AutoCloner

Multiple sequence alignment - TraesCS7A01G451800

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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	TraesCS7A01G451800	chr7A	100.000	2751	0	0	1	2751	644734138	644736888	0.000000e+00	5081.0
1	TraesCS7A01G451800	chr7A	85.653	1645	161	36	633	2254	644721699	644723291	0.000000e+00	1661.0
2	TraesCS7A01G451800	chr7A	85.069	1661	175	41	627	2254	644768307	644769927	0.000000e+00	1626.0
3	TraesCS7A01G451800	chr7A	89.230	1272	89	28	662	1917	644784894	644786133	0.000000e+00	1546.0
4	TraesCS7A01G451800	chr7A	87.590	975	96	16	882	1840	644710470	644711435	0.000000e+00	1107.0
5	TraesCS7A01G451800	chr7A	81.782	505	69	12	2242	2745	644769958	644770440	4.270000e-108	401.0
6	TraesCS7A01G451800	chr7D	89.793	1646	108	29	633	2254	560596915	560598524	0.000000e+00	2054.0
7	TraesCS7A01G451800	chr7D	84.961	1669	169	53	627	2254	560602790	560604417	0.000000e+00	1616.0
8	TraesCS7A01G451800	chr7D	88.253	1311	100	29	627	1916	560682629	560683906	0.000000e+00	1519.0
9	TraesCS7A01G451800	chr7D	88.253	1311	99	30	627	1916	560701594	560702870	0.000000e+00	1517.0
10	TraesCS7A01G451800	chr7D	85.792	915	82	20	1304	2204	560590253	560591133	0.000000e+00	926.0
11	TraesCS7A01G451800	chr7D	93.861	505	29	2	2248	2751	560598565	560599068	0.000000e+00	760.0
12	TraesCS7A01G451800	chr7D	88.156	591	68	2	4	593	88136084	88135495	0.000000e+00	702.0
13	TraesCS7A01G451800	chr7D	84.190	506	74	6	2242	2745	560604449	560604950	1.150000e-133	486.0
14	TraesCS7A01G451800	chr7D	89.474	57	4	1	2198	2254	625908440	625908386	1.370000e-08	71.3
15	TraesCS7A01G451800	chr7B	87.203	1641	134	36	633	2249	608391952	608393540	0.000000e+00	1797.0
16	TraesCS7A01G451800	chr7B	85.907	1405	154	30	868	2254	608405192	608406570	0.000000e+00	1458.0
17	TraesCS7A01G451800	chr7B	87.119	1312	112	30	627	1917	608414770	608416045	0.000000e+00	1434.0
18	TraesCS7A01G451800	chr7B	86.279	1341	127	30	882	2204	608379924	608381225	0.000000e+00	1404.0
19	TraesCS7A01G451800	chr7B	88.822	501	52	4	2246	2745	608393585	608394082	1.810000e-171	612.0
20	TraesCS7A01G451800	chr7B	84.175	594	83	10	4	593	581438772	581439358	1.430000e-157	566.0
21	TraesCS7A01G451800	chr1A	90.153	589	58	0	4	592	6302073	6301485	0.000000e+00	767.0
22	TraesCS7A01G451800	chr5A	90.809	544	47	3	4	546	468354220	468353679	0.000000e+00	725.0
23	TraesCS7A01G451800	chr5D	87.946	589	69	2	4	591	243815609	243816196	0.000000e+00	693.0
24	TraesCS7A01G451800	chr6A	86.633	591	74	4	4	593	46566054	46566640	0.000000e+00	649.0
25	TraesCS7A01G451800	chr6B	84.538	595	79	11	4	591	50337190	50336602	6.610000e-161	577.0
26	TraesCS7A01G451800	chr6B	82.293	593	97	8	4	592	583292926	583292338	8.790000e-140	507.0
