AutoCloner

Multiple sequence alignment - TraesCS1B01G302300

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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	TraesCS1B01G302300	chr1B	100.000	4566	0	0	1	4566	523007525	523012090	0.000000e+00	8432.0
1	TraesCS1B01G302300	chr1B	96.452	4453	102	21	42	4466	523151850	523147426	0.000000e+00	7297.0
2	TraesCS1B01G302300	chr1B	79.567	832	133	23	1022	1833	522753696	522754510	1.110000e-155	560.0
3	TraesCS1B01G302300	chr1B	89.286	56	6	0	1394	1449	523338654	523338709	2.280000e-08	71.3
4	TraesCS1B01G302300	chr1D	93.147	2320	106	25	788	3095	390665312	390667590	0.000000e+00	3354.0
5	TraesCS1B01G302300	chr1D	86.273	1916	155	55	2558	4398	390681415	390679533	0.000000e+00	1982.0
6	TraesCS1B01G302300	chr1D	92.169	1277	83	9	989	2253	390686969	390685698	0.000000e+00	1788.0
7	TraesCS1B01G302300	chr1D	91.022	646	40	9	2258	2893	390682147	390681510	0.000000e+00	856.0
8	TraesCS1B01G302300	chr1D	78.734	1011	169	25	1236	2210	389796737	389797737	6.440000e-178	634.0
9	TraesCS1B01G302300	chr1D	78.888	971	160	25	1272	2210	389429592	389428635	2.330000e-172	616.0
10	TraesCS1B01G302300	chr1D	87.677	495	28	11	4099	4565	390667970	390668459	3.110000e-151	545.0
11	TraesCS1B01G302300	chr1D	93.266	297	11	5	3811	4098	390667644	390667940	3.260000e-116	429.0
12	TraesCS1B01G302300	chr1D	73.391	466	98	19	996	1454	389953083	389952637	2.850000e-32	150.0
13	TraesCS1B01G302300	chr1D	79.375	160	20	8	854	1007	390687160	390687008	2.910000e-17	100.0
14	TraesCS1B01G302300	chr1A	94.114	1495	68	8	2297	3781	488227775	488226291	0.000000e+00	2255.0
15	TraesCS1B01G302300	chr1A	92.984	1468	79	17	788	2248	488229974	488228524	0.000000e+00	2119.0
16	TraesCS1B01G302300	chr1A	84.584	746	70	25	2286	3001	488228515	488227785	0.000000e+00	699.0
17	TraesCS1B01G302300	chr1A	95.272	423	13	4	3682	4098	142891484	142891905	0.000000e+00	664.0
18	TraesCS1B01G302300	chr1A	76.685	1261	202	57	996	2210	488186801	488188015	2.330000e-172	616.0
19	TraesCS1B01G302300	chr1A	93.680	269	16	1	3415	3683	142891117	142891384	7.120000e-108	401.0
20	TraesCS1B01G302300	chr1A	95.798	119	5	0	3976	4094	488226153	488226035	4.660000e-45	193.0
21	TraesCS1B01G302300	chr1A	94.400	125	5	2	3867	3990	488226293	488226170	1.680000e-44	191.0
22	TraesCS1B01G302300	chr1A	80.513	195	18	6	4099	4288	488225998	488225819	1.030000e-26	132.0
23	TraesCS1B01G302300	chr3B	90.043	1155	67	16	2449	3585	225991012	225992136	0.000000e+00	1452.0
24	TraesCS1B01G302300	chr3B	92.742	248	12	3	3595	3837	647525803	647525557	2.020000e-93	353.0
