AutoCloner

Multiple sequence alignment - TraesCS2A01G295500

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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	TraesCS2A01G295500	chr2A	100.000	3017	0	0	1	3017	508072514	508069498	0.000000e+00	5572.0
1	TraesCS2A01G295500	chr5A	94.636	2237	91	7	807	3017	28709883	28707650	0.000000e+00	3439.0
2	TraesCS2A01G295500	chr5A	95.934	1574	56	5	1445	3017	604305906	604307472	0.000000e+00	2545.0
3	TraesCS2A01G295500	chr5A	90.638	737	38	14	742	1448	604296167	604296902	0.000000e+00	950.0
4	TraesCS2A01G295500	chr6A	95.656	2095	78	10	751	2838	501184182	501186270	0.000000e+00	3352.0
5	TraesCS2A01G295500	chr7D	92.778	2174	103	14	874	3017	261862031	261859882	0.000000e+00	3096.0
6	TraesCS2A01G295500	chr1B	92.530	2182	107	22	874	3017	346656921	346654758	0.000000e+00	3075.0
7	TraesCS2A01G295500	chr2D	92.345	2077	105	23	795	2838	640774660	640776715	0.000000e+00	2905.0
8	TraesCS2A01G295500	chr2D	89.877	1709	135	24	874	2566	504170543	504172229	0.000000e+00	2163.0
9	TraesCS2A01G295500	chr2D	93.627	1067	51	7	748	1800	595446108	595447171	0.000000e+00	1578.0
10	TraesCS2A01G295500	chr2D	93.987	948	30	7	1947	2870	595447531	595448475	0.000000e+00	1410.0
11	TraesCS2A01G295500	chr2D	89.343	685	34	13	63	715	375605283	375604606	0.000000e+00	824.0
12	TraesCS2A01G295500	chr2D	89.343	685	34	13	63	715	375625459	375624782	0.000000e+00	824.0
13	TraesCS2A01G295500	chr2D	89.343	685	34	13	63	715	375637120	375636443	0.000000e+00	824.0
14	TraesCS2A01G295500	chr2D	100.000	31	0	0	720	750	375604579	375604549	1.170000e-04	58.4
15	TraesCS2A01G295500	chr2D	100.000	31	0	0	720	750	375624755	375624725	1.170000e-04	58.4
16	TraesCS2A01G295500	chr2D	100.000	31	0	0	720	750	375636416	375636386	1.170000e-04	58.4
17	TraesCS2A01G295500	chr5D	89.546	2334	166	32	747	3017	395682041	395684359	0.000000e+00	2887.0
18	TraesCS2A01G295500	chr5D	93.557	1133	57	6	751	1868	516814529	516813398	0.000000e+00	1674.0
19	TraesCS2A01G295500	chr5D	94.833	1045	27	6	1997	3017	516813091	516812050	0.000000e+00	1605.0
20	TraesCS2A01G295500	chr3D	90.400	1927	118	23	1124	3017	30636283	30638175	0.000000e+00	2471.0
21	TraesCS2A01G295500	chr1D	92.775	1038	36	13	2010	3017	339349064	339350092	0.000000e+00	1465.0
22	TraesCS2A01G295500	chr1D	88.328	1148	124	9	874	2016	339342797	339343939	0.000000e+00	1369.0
