AutoCloner

Multiple sequence alignment - TraesCS1D01G015500

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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	TraesCS1D01G015500	chr1D	100.000	4751	0	0	1	4751	7281355	7276605	0.000000e+00	8774
1	TraesCS1D01G015500	chr1D	94.211	2833	102	11	1953	4751	7821407	7824211	0.000000e+00	4266
2	TraesCS1D01G015500	chr1D	84.967	3213	443	24	826	4017	7606079	7609272	0.000000e+00	3221
3	TraesCS1D01G015500	chr1D	84.525	2798	427	5	963	3755	10663401	10660605	0.000000e+00	2763
4	TraesCS1D01G015500	chr1D	78.072	2344	460	40	1446	3765	494860357	494858044	0.000000e+00	1432
5	TraesCS1D01G015500	chr1D	93.610	939	51	6	410	1347	7820477	7821407	0.000000e+00	1393
6	TraesCS1D01G015500	chr1D	80.218	551	64	22	1	548	37894932	37894424	5.810000e-99	372
7	TraesCS1D01G015500	chr1B	94.293	4766	216	24	1	4751	9988614	9993338	0.000000e+00	7243
8	TraesCS1D01G015500	chr1B	85.119	3145	417	26	900	4017	9558665	9555545	0.000000e+00	3168
9	TraesCS1D01G015500	chr1B	84.602	2260	332	11	1505	3752	15877084	15879339	0.000000e+00	2231
10	TraesCS1D01G015500	chr1A	85.961	3184	400	22	898	4041	8718529	8715353	0.000000e+00	3360
11	TraesCS1D01G015500	chr1A	84.541	2801	417	12	963	3752	12503859	12506654	0.000000e+00	2760
12	TraesCS1D01G015500	chr1A	84.393	2800	427	9	963	3755	12306461	12303665	0.000000e+00	2741
13	TraesCS1D01G015500	chr1A	83.751	2794	449	5	963	3752	12210636	12207844	0.000000e+00	2639
14	TraesCS1D01G015500	chr1A	96.659	419	13	1	1246	1663	9251945	9252363	0.000000e+00	695
15	TraesCS1D01G015500	chr1A	92.388	289	22	0	4090	4378	9252437	9252725	3.420000e-111	412
16	TraesCS1D01G015500	chr1A	85.547	256	32	4	4501	4751	9253082	9253337	3.650000e-66	263
17	TraesCS1D01G015500	chr2A	77.080	3089	630	52	955	4014	46826423	46823384	0.000000e+00	1711

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	TraesCS1D01G015500	chr1D	7276605	7281355	4750	True	8774.000000	8774	100.000000	1	4751	1	chr1D.!!$R1	4750
1	TraesCS1D01G015500	chr1D	7606079	7609272	3193	False	3221.000000	3221	84.967000	826	4017	1	chr1D.!!$F1	3191
2	TraesCS1D01G015500	chr1D	7820477	7824211	3734	False	2829.500000	4266	93.910500	410	4751	2	chr1D.!!$F2	4341
3	TraesCS1D01G015500	chr1D	10660605	10663401	2796	True	2763.000000	2763	84.525000	963	3755	1	chr1D.!!$R2	2792
4	TraesCS1D01G015500	chr1D	494858044	494860357	2313	True	1432.000000	1432	78.072000	1446	3765	1	chr1D.!!$R4	2319
5	TraesCS1D01G015500	chr1D	37894424	37894932	508	True	372.000000	372	80.218000	1	548	1	chr1D.!!$R3	547
6	TraesCS1D01G015500	chr1B	9988614	9993338	4724	False	7243.000000	7243	94.293000	1	4751	1	chr1B.!!$F1	4750