25	TraesCS1B01G302300	chr3B	98.851	87	0	1	4246	4332	708717766	708717851	2.200000e-33	154.0
26	TraesCS1B01G302300	chr3B	94.253	87	4	1	4246	4332	225992132	225992217	1.030000e-26	132.0
27	TraesCS1B01G302300	chr4A	96.244	639	18	2	2807	3439	717673728	717673090	0.000000e+00	1042.0
28	TraesCS1B01G302300	chr4A	93.760	641	28	5	2807	3437	721669251	721668613	0.000000e+00	952.0
29	TraesCS1B01G302300	chr4A	93.128	553	32	2	3039	3585	92766731	92766179	0.000000e+00	806.0
30	TraesCS1B01G302300	chr4A	92.651	381	23	3	3460	3837	594053809	594054187	1.120000e-150	544.0
31	TraesCS1B01G302300	chr4A	97.701	87	1	1	4246	4332	92766183	92766098	1.020000e-31	148.0
32	TraesCS1B01G302300	chrUn	95.419	633	22	3	2807	3434	66300685	66301315	0.000000e+00	1002.0
33	TraesCS1B01G302300	chrUn	92.138	318	18	5	3523	3837	317014635	317014948	4.190000e-120	442.0
34	TraesCS1B01G302300	chr7B	96.623	533	16	2	2908	3439	426808117	426807586	0.000000e+00	883.0
35	TraesCS1B01G302300	chr7D	92.896	549	31	4	3044	3585	477930824	477930277	0.000000e+00	791.0
36	TraesCS1B01G302300	chr7D	93.805	113	6	1	661	772	561540228	561540340	7.860000e-38	169.0
37	TraesCS1B01G302300	chr7D	91.150	113	9	1	661	772	418916671	418916783	7.910000e-33	152.0
38	TraesCS1B01G302300	chr7D	97.701	87	1	1	4246	4332	477930281	477930196	1.020000e-31	148.0
39	TraesCS1B01G302300	chr6D	90.789	152	11	3	331	480	389978166	389978316	2.790000e-47	200.0
40	TraesCS1B01G302300	chr6D	87.037	54	4	2	335	388	411548076	411548026	1.770000e-04	58.4
41	TraesCS1B01G302300	chr2D	90.265	113	10	1	661	772	28409891	28409779	3.680000e-31	147.0
42	TraesCS1B01G302300	chr2D	86.792	53	3	2	335	386	565591504	565591553	6.380000e-04	56.5
43	TraesCS1B01G302300	chr5B	96.552	87	2	1	4246	4332	473280809	473280724	4.760000e-30	143.0
44	TraesCS1B01G302300	chr5B	94.203	69	3	1	661	728	691958693	691958761	2.250000e-18	104.0
45	TraesCS1B01G302300	chr5D	90.000	60	4	2	328	387	485360025	485360082	4.900000e-10	76.8
46	TraesCS1B01G302300	chr4B	89.831	59	6	0	5	63	406551263	406551321	4.900000e-10	76.8
47	TraesCS1B01G302300	chr3A	86.667	60	4	2	331	389	740388558	740388502	3.810000e-06	63.9
48	TraesCS1B01G302300	chr4D	100.000	31	0	0	359	389	461261347	461261317	1.770000e-04	58.4
49	TraesCS1B01G302300	chr3D	100.000	30	0	0	359	388	2191945	2191916	6.380000e-04	56.5
50	TraesCS1B01G302300	chr2B	92.308	39	3	0	360	398	592057095	592057057	6.380000e-04	56.5

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	TraesCS1B01G302300	chr1B	523007525	523012090	4565	False	8432.000000	8432	100.000000	1	4566	1	chr1B.!!$F2	4565
1	TraesCS1B01G302300	chr1B	523147426	523151850	4424	True	7297.000000	7297	96.452000	42	4466	1	chr1B.!!$R1	4424