23	TraesCS2A01G295500	chr6D	90.766	509	29	4	751	1242	27685301	27685808	0.000000e+00	664.0
24	TraesCS2A01G295500	chr2B	88.817	465	23	7	63	507	446114969	446114514	7.360000e-151	544.0
25	TraesCS2A01G295500	chr3B	86.842	190	18	6	750	939	265856306	265856124	3.940000e-49	206.0
26	TraesCS2A01G295500	chr3B	83.173	208	15	9	750	939	741307816	741307611	4.000000e-39	172.0
27	TraesCS2A01G295500	chr7B	86.154	195	19	7	750	940	337401582	337401772	1.420000e-48	204.0
28	TraesCS2A01G295500	chr7B	85.128	195	20	8	750	940	337402288	337402477	1.100000e-44	191.0
29	TraesCS2A01G295500	chr7B	84.615	195	22	7	750	940	337403120	337403310	1.430000e-43	187.0
30	TraesCS2A01G295500	chr7B	84.615	195	22	7	750	940	337403827	337404017	1.430000e-43	187.0
31	TraesCS2A01G295500	chr7B	83.962	106	12	4	750	852	337404533	337404636	2.480000e-16	97.1

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	TraesCS2A01G295500	chr2A	508069498	508072514	3016	True	5572.0	5572	100.0000	1	3017	1	chr2A.!!$R1	3016
1	TraesCS2A01G295500	chr5A	28707650	28709883	2233	True	3439.0	3439	94.6360	807	3017	1	chr5A.!!$R1	2210
2	TraesCS2A01G295500	chr5A	604305906	604307472	1566	False	2545.0	2545	95.9340	1445	3017	1	chr5A.!!$F2	1572
3	TraesCS2A01G295500	chr5A	604296167	604296902	735	False	950.0	950	90.6380	742	1448	1	chr5A.!!$F1	706
4	TraesCS2A01G295500	chr6A	501184182	501186270	2088	False	3352.0	3352	95.6560	751	2838	1	chr6A.!!$F1	2087
5	TraesCS2A01G295500	chr7D	261859882	261862031	2149	True	3096.0	3096	92.7780	874	3017	1	chr7D.!!$R1	2143
6	TraesCS2A01G295500	chr1B	346654758	346656921	2163	True	3075.0	3075	92.5300	874	3017	1	chr1B.!!$R1	2143
7	TraesCS2A01G295500	chr2D	640774660	640776715	2055	False	2905.0	2905	92.3450	795	2838	1	chr2D.!!$F2	2043
8	TraesCS2A01G295500	chr2D	504170543	504172229	1686	False	2163.0	2163	89.8770	874	2566	1	chr2D.!!$F1	1692
9	TraesCS2A01G295500	chr2D	595446108	595448475	2367	False	1494.0	1578	93.8070	748	2870	2	chr2D.!!$F3	2122
10	TraesCS2A01G295500	chr2D	375604549	375605283	734	True	441.2	824	94.6715	63	750	2	chr2D.!!$R1	687
11	TraesCS2A01G295500	chr2D	375624725	375625459	734	True	441.2	824	94.6715	63	750	2	chr2D.!!$R2	687
12	TraesCS2A01G295500	chr2D	375636386	375637120	734	True	441.2	824	94.6715	63	750	2	chr2D.!!$R3	687