7	TraesCS1D01G015500	chr1B	9555545	9558665	3120	True	3168.000000	3168	85.119000	900	4017	1	chr1B.!!$R1	3117
8	TraesCS1D01G015500	chr1B	15877084	15879339	2255	False	2231.000000	2231	84.602000	1505	3752	1	chr1B.!!$F2	2247
9	TraesCS1D01G015500	chr1A	8715353	8718529	3176	True	3360.000000	3360	85.961000	898	4041	1	chr1A.!!$R1	3143
10	TraesCS1D01G015500	chr1A	12503859	12506654	2795	False	2760.000000	2760	84.541000	963	3752	1	chr1A.!!$F1	2789
11	TraesCS1D01G015500	chr1A	12303665	12306461	2796	True	2741.000000	2741	84.393000	963	3755	1	chr1A.!!$R3	2792
12	TraesCS1D01G015500	chr1A	12207844	12210636	2792	True	2639.000000	2639	83.751000	963	3752	1	chr1A.!!$R2	2789
13	TraesCS1D01G015500	chr1A	9251945	9253337	1392	False	456.666667	695	91.531333	1246	4751	3	chr1A.!!$F2	3505
14	TraesCS1D01G015500	chr2A	46823384	46826423	3039	True	1711.000000	1711	77.080000	955	4014	1	chr2A.!!$R1	3059

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	Hairpin	End Stability	Orientation
402	409	0.172803	ATGTGTACGACGAAGGAGGC	59.827	55.000	0.00	0.00	4.70	F
404	411	0.172803	GTGTACGACGAAGGAGGCAT	59.827	55.000	0.00	0.00	4.40	F
779	794	0.397941	AAAGTGCACTCAGCCTGCTA	59.602	50.000	21.95	44.83	3.49	F
787	802	1.548269	ACTCAGCCTGCTAGAACTGAC	59.452	52.381	0.00	35.42	3.51	F
2542	2572	0.523519	GGCTCTTGCTGTGGCTAAAC	59.476	55.000	0.00	39.59	2.01	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1666	1685	0.744874	ATCCAAGCATGTGCATCAGC	59.255	50.000	7.83	45.16	4.26	R
2059	2086	1.070786	GAGGGCACTCACGGTTCAA	59.929	57.895	12.23	43.41	2.69	R
2542	2572	0.676151	GCAGAGCCAAACCTCTCCTG	60.676	60.000	0.00	40.11	3.86	R
2565	2595	1.186200	GAATCAGTTCTTTGGGGGCC	58.814	55.000	0.00	0.00	5.80	R
4167	4273	1.595311	TGGATGGGCCACTTCTGTAT	58.405	50.000	9.28	43.33	2.29	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
148	154	6.265577	AGTTCATAATTTTAGCAACATCGCC	58.734	36.000	0.00	0.00	0.00	5.54
206	212	8.408601	GGATAGCAATTCACAACACTATGAAAT	58.591	33.333	0.00	0.00	38.29	2.17
218	224	7.607991	ACAACACTATGAAATTAGAGGGTGAAG	59.392	37.037	0.00	0.00	0.00	3.02
303	309	1.889829	CCAAACCAACTCCCGCATTAA	59.110	47.619	0.00	0.00	0.00	1.40
307	313	1.564348	ACCAACTCCCGCATTAAGGAT	59.436	47.619	0.00	0.00	0.00	3.24
313	319	3.008049	ACTCCCGCATTAAGGATATCCAC	59.992	47.826	23.81	4.92	38.89	4.02
321	327	6.039270	CGCATTAAGGATATCCACTCCAAAAA	59.961	38.462	23.81	6.14	38.89	1.94
322	328	7.255590	CGCATTAAGGATATCCACTCCAAAAAT	60.256	37.037	23.81	7.96	38.89	1.82
323	329	8.084684	GCATTAAGGATATCCACTCCAAAAATC	58.915	37.037	23.81	0.00	38.89	2.17
333	339	3.922240	CACTCCAAAAATCAAATGGCTCG	59.078	43.478	0.00	0.00	34.13	5.03
346	352	2.805546	GCTCGGATGCCTACGACA	59.194	61.111	0.00	0.00	35.04	4.35
