AutoCloner

Multiple sequence alignment - TraesCS3D01G047800

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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	TraesCS3D01G047800	chr3D	100.000	3314	0	0	1	3314	17779523	17776210	0.000000e+00	6120.0
1	TraesCS3D01G047800	chr3D	85.722	1961	224	26	438	2353	17748520	17746571	0.000000e+00	2019.0
2	TraesCS3D01G047800	chr3D	83.204	387	36	16	1	384	17749623	17749263	8.870000e-86	327.0
3	TraesCS3D01G047800	chr3A	94.197	2671	114	19	228	2872	18838080	18835425	0.000000e+00	4036.0
4	TraesCS3D01G047800	chr3A	84.469	1938	242	31	443	2337	18831594	18829673	0.000000e+00	1857.0
5	TraesCS3D01G047800	chr3A	88.729	417	36	1	2909	3314	18835094	18834678	1.780000e-137	499.0
6	TraesCS3D01G047800	chr3A	92.661	218	11	3	3	215	18838281	18838064	3.210000e-80	309.0
7	TraesCS3D01G047800	chr3A	81.395	387	39	16	1	384	18832695	18832339	5.410000e-73	285.0
8	TraesCS3D01G047800	chr3A	80.000	100	17	3	3149	3247	574450374	574450277	1.650000e-08	71.3
9	TraesCS3D01G047800	chr3A	97.222	36	1	0	382	417	18837867	18837832	9.930000e-06	62.1
10	TraesCS3D01G047800	chrUn	92.795	1374	94	4	1059	2431	37181801	37180432	0.000000e+00	1984.0
11	TraesCS3D01G047800	chrUn	88.570	1636	159	20	731	2357	37504139	37505755	0.000000e+00	1960.0
12	TraesCS3D01G047800	chrUn	85.354	1427	162	13	438	1824	37705839	37704420	0.000000e+00	1434.0
13	TraesCS3D01G047800	chrUn	92.555	497	34	2	969	1462	37869673	37870169	0.000000e+00	710.0
14	TraesCS3D01G047800	chrUn	92.555	497	34	2	969	1462	333562661	333563157	0.000000e+00	710.0
15	TraesCS3D01G047800	chrUn	85.827	635	50	16	461	1062	37795660	37796287	3.610000e-179	638.0
16	TraesCS3D01G047800	chrUn	90.535	486	38	3	2431	2908	37177730	37177245	1.300000e-178	636.0
17	TraesCS3D01G047800	chrUn	89.583	384	29	7	2213	2587	37160260	37160641	8.320000e-131	477.0
18	TraesCS3D01G047800	chrUn	93.851	309	15	2	2449	2753	37870168	37870476	2.330000e-126	462.0
19	TraesCS3D01G047800	chrUn	93.851	309	15	2	2449	2753	333563156	333563464	2.330000e-126	462.0
20	TraesCS3D01G047800	chrUn	86.811	417	26	6	2909	3314	37709472	37709074	3.930000e-119	438.0
21	TraesCS3D01G047800	chrUn	85.849	424	38	9	2909	3314	37161302	37161721	6.570000e-117	431.0
22	TraesCS3D01G047800	chrUn	84.071	452	62	8	1905	2353	37704355	37703911	8.500000e-116	427.0
23	TraesCS3D01G047800	chrUn	92.883	281	20	0	2574	2854	37160945	37161225	3.080000e-110	409.0
24	TraesCS3D01G047800	chrUn	80.597	402	72	5	1925	2321	10148958	10149358	4.150000e-79	305.0