2	TraesCS1B01G302300	chr1B	522753696	522754510	814	False	560.000000	560	79.567000	1022	1833	1	chr1B.!!$F1	811
3	TraesCS1B01G302300	chr1D	390665312	390668459	3147	False	1442.666667	3354	91.363333	788	4565	3	chr1D.!!$F2	3777
4	TraesCS1B01G302300	chr1D	390679533	390687160	7627	True	1181.500000	1982	87.209750	854	4398	4	chr1D.!!$R3	3544
5	TraesCS1B01G302300	chr1D	389796737	389797737	1000	False	634.000000	634	78.734000	1236	2210	1	chr1D.!!$F1	974
6	TraesCS1B01G302300	chr1D	389428635	389429592	957	True	616.000000	616	78.888000	1272	2210	1	chr1D.!!$R1	938
7	TraesCS1B01G302300	chr1A	488225819	488229974	4155	True	931.500000	2255	90.398833	788	4288	6	chr1A.!!$R1	3500
8	TraesCS1B01G302300	chr1A	488186801	488188015	1214	False	616.000000	616	76.685000	996	2210	1	chr1A.!!$F1	1214
9	TraesCS1B01G302300	chr1A	142891117	142891905	788	False	532.500000	664	94.476000	3415	4098	2	chr1A.!!$F2	683
10	TraesCS1B01G302300	chr3B	225991012	225992217	1205	False	792.000000	1452	92.148000	2449	4332	2	chr3B.!!$F2	1883
11	TraesCS1B01G302300	chr4A	717673090	717673728	638	True	1042.000000	1042	96.244000	2807	3439	1	chr4A.!!$R1	632
12	TraesCS1B01G302300	chr4A	721668613	721669251	638	True	952.000000	952	93.760000	2807	3437	1	chr4A.!!$R2	630
13	TraesCS1B01G302300	chr4A	92766098	92766731	633	True	477.000000	806	95.414500	3039	4332	2	chr4A.!!$R3	1293
14	TraesCS1B01G302300	chrUn	66300685	66301315	630	False	1002.000000	1002	95.419000	2807	3434	1	chrUn.!!$F1	627
15	TraesCS1B01G302300	chr7B	426807586	426808117	531	True	883.000000	883	96.623000	2908	3439	1	chr7B.!!$R1	531
16	TraesCS1B01G302300	chr7D	477930196	477930824	628	True	469.500000	791	95.298500	3044	4332	2	chr7D.!!$R1	1288

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
37	38	0.457851	CTCTCTCGAAGGATTGGCGT	59.542	55.0	0.00	0.00	0.00	5.68	F
38	39	0.895530	TCTCTCGAAGGATTGGCGTT	59.104	50.0	0.00	0.00	0.00	4.84	F
2133	2255	1.464734	TAACAGGGAGCTCTCGTCTG	58.535	55.0	14.64	16.94	37.48	3.51	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2133	2255	0.693092	TGGGGACACTGGGTATAGCC	60.693	60.000	14.30	14.3	33.40	3.93	R
2441	6853	7.730332	TGGATGCACTTCTCCTCTTATATCTAA	59.270	37.037	5.69	0.0	32.47	2.10	R
4469	9553	0.179018	AACTCCAGGAGCCAACACAC	60.179	55.000	17.31	0.0	32.04	3.82	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
26	27	7.611213	AAAAACAAGTTTTCTTCTCTCTCGA	57.389	32.000	10.96	0.00	41.45	4.04
27	28	7.611213	AAAACAAGTTTTCTTCTCTCTCGAA	57.389	32.000	5.16	0.00	38.27	3.71
28	29	6.836577	AACAAGTTTTCTTCTCTCTCGAAG	57.163	37.500	0.00	0.00	41.32	3.79
