AutoCloner

Multiple sequence alignment - TraesCS1B01G204800

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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	TraesCS1B01G204800	chr1B	100.000	3636	0	0	1	3636	368681815	368678180	0.000000e+00	6715.0
1	TraesCS1B01G204800	chr1D	93.824	2866	108	22	31	2838	233926639	233923785	0.000000e+00	4248.0
2	TraesCS1B01G204800	chr1D	96.524	633	19	1	2836	3468	282720294	282720923	0.000000e+00	1044.0
3	TraesCS1B01G204800	chr1D	96.051	633	21	1	2836	3468	474237457	474236829	0.000000e+00	1027.0
4	TraesCS1B01G204800	chr1D	98.246	171	3	0	3465	3635	474236882	474236712	2.120000e-77	300.0
5	TraesCS1B01G204800	chr1A	95.824	2347	74	13	505	2839	313590017	313592351	0.000000e+00	3770.0
6	TraesCS1B01G204800	chr1A	89.933	298	28	2	1	297	313493874	313494170	2.050000e-102	383.0
7	TraesCS1B01G204800	chr1A	100.000	28	0	0	760	787	8335854	8335827	7.000000e-03	52.8
8	TraesCS1B01G204800	chr3D	96.682	633	19	2	2836	3468	286898990	286899620	0.000000e+00	1051.0
9	TraesCS1B01G204800	chr3D	97.688	173	3	1	3465	3636	286899567	286899739	2.750000e-76	296.0
10	TraesCS1B01G204800	chr2D	96.367	633	20	1	2836	3468	89209515	89210144	0.000000e+00	1038.0
11	TraesCS1B01G204800	chr2D	95.893	633	23	1	2836	3468	104908009	104907380	0.000000e+00	1022.0
12	TraesCS1B01G204800	chr2D	98.246	171	3	0	3465	3635	89210091	89210261	2.120000e-77	300.0
13	TraesCS1B01G204800	chr2D	98.246	171	3	0	3465	3635	104907433	104907263	2.120000e-77	300.0
14	TraesCS1B01G204800	chr2D	89.573	211	22	0	1	211	615052087	615052297	5.980000e-68	268.0
15	TraesCS1B01G204800	chr5B	96.209	633	24	0	2836	3468	36737045	36737677	0.000000e+00	1037.0
16	TraesCS1B01G204800	chr5B	97.110	173	4	1	3465	3636	473119165	473119337	1.280000e-74	291.0
17	TraesCS1B01G204800	chr5D	96.051	633	24	1	2836	3468	507220311	507219680	0.000000e+00	1029.0
18	TraesCS1B01G204800	chr5D	86.730	211	28	0	1	211	484028973	484028763	6.070000e-58	235.0
19	TraesCS1B01G204800	chr5D	87.952	83	6	3	599	679	340948982	340948902	1.070000e-15	95.3
20	TraesCS1B01G204800	chr5D	76.471	102	24	0	442	543	320444712	320444813	5.070000e-04	56.5
21	TraesCS1B01G204800	chr5D	100.000	28	0	0	551	578	533116146	533116119	7.000000e-03	52.8
22	TraesCS1B01G204800	chr3A	95.419	633	26	1	2836	3468	681394098	681394727	0.000000e+00	1005.0
23	TraesCS1B01G204800	chr3A	96.532	173	5	1	3465	3636	681394674	681394846	5.940000e-73	285.0