25	TraesCS3D01G047800	chrUn	80.320	437	42	22	3	423	37503218	37503626	1.160000e-74	291.0
26	TraesCS3D01G047800	chrUn	81.654	387	30	19	4	378	37706933	37706576	1.950000e-72	283.0
27	TraesCS3D01G047800	chrUn	81.437	334	53	8	625	954	37869233	37869561	7.050000e-67	265.0
28	TraesCS3D01G047800	chrUn	81.437	334	53	8	625	954	333562221	333562549	7.050000e-67	265.0
29	TraesCS3D01G047800	chrUn	84.127	252	31	8	2909	3156	37177145	37176899	5.530000e-58	235.0
30	TraesCS3D01G047800	chrUn	85.778	225	15	6	1	215	37707365	37707148	4.300000e-54	222.0
31	TraesCS3D01G047800	chrUn	94.444	54	3	0	574	627	37503980	37504033	2.120000e-12	84.2
32	TraesCS3D01G047800	chrUn	85.185	81	11	1	2571	2651	37703700	37703621	7.620000e-12	82.4
33	TraesCS3D01G047800	chr4B	80.153	786	151	3	1017	1801	577016189	577015408	1.710000e-162	582.0
34	TraesCS3D01G047800	chr4B	82.687	335	54	4	1983	2315	644366705	644366373	8.990000e-76	294.0
35	TraesCS3D01G047800	chr4B	74.138	174	32	8	3153	3314	571904264	571904092	3.570000e-05	60.2
36	TraesCS3D01G047800	chr4D	79.135	786	155	6	1017	1801	461562125	461561348	4.870000e-148	534.0
37	TraesCS3D01G047800	chr4D	80.597	402	72	5	1925	2321	500529094	500529494	4.150000e-79	305.0
38	TraesCS3D01G047800	chr4D	75.287	348	63	15	2988	3314	76612428	76612773	9.580000e-31	145.0
39	TraesCS3D01G047800	chr2D	76.653	968	178	32	856	1801	639460068	639461009	2.970000e-135	492.0
40	TraesCS3D01G047800	chr5A	83.537	164	26	1	2988	3150	687161516	687161679	5.730000e-33	152.0
41	TraesCS3D01G047800	chr6D	81.098	164	27	4	2995	3155	29379044	29379206	9.650000e-26	128.0
42	TraesCS3D01G047800	chr1B	79.762	168	33	1	2988	3154	372143034	372143201	1.620000e-23	121.0
43	TraesCS3D01G047800	chr7D	83.465	127	21	0	3030	3156	530338106	530338232	5.810000e-23	119.0
44	TraesCS3D01G047800	chr7D	74.910	279	49	12	2988	3248	37872494	37872769	1.260000e-19	108.0
45	TraesCS3D01G047800	chr7D	77.863	131	19	4	3194	3314	578623900	578624030	4.590000e-09	73.1
46	TraesCS3D01G047800	chr7D	85.938	64	9	0	3251	3314	330422634	330422697	5.930000e-08	69.4
47	TraesCS3D01G047800	chr5B	76.774	155	26	5	3170	3314	711989385	711989231	9.860000e-11	78.7
48	TraesCS3D01G047800	chr4A	87.879	66	6	2	3250	3314	681831181	681831245	3.550000e-10	76.8

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	TraesCS3D01G047800	chr3D	17776210	17779523	3313	True	6120.000000	6120	100.000000	1	3314	1	chr3D.!!$R1	3313
1	TraesCS3D01G047800	chr3D	17746571	17749623	3052	True	1173.000000	2019	84.463000	1	2353	2	chr3D.!!$R2	2352