29	30	5.293560	ACAAGTTTTCTTCTCTCTCGAAGG	58.706	41.667	0.00	0.00	40.56	3.46
30	31	5.069251	ACAAGTTTTCTTCTCTCTCGAAGGA	59.931	40.000	0.00	0.00	40.56	3.36
31	32	5.993748	AGTTTTCTTCTCTCTCGAAGGAT	57.006	39.130	0.00	0.00	40.56	3.24
32	33	6.353404	AGTTTTCTTCTCTCTCGAAGGATT	57.647	37.500	0.00	0.00	40.56	3.01
33	34	6.162777	AGTTTTCTTCTCTCTCGAAGGATTG	58.837	40.000	0.00	0.00	40.56	2.67
34	35	4.727507	TTCTTCTCTCTCGAAGGATTGG	57.272	45.455	0.00	0.00	40.56	3.16
35	36	2.428890	TCTTCTCTCTCGAAGGATTGGC	59.571	50.000	0.00	0.00	40.56	4.52
36	37	0.741326	TCTCTCTCGAAGGATTGGCG	59.259	55.000	0.00	0.00	0.00	5.69
37	38	0.457851	CTCTCTCGAAGGATTGGCGT	59.542	55.000	0.00	0.00	0.00	5.68
38	39	0.895530	TCTCTCGAAGGATTGGCGTT	59.104	50.000	0.00	0.00	0.00	4.84
39	40	2.097036	TCTCTCGAAGGATTGGCGTTA	58.903	47.619	0.00	0.00	0.00	3.18
40	41	2.099263	TCTCTCGAAGGATTGGCGTTAG	59.901	50.000	0.00	0.00	0.00	2.34
47	48	5.292589	TCGAAGGATTGGCGTTAGAAATAAC	59.707	40.000	0.00	0.00	0.00	1.89
48	49	5.293569	CGAAGGATTGGCGTTAGAAATAACT	59.706	40.000	0.00	0.00	0.00	2.24
55	56	7.681939	TTGGCGTTAGAAATAACTGAGAAAT	57.318	32.000	0.00	0.00	0.00	2.17
58	59	7.148474	TGGCGTTAGAAATAACTGAGAAATGAC	60.148	37.037	0.00	0.00	0.00	3.06
65	66	9.750125	AGAAATAACTGAGAAATGACAAAAACC	57.250	29.630	0.00	0.00	0.00	3.27
66	67	8.887036	AAATAACTGAGAAATGACAAAAACCC	57.113	30.769	0.00	0.00	0.00	4.11
78	79	4.081642	TGACAAAAACCCGATGAAAACCAA	60.082	37.500	0.00	0.00	0.00	3.67
84	85	2.884639	ACCCGATGAAAACCAAGTCAAG	59.115	45.455	0.00	0.00	0.00	3.02
93	94	5.820947	TGAAAACCAAGTCAAGACTCCTTAC	59.179	40.000	2.78	0.00	41.58	2.34
108	109	6.043854	ACTCCTTACAAAAAGCCACAAAAA	57.956	33.333	0.00	0.00	0.00	1.94
109	110	6.649155	ACTCCTTACAAAAAGCCACAAAAAT	58.351	32.000	0.00	0.00	0.00	1.82
111	112	6.883744	TCCTTACAAAAAGCCACAAAAATCT	58.116	32.000	0.00	0.00	0.00	2.40
112	113	8.012957	TCCTTACAAAAAGCCACAAAAATCTA	57.987	30.769	0.00	0.00	0.00	1.98
113	114	8.141268	TCCTTACAAAAAGCCACAAAAATCTAG	58.859	33.333	0.00	0.00	0.00	2.43
115	116	9.185192	CTTACAAAAAGCCACAAAAATCTAGAG	57.815	33.333	0.00	0.00	0.00	2.43
333	334	7.382898	TCACATATAATCGCTAGGCAAATGTA	58.617	34.615	0.00	0.00	0.00	2.29
393	394	7.098477	TCATTAATGAAACCAAAAGCATCCAG	58.902	34.615	15.82	0.00	33.08	3.86
429	430	6.385649	AGGTTCAAAGAAAAACATAAGCGA	57.614	33.333	0.00	0.00	0.00	4.93
450	451	5.333875	GCGAAAAGGAGTTTAAACGACATCT	60.334	40.000	12.54	4.80	0.00	2.90
636	637	4.124851	AGACGGTTCTCCACATTATCAC	57.875	45.455	0.00	0.00	0.00	3.06
684	685	6.654582	TGATGTTATGTGTGTAGCAGATGTTT	59.345	34.615	0.00	0.00	32.89	2.83
2133	2255	1.464734	TAACAGGGAGCTCTCGTCTG	58.535	55.000	14.64	16.94	37.48	3.51