13	TraesCS2A01G295500	chr5D	395682041	395684359	2318	False	2887.0	2887	89.5460	747	3017	1	chr5D.!!$F1	2270
14	TraesCS2A01G295500	chr5D	516812050	516814529	2479	True	1639.5	1674	94.1950	751	3017	2	chr5D.!!$R1	2266
15	TraesCS2A01G295500	chr3D	30636283	30638175	1892	False	2471.0	2471	90.4000	1124	3017	1	chr3D.!!$F1	1893
16	TraesCS2A01G295500	chr1D	339349064	339350092	1028	False	1465.0	1465	92.7750	2010	3017	1	chr1D.!!$F2	1007
17	TraesCS2A01G295500	chr1D	339342797	339343939	1142	False	1369.0	1369	88.3280	874	2016	1	chr1D.!!$F1	1142
18	TraesCS2A01G295500	chr6D	27685301	27685808	507	False	664.0	664	90.7660	751	1242	1	chr6D.!!$F1	491

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
661	694	0.042188	CTTCACAAACGACCGCTGTG	60.042	55.0	15.02	15.02	41.47	3.66	F
716	749	0.306533	CAGTTTTCCGTGTTCCCGTG	59.693	55.0	0.00	0.00	0.00	4.94	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1929	2068	1.068921	GCGATCTTCAGGAGGAGGC	59.931	63.158	0.0	0.0	0.00	4.70	R
2654	3050	7.953158	TGAGAACCAGATAATCGATCAATTC	57.047	36.000	0.0	0.0	36.98	2.17	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
25	26	2.829741	GCAGGGTCCTGACAGATATC	57.170	55.000	20.22	0.00	46.30	1.63
26	27	1.346068	GCAGGGTCCTGACAGATATCC	59.654	57.143	20.22	1.36	46.30	2.59
27	28	2.682594	CAGGGTCCTGACAGATATCCA	58.317	52.381	11.39	0.00	46.30	3.41
28	29	3.246301	CAGGGTCCTGACAGATATCCAT	58.754	50.000	11.39	0.00	46.30	3.41
29	30	3.007723	CAGGGTCCTGACAGATATCCATG	59.992	52.174	11.39	4.97	46.30	3.66
30	31	3.116590	AGGGTCCTGACAGATATCCATGA	60.117	47.826	3.32	0.00	0.00	3.07
31	32	3.843027	GGGTCCTGACAGATATCCATGAT	59.157	47.826	3.32	0.00	0.00	2.45
32	33	4.323333	GGGTCCTGACAGATATCCATGATG	60.323	50.000	3.32	0.00	0.00	3.07
33	34	4.285517	GGTCCTGACAGATATCCATGATGT	59.714	45.833	3.32	0.00	0.00	3.06
34	35	5.221803	GGTCCTGACAGATATCCATGATGTT	60.222	44.000	3.32	0.00	0.00	2.71
35	36	6.294473	GTCCTGACAGATATCCATGATGTTT	58.706	40.000	3.32	0.00	0.00	2.83
36	37	7.445121	GTCCTGACAGATATCCATGATGTTTA	58.555	38.462	3.32	0.00	0.00	2.01
37	38	8.099537	GTCCTGACAGATATCCATGATGTTTAT	58.900	37.037	3.32	0.00	0.00	1.40
38	39	8.663167	TCCTGACAGATATCCATGATGTTTATT	58.337	33.333	3.32	0.00	0.00	1.40
39	40	9.293404	CCTGACAGATATCCATGATGTTTATTT	57.707	33.333	3.32	0.00	0.00	1.40
48	49	8.991243	ATCCATGATGTTTATTTTGTGTTGAG	57.009	30.769	0.00	0.00	0.00	3.02
49	50	6.867816	TCCATGATGTTTATTTTGTGTTGAGC	59.132	34.615	0.00	0.00	0.00	4.26
