AutoCloner

Multiple sequence alignment - TraesCS5A01G333900

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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	TraesCS5A01G333900	chr5A	100.000	2859	0	0	1	2859	543566912	543569770	0.000000e+00	5280.0
1	TraesCS5A01G333900	chr5A	78.669	511	70	22	1102	1579	542063103	542063607	1.290000e-78	303.0
2	TraesCS5A01G333900	chr5A	78.378	333	46	15	1102	1418	643297827	643298149	2.910000e-45	193.0
3	TraesCS5A01G333900	chr5A	80.569	211	23	9	2334	2543	707525733	707525926	2.300000e-31	147.0
4	TraesCS5A01G333900	chr5B	88.807	2028	134	38	748	2726	517417473	517419456	0.000000e+00	2401.0
5	TraesCS5A01G333900	chr5B	83.796	685	81	17	2186	2857	575068097	575067430	8.700000e-175	623.0
6	TraesCS5A01G333900	chr5B	88.508	496	46	4	260	747	517416902	517417394	8.820000e-165	590.0
7	TraesCS5A01G333900	chr5B	78.274	649	92	27	1102	1723	517215784	517216410	3.480000e-99	372.0
8	TraesCS5A01G333900	chr5B	87.072	263	25	9	6	262	517412027	517412286	3.600000e-74	289.0
9	TraesCS5A01G333900	chr5D	94.334	1006	42	6	792	1784	428238140	428239143	0.000000e+00	1528.0
10	TraesCS5A01G333900	chr5D	85.485	1123	93	30	1774	2856	428241610	428242702	0.000000e+00	1107.0
11	TraesCS5A01G333900	chr5D	91.763	777	50	10	6	779	428237072	428237837	0.000000e+00	1068.0
12	TraesCS5A01G333900	chr5D	82.097	849	110	25	2026	2856	489771881	489772705	0.000000e+00	688.0
13	TraesCS5A01G333900	chr5D	81.007	874	116	32	2004	2859	468356548	468355707	0.000000e+00	649.0
14	TraesCS5A01G333900	chr5D	83.830	637	80	11	2219	2851	292818847	292818230	4.100000e-163	584.0
15	TraesCS5A01G333900	chr5D	78.066	693	109	28	2038	2718	368800361	368799700	5.740000e-107	398.0
16	TraesCS5A01G333900	chr5D	82.186	247	29	8	1483	1723	427582446	427582683	6.250000e-47	198.0
17	TraesCS5A01G333900	chr5D	77.593	241	32	9	1102	1325	427569041	427569276	2.990000e-25	126.0
18	TraesCS5A01G333900	chr3D	83.077	845	108	17	2026	2856	86365578	86366401	0.000000e+00	736.0
19	TraesCS5A01G333900	chr3D	90.141	71	7	0	2132	2202	179182649	179182719	3.030000e-15	93.5
20	TraesCS5A01G333900	chr2A	83.609	726	89	17	2145	2859	194478073	194477367	0.000000e+00	654.0
21	TraesCS5A01G333900	chr2D	81.784	796	96	18	2081	2856	33326496	33327262	3.130000e-174	621.0
22	TraesCS5A01G333900	chr2D	79.766	855	112	28	2026	2859	161397241	161396427	5.350000e-157	564.0
23	TraesCS5A01G333900	chr2D	83.473	478	55	14	2378	2853	448101865	448102320	9.470000e-115	424.0
