AutoCloner

Multiple sequence alignment - TraesCS1D01G445000

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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	TraesCS1D01G445000	chr1D	100.000	2915	0	0	1	2915	487909449	487912363	0.000000e+00	5384.0
1	TraesCS1D01G445000	chr1D	77.994	718	88	44	626	1313	488545968	488545291	1.270000e-103	387.0
2	TraesCS1D01G445000	chr1D	80.819	537	35	44	817	1318	487948857	487949360	2.760000e-95	359.0
3	TraesCS1D01G445000	chr1A	90.249	1364	78	27	1	1344	586936606	586937934	0.000000e+00	1731.0
4	TraesCS1D01G445000	chr1A	94.337	671	28	3	1397	2061	586938041	586938707	0.000000e+00	1020.0
5	TraesCS1D01G445000	chr1A	86.781	643	74	8	2186	2822	534141585	534142222	0.000000e+00	706.0
6	TraesCS1D01G445000	chr1A	88.757	338	29	7	984	1318	586950112	586950443	3.500000e-109	405.0
7	TraesCS1D01G445000	chr1A	80.106	568	83	12	1368	1920	586950760	586951312	2.110000e-106	396.0
8	TraesCS1D01G445000	chr1A	93.007	143	10	0	2046	2188	586942550	586942692	2.940000e-50	209.0
9	TraesCS1D01G445000	chr1B	93.159	804	34	5	1397	2188	679723302	679724096	0.000000e+00	1160.0
10	TraesCS1D01G445000	chr1B	92.115	799	30	14	565	1347	679722423	679723204	0.000000e+00	1096.0
11	TraesCS1D01G445000	chr1B	79.429	525	60	29	817	1318	679744802	679745301	7.790000e-86	327.0
12	TraesCS1D01G445000	chr1B	78.464	534	82	17	1397	1921	679745707	679746216	4.690000e-83	318.0
13	TraesCS1D01G445000	chr1B	81.671	371	33	14	1833	2187	679717496	679717847	2.860000e-70	276.0
14	TraesCS1D01G445000	chr1B	82.667	225	22	8	220	437	679722205	679722419	1.780000e-42	183.0
15	TraesCS1D01G445000	chr1B	88.060	67	1	2	2848	2914	679726367	679726426	4.030000e-09	73.1
16	TraesCS1D01G445000	chr5D	88.273	631	66	5	2193	2819	525730610	525731236	0.000000e+00	749.0
17	TraesCS1D01G445000	chr4D	87.578	644	68	8	2186	2823	464994401	464993764	0.000000e+00	736.0
18	TraesCS1D01G445000	chr3D	87.520	641	73	3	2186	2822	587396396	587397033	0.000000e+00	734.0
19	TraesCS1D01G445000	chr5A	87.211	649	70	10	2178	2820	708702719	708702078	0.000000e+00	726.0
20	TraesCS1D01G445000	chr5A	87.200	125	9	3	723	847	28653344	28653227	5.070000e-28	135.0
21	TraesCS1D01G445000	chr5A	87.719	114	7	3	734	847	640275602	640275496	3.050000e-25	126.0
22	TraesCS1D01G445000	chr7D	87.072	642	75	5	2186	2822	131826076	131826714	0.000000e+00	719.0
23	TraesCS1D01G445000	chr7D	80.896	335	40	15	987	1317	586029350	586029664	2.900000e-60	243.0