27	TraesCS7A01G451800	chr4B	83.390	590	93	5	4	592	448807057	448806472	2.410000e-150	542.0
28	TraesCS7A01G451800	chr1B	82.036	167	25	5	2084	2246	306591907	306592072	1.330000e-28	137.0

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	TraesCS7A01G451800	chr7A	644734138	644736888	2750	False	5081.0	5081	100.00000	1	2751	1	chr7A.!!$F3	2750
1	TraesCS7A01G451800	chr7A	644721699	644723291	1592	False	1661.0	1661	85.65300	633	2254	1	chr7A.!!$F2	1621
2	TraesCS7A01G451800	chr7A	644784894	644786133	1239	False	1546.0	1546	89.23000	662	1917	1	chr7A.!!$F4	1255
3	TraesCS7A01G451800	chr7A	644710470	644711435	965	False	1107.0	1107	87.59000	882	1840	1	chr7A.!!$F1	958
4	TraesCS7A01G451800	chr7A	644768307	644770440	2133	False	1013.5	1626	83.42550	627	2745	2	chr7A.!!$F5	2118
5	TraesCS7A01G451800	chr7D	560682629	560683906	1277	False	1519.0	1519	88.25300	627	1916	1	chr7D.!!$F2	1289
6	TraesCS7A01G451800	chr7D	560701594	560702870	1276	False	1517.0	1517	88.25300	627	1916	1	chr7D.!!$F3	1289
7	TraesCS7A01G451800	chr7D	560596915	560604950	8035	False	1229.0	2054	88.20125	627	2751	4	chr7D.!!$F4	2124
8	TraesCS7A01G451800	chr7D	560590253	560591133	880	False	926.0	926	85.79200	1304	2204	1	chr7D.!!$F1	900
9	TraesCS7A01G451800	chr7D	88135495	88136084	589	True	702.0	702	88.15600	4	593	1	chr7D.!!$R1	589
10	TraesCS7A01G451800	chr7B	608405192	608406570	1378	False	1458.0	1458	85.90700	868	2254	1	chr7B.!!$F3	1386
11	TraesCS7A01G451800	chr7B	608414770	608416045	1275	False	1434.0	1434	87.11900	627	1917	1	chr7B.!!$F4	1290
12	TraesCS7A01G451800	chr7B	608379924	608381225	1301	False	1404.0	1404	86.27900	882	2204	1	chr7B.!!$F2	1322
13	TraesCS7A01G451800	chr7B	608391952	608394082	2130	False	1204.5	1797	88.01250	633	2745	2	chr7B.!!$F5	2112
14	TraesCS7A01G451800	chr7B	581438772	581439358	586	False	566.0	566	84.17500	4	593	1	chr7B.!!$F1	589
15	TraesCS7A01G451800	chr1A	6301485	6302073	588	True	767.0	767	90.15300	4	592	1	chr1A.!!$R1	588
16	TraesCS7A01G451800	chr5A	468353679	468354220	541	True	725.0	725	90.80900	4	546	1	chr5A.!!$R1	542
17	TraesCS7A01G451800	chr5D	243815609	243816196	587	False	693.0	693	87.94600	4	591	1	chr5D.!!$F1	587
18	TraesCS7A01G451800	chr6A	46566054	46566640	586	False	649.0	649	86.63300	4	593	1	chr6A.!!$F1	589
19	TraesCS7A01G451800	chr6B	50336602	50337190	588	True	577.0	577	84.53800	4	591	1	chr6B.!!$R1	587
20	TraesCS7A01G451800	chr6B	583292338	583292926	588	True	507.0	507	82.29300	4	592	1	chr6B.!!$R2	588
21	TraesCS7A01G451800	chr4B	448806472	448807057	585	True	542.0	542	83.39000	4	592	1	chr4B.!!$R1	588

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
610	615	0.392998	CCCTGGTCGAGAAATGGTGG	60.393	60.0	0.0	0.0	0.0	4.61	F
