AutoCloner

Multiple sequence alignment - TraesCS3B01G250900

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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	TraesCS3B01G250900	chr3B	100.000	7693	0	0	1	7693	401287458	401279766	0.000000e+00	14207.0
1	TraesCS3B01G250900	chr3B	96.104	154	6	0	7346	7499	201554737	201554584	1.280000e-62	252.0
2	TraesCS3B01G250900	chr3B	98.387	62	1	0	6778	6839	401280643	401280582	8.160000e-20	110.0
3	TraesCS3B01G250900	chr3B	98.387	62	1	0	6816	6877	401280681	401280620	8.160000e-20	110.0
4	TraesCS3B01G250900	chr3D	95.747	7125	185	33	1	7030	318504662	318511763	0.000000e+00	11370.0
5	TraesCS3B01G250900	chr3D	92.954	667	33	8	7023	7679	318512794	318513456	0.000000e+00	959.0
6	TraesCS3B01G250900	chr3D	96.104	154	6	0	7346	7499	589248896	589249049	1.280000e-62	252.0
7	TraesCS3B01G250900	chr3D	90.710	183	12	3	7500	7679	255424450	255424630	9.980000e-59	239.0
8	TraesCS3B01G250900	chr3D	95.082	61	3	0	6817	6877	318511515	318511575	6.350000e-16	97.1
9	TraesCS3B01G250900	chr3D	91.935	62	3	1	7235	7294	416191856	416191795	1.380000e-12	86.1
10	TraesCS3B01G250900	chr3A	93.291	2996	120	26	1	2933	408034148	408031171	0.000000e+00	4344.0
11	TraesCS3B01G250900	chr3A	96.382	1824	34	4	2929	4721	408029254	408027432	0.000000e+00	2974.0
12	TraesCS3B01G250900	chr3A	98.122	1331	23	1	4748	6076	408027437	408026107	0.000000e+00	2318.0
13	TraesCS3B01G250900	chr3A	96.312	922	24	5	5922	6839	408026115	408025200	0.000000e+00	1506.0
14	TraesCS3B01G250900	chr3A	92.879	323	14	3	6819	7141	408025257	408024944	1.960000e-125	460.0
15	TraesCS3B01G250900	chr3A	90.710	183	15	2	7505	7685	587584956	587584774	7.710000e-60	243.0
16	TraesCS3B01G250900	chr3A	94.828	58	3	0	7237	7294	99264135	99264078	2.960000e-14	91.6
17	TraesCS3B01G250900	chr3A	94.872	39	2	0	3495	3533	12784338	12784300	2.320000e-05	62.1
18	TraesCS3B01G250900	chr2D	84.215	1305	168	22	4920	6214	382444670	382443394	0.000000e+00	1234.0
19	TraesCS3B01G250900	chr2D	82.300	774	86	24	3553	4282	382449323	382448557	2.360000e-174	623.0
20	TraesCS3B01G250900	chr2D	82.803	692	95	17	2647	3333	382449996	382449324	1.430000e-166	597.0
21	TraesCS3B01G250900	chr2D	87.892	223	25	1	4750	4970	382444897	382444675	2.130000e-65	261.0
22	TraesCS3B01G250900	chr2B	84.364	1164	152	23	4920	6068	453231600	453230452	0.000000e+00	1114.0
23	TraesCS3B01G250900	chr2B	84.130	523	67	6	3555	4064	453237897	453237378	6.940000e-135	492.0
24	TraesCS3B01G250900	chr2B	81.000	600	91	20	4111	4691	453237215	453236620	9.100000e-124	455.0
25	TraesCS3B01G250900	chr2B	81.013	395	67	8	2954	3346	453238276	453237888	2.700000e-79	307.0
26	TraesCS3B01G250900	chr2B	82.428	313	38	9	2647	2956	453259715	453259417	2.750000e-64	257.0
27	TraesCS3B01G250900	chr2B	84.528	265	33	3	4696	4953	453231883	453231620	9.910000e-64	255.0