2189	2317	1.635663	CCGACGTGGCTGGAATCAAC	61.636	60.000	0.00	0.00	0.00	3.18
3264	8128	2.092968	GGACCAGTGATTGCTGTATCCA	60.093	50.000	0.00	0.00	38.60	3.41
3506	8396	0.955919	GACCGCTGTGAAAAGGGAGG	60.956	60.000	0.00	0.00	32.03	4.30
3621	8511	7.889589	TCGCATAACCTATCTTCATGTATTG	57.110	36.000	0.00	0.00	0.00	1.90
3647	8537	3.405831	TCACAGTCCATTTCTCTTGCAG	58.594	45.455	0.00	0.00	0.00	4.41
3795	8789	2.872245	AGAGTGTGAAAACACGGTGATG	59.128	45.455	16.29	0.00	44.71	3.07
3826	8823	5.074746	TGAGGTTAGCAGATACCCAGATA	57.925	43.478	0.00	0.00	34.90	1.98
3936	8933	6.267471	TGAACCCTCTTGCTTCATTTATTGTT	59.733	34.615	0.00	0.00	0.00	2.83
3944	8941	5.599732	TGCTTCATTTATTGTTGCAACAGT	58.400	33.333	29.50	28.51	40.50	3.55
4029	9058	2.040947	TGTGGATGGGAATGTGCTTGTA	59.959	45.455	0.00	0.00	0.00	2.41
4147	9216	4.931002	TCCCTAGTGTTTAATCCGTTTTCG	59.069	41.667	0.00	0.00	43.67	3.46
4190	9260	5.935206	TGGCGAGACTCATGTTTACAATTTA	59.065	36.000	2.82	0.00	0.00	1.40
4193	9263	7.277098	GGCGAGACTCATGTTTACAATTTACTA	59.723	37.037	2.82	0.00	0.00	1.82
4232	9307	6.705863	ATTGTCAGATAAGATTTGGAAGCC	57.294	37.500	0.00	0.00	0.00	4.35
4346	9422	5.552178	TGGGTGTTTTACATATTTTTGGCC	58.448	37.500	0.00	0.00	0.00	5.36
4368	9452	4.320494	CCTTGTTTTACATGGCTCAGTGTC	60.320	45.833	0.00	0.00	36.75	3.67
4398	9482	8.167392	TCCTTTTAACTTTGGATGGATCAGTAA	58.833	33.333	0.00	0.00	0.00	2.24
4400	9484	9.793252	CTTTTAACTTTGGATGGATCAGTAATG	57.207	33.333	0.00	0.00	0.00	1.90
4468	9552	6.174720	AGAATGTTCTGGTGTCTTGTTCTA	57.825	37.500	0.00	0.00	35.89	2.10
4469	9553	6.226787	AGAATGTTCTGGTGTCTTGTTCTAG	58.773	40.000	0.00	0.00	35.89	2.43
4471	9555	4.693283	TGTTCTGGTGTCTTGTTCTAGTG	58.307	43.478	0.00	0.00	0.00	2.74
4472	9556	4.161565	TGTTCTGGTGTCTTGTTCTAGTGT	59.838	41.667	0.00	0.00	0.00	3.55
4474	9558	3.704566	TCTGGTGTCTTGTTCTAGTGTGT	59.295	43.478	0.00	0.00	0.00	3.72
4476	9560	4.188462	TGGTGTCTTGTTCTAGTGTGTTG	58.812	43.478	0.00	0.00	0.00	3.33
4477	9561	3.560068	GGTGTCTTGTTCTAGTGTGTTGG	59.440	47.826	0.00	0.00	0.00	3.77
4540	9647	4.811024	TGATGGCGAGATGAACTTGTATTC	59.189	41.667	0.00	0.00	32.82	1.75
4555	9662	9.886132	GAACTTGTATTCTGGAGAGGTTTATTA	57.114	33.333	0.00	0.00	0.00	0.98
4561	9668	6.620877	TTCTGGAGAGGTTTATTAAGCTGA	57.379	37.500	0.12	0.00	41.92	4.26
4565	9672	5.590259	TGGAGAGGTTTATTAAGCTGATTGC	59.410	40.000	0.12	0.00	41.92	3.56

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
2	3	7.611213	TCGAGAGAGAAGAAAACTTGTTTTT	57.389	32.000	11.99	0.00	36.40	1.94
15	16	2.797792	CGCCAATCCTTCGAGAGAGAAG	60.798	54.545	0.14	0.14	45.26	2.85
16	17	1.135139	CGCCAATCCTTCGAGAGAGAA	59.865	52.381	0.00	0.00	43.69	2.87