24	TraesCS1B01G204800	chr3B	94.787	633	30	1	2836	3468	663178596	663177967	0.000000e+00	983.0
25	TraesCS1B01G204800	chr3B	97.076	171	5	0	3465	3635	663178020	663177850	4.590000e-74	289.0
26	TraesCS1B01G204800	chr3B	84.472	161	25	0	1	161	612800940	612800780	3.760000e-35	159.0
27	TraesCS1B01G204800	chr5A	98.246	171	3	0	3465	3635	491696632	491696802	2.120000e-77	300.0
28	TraesCS1B01G204800	chr5A	97.110	173	4	1	3465	3636	491702736	491702908	1.280000e-74	291.0
29	TraesCS1B01G204800	chr2B	87.736	212	26	0	1	212	323087462	323087673	7.800000e-62	248.0
30	TraesCS1B01G204800	chr2B	97.143	35	0	1	178	211	783006143	783006109	1.410000e-04	58.4
31	TraesCS1B01G204800	chr4A	86.916	214	28	0	1	214	59272757	59272544	1.300000e-59	241.0
32	TraesCS1B01G204800	chr7D	84.434	212	32	1	1	211	500254643	500254432	1.320000e-49	207.0
33	TraesCS1B01G204800	chr4D	93.902	82	5	0	130	211	15779158	15779239	1.370000e-24	124.0

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	TraesCS1B01G204800	chr1B	368678180	368681815	3635	True	6715.0	6715	100.0000	1	3636	1	chr1B.!!$R1	3635
1	TraesCS1B01G204800	chr1D	233923785	233926639	2854	True	4248.0	4248	93.8240	31	2838	1	chr1D.!!$R1	2807
2	TraesCS1B01G204800	chr1D	282720294	282720923	629	False	1044.0	1044	96.5240	2836	3468	1	chr1D.!!$F1	632
3	TraesCS1B01G204800	chr1D	474236712	474237457	745	True	663.5	1027	97.1485	2836	3635	2	chr1D.!!$R2	799
4	TraesCS1B01G204800	chr1A	313590017	313592351	2334	False	3770.0	3770	95.8240	505	2839	1	chr1A.!!$F2	2334
5	TraesCS1B01G204800	chr3D	286898990	286899739	749	False	673.5	1051	97.1850	2836	3636	2	chr3D.!!$F1	800
6	TraesCS1B01G204800	chr2D	89209515	89210261	746	False	669.0	1038	97.3065	2836	3635	2	chr2D.!!$F2	799
7	TraesCS1B01G204800	chr2D	104907263	104908009	746	True	661.0	1022	97.0695	2836	3635	2	chr2D.!!$R1	799
8	TraesCS1B01G204800	chr5B	36737045	36737677	632	False	1037.0	1037	96.2090	2836	3468	1	chr5B.!!$F1	632
9	TraesCS1B01G204800	chr5D	507219680	507220311	631	True	1029.0	1029	96.0510	2836	3468	1	chr5D.!!$R3	632
10	TraesCS1B01G204800	chr3A	681394098	681394846	748	False	645.0	1005	95.9755	2836	3636	2	chr3A.!!$F1	800
11	TraesCS1B01G204800	chr3B	663177850	663178596	746	True	636.0	983	95.9315	2836	3635	2	chr3B.!!$R2	799

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