28	TraesCS3B01G250900	chr2B	94.231	156	9	0	6059	6214	453228580	453228425	9.980000e-59	239.0
29	TraesCS3B01G250900	chr2B	92.857	56	3	1	7239	7294	466014149	466014095	6.400000e-11	80.5
30	TraesCS3B01G250900	chr2A	84.533	653	79	18	5583	6227	516745024	516744386	1.820000e-175	627.0
31	TraesCS3B01G250900	chr2A	82.988	676	93	14	4920	5588	516746979	516746319	6.650000e-165	592.0
32	TraesCS3B01G250900	chr2A	81.323	771	94	21	3555	4282	516827524	516826761	1.440000e-161	580.0
33	TraesCS3B01G250900	chr2A	80.312	706	111	20	2647	3346	516828198	516827515	6.890000e-140	508.0
34	TraesCS3B01G250900	chr2A	86.364	220	28	1	4753	4970	516747203	516746984	9.980000e-59	239.0
35	TraesCS3B01G250900	chr5D	96.753	154	5	0	7346	7499	500976344	500976497	2.750000e-64	257.0
36	TraesCS3B01G250900	chr5D	90.659	182	14	2	7505	7685	451067364	451067185	9.980000e-59	239.0
37	TraesCS3B01G250900	chr5D	96.296	54	2	0	7243	7296	281009439	281009386	1.060000e-13	89.8
38	TraesCS3B01G250900	chr5B	96.104	154	6	0	7346	7499	622512026	622512179	1.280000e-62	252.0
39	TraesCS3B01G250900	chr5A	96.104	154	6	0	7346	7499	482023328	482023175	1.280000e-62	252.0
40	TraesCS3B01G250900	chr6B	95.455	154	7	0	7346	7499	158664196	158664349	5.960000e-61	246.0
41	TraesCS3B01G250900	chr4A	95.455	154	7	0	7346	7499	219303966	219303813	5.960000e-61	246.0
42	TraesCS3B01G250900	chr4A	90.659	182	13	3	7505	7685	26977975	26978153	9.980000e-59	239.0
43	TraesCS3B01G250900	chr1D	95.455	154	7	0	7346	7499	200551601	200551754	5.960000e-61	246.0
44	TraesCS3B01G250900	chr1D	97.727	44	1	0	7295	7338	151601706	151601749	8.280000e-10	76.8
45	TraesCS3B01G250900	chr1D	97.727	44	1	0	7295	7338	244400445	244400488	8.280000e-10	76.8
46	TraesCS3B01G250900	chr1D	97.727	44	1	0	7295	7338	244406894	244406937	8.280000e-10	76.8
47	TraesCS3B01G250900	chr1D	97.727	44	1	0	7295	7338	254487972	254488015	8.280000e-10	76.8
48	TraesCS3B01G250900	chr4D	91.954	174	12	2	7505	7676	506748089	506747916	7.710000e-60	243.0
49	TraesCS3B01G250900	chr1B	90.323	186	13	5	7500	7682	634236794	634236977	9.980000e-59	239.0
50	TraesCS3B01G250900	chr1B	96.552	58	2	0	7237	7294	509106328	509106271	6.350000e-16	97.1
51	TraesCS3B01G250900	chr1B	95.000	60	1	2	7237	7294	625938094	625938035	8.220000e-15	93.5
52	TraesCS3B01G250900	chr1B	95.833	48	2	0	7295	7342	347446665	347446712	2.300000e-10	78.7
53	TraesCS3B01G250900	chr6D	90.710	183	10	6	7500	7679	26033707	26033885	3.590000e-58	237.0
54	TraesCS3B01G250900	chr6D	89.947	189	12	4	7500	7685	461412780	461412964	3.590000e-58	237.0
55	TraesCS3B01G250900	chr6D	90.323	62	5	1	7238	7299	38888727	38888667	6.400000e-11	80.5
56	TraesCS3B01G250900	chr7A	94.737	57	2	1	7238	7294	104650573	104650628	3.820000e-13	87.9