24	TraesCS1D01G445000	chr2D	87.072	642	73	5	2186	2822	66853525	66852889	0.000000e+00	717.0
25	TraesCS1D01G445000	chr2B	86.667	645	74	8	2186	2823	774540212	774539573	0.000000e+00	704.0
26	TraesCS1D01G445000	chr3B	86.308	650	81	7	2178	2822	42493208	42492562	0.000000e+00	701.0
27	TraesCS1D01G445000	chr7B	81.481	351	46	13	986	1334	656419852	656420185	1.330000e-68	270.0
28	TraesCS1D01G445000	chr7B	81.437	334	43	13	986	1317	656286806	656287122	3.730000e-64	255.0
29	TraesCS1D01G445000	chr7A	80.299	335	45	14	986	1317	682175804	682175488	1.750000e-57	233.0
30	TraesCS1D01G445000	chr3A	87.200	125	9	3	723	847	118573767	118573884	5.070000e-28	135.0
31	TraesCS1D01G445000	chr3A	87.755	98	7	1	750	847	691473283	691473375	3.070000e-20	110.0
32	TraesCS1D01G445000	chr2A	87.200	125	9	4	723	847	60075782	60075665	5.070000e-28	135.0

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	TraesCS1D01G445000	chr1D	487909449	487912363	2914	False	5384.000000	5384	100.00000	1	2915	1	chr1D.!!$F1	2914
1	TraesCS1D01G445000	chr1D	488545291	488545968	677	True	387.000000	387	77.99400	626	1313	1	chr1D.!!$R1	687
2	TraesCS1D01G445000	chr1D	487948857	487949360	503	False	359.000000	359	80.81900	817	1318	1	chr1D.!!$F2	501
3	TraesCS1D01G445000	chr1A	586936606	586942692	6086	False	986.666667	1731	92.53100	1	2188	3	chr1A.!!$F2	2187
4	TraesCS1D01G445000	chr1A	534141585	534142222	637	False	706.000000	706	86.78100	2186	2822	1	chr1A.!!$F1	636
5	TraesCS1D01G445000	chr1A	586950112	586951312	1200	False	400.500000	405	84.43150	984	1920	2	chr1A.!!$F3	936
6	TraesCS1D01G445000	chr1B	679722205	679726426	4221	False	628.025000	1160	89.00025	220	2914	4	chr1B.!!$F2	2694
7	TraesCS1D01G445000	chr1B	679744802	679746216	1414	False	322.500000	327	78.94650	817	1921	2	chr1B.!!$F3	1104
8	TraesCS1D01G445000	chr5D	525730610	525731236	626	False	749.000000	749	88.27300	2193	2819	1	chr5D.!!$F1	626
9	TraesCS1D01G445000	chr4D	464993764	464994401	637	True	736.000000	736	87.57800	2186	2823	1	chr4D.!!$R1	637
10	TraesCS1D01G445000	chr3D	587396396	587397033	637	False	734.000000	734	87.52000	2186	2822	1	chr3D.!!$F1	636
11	TraesCS1D01G445000	chr5A	708702078	708702719	641	True	726.000000	726	87.21100	2178	2820	1	chr5A.!!$R3	642
12	TraesCS1D01G445000	chr7D	131826076	131826714	638	False	719.000000	719	87.07200	2186	2822	1	chr7D.!!$F1	636
13	TraesCS1D01G445000	chr2D	66852889	66853525	636	True	717.000000	717	87.07200	2186	2822	1	chr2D.!!$R1	636