24	TraesCS5A01G333900	chr6B	81.692	721	99	14	2148	2856	446293901	446294600	1.150000e-158	569.0
25	TraesCS5A01G333900	chr7D	89.831	413	39	3	2448	2859	186832681	186832271	7.020000e-146	527.0
26	TraesCS5A01G333900	chr7D	83.333	90	11	4	2081	2167	72118929	72119017	2.360000e-11	80.5
27	TraesCS5A01G333900	chr1A	86.611	478	52	8	2378	2853	32858001	32858468	4.220000e-143	518.0
28	TraesCS5A01G333900	chr1A	77.219	338	46	22	1102	1422	86559493	86559816	4.900000e-38	169.0
29	TraesCS5A01G333900	chr1A	73.578	545	101	19	2085	2607	278464761	278465284	4.900000e-38	169.0
30	TraesCS5A01G333900	chr1B	85.535	477	62	7	2378	2851	410054320	410053848	2.560000e-135	492.0
31	TraesCS5A01G333900	chr1B	96.970	33	1	0	1982	2014	577031737	577031769	3.980000e-04	56.5
32	TraesCS5A01G333900	chr2B	84.310	478	63	9	2378	2853	527868669	527869136	9.340000e-125	457.0
33	TraesCS5A01G333900	chr2B	79.612	103	15	4	2026	2126	615797090	615796992	5.110000e-08	69.4
34	TraesCS5A01G333900	chr6D	82.959	534	57	12	2326	2856	459790559	459791061	4.340000e-123	451.0
35	TraesCS5A01G333900	chr4A	81.373	102	17	2	2026	2125	80020749	80020850	6.570000e-12	82.4
36	TraesCS5A01G333900	chr3A	77.465	142	25	6	2026	2162	65824406	65824545	8.490000e-11	78.7
37	TraesCS5A01G333900	chrUn	100.000	34	0	0	1981	2014	372172440	372172407	2.380000e-06	63.9
38	TraesCS5A01G333900	chrUn	94.444	36	2	0	1986	2021	63180378	63180343	3.980000e-04	56.5
39	TraesCS5A01G333900	chr7A	100.000	34	0	0	2089	2122	675573332	675573299	2.380000e-06	63.9

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	TraesCS5A01G333900	chr5A	543566912	543569770	2858	False	5280.000000	5280	100.000000	1	2859	1	chr5A.!!$F2	2858
1	TraesCS5A01G333900	chr5A	542063103	542063607	504	False	303.000000	303	78.669000	1102	1579	1	chr5A.!!$F1	477
2	TraesCS5A01G333900	chr5B	517416902	517419456	2554	False	1495.500000	2401	88.657500	260	2726	2	chr5B.!!$F3	2466
3	TraesCS5A01G333900	chr5B	575067430	575068097	667	True	623.000000	623	83.796000	2186	2857	1	chr5B.!!$R1	671
4	TraesCS5A01G333900	chr5B	517215784	517216410	626	False	372.000000	372	78.274000	1102	1723	1	chr5B.!!$F1	621
5	TraesCS5A01G333900	chr5D	428237072	428242702	5630	False	1234.333333	1528	90.527333	6	2856	3	chr5D.!!$F4	2850
6	TraesCS5A01G333900	chr5D	489771881	489772705	824	False	688.000000	688	82.097000	2026	2856	1	chr5D.!!$F3	830
7	TraesCS5A01G333900	chr5D	468355707	468356548	841	True	649.000000	649	81.007000	2004	2859	1	chr5D.!!$R3	855
8	TraesCS5A01G333900	chr5D	292818230	292818847	617	True	584.000000	584	83.830000	2219	2851	1	chr5D.!!$R1	632