356	363	6.094325	TCGGATGCCTACGACAAAATAAAAAT	59.906	34.615	0.00	0.00	33.69	1.82
357	364	7.280428	TCGGATGCCTACGACAAAATAAAAATA	59.720	33.333	0.00	0.00	33.69	1.40
386	393	6.469782	AACACAAGAAAATGGTTCAGATGT	57.530	33.333	0.00	0.00	0.00	3.06
400	407	2.418976	TCAGATGTGTACGACGAAGGAG	59.581	50.000	0.00	0.00	0.00	3.69
401	408	1.743958	AGATGTGTACGACGAAGGAGG	59.256	52.381	0.00	0.00	0.00	4.30
402	409	0.172803	ATGTGTACGACGAAGGAGGC	59.827	55.000	0.00	0.00	0.00	4.70
403	410	1.174078	TGTGTACGACGAAGGAGGCA	61.174	55.000	0.00	0.00	0.00	4.75
404	411	0.172803	GTGTACGACGAAGGAGGCAT	59.827	55.000	0.00	0.00	0.00	4.40
406	413	0.454600	GTACGACGAAGGAGGCATGA	59.545	55.000	0.00	0.00	0.00	3.07
408	415	1.215382	CGACGAAGGAGGCATGACA	59.785	57.895	0.00	0.00	0.00	3.58
428	435	5.663106	TGACACTGCCTCTTATCCTATCTTT	59.337	40.000	0.00	0.00	0.00	2.52
545	560	3.310860	AAGGAATCGGGAAGCGCGT	62.311	57.895	8.43	0.00	40.60	6.01
649	664	1.838112	TCCTATGGCCTGCAACAAAG	58.162	50.000	3.32	0.00	0.00	2.77
693	708	0.489567	AAATTTGGGGCCCTGTACCA	59.510	50.000	25.93	7.83	0.00	3.25
696	711	1.143329	TTTGGGGCCCTGTACCATCA	61.143	55.000	25.93	5.18	33.63	3.07
703	718	1.993391	CCTGTACCATCACCCGGGT	60.993	63.158	24.16	24.16	41.21	5.28
704	719	1.220749	CTGTACCATCACCCGGGTG	59.779	63.158	42.62	42.62	46.64	4.61
717	732	4.416738	GGGTGGGTGGAGCTGAGC	62.417	72.222	0.00	0.00	0.00	4.26
718	733	4.767255	GGTGGGTGGAGCTGAGCG	62.767	72.222	0.00	0.00	0.00	5.03
719	734	4.767255	GTGGGTGGAGCTGAGCGG	62.767	72.222	0.00	0.00	0.00	5.52
747	762	5.405797	GTGGGCTTCAGAGAAAATTGAATC	58.594	41.667	0.00	0.00	33.25	2.52
754	769	7.699812	GCTTCAGAGAAAATTGAATCGCTAATT	59.300	33.333	0.00	0.00	33.25	1.40
766	781	4.802876	ATCGCTAATTGCTAGAAAGTGC	57.197	40.909	0.00	0.00	40.11	4.40
779	794	0.397941	AAAGTGCACTCAGCCTGCTA	59.602	50.000	21.95	0.00	44.83	3.49
787	802	1.548269	ACTCAGCCTGCTAGAACTGAC	59.452	52.381	0.00	0.00	35.42	3.51
819	834	9.712305	ACTATTACCATGCATCTACTTTATGTC	57.288	33.333	0.00	0.00	0.00	3.06
821	836	8.839310	ATTACCATGCATCTACTTTATGTCTC	57.161	34.615	0.00	0.00	0.00	3.36
823	838	4.687948	CCATGCATCTACTTTATGTCTCCG	59.312	45.833	0.00	0.00	0.00	4.63
1666	1685	2.433868	TCGGGAGAAAGTCAACTTCG	57.566	50.000	0.00	0.00	34.61	3.79
1692	1711	1.818060	GCACATGCTTGGATTGTGGTA	59.182	47.619	4.44	0.00	40.79	3.25
1765	1787	1.593006	GACACACACAAGAGTCAACGG	59.407	52.381	0.00	0.00	0.00	4.44
2052	2079	2.014010	TTTGCTCAAGGGCTTTCCAT	57.986	45.000	0.00	0.00	38.24	3.41
2059	2086	2.041620	TCAAGGGCTTTCCATAGCAACT	59.958	45.455	0.00	0.00	43.02	3.16
2542	2572	0.523519	GGCTCTTGCTGTGGCTAAAC	59.476	55.000	0.00	0.00	39.59	2.01
2565	2595	0.321122	AGAGGTTTGGCTCTGCGAAG	60.321	55.000	0.00	0.00	0.00	3.79