14	TraesCS1D01G445000	chr2B	774539573	774540212	639	True	704.000000	704	86.66700	2186	2823	1	chr2B.!!$R1	637
15	TraesCS1D01G445000	chr3B	42492562	42493208	646	True	701.000000	701	86.30800	2178	2822	1	chr3B.!!$R1	644

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
791	824	0.041926	CACGTATGCATGCATGGTCG	60.042	55.0	37.43	34.25	37.82	4.79	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2704	7049	0.039618	ATCAAGCCACCCGAAACCAT	59.96	50.0	0.0	0.0	0.0	3.55	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
27	28	3.367025	GCAAAGTTAGCTACTGTACACCG	59.633	47.826	0.00	0.00	37.12	4.94
32	33	4.335874	AGTTAGCTACTGTACACCGAGATG	59.664	45.833	0.00	0.00	35.19	2.90
33	34	2.724454	AGCTACTGTACACCGAGATGT	58.276	47.619	0.00	0.00	36.56	3.06
92	93	6.982141	GCATGTGGAATCAATGTGATAATTGT	59.018	34.615	0.00	0.00	35.76	2.71
125	126	0.401738	TTTCAGCTGTGGGGAAGGAG	59.598	55.000	14.67	0.00	0.00	3.69
144	145	6.470456	AGGAGAAAACCTTTTTATCTCCCT	57.530	37.500	14.71	2.48	38.48	4.20
145	146	7.584396	AGGAGAAAACCTTTTTATCTCCCTA	57.416	36.000	14.71	0.00	38.48	3.53
196	197	0.459411	TCGAAAATCTGATGGCGCGA	60.459	50.000	12.10	0.00	0.00	5.87
213	214	5.797934	TGGCGCGAGTTTATTCTTTATTTTG	59.202	36.000	12.10	0.00	0.00	2.44
258	261	3.368495	GGTTTTGCCTTAGTGTGTTTCG	58.632	45.455	0.00	0.00	0.00	3.46
314	319	9.956640	TTGGCATTTTTCCATAAGAATACAAAT	57.043	25.926	0.00	0.00	33.44	2.32
324	329	9.812347	TCCATAAGAATACAAATGAATATGCCT	57.188	29.630	0.00	0.00	0.00	4.75
367	374	3.554692	CGTCCTCCGTTCATGCGC	61.555	66.667	0.00	0.00	0.00	6.09
524	531	1.497161	GGGTGCTAGTGACATACCCT	58.503	55.000	0.00	0.00	45.94	4.34
553	560	2.825836	GCCGCACATAGCTTGGCT	60.826	61.111	0.00	0.00	43.80	4.75
571	578	0.098200	CTGCCACGATGATGCACAAG	59.902	55.000	0.00	0.00	0.00	3.16
599	606	5.946942	TCTCTTCTTCACATCCATAGCTT	57.053	39.130	0.00	0.00	0.00	3.74
600	607	7.440198	CATCTCTTCTTCACATCCATAGCTTA	58.560	38.462	0.00	0.00	0.00	3.09
601	608	7.048629	TCTCTTCTTCACATCCATAGCTTAG	57.951	40.000	0.00	0.00	0.00	2.18
602	609	5.605534	TCTTCTTCACATCCATAGCTTAGC	58.394	41.667	0.00	0.00	0.00	3.09
603	610	5.365025	TCTTCTTCACATCCATAGCTTAGCT	59.635	40.000	12.67	12.67	43.41	3.32
647	659	4.744795	TCTTTCTTCACCTCCATAGCTC	57.255	45.455	0.00	0.00	0.00	4.09
666	678	1.531602	AGCTTGCCACCCTGGAAAC	60.532	57.895	0.00	0.00	40.96	2.78
713	733	2.913617	CCTAAACCTTTCCTCCTCACCT	59.086	50.000	0.00	0.00	0.00	4.00