2	TraesCS3D01G047800	chr3A	18829673	18838281	8608	True	1174.683333	4036	89.778833	1	3314	6	chr3A.!!$R2	3313
3	TraesCS3D01G047800	chrUn	37176899	37181801	4902	True	951.666667	1984	89.152333	1059	3156	3	chrUn.!!$R1	2097
4	TraesCS3D01G047800	chrUn	37503218	37505755	2537	False	778.400000	1960	87.778000	3	2357	3	chrUn.!!$F4	2354
5	TraesCS3D01G047800	chrUn	37795660	37796287	627	False	638.000000	638	85.827000	461	1062	1	chrUn.!!$F2	601
6	TraesCS3D01G047800	chrUn	37703621	37709472	5851	True	481.066667	1434	84.808833	1	3314	6	chrUn.!!$R2	3313
7	TraesCS3D01G047800	chrUn	37869233	37870476	1243	False	479.000000	710	89.281000	625	2753	3	chrUn.!!$F5	2128
8	TraesCS3D01G047800	chrUn	333562221	333563464	1243	False	479.000000	710	89.281000	625	2753	3	chrUn.!!$F6	2128
9	TraesCS3D01G047800	chrUn	37160260	37161721	1461	False	439.000000	477	89.438333	2213	3314	3	chrUn.!!$F3	1101
10	TraesCS3D01G047800	chr4B	577015408	577016189	781	True	582.000000	582	80.153000	1017	1801	1	chr4B.!!$R2	784
11	TraesCS3D01G047800	chr4D	461561348	461562125	777	True	534.000000	534	79.135000	1017	1801	1	chr4D.!!$R1	784
12	TraesCS3D01G047800	chr2D	639460068	639461009	941	False	492.000000	492	76.653000	856	1801	1	chr2D.!!$F1	945

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
772	4343	0.109781	GTGCGTAACAAGCCATGTGG	60.11	55.0	0.0	0.0	42.99	4.17	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2491	15231	0.676736	GCCCCAAACGTTTCATCCAA	59.323	50.0	11.37	0.0	0.0	3.53	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
160	2706	2.823829	GCTATTTGCAGGTCGCCGG	61.824	63.158	0.00	0.00	41.33	6.13
201	2750	1.532868	GCGCTGTGTGATGTCTCTTTT	59.467	47.619	0.00	0.00	0.00	2.27
215	2764	6.371809	TGTCTCTTTTTCGTGCATAACTTT	57.628	33.333	0.00	0.00	0.00	2.66
216	2765	6.791303	TGTCTCTTTTTCGTGCATAACTTTT	58.209	32.000	0.00	0.00	0.00	2.27
236	2785	3.482722	TTTTAACGGTGTTTTCGTGCA	57.517	38.095	0.00	0.00	40.96	4.57
237	2786	3.694535	TTTAACGGTGTTTTCGTGCAT	57.305	38.095	0.00	0.00	40.96	3.96
318	2869	6.473455	GGCTTGGATTCATAACGAAAAATCTG	59.527	38.462	0.00	0.00	37.12	2.90
329	2880	3.963724	ACGAAAAATCTGTAAACGCGTTG	59.036	39.130	27.34	13.19	0.00	4.10
366	2926	8.448008	AGAGCTAATCCTATCCTATATCCTCTG	58.552	40.741	0.00	0.00	0.00	3.35
407	2967	5.068234	AGTTGATCCATTTTGAGCACATG	57.932	39.130	0.00	0.00	28.88	3.21
411	2971	3.306917	TCCATTTTGAGCACATGCAAG	57.693	42.857	6.64	0.00	45.16	4.01
434	3700	5.247110	AGCCCTCACGTCAAATATCATCTAT	59.753	40.000	0.00	0.00	0.00	1.98