9	TraesCS5A01G333900	chr5D	368799700	368800361	661	True	398.000000	398	78.066000	2038	2718	1	chr5D.!!$R2	680
10	TraesCS5A01G333900	chr3D	86365578	86366401	823	False	736.000000	736	83.077000	2026	2856	1	chr3D.!!$F1	830
11	TraesCS5A01G333900	chr2A	194477367	194478073	706	True	654.000000	654	83.609000	2145	2859	1	chr2A.!!$R1	714
12	TraesCS5A01G333900	chr2D	33326496	33327262	766	False	621.000000	621	81.784000	2081	2856	1	chr2D.!!$F1	775
13	TraesCS5A01G333900	chr2D	161396427	161397241	814	True	564.000000	564	79.766000	2026	2859	1	chr2D.!!$R1	833
14	TraesCS5A01G333900	chr6B	446293901	446294600	699	False	569.000000	569	81.692000	2148	2856	1	chr6B.!!$F1	708
15	TraesCS5A01G333900	chr6D	459790559	459791061	502	False	451.000000	451	82.959000	2326	2856	1	chr6D.!!$F1	530

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
147	148	0.683973	TTAACCTTTGGCGGTACCGA	59.316	50.0	37.62	15.62	43.94	4.69	F
478	481	0.895530	GACTTCGATGACAGGGACCA	59.104	55.0	5.16	0.00	0.00	4.02	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1329	1730	0.044702	TCCATGGACCCCAGAGACAT	59.955	55.0	11.44	0.0	36.75	3.06	R
2294	5249	0.317479	AACGCAGAAGCTAGGAACGT	59.683	50.0	0.00	0.0	39.10	3.99	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
76	77	3.381908	ACCCAAGTAAGAGATAGACGCAG	59.618	47.826	0.00	0.00	0.00	5.18
78	79	3.243569	CCAAGTAAGAGATAGACGCAGGG	60.244	52.174	0.00	0.00	0.00	4.45
97	98	4.520492	CAGGGAAAGTAGTGCAGAAAACAT	59.480	41.667	0.00	0.00	0.00	2.71
101	102	6.348540	GGGAAAGTAGTGCAGAAAACATACAG	60.349	42.308	0.00	0.00	0.00	2.74
111	112	3.330701	AGAAAACATACAGGGAAGGCTGA	59.669	43.478	0.00	0.00	0.00	4.26
112	113	2.789409	AACATACAGGGAAGGCTGAC	57.211	50.000	0.00	0.00	0.00	3.51
128	129	4.646492	AGGCTGACAACTCAAGACAAAAAT	59.354	37.500	0.00	0.00	0.00	1.82
147	148	0.683973	TTAACCTTTGGCGGTACCGA	59.316	50.000	37.62	15.62	43.94	4.69
204	206	3.605922	GCATGTCATGAACGACGACAAAA	60.606	43.478	17.24	0.00	42.53	2.44
205	207	3.852471	TGTCATGAACGACGACAAAAG	57.148	42.857	0.00	0.00	38.84	2.27
206	208	3.449632	TGTCATGAACGACGACAAAAGA	58.550	40.909	0.00	0.00	38.84	2.52
207	209	3.244345	TGTCATGAACGACGACAAAAGAC	59.756	43.478	0.00	11.19	38.84	3.01
208	210	2.469886	TCATGAACGACGACAAAAGACG	59.530	45.455	0.00	0.00	0.00	4.18
209	211	1.912001	TGAACGACGACAAAAGACGT	58.088	45.000	0.00	0.00	45.32	4.34
210	212	1.584761	TGAACGACGACAAAAGACGTG	59.415	47.619	0.00	0.00	42.74	4.49
211	213	1.585214	GAACGACGACAAAAGACGTGT	59.415	47.619	0.00	0.00	42.74	4.49