730	755	0.752658	CCTATGCACGACTCCATGGA	59.247	55.000	15.27	15.27	0.00	3.41
732	757	2.410939	CTATGCACGACTCCATGGATG	58.589	52.381	16.63	11.93	0.00	3.51
733	758	0.543277	ATGCACGACTCCATGGATGT	59.457	50.000	16.63	15.28	0.00	3.06
734	759	1.190643	TGCACGACTCCATGGATGTA	58.809	50.000	16.63	7.37	0.00	2.29
735	760	1.134818	TGCACGACTCCATGGATGTAC	60.135	52.381	16.63	9.74	0.00	2.90
789	822	2.212652	CTACACGTATGCATGCATGGT	58.787	47.619	37.43	30.56	37.82	3.55
790	823	1.016627	ACACGTATGCATGCATGGTC	58.983	50.000	37.43	25.78	37.82	4.02
791	824	0.041926	CACGTATGCATGCATGGTCG	60.042	55.000	37.43	34.25	37.82	4.79
792	825	1.159713	ACGTATGCATGCATGGTCGG	61.160	55.000	37.43	23.87	37.82	4.79
793	826	1.283793	GTATGCATGCATGGTCGGC	59.716	57.895	37.43	18.57	37.82	5.54
849	882	0.902048	CCACCTCTCTCCTCACAGCA	60.902	60.000	0.00	0.00	0.00	4.41
850	883	0.246086	CACCTCTCTCCTCACAGCAC	59.754	60.000	0.00	0.00	0.00	4.40
865	898	1.021390	AGCACCCAAGCTTCGAATCG	61.021	55.000	0.00	0.00	43.70	3.34
905	957	5.184479	ACACCTTCATATATATACACGGCGT	59.816	40.000	6.77	6.77	0.00	5.68
972	1034	1.760086	CCACCAAGGCACCAACCAA	60.760	57.895	0.00	0.00	0.00	3.67
974	1036	2.124693	ACCAAGGCACCAACCAACG	61.125	57.895	0.00	0.00	0.00	4.10
1091	1201	0.616111	GAGTGGGCAGAGAAGGAGGA	60.616	60.000	0.00	0.00	0.00	3.71
1248	1361	4.577677	TTCCAGCTGCCCGCAACA	62.578	61.111	8.66	0.00	42.61	3.33
1350	1508	1.158466	TGTGGCCAAGGAGGAGAGA	59.842	57.895	7.24	0.00	41.22	3.10
1351	1509	1.194781	TGTGGCCAAGGAGGAGAGAC	61.195	60.000	7.24	0.00	41.22	3.36
1352	1510	0.907230	GTGGCCAAGGAGGAGAGACT	60.907	60.000	7.24	0.00	41.22	3.24
1360	1812	0.678366	GGAGGAGAGACTCAGCGACA	60.678	60.000	5.02	0.00	39.27	4.35
1361	1813	0.450184	GAGGAGAGACTCAGCGACAC	59.550	60.000	5.02	0.00	37.44	3.67
1364	1816	1.579084	GAGAGACTCAGCGACACCGT	61.579	60.000	5.02	0.00	38.24	4.83
1366	1818	2.126424	GACTCAGCGACACCGTCC	60.126	66.667	0.00	0.00	38.24	4.79
1371	1823	1.300620	CAGCGACACCGTCCAGAAA	60.301	57.895	0.00	0.00	38.24	2.52
1381	1833	1.604604	CGTCCAGAAAAAGGAAGCCA	58.395	50.000	0.00	0.00	36.80	4.75
1382	1834	1.266989	CGTCCAGAAAAAGGAAGCCAC	59.733	52.381	0.00	0.00	36.80	5.01
1385	1837	1.604604	CAGAAAAAGGAAGCCACCGA	58.395	50.000	0.00	0.00	34.73	4.69
1521	1976	2.815647	GCGGCGAAGAAGGACCAG	60.816	66.667	12.98	0.00	0.00	4.00
1788	2261	0.178873	TTGTAGGGGAGCTGAAGGGT	60.179	55.000	0.00	0.00	0.00	4.34
1897	2370	1.448717	GGCTTCTTCGTCTCCCAGC	60.449	63.158	0.00	0.00	0.00	4.85