2567	2597	2.563427	GTTTGGCTCTGCGAAGGC	59.437	61.111	4.93	4.93	41.95	4.35
2578	2608	2.636412	GCGAAGGCCCCCAAAGAAC	61.636	63.158	0.00	0.00	0.00	3.01
2591	2621	3.194116	CCCAAAGAACTGATTCACATGGG	59.806	47.826	0.00	0.00	42.71	4.00
2938	2992	3.629142	AGCTACCACCAGGAATTGTAC	57.371	47.619	0.00	0.00	38.69	2.90
3101	3155	2.224314	GCAAAGACTTGTCACTACAGCC	59.776	50.000	3.49	0.00	36.83	4.85
3123	3177	2.921754	GCAGAAAATGATGAAGCTGCAC	59.078	45.455	0.00	0.00	45.78	4.57
3163	3217	7.400599	AACATCAATGCATCTAACTGTGATT	57.599	32.000	0.00	0.00	0.00	2.57
3765	3830	3.633065	GTGTCTAGTAGCCTACCTCCTTG	59.367	52.174	0.00	0.00	0.00	3.61
3911	3983	2.052891	CATGCATTGTTGGTTGTGTCG	58.947	47.619	0.00	0.00	0.00	4.35
4077	4179	4.262420	GCCCATCTCTCTGTTTCCTAGATC	60.262	50.000	0.00	0.00	0.00	2.75
4148	4254	2.569059	CCTATTGGGCTCATGAGTGTG	58.431	52.381	23.38	0.00	0.00	3.82
4166	4272	7.650890	TGAGTGTGTACGTTCTAGTTCAAATA	58.349	34.615	0.00	0.00	0.00	1.40
4167	4273	8.136800	TGAGTGTGTACGTTCTAGTTCAAATAA	58.863	33.333	0.00	0.00	0.00	1.40
4184	4290	5.827797	TCAAATAATACAGAAGTGGCCCATC	59.172	40.000	0.00	0.00	0.00	3.51
4196	4302	1.034838	GGCCCATCCAAATACGTGCA	61.035	55.000	0.00	0.00	34.01	4.57
4261	4367	1.268352	GCGGTAATTTCCTGTGCACAA	59.732	47.619	21.98	6.15	0.00	3.33
4263	4369	2.292016	CGGTAATTTCCTGTGCACAACA	59.708	45.455	21.98	7.17	37.22	3.33
4272	4378	1.727467	GTGCACAACACTGGGACAC	59.273	57.895	13.17	0.00	46.41	3.67
4287	4393	2.159170	GGGACACTGAGTCTACTGCATC	60.159	54.545	5.26	0.00	46.72	3.91
4398	4512	1.584724	CTCTCCCCTTGCCCTAAAGA	58.415	55.000	0.00	0.00	0.00	2.52
4440	4557	9.802039	AACTGAAATTTTAGGGAGTTACATACA	57.198	29.630	13.89	0.00	0.00	2.29
4512	4894	2.037121	GGTCCCAAAACATCCCAACTTG	59.963	50.000	0.00	0.00	0.00	3.16
4529	4911	6.459710	CCCAACTTGTCAAAAGTAGAGAAACC	60.460	42.308	0.00	0.00	0.00	3.27
4598	4980	1.894756	GTTGTACTGCCCGCCAACA	60.895	57.895	0.00	0.00	37.66	3.33
4663	5048	3.506096	CTCTCCACGCGTCGCCTA	61.506	66.667	9.86	0.00	0.00	3.93
4695	5080	6.112734	TCCTACTATATGTTGTGCTTTGTGG	58.887	40.000	0.00	0.00	0.00	4.17
4736	5121	4.041691	GCCATTTGAGCCCCTTATAGTAGA	59.958	45.833	0.00	0.00	0.00	2.59

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
148	154	0.387622	TTAACGGTCGGAAGTCTGCG	60.388	55.000	0.00	0.00	37.81	5.18
206	212	3.008704	GCCCTTGTTACTTCACCCTCTAA	59.991	47.826	0.00	0.00	0.00	2.10
218	224	3.440415	GCCGGCAGCCCTTGTTAC	61.440	66.667	24.80	0.00	34.35	2.50
265	271	0.177373	GGTTCGGCCGATTCCTAACT	59.823	55.000	31.56	0.00	33.69	2.24
303	309	7.070322	CCATTTGATTTTTGGAGTGGATATCCT	59.930	37.037	22.35	3.01	37.74	3.24
307	313	5.721000	AGCCATTTGATTTTTGGAGTGGATA	59.279	36.000	0.00	0.00	31.94	2.59