17	18	0.741326	CGCCAATCCTTCGAGAGAGA	59.259	55.000	0.00	0.00	43.69	3.10
18	19	0.457851	ACGCCAATCCTTCGAGAGAG	59.542	55.000	0.00	0.00	43.69	3.20
19	20	0.895530	AACGCCAATCCTTCGAGAGA	59.104	50.000	0.00	0.00	39.20	3.10
20	21	2.099263	TCTAACGCCAATCCTTCGAGAG	59.901	50.000	0.00	0.00	0.00	3.20
21	22	2.097036	TCTAACGCCAATCCTTCGAGA	58.903	47.619	0.00	0.00	0.00	4.04
22	23	2.579207	TCTAACGCCAATCCTTCGAG	57.421	50.000	0.00	0.00	0.00	4.04
23	24	3.322211	TTTCTAACGCCAATCCTTCGA	57.678	42.857	0.00	0.00	0.00	3.71
24	25	5.293569	AGTTATTTCTAACGCCAATCCTTCG	59.706	40.000	0.00	0.00	41.77	3.79
25	26	6.315393	TCAGTTATTTCTAACGCCAATCCTTC	59.685	38.462	0.00	0.00	41.77	3.46
26	27	6.177610	TCAGTTATTTCTAACGCCAATCCTT	58.822	36.000	0.00	0.00	41.77	3.36
27	28	5.741011	TCAGTTATTTCTAACGCCAATCCT	58.259	37.500	0.00	0.00	41.77	3.24
28	29	5.815740	TCTCAGTTATTTCTAACGCCAATCC	59.184	40.000	0.00	0.00	41.77	3.01
29	30	6.903883	TCTCAGTTATTTCTAACGCCAATC	57.096	37.500	0.00	0.00	41.77	2.67
30	31	7.681939	TTTCTCAGTTATTTCTAACGCCAAT	57.318	32.000	0.00	0.00	41.77	3.16
31	32	7.389330	TCATTTCTCAGTTATTTCTAACGCCAA	59.611	33.333	0.00	0.00	41.77	4.52
32	33	6.876789	TCATTTCTCAGTTATTTCTAACGCCA	59.123	34.615	0.00	0.00	41.77	5.69
33	34	7.148474	TGTCATTTCTCAGTTATTTCTAACGCC	60.148	37.037	0.00	0.00	41.77	5.68
34	35	7.739295	TGTCATTTCTCAGTTATTTCTAACGC	58.261	34.615	0.00	0.00	41.77	4.84
39	40	9.750125	GGTTTTTGTCATTTCTCAGTTATTTCT	57.250	29.630	0.00	0.00	0.00	2.52
40	41	8.978539	GGGTTTTTGTCATTTCTCAGTTATTTC	58.021	33.333	0.00	0.00	0.00	2.17
47	48	4.829064	TCGGGTTTTTGTCATTTCTCAG	57.171	40.909	0.00	0.00	0.00	3.35
48	49	4.824537	TCATCGGGTTTTTGTCATTTCTCA	59.175	37.500	0.00	0.00	0.00	3.27
55	56	3.447586	TGGTTTTCATCGGGTTTTTGTCA	59.552	39.130	0.00	0.00	0.00	3.58
58	59	4.438148	ACTTGGTTTTCATCGGGTTTTTG	58.562	39.130	0.00	0.00	0.00	2.44
65	66	3.815401	AGTCTTGACTTGGTTTTCATCGG	59.185	43.478	0.00	0.00	0.00	4.18
66	67	4.083802	GGAGTCTTGACTTGGTTTTCATCG	60.084	45.833	4.67	0.00	0.00	3.84
78	79	4.822350	GGCTTTTTGTAAGGAGTCTTGACT	59.178	41.667	2.59	2.59	34.59	3.41
84	85	4.911514	TTGTGGCTTTTTGTAAGGAGTC	57.088	40.909	0.00	0.00	0.00	3.36
93	94	5.406477	GGCTCTAGATTTTTGTGGCTTTTTG	59.594	40.000	0.00	0.00	0.00	2.44
108	109	5.104193	ACAATCCAACTTGATGGCTCTAGAT	60.104	40.000	0.00	0.00	40.46	1.98
109	110	4.225942	ACAATCCAACTTGATGGCTCTAGA	59.774	41.667	0.00	0.00	40.46	2.43
111	112	4.574674	ACAATCCAACTTGATGGCTCTA	57.425	40.909	0.00	0.00	40.46	2.43
112	113	3.446442	ACAATCCAACTTGATGGCTCT	57.554	42.857	0.00	0.00	40.46	4.09
113	114	3.367703	CCAACAATCCAACTTGATGGCTC	60.368	47.826	0.98	0.00	40.68	4.70