1935	2411	0.447801	CAGCAATGCGTACCAAGGAC	59.552	55.000	0.00	0.00	0.00	3.85
1952	2428	3.300388	AGGACGACCATCTCACATACAT	58.700	45.455	6.71	0.00	38.94	2.29
2035	2514	8.492673	TTGACTCAACAACCATGTAAGATATC	57.507	34.615	0.00	0.00	39.40	1.63
2072	6409	5.991328	AAGTGTGTACATTCAGACAACAG	57.009	39.130	0.00	0.00	34.66	3.16
2188	6527	0.903454	ACTTCATCCGTCCGTCCCTT	60.903	55.000	0.00	0.00	0.00	3.95
2292	6631	0.178964	ACAATGGTGTGGAGGTTGGG	60.179	55.000	0.00	0.00	36.31	4.12
2297	6636	1.423794	GGTGTGGAGGTTGGGAGGAA	61.424	60.000	0.00	0.00	0.00	3.36
2301	6640	0.193574	TGGAGGTTGGGAGGAAGAGT	59.806	55.000	0.00	0.00	0.00	3.24
2311	6653	1.757699	GGAGGAAGAGTGGCGTTCTAT	59.242	52.381	0.00	0.00	0.00	1.98
2314	6656	1.480954	GGAAGAGTGGCGTTCTATCCA	59.519	52.381	11.05	0.00	0.00	3.41
2437	6779	0.395311	AGAGTCTCCGCGTTGGGATA	60.395	55.000	4.92	0.00	38.76	2.59
2465	6807	3.134127	GGGCGGTGGAGTCATTGC	61.134	66.667	0.00	0.00	0.00	3.56
2484	6826	2.962786	CGTTGTGGTGGCGTCGAA	60.963	61.111	0.00	0.00	0.00	3.71
2498	6840	1.076559	TCGAAGGATGGCCGGACTA	60.077	57.895	9.82	0.00	39.96	2.59
2522	6864	4.142071	GCAAGGATGATGCGGATATCTCTA	60.142	45.833	2.05	0.00	33.57	2.43
2567	6912	2.273557	GATGGCGGCTTCTAAAACGTA	58.726	47.619	16.43	0.00	0.00	3.57
2582	6927	7.266400	TCTAAAACGTATGCATGTGGTGTATA	58.734	34.615	10.16	0.00	34.75	1.47
2601	6946	0.764890	ACTTTAGGTCTGCTGCACCA	59.235	50.000	11.35	0.00	36.23	4.17
2612	6957	2.095461	TGCTGCACCAGTTGTTTGTTA	58.905	42.857	0.00	0.00	33.43	2.41
2619	6964	4.024725	GCACCAGTTGTTTGTTACGATACA	60.025	41.667	0.00	0.00	0.00	2.29
2637	6982	8.112016	ACGATACATTATATGGATAGATCGGG	57.888	38.462	0.00	0.00	38.31	5.14
2658	7003	4.460382	GGGGACGACATCGGTTATAGATAA	59.540	45.833	6.21	0.00	44.95	1.75
2704	7049	4.746535	TCAAGTTTGTAGGTGTGAGTGA	57.253	40.909	0.00	0.00	0.00	3.41
2708	7053	3.391296	AGTTTGTAGGTGTGAGTGATGGT	59.609	43.478	0.00	0.00	0.00	3.55
2746	7092	3.692257	ATGTTCTTGTCAGACCCTCAG	57.308	47.619	0.00	0.00	0.00	3.35
2754	7541	5.186021	TCTTGTCAGACCCTCAGAGAATAAC	59.814	44.000	0.00	0.00	0.00	1.89
2761	7549	9.488762	TCAGACCCTCAGAGAATAACTAATAAA	57.511	33.333	0.00	0.00	0.00	1.40
2785	7573	6.494200	AATGGCTACATGCATCGATTGATGT	61.494	40.000	21.57	18.49	44.25	3.06
2836	7896	2.554370	AAAAATCCGTTCGTCCCTCA	57.446	45.000	0.00	0.00	0.00	3.86
2837	7897	2.781681	AAAATCCGTTCGTCCCTCAT	57.218	45.000	0.00	0.00	0.00	2.90
2838	7898	2.311124	AAATCCGTTCGTCCCTCATC	57.689	50.000	0.00	0.00	0.00	2.92
