34	TraesCS4D01G165200	chr5A	85.542	83	12	0	352	434	433564030	433564112	1.390000e-13	87.9

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	TraesCS4D01G165200	chr4D	272993649	272996458	2809	True	5190.000000	5190	100.0000	1	2810	1	chr4D.!!$R1	2809
1	TraesCS4D01G165200	chr4A	307086766	307089336	2570	False	1348.000000	2165	90.7125	100	2065	2	chr4A.!!$F1	1965
2	TraesCS4D01G165200	chr4B	276359963	276362147	2184	False	997.333333	1794	93.5010	100	2058	3	chr4B.!!$F1	1958
3	TraesCS4D01G165200	chr5D	114362388	114363067	679	False	1171.000000	1171	97.7940	2132	2810	1	chr5D.!!$F1	678
4	TraesCS4D01G165200	chr2A	649506431	649507110	679	True	1171.000000	1171	97.7940	2132	2810	1	chr2A.!!$R1	678
5	TraesCS4D01G165200	chr2A	760300231	760300910	679	False	1160.000000	1160	97.5000	2132	2810	1	chr2A.!!$F1	678
6	TraesCS4D01G165200	chr3D	548508346	548509030	684	True	1122.000000	1122	96.3500	2132	2810	1	chr3D.!!$R1	678
7	TraesCS4D01G165200	chr3D	93487527	93488326	799	True	646.000000	1160	96.3690	2063	2810	2	chr3D.!!$R2	747
8	TraesCS4D01G165200	chr7A	81791698	81792497	799	True	637.000000	1155	96.6215	2063	2810	2	chr7A.!!$R1	747
9	TraesCS4D01G165200	chr1A	500968448	500969126	678	False	1138.000000	1138	96.9120	2132	2810	1	chr1A.!!$F1	678
10	TraesCS4D01G165200	chr3A	124549820	124550494	674	True	1109.000000	1109	96.2960	2136	2810	1	chr3A.!!$R1	674
11	TraesCS4D01G165200	chr6A	224093496	224094295	799	True	606.500000	1094	95.8125	2063	2810	2	chr6A.!!$R1	747

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
32	33	0.106149	GACGGGGTCACAGTTCTGTT	59.894	55.0	2.47	0.00	32.09	3.16	F
488	490	0.378610	TTTGTCGTGCGTTGCAATGA	59.621	45.0	22.81	4.86	41.47	2.57	F
1350	1977	0.027455	CAAACAACGACAGCAGCGAA	59.973	50.0	0.00	0.00	0.00	4.70	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1200	1827	0.247537	CATCGTCGTCGTCGTCATCA	60.248	55.0	11.41	38.33	3.07	R
1740	2385	0.596600	CGACGTACTTGTGCTGTGGT	60.597	55.0	0.00	0.00	4.16	R
2645	3347	2.060326	TCCGTAGAAAAGTGACGCAG	57.940	50.0	0.00	35.28	5.18	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
27	28	4.309950	GCCGACGGGGTCACAGTT	62.310	66.667	17.22	0.00	38.44	3.16
28	29	2.048503	CCGACGGGGTCACAGTTC	60.049	66.667	5.81	0.00	32.09	3.01
29	30	2.571216	CCGACGGGGTCACAGTTCT	61.571	63.158	5.81	0.00	32.09	3.01
30	31	1.372997	CGACGGGGTCACAGTTCTG	60.373	63.158	0.00	0.00	32.09	3.02
31	32	1.746517	GACGGGGTCACAGTTCTGT	59.253	57.895	0.00	0.00	32.09	3.41
32	33	0.106149	GACGGGGTCACAGTTCTGTT	59.894	55.000	2.47	0.00	32.09	3.16
33	34	0.544697	ACGGGGTCACAGTTCTGTTT	59.455	50.000	2.47	0.00	0.00	2.83