332	335	5.934935	AAAAACGACAACGATACCTCAAT	57.065	34.783	0.00	0.00	42.66	2.57
342	345	3.759618	ACGATACCTCAATAGCCTAGAGC	59.240	47.826	0.00	0.00	44.25	4.09
360	363	2.422231	CCGAGAGTCTGCTCAGGGG	61.422	68.421	0.00	0.00	44.00	4.79
362	365	1.383456	CGAGAGTCTGCTCAGGGGAG	61.383	65.000	0.00	0.00	44.00	4.30
377	380	2.197465	GGGGAGAACTAGAACACCCAT	58.803	52.381	20.09	0.00	38.38	4.00
380	383	4.412528	GGGGAGAACTAGAACACCCATATT	59.587	45.833	20.09	0.00	38.38	1.28
381	384	5.368989	GGGAGAACTAGAACACCCATATTG	58.631	45.833	16.24	0.00	37.00	1.90
383	386	6.183361	GGGAGAACTAGAACACCCATATTGAT	60.183	42.308	16.24	0.00	37.00	2.57
387	390	9.213777	AGAACTAGAACACCCATATTGATAAGA	57.786	33.333	0.00	0.00	0.00	2.10
410	413	2.499289	ACATCAGCAGGACTAGAAGTGG	59.501	50.000	0.00	0.00	0.00	4.00
478	481	0.895530	GACTTCGATGACAGGGACCA	59.104	55.000	5.16	0.00	0.00	4.02
517	521	4.377839	TTCAATGTTTTCGGTTTGCTCA	57.622	36.364	0.00	0.00	0.00	4.26
522	526	4.377839	TGTTTTCGGTTTGCTCAATTCA	57.622	36.364	0.00	0.00	0.00	2.57
525	529	5.066634	TGTTTTCGGTTTGCTCAATTCAGTA	59.933	36.000	0.00	0.00	0.00	2.74
529	533	6.325919	TCGGTTTGCTCAATTCAGTATTTT	57.674	33.333	0.00	0.00	0.00	1.82
554	558	8.690203	TTAGAATTCAGTCTTCCATTTTGACA	57.310	30.769	8.44	0.00	33.56	3.58
572	576	6.477053	TTGACAATCAAATTGGTCTTTCCA	57.523	33.333	4.82	0.00	44.42	3.53
600	605	5.930837	TCATTGTTTGGTCTTTGGTCTTT	57.069	34.783	0.00	0.00	0.00	2.52
601	606	7.340743	TCTTCATTGTTTGGTCTTTGGTCTTTA	59.659	33.333	0.00	0.00	0.00	1.85
630	642	8.088463	AGGATGATAATTTGCCAAATAAACCA	57.912	30.769	2.54	0.73	0.00	3.67
680	692	7.167302	GTCTCATTCTACAACTCAGATTCATCG	59.833	40.741	0.00	0.00	0.00	3.84
732	744	3.196039	TGCAGCATTAAAATCACCAGCAT	59.804	39.130	0.00	0.00	0.00	3.79
795	1175	3.535629	TTGTGACCGCAGCCTCAGG	62.536	63.158	0.00	0.00	0.00	3.86
810	1190	4.796231	AGGCACGCGTCATCGTCC	62.796	66.667	9.86	4.22	41.21	4.79
883	1263	0.981183	ATTCCGTCTACCAGCACCAA	59.019	50.000	0.00	0.00	0.00	3.67
933	1313	4.063967	CGGCACCCACGTCTGCTA	62.064	66.667	8.79	0.00	33.63	3.49
1255	1653	2.761195	CGATGACGTCCTCCTCGCA	61.761	63.158	14.12	0.00	31.42	5.10
1309	1710	4.200283	CGACGCTGAGGAGGAGCC	62.200	72.222	0.00	0.00	32.41	4.70
1329	1730	0.532573	GATCGTCAAGGAGACTGCCA	59.467	55.000	0.00	0.00	45.32	4.92
1349	1750	0.909610	TGTCTCTGGGGTCCATGGAC	60.910	60.000	33.14	33.14	43.87	4.02
1385	1786	1.213013	GAAGAGCTCGGCGAACTCA	59.787	57.895	33.73	4.05	32.71	3.41
1406	1807	4.373116	TGCAAGGACCTCGCCGTC	62.373	66.667	0.92	0.00	0.00	4.79