332	333	0.033796	CCCGGACGCCCCTATATCTA	60.034	60.000	0.73	0.0	0.0	1.98	F
382	383	1.306997	AAAGGGGAGCGAGATGGGA	60.307	57.895	0.00	0.0	0.0	4.37	F
1147	1210	1.597461	GAGTAGCCCGGCTGTTCTT	59.403	57.895	22.95	2.5	40.1	2.52	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1224	1287	0.388659	CCCTCTCTCTCCAGAATGCG	59.611	60.0	0.0	0.00	31.97	4.73	R
1604	1667	0.457035	TCGTGTTATGGCGGTACCTC	59.543	55.0	10.9	0.69	40.22	3.85	R
2869	2934	0.550147	ACTGGCCCTCAACCCTGTAT	60.550	55.0	0.0	0.00	32.40	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
19	20	1.873698	TTTGGACTAGGCACGACAAC	58.126	50.000	0.00	0.00	0.00	3.32
20	21	0.319211	TTGGACTAGGCACGACAACG	60.319	55.000	0.00	0.00	45.75	4.10
87	88	5.222027	TGTGATGACAAAGGGGATTAAGTCA	60.222	40.000	0.00	0.00	39.17	3.41
89	90	6.625873	GATGACAAAGGGGATTAAGTCATC	57.374	41.667	14.97	14.97	45.79	2.92
96	97	2.158957	GGGGATTAAGTCATCGACTGCA	60.159	50.000	0.00	0.00	42.59	4.41
111	112	0.106335	CTGCAGGTGCTGATAGGAGG	59.894	60.000	5.57	0.00	41.71	4.30
127	128	4.906537	GGGGGTTGTGCGGGTGTT	62.907	66.667	0.00	0.00	0.00	3.32
128	129	2.835895	GGGGTTGTGCGGGTGTTT	60.836	61.111	0.00	0.00	0.00	2.83
134	135	2.223852	GGTTGTGCGGGTGTTTGTTTAT	60.224	45.455	0.00	0.00	0.00	1.40
156	157	0.613260	CGAGACAATTGTCCCTCCCA	59.387	55.000	30.34	0.00	45.85	4.37
157	158	1.210478	CGAGACAATTGTCCCTCCCAT	59.790	52.381	30.34	13.60	45.85	4.00
176	177	6.772605	TCCCATTGTGAGACTATGAATATGG	58.227	40.000	0.00	0.00	34.07	2.74
219	220	2.094417	GCATTGTGCTAGTCTTTCCGAC	59.906	50.000	0.00	0.00	40.96	4.79
229	230	4.351874	AGTCTTTCCGACATTGGAGAAA	57.648	40.909	0.00	0.00	45.32	2.52
236	237	1.134946	CGACATTGGAGAAATTGGGCC	59.865	52.381	0.00	0.00	0.00	5.80
241	242	1.631405	TGGAGAAATTGGGCCAACAG	58.369	50.000	23.59	0.00	0.00	3.16
247	248	4.450976	AGAAATTGGGCCAACAGAAAAAC	58.549	39.130	23.59	7.42	0.00	2.43
248	249	3.922171	AATTGGGCCAACAGAAAAACA	57.078	38.095	23.59	0.00	0.00	2.83
250	251	2.682155	TGGGCCAACAGAAAAACAAC	57.318	45.000	2.13	0.00	0.00	3.32
251	252	1.208293	TGGGCCAACAGAAAAACAACC	59.792	47.619	2.13	0.00	0.00	3.77
264	265	2.765689	AACAACCCCCAACATCTTGA	57.234	45.000	0.00	0.00	0.00	3.02
270	271	3.379452	ACCCCCAACATCTTGAAAACAA	58.621	40.909	0.00	0.00	0.00	2.83
279	280	3.878160	TCTTGAAAACAACCCAACACC	57.122	42.857	0.00	0.00	0.00	4.16
280	281	3.436243	TCTTGAAAACAACCCAACACCT	58.564	40.909	0.00	0.00	0.00	4.00