57	TraesCS3B01G250900	chrUn	97.727	44	1	0	7295	7338	453774738	453774781	8.280000e-10	76.8
58	TraesCS3B01G250900	chrUn	95.745	47	2	0	7295	7341	463114019	463113973	8.280000e-10	76.8
59	TraesCS3B01G250900	chrUn	95.745	47	2	0	7295	7341	465624478	465624432	8.280000e-10	76.8

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	TraesCS3B01G250900	chr3B	401279766	401287458	7692	True	14207.000000	14207	100.000000	1	7693	1	chr3B.!!$R2	7692
1	TraesCS3B01G250900	chr3D	318504662	318513456	8794	False	4142.033333	11370	94.594333	1	7679	3	chr3D.!!$F3	7678
2	TraesCS3B01G250900	chr3A	408024944	408034148	9204	True	2320.400000	4344	95.397200	1	7141	5	chr3A.!!$R4	7140
3	TraesCS3B01G250900	chr2D	382443394	382449996	6602	True	678.750000	1234	84.302500	2647	6214	4	chr2D.!!$R1	3567
4	TraesCS3B01G250900	chr2B	453228425	453231883	3458	True	536.000000	1114	87.707667	4696	6214	3	chr2B.!!$R3	1518
5	TraesCS3B01G250900	chr2B	453236620	453238276	1656	True	418.000000	492	82.047667	2954	4691	3	chr2B.!!$R4	1737
6	TraesCS3B01G250900	chr2A	516826761	516828198	1437	True	544.000000	580	80.817500	2647	4282	2	chr2A.!!$R2	1635
7	TraesCS3B01G250900	chr2A	516744386	516747203	2817	True	486.000000	627	84.628333	4753	6227	3	chr2A.!!$R1	1474

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
882	917	0.254462	GCTAAAGCAAGCCCTCCTCT	59.746	55.000	0.00	0.00	41.59	3.69	F
1780	1850	0.393537	CCACCATCTGCCAACTCCTC	60.394	60.000	0.00	0.00	0.00	3.71	F
2187	2257	3.257873	AGAGGAGGTCATGATCTTATGCG	59.742	47.826	10.51	0.00	0.00	4.73	F
4227	6374	1.450848	ACTGCAGATGGCCATCACG	60.451	57.895	40.05	31.63	43.89	4.35	F
6217	15003	0.393132	GGGTAAGCAGCTGAACCTCC	60.393	60.000	20.43	11.92	32.38	4.30	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2821	2894	1.202114	TGGAAATGATGCTTCGCCAAC	59.798	47.619	0.00	0.00	0.00	3.77	R
4227	6374	1.945394	CTGTCATGTCCTAATGCTGCC	59.055	52.381	0.00	0.00	0.00	4.85	R
4290	6437	4.516698	GCAATCACGTCATCCATATTTCCT	59.483	41.667	0.00	0.00	0.00	3.36	R
6503	15289	0.382880	GCCATTTTGTTTTGCACGCG	60.383	50.000	3.53	3.53	0.00	6.01	R
7109	16941	2.115910	TGCAAGCCAAGGGGTCTG	59.884	61.111	0.00	0.00	36.17	3.51	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
33	34	9.277783	CAACGAAGAGATGATTTATATTTCCCT	57.722	33.333	0.00	0.00	0.00	4.20
34	35	8.839310	ACGAAGAGATGATTTATATTTCCCTG	57.161	34.615	0.00	0.00	0.00	4.45
35	36	7.389053	ACGAAGAGATGATTTATATTTCCCTGC	59.611	37.037	0.00	0.00	0.00	4.85
37	38	9.950496	GAAGAGATGATTTATATTTCCCTGCTA	57.050	33.333	0.00	0.00	0.00	3.49
38	39	9.956640	AAGAGATGATTTATATTTCCCTGCTAG	57.043	33.333	0.00	0.00	0.00	3.42
224	227	3.195610	TGGTTGTACACAGATCTAGCAGG	59.804	47.826	0.00	0.00	0.00	4.85
230	233	2.093235	ACACAGATCTAGCAGGAAAGCC	60.093	50.000	0.00	0.00	34.23	4.35
248	251	6.013293	GGAAAGCCACCTCTACTATTCCATAT	60.013	42.308	0.00	0.00	36.09	1.78