313	319	3.193267	TCCGAGCCATTTGATTTTTGGAG	59.807	43.478	0.00	0.00	31.94	3.86
356	363	9.311916	CTGAACCATTTTCTTGTGTTTGATTTA	57.688	29.630	0.00	0.00	0.00	1.40
357	364	8.040132	TCTGAACCATTTTCTTGTGTTTGATTT	58.960	29.630	0.00	0.00	0.00	2.17
386	393	0.172578	CATGCCTCCTTCGTCGTACA	59.827	55.000	0.00	0.00	0.00	2.90
401	408	2.158842	AGGATAAGAGGCAGTGTCATGC	60.159	50.000	0.00	0.00	45.74	4.06
402	409	3.834489	AGGATAAGAGGCAGTGTCATG	57.166	47.619	0.00	0.00	0.00	3.07
403	410	5.401750	AGATAGGATAAGAGGCAGTGTCAT	58.598	41.667	0.00	0.00	0.00	3.06
404	411	4.809193	AGATAGGATAAGAGGCAGTGTCA	58.191	43.478	0.00	0.00	0.00	3.58
406	413	5.426833	ACAAAGATAGGATAAGAGGCAGTGT	59.573	40.000	0.00	0.00	0.00	3.55
408	415	6.352516	CAACAAAGATAGGATAAGAGGCAGT	58.647	40.000	0.00	0.00	0.00	4.40
428	435	1.153647	CCGGAGATGCTACGCAACA	60.154	57.895	0.00	0.00	43.62	3.33
545	560	3.824443	TGAGTCTCTTACGACATGGTTCA	59.176	43.478	0.65	0.00	36.38	3.18
649	664	1.449778	GCCCCGAGTTTCCTAGCAC	60.450	63.158	0.00	0.00	0.00	4.40
719	734	4.785453	CTCTGAAGCCCACCCGCC	62.785	72.222	0.00	0.00	0.00	6.13
720	735	2.748058	TTTCTCTGAAGCCCACCCGC	62.748	60.000	0.00	0.00	0.00	6.13
721	736	0.250727	TTTTCTCTGAAGCCCACCCG	60.251	55.000	0.00	0.00	0.00	5.28
724	739	4.853924	TTCAATTTTCTCTGAAGCCCAC	57.146	40.909	0.00	0.00	0.00	4.61
727	742	4.101235	GCGATTCAATTTTCTCTGAAGCC	58.899	43.478	0.00	0.00	35.11	4.35
728	743	4.979388	AGCGATTCAATTTTCTCTGAAGC	58.021	39.130	0.00	0.00	35.14	3.86
729	744	9.007252	CAATTAGCGATTCAATTTTCTCTGAAG	57.993	33.333	0.00	0.00	35.14	3.02
730	745	7.485913	GCAATTAGCGATTCAATTTTCTCTGAA	59.514	33.333	0.00	0.00	36.08	3.02
731	746	6.968904	GCAATTAGCGATTCAATTTTCTCTGA	59.031	34.615	0.00	0.00	0.00	3.27
732	747	7.146368	GCAATTAGCGATTCAATTTTCTCTG	57.854	36.000	0.00	0.00	0.00	3.35
754	769	1.609061	GGCTGAGTGCACTTTCTAGCA	60.609	52.381	29.98	19.80	45.15	3.49
766	781	1.547820	TCAGTTCTAGCAGGCTGAGTG	59.452	52.381	20.86	10.10	33.62	3.51
779	794	8.361139	GCATGGTAATAGTACATAGTCAGTTCT	58.639	37.037	2.37	0.00	31.21	3.01
819	834	2.095768	CACACATTAACTTGGCACGGAG	60.096	50.000	0.00	0.00	0.00	4.63
821	836	1.606668	ACACACATTAACTTGGCACGG	59.393	47.619	0.00	0.00	0.00	4.94
823	838	4.822036	TGTACACACATTAACTTGGCAC	57.178	40.909	0.00	0.00	0.00	5.01
858	873	5.659440	TCAGAATATGGCGTAGATGCATA	57.341	39.130	0.00	0.00	36.28	3.14
868	883	7.993821	AGATAAATACGATCAGAATATGGCG	57.006	36.000	0.00	0.00	34.61	5.69
917	932	5.854338	GCATCGAGTACAATAAGACTAGCTC	59.146	44.000	0.00	0.00	0.00	4.09
1666	1685	0.744874	ATCCAAGCATGTGCATCAGC	59.255	50.000	7.83	0.00	45.16	4.26
1765	1787	1.153549	CGCTAAGAGGAGGTGGTGC	60.154	63.158	0.00	0.00	0.00	5.01