287	288	0.474184	CAACCCAACACCTCCTCTGT	59.526	55.000	0.00	0.00	0.00	3.41
295	296	4.225267	CCAACACCTCCTCTGTATTAAGGT	59.775	45.833	0.00	0.00	40.97	3.50
318	319	1.302949	CTGGATTTTCCTGCCCGGA	59.697	57.895	0.73	0.00	41.06	5.14
332	333	0.033796	CCCGGACGCCCCTATATCTA	60.034	60.000	0.73	0.00	0.00	1.98
335	336	1.848652	GGACGCCCCTATATCTAGCA	58.151	55.000	0.00	0.00	0.00	3.49
340	341	3.449018	ACGCCCCTATATCTAGCATTCAG	59.551	47.826	0.00	0.00	0.00	3.02
354	355	2.481104	GCATTCAGCGAGTCTAGCTTCT	60.481	50.000	4.51	0.00	44.06	2.85
366	367	4.702612	AGTCTAGCTTCTGACTCGATGAAA	59.297	41.667	9.86	0.00	39.04	2.69
382	383	1.306997	AAAGGGGAGCGAGATGGGA	60.307	57.895	0.00	0.00	0.00	4.37
442	443	2.492484	GAGAGTGAGTTTTCGGGAGCTA	59.508	50.000	0.00	0.00	0.00	3.32
494	495	4.815846	GGGATACTAAAAACGCGGGAATAA	59.184	41.667	12.47	0.00	0.00	1.40
553	576	6.894339	ATCCTACAAGATTTTGGTTCGTTT	57.106	33.333	0.57	0.00	38.66	3.60
559	582	6.337356	ACAAGATTTTGGTTCGTTTGATTGT	58.663	32.000	0.57	0.00	38.66	2.71
567	590	4.634004	TGGTTCGTTTGATTGTAGCATAGG	59.366	41.667	0.00	0.00	0.00	2.57
665	689	4.163441	TCAACAAGGTTTGAGTGGATGA	57.837	40.909	0.00	0.00	31.68	2.92
679	703	3.711704	AGTGGATGATAGAAATCCCGTGT	59.288	43.478	0.18	0.00	42.63	4.49
740	772	9.787532	AATTCTATGAATCAAATAACCAACGTG	57.212	29.630	0.00	0.00	0.00	4.49
741	773	7.315247	TCTATGAATCAAATAACCAACGTGG	57.685	36.000	0.00	0.00	45.02	4.94
951	1014	3.787001	CCGCCTCCTCTTCCCCAC	61.787	72.222	0.00	0.00	0.00	4.61
1147	1210	1.597461	GAGTAGCCCGGCTGTTCTT	59.403	57.895	22.95	2.50	40.10	2.52
1251	1314	4.116585	AGAGAGAGGGCGAGGCGA	62.117	66.667	0.00	0.00	0.00	5.54
1404	1467	3.840831	CGTGAGGAATTGAGGCTGA	57.159	52.632	0.00	0.00	0.00	4.26
1535	1598	5.041951	TGTTCAAGTTTGTTGTGTCTGTC	57.958	39.130	0.00	0.00	0.00	3.51
1550	1613	2.095364	GTCTGTCGATAGTGTCAACCGT	60.095	50.000	9.16	0.00	37.40	4.83
1553	1616	2.293955	TGTCGATAGTGTCAACCGTGAA	59.706	45.455	0.00	0.00	34.10	3.18
1799	1862	0.890683	GGCTGGTGGAAAGGTTCATG	59.109	55.000	0.00	0.00	0.00	3.07
2141	2204	1.032014	GTGATGTTGGTTGTGTGCCT	58.968	50.000	0.00	0.00	0.00	4.75
2333	2396	7.148086	GCCCAGAAGTTGTTTGATGATATGTTA	60.148	37.037	0.00	0.00	0.00	2.41
2381	2444	8.600625	GTGTACACATACAATTCAATGATACGT	58.399	33.333	21.14	0.00	42.99	3.57
2416	2479	9.817809	CATAGTAGGTGAGTTTGATAAAGCTTA	57.182	33.333	0.00	0.00	0.00	3.09
2489	2552	7.040892	TCAGTGTACAGTACTTTAGTGTGTAGG	60.041	40.741	12.07	0.00	42.07	3.18