50	51	6.645827	CCATGATGTTTATTTTGTGTTGAGCA	59.354	34.615	0.00	0.00	0.00	4.26
51	52	7.148705	CCATGATGTTTATTTTGTGTTGAGCAG	60.149	37.037	0.00	0.00	0.00	4.24
52	53	7.036996	TGATGTTTATTTTGTGTTGAGCAGA	57.963	32.000	0.00	0.00	0.00	4.26
53	54	7.140705	TGATGTTTATTTTGTGTTGAGCAGAG	58.859	34.615	0.00	0.00	0.00	3.35
54	55	5.830912	TGTTTATTTTGTGTTGAGCAGAGG	58.169	37.500	0.00	0.00	0.00	3.69
55	56	5.592282	TGTTTATTTTGTGTTGAGCAGAGGA	59.408	36.000	0.00	0.00	0.00	3.71
56	57	6.265196	TGTTTATTTTGTGTTGAGCAGAGGAT	59.735	34.615	0.00	0.00	0.00	3.24
57	58	4.778534	ATTTTGTGTTGAGCAGAGGATG	57.221	40.909	0.00	0.00	0.00	3.51
58	59	2.936919	TTGTGTTGAGCAGAGGATGT	57.063	45.000	0.00	0.00	0.00	3.06
59	60	2.936919	TGTGTTGAGCAGAGGATGTT	57.063	45.000	0.00	0.00	0.00	2.71
60	61	3.213206	TGTGTTGAGCAGAGGATGTTT	57.787	42.857	0.00	0.00	0.00	2.83
61	62	3.554934	TGTGTTGAGCAGAGGATGTTTT	58.445	40.909	0.00	0.00	0.00	2.43
70	71	6.071952	TGAGCAGAGGATGTTTTATTTTCCAC	60.072	38.462	0.00	0.00	0.00	4.02
148	150	1.996748	GGATGTTACCCCGGTCCCA	60.997	63.158	0.00	0.00	0.00	4.37
245	247	6.211584	ACAATACCAAGCTATCGATATCCTGT	59.788	38.462	5.40	2.43	0.00	4.00
355	357	4.521256	TGTTTAGAAAATGACCCTTTCCCG	59.479	41.667	0.00	0.00	34.00	5.14
356	358	2.215942	AGAAAATGACCCTTTCCCGG	57.784	50.000	0.00	0.00	34.00	5.73
386	389	7.560991	TGAATCAAGTGGTTGCCATCTATTATT	59.439	33.333	0.00	0.00	35.28	1.40
389	392	7.342581	TCAAGTGGTTGCCATCTATTATTACA	58.657	34.615	0.00	0.00	35.28	2.41
393	396	7.499232	AGTGGTTGCCATCTATTATTACACTTC	59.501	37.037	0.00	0.00	35.28	3.01
394	397	6.481976	TGGTTGCCATCTATTATTACACTTCG	59.518	38.462	0.00	0.00	0.00	3.79
438	443	3.917380	CGTCTTGTTGTTGCTTGTTTCAA	59.083	39.130	0.00	0.00	0.00	2.69
439	444	4.562394	CGTCTTGTTGTTGCTTGTTTCAAT	59.438	37.500	0.00	0.00	0.00	2.57
440	445	5.275881	CGTCTTGTTGTTGCTTGTTTCAATC	60.276	40.000	0.00	0.00	0.00	2.67
441	446	5.576384	GTCTTGTTGTTGCTTGTTTCAATCA	59.424	36.000	0.00	0.00	0.00	2.57
443	448	5.970140	TGTTGTTGCTTGTTTCAATCATG	57.030	34.783	0.00	0.00	0.00	3.07
445	450	5.291371	TGTTGTTGCTTGTTTCAATCATGTG	59.709	36.000	0.00	0.00	0.00	3.21
446	451	5.008619	TGTTGCTTGTTTCAATCATGTGT	57.991	34.783	0.00	0.00	0.00	3.72
447	452	5.042593	TGTTGCTTGTTTCAATCATGTGTC	58.957	37.500	0.00	0.00	0.00	3.67
448	453	4.915158	TGCTTGTTTCAATCATGTGTCA	57.085	36.364	0.00	0.00	0.00	3.58