1288	1340	0.261991	TCTACTTCTCCGGCCTCCAT	59.738	55.0	0.0	0.0	0.0	3.41	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1643	1695	1.649815	CAAACACCGCGTTGGCTAA	59.350	52.632	8.96	0.0	43.94	3.09	R
2229	8211	2.727123	TTGTGCTTTTCCAGTCCTCA	57.273	45.000	0.00	0.0	0.00	3.86	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
105	106	1.270625	GCCGTGCCTATTATACCTGCA	60.271	52.381	0.00	0.00	0.00	4.41
114	115	5.798132	CCTATTATACCTGCATTGCTCTCA	58.202	41.667	10.49	0.00	0.00	3.27
125	126	2.859165	TTGCTCTCACAAACCCTAGG	57.141	50.000	0.06	0.06	0.00	3.02
222	224	1.923395	AAGGATTCCCGGTCCAGCA	60.923	57.895	11.86	0.00	38.25	4.41
486	491	1.081094	CATGTTCATCGAGCAGCACA	58.919	50.000	0.00	0.00	0.00	4.57
543	548	4.194720	GCCAGCGAGATCCGTCGT	62.195	66.667	6.28	0.00	42.17	4.34
598	603	4.176752	GGGCGTCCATCCCTGGTC	62.177	72.222	0.00	0.00	43.61	4.02
602	607	4.356979	GTCCATCCCTGGTCGAGA	57.643	61.111	0.00	0.00	43.61	4.04
603	608	2.591915	GTCCATCCCTGGTCGAGAA	58.408	57.895	0.00	0.00	43.61	2.87
604	609	0.902531	GTCCATCCCTGGTCGAGAAA	59.097	55.000	0.00	0.00	43.61	2.52
605	610	1.486726	GTCCATCCCTGGTCGAGAAAT	59.513	52.381	0.00	0.00	43.61	2.17
606	611	1.486310	TCCATCCCTGGTCGAGAAATG	59.514	52.381	0.00	0.00	43.61	2.32
607	612	1.475751	CCATCCCTGGTCGAGAAATGG	60.476	57.143	0.00	2.57	37.79	3.16
608	613	1.210478	CATCCCTGGTCGAGAAATGGT	59.790	52.381	0.00	0.00	0.00	3.55
609	614	0.613260	TCCCTGGTCGAGAAATGGTG	59.387	55.000	0.00	0.00	0.00	4.17
610	615	0.392998	CCCTGGTCGAGAAATGGTGG	60.393	60.000	0.00	0.00	0.00	4.61
611	616	0.392998	CCTGGTCGAGAAATGGTGGG	60.393	60.000	0.00	0.00	0.00	4.61
612	617	0.613260	CTGGTCGAGAAATGGTGGGA	59.387	55.000	0.00	0.00	0.00	4.37
613	618	0.613260	TGGTCGAGAAATGGTGGGAG	59.387	55.000	0.00	0.00	0.00	4.30
614	619	0.902531	GGTCGAGAAATGGTGGGAGA	59.097	55.000	0.00	0.00	0.00	3.71
615	620	1.486726	GGTCGAGAAATGGTGGGAGAT	59.513	52.381	0.00	0.00	0.00	2.75
616	621	2.483889	GGTCGAGAAATGGTGGGAGATC	60.484	54.545	0.00	0.00	0.00	2.75
617	622	1.409064	TCGAGAAATGGTGGGAGATCG	59.591	52.381	0.00	0.00	0.00	3.69
618	623	1.409064	CGAGAAATGGTGGGAGATCGA	59.591	52.381	0.00	0.00	0.00	3.59
619	624	2.544694	CGAGAAATGGTGGGAGATCGAG	60.545	54.545	0.00	0.00	0.00	4.04
620	625	1.139853	AGAAATGGTGGGAGATCGAGC	59.860	52.381	0.00	0.00	0.00	5.03
621	626	0.911769	AAATGGTGGGAGATCGAGCA	59.088	50.000	2.38	0.00	36.12	4.26
622	627	0.467384	AATGGTGGGAGATCGAGCAG	59.533	55.000	2.38	0.00	35.21	4.24
623	628	2.037620	ATGGTGGGAGATCGAGCAGC	62.038	60.000	2.38	0.00	35.21	5.25
624	629	2.725312	GGTGGGAGATCGAGCAGCA	61.725	63.158	2.38	0.00	0.00	4.41
625	630	1.520342	GTGGGAGATCGAGCAGCAC	60.520	63.158	2.38	0.00	0.00	4.40
672	677	4.041740	TGTTGATATGTACAGGCGACTC	57.958	45.455	0.33	0.00	40.21	3.36
