AutoCloner

Multiple sequence alignment - TraesCS3D01G539300

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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	TraesCS3D01G539300	chr3D	100.000	2630	0	0	1	2630	611406334	611408963	0.000000e+00	4857.0
1	TraesCS3D01G539300	chr3A	89.828	1632	103	18	1	1600	746260413	746262013	0.000000e+00	2036.0
2	TraesCS3D01G539300	chr3A	85.154	714	51	21	1550	2213	746262026	746262734	0.000000e+00	680.0
3	TraesCS3D01G539300	chr3A	94.865	370	15	3	2262	2630	746262857	746263223	2.270000e-160	575.0
4	TraesCS3D01G539300	chr3A	84.564	149	20	3	2302	2450	746289948	746290093	7.590000e-31	145.0
5	TraesCS3D01G539300	chr3A	94.444	54	3	0	2210	2263	746262773	746262826	1.680000e-12	84.2
6	TraesCS3D01G539300	chr3B	87.383	1823	102	42	852	2630	829112868	829114606	0.000000e+00	1975.0
7	TraesCS3D01G539300	chr3B	80.769	234	14	7	591	808	829112653	829112871	1.260000e-33	154.0
8	TraesCS3D01G539300	chr6B	81.961	765	98	32	740	1489	28925791	28926530	1.730000e-171	612.0
9	TraesCS3D01G539300	chr6B	81.358	692	90	32	810	1489	28256808	28256144	6.450000e-146	527.0
10	TraesCS3D01G539300	chr6D	82.733	666	74	29	864	1512	24001443	24002084	2.960000e-154	555.0
11	TraesCS3D01G539300	chr6D	80.497	764	105	29	739	1489	16529762	16529030	1.780000e-151	545.0
12	TraesCS3D01G539300	chr6D	80.403	694	105	26	810	1489	16307426	16306750	1.410000e-137	499.0
13	TraesCS3D01G539300	chr6D	85.371	499	48	14	999	1489	16390085	16389604	6.540000e-136	494.0
14	TraesCS3D01G539300	chr6D	96.970	33	1	0	2481	2513	267129850	267129818	3.660000e-04	56.5
15	TraesCS3D01G539300	chr5D	80.313	767	107	32	739	1489	514924342	514923604	8.280000e-150	540.0
16	TraesCS3D01G539300	chr5D	83.544	474	63	12	1	465	59966566	59967033	1.870000e-116	429.0
17	TraesCS3D01G539300	chr5D	81.143	175	25	2	1998	2164	213079478	213079652	1.640000e-27	134.0
18	TraesCS3D01G539300	chr5D	81.897	116	19	2	2312	2427	213079865	213079978	2.150000e-16	97.1
19	TraesCS3D01G539300	chr5D	79.208	101	19	2	2472	2572	213080058	213080156	4.700000e-08	69.4
20	TraesCS3D01G539300	chr6A	79.844	769	117	27	740	1489	16802284	16801535	6.450000e-146	527.0
21	TraesCS3D01G539300	chr6A	83.662	557	63	22	946	1489	16720242	16719701	1.410000e-137	499.0
22	TraesCS3D01G539300	chr1B	84.324	555	60	22	946	1489	587472841	587473379	3.880000e-143	518.0