459	3725	7.962995	TGGAGATGTTCTAAGTAGTTGATCT	57.037	36.000	0.00	0.00	0.00	2.75
473	3739	8.798859	AGTAGTTGATCTATTTTGAGCACATT	57.201	30.769	0.00	0.00	31.72	2.71
474	3740	9.236006	AGTAGTTGATCTATTTTGAGCACATTT	57.764	29.630	0.00	0.00	31.72	2.32
525	3792	8.461222	TGCAATCATTTACATTCCACTTTCTAG	58.539	33.333	0.00	0.00	0.00	2.43
549	4077	0.736053	TGCAAACCTCCACGTCAAAC	59.264	50.000	0.00	0.00	0.00	2.93
681	4252	5.979993	TGTCCGTTAAGTAATTATCTGGCA	58.020	37.500	0.00	0.00	0.00	4.92
705	4276	7.047891	CAGTATAGTGCAAAGGAATCTTGGTA	58.952	38.462	0.00	0.00	32.75	3.25
714	4285	6.205658	GCAAAGGAATCTTGGTAGTATCATCC	59.794	42.308	0.00	0.00	32.75	3.51
734	4305	1.535462	CGTCCATCAACAAACAGACCC	59.465	52.381	0.00	0.00	0.00	4.46
739	4310	2.203437	AACAAACAGACCCGCCCC	60.203	61.111	0.00	0.00	0.00	5.80
746	4317	4.332543	AGACCCGCCCCTCTCCAA	62.333	66.667	0.00	0.00	0.00	3.53
772	4343	0.109781	GTGCGTAACAAGCCATGTGG	60.110	55.000	0.00	0.00	42.99	4.17
801	10678	1.109323	GCCCTGTCCTGCAACAAACT	61.109	55.000	0.00	0.00	0.00	2.66
943	10826	6.407525	GGATGCTATATAAACCCTCCTAGCTG	60.408	46.154	0.00	0.00	34.21	4.24
991	10977	1.761784	ACCAGCCTCATAGCAAGAGAG	59.238	52.381	2.12	0.00	35.09	3.20
1022	11010	0.250513	GCTGACAAGTCTTCCCCGAT	59.749	55.000	1.53	0.00	0.00	4.18
1062	11050	0.462581	CTGAGCTAATCCAGGCGCAA	60.463	55.000	10.83	0.00	37.75	4.85
1182	11176	2.260434	GCGTCGTTGCCTGACCTA	59.740	61.111	0.00	0.00	32.68	3.08
1238	11232	1.471829	TTCCTCAGCCGTCTCTTGCA	61.472	55.000	0.00	0.00	0.00	4.08
1279	11273	0.744414	GCTGGCATCAAACGAGGCTA	60.744	55.000	0.00	0.00	40.06	3.93
1449	11444	3.499737	GCTCAACCCGTGCCATCG	61.500	66.667	0.00	0.00	0.00	3.84
1784	11779	0.842030	TCCATCCCACCTGCTCAAGT	60.842	55.000	0.00	0.00	0.00	3.16
1864	11867	5.446473	GCATTCTGTACCGCATAGATATTGC	60.446	44.000	0.00	0.00	36.74	3.56
1865	11868	4.864704	TCTGTACCGCATAGATATTGCA	57.135	40.909	0.00	0.00	40.14	4.08
1867	11870	5.606505	TCTGTACCGCATAGATATTGCAAA	58.393	37.500	1.71	0.00	40.14	3.68
1888	11891	0.109458	TTGCGTCACTAGTAGGCACG	60.109	55.000	15.36	15.36	37.45	5.34
2008	12013	9.069078	CATTGCTTGACTGTAAAGATATTTGTG	57.931	33.333	9.15	0.00	0.00	3.33
2046	12051	0.681564	ACTTCTGGAGCGACGAGGAT	60.682	55.000	0.00	0.00	0.00	3.24
2149	12154	1.996798	TGACTCTTCTTCAGGACCGT	58.003	50.000	0.00	0.00	0.00	4.83
2151	12156	3.493334	TGACTCTTCTTCAGGACCGTTA	58.507	45.455	0.00	0.00	0.00	3.18
2325	12330	4.026804	GTCTATCCATAAGTTCGTGTTGCG	60.027	45.833	0.00	0.00	43.01	4.85
2337	12342	1.069296	CGTGTTGCGAATGGTGTGATT	60.069	47.619	0.00	0.00	44.77	2.57