746	765	1.140052	CCTGCCGTCCCACATACATAA	59.860	52.381	0.00	0.00	0.00	1.90
803	827	2.564975	GCAGGCTGCACACATCAC	59.435	61.111	33.33	0.49	44.26	3.06
804	828	2.263021	GCAGGCTGCACACATCACA	61.263	57.895	33.33	0.00	44.26	3.58
805	829	1.798234	GCAGGCTGCACACATCACAA	61.798	55.000	33.33	0.00	44.26	3.33
806	830	0.885879	CAGGCTGCACACATCACAAT	59.114	50.000	0.00	0.00	0.00	2.71
849	875	5.013704	AGACCCAACCATGTGTATCTAAACA	59.986	40.000	0.00	0.00	0.00	2.83
850	876	5.826643	ACCCAACCATGTGTATCTAAACAT	58.173	37.500	0.00	0.00	37.50	2.71
859	885	7.428020	CATGTGTATCTAAACATGGGAAATGG	58.572	38.462	11.24	0.00	46.43	3.16
860	886	5.890985	TGTGTATCTAAACATGGGAAATGGG	59.109	40.000	0.00	0.00	0.00	4.00
870	896	8.650143	AAACATGGGAAATGGGATACATATAC	57.350	34.615	0.00	0.00	39.40	1.47
879	905	3.441222	TGGGATACATATACGTACGGCAG	59.559	47.826	21.06	7.04	39.74	4.85
925	954	6.426980	TTCATTGCATAGAGATCACACAAC	57.573	37.500	0.00	0.00	0.00	3.32
969	1004	4.900154	AGCTCGACTGCTTGCTAC	57.100	55.556	0.00	0.00	40.93	3.58
1125	1160	1.201880	GACAAGACGTCTCCAGGTACC	59.798	57.143	20.33	2.73	41.81	3.34
1288	1340	0.261991	TCTACTTCTCCGGCCTCCAT	59.738	55.000	0.00	0.00	0.00	3.41
1477	1529	0.698238	TAGAGGGTTGCCTGCATGTT	59.302	50.000	0.00	0.00	0.00	2.71
1643	1695	0.608640	GAACCCTGGAGTGATCACGT	59.391	55.000	19.85	8.01	36.20	4.49
1773	1834	5.646606	AGTTAATGAGTGCGTTTGTTTGTT	58.353	33.333	0.00	0.00	0.00	2.83
1775	1840	4.838665	AATGAGTGCGTTTGTTTGTTTG	57.161	36.364	0.00	0.00	0.00	2.93
1776	1841	3.290308	TGAGTGCGTTTGTTTGTTTGT	57.710	38.095	0.00	0.00	0.00	2.83
1777	1842	4.421033	TGAGTGCGTTTGTTTGTTTGTA	57.579	36.364	0.00	0.00	0.00	2.41
1786	1852	6.557171	GCGTTTGTTTGTTTGTAAGAATCGAC	60.557	38.462	0.00	0.00	0.00	4.20
1911	7886	8.641499	TTTTTCCTGTTTAATGTTGATGTGTC	57.359	30.769	0.00	0.00	0.00	3.67
1912	7887	5.605564	TCCTGTTTAATGTTGATGTGTCG	57.394	39.130	0.00	0.00	0.00	4.35
1913	7888	5.060506	TCCTGTTTAATGTTGATGTGTCGT	58.939	37.500	0.00	0.00	0.00	4.34
1914	7889	5.049749	TCCTGTTTAATGTTGATGTGTCGTG	60.050	40.000	0.00	0.00	0.00	4.35
1915	7890	5.102020	TGTTTAATGTTGATGTGTCGTGG	57.898	39.130	0.00	0.00	0.00	4.94
1916	7891	3.822594	TTAATGTTGATGTGTCGTGGC	57.177	42.857	0.00	0.00	0.00	5.01
1917	7892	0.881118	AATGTTGATGTGTCGTGGCC	59.119	50.000	0.00	0.00	0.00	5.36
1918	7893	0.036732	ATGTTGATGTGTCGTGGCCT	59.963	50.000	3.32	0.00	0.00	5.19
1919	7894	0.602638	TGTTGATGTGTCGTGGCCTC	60.603	55.000	3.32	0.00	0.00	4.70
2050	8029	7.448748	AATTGTTCTTTTCCTGCGTAACTAT	57.551	32.000	0.00	0.00	0.00	2.12
2090	8069	2.863739	GCAAGGGCAACGTCTTTATTC	58.136	47.619	0.00	0.00	40.72	1.75
2093	8074	4.558697	GCAAGGGCAACGTCTTTATTCTTT	60.559	41.667	0.00	0.00	40.72	2.52
2199	8180	5.067805	GGCCTCTTTGGTATGTAGGATTTTG	59.932	44.000	0.00	0.00	38.35	2.44