249	252	6.613153	AAGCCACCTCTACTATTCCATATC	57.387	41.667	0.00	0.00	0.00	1.63
250	253	5.026790	AGCCACCTCTACTATTCCATATCC	58.973	45.833	0.00	0.00	0.00	2.59
290	293	6.599638	GCCTTTTCAATAGGTCTCAGTGTTAT	59.400	38.462	0.00	0.00	35.13	1.89
345	348	5.352569	CCAAATCATCTCGTTAGCAGAAAGT	59.647	40.000	0.00	0.00	0.00	2.66
488	493	5.360649	ACTCTAGGAAACAATAGGAAGGC	57.639	43.478	0.00	0.00	0.00	4.35
489	494	5.033522	ACTCTAGGAAACAATAGGAAGGCT	58.966	41.667	0.00	0.00	0.00	4.58
490	495	5.104735	ACTCTAGGAAACAATAGGAAGGCTG	60.105	44.000	0.00	0.00	0.00	4.85
492	497	3.956744	AGGAAACAATAGGAAGGCTGAC	58.043	45.455	0.00	0.00	0.00	3.51
513	531	0.534203	TTTGACCGAACACCTGCCTC	60.534	55.000	0.00	0.00	0.00	4.70
604	622	2.746277	GTCTGGACGCCCGCAAAT	60.746	61.111	0.00	0.00	34.29	2.32
613	631	2.358619	CCCGCAAATCTCCCCCAA	59.641	61.111	0.00	0.00	0.00	4.12
635	664	2.791383	TGCAGGAATTTGGACAAACG	57.209	45.000	0.00	0.00	32.51	3.60
636	665	1.339610	TGCAGGAATTTGGACAAACGG	59.660	47.619	0.00	0.00	32.51	4.44
640	669	3.255642	CAGGAATTTGGACAAACGGATGT	59.744	43.478	0.00	0.00	35.90	3.06
681	716	5.643379	AAACGCATTGGATGACAAACTAT	57.357	34.783	0.00	0.00	43.46	2.12
682	717	6.751514	AAACGCATTGGATGACAAACTATA	57.248	33.333	0.00	0.00	43.46	1.31
755	790	5.602628	AGAGAAAATCGGTTATCTGGTAGC	58.397	41.667	0.00	0.00	0.00	3.58
801	836	4.537135	TTCGAAGTCCTATTTGCAGACT	57.463	40.909	0.00	0.00	42.58	3.24
845	880	4.433805	CCTTCACGAAACGTAATACTGCAC	60.434	45.833	0.00	0.00	38.32	4.57
882	917	0.254462	GCTAAAGCAAGCCCTCCTCT	59.746	55.000	0.00	0.00	41.59	3.69
888	923	2.200081	AGCAAGCCCTCCTCTAATTGA	58.800	47.619	0.00	0.00	0.00	2.57
896	931	4.273318	CCCTCCTCTAATTGAAAGGGTTG	58.727	47.826	12.31	3.02	40.43	3.77
904	939	4.670896	AATTGAAAGGGTTGTCCAACAG	57.329	40.909	11.89	0.00	42.85	3.16
1051	1098	1.204146	GCTGGAGTTAGACCCCATCA	58.796	55.000	0.00	0.00	0.00	3.07
1166	1213	3.924013	ATCCTCCCACTCGCCCACA	62.924	63.158	0.00	0.00	0.00	4.17
1258	1305	3.670991	CGCTACTCCTAGATTTTGCGATC	59.329	47.826	11.81	0.00	44.02	3.69
1425	1472	1.401539	GGCTTGAGTTTTCGCATGTCC	60.402	52.381	0.00	0.00	0.00	4.02
1510	1557	2.368548	TCTGCTTGTGCACTTTCCTCTA	59.631	45.455	19.41	0.00	45.31	2.43
1563	1632	3.944015	CAGGAGAAGTAGCATTTCCCTTG	59.056	47.826	0.00	0.00	0.00	3.61
1627	1697	0.611200	TTCGTCCATGTGTGTAGGGG	59.389	55.000	0.00	0.00	0.00	4.79
1780	1850	0.393537	CCACCATCTGCCAACTCCTC	60.394	60.000	0.00	0.00	0.00	3.71
2078	2148	4.578105	GCGGATCTGAAGAATTGGAAGATT	59.422	41.667	5.48	0.00	0.00	2.40
2187	2257	3.257873	AGAGGAGGTCATGATCTTATGCG	59.742	47.826	10.51	0.00	0.00	4.73
2380	2450	7.759489	TTGATAGCTTGTTGTTAATTGGTCT	57.241	32.000	0.00	0.00	0.00	3.85
2821	2894	5.927819	AGCTTGATCTAGAGAAATCCCTTG	58.072	41.667	8.45	0.00	0.00	3.61
3339	5337	5.836024	AACAAACTGTAATACTCCCTCCA	57.164	39.130	0.00	0.00	0.00	3.86