2602	2665	3.118445	GGGGGATATAGAAGATGCTGAGC	60.118	52.174	0.00	0.00	0.00	4.26
2869	2934	1.198713	CTGCTTAGGAGGGCTCTTCA	58.801	55.000	0.00	0.00	0.00	3.02
2885	2950	0.623723	TTCATACAGGGTTGAGGGCC	59.376	55.000	0.00	0.00	0.00	5.80
3263	3328	2.147150	GCTCCAACTCCAACTCAGTTC	58.853	52.381	0.00	0.00	31.40	3.01
3474	3540	3.770625	GCTTCAGCTCCTTACCCTC	57.229	57.895	0.00	0.00	38.21	4.30
3475	3541	1.199615	GCTTCAGCTCCTTACCCTCT	58.800	55.000	0.00	0.00	38.21	3.69
3476	3542	2.389715	GCTTCAGCTCCTTACCCTCTA	58.610	52.381	0.00	0.00	38.21	2.43
3477	3543	2.766828	GCTTCAGCTCCTTACCCTCTAA	59.233	50.000	0.00	0.00	38.21	2.10
3478	3544	3.389656	GCTTCAGCTCCTTACCCTCTAAT	59.610	47.826	0.00	0.00	38.21	1.73
3479	3545	4.502431	GCTTCAGCTCCTTACCCTCTAATC	60.502	50.000	0.00	0.00	38.21	1.75
3480	3546	3.223435	TCAGCTCCTTACCCTCTAATCG	58.777	50.000	0.00	0.00	0.00	3.34
3481	3547	3.117625	TCAGCTCCTTACCCTCTAATCGA	60.118	47.826	0.00	0.00	0.00	3.59
3482	3548	3.254657	CAGCTCCTTACCCTCTAATCGAG	59.745	52.174	0.00	0.00	39.57	4.04
3495	3561	6.573664	CTCTAATCGAGGAGAGATCAATGT	57.426	41.667	17.51	0.00	41.55	2.71
3496	3562	6.324561	TCTAATCGAGGAGAGATCAATGTG	57.675	41.667	0.00	0.00	0.00	3.21
3497	3563	2.879002	TCGAGGAGAGATCAATGTGC	57.121	50.000	0.00	0.00	0.00	4.57
3498	3564	2.102578	TCGAGGAGAGATCAATGTGCA	58.897	47.619	0.00	0.00	0.00	4.57
3499	3565	2.497273	TCGAGGAGAGATCAATGTGCAA	59.503	45.455	0.00	0.00	0.00	4.08
3500	3566	2.864946	CGAGGAGAGATCAATGTGCAAG	59.135	50.000	0.00	0.00	0.00	4.01
3501	3567	3.678252	CGAGGAGAGATCAATGTGCAAGT	60.678	47.826	0.00	0.00	0.00	3.16
3502	3568	3.607741	AGGAGAGATCAATGTGCAAGTG	58.392	45.455	0.00	0.00	0.00	3.16
3503	3569	2.097142	GGAGAGATCAATGTGCAAGTGC	59.903	50.000	0.00	0.00	42.50	4.40
3513	3579	4.240049	GCAAGTGCAAGCTTCAGC	57.760	55.556	0.00	0.00	41.59	4.26
3597	3663	3.727079	GCATCTCAACTCAACATTGCTCG	60.727	47.826	0.00	0.00	0.00	5.03
3635	3701	2.212900	CTGCTTGGTTTTAGCGGGGC	62.213	60.000	0.00	0.00	41.54	5.80

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	1.870580	CGTTGTCGTGCCTAGTCCAAA	60.871	52.381	0.00	0.00	0.00	3.28
1	2	0.319211	CGTTGTCGTGCCTAGTCCAA	60.319	55.000	0.00	0.00	0.00	3.53
2	3	1.287815	CGTTGTCGTGCCTAGTCCA	59.712	57.895	0.00	0.00	0.00	4.02
3	4	4.164252	CGTTGTCGTGCCTAGTCC	57.836	61.111	0.00	0.00	0.00	3.85
13	14	4.903638	AAGTTATGTCATCACGTTGTCG	57.096	40.909	0.00	0.00	43.34	4.35