23	TraesCS3D01G539300	chr5B	79.716	774	110	30	739	1489	647387578	647386829	1.400000e-142	516.0
24	TraesCS3D01G539300	chr5B	82.526	475	64	15	1	465	682461563	682462028	1.470000e-107	399.0
25	TraesCS3D01G539300	chr5B	80.337	178	26	5	1998	2167	690061818	690061642	2.750000e-25	126.0
26	TraesCS3D01G539300	chr5A	84.483	464	61	7	1	457	524742771	524742312	5.160000e-122	448.0
27	TraesCS3D01G539300	chr1A	83.918	485	57	15	1021	1499	21022856	21023325	6.680000e-121	444.0
28	TraesCS3D01G539300	chr7D	82.178	505	75	13	1020	1512	617735752	617735251	1.130000e-113	420.0
29	TraesCS3D01G539300	chr7D	84.483	116	16	2	2312	2427	52623761	52623874	2.140000e-21	113.0
30	TraesCS3D01G539300	chr7A	82.479	468	59	16	1	456	189712842	189713298	3.170000e-104	388.0
31	TraesCS3D01G539300	chr7B	82.265	468	64	14	1	458	572030583	572030125	1.140000e-103	387.0
32	TraesCS3D01G539300	chr7B	80.901	466	73	13	1	458	735910326	735910783	1.160000e-93	353.0
33	TraesCS3D01G539300	chr2B	81.551	477	65	19	1	465	63263247	63263712	3.200000e-99	372.0
34	TraesCS3D01G539300	chr2B	80.720	472	70	14	4	465	151622567	151622107	5.390000e-92	348.0
35	TraesCS3D01G539300	chr2D	82.022	178	24	2	1998	2167	56185008	56184831	7.590000e-31	145.0
36	TraesCS3D01G539300	chr2D	84.071	113	16	2	2315	2427	56184618	56184508	9.950000e-20	108.0

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	TraesCS3D01G539300	chr3D	611406334	611408963	2629	False	4857.0	4857	100.00000	1	2630	1	chr3D.!!$F1	2629
1	TraesCS3D01G539300	chr3A	746260413	746263223	2810	False	843.8	2036	91.07275	1	2630	4	chr3A.!!$F2	2629
2	TraesCS3D01G539300	chr3B	829112653	829114606	1953	False	1064.5	1975	84.07600	591	2630	2	chr3B.!!$F1	2039
3	TraesCS3D01G539300	chr6B	28925791	28926530	739	False	612.0	612	81.96100	740	1489	1	chr6B.!!$F1	749
4	TraesCS3D01G539300	chr6B	28256144	28256808	664	True	527.0	527	81.35800	810	1489	1	chr6B.!!$R1	679
5	TraesCS3D01G539300	chr6D	24001443	24002084	641	False	555.0	555	82.73300	864	1512	1	chr6D.!!$F1	648
6	TraesCS3D01G539300	chr6D	16529030	16529762	732	True	545.0	545	80.49700	739	1489	1	chr6D.!!$R3	750
7	TraesCS3D01G539300	chr6D	16306750	16307426	676	True	499.0	499	80.40300	810	1489	1	chr6D.!!$R1	679
8	TraesCS3D01G539300	chr5D	514923604	514924342	738	True	540.0	540	80.31300	739	1489	1	chr5D.!!$R1	750
9	TraesCS3D01G539300	chr6A	16801535	16802284	749	True	527.0	527	79.84400	740	1489	1	chr6A.!!$R2	749