2348	12353	4.842531	ATGGTGTGATTGTGACCATCTA	57.157	40.909	0.00	0.00	45.56	1.98
2357	12369	9.764363	TGTGATTGTGACCATCTAGTATAAATC	57.236	33.333	0.00	0.00	0.00	2.17
2367	12379	5.362556	TCTAGTATAAATCGGCGTGGTAC	57.637	43.478	6.85	4.84	0.00	3.34
2417	12455	4.982916	GTGGTGCGTTACTATCTAATGGAG	59.017	45.833	0.00	0.00	0.00	3.86
2420	12458	6.041637	TGGTGCGTTACTATCTAATGGAGAAT	59.958	38.462	0.00	0.00	37.85	2.40
2467	15207	5.977489	AAAACTTTAAGGGCTACCACATC	57.023	39.130	0.00	0.00	40.13	3.06
2491	15231	3.507233	CACATGTGGTAAGCAATCCAAGT	59.493	43.478	18.51	0.00	35.38	3.16
2493	15233	4.022068	ACATGTGGTAAGCAATCCAAGTTG	60.022	41.667	0.00	0.00	35.38	3.16
2655	15718	9.271921	ACATGAGGAGATATTATGCTTACCATA	57.728	33.333	0.00	0.00	35.34	2.74
2779	15842	3.966215	TGCGTTGGTAGCAGCTTC	58.034	55.556	0.00	0.00	40.01	3.86
2876	15939	9.112725	TCATTCGAGATGTTTGATATTTCATGT	57.887	29.630	0.00	0.00	0.00	3.21
2894	15957	6.134535	TCATGTTTACCTTGTAACAGGGAT	57.865	37.500	2.49	0.00	38.42	3.85
2898	15961	1.296002	ACCTTGTAACAGGGATCCCC	58.704	55.000	28.11	12.16	45.90	4.81
2978	16142	4.822026	AGAACATGTGGTAGTCTAGCAAC	58.178	43.478	13.21	8.55	37.99	4.17
2979	16143	4.528596	AGAACATGTGGTAGTCTAGCAACT	59.471	41.667	13.21	1.56	37.99	3.16
2990	16154	9.251440	TGGTAGTCTAGCAACTAATAGAAAAGA	57.749	33.333	9.32	0.00	33.68	2.52
3027	16192	1.573108	CCCTCCCAAGCTAGAGTTGA	58.427	55.000	6.80	0.00	0.00	3.18
3028	16193	1.484240	CCCTCCCAAGCTAGAGTTGAG	59.516	57.143	6.80	0.00	0.00	3.02
3032	16197	4.263068	CCTCCCAAGCTAGAGTTGAGAAAA	60.263	45.833	6.80	0.00	0.00	2.29
3045	16210	6.037610	AGAGTTGAGAAAACTTGTTGTAGCAG	59.962	38.462	0.00	0.00	0.00	4.24
3057	16222	3.627395	TTGTAGCAGACAATCGGGAAT	57.373	42.857	0.38	0.00	43.30	3.01
3061	16226	0.028110	GCAGACAATCGGGAATTCGC	59.972	55.000	12.30	12.30	0.00	4.70
3098	16264	2.991250	AGGACTAGCGCATCAAAACAT	58.009	42.857	11.47	0.00	0.00	2.71
3107	16273	1.616620	CATCAAAACATCAACCGCCG	58.383	50.000	0.00	0.00	0.00	6.46
3150	16316	3.519510	TCGGAAGGATCCAACTTGAAGAT	59.480	43.478	15.82	0.00	46.97	2.40
3165	16331	4.203950	TGAAGATACACGCAAACACAAC	57.796	40.909	0.00	0.00	0.00	3.32
3198	16364	4.564782	TCATGAGAGTTTCATTGGAGCT	57.435	40.909	0.00	0.00	44.14	4.09
3217	16383	2.725127	TACACCTCCACACGCCCTCT	62.725	60.000	0.00	0.00	0.00	3.69
3220	16386	2.362369	CCTCCACACGCCCTCTGAT	61.362	63.158	0.00	0.00	0.00	2.90
3222	16388	1.607801	CTCCACACGCCCTCTGATGA	61.608	60.000	0.00	0.00	0.00	2.92
3224	16390	0.812811	CCACACGCCCTCTGATGATG	60.813	60.000	0.00	0.00	0.00	3.07