1418	1819	3.437795	GCCGTCGACGAGGAGGAA	61.438	66.667	37.65	0.00	43.02	3.36
1463	1876	3.550431	CCGCTGGGGTCGATGGAT	61.550	66.667	1.98	0.00	0.00	3.41
1630	2064	2.101582	GGTACGGAGACTACTCGGAGTA	59.898	54.545	16.50	16.50	43.21	2.59
1694	2130	3.365820	CGTTTCGTTTCACCGTAGCTATT	59.634	43.478	0.00	0.00	0.00	1.73
1825	4738	1.980036	GAACCCACCCAACTACTACCA	59.020	52.381	0.00	0.00	0.00	3.25
1829	4742	1.553704	CCACCCAACTACTACCACCTC	59.446	57.143	0.00	0.00	0.00	3.85
1836	4749	1.183549	CTACTACCACCTCCGTGCTT	58.816	55.000	0.00	0.00	38.79	3.91
1843	4756	1.613255	CCACCTCCGTGCTTATTGGTT	60.613	52.381	0.00	0.00	38.79	3.67
1847	4760	2.420022	CCTCCGTGCTTATTGGTTCAAG	59.580	50.000	0.00	0.00	0.00	3.02
1857	4770	3.691049	ATTGGTTCAAGTGTGTGTTCG	57.309	42.857	0.00	0.00	0.00	3.95
1888	4801	4.937620	CCTCCTTCGTGATTTGAATCTGAA	59.062	41.667	5.42	8.01	36.39	3.02
1889	4802	5.412594	CCTCCTTCGTGATTTGAATCTGAAA	59.587	40.000	5.42	0.00	36.39	2.69
1977	4890	2.942905	ACTCCCTCCCTCCCAAAATTA	58.057	47.619	0.00	0.00	0.00	1.40
2021	4934	2.027625	CGCCTCAAACCCGTCTCAC	61.028	63.158	0.00	0.00	0.00	3.51
2022	4935	1.671379	GCCTCAAACCCGTCTCACC	60.671	63.158	0.00	0.00	0.00	4.02
2082	5010	1.201414	CCCCCTTAAACGTGCATCAAC	59.799	52.381	0.00	0.00	0.00	3.18
2114	5044	1.971357	CGACACCCCTTATATCCAGCT	59.029	52.381	0.00	0.00	0.00	4.24
2217	5169	1.923395	CCACCCCCAAGACCTGCTA	60.923	63.158	0.00	0.00	0.00	3.49
2247	5201	4.534647	TGCTATCCTCTCTTCTTCCTCT	57.465	45.455	0.00	0.00	0.00	3.69
2250	5204	4.039124	GCTATCCTCTCTTCTTCCTCTTGG	59.961	50.000	0.00	0.00	0.00	3.61
2271	5225	1.016130	CGATGTCCGTCTTGCAGCTT	61.016	55.000	0.00	0.00	0.00	3.74
2273	5227	0.035317	ATGTCCGTCTTGCAGCTTCA	59.965	50.000	0.00	0.00	0.00	3.02
2277	5232	1.016130	CCGTCTTGCAGCTTCATCGT	61.016	55.000	0.00	0.00	0.00	3.73
2305	5260	1.178276	CTCCACAGACGTTCCTAGCT	58.822	55.000	0.00	0.00	0.00	3.32
2312	5267	0.109226	GACGTTCCTAGCTTCTGCGT	60.109	55.000	0.00	0.00	45.42	5.24
2322	5277	1.670406	CTTCTGCGTTGCCAGCTCT	60.670	57.895	0.00	0.00	35.28	4.09
2339	5300	3.071206	TGCAGTCCTCTCTCCCGC	61.071	66.667	0.00	0.00	0.00	6.13
2739	5706	1.625818	CACAGGGACTACTTTGCTCCT	59.374	52.381	0.00	0.00	36.02	3.69
2832	5810	2.224159	TGAAGGGAGTGGAGGCACC	61.224	63.158	0.00	0.00	39.54	5.01

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
1	2	0.464036	TGCGCCCCTTATAGTCAGTG	59.536	55.000	4.18	0.00	0.00	3.66
2	3	1.424638	ATGCGCCCCTTATAGTCAGT	58.575	50.000	4.18	0.00	0.00	3.41
3	4	3.895232	ATATGCGCCCCTTATAGTCAG	57.105	47.619	4.18	0.00	0.00	3.51