449	454	5.259832	TGCTTGTTTCAATCATGTGTCAA	57.740	34.783	0.00	0.00	0.00	3.18
450	455	5.658468	TGCTTGTTTCAATCATGTGTCAAA	58.342	33.333	0.00	0.00	0.00	2.69
451	456	6.104665	TGCTTGTTTCAATCATGTGTCAAAA	58.895	32.000	0.00	0.00	0.00	2.44
498	503	3.616219	TGTGTCAACTAACCTGCAGTTT	58.384	40.909	13.81	7.46	40.05	2.66
507	512	1.915141	ACCTGCAGTTTGCTTGCTAT	58.085	45.000	13.81	0.00	45.31	2.97
508	513	2.242043	ACCTGCAGTTTGCTTGCTATT	58.758	42.857	13.81	0.00	45.31	1.73
510	515	3.070015	ACCTGCAGTTTGCTTGCTATTTT	59.930	39.130	13.81	0.00	45.31	1.82
511	516	3.430895	CCTGCAGTTTGCTTGCTATTTTG	59.569	43.478	13.81	0.00	45.31	2.44
512	517	4.300803	CTGCAGTTTGCTTGCTATTTTGA	58.699	39.130	5.25	0.00	45.31	2.69
537	560	0.458370	GCTTTGCTAAATGGGTGGCG	60.458	55.000	0.00	0.00	0.00	5.69
552	578	3.467803	GGTGGCGCATAAGATCTACTTT	58.532	45.455	10.83	0.00	39.72	2.66
556	582	4.991056	TGGCGCATAAGATCTACTTTGATC	59.009	41.667	10.83	0.00	42.18	2.92
561	587	6.870439	CGCATAAGATCTACTTTGATCCATGA	59.130	38.462	15.05	0.00	42.68	3.07
585	612	2.042741	CTCCCATGGGCCATGCAA	60.043	61.111	35.99	24.99	40.20	4.08
594	621	1.453015	GGCCATGCAATACCCACGA	60.453	57.895	0.00	0.00	0.00	4.35
648	681	2.040278	CCCTCTTCAACCCATCTTCACA	59.960	50.000	0.00	0.00	0.00	3.58
661	694	0.042188	CTTCACAAACGACCGCTGTG	60.042	55.000	15.02	15.02	41.47	3.66
663	696	2.203015	ACAAACGACCGCTGTGCT	60.203	55.556	0.00	0.00	0.00	4.40
669	702	2.435059	GACCGCTGTGCTTCTCCC	60.435	66.667	0.00	0.00	0.00	4.30
678	711	2.125350	GCTTCTCCCTGCTCCACG	60.125	66.667	0.00	0.00	0.00	4.94
680	713	3.003173	TTCTCCCTGCTCCACGGG	61.003	66.667	0.00	0.00	45.52	5.28
703	736	3.380004	TGTCCTTTTGATCGTGCAGTTTT	59.620	39.130	0.00	0.00	0.00	2.43
704	737	3.975035	GTCCTTTTGATCGTGCAGTTTTC	59.025	43.478	0.00	0.00	0.00	2.29
712	745	0.316689	CGTGCAGTTTTCCGTGTTCC	60.317	55.000	0.00	0.00	0.00	3.62
715	748	1.441732	GCAGTTTTCCGTGTTCCCGT	61.442	55.000	0.00	0.00	0.00	5.28
716	749	0.306533	CAGTTTTCCGTGTTCCCGTG	59.693	55.000	0.00	0.00	0.00	4.94
717	750	1.009335	GTTTTCCGTGTTCCCGTGC	60.009	57.895	0.00	0.00	0.00	5.34
718	751	2.188161	TTTTCCGTGTTCCCGTGCC	61.188	57.895	0.00	0.00	0.00	5.01
811	866	1.004320	TGTGTCCAAAGCGCCGTAT	60.004	52.632	2.29	0.00	0.00	3.06
826	902	0.377554	CGTATGGAGCGTCTTCTCGT	59.622	55.000	0.00	0.00	33.98	4.18
848	924	1.962306	ACGGGCGCGTGTTGTAAAT	60.962	52.632	28.99	0.00	0.00	1.40