3239	16405	0.172578	TGATGCTAGACGAACCACCG	59.827	55.000	0.00	0.00	0.00	4.94
3243	16409	0.735287	GCTAGACGAACCACCGGAAC	60.735	60.000	9.46	0.00	0.00	3.62
3271	16448	5.755849	GGAACCTTATTCCATCTTCAAGGA	58.244	41.667	5.71	0.00	38.42	3.36
3272	16449	5.825151	GGAACCTTATTCCATCTTCAAGGAG	59.175	44.000	5.71	0.00	38.42	3.69
3273	16450	4.786425	ACCTTATTCCATCTTCAAGGAGC	58.214	43.478	5.71	0.00	38.42	4.70
3274	16451	4.476479	ACCTTATTCCATCTTCAAGGAGCT	59.524	41.667	5.71	0.00	38.42	4.09
3280	16462	2.376109	CATCTTCAAGGAGCTGCCATT	58.624	47.619	0.00	0.00	40.02	3.16
3291	16473	0.723981	GCTGCCATTGTCTCGTCTTC	59.276	55.000	0.00	0.00	0.00	2.87
3293	16475	0.036388	TGCCATTGTCTCGTCTTCCC	60.036	55.000	0.00	0.00	0.00	3.97
3300	16482	3.592070	CTCGTCTTCCCGAGCAGA	58.408	61.111	0.00	0.00	46.64	4.26

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
102	2640	1.490574	CAACAAAGGTGGGGTTCCAA	58.509	50.000	0.00	0.00	46.04	3.53
160	2706	0.725117	CGTCATAAACCGAACAGCCC	59.275	55.000	0.00	0.00	0.00	5.19
169	2715	2.021380	CAGCGCGCGTCATAAACC	59.979	61.111	32.35	11.90	0.00	3.27
215	2764	3.829948	TGCACGAAAACACCGTTAAAAA	58.170	36.364	0.00	0.00	38.29	1.94
216	2765	3.482722	TGCACGAAAACACCGTTAAAA	57.517	38.095	0.00	0.00	38.29	1.52
218	2767	4.272991	AGTTATGCACGAAAACACCGTTAA	59.727	37.500	0.00	0.00	38.29	2.01
219	2768	3.808726	AGTTATGCACGAAAACACCGTTA	59.191	39.130	0.00	0.00	38.29	3.18
220	2769	2.614983	AGTTATGCACGAAAACACCGTT	59.385	40.909	0.00	0.00	38.29	4.44
221	2770	2.215196	AGTTATGCACGAAAACACCGT	58.785	42.857	0.00	0.00	41.36	4.83
222	2771	2.961522	AGTTATGCACGAAAACACCG	57.038	45.000	0.00	0.00	0.00	4.94
235	2784	4.804139	CGACCAACCTACTAGCAAGTTATG	59.196	45.833	0.00	0.00	37.15	1.90
236	2785	4.708421	TCGACCAACCTACTAGCAAGTTAT	59.292	41.667	0.00	0.00	37.15	1.89
237	2786	4.081406	TCGACCAACCTACTAGCAAGTTA	58.919	43.478	0.00	0.00	37.15	2.24
253	2802	1.899437	GAGTGGAGGCCAATCGACCA	61.899	60.000	5.01	1.37	38.82	4.02
329	2880	4.826556	AGGATTAGCTCTCAAATATCGCC	58.173	43.478	0.00	0.00	0.00	5.54
366	2926	9.447040	GATCAACTACTTGGAAACTTACAAAAC	57.553	33.333	0.00	0.00	28.96	2.43
407	2967	1.448985	TATTTGACGTGAGGGCTTGC	58.551	50.000	0.00	0.00	0.00	4.01
411	2971	3.733337	AGATGATATTTGACGTGAGGGC	58.267	45.455	0.00	0.00	0.00	5.19
434	3700	8.367660	AGATCAACTACTTAGAACATCTCCAA	57.632	34.615	0.00	0.00	0.00	3.53
459	3725	6.349777	CGGAGGGTTTAAATGTGCTCAAAATA	60.350	38.462	0.00	0.00	0.00	1.40
473	3739	3.078837	GTTGATGAAGCGGAGGGTTTAA	58.921	45.455	0.00	0.00	33.17	1.52