1834	1856	7.852945	CACAATCAAACACTTCTTCTCTTGTAC	59.147	37.037	0.00	0.00	0.00	2.90
1842	1864	5.581605	TCAAGCACAATCAAACACTTCTTC	58.418	37.500	0.00	0.00	0.00	2.87
2052	2079	2.479837	CACTCACGGTTCAAGTTGCTA	58.520	47.619	0.00	0.00	0.00	3.49
2059	2086	1.070786	GAGGGCACTCACGGTTCAA	59.929	57.895	12.23	0.00	43.41	2.69
2542	2572	0.676151	GCAGAGCCAAACCTCTCCTG	60.676	60.000	0.00	0.00	40.11	3.86
2565	2595	1.186200	GAATCAGTTCTTTGGGGGCC	58.814	55.000	0.00	0.00	0.00	5.80
2567	2597	2.875296	TGTGAATCAGTTCTTTGGGGG	58.125	47.619	0.00	0.00	35.33	5.40
2578	2608	6.402550	CGAACTTCTTTACCCATGTGAATCAG	60.403	42.308	0.00	0.00	0.00	2.90
2591	2621	3.360168	CGAGAACCGACGAACTTCTTTAC	59.640	47.826	0.00	0.00	41.76	2.01
2938	2992	2.802816	GGTGCCGTAGCTTCTCAATATG	59.197	50.000	0.00	0.00	40.80	1.78
3101	3155	2.182825	GCAGCTTCATCATTTTCTGCG	58.817	47.619	0.00	0.00	37.73	5.18
3123	3177	5.703978	TGATGTTATCAACCCAAACTGTG	57.296	39.130	0.00	0.00	36.11	3.66
3163	3217	8.651389	CATATCTGAGAGGGTTTTCAATAGGTA	58.349	37.037	0.00	0.00	0.00	3.08
3401	3455	2.089980	GATGAGATGCCAACAACTGCT	58.910	47.619	0.00	0.00	0.00	4.24
3573	3627	4.843728	ACACAATGTAGATCCCGTCAATT	58.156	39.130	0.00	0.00	0.00	2.32
3806	3871	9.602568	TCATCACAAATAATAAAAAGCATGCAT	57.397	25.926	21.98	4.57	0.00	3.96
4166	4272	1.922447	TGGATGGGCCACTTCTGTATT	59.078	47.619	9.28	0.00	43.33	1.89
4167	4273	1.595311	TGGATGGGCCACTTCTGTAT	58.405	50.000	9.28	0.00	43.33	2.29
4184	4290	3.829886	AGATGTTGTGCACGTATTTGG	57.170	42.857	13.13	0.00	0.00	3.28
4235	4341	2.347452	CACAGGAAATTACCGCTACACG	59.653	50.000	0.00	0.00	43.15	4.49
4243	4349	3.638484	GTGTTGTGCACAGGAAATTACC	58.362	45.455	20.59	4.29	46.91	2.85
4261	4367	2.158445	AGTAGACTCAGTGTCCCAGTGT	60.158	50.000	0.00	0.00	46.46	3.55
4263	4369	2.520069	CAGTAGACTCAGTGTCCCAGT	58.480	52.381	0.00	0.00	46.46	4.00
4272	4378	6.293407	GCTACTTCTAGATGCAGTAGACTCAG	60.293	46.154	24.79	8.38	42.50	3.35
4287	4393	7.585867	TGCGTCTTGATATAAGCTACTTCTAG	58.414	38.462	0.00	0.00	0.00	2.43
4437	4554	7.994334	ACTTACAGAAAGTGTTAATTGGGTGTA	59.006	33.333	0.00	0.00	46.90	2.90
4438	4555	6.831868	ACTTACAGAAAGTGTTAATTGGGTGT	59.168	34.615	0.00	0.00	46.90	4.16
4439	4556	7.272037	ACTTACAGAAAGTGTTAATTGGGTG	57.728	36.000	0.00	0.00	46.90	4.61
4479	4596	4.343814	TGTTTTGGGACCTTTCCTCATTTC	59.656	41.667	0.00	0.00	42.38	2.17
4512	4894	5.548406	TGGCTAGGTTTCTCTACTTTTGAC	58.452	41.667	0.00	0.00	0.00	3.18
4529	4911	4.020662	GGGAGTTGGATAGAGAATGGCTAG	60.021	50.000	0.00	0.00	0.00	3.42
4663	5048	6.464465	GCACAACATATAGTAGGATGGGAAGT	60.464	42.308	1.17	0.00	0.00	3.01
4695	5080	2.289569	TGGCTTCCATCAACATTTTGCC	60.290	45.455	0.00	0.00	38.42	4.52

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.