10	TraesCS3D01G539300	chr6A	16719701	16720242	541	True	499.0	499	83.66200	946	1489	1	chr6A.!!$R1	543
11	TraesCS3D01G539300	chr1B	587472841	587473379	538	False	518.0	518	84.32400	946	1489	1	chr1B.!!$F1	543
12	TraesCS3D01G539300	chr5B	647386829	647387578	749	True	516.0	516	79.71600	739	1489	1	chr5B.!!$R1	750
13	TraesCS3D01G539300	chr7D	617735251	617735752	501	True	420.0	420	82.17800	1020	1512	1	chr7D.!!$R1	492

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
179	181	0.040425	GACGCCGTGAGCAAAACAAT	60.04	50.0	0.0	0.0	44.04	2.71	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1983	2228	0.039035	CCCAAATCCTTCGTTCCCCA	59.961	55.0	0.0	0.0	0.0	4.96	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
17	18	4.549793	ACACATGGCACGAACACA	57.450	50.000	0.00	0.00	0.00	3.72
37	38	2.282180	GGGGCGTGAACATGGTGT	60.282	61.111	0.00	0.00	0.00	4.16
40	41	1.599518	GGCGTGAACATGGTGTCCA	60.600	57.895	0.00	0.00	38.19	4.02
42	43	0.238289	GCGTGAACATGGTGTCCAAG	59.762	55.000	0.00	0.00	36.95	3.61
45	46	0.888736	TGAACATGGTGTCCAAGGCG	60.889	55.000	0.00	0.00	36.95	5.52
60	61	1.110442	AGGCGGAGAGACAAGAGATG	58.890	55.000	0.00	0.00	0.00	2.90
64	65	1.747924	CGGAGAGACAAGAGATGCTCA	59.252	52.381	0.00	0.00	35.76	4.26
93	95	8.432359	CCAAAACAAAGAAGAACACAACTAAAC	58.568	33.333	0.00	0.00	0.00	2.01
97	99	5.405331	AAGAAGAACACAACTAAACTCGC	57.595	39.130	0.00	0.00	0.00	5.03
132	134	2.025898	ACCCAACCAACAACTAAACGG	58.974	47.619	0.00	0.00	0.00	4.44
156	158	5.622233	GCCAAACATCTCCAAATCTAACACC	60.622	44.000	0.00	0.00	0.00	4.16
160	162	3.887621	TCTCCAAATCTAACACCGAGG	57.112	47.619	0.00	0.00	0.00	4.63
162	164	3.194968	TCTCCAAATCTAACACCGAGGAC	59.805	47.826	0.00	0.00	0.00	3.85
167	169	2.985282	TAACACCGAGGACGCCGT	60.985	61.111	0.00	0.00	38.29	5.68
168	170	3.271706	TAACACCGAGGACGCCGTG	62.272	63.158	0.00	0.00	37.57	4.94
179	181	0.040425	GACGCCGTGAGCAAAACAAT	60.040	50.000	0.00	0.00	44.04	2.71
185	187	2.970609	CCGTGAGCAAAACAATACAACG	59.029	45.455	0.00	0.00	0.00	4.10
211	213	1.859427	CGAAGGAGAACGACACCGGA	61.859	60.000	9.46	0.00	40.78	5.14
255	257	1.203441	AACCGGACCTAGGGTTTCCC	61.203	60.000	14.81	5.14	43.84	3.97
295	297	3.141398	CACGAATAATGGCCATAGCAGT	58.859	45.455	21.15	12.89	42.56	4.40
335	344	4.147449	TGTCGCCGCTGCTAGCAT	62.147	61.111	19.72	0.00	42.58	3.79
336	345	2.027605	GTCGCCGCTGCTAGCATA	59.972	61.111	19.72	0.00	42.58	3.14
339	348	0.875908	TCGCCGCTGCTAGCATAAAG	60.876	55.000	19.72	7.67	42.58	1.85