3589	5594	9.968870	ACAAACTTAAATAAAATCGGCACTTAA	57.031	25.926	0.00	0.00	0.00	1.85
3593	5598	9.968870	ACTTAAATAAAATCGGCACTTAAACAA	57.031	25.926	0.00	0.00	0.00	2.83
4227	6374	1.450848	ACTGCAGATGGCCATCACG	60.451	57.895	40.05	31.63	43.89	4.35
4290	6437	1.072331	GCTGGTCCAGGAACAAGAAGA	59.928	52.381	20.72	0.00	31.21	2.87
4401	6548	3.992427	ACGATACGACTTCCCTTTTCAAC	59.008	43.478	0.00	0.00	0.00	3.18
4623	6793	4.141482	CCAGAGGGGTAAGCTGCTAAATAA	60.141	45.833	0.90	0.00	0.00	1.40
4731	10112	9.275398	AGAAAACTAATCAATAAACGTACACCA	57.725	29.630	0.00	0.00	0.00	4.17
4887	10275	5.769662	ACTGTGATAAGCAATTCCTCAAACA	59.230	36.000	0.00	0.00	0.00	2.83
5326	10776	4.752101	CAGGATTATGGTGTTCGGAATCTC	59.248	45.833	0.00	0.00	0.00	2.75
5370	10820	4.756642	TGTTGTTGTGTCAAATTTGGCAAA	59.243	33.333	26.06	19.14	45.39	3.68
5479	10929	3.510531	AGTTTTCACTTCCCTTCCCTC	57.489	47.619	0.00	0.00	0.00	4.30
5484	10934	2.266279	TCACTTCCCTTCCCTCGAAAT	58.734	47.619	0.00	0.00	0.00	2.17
5642	12397	2.356382	CGTCTCCAGGAGTTAGTAGCTG	59.644	54.545	16.65	0.00	0.00	4.24
5811	12567	7.066284	CCCATTATACTGCAGATTGCTATTACC	59.934	40.741	23.35	0.00	45.31	2.85
5853	12609	2.777972	CCTTGCCATGCGACATGGG	61.778	63.158	28.38	17.56	39.53	4.00
5867	12623	1.623686	ATGGGGCTGGTCCAGGAAT	60.624	57.895	20.72	0.00	37.75	3.01
6217	15003	0.393132	GGGTAAGCAGCTGAACCTCC	60.393	60.000	20.43	11.92	32.38	4.30
6255	15041	4.463050	AAAGGTGGGTGAGGAAACAATA	57.537	40.909	0.00	0.00	0.00	1.90
6281	15067	7.719633	ACAAGTGATGGTTGATTTACTTACTGT	59.280	33.333	0.00	0.00	0.00	3.55
6503	15289	8.816144	TGTTTTGAAAACTTTGCTGATACATTC	58.184	29.630	20.06	0.00	0.00	2.67
6677	15467	2.251893	GATGAAGTTGACGACGAGGAC	58.748	52.381	0.00	0.00	0.00	3.85
6755	15545	7.609146	AGAGATTGATTGTTAGAGTTGCATTCA	59.391	33.333	0.00	0.00	0.00	2.57
6915	15709	1.174783	TAGCTCGTGAGGGTGTTCTC	58.825	55.000	0.00	0.00	0.00	2.87
6916	15710	1.079750	GCTCGTGAGGGTGTTCTCC	60.080	63.158	0.00	0.00	33.04	3.71
6917	15711	1.536943	GCTCGTGAGGGTGTTCTCCT	61.537	60.000	0.00	0.00	37.33	3.69
7047	16879	4.920640	ATCGTACCTGATACACCTTGAG	57.079	45.455	0.00	0.00	32.79	3.02
7109	16941	1.660264	CCGCCGTTCAGTTTTTGCC	60.660	57.895	0.00	0.00	0.00	4.52
7130	16962	2.521465	CCCCTTGGCTTGCACACA	60.521	61.111	0.00	0.00	0.00	3.72
7161	16993	3.160748	GCCTGAGCCTCCTCCCTC	61.161	72.222	0.00	0.00	37.29	4.30
7180	17012	6.485171	TCCCTCTTCTTATTTTCCTCTTTGG	58.515	40.000	0.00	0.00	37.10	3.28
7210	17042	3.842869	AGCTCCCGCTGTTTCTTAG	57.157	52.632	0.00	0.00	46.86	2.18
7281	17116	6.500910	ACGTAAGGTTTTCATTTCACCTTTC	58.499	36.000	8.08	2.95	46.85	2.62
7288	17123	5.529581	TTTCATTTCACCTTTCTTCCCAC	57.470	39.130	0.00	0.00	0.00	4.61
7304	17139	5.791664	TCTTCCCACCACCCTTAGTTTATTA	59.208	40.000	0.00	0.00	0.00	0.98
7307	17142	5.190330	TCCCACCACCCTTAGTTTATTACTC	59.810	44.000	0.00	0.00	38.33	2.59