474	3740	2.617021	GGTTGATGAAGCGGAGGGTTTA	60.617	50.000	0.00	0.00	33.17	2.01
525	3792	1.081242	CGTGGAGGTTTGCATGTGC	60.081	57.895	0.00	0.00	42.50	4.57
549	4077	1.601759	CGGGGAGGGCTTGCATATG	60.602	63.158	0.00	0.00	0.00	1.78
645	4216	9.826574	TTACTTAACGGACAGCTCATTAATTAT	57.173	29.630	0.00	0.00	0.00	1.28
681	4252	6.067217	ACCAAGATTCCTTTGCACTATACT	57.933	37.500	0.00	0.00	0.00	2.12
705	4276	4.753516	TTGTTGATGGACGGATGATACT	57.246	40.909	0.00	0.00	0.00	2.12
714	4285	1.535462	GGGTCTGTTTGTTGATGGACG	59.465	52.381	0.00	0.00	0.00	4.79
734	4305	2.437359	CTGCTTTGGAGAGGGGCG	60.437	66.667	0.00	0.00	0.00	6.13
739	4310	0.882042	ACGCACACTGCTTTGGAGAG	60.882	55.000	0.00	0.00	42.25	3.20
746	4317	0.307760	GCTTGTTACGCACACTGCTT	59.692	50.000	5.68	0.00	42.25	3.91
772	4343	2.962253	GACAGGGCTATGCGCGTC	60.962	66.667	4.79	0.00	46.18	5.19
943	10826	6.183360	TGTGTTTGTGTGTTGATTACTTACCC	60.183	38.462	0.00	0.00	0.00	3.69
1007	10995	2.093447	GTCATCATCGGGGAAGACTTGT	60.093	50.000	0.00	0.00	33.83	3.16
1022	11010	0.251916	GTCGGTGGGGATTGTCATCA	59.748	55.000	0.00	0.00	0.00	3.07
1062	11050	4.269523	TGGCGCCAAAGGTCAGCT	62.270	61.111	30.74	0.00	0.00	4.24
1238	11232	4.363990	CCGTCGTGGACAGCAGCT	62.364	66.667	0.00	0.00	42.00	4.24
1266	11260	4.215908	TGTAGATCCTAGCCTCGTTTGAT	58.784	43.478	0.00	0.00	0.00	2.57
1279	11273	0.468400	GGGACGAGGCTGTAGATCCT	60.468	60.000	0.00	0.00	34.90	3.24
1495	11490	2.361357	CTCAGGGTCGAGGACGGT	60.361	66.667	0.00	0.00	40.21	4.83
1784	11779	5.240623	CCAGTTTGTACCTTGAGCATTACAA	59.759	40.000	0.00	0.00	33.62	2.41
1841	11844	5.639082	TGCAATATCTATGCGGTACAGAATG	59.361	40.000	0.00	0.00	46.76	2.67
1951	11955	8.062065	TCAAGGACAAACAGTTTATGAACTTT	57.938	30.769	0.00	0.00	43.48	2.66
1952	11956	7.639113	TCAAGGACAAACAGTTTATGAACTT	57.361	32.000	0.00	0.00	43.48	2.66
2008	12013	1.135575	GTGTAGAACAAGCTGGCATGC	60.136	52.381	9.90	9.90	0.00	4.06
2046	12051	6.546772	TGCATTGAGTTAGGATATTGATGCAA	59.453	34.615	4.87	0.00	42.78	4.08
2149	12154	5.394005	CCATCAGCATTTGGGTTTCGAATAA	60.394	40.000	0.00	0.00	0.00	1.40
2151	12156	3.119029	CCATCAGCATTTGGGTTTCGAAT	60.119	43.478	0.00	0.00	0.00	3.34
2337	12342	5.564063	CGCCGATTTATACTAGATGGTCACA	60.564	44.000	0.00	0.00	0.00	3.58
2348	12353	4.389890	TTGTACCACGCCGATTTATACT	57.610	40.909	0.00	0.00	0.00	2.12
2367	12379	9.607285	ACGCCTCGCTTATTTATTTATTTATTG	57.393	29.630	0.00	0.00	0.00	1.90
2467	15207	1.202177	GGATTGCTTACCACATGTGCG	60.202	52.381	20.81	15.44	0.00	5.34
2491	15231	0.676736	GCCCCAAACGTTTCATCCAA	59.323	50.000	11.37	0.00	0.00	3.53