14	15	7.347508	AGTTAAGTTATGTCATCACGTTGTC	57.652	36.000	0.00	0.00	0.00	3.18
15	16	8.086522	AGTAGTTAAGTTATGTCATCACGTTGT	58.913	33.333	0.00	0.00	0.00	3.32
16	17	8.462143	AGTAGTTAAGTTATGTCATCACGTTG	57.538	34.615	0.00	0.00	0.00	4.10
18	19	9.731819	CATAGTAGTTAAGTTATGTCATCACGT	57.268	33.333	0.00	0.00	0.00	4.49
19	20	9.731819	ACATAGTAGTTAAGTTATGTCATCACG	57.268	33.333	2.92	0.00	32.80	4.35
75	76	2.158957	TGCAGTCGATGACTTAATCCCC	60.159	50.000	0.00	0.00	41.37	4.81
87	88	1.068281	CTATCAGCACCTGCAGTCGAT	59.932	52.381	13.81	9.02	45.16	3.59
89	90	0.529337	CCTATCAGCACCTGCAGTCG	60.529	60.000	13.81	3.96	45.16	4.18
96	97	1.074167	CCCCCTCCTATCAGCACCT	60.074	63.158	0.00	0.00	0.00	4.00
111	112	2.835895	AAACACCCGCACAACCCC	60.836	61.111	0.00	0.00	0.00	4.95
123	124	7.075741	ACAATTGTCTCGCTATAAACAAACAC	58.924	34.615	4.92	0.00	35.46	3.32
127	128	5.353123	GGGACAATTGTCTCGCTATAAACAA	59.647	40.000	31.81	0.00	44.20	2.83
128	129	4.873827	GGGACAATTGTCTCGCTATAAACA	59.126	41.667	31.81	0.00	44.20	2.83
156	157	8.153550	GGAGAACCATATTCATAGTCTCACAAT	58.846	37.037	0.00	0.00	35.97	2.71
157	158	7.419057	GGGAGAACCATATTCATAGTCTCACAA	60.419	40.741	0.00	0.00	39.85	3.33
216	217	1.134946	GGCCCAATTTCTCCAATGTCG	59.865	52.381	0.00	0.00	0.00	4.35
219	220	2.302445	TGTTGGCCCAATTTCTCCAATG	59.698	45.455	0.00	0.00	40.29	2.82
229	230	3.540617	GTTGTTTTTCTGTTGGCCCAAT	58.459	40.909	0.00	0.00	0.00	3.16
236	237	3.266636	GTTGGGGGTTGTTTTTCTGTTG	58.733	45.455	0.00	0.00	0.00	3.33
241	242	4.126437	CAAGATGTTGGGGGTTGTTTTTC	58.874	43.478	0.00	0.00	0.00	2.29
247	248	3.133721	TGTTTTCAAGATGTTGGGGGTTG	59.866	43.478	2.33	0.00	34.09	3.77
248	249	3.379452	TGTTTTCAAGATGTTGGGGGTT	58.621	40.909	2.33	0.00	34.09	4.11
250	251	3.494223	GGTTGTTTTCAAGATGTTGGGGG	60.494	47.826	2.33	0.00	40.74	5.40
251	252	3.494223	GGGTTGTTTTCAAGATGTTGGGG	60.494	47.826	2.33	0.00	40.74	4.96
264	265	2.024369	AGAGGAGGTGTTGGGTTGTTTT	60.024	45.455	0.00	0.00	0.00	2.43
270	271	2.344093	ATACAGAGGAGGTGTTGGGT	57.656	50.000	0.00	0.00	0.00	4.51
279	280	3.964031	AGCTCCACCTTAATACAGAGGAG	59.036	47.826	0.00	0.00	43.04	3.69
280	281	3.706594	CAGCTCCACCTTAATACAGAGGA	59.293	47.826	0.00	0.00	36.84	3.71
287	288	5.193728	AGGAAAATCCAGCTCCACCTTAATA	59.806	40.000	0.00	0.00	39.61	0.98
295	296	0.323725	GGCAGGAAAATCCAGCTCCA	60.324	55.000	12.63	0.00	46.79	3.86
296	297	1.039785	GGGCAGGAAAATCCAGCTCC	61.040	60.000	12.63	8.93	43.03	4.70