7329	17164	7.519002	ACTCGAAACTAAATCAAGGATTTTCG	58.481	34.615	9.24	11.63	41.64	3.46
7330	17165	6.837992	TCGAAACTAAATCAAGGATTTTCGG	58.162	36.000	16.80	9.04	41.64	4.30
7331	17166	6.027749	CGAAACTAAATCAAGGATTTTCGGG	58.972	40.000	9.24	2.32	41.64	5.14
7338	17173	7.718334	AAATCAAGGATTTTCGGGATACTTT	57.282	32.000	0.00	0.00	38.89	2.66
7398	17237	2.507886	TGGTTTTGGAGAAGACAGGTGA	59.492	45.455	0.00	0.00	0.00	4.02
7515	17356	6.884832	TGATAGGATTCGTAACCTTTCATGT	58.115	36.000	7.24	0.00	38.57	3.21
7516	17357	8.014070	TGATAGGATTCGTAACCTTTCATGTA	57.986	34.615	7.24	0.00	38.57	2.29
7679	17521	7.867305	TTGACAGGTAAATCACAAACTAACA	57.133	32.000	0.00	0.00	0.00	2.41
7680	17522	8.458573	TTGACAGGTAAATCACAAACTAACAT	57.541	30.769	0.00	0.00	0.00	2.71
7681	17523	9.562408	TTGACAGGTAAATCACAAACTAACATA	57.438	29.630	0.00	0.00	0.00	2.29
7682	17524	9.733556	TGACAGGTAAATCACAAACTAACATAT	57.266	29.630	0.00	0.00	0.00	1.78

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
29	30	1.145119	TCGCTTCTATCCTAGCAGGGA	59.855	52.381	0.20	0.20	38.32	4.20
30	31	1.271102	GTCGCTTCTATCCTAGCAGGG	59.729	57.143	0.00	0.00	37.23	4.45
33	34	2.375146	TGTGTCGCTTCTATCCTAGCA	58.625	47.619	0.00	0.00	37.23	3.49
34	35	3.438297	TTGTGTCGCTTCTATCCTAGC	57.562	47.619	0.00	0.00	0.00	3.42
35	36	4.363999	CCTTTGTGTCGCTTCTATCCTAG	58.636	47.826	0.00	0.00	0.00	3.02
37	38	2.093447	CCCTTTGTGTCGCTTCTATCCT	60.093	50.000	0.00	0.00	0.00	3.24
38	39	2.280628	CCCTTTGTGTCGCTTCTATCC	58.719	52.381	0.00	0.00	0.00	2.59
109	111	1.001860	TGGCTTTGGCTAATTTGGCAC	59.998	47.619	15.30	5.40	42.23	5.01
189	192	5.592282	TGTGTACAACCATTTGTCTGACATT	59.408	36.000	11.86	0.00	42.67	2.71
196	199	6.183360	GCTAGATCTGTGTACAACCATTTGTC	60.183	42.308	5.18	0.00	42.67	3.18
220	223	0.615850	AGTAGAGGTGGCTTTCCTGC	59.384	55.000	1.69	0.00	35.20	4.85
224	227	4.755266	TGGAATAGTAGAGGTGGCTTTC	57.245	45.455	0.00	0.00	0.00	2.62
230	233	6.256819	TGGAGGATATGGAATAGTAGAGGTG	58.743	44.000	0.00	0.00	28.50	4.00
248	251	5.994416	AAAGGCTATTCCTAAATGGAGGA	57.006	39.130	0.00	0.00	46.94	3.71
249	252	6.129179	TGAAAAGGCTATTCCTAAATGGAGG	58.871	40.000	0.00	0.00	46.94	4.30
250	253	7.645058	TTGAAAAGGCTATTCCTAAATGGAG	57.355	36.000	0.00	0.00	46.94	3.86
263	266	5.248477	ACACTGAGACCTATTGAAAAGGCTA	59.752	40.000	0.00	0.00	37.67	3.93
265	268	4.327680	ACACTGAGACCTATTGAAAAGGC	58.672	43.478	0.00	0.00	37.67	4.35
269	272	9.871238	GTTCTATAACACTGAGACCTATTGAAA	57.129	33.333	0.00	0.00	35.56	2.69
290	293	9.201989	ACAGACTAAGGATAATCATGTGTTCTA	57.798	33.333	0.00	0.00	0.00	2.10
299	302	7.432148	TGGCTTAACAGACTAAGGATAATCA	57.568	36.000	0.00	0.00	30.79	2.57
402	407	6.013119	TGCACTATATGAGGTCCATCATGATT	60.013	38.462	5.16	0.00	40.16	2.57
409	414	2.974794	TGCTGCACTATATGAGGTCCAT	59.025	45.455	0.00	0.00	39.25	3.41
410	415	2.397597	TGCTGCACTATATGAGGTCCA	58.602	47.619	0.00	0.00	0.00	4.02