115	116	2.354003	CCCAACAATCCAACTTGATGGC	60.354	50.000	7.39	0.00	43.82	4.40
393	394	9.924650	TTTTCTTTGAACCTATCTAGTAGTGTC	57.075	33.333	0.00	0.00	0.00	3.67
2133	2255	0.693092	TGGGGACACTGGGTATAGCC	60.693	60.000	14.30	14.30	33.40	3.93
2441	6853	7.730332	TGGATGCACTTCTCCTCTTATATCTAA	59.270	37.037	5.69	0.00	32.47	2.10
3264	8128	5.591099	GTGACATGACACTTCCAAAAACAT	58.409	37.500	19.10	0.00	37.73	2.71
3506	8396	1.026182	TTGACCATGTCAGGCGATGC	61.026	55.000	0.00	0.00	43.69	3.91
3621	8511	4.213564	AGAGAAATGGACTGTGATGGAC	57.786	45.455	0.00	0.00	0.00	4.02
3647	8537	3.563808	TCCAAATAACACACTGCTGACAC	59.436	43.478	0.00	0.00	0.00	3.67
3795	8789	2.490903	TCTGCTAACCTCAACTACCGTC	59.509	50.000	0.00	0.00	0.00	4.79
3826	8823	6.131264	TGAAGATGGCTCATCATAACCAAAT	58.869	36.000	14.93	0.00	42.72	2.32
3936	8933	9.703892	AATATGCTTTGTTTATTTACTGTTGCA	57.296	25.926	0.00	0.00	0.00	4.08
3944	8941	7.032580	ACGCTGCAATATGCTTTGTTTATTTA	58.967	30.769	0.00	0.00	45.31	1.40
4029	9058	9.507329	AACATGAGTTCAGACATAAATAACAGT	57.493	29.630	0.00	0.00	30.46	3.55
4109	9178	4.022762	CACTAGGGACATCTGAATACTCCG	60.023	50.000	0.00	0.00	0.00	4.63
4147	9216	4.795278	CGCCAATCTCTTTGCAGTAATTTC	59.205	41.667	0.00	0.00	33.73	2.17
4158	9227	3.055530	ACATGAGTCTCGCCAATCTCTTT	60.056	43.478	0.00	0.00	0.00	2.52
4190	9260	8.023021	TGACAATTTAGAGATACCTGCATAGT	57.977	34.615	0.00	0.00	0.00	2.12
4193	9263	7.129457	TCTGACAATTTAGAGATACCTGCAT	57.871	36.000	0.00	0.00	0.00	3.96
4229	9304	3.041946	CAGGAAACTACCATCCTAGGCT	58.958	50.000	2.96	0.00	44.26	4.58
4232	9307	5.600484	AGATGTCAGGAAACTACCATCCTAG	59.400	44.000	0.00	0.00	44.26	3.02
4346	9422	4.275689	TGACACTGAGCCATGTAAAACAAG	59.724	41.667	0.00	0.00	0.00	3.16
4368	9452	6.588719	TCCATCCAAAGTTAAAAGGACATG	57.411	37.500	0.00	0.00	32.04	3.21
4398	9482	6.893020	ACTTCACCCTCTAAAAGATACCAT	57.107	37.500	0.00	0.00	0.00	3.55
4400	9484	8.075761	TCTAACTTCACCCTCTAAAAGATACC	57.924	38.462	0.00	0.00	0.00	2.73
4468	9552	1.056700	ACTCCAGGAGCCAACACACT	61.057	55.000	17.31	0.00	32.04	3.55
4469	9553	0.179018	AACTCCAGGAGCCAACACAC	60.179	55.000	17.31	0.00	32.04	3.82
4471	9555	2.427506	CTAAACTCCAGGAGCCAACAC	58.572	52.381	17.31	0.00	32.04	3.32
4472	9556	1.271379	GCTAAACTCCAGGAGCCAACA	60.271	52.381	17.31	0.00	32.04	3.33
4474	9558	1.362224	AGCTAAACTCCAGGAGCCAA	58.638	50.000	17.31	0.63	35.45	4.52
4476	9560	3.629142	TTAAGCTAAACTCCAGGAGCC	57.371	47.619	17.31	0.21	35.45	4.70
4477	9561	3.371285	CGTTTAAGCTAAACTCCAGGAGC	59.629	47.826	17.31	2.61	44.40	4.70
4540	9647	6.238593	GCAATCAGCTTAATAAACCTCTCCAG	60.239	42.308	0.00	0.00	41.15	3.86

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.