357	366	0.835941	AGATGCAGAGATTTCGCCCT	59.164	50.000	0.00	0.00	0.00	5.19
358	367	1.202627	AGATGCAGAGATTTCGCCCTC	60.203	52.381	0.00	0.00	0.00	4.30
397	406	1.004277	CAAGTCGTCGGAGCACAGAC	61.004	60.000	4.43	4.43	37.74	3.51
404	413	2.574399	GGAGCACAGACCGGAGAC	59.426	66.667	9.46	0.00	0.00	3.36
425	434	2.590007	GCAGCTGGTCATAGGCCG	60.590	66.667	17.12	0.00	0.00	6.13
431	440	1.971505	CTGGTCATAGGCCGGAGCAA	61.972	60.000	21.54	10.41	40.57	3.91
433	442	1.883084	GTCATAGGCCGGAGCAACG	60.883	63.158	5.05	0.00	42.56	4.10
434	443	2.055633	TCATAGGCCGGAGCAACGA	61.056	57.895	5.05	0.00	42.56	3.85
450	459	2.993853	GACTGCAGGAAGGGGAGG	59.006	66.667	19.93	0.00	0.00	4.30
499	528	1.977544	CGGAGGAGGACGAGGTTGT	60.978	63.158	0.00	0.00	0.00	3.32
529	559	4.479158	GCATATCCCAACCCCTATTTGAA	58.521	43.478	0.00	0.00	0.00	2.69
533	563	2.176045	CCCAACCCCTATTTGAACCAC	58.824	52.381	0.00	0.00	0.00	4.16
536	566	0.675522	ACCCCTATTTGAACCACGCG	60.676	55.000	3.53	3.53	0.00	6.01
540	570	2.094734	CCCTATTTGAACCACGCGTAAC	59.905	50.000	13.44	4.22	0.00	2.50
553	583	1.194495	GCGTAACGATGAACCTACCG	58.806	55.000	0.00	0.00	0.00	4.02
554	584	1.194495	CGTAACGATGAACCTACCGC	58.806	55.000	0.00	0.00	0.00	5.68
555	585	1.194495	GTAACGATGAACCTACCGCG	58.806	55.000	0.00	0.00	0.00	6.46
556	586	1.093972	TAACGATGAACCTACCGCGA	58.906	50.000	8.23	0.00	0.00	5.87
557	587	0.458669	AACGATGAACCTACCGCGAT	59.541	50.000	8.23	0.00	0.00	4.58
558	588	0.248907	ACGATGAACCTACCGCGATG	60.249	55.000	8.23	0.00	0.00	3.84
575	605	5.208624	GCGATGCGATGTAATTATGTGAT	57.791	39.130	0.00	0.00	0.00	3.06
577	607	6.937457	GCGATGCGATGTAATTATGTGATAT	58.063	36.000	0.00	0.00	0.00	1.63
615	648	4.741321	ACCAGCAACAAAATGGGATATG	57.259	40.909	0.00	0.00	38.48	1.78
616	649	4.352009	ACCAGCAACAAAATGGGATATGA	58.648	39.130	0.00	0.00	38.48	2.15
668	701	4.801221	CGCCTGAAAAGAGCGCGC	62.801	66.667	26.66	26.66	43.72	6.86
725	770	1.334689	GCACGAAAGGAAAGAAACGGG	60.335	52.381	0.00	0.00	0.00	5.28
1181	1257	4.745751	CGCCGCCGAGGTAACCAA	62.746	66.667	0.00	0.00	43.70	3.67
1222	1316	3.070748	GTTCCTGCTCTGTTCTTTCTCC	58.929	50.000	0.00	0.00	0.00	3.71
1224	1318	1.339535	CCTGCTCTGTTCTTTCTCCCC	60.340	57.143	0.00	0.00	0.00	4.81
1586	1750	1.667830	CCGCCGCTGACAAGAAGAA	60.668	57.895	0.00	0.00	0.00	2.52
1587	1751	1.630244	CCGCCGCTGACAAGAAGAAG	61.630	60.000	0.00	0.00	0.00	2.85
1668	1864	2.542618	CGCGTAGTTCTGCATCTGAGAT	60.543	50.000	0.00	0.00	0.00	2.75