2839	7899	1.486211	AATCCGTTCGTCCCTCATCT	58.514	50.000	0.00	0.00	0.00	2.90
2840	7900	1.033574	ATCCGTTCGTCCCTCATCTC	58.966	55.000	0.00	0.00	0.00	2.75
2841	7901	0.034380	TCCGTTCGTCCCTCATCTCT	60.034	55.000	0.00	0.00	0.00	3.10
2842	7902	1.211212	TCCGTTCGTCCCTCATCTCTA	59.789	52.381	0.00	0.00	0.00	2.43
2843	7903	1.334243	CCGTTCGTCCCTCATCTCTAC	59.666	57.143	0.00	0.00	0.00	2.59
2845	7905	2.422479	CGTTCGTCCCTCATCTCTACAA	59.578	50.000	0.00	0.00	0.00	2.41
2846	7906	3.731264	CGTTCGTCCCTCATCTCTACAAC	60.731	52.174	0.00	0.00	0.00	3.32
2855	9157	4.021544	CCTCATCTCTACAACTCCCTATGC	60.022	50.000	0.00	0.00	0.00	3.14
2867	9169	2.203070	CTATGCGTGCCCCACTCC	60.203	66.667	0.00	0.00	31.34	3.85
2871	9173	4.767255	GCGTGCCCCACTCCAGAG	62.767	72.222	0.00	0.00	31.34	3.35
2873	9175	2.665603	GTGCCCCACTCCAGAGTC	59.334	66.667	0.00	0.00	40.20	3.36
2914	9262	3.055891	CCCAGTATCCGCATGATGTGATA	60.056	47.826	7.69	5.27	34.76	2.15

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
5	6	3.367025	CGGTGTACAGTAGCTAACTTTGC	59.633	47.826	0.00	0.00	35.76	3.68
56	57	6.647334	TGATTCCACATGCAGAAAAACTAA	57.353	33.333	2.44	0.00	0.00	2.24
92	93	3.005050	CAGCTGAAAGAAGGTTCATGCAA	59.995	43.478	8.42	0.00	36.92	4.08
213	214	7.725844	ACCCCTTCCAATCATAATAGATTTCAC	59.274	37.037	0.00	0.00	36.13	3.18
553	560	0.321475	TCTTGTGCATCATCGTGGCA	60.321	50.000	0.00	0.00	34.70	4.92
647	659	1.531365	TTTCCAGGGTGGCAAGCTG	60.531	57.895	0.00	0.00	37.47	4.24
666	678	2.203153	CGCGGGAGGGTAAATGGG	60.203	66.667	0.00	0.00	38.10	4.00
713	733	1.762370	ACATCCATGGAGTCGTGCATA	59.238	47.619	21.33	0.00	31.91	3.14
849	882	0.391263	GGTCGATTCGAAGCTTGGGT	60.391	55.000	10.87	0.00	37.72	4.51
850	883	0.391130	TGGTCGATTCGAAGCTTGGG	60.391	55.000	10.87	0.00	37.72	4.12
865	898	2.045708	TGTTGGCATGGCGATGGTC	61.046	57.895	13.07	0.02	0.00	4.02
905	957	5.848369	AGATGAGATGGGAAGGTTCATGATA	59.152	40.000	0.00	0.00	0.00	2.15
972	1034	0.528470	GTAGGCAAGAGCTCTGTCGT	59.472	55.000	19.06	15.28	41.70	4.34
974	1036	0.804156	GCGTAGGCAAGAGCTCTGTC	60.804	60.000	19.06	13.03	41.70	3.51
1080	1190	1.004979	ACGTAGCTGTCCTCCTTCTCT	59.995	52.381	0.00	0.00	0.00	3.10
1248	1361	2.364842	ATGTCCTCGAGGCTGGCT	60.365	61.111	27.39	2.24	34.44	4.75
1350	1508	2.910479	TGGACGGTGTCGCTGAGT	60.910	61.111	0.00	0.00	40.63	3.41
1351	1509	2.126307	CTGGACGGTGTCGCTGAG	60.126	66.667	0.00	0.00	40.63	3.35
1352	1510	1.740332	TTTCTGGACGGTGTCGCTGA	61.740	55.000	0.00	0.00	40.63	4.26