297	298	1.379642	CGGGCAGGAAAATCCAGCTC	61.380	60.000	12.63	8.45	46.79	4.09
316	317	1.848652	TGCTAGATATAGGGGCGTCC	58.151	55.000	0.00	0.00	0.00	4.79
318	319	3.441101	TGAATGCTAGATATAGGGGCGT	58.559	45.455	0.00	0.00	0.00	5.68
332	333	1.110442	AGCTAGACTCGCTGAATGCT	58.890	50.000	0.00	0.00	40.11	3.79
335	336	3.020274	TCAGAAGCTAGACTCGCTGAAT	58.980	45.455	1.68	0.00	37.01	2.57
354	355	0.537188	GCTCCCCTTTCATCGAGTCA	59.463	55.000	0.00	0.00	0.00	3.41
359	360	0.390860	ATCTCGCTCCCCTTTCATCG	59.609	55.000	0.00	0.00	0.00	3.84
366	367	2.444895	GTCCCATCTCGCTCCCCT	60.445	66.667	0.00	0.00	0.00	4.79
402	403	4.956085	TCTCAAATCAAAGAGGTCGTTGA	58.044	39.130	10.20	10.20	45.46	3.18
404	405	4.752101	CACTCTCAAATCAAAGAGGTCGTT	59.248	41.667	4.57	0.00	42.72	3.85
408	409	5.559148	ACTCACTCTCAAATCAAAGAGGT	57.441	39.130	4.57	0.00	42.72	3.85
503	526	8.680001	TGAGATTAACATGACATTTCAATCCTG	58.320	33.333	0.00	0.00	34.61	3.86
642	666	4.338118	TCATCCACTCAAACCTTGTTGAAC	59.662	41.667	0.00	0.00	37.08	3.18
648	672	7.201767	GGATTTCTATCATCCACTCAAACCTTG	60.202	40.741	0.00	0.00	40.21	3.61
665	689	4.287552	ACTACCTCACACGGGATTTCTAT	58.712	43.478	0.00	0.00	0.00	1.98
717	749	6.317642	CCCACGTTGGTTATTTGATTCATAGA	59.682	38.462	0.00	0.00	35.17	1.98
783	815	5.010708	TCCTAAGGGCTCCTTTGATTTTT	57.989	39.130	11.15	0.00	41.69	1.94
863	919	4.494811	CACGCTCGTGCCAGATTA	57.505	55.556	9.55	0.00	39.39	1.75
951	1014	2.620115	AGATGGTTTGAGTTGCAGTGTG	59.380	45.455	0.00	0.00	0.00	3.82
1171	1234	1.667756	CGACACCGGTTCTTGAATCGA	60.668	52.381	16.38	0.00	0.00	3.59
1224	1287	0.388659	CCCTCTCTCTCCAGAATGCG	59.611	60.000	0.00	0.00	31.97	4.73
1404	1467	4.653341	CAGGACCTTGAGAATCCTATCTGT	59.347	45.833	0.00	0.00	41.07	3.41
1535	1598	2.666508	CCTTTCACGGTTGACACTATCG	59.333	50.000	0.00	0.00	0.00	2.92
1604	1667	0.457035	TCGTGTTATGGCGGTACCTC	59.543	55.000	10.90	0.69	40.22	3.85
1605	1668	0.458669	CTCGTGTTATGGCGGTACCT	59.541	55.000	10.90	0.00	40.22	3.08
2141	2204	4.460263	AGTTTGTGAAATGGAGCACACTA	58.540	39.130	0.00	0.00	43.97	2.74
2381	2444	1.912731	TCACCTACTATGCAAAGCCCA	59.087	47.619	0.00	0.00	0.00	5.36
2416	2479	5.401750	AGTCCATATCCTTCAGCATAGAGT	58.598	41.667	0.00	0.00	0.00	3.24
2489	2552	1.269448	TCCTTTCCAGCATTTCGCAAC	59.731	47.619	0.00	0.00	46.13	4.17
2602	2665	5.221722	TGCATTTTACTATAGGCCCTCTCAG	60.222	44.000	0.00	0.00	0.00	3.35
2869	2934	0.550147	ACTGGCCCTCAACCCTGTAT	60.550	55.000	0.00	0.00	32.40	2.29