4	5	4.081862	GTGTATATGCGCCCCTTATAGTCA	60.082	45.833	4.18	0.00	0.00	3.41
17	18	5.378292	ACTCTCTATGTGGTGTATATGCG	57.622	43.478	0.00	0.00	0.00	4.73
76	77	5.472137	TGTATGTTTTCTGCACTACTTTCCC	59.528	40.000	0.00	0.00	0.00	3.97
78	79	6.348540	CCCTGTATGTTTTCTGCACTACTTTC	60.349	42.308	0.00	0.00	0.00	2.62
97	98	1.623811	GAGTTGTCAGCCTTCCCTGTA	59.376	52.381	0.00	0.00	34.47	2.74
101	102	1.072331	TCTTGAGTTGTCAGCCTTCCC	59.928	52.381	0.00	0.00	32.98	3.97
111	112	9.150348	CAAAGGTTAATTTTTGTCTTGAGTTGT	57.850	29.630	6.52	0.00	31.36	3.32
112	113	8.603181	CCAAAGGTTAATTTTTGTCTTGAGTTG	58.397	33.333	11.39	0.00	33.52	3.16
128	129	0.683973	TCGGTACCGCCAAAGGTTAA	59.316	50.000	29.64	5.07	43.00	2.01
147	148	3.034635	AGGCTTCGTCTCATGAGGTATT	58.965	45.455	22.42	0.00	0.00	1.89
194	196	2.706760	AAACACGTCTTTTGTCGTCG	57.293	45.000	0.00	0.00	41.75	5.12
204	206	5.334879	GGCATAGAATCAACAAAACACGTCT	60.335	40.000	0.00	0.00	0.00	4.18
205	207	4.851558	GGCATAGAATCAACAAAACACGTC	59.148	41.667	0.00	0.00	0.00	4.34
206	208	4.277174	TGGCATAGAATCAACAAAACACGT	59.723	37.500	0.00	0.00	0.00	4.49
207	209	4.616802	GTGGCATAGAATCAACAAAACACG	59.383	41.667	0.00	0.00	0.00	4.49
208	210	5.527951	TGTGGCATAGAATCAACAAAACAC	58.472	37.500	0.00	0.00	0.00	3.32
209	211	5.781210	TGTGGCATAGAATCAACAAAACA	57.219	34.783	0.00	0.00	0.00	2.83
210	212	5.982516	TGTTGTGGCATAGAATCAACAAAAC	59.017	36.000	14.37	0.00	43.02	2.43
211	213	6.154203	TGTTGTGGCATAGAATCAACAAAA	57.846	33.333	14.37	0.00	43.02	2.44
215	217	5.565592	TCATGTTGTGGCATAGAATCAAC	57.434	39.130	8.87	8.87	38.82	3.18
258	260	4.096984	CACCTCCACTTTATGATGCCTTTC	59.903	45.833	0.00	0.00	0.00	2.62
314	317	3.490419	GGCTATTGAGGTATCGTTGTCGT	60.490	47.826	0.00	0.00	38.33	4.34
315	318	3.050619	GGCTATTGAGGTATCGTTGTCG	58.949	50.000	0.00	0.00	38.55	4.35
316	319	4.323553	AGGCTATTGAGGTATCGTTGTC	57.676	45.455	0.00	0.00	0.00	3.18
317	320	5.138276	TCTAGGCTATTGAGGTATCGTTGT	58.862	41.667	0.00	0.00	0.00	3.32
332	335	1.133363	AGACTCTCGGCTCTAGGCTA	58.867	55.000	1.82	0.00	41.46	3.93
342	345	2.422231	CCCCTGAGCAGACTCTCGG	61.422	68.421	0.00	4.59	43.85	4.63
360	363	9.482627	CTTATCAATATGGGTGTTCTAGTTCTC	57.517	37.037	0.00	0.00	0.00	2.87
362	365	9.832445	TTCTTATCAATATGGGTGTTCTAGTTC	57.168	33.333	0.00	0.00	0.00	3.01
377	380	7.568349	AGTCCTGCTGATGTTTCTTATCAATA	58.432	34.615	0.00	0.00	34.41	1.90
380	383	5.426689	AGTCCTGCTGATGTTTCTTATCA	57.573	39.130	0.00	0.00	33.76	2.15
381	384	6.810911	TCTAGTCCTGCTGATGTTTCTTATC	58.189	40.000	0.00	0.00	0.00	1.75