411	416	3.475566	TTGCTGCACTATATGAGGTCC	57.524	47.619	0.00	0.00	0.00	4.46
481	486	1.611673	CGGTCAAATGTCAGCCTTCCT	60.612	52.381	0.00	0.00	0.00	3.36
488	493	2.224079	CAGGTGTTCGGTCAAATGTCAG	59.776	50.000	0.00	0.00	0.00	3.51
489	494	2.217750	CAGGTGTTCGGTCAAATGTCA	58.782	47.619	0.00	0.00	0.00	3.58
490	495	1.069227	GCAGGTGTTCGGTCAAATGTC	60.069	52.381	0.00	0.00	0.00	3.06
492	497	0.240945	GGCAGGTGTTCGGTCAAATG	59.759	55.000	0.00	0.00	0.00	2.32
513	531	2.472059	CCAACGCCATCCATGACGG	61.472	63.158	0.00	0.00	38.00	4.79
604	622	0.783206	TTCCTGCAAATTGGGGGAGA	59.217	50.000	0.00	0.00	0.00	3.71
613	631	4.057432	CGTTTGTCCAAATTCCTGCAAAT	58.943	39.130	0.00	0.00	32.36	2.32
658	687	4.320608	AGTTTGTCATCCAATGCGTTTT	57.679	36.364	0.00	0.00	31.81	2.43
659	688	5.643379	ATAGTTTGTCATCCAATGCGTTT	57.357	34.783	0.00	0.00	31.81	3.60
660	689	6.751514	TTATAGTTTGTCATCCAATGCGTT	57.248	33.333	0.00	0.00	31.81	4.84
681	716	9.561069	GAAGAAAGATAGTAAAGGGCATCATTA	57.439	33.333	0.00	0.00	0.00	1.90
682	717	8.277918	AGAAGAAAGATAGTAAAGGGCATCATT	58.722	33.333	0.00	0.00	0.00	2.57
717	752	9.899226	CCGATTTTCTCTCTTCTTTTTACATTT	57.101	29.630	0.00	0.00	0.00	2.32
718	753	9.067986	ACCGATTTTCTCTCTTCTTTTTACATT	57.932	29.630	0.00	0.00	0.00	2.71
720	755	8.446599	AACCGATTTTCTCTCTTCTTTTTACA	57.553	30.769	0.00	0.00	0.00	2.41
729	764	6.301169	ACCAGATAACCGATTTTCTCTCTT	57.699	37.500	0.00	0.00	0.00	2.85
845	880	2.192463	GCGTATGTATAACTTGCGCG	57.808	50.000	0.00	0.00	44.08	6.86
882	917	5.450453	TCTGTTGGACAACCCTTTCAATTA	58.550	37.500	12.21	0.00	40.46	1.40
888	923	5.061721	AGTTATCTGTTGGACAACCCTTT	57.938	39.130	12.21	0.00	40.46	3.11
939	977	1.799258	CGTGGGCTGCTTCTGCTTTT	61.799	55.000	0.00	0.00	40.48	2.27
1166	1213	2.426381	GAGAATTACGAGAGGAACGGGT	59.574	50.000	0.00	0.00	36.24	5.28
1258	1305	1.359848	GCCACCAACTCATACACGAG	58.640	55.000	0.00	0.00	39.05	4.18
1449	1496	7.463431	ACTACACCAACAATAACCCATCTAAA	58.537	34.615	0.00	0.00	0.00	1.85
1533	1602	3.034635	TGCTACTTCTCCTGAGGAATCC	58.965	50.000	1.41	0.00	0.00	3.01
1605	1674	2.337583	CCTACACACATGGACGAACAG	58.662	52.381	0.00	0.00	0.00	3.16
1627	1697	3.939592	AGAATACAAAAAGACTAGGCGCC	59.060	43.478	21.89	21.89	0.00	6.53
1702	1772	4.202336	ACATTTTTGGATGTGTGCATGGAA	60.202	37.500	0.00	0.00	38.75	3.53
1746	1816	3.281727	TGGTGGCACTAATGATTCTCC	57.718	47.619	18.45	0.00	0.00	3.71
1780	1850	2.167487	GGACAAGAGTTCCTAGAGCCAG	59.833	54.545	0.00	0.00	0.00	4.85
1853	1923	5.626142	TCTCTCAGTAGATACTCCACATCC	58.374	45.833	0.00	0.00	33.46	3.51
2078	2148	4.929479	AGGGGAATGCAACACTGTAATAA	58.071	39.130	0.00	0.00	0.00	1.40
2821	2894	1.202114	TGGAAATGATGCTTCGCCAAC	59.798	47.619	0.00	0.00	0.00	3.77
4227	6374	1.945394	CTGTCATGTCCTAATGCTGCC	59.055	52.381	0.00	0.00	0.00	4.85
4290	6437	4.516698	GCAATCACGTCATCCATATTTCCT	59.483	41.667	0.00	0.00	0.00	3.36