1039	1134	3.071602	GCATAGAATCACCTCTGCCCTTA	59.928	47.826	0.00	0.00	32.23	2.69
1654	1789	2.030562	CCGTTGTGAAGCCGGAGT	59.969	61.111	5.05	0.00	44.41	3.85
1759	1895	2.150719	TCGTCTTCCAAGGCCCCAA	61.151	57.895	0.00	0.00	0.00	4.12
2074	2427	4.521062	GTCTCCATCAGCGGCGCT	62.521	66.667	31.35	31.35	40.77	5.92
2215	2587	6.544931	TCGTGCATTAGTCCAACTACTAGTAT	59.455	38.462	2.33	0.00	33.62	2.12
2323	2695	8.918202	TTGTCATGTTTTAGACCTTGTATCTT	57.082	30.769	0.00	0.00	33.89	2.40
2420	2792	6.922247	ATGTTCAATGTGTTTGCAATTTGA	57.078	29.167	0.00	2.85	35.16	2.69
2509	2881	7.264221	TGCAACTCAAATATTAATTCGCCATT	58.736	30.769	0.00	0.00	0.00	3.16
2856	3252	6.893958	TTGCACAATTAAACGAACAACAAT	57.106	29.167	0.00	0.00	0.00	2.71
2902	3298	2.356535	GGCACCATATCCATCCAGATCC	60.357	54.545	0.00	0.00	0.00	3.36

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
4	5	0.339859	TATCTGTCAGGACCCTGCCT	59.660	55.000	11.11	0.00	43.31	4.75
5	6	1.346068	GATATCTGTCAGGACCCTGCC	59.654	57.143	11.11	0.29	43.31	4.85
6	7	1.346068	GGATATCTGTCAGGACCCTGC	59.654	57.143	11.11	7.25	43.31	4.85
8	9	3.116590	TCATGGATATCTGTCAGGACCCT	60.117	47.826	2.05	0.00	0.00	4.34
9	10	3.242867	TCATGGATATCTGTCAGGACCC	58.757	50.000	2.05	0.00	0.00	4.46
10	11	4.285517	ACATCATGGATATCTGTCAGGACC	59.714	45.833	2.05	0.00	0.00	4.46
11	12	5.480642	ACATCATGGATATCTGTCAGGAC	57.519	43.478	2.05	0.00	0.00	3.85
12	13	6.505048	AAACATCATGGATATCTGTCAGGA	57.495	37.500	2.05	0.10	0.00	3.86
13	14	8.859236	AATAAACATCATGGATATCTGTCAGG	57.141	34.615	2.05	0.00	0.00	3.86
23	24	7.546667	GCTCAACACAAAATAAACATCATGGAT	59.453	33.333	0.00	0.00	0.00	3.41
24	25	6.867816	GCTCAACACAAAATAAACATCATGGA	59.132	34.615	0.00	0.00	0.00	3.41
25	26	6.645827	TGCTCAACACAAAATAAACATCATGG	59.354	34.615	0.00	0.00	0.00	3.66
26	27	7.595875	TCTGCTCAACACAAAATAAACATCATG	59.404	33.333	0.00	0.00	0.00	3.07
27	28	7.660112	TCTGCTCAACACAAAATAAACATCAT	58.340	30.769	0.00	0.00	0.00	2.45
28	29	7.036996	TCTGCTCAACACAAAATAAACATCA	57.963	32.000	0.00	0.00	0.00	3.07
29	30	6.583806	CCTCTGCTCAACACAAAATAAACATC	59.416	38.462	0.00	0.00	0.00	3.06
30	31	6.265196	TCCTCTGCTCAACACAAAATAAACAT	59.735	34.615	0.00	0.00	0.00	2.71
31	32	5.592282	TCCTCTGCTCAACACAAAATAAACA	59.408	36.000	0.00	0.00	0.00	2.83
32	33	6.072112	TCCTCTGCTCAACACAAAATAAAC	57.928	37.500	0.00	0.00	0.00	2.01
33	34	6.265196	ACATCCTCTGCTCAACACAAAATAAA	59.735	34.615	0.00	0.00	0.00	1.40