1687	1884	5.103558	TGAGATGGGAGAGAAAGAGAGAGAT	60.104	44.000	0.00	0.00	0.00	2.75
1692	1889	4.895297	GGGAGAGAAAGAGAGAGATCATGT	59.105	45.833	0.00	0.00	0.00	3.21
1717	1914	3.780294	TCCTGTATGTAATGCCTGGTCTT	59.220	43.478	0.00	0.00	0.00	3.01
1772	1998	6.402875	CGATTGATCTTGAATCACTGCTGAAA	60.403	38.462	0.00	0.00	31.26	2.69
1827	2053	4.382470	CCAATCTTCTCCGTGTCAATCTCT	60.382	45.833	0.00	0.00	0.00	3.10
1849	2075	3.068024	TCGAATTTTTGCTGGTTCTTGCT	59.932	39.130	0.00	0.00	0.00	3.91
1882	2114	1.577468	TCGTCTGCACATTTGTTCGT	58.423	45.000	0.00	0.00	0.00	3.85
1899	2142	6.671614	TGTTCGTACAATTTCACTTCTTGT	57.328	33.333	0.00	0.00	37.00	3.16
1925	2168	4.335594	GCGATTTGGCAATAACTAGGTTCT	59.664	41.667	0.00	0.00	0.00	3.01
1939	2182	2.112297	TTCTGTGGGGTGCGGTTC	59.888	61.111	0.00	0.00	0.00	3.62
1979	2224	3.878667	GATCTGCGGGGAAGGGGG	61.879	72.222	0.00	0.00	0.00	5.40
1980	2225	4.431524	ATCTGCGGGGAAGGGGGA	62.432	66.667	0.00	0.00	0.00	4.81
1981	2226	3.739080	ATCTGCGGGGAAGGGGGAT	62.739	63.158	0.00	0.00	0.00	3.85
1982	2227	3.878667	CTGCGGGGAAGGGGGATC	61.879	72.222	0.00	0.00	0.00	3.36
1983	2228	4.431524	TGCGGGGAAGGGGGATCT	62.432	66.667	0.00	0.00	0.00	2.75
1987	2232	2.778717	GGGAAGGGGGATCTGGGG	60.779	72.222	0.00	0.00	0.00	4.96
1988	2233	2.376842	GGAAGGGGGATCTGGGGA	59.623	66.667	0.00	0.00	0.00	4.81
1989	2234	1.308746	GGAAGGGGGATCTGGGGAA	60.309	63.158	0.00	0.00	0.00	3.97
2104	2356	3.565910	CTGCTAGATCGGAGCGCCC	62.566	68.421	2.29	3.94	43.19	6.13
2124	2376	1.433534	GTTTCTCGTCAGGCTCCAAG	58.566	55.000	0.00	0.00	0.00	3.61
2136	2388	1.738099	CTCCAAGCTGTTCGTCGGG	60.738	63.158	0.00	0.00	0.00	5.14
2149	2401	1.024271	CGTCGGGGGTAAGATTCGTA	58.976	55.000	0.00	0.00	0.00	3.43
2150	2402	1.268743	CGTCGGGGGTAAGATTCGTAC	60.269	57.143	1.60	1.60	0.00	3.67
2156	2408	2.288640	GGGGTAAGATTCGTACATCCCG	60.289	54.545	11.12	0.00	34.99	5.14
2164	2416	2.022764	TCGTACATCCCGTTCTCGTA	57.977	50.000	0.00	0.00	35.01	3.43
2205	2457	2.493035	GGAATTTGTTTGGTGCTTGGG	58.507	47.619	0.00	0.00	0.00	4.12
2218	2470	1.264045	GCTTGGGCCCCAATTTGCTA	61.264	55.000	22.27	0.00	43.07	3.49
2263	2557	3.009916	AGTTCCTCAATCATCCTGCTTGT	59.990	43.478	0.00	0.00	0.00	3.16
2289	2616	0.318955	ATTTGGTGCAAACGCTCTGC	60.319	50.000	0.00	0.00	36.13	4.26
2342	2669	6.339730	AGAAATCTGTTTGAACATTGCACAA	58.660	32.000	0.00	0.00	38.41	3.33