34	35	1.064979	ACGGGGTCACAGTTCTGTTTT	60.065	47.619	2.47	0.00	0.00	2.43
35	36	2.021457	CGGGGTCACAGTTCTGTTTTT	58.979	47.619	2.47	0.00	0.00	1.94
58	59	6.987403	TTTTTCCTTTGGGTGCTATAGTTT	57.013	33.333	0.84	0.00	0.00	2.66
59	60	6.584185	TTTTCCTTTGGGTGCTATAGTTTC	57.416	37.500	0.84	0.00	0.00	2.78
60	61	4.230745	TCCTTTGGGTGCTATAGTTTCC	57.769	45.455	0.84	2.01	0.00	3.13
61	62	2.943033	CCTTTGGGTGCTATAGTTTCCG	59.057	50.000	0.84	0.00	0.00	4.30
62	63	3.370103	CCTTTGGGTGCTATAGTTTCCGA	60.370	47.826	0.84	0.00	0.00	4.55
63	64	3.985019	TTGGGTGCTATAGTTTCCGAA	57.015	42.857	0.84	3.10	0.00	4.30
64	65	4.497291	TTGGGTGCTATAGTTTCCGAAT	57.503	40.909	0.84	0.00	0.00	3.34
65	66	4.497291	TGGGTGCTATAGTTTCCGAATT	57.503	40.909	0.84	0.00	0.00	2.17
66	67	4.850680	TGGGTGCTATAGTTTCCGAATTT	58.149	39.130	0.84	0.00	0.00	1.82
67	68	4.638421	TGGGTGCTATAGTTTCCGAATTTG	59.362	41.667	0.84	0.00	0.00	2.32
68	69	4.497507	GGGTGCTATAGTTTCCGAATTTGC	60.498	45.833	0.84	0.00	0.00	3.68
69	70	4.335594	GGTGCTATAGTTTCCGAATTTGCT	59.664	41.667	0.84	0.00	0.00	3.91
70	71	5.526111	GGTGCTATAGTTTCCGAATTTGCTA	59.474	40.000	0.84	0.00	0.00	3.49
71	72	6.204882	GGTGCTATAGTTTCCGAATTTGCTAT	59.795	38.462	0.84	0.00	0.00	2.97
72	73	7.386848	GGTGCTATAGTTTCCGAATTTGCTATA	59.613	37.037	0.84	0.00	0.00	1.31
73	74	8.770828	GTGCTATAGTTTCCGAATTTGCTATAA	58.229	33.333	0.84	0.00	0.00	0.98
74	75	9.332502	TGCTATAGTTTCCGAATTTGCTATAAA	57.667	29.630	0.84	0.00	0.00	1.40
78	79	7.790861	AGTTTCCGAATTTGCTATAAAAACG	57.209	32.000	0.00	0.00	31.29	3.60
79	80	7.364970	AGTTTCCGAATTTGCTATAAAAACGT	58.635	30.769	0.00	0.00	31.29	3.99
80	81	7.325097	AGTTTCCGAATTTGCTATAAAAACGTG	59.675	33.333	0.00	0.00	31.29	4.49
81	82	6.483385	TCCGAATTTGCTATAAAAACGTGA	57.517	33.333	0.00	0.00	0.00	4.35
82	83	7.079182	TCCGAATTTGCTATAAAAACGTGAT	57.921	32.000	0.00	0.00	0.00	3.06
83	84	8.199176	TCCGAATTTGCTATAAAAACGTGATA	57.801	30.769	0.00	0.00	0.00	2.15
84	85	8.332464	TCCGAATTTGCTATAAAAACGTGATAG	58.668	33.333	0.00	0.00	0.00	2.08
85	86	8.120465	CCGAATTTGCTATAAAAACGTGATAGT	58.880	33.333	0.00	0.00	0.00	2.12
86	87	9.485591	CGAATTTGCTATAAAAACGTGATAGTT	57.514	29.630	0.00	0.00	35.59	2.24
159	160	0.740737	CATTCGGGGCAGTGAAATCC	59.259	55.000	0.00	0.00	0.00	3.01
170	171	2.057922	AGTGAAATCCAGTGTCAGGGT	58.942	47.619	0.00	0.00	0.00	4.34
270	272	1.496060	AGACATCCGGGCTGTCATTA	58.504	50.000	27.38	0.00	44.37	1.90
333	335	1.203928	GTCGATGACTCATTCTGGCG	58.796	55.000	0.00	0.00	0.00	5.69
339	341	1.078848	ACTCATTCTGGCGAGTGGC	60.079	57.895	0.00	0.00	40.92	5.01
488	490	0.378610	TTTGTCGTGCGTTGCAATGA	59.621	45.000	22.81	4.86	41.47	2.57