383	386	6.211584	ACTTCTAGTCCTGCTGATGTTTCTTA	59.788	38.462	0.00	0.00	0.00	2.10
387	390	4.564406	CCACTTCTAGTCCTGCTGATGTTT	60.564	45.833	0.00	0.00	0.00	2.83
410	413	8.556194	TGTTATTTGTTGTCTAGTGTGTTCATC	58.444	33.333	0.00	0.00	0.00	2.92
478	481	0.823356	AATGCCTGGCTTTGTCGTGT	60.823	50.000	21.03	0.00	0.00	4.49
529	533	8.690203	TGTCAAAATGGAAGACTGAATTCTAA	57.310	30.769	7.05	0.00	33.56	2.10
572	576	5.422012	ACCAAAGACCAAACAATGAAGAACT	59.578	36.000	0.00	0.00	0.00	3.01
630	642	6.210185	ACTTGAGAGCAGGCTTTATGAAATTT	59.790	34.615	0.00	0.00	0.00	1.82
642	654	2.093553	AGAATGAGACTTGAGAGCAGGC	60.094	50.000	0.00	0.00	0.00	4.85
680	692	9.558396	ACCTACTGTGTATTCTATACTAGACAC	57.442	37.037	0.00	0.00	33.84	3.67
757	847	3.412237	AGCACCAGTGTAAAATACCGT	57.588	42.857	0.00	0.00	0.00	4.83
883	1263	1.125711	GTGGGGTACAGGTGTCTGGT	61.126	60.000	0.00	0.00	44.99	4.00
1329	1730	0.044702	TCCATGGACCCCAGAGACAT	59.955	55.000	11.44	0.00	36.75	3.06
1349	1750	2.055042	CCTCGTCCTCCAGTCCAGG	61.055	68.421	0.00	0.00	0.00	4.45
1385	1786	2.437359	GCGAGGTCCTTGCAGCAT	60.437	61.111	24.27	0.00	40.38	3.79
1406	1807	2.405594	CGCTCTTCCTCCTCGTCG	59.594	66.667	0.00	0.00	0.00	5.12
1418	1819	2.282958	TCCTTGACGACCCGCTCT	60.283	61.111	0.00	0.00	0.00	4.09
1463	1876	0.475632	TCCTTGCCCTCCTTTCCAGA	60.476	55.000	0.00	0.00	0.00	3.86
1624	2058	2.146920	AACCCCTTCTCTCTACTCCG	57.853	55.000	0.00	0.00	0.00	4.63
1630	2064	2.695585	ACACAGAAACCCCTTCTCTCT	58.304	47.619	0.00	0.00	42.84	3.10
1631	2065	4.618920	TTACACAGAAACCCCTTCTCTC	57.381	45.455	0.00	0.00	42.84	3.20
1632	2066	5.584551	AATTACACAGAAACCCCTTCTCT	57.415	39.130	0.00	0.00	42.84	3.10
1694	2130	5.968848	CGTTTTCCATTTCGTCTCTGAAAAA	59.031	36.000	0.00	0.00	40.90	1.94
1755	2191	5.008712	CGCTAACCACCTTCTTTTTCTTCTT	59.991	40.000	0.00	0.00	0.00	2.52
1825	4738	1.349688	TGAACCAATAAGCACGGAGGT	59.650	47.619	0.00	0.00	0.00	3.85
1829	4742	2.552315	ACACTTGAACCAATAAGCACGG	59.448	45.455	0.00	0.00	0.00	4.94
1836	4749	3.562141	CCGAACACACACTTGAACCAATA	59.438	43.478	0.00	0.00	0.00	1.90
1843	4756	3.810941	GGAAATACCGAACACACACTTGA	59.189	43.478	0.00	0.00	0.00	3.02
1847	4760	2.740447	GAGGGAAATACCGAACACACAC	59.260	50.000	0.00	0.00	40.11	3.82
1857	4770	3.840124	ATCACGAAGGAGGGAAATACC	57.160	47.619	0.00	0.00	38.08	2.73
1929	4842	4.987408	TCAATATGCCTTCCACACAATG	57.013	40.909	0.00	0.00	0.00	2.82
1940	4853	5.348833	AGGGAGTAGATGATCAATATGCCT	58.651	41.667	0.00	1.77	0.00	4.75
1977	4890	5.453057	CCAGCTGTAGATGCTCTAAGACAAT	60.453	44.000	13.81	0.00	38.92	2.71