2343	2670	6.987992	AGAAATCTGTTTGAACATTGCACAAT	59.012	30.769	0.00	0.00	38.41	2.71
2424	2751	3.952323	CTGATTGATGCCTGAACCTGAAT	59.048	43.478	0.00	0.00	0.00	2.57
2449	2776	2.144078	TCCGTTGGAGACCTGCCAA	61.144	57.895	0.00	0.00	42.81	4.52
2513	2843	5.684626	GCTGATTTTGCTAGCACAATGTATC	59.315	40.000	28.92	17.77	37.40	2.24
2521	2851	5.177511	TGCTAGCACAATGTATCTATTTCGC	59.822	40.000	14.93	0.00	0.00	4.70
2541	2871	1.339610	CCCAGTGAAATTCCGTGCAAA	59.660	47.619	0.00	0.00	0.00	3.68

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
7	8	2.335011	GCCCCTTTGTGTTCGTGC	59.665	61.111	0.00	0.00	0.00	5.34
16	17	1.178534	ACCATGTTCACGCCCCTTTG	61.179	55.000	0.00	0.00	0.00	2.77
17	18	1.152830	ACCATGTTCACGCCCCTTT	59.847	52.632	0.00	0.00	0.00	3.11
40	41	1.480137	CATCTCTTGTCTCTCCGCCTT	59.520	52.381	0.00	0.00	0.00	4.35
42	43	0.529555	GCATCTCTTGTCTCTCCGCC	60.530	60.000	0.00	0.00	0.00	6.13
45	46	3.520569	GTTGAGCATCTCTTGTCTCTCC	58.479	50.000	0.00	0.00	34.92	3.71
52	53	3.318839	TGTTTTGGGTTGAGCATCTCTTG	59.681	43.478	0.00	0.00	34.92	3.02
60	61	4.385358	TCTTCTTTGTTTTGGGTTGAGC	57.615	40.909	0.00	0.00	0.00	4.26
64	65	5.476091	TGTGTTCTTCTTTGTTTTGGGTT	57.524	34.783	0.00	0.00	0.00	4.11
93	95	1.377366	TAGCTTCTCTGGTCGGCGAG	61.377	60.000	11.20	0.00	0.00	5.03
97	99	0.970937	TGGGTAGCTTCTCTGGTCGG	60.971	60.000	0.00	0.00	0.00	4.79
132	134	5.402398	GTGTTAGATTTGGAGATGTTTGGC	58.598	41.667	0.00	0.00	0.00	4.52
156	158	4.717629	TTGCTCACGGCGTCCTCG	62.718	66.667	10.85	0.00	45.43	4.63
160	162	0.040425	ATTGTTTTGCTCACGGCGTC	60.040	50.000	10.85	0.00	45.43	5.19
162	164	1.069568	TGTATTGTTTTGCTCACGGCG	60.070	47.619	4.80	4.80	45.43	6.46
167	169	2.621055	AGGCGTTGTATTGTTTTGCTCA	59.379	40.909	0.00	0.00	0.00	4.26
168	170	3.282831	AGGCGTTGTATTGTTTTGCTC	57.717	42.857	0.00	0.00	0.00	4.26
255	257	0.813210	GCCCCTCTTCGAGCATCAAG	60.813	60.000	0.00	0.00	33.17	3.02
276	278	2.095567	GCACTGCTATGGCCATTATTCG	60.096	50.000	26.37	11.50	37.74	3.34
278	280	2.242043	GGCACTGCTATGGCCATTATT	58.758	47.619	26.37	1.70	46.92	1.40
335	344	3.118261	AGGGCGAAATCTCTGCATCTTTA	60.118	43.478	0.00	0.00	0.00	1.85
336	345	2.019984	GGGCGAAATCTCTGCATCTTT	58.980	47.619	0.00	0.00	0.00	2.52
339	348	1.224965	GAGGGCGAAATCTCTGCATC	58.775	55.000	0.00	0.00	0.00	3.91
346	355	1.002624	TTTGGCGAGGGCGAAATCT	60.003	52.632	0.00	0.00	41.14	2.40
357	366	0.732571	GATTGCTCGGAATTTGGCGA	59.267	50.000	0.00	0.00	0.00	5.54