34	35	5.769662	ACATCCTCTGCTCAACACAAAATAA	59.230	36.000	0.00	0.00	0.00	1.40
35	36	5.316167	ACATCCTCTGCTCAACACAAAATA	58.684	37.500	0.00	0.00	0.00	1.40
36	37	4.147321	ACATCCTCTGCTCAACACAAAAT	58.853	39.130	0.00	0.00	0.00	1.82
37	38	3.554934	ACATCCTCTGCTCAACACAAAA	58.445	40.909	0.00	0.00	0.00	2.44
38	39	3.213206	ACATCCTCTGCTCAACACAAA	57.787	42.857	0.00	0.00	0.00	2.83
39	40	2.936919	ACATCCTCTGCTCAACACAA	57.063	45.000	0.00	0.00	0.00	3.33
40	41	2.936919	AACATCCTCTGCTCAACACA	57.063	45.000	0.00	0.00	0.00	3.72
41	42	5.886960	ATAAAACATCCTCTGCTCAACAC	57.113	39.130	0.00	0.00	0.00	3.32
42	43	6.899393	AAATAAAACATCCTCTGCTCAACA	57.101	33.333	0.00	0.00	0.00	3.33
43	44	6.808704	GGAAAATAAAACATCCTCTGCTCAAC	59.191	38.462	0.00	0.00	0.00	3.18
44	45	6.493115	TGGAAAATAAAACATCCTCTGCTCAA	59.507	34.615	0.00	0.00	33.02	3.02
45	46	6.009589	TGGAAAATAAAACATCCTCTGCTCA	58.990	36.000	0.00	0.00	33.02	4.26
46	47	6.151817	AGTGGAAAATAAAACATCCTCTGCTC	59.848	38.462	0.00	0.00	35.20	4.26
47	48	6.012745	AGTGGAAAATAAAACATCCTCTGCT	58.987	36.000	0.00	0.00	35.20	4.24
48	49	6.272822	AGTGGAAAATAAAACATCCTCTGC	57.727	37.500	0.00	0.00	35.20	4.26
49	50	9.846248	CTAAAGTGGAAAATAAAACATCCTCTG	57.154	33.333	0.00	0.00	36.29	3.35
50	51	9.588096	ACTAAAGTGGAAAATAAAACATCCTCT	57.412	29.630	0.00	0.00	37.38	3.69
70	71	7.438160	TCCGCTGTATGACATCATAAACTAAAG	59.562	37.037	3.15	0.00	40.18	1.85
112	113	4.037208	ACATCCTCTGCTCAACACAAAAAG	59.963	41.667	0.00	0.00	0.00	2.27
119	121	2.027192	GGGTAACATCCTCTGCTCAACA	60.027	50.000	0.00	0.00	39.74	3.33
148	150	4.988598	CGGCGGGTGCTGTCAGTT	62.989	66.667	0.00	0.00	42.79	3.16
245	247	4.513442	AGTACAGAACAAGTTGCAAGACA	58.487	39.130	0.00	0.00	0.00	3.41
355	357	2.407090	GCAACCACTTGATTCAAAGCC	58.593	47.619	0.01	0.00	0.00	4.35
356	358	2.224018	TGGCAACCACTTGATTCAAAGC	60.224	45.455	0.01	0.00	0.00	3.51
386	389	7.101054	AGTAAATCCATAGCAAACGAAGTGTA	58.899	34.615	0.00	0.00	45.00	2.90
393	396	5.003402	CGCAAAAGTAAATCCATAGCAAACG	59.997	40.000	0.00	0.00	0.00	3.60
394	397	5.861787	ACGCAAAAGTAAATCCATAGCAAAC	59.138	36.000	0.00	0.00	0.00	2.93
450	455	3.569250	ACAACAGCGTGTCAAGTTTTT	57.431	38.095	0.00	0.00	0.00	1.94
451	456	3.486875	GCTACAACAGCGTGTCAAGTTTT	60.487	43.478	0.00	0.00	41.37	2.43
479	484	2.357637	GCAAACTGCAGGTTAGTTGACA	59.642	45.455	18.48	0.00	44.26	3.58