1360	1812	1.605753	GCTTCCTTTTTCTGGACGGT	58.394	50.000	0.00	0.00	32.65	4.83
1361	1813	0.881796	GGCTTCCTTTTTCTGGACGG	59.118	55.000	0.00	0.00	32.65	4.79
1364	1816	1.817740	CGGTGGCTTCCTTTTTCTGGA	60.818	52.381	0.00	0.00	0.00	3.86
1366	1818	1.604604	TCGGTGGCTTCCTTTTTCTG	58.395	50.000	0.00	0.00	0.00	3.02
1371	1823	0.035056	CTCCATCGGTGGCTTCCTTT	60.035	55.000	10.80	0.00	45.63	3.11
1381	1833	2.579201	CTTCACGGCTCCATCGGT	59.421	61.111	0.00	0.00	0.00	4.69
1382	1834	2.202932	CCTTCACGGCTCCATCGG	60.203	66.667	0.00	0.00	0.00	4.18
1385	1837	1.965754	GCTCTCCTTCACGGCTCCAT	61.966	60.000	0.00	0.00	0.00	3.41
1389	1841	2.659610	GTGCTCTCCTTCACGGCT	59.340	61.111	0.00	0.00	0.00	5.52
1394	1846	1.588597	CTGAGCGTGCTCTCCTTCA	59.411	57.895	21.36	1.59	43.12	3.02
1662	2129	0.401738	CCTTGGCCCTCACTTCTTCA	59.598	55.000	0.00	0.00	0.00	3.02
1665	2132	2.134630	CTGCCTTGGCCCTCACTTCT	62.135	60.000	9.35	0.00	0.00	2.85
1788	2261	1.002430	GCCCACTTCATGTCTGTCAGA	59.998	52.381	0.00	0.00	0.00	3.27
1897	2370	0.802607	GCTCACTTACCGAAGAGCCG	60.803	60.000	0.00	0.00	45.79	5.52
1935	2411	4.202111	TGGTGTATGTATGTGAGATGGTCG	60.202	45.833	0.00	0.00	0.00	4.79
1952	2428	1.412079	ACGTACCCACTGTTGGTGTA	58.588	50.000	13.42	4.39	43.94	2.90
1964	2440	4.861102	AGCCTGTACATATTACGTACCC	57.139	45.455	0.00	0.00	38.77	3.69
1967	2443	8.415553	ACAACAATAGCCTGTACATATTACGTA	58.584	33.333	0.00	0.00	0.00	3.57
2035	2514	5.443185	ACACACTTTGATTGATTCCACAG	57.557	39.130	0.00	0.00	0.00	3.66
2072	6409	6.594547	CCAGATATGATGATTGACTCCATGTC	59.405	42.308	0.00	0.00	45.54	3.06
2188	6527	3.390521	AAGACGGCGCCTCCATGA	61.391	61.111	26.68	0.00	34.01	3.07
2273	6612	0.178964	CCCAACCTCCACACCATTGT	60.179	55.000	0.00	0.00	35.84	2.71
2292	6631	2.223852	GGATAGAACGCCACTCTTCCTC	60.224	54.545	0.00	0.00	0.00	3.71
2301	6640	2.185867	GCCGTGGATAGAACGCCA	59.814	61.111	0.00	0.00	39.69	5.69
2311	6653	4.794439	CGCATCTGACGCCGTGGA	62.794	66.667	0.00	0.00	0.00	4.02
2314	6656	3.749064	AGACGCATCTGACGCCGT	61.749	61.111	0.00	0.00	32.29	5.68
2373	6715	1.302431	CCGACCAGGCATGACACAA	60.302	57.895	0.00	0.00	0.00	3.33
2461	6803	4.341502	GCCACCACAACGCGCAAT	62.342	61.111	5.73	0.00	0.00	3.56
2484	6826	1.689233	TTGCTAGTCCGGCCATCCT	60.689	57.895	2.24	0.00	0.00	3.24
2498	6840	2.570752	AGATATCCGCATCATCCTTGCT	59.429	45.455	0.00	0.00	37.96	3.91
2522	6864	3.337694	TCGAACCGTTGTCCCATATTT	57.662	42.857	0.00	0.00	0.00	1.40
2567	6912	6.001449	ACCTAAAGTATACACCACATGCAT	57.999	37.500	5.50	0.00	0.00	3.96