2885	2950	9.695526	TTTGAAATGTGAATGGAAAATCTACTG	57.304	29.630	0.00	0.00	0.00	2.74
2953	3018	5.173854	CGAGAAAAAGAGCACATGAAAAACC	59.826	40.000	0.00	0.00	0.00	3.27
3263	3328	7.256286	CAGGCAAAGGAATTTGATTAGAAGAG	58.744	38.462	4.96	0.00	33.95	2.85
3472	3538	6.380995	CACATTGATCTCTCCTCGATTAGAG	58.619	44.000	14.90	14.90	46.44	2.43
3473	3539	5.278709	GCACATTGATCTCTCCTCGATTAGA	60.279	44.000	0.00	0.00	0.00	2.10
3474	3540	4.922692	GCACATTGATCTCTCCTCGATTAG	59.077	45.833	0.00	0.00	0.00	1.73
3475	3541	4.342092	TGCACATTGATCTCTCCTCGATTA	59.658	41.667	0.00	0.00	0.00	1.75
3476	3542	3.133542	TGCACATTGATCTCTCCTCGATT	59.866	43.478	0.00	0.00	0.00	3.34
3477	3543	2.697229	TGCACATTGATCTCTCCTCGAT	59.303	45.455	0.00	0.00	0.00	3.59
3478	3544	2.102578	TGCACATTGATCTCTCCTCGA	58.897	47.619	0.00	0.00	0.00	4.04
3479	3545	2.591571	TGCACATTGATCTCTCCTCG	57.408	50.000	0.00	0.00	0.00	4.63
3480	3546	3.622163	CACTTGCACATTGATCTCTCCTC	59.378	47.826	0.00	0.00	0.00	3.71
3481	3547	3.607741	CACTTGCACATTGATCTCTCCT	58.392	45.455	0.00	0.00	0.00	3.69
3482	3548	2.097142	GCACTTGCACATTGATCTCTCC	59.903	50.000	0.00	0.00	41.59	3.71
3483	3549	3.402058	GCACTTGCACATTGATCTCTC	57.598	47.619	0.00	0.00	41.59	3.20
3496	3562	4.240049	GCTGAAGCTTGCACTTGC	57.760	55.556	2.10	0.00	38.76	4.01
3506	3572	1.003003	AGAAGTTGGAGGAGCTGAAGC	59.997	52.381	0.00	0.00	42.49	3.86
3507	3573	3.513515	AGTAGAAGTTGGAGGAGCTGAAG	59.486	47.826	0.00	0.00	0.00	3.02
3508	3574	3.511477	AGTAGAAGTTGGAGGAGCTGAA	58.489	45.455	0.00	0.00	0.00	3.02
3509	3575	3.093057	GAGTAGAAGTTGGAGGAGCTGA	58.907	50.000	0.00	0.00	0.00	4.26
3510	3576	2.167487	GGAGTAGAAGTTGGAGGAGCTG	59.833	54.545	0.00	0.00	0.00	4.24
3511	3577	2.043801	AGGAGTAGAAGTTGGAGGAGCT	59.956	50.000	0.00	0.00	0.00	4.09
3512	3578	2.429250	GAGGAGTAGAAGTTGGAGGAGC	59.571	54.545	0.00	0.00	0.00	4.70
3513	3579	3.699038	CAGAGGAGTAGAAGTTGGAGGAG	59.301	52.174	0.00	0.00	0.00	3.69
3514	3580	3.702792	CAGAGGAGTAGAAGTTGGAGGA	58.297	50.000	0.00	0.00	0.00	3.71
3515	3581	2.167487	GCAGAGGAGTAGAAGTTGGAGG	59.833	54.545	0.00	0.00	0.00	4.30
3516	3582	2.828520	TGCAGAGGAGTAGAAGTTGGAG	59.171	50.000	0.00	0.00	0.00	3.86
3517	3583	2.889512	TGCAGAGGAGTAGAAGTTGGA	58.110	47.619	0.00	0.00	0.00	3.53
3597	3663	1.275573	AGTCCGTCAGAAAAGTAGGCC	59.724	52.381	0.00	0.00	0.00	5.19

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.