358	367	0.248621	GGATTGCTCGGAATTTGGCG	60.249	55.000	0.00	0.00	0.00	5.69
397	406	4.504916	CAGCTGCCTCGTCTCCGG	62.505	72.222	0.00	0.00	33.95	5.14
399	408	3.363844	GACCAGCTGCCTCGTCTCC	62.364	68.421	8.66	0.00	0.00	3.71
400	409	1.954362	ATGACCAGCTGCCTCGTCTC	61.954	60.000	17.95	0.00	31.42	3.36
404	413	1.068753	CCTATGACCAGCTGCCTCG	59.931	63.158	8.66	0.00	0.00	4.63
410	419	2.041922	TCCGGCCTATGACCAGCT	60.042	61.111	0.00	0.00	0.00	4.24
413	422	1.992834	TTGCTCCGGCCTATGACCA	60.993	57.895	0.00	0.00	37.74	4.02
415	424	1.883084	CGTTGCTCCGGCCTATGAC	60.883	63.158	0.00	0.00	37.74	3.06
431	440	2.203788	TCCCCTTCCTGCAGTCGT	60.204	61.111	13.81	0.00	0.00	4.34
433	442	2.993853	CCTCCCCTTCCTGCAGTC	59.006	66.667	13.81	0.00	0.00	3.51
434	443	3.334054	GCCTCCCCTTCCTGCAGT	61.334	66.667	13.81	0.00	0.00	4.40
529	559	1.010419	GGTTCATCGTTACGCGTGGT	61.010	55.000	24.59	0.00	42.13	4.16
533	563	1.194495	GGTAGGTTCATCGTTACGCG	58.806	55.000	3.53	3.53	43.01	6.01
536	566	1.194495	CGCGGTAGGTTCATCGTTAC	58.806	55.000	0.00	0.00	0.00	2.50
540	570	1.548973	GCATCGCGGTAGGTTCATCG	61.549	60.000	6.13	0.00	0.00	3.84
548	578	1.698165	ATTACATCGCATCGCGGTAG	58.302	50.000	6.13	0.00	46.38	3.18
553	583	4.645667	TCACATAATTACATCGCATCGC	57.354	40.909	0.00	0.00	0.00	4.58
577	607	7.831690	TGTTGCTGGTATATTGAGTGGAATTTA	59.168	33.333	0.00	0.00	0.00	1.40
630	663	3.619487	CGGAGGGGTTTTCGGTTATGTTA	60.619	47.826	0.00	0.00	0.00	2.41
668	701	4.757355	TTGGGGGCAGCGGGAATG	62.757	66.667	0.00	0.00	0.00	2.67
677	710	1.616374	GAGTTCGAAAATTTGGGGGCA	59.384	47.619	0.00	0.00	0.00	5.36
725	770	2.180769	GCGCACCGATTTTTCCCC	59.819	61.111	0.30	0.00	0.00	4.81
737	782	3.869272	CGGCCAATCAGAGCGCAC	61.869	66.667	11.47	2.25	0.00	5.34
912	961	2.652941	TGGGAATGCTTCGAATTTGC	57.347	45.000	0.00	0.00	0.00	3.68
1181	1257	1.321074	GGAGGACGAGATCGGTTGGT	61.321	60.000	7.22	0.00	44.95	3.67
1224	1318	2.182030	GTCAGCCCTCCGTCGAAG	59.818	66.667	0.00	0.00	0.00	3.79
1254	1360	1.737236	TGCGAATCCATCCAAAGAACG	59.263	47.619	0.00	0.00	0.00	3.95
1668	1864	4.599720	TGATCTCTCTCTTTCTCTCCCA	57.400	45.455	0.00	0.00	0.00	4.37
1687	1884	5.072193	AGGCATTACATACAGGATCACATGA	59.928	40.000	0.00	0.00	0.00	3.07
1692	1889	3.716353	ACCAGGCATTACATACAGGATCA	59.284	43.478	0.00	0.00	0.00	2.92
1717	1914	3.008813	AGACTACTACCAGTTCGGACTCA	59.991	47.826	0.00	0.00	38.63	3.41
1772	1998	3.679389	ACGATCAAGTTTCCAGCTTCAT	58.321	40.909	0.00	0.00	0.00	2.57