4721	10102	2.303600	TCCTTAAGGCATGGTGTACGTT	59.696	45.455	17.32	0.00	34.44	3.99
5326	10776	3.858812	CACAACCACTGTCAACAATTGTG	59.141	43.478	12.82	6.76	39.41	3.33
5370	10820	8.403236	GGTCTTTAGTTGTGTAAAGTGATTGTT	58.597	33.333	3.89	0.00	39.87	2.83
5642	12397	1.404391	CAAGAAGACAGCATCATGGGC	59.596	52.381	0.00	0.00	0.00	5.36
5811	12567	2.223923	GCTATCATATCCTAGGGCTGCG	60.224	54.545	9.46	0.00	0.00	5.18
5853	12609	3.633986	CAGAATTTATTCCTGGACCAGCC	59.366	47.826	16.72	0.00	37.51	4.85
6217	15003	4.396166	CACCTTTTACATAGCAGGTTCCAG	59.604	45.833	0.00	0.00	37.56	3.86
6255	15041	7.719633	ACAGTAAGTAAATCAACCATCACTTGT	59.280	33.333	0.00	0.00	0.00	3.16
6281	15067	3.136260	TGGAGCATGTATCCTGCACAATA	59.864	43.478	16.91	0.00	42.15	1.90
6503	15289	0.382880	GCCATTTTGTTTTGCACGCG	60.383	50.000	3.53	3.53	0.00	6.01
6677	15467	4.685169	ATAAAGTCACATGTCGGCAAAG	57.315	40.909	0.00	0.00	0.00	2.77
6777	15567	8.450964	GTTGAATCAATCTCCGAAGAATTTACA	58.549	33.333	0.00	0.00	34.49	2.41
6853	15644	6.592220	TCGAATCAATGTCCGAAGAATTTACA	59.408	34.615	0.00	0.00	0.00	2.41
6915	15709	8.812972	TGGAGGTTGTAGCTAATATGTATAAGG	58.187	37.037	0.00	0.00	0.00	2.69
6916	15710	9.862371	CTGGAGGTTGTAGCTAATATGTATAAG	57.138	37.037	0.00	0.00	0.00	1.73
6917	15711	8.812972	CCTGGAGGTTGTAGCTAATATGTATAA	58.187	37.037	0.00	0.00	0.00	0.98
7024	15818	5.006153	TCAAGGTGTATCAGGTACGATTG	57.994	43.478	0.00	0.00	36.01	2.67
7109	16941	2.115910	TGCAAGCCAAGGGGTCTG	59.884	61.111	0.00	0.00	36.17	3.51
7161	16993	5.243730	TGCCACCAAAGAGGAAAATAAGAAG	59.756	40.000	0.00	0.00	41.22	2.85
7210	17042	9.620259	AGAGATGTAAATTTGGATAGGAACTTC	57.380	33.333	0.00	0.00	41.75	3.01
7250	17085	8.529102	GTGAAATGAAAACCTTACGTTCTTTTC	58.471	33.333	0.00	4.59	41.31	2.29
7255	17090	6.068473	AGGTGAAATGAAAACCTTACGTTC	57.932	37.500	0.00	0.00	41.65	3.95
7267	17102	3.895041	GGTGGGAAGAAAGGTGAAATGAA	59.105	43.478	0.00	0.00	0.00	2.57
7281	17116	2.971901	AAACTAAGGGTGGTGGGAAG	57.028	50.000	0.00	0.00	0.00	3.46
7288	17123	7.101700	AGTTTCGAGTAATAAACTAAGGGTGG	58.898	38.462	0.00	0.00	39.07	4.61
7304	17139	7.360946	CCGAAAATCCTTGATTTAGTTTCGAGT	60.361	37.037	15.62	0.00	40.77	4.18
7307	17142	6.027749	CCCGAAAATCCTTGATTTAGTTTCG	58.972	40.000	9.18	9.18	40.77	3.46
7329	17164	6.120507	AGAGCATATTCCAGAAAGTATCCC	57.879	41.667	0.00	0.00	0.00	3.85
7330	17165	9.732130	AATAAGAGCATATTCCAGAAAGTATCC	57.268	33.333	0.00	0.00	0.00	2.59
7379	17218	4.640647	ACTTTCACCTGTCTTCTCCAAAAC	59.359	41.667	0.00	0.00	0.00	2.43
7488	17327	7.786178	TGAAAGGTTACGAATCCTATCAATG	57.214	36.000	0.00	0.00	33.27	2.82
7544	17385	8.528044	AAAGTGTAATTGGTTCAGAAGGTAAA	57.472	30.769	0.00	0.00	0.00	2.01
7545	17386	9.629878	TTAAAGTGTAATTGGTTCAGAAGGTAA	57.370	29.630	0.00	0.00	0.00	2.85

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.