524	526	2.803956	AGTAGATTGACCGGTGACTGA	58.196	47.619	14.63	0.00	0.00	3.41
525	527	3.366396	AGTAGATTGACCGGTGACTGAT	58.634	45.455	14.63	0.00	0.00	2.90
526	528	3.769844	AGTAGATTGACCGGTGACTGATT	59.230	43.478	14.63	0.00	0.00	2.57
528	530	3.338249	AGATTGACCGGTGACTGATTTG	58.662	45.455	14.63	0.00	0.00	2.32
529	531	2.920724	TTGACCGGTGACTGATTTGA	57.079	45.000	14.63	0.00	0.00	2.69
530	532	2.163818	TGACCGGTGACTGATTTGAC	57.836	50.000	14.63	0.00	0.00	3.18
531	533	1.414550	TGACCGGTGACTGATTTGACA	59.585	47.619	14.63	0.00	0.00	3.58
532	534	2.158885	TGACCGGTGACTGATTTGACAA	60.159	45.455	14.63	0.00	0.00	3.18
538	1102	5.123820	CCGGTGACTGATTTGACAATTGTAT	59.876	40.000	11.95	0.98	0.00	2.29
625	1192	3.564225	AGCGGGTAAAAGAAGAAACACAG	59.436	43.478	0.00	0.00	0.00	3.66
655	1228	6.138761	CACAGCTTAAGAAGTGCAAACTAAG	58.861	40.000	6.67	0.00	0.00	2.18
690	1263	3.181530	CGCGGACTTGTGTAAAGATTGAG	60.182	47.826	0.00	0.00	0.00	3.02
896	1471	3.155167	CACTCCCTACCCGGCCTC	61.155	72.222	0.00	0.00	0.00	4.70
921	1499	6.309389	ACCCCAACTACTTAATAACCTCTG	57.691	41.667	0.00	0.00	0.00	3.35
943	1553	3.855689	AATGCACATTACTGACTTGGC	57.144	42.857	0.00	0.00	0.00	4.52
1194	1818	2.430382	ATCACCACCACCACGACGAC	62.430	60.000	0.00	0.00	0.00	4.34
1200	1827	1.138883	CCACCACGACGACGATGAT	59.861	57.895	15.32	0.00	42.66	2.45
1203	1830	0.738975	ACCACGACGACGATGATGAT	59.261	50.000	15.32	0.00	42.66	2.45
1349	1976	1.641140	CAAACAACGACAGCAGCGA	59.359	52.632	0.00	0.00	0.00	4.93
1350	1977	0.027455	CAAACAACGACAGCAGCGAA	59.973	50.000	0.00	0.00	0.00	4.70
1479	2118	2.494918	GACGGTGATGAGGACCCG	59.505	66.667	0.00	0.00	45.72	5.28
1527	2166	1.072806	CCCGACCATGATGATGACCAT	59.927	52.381	0.00	0.00	38.43	3.55
1537	2176	2.557555	TGATGACCATGAGGAGGACT	57.442	50.000	0.00	0.00	38.69	3.85
1568	2207	1.069378	GACGACCATGACGACGAACC	61.069	60.000	16.44	0.00	34.70	3.62
1647	2292	2.651361	CACCACGACGAGGAGCTT	59.349	61.111	18.62	0.00	0.00	3.74
1740	2385	2.356553	CCGCCGTTCCTCGTGAAA	60.357	61.111	0.00	0.00	37.94	2.69
1953	2598	6.057321	TGGATCGGGTGTAATTTTTCTACT	57.943	37.500	0.00	0.00	0.00	2.57
1954	2599	7.185318	TGGATCGGGTGTAATTTTTCTACTA	57.815	36.000	0.00	0.00	0.00	1.82
2054	2699	9.007901	TGACAAGGAGTTTACTAGTAGTAAGTC	57.992	37.037	19.48	19.53	41.23	3.01
2055	2700	9.230122	GACAAGGAGTTTACTAGTAGTAAGTCT	57.770	37.037	19.48	19.85	41.23	3.24
2153	2849	9.535878	GAGCTTACAGTAACTAAAATGAGCTAT	57.464	33.333	0.00	0.00	36.93	2.97
2328	3024	2.304761	TGATTCAGCTTCTACCCGGTTT	59.695	45.455	0.00	0.00	0.00	3.27
2398	3094	3.088532	TCTGTTGTTATTGCATCCACCC	58.911	45.455	0.00	0.00	0.00	4.61
2645	3347	4.190370	AGGGGGAGGAATTGATTCATTC	57.810	45.455	6.11	0.00	38.53	2.67