2582	6927	0.764890	TGGTGCAGCAGACCTAAAGT	59.235	50.000	15.99	0.00	34.26	2.66
2612	6957	7.176865	CCCCGATCTATCCATATAATGTATCGT	59.823	40.741	0.00	0.00	33.67	3.73
2619	6964	5.535406	GTCGTCCCCGATCTATCCATATAAT	59.465	44.000	0.00	0.00	46.30	1.28
2630	6975	2.194212	CCGATGTCGTCCCCGATCT	61.194	63.158	1.44	0.00	46.30	2.75
2637	6982	5.392811	CCCTTATCTATAACCGATGTCGTCC	60.393	48.000	1.44	0.00	37.74	4.79
2704	7049	0.039618	ATCAAGCCACCCGAAACCAT	59.960	50.000	0.00	0.00	0.00	3.55
2708	7053	2.290641	ACATACATCAAGCCACCCGAAA	60.291	45.455	0.00	0.00	0.00	3.46
2754	7541	7.132694	TCGATGCATGTAGCCATTTTATTAG	57.867	36.000	2.46	0.00	44.83	1.73
2761	7549	3.479489	TCAATCGATGCATGTAGCCATT	58.521	40.909	2.46	0.00	44.83	3.16
2785	7573	4.657039	AGGAAGTTAAACCTCCGGCATATA	59.343	41.667	0.00	0.00	0.00	0.86
2789	7757	1.061546	AGGAAGTTAAACCTCCGGCA	58.938	50.000	0.00	0.00	0.00	5.69
2823	7883	1.334243	GTAGAGATGAGGGACGAACGG	59.666	57.143	0.00	0.00	0.00	4.44
2824	7884	2.014857	TGTAGAGATGAGGGACGAACG	58.985	52.381	0.00	0.00	0.00	3.95
2825	7885	3.444388	AGTTGTAGAGATGAGGGACGAAC	59.556	47.826	0.00	0.00	0.00	3.95
2827	7887	3.280295	GAGTTGTAGAGATGAGGGACGA	58.720	50.000	0.00	0.00	0.00	4.20
2828	7888	2.359531	GGAGTTGTAGAGATGAGGGACG	59.640	54.545	0.00	0.00	0.00	4.79
2830	7890	2.587777	AGGGAGTTGTAGAGATGAGGGA	59.412	50.000	0.00	0.00	0.00	4.20
2831	7891	3.039252	AGGGAGTTGTAGAGATGAGGG	57.961	52.381	0.00	0.00	0.00	4.30
2833	7893	4.320861	CGCATAGGGAGTTGTAGAGATGAG	60.321	50.000	0.00	0.00	0.00	2.90
2835	7895	3.319405	ACGCATAGGGAGTTGTAGAGATG	59.681	47.826	0.00	0.00	0.00	2.90
2836	7896	3.319405	CACGCATAGGGAGTTGTAGAGAT	59.681	47.826	0.00	0.00	0.00	2.75
2837	7897	2.688446	CACGCATAGGGAGTTGTAGAGA	59.312	50.000	0.00	0.00	0.00	3.10
2838	7898	2.799917	GCACGCATAGGGAGTTGTAGAG	60.800	54.545	0.00	0.00	0.00	2.43
2839	7899	1.136305	GCACGCATAGGGAGTTGTAGA	59.864	52.381	0.00	0.00	0.00	2.59
2840	7900	1.571919	GCACGCATAGGGAGTTGTAG	58.428	55.000	0.00	0.00	0.00	2.74
2841	7901	0.177141	GGCACGCATAGGGAGTTGTA	59.823	55.000	0.00	0.00	0.00	2.41
2842	7902	1.078426	GGCACGCATAGGGAGTTGT	60.078	57.895	0.00	0.00	0.00	3.32
2843	7903	1.819632	GGGCACGCATAGGGAGTTG	60.820	63.158	0.00	0.00	0.00	3.16
2845	7905	3.480133	GGGGCACGCATAGGGAGT	61.480	66.667	0.00	0.00	42.57	3.85
2855	9157	3.302347	GACTCTGGAGTGGGGCACG	62.302	68.421	8.06	0.00	42.66	5.34

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.