498	503	3.258872	AGCCACAATCAAAATAGCAAGCA	59.741	39.130	0.00	0.00	0.00	3.91
507	512	5.469421	CCATTTAGCAAAGCCACAATCAAAA	59.531	36.000	0.00	0.00	0.00	2.44
508	513	4.996122	CCATTTAGCAAAGCCACAATCAAA	59.004	37.500	0.00	0.00	0.00	2.69
510	515	3.055963	CCCATTTAGCAAAGCCACAATCA	60.056	43.478	0.00	0.00	0.00	2.57
511	516	3.055891	ACCCATTTAGCAAAGCCACAATC	60.056	43.478	0.00	0.00	0.00	2.67
512	517	2.905736	ACCCATTTAGCAAAGCCACAAT	59.094	40.909	0.00	0.00	0.00	2.71
537	560	8.613060	TTCATGGATCAAAGTAGATCTTATGC	57.387	34.615	0.00	0.00	43.11	3.14
556	582	1.414919	CCATGGGAGCCAATTTCATGG	59.585	52.381	2.85	6.30	45.64	3.66
561	587	4.055178	GCCCATGGGAGCCAATTT	57.945	55.556	36.00	0.00	36.95	1.82
594	621	1.226435	GACGCGAGCGAGTGATTCT	60.226	57.895	24.72	0.00	42.83	2.40
606	633	1.132453	CTAAGGATGTCACTGACGCGA	59.868	52.381	15.93	0.00	34.95	5.87
648	681	1.222115	GAGAAGCACAGCGGTCGTTT	61.222	55.000	0.00	0.00	0.00	3.60
661	694	2.125350	CGTGGAGCAGGGAGAAGC	60.125	66.667	0.00	0.00	0.00	3.86
669	702	2.397413	AAAGGACACCCGTGGAGCAG	62.397	60.000	0.00	0.00	37.58	4.24
678	711	0.521735	GCACGATCAAAAGGACACCC	59.478	55.000	0.00	0.00	0.00	4.61
680	713	1.873591	ACTGCACGATCAAAAGGACAC	59.126	47.619	0.00	0.00	0.00	3.67
703	736	4.308458	CAGGCACGGGAACACGGA	62.308	66.667	0.80	0.00	38.39	4.69
704	737	4.308458	TCAGGCACGGGAACACGG	62.308	66.667	0.80	0.00	38.39	4.94
712	745	1.512926	GCCATAATAGTCAGGCACGG	58.487	55.000	0.00	0.00	46.26	4.94
716	749	4.265073	CCATAAGGCCATAATAGTCAGGC	58.735	47.826	5.01	0.00	46.28	4.85
717	750	4.536090	TCCCATAAGGCCATAATAGTCAGG	59.464	45.833	5.01	0.00	34.51	3.86
718	751	5.762179	TCCCATAAGGCCATAATAGTCAG	57.238	43.478	5.01	0.00	34.51	3.51
811	866	2.258591	GCACGAGAAGACGCTCCA	59.741	61.111	0.00	0.00	36.70	3.86
838	914	2.415512	GAGAGGCGTCCATTTACAACAC	59.584	50.000	2.06	0.00	0.00	3.32
1039	1134	2.434336	TCTCCCGTCCAATGAATCGAAT	59.566	45.455	0.00	0.00	0.00	3.34
1072	1167	3.550431	AGCACTGTGGCGTCTGGT	61.550	61.111	10.21	0.00	39.27	4.00
1344	1479	0.677288	CATCCATGCCATTGCCGAAT	59.323	50.000	0.00	0.00	36.33	3.34
1929	2068	1.068921	GCGATCTTCAGGAGGAGGC	59.931	63.158	0.00	0.00	0.00	4.70
2215	2587	9.405587	GCTAAAACATGACAAGCACTAAATTAA	57.594	29.630	0.00	0.00	33.38	1.40
2654	3050	7.953158	TGAGAACCAGATAATCGATCAATTC	57.047	36.000	0.00	0.00	36.98	2.17

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.