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
10	11	4.309950	AACTGTGACCCCGTCGGC	62.310	66.667	5.50	0.00	34.95	5.54
11	12	2.048503	GAACTGTGACCCCGTCGG	60.049	66.667	3.60	3.60	34.95	4.79
12	13	1.372997	CAGAACTGTGACCCCGTCG	60.373	63.158	0.00	0.00	34.95	5.12
13	14	0.106149	AACAGAACTGTGACCCCGTC	59.894	55.000	8.25	0.00	44.13	4.79
14	15	0.544697	AAACAGAACTGTGACCCCGT	59.455	50.000	8.25	0.00	44.13	5.28
15	16	1.675552	AAAACAGAACTGTGACCCCG	58.324	50.000	8.25	0.00	44.13	5.73
35	36	6.014925	GGAAACTATAGCACCCAAAGGAAAAA	60.015	38.462	0.00	0.00	36.73	1.94
36	37	5.479027	GGAAACTATAGCACCCAAAGGAAAA	59.521	40.000	0.00	0.00	36.73	2.29
37	38	5.014202	GGAAACTATAGCACCCAAAGGAAA	58.986	41.667	0.00	0.00	36.73	3.13
38	39	4.595986	GGAAACTATAGCACCCAAAGGAA	58.404	43.478	0.00	0.00	36.73	3.36
39	40	3.370103	CGGAAACTATAGCACCCAAAGGA	60.370	47.826	0.00	0.00	36.73	3.36
40	41	2.943033	CGGAAACTATAGCACCCAAAGG	59.057	50.000	0.00	0.00	40.04	3.11
41	42	3.869065	TCGGAAACTATAGCACCCAAAG	58.131	45.455	0.00	0.00	0.00	2.77
42	43	3.985019	TCGGAAACTATAGCACCCAAA	57.015	42.857	0.00	0.00	0.00	3.28
43	44	3.985019	TTCGGAAACTATAGCACCCAA	57.015	42.857	0.00	0.00	0.00	4.12
44	45	4.497291	AATTCGGAAACTATAGCACCCA	57.503	40.909	0.00	0.00	0.00	4.51
45	46	4.497507	GCAAATTCGGAAACTATAGCACCC	60.498	45.833	0.00	0.00	0.00	4.61
46	47	4.335594	AGCAAATTCGGAAACTATAGCACC	59.664	41.667	0.00	0.23	0.00	5.01
47	48	5.485662	AGCAAATTCGGAAACTATAGCAC	57.514	39.130	0.00	0.00	0.00	4.40
48	49	8.896320	TTATAGCAAATTCGGAAACTATAGCA	57.104	30.769	0.00	0.00	0.00	3.49
52	53	9.498307	CGTTTTTATAGCAAATTCGGAAACTAT	57.502	29.630	0.00	3.39	0.00	2.12
53	54	8.505625	ACGTTTTTATAGCAAATTCGGAAACTA	58.494	29.630	0.00	0.00	0.00	2.24
54	55	7.325097	CACGTTTTTATAGCAAATTCGGAAACT	59.675	33.333	0.00	0.00	0.00	2.66
55	56	7.324135	TCACGTTTTTATAGCAAATTCGGAAAC	59.676	33.333	0.00	0.00	0.00	2.78
56	57	7.361127	TCACGTTTTTATAGCAAATTCGGAAA	58.639	30.769	0.00	0.00	0.00	3.13
57	58	6.900189	TCACGTTTTTATAGCAAATTCGGAA	58.100	32.000	0.00	0.00	0.00	4.30
58	59	6.483385	TCACGTTTTTATAGCAAATTCGGA	57.517	33.333	0.00	0.00	0.00	4.55
59	60	8.120465	ACTATCACGTTTTTATAGCAAATTCGG	58.880	33.333	0.00	0.00	0.00	4.30
60	61	9.485591	AACTATCACGTTTTTATAGCAAATTCG	57.514	29.630	0.00	0.00	0.00	3.34
159	160	3.313012	TGATACGAAACCCTGACACTG	57.687	47.619	0.00	0.00	0.00	3.66
165	166	7.843490	TCTCTTAAATTGATACGAAACCCTG	57.157	36.000	0.00	0.00	0.00	4.45
170	171	9.361315	TCGTTGATCTCTTAAATTGATACGAAA	57.639	29.630	0.00	0.00	32.13	3.46
270	272	1.053264	AGAGCCGGCCTGATCTTGAT	61.053	55.000	26.15	0.00	0.00	2.57
333	335	1.742768	CCCACTAGATCCGCCACTC	59.257	63.158	0.00	0.00	0.00	3.51