2002	4915	2.342648	GAGACGGGTTTGAGGCGT	59.657	61.111	0.00	0.00	0.00	5.68
2021	4934	1.033574	GACCAGATAGTGACCGAGGG	58.966	60.000	0.00	0.00	0.00	4.30
2022	4935	1.763968	TGACCAGATAGTGACCGAGG	58.236	55.000	0.00	0.00	0.00	4.63
2096	5026	3.060479	TGAGCTGGATATAAGGGGTGT	57.940	47.619	0.00	0.00	0.00	4.16
2114	5044	3.013921	GCCCGAACACCTTCATATTTGA	58.986	45.455	0.00	0.00	0.00	2.69
2174	5125	5.495926	TTGATGCAATTTACAATGGGGTT	57.504	34.783	0.00	0.00	0.00	4.11
2217	5169	5.845614	AGAAGAGAGGATAGCAAATGGATCT	59.154	40.000	0.00	0.00	0.00	2.75
2247	5201	1.375396	CAAGACGGACATCGCCCAA	60.375	57.895	0.00	0.00	43.89	4.12
2250	5204	2.434185	TGCAAGACGGACATCGCC	60.434	61.111	0.00	0.00	43.89	5.54
2294	5249	0.317479	AACGCAGAAGCTAGGAACGT	59.683	50.000	0.00	0.00	39.10	3.99
2305	5260	1.962822	CAGAGCTGGCAACGCAGAA	60.963	57.895	0.00	0.00	38.34	3.02
2312	5267	2.033141	GGACTGCAGAGCTGGCAA	59.967	61.111	23.35	0.00	41.39	4.52
2322	5277	3.071206	GCGGGAGAGAGGACTGCA	61.071	66.667	0.00	0.00	36.53	4.41
2339	5300	4.275508	CATCCCCCATGGCGAGGG	62.276	72.222	16.53	16.53	46.36	4.30
2374	5335	4.386951	CCATGGTGGCGTCCGACA	62.387	66.667	2.57	0.00	0.00	4.35
2375	5336	2.306255	ATACCATGGTGGCGTCCGAC	62.306	60.000	28.17	0.00	42.67	4.79
2376	5337	2.061578	ATACCATGGTGGCGTCCGA	61.062	57.895	28.17	4.74	42.67	4.55
2377	5338	1.887242	CATACCATGGTGGCGTCCG	60.887	63.158	28.17	3.79	42.67	4.79
2378	5339	0.814010	GACATACCATGGTGGCGTCC	60.814	60.000	28.17	11.00	42.67	4.79
2379	5340	0.814010	GGACATACCATGGTGGCGTC	60.814	60.000	28.17	25.81	42.67	5.19
2380	5341	1.223487	GGACATACCATGGTGGCGT	59.777	57.895	28.17	20.01	42.67	5.68
2381	5342	1.887242	CGGACATACCATGGTGGCG	60.887	63.158	28.17	16.94	42.67	5.69
2440	5402	3.322211	TCGGTCGGACAATGTGTTAAT	57.678	42.857	10.76	0.00	0.00	1.40
2441	5403	2.816204	TCGGTCGGACAATGTGTTAA	57.184	45.000	10.76	0.00	0.00	2.01
2442	5404	2.816204	TTCGGTCGGACAATGTGTTA	57.184	45.000	10.76	0.00	0.00	2.41
2443	5405	2.178912	ATTCGGTCGGACAATGTGTT	57.821	45.000	10.76	0.00	0.00	3.32
2444	5406	2.178912	AATTCGGTCGGACAATGTGT	57.821	45.000	10.76	0.00	0.00	3.72
2445	5407	3.552604	AAAATTCGGTCGGACAATGTG	57.447	42.857	10.76	0.00	0.00	3.21
2619	5585	1.283613	TCCACTTGCCGGTCCATTTAT	59.716	47.619	1.90	0.00	0.00	1.40
2620	5586	0.693622	TCCACTTGCCGGTCCATTTA	59.306	50.000	1.90	0.00	0.00	1.40
2739	5706	3.017048	TCGTCCGGGAAAGTAGGATTA	57.983	47.619	0.00	0.00	36.34	1.75
2832	5810	0.784778	GAGCTTGAAGTTGTCGTCGG	59.215	55.000	0.00	0.00	0.00	4.79

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.