1827	2053	3.068024	AGCAAGAACCAGCAAAAATTCGA	59.932	39.130	0.00	0.00	0.00	3.71
1849	2075	2.778299	CAGACGAACAAGGGGATCAAA	58.222	47.619	0.00	0.00	0.00	2.69
1899	2142	1.846007	AGTTATTGCCAAATCGCCCA	58.154	45.000	0.00	0.00	0.00	5.36
1925	2168	4.920112	CACGAACCGCACCCCACA	62.920	66.667	0.00	0.00	0.00	4.17
1939	2182	3.552068	GGTTGACCCCAAGAAATTTCACG	60.552	47.826	19.99	9.97	32.06	4.35
1979	2224	2.945668	CAAATCCTTCGTTCCCCAGATC	59.054	50.000	0.00	0.00	0.00	2.75
1980	2225	2.357154	CCAAATCCTTCGTTCCCCAGAT	60.357	50.000	0.00	0.00	0.00	2.90
1981	2226	1.004277	CCAAATCCTTCGTTCCCCAGA	59.996	52.381	0.00	0.00	0.00	3.86
1982	2227	1.463674	CCAAATCCTTCGTTCCCCAG	58.536	55.000	0.00	0.00	0.00	4.45
1983	2228	0.039035	CCCAAATCCTTCGTTCCCCA	59.961	55.000	0.00	0.00	0.00	4.96
1987	2232	6.321435	AGAAATAATCCCCAAATCCTTCGTTC	59.679	38.462	0.00	0.00	0.00	3.95
1988	2233	6.194967	AGAAATAATCCCCAAATCCTTCGTT	58.805	36.000	0.00	0.00	0.00	3.85
1989	2234	5.766590	AGAAATAATCCCCAAATCCTTCGT	58.233	37.500	0.00	0.00	0.00	3.85
2124	2376	1.447314	CTTACCCCCGACGAACAGC	60.447	63.158	0.00	0.00	0.00	4.40
2136	2388	2.363359	ACGGGATGTACGAATCTTACCC	59.637	50.000	0.00	0.00	34.93	3.69
2149	2401	2.361438	GGAGAATACGAGAACGGGATGT	59.639	50.000	0.00	0.00	44.46	3.06
2150	2402	2.623889	AGGAGAATACGAGAACGGGATG	59.376	50.000	0.00	0.00	44.46	3.51
2156	2408	5.213675	CGAATACCAGGAGAATACGAGAAC	58.786	45.833	0.00	0.00	0.00	3.01
2164	2416	3.371595	CCCAAACCGAATACCAGGAGAAT	60.372	47.826	0.00	0.00	0.00	2.40
2205	2457	3.401033	AGTTTGTTAGCAAATTGGGGC	57.599	42.857	8.05	0.00	45.11	5.80
2218	2470	7.398024	ACTAGCATGATCTTCCTAAGTTTGTT	58.602	34.615	0.00	0.00	0.00	2.83
2263	2557	2.544685	CGTTTGCACCAAATTCACCAA	58.455	42.857	0.00	0.00	35.74	3.67
2289	2616	5.455392	CACTTGCAGTTTGTTCAGATTAGG	58.545	41.667	0.00	0.00	0.00	2.69
2342	2669	4.730949	AGTCAGCAGCATTTTTGCATAT	57.269	36.364	0.00	0.00	43.92	1.78
2343	2670	4.524316	AAGTCAGCAGCATTTTTGCATA	57.476	36.364	0.00	0.00	43.92	3.14
2350	2677	4.081406	TGAACCATAAGTCAGCAGCATTT	58.919	39.130	0.00	0.00	0.00	2.32
2449	2776	7.349598	AGAAACTAGCATGACCTGGATAAATT	58.650	34.615	0.00	0.00	0.00	1.82
2513	2843	3.242739	CGGAATTTCACTGGGCGAAATAG	60.243	47.826	0.00	0.00	41.16	1.73
2521	2851	0.958091	TTGCACGGAATTTCACTGGG	59.042	50.000	0.00	0.00	0.00	4.45
2541	2871	8.730680	ACATTTATTTAAGATTGAACTCGCTGT	58.269	29.630	0.00	0.00	0.00	4.40

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.