339	341	2.808206	GGGTGCCCCACTAGATCCG	61.808	68.421	0.00	0.00	44.65	4.18
473	475	1.501292	CCATCATTGCAACGCACGA	59.499	52.632	0.00	0.00	38.71	4.35
505	507	3.802948	ATCAGTCACCGGTCAATCTAC	57.197	47.619	2.59	0.00	0.00	2.59
516	518	8.299570	AGAAATACAATTGTCAAATCAGTCACC	58.700	33.333	15.85	0.00	0.00	4.02
570	1134	9.339850	ACGACAGAATGATAAGTACATACTACT	57.660	33.333	0.00	0.00	39.69	2.57
571	1135	9.947669	AACGACAGAATGATAAGTACATACTAC	57.052	33.333	0.00	0.00	39.69	2.73
601	1165	2.292292	TGTTTCTTCTTTTACCCGCTGC	59.708	45.455	0.00	0.00	0.00	5.25
625	1192	4.272504	TGCACTTCTTAAGCTGTGTTACAC	59.727	41.667	20.66	8.76	33.44	2.90
655	1228	4.201783	ACAAGTCCGCGTAATTTAGAATGC	60.202	41.667	4.92	0.00	0.00	3.56
732	1305	1.619654	CATTGTTGGTGAGAGGCCAA	58.380	50.000	5.01	0.00	43.04	4.52
896	1471	5.128335	AGAGGTTATTAAGTAGTTGGGGTCG	59.872	44.000	0.00	0.00	0.00	4.79
943	1553	4.750098	CCGGCCACTTATAAAGATGTGTAG	59.250	45.833	2.24	0.00	0.00	2.74
1029	1653	3.164269	AGGAGTATGGCGGCCAGG	61.164	66.667	27.62	0.00	36.75	4.45
1039	1663	3.211000	AGGGAAGGGATGAAGAGGAGTAT	59.789	47.826	0.00	0.00	0.00	2.12
1041	1665	1.367848	AGGGAAGGGATGAAGAGGAGT	59.632	52.381	0.00	0.00	0.00	3.85
1194	1818	1.037998	CGTCGTCGTCATCATCATCG	58.962	55.000	0.00	0.00	0.00	3.84
1200	1827	0.247537	CATCGTCGTCGTCGTCATCA	60.248	55.000	11.41	0.00	38.33	3.07
1203	1830	1.131218	GTCATCGTCGTCGTCGTCA	59.869	57.895	11.41	0.00	38.33	4.35
1349	1976	2.477189	CCGTTTCTTGCAACGTGAACTT	60.477	45.455	7.78	0.00	46.64	2.66
1350	1977	1.063469	CCGTTTCTTGCAACGTGAACT	59.937	47.619	7.78	0.00	46.64	3.01
1479	2118	1.445582	GTGGTCGTCGTCATGGTCC	60.446	63.158	0.00	0.00	0.00	4.46
1537	2176	3.716006	GTCGTCGTCGTGGTCGGA	61.716	66.667	1.33	0.00	38.33	4.55
1568	2207	1.457738	GTCGTCGTCATCGTCATCAG	58.542	55.000	0.00	0.00	38.33	2.90
1740	2385	0.596600	CGACGTACTTGTGCTGTGGT	60.597	55.000	0.00	0.00	0.00	4.16
1879	2524	4.051922	ACGTAGACTGAAGAGCAAAACAG	58.948	43.478	0.00	0.00	36.58	3.16
1953	2598	8.665643	TCGAAAAACTTTGAGGACAATACTTA	57.334	30.769	0.00	0.00	35.85	2.24
1954	2599	7.562454	TCGAAAAACTTTGAGGACAATACTT	57.438	32.000	0.00	0.00	35.85	2.24
2029	2674	9.230122	AGACTTACTACTAGTAAACTCCTTGTC	57.770	37.037	3.76	10.42	39.89	3.18
2111	2756	9.911857	ACTGTAAGCTCGTAGACGATGTAAACG	62.912	44.444	5.05	0.00	42.54	3.60
2328	3024	3.586470	TTTGCTAACTCCTTTGGGTGA	57.414	42.857	0.00	0.00	0.00	4.02
2398	3094	5.410067	CCAATGCAAGTTTATACCTGTTGG	58.590	41.667	0.00	0.00	39.83	3.77
2645	3347	2.060326	TCCGTAGAAAAGTGACGCAG	57.940	50.000	0.00	0.00	35.28	5.18

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.