2493	15233	1.211709	CGCCCCAAACGTTTCATCC	59.788	57.895	11.37	0.00	0.00	3.51
2543	15289	5.647658	CCAACTTTCATGCACATACTTCCTA	59.352	40.000	0.00	0.00	0.00	2.94
2603	15666	3.861113	AGTATACAAACATGGCACGTACG	59.139	43.478	15.01	15.01	0.00	3.67
2689	15752	3.801114	GCCGAGGGCTTAATTTTTCAT	57.199	42.857	0.00	0.00	46.69	2.57
2855	15918	9.438291	GGTAAACATGAAATATCAAACATCTCG	57.562	33.333	0.00	0.00	39.49	4.04
2874	15937	4.263594	GGGATCCCTGTTACAAGGTAAACA	60.264	45.833	24.69	0.00	35.34	2.83
2876	15939	3.267551	GGGGATCCCTGTTACAAGGTAAA	59.732	47.826	30.08	0.00	41.34	2.01
2904	15967	1.068333	CGTGTTTTTCTGCTGATGGGG	60.068	52.381	0.00	0.00	0.00	4.96
3045	16210	1.264288	GATGGCGAATTCCCGATTGTC	59.736	52.381	0.00	0.00	0.00	3.18
3061	16226	0.995024	CCTATGGGGCCTTAGGATGG	59.005	60.000	21.56	5.44	42.87	3.51
3098	16264	1.445410	CTTCATCGACGGCGGTTGA	60.445	57.895	12.58	15.94	40.79	3.18
3107	16273	5.444877	CCGATCTACGTATCTCTTCATCGAC	60.445	48.000	0.00	0.00	40.78	4.20
3150	16316	0.733729	GGTGGTTGTGTTTGCGTGTA	59.266	50.000	0.00	0.00	0.00	2.90
3165	16331	0.459899	TCTCATGATTCGGTCGGTGG	59.540	55.000	0.00	0.00	0.00	4.61
3198	16364	2.203728	AGGGCGTGTGGAGGTGTA	60.204	61.111	0.00	0.00	0.00	2.90
3217	16383	2.159099	GGTGGTTCGTCTAGCATCATCA	60.159	50.000	0.00	0.00	0.00	3.07
3220	16386	0.172578	CGGTGGTTCGTCTAGCATCA	59.827	55.000	0.00	0.00	0.00	3.07
3222	16388	0.968901	TCCGGTGGTTCGTCTAGCAT	60.969	55.000	0.00	0.00	0.00	3.79
3224	16390	0.735287	GTTCCGGTGGTTCGTCTAGC	60.735	60.000	0.00	0.00	0.00	3.42
3249	16415	5.298026	GCTCCTTGAAGATGGAATAAGGTTC	59.702	44.000	0.00	0.00	39.11	3.62
3261	16438	2.291411	ACAATGGCAGCTCCTTGAAGAT	60.291	45.455	4.88	0.00	35.26	2.40
3266	16443	1.093159	GAGACAATGGCAGCTCCTTG	58.907	55.000	0.00	0.00	35.26	3.61
3267	16444	0.392193	CGAGACAATGGCAGCTCCTT	60.392	55.000	0.00	0.00	35.26	3.36
3268	16445	1.220206	CGAGACAATGGCAGCTCCT	59.780	57.895	0.00	0.00	35.26	3.69
3269	16446	1.078848	ACGAGACAATGGCAGCTCC	60.079	57.895	0.00	0.00	0.00	4.70
3270	16447	0.108424	AGACGAGACAATGGCAGCTC	60.108	55.000	0.00	0.00	0.00	4.09
3271	16448	0.322975	AAGACGAGACAATGGCAGCT	59.677	50.000	0.00	0.00	0.00	4.24
3272	16449	0.723981	GAAGACGAGACAATGGCAGC	59.276	55.000	0.00	0.00	0.00	5.25
3273	16450	1.363744	GGAAGACGAGACAATGGCAG	58.636	55.000	0.00	0.00	0.00	4.85
3274	16451	0.036388	GGGAAGACGAGACAATGGCA	60.036	55.000	0.00	0.00	0.00	4.92
3291	16473	1.065418	AGGGTTTGTATTCTGCTCGGG	60.065	52.381	0.00	0.00	0.00	5.14

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.