2242	8224	6.572519	CAAGTTCAAATTGAGGACTGGAAAA	58.427	36.000	1.54	0.00	0.00	2.29
2243	8225	6.396829	AGTTCAAATTGAGGACTGGAAAAG	57.603	37.500	0.00	0.00	0.00	2.27
2244	8226	4.853924	TCAAATTGAGGACTGGAAAAGC	57.146	40.909	0.00	0.00	0.00	3.51
2245	8227	4.214310	TCAAATTGAGGACTGGAAAAGCA	58.786	39.130	0.00	0.00	0.00	3.91
2246	8228	4.037923	TCAAATTGAGGACTGGAAAAGCAC	59.962	41.667	0.00	0.00	0.00	4.40
2253	8276	5.774690	TGAGGACTGGAAAAGCACAATAATT	59.225	36.000	0.00	0.00	0.00	1.40
2267	8299	7.547227	AGCACAATAATTACTCCATTTGTTCC	58.453	34.615	0.00	0.00	0.00	3.62
2269	8301	6.972328	CACAATAATTACTCCATTTGTTCCGG	59.028	38.462	0.00	0.00	0.00	5.14
2284	8316	9.507280	CATTTGTTCCGGAATATATTGCATATC	57.493	33.333	22.04	2.76	0.00	1.63
2285	8317	6.902224	TGTTCCGGAATATATTGCATATCG	57.098	37.500	22.04	0.72	0.00	2.92
2292	8324	7.857389	CCGGAATATATTGCATATCGGATTTTG	59.143	37.037	16.12	0.00	33.29	2.44
2331	8363	7.790823	TGTAAAGTTTGACCTAAGTTGGTAC	57.209	36.000	0.00	0.00	41.00	3.34
2364	8397	5.640357	TCAACGTCTACAATACCAAACCATC	59.360	40.000	0.00	0.00	0.00	3.51
2466	8516	6.310224	ACTTTTTGAGAAAACCAAATCACACG	59.690	34.615	0.00	0.00	34.02	4.49
2467	8517	3.980646	TGAGAAAACCAAATCACACGG	57.019	42.857	0.00	0.00	0.00	4.94
2478	8528	5.355910	ACCAAATCACACGGTATTATGGAAC	59.644	40.000	0.00	0.00	0.00	3.62
2522	8572	7.548196	TTTTCTTATGCCACTAAATACCTCG	57.452	36.000	0.00	0.00	0.00	4.63
2612	8663	9.175312	GATGGATATCACATTTTATGCTCTCAT	57.825	33.333	4.83	0.00	33.80	2.90
2628	8680	5.521372	TGCTCTCATATCATGTCTTTTCGTG	59.479	40.000	0.00	0.00	0.00	4.35
2686	8738	8.588472	ACCTTTTGAAATCCCTGATCTTTTTAG	58.412	33.333	0.00	0.00	0.00	1.85
2689	8741	9.981114	TTTTGAAATCCCTGATCTTTTTAGAAC	57.019	29.630	0.00	0.00	0.00	3.01

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	1.831736	CCGGTCAGATCTAGGGTTTGT	59.168	52.381	0.00	0.00	0.00	2.83
1	2	2.101582	CTCCGGTCAGATCTAGGGTTTG	59.898	54.545	0.00	0.00	0.00	2.93
2	3	2.389715	CTCCGGTCAGATCTAGGGTTT	58.610	52.381	0.00	0.00	0.00	3.27
94	95	5.039920	TGTGAGAGCAATGCAGGTATAAT	57.960	39.130	8.35	0.00	0.00	1.28
105	106	2.025887	CCCTAGGGTTTGTGAGAGCAAT	60.026	50.000	20.88	0.00	0.00	3.56
222	224	1.172812	GGTTTTTGCCTGCCTCGACT	61.173	55.000	0.00	0.00	0.00	4.18
503	508	4.803426	GCGTGGTCTGGCTCCGAG	62.803	72.222	0.00	0.00	0.00	4.63
593	598	0.613260	TCCCACCATTTCTCGACCAG	59.387	55.000	0.00	0.00	0.00	4.00
594	599	0.613260	CTCCCACCATTTCTCGACCA	59.387	55.000	0.00	0.00	0.00	4.02
595	600	0.902531	TCTCCCACCATTTCTCGACC	59.097	55.000	0.00	0.00	0.00	4.79
596	601	2.799917	CGATCTCCCACCATTTCTCGAC	60.800	54.545	0.00	0.00	0.00	4.20
597	602	1.409064	CGATCTCCCACCATTTCTCGA	59.591	52.381	0.00	0.00	0.00	4.04
598	603	1.409064	TCGATCTCCCACCATTTCTCG	59.591	52.381	0.00	0.00	0.00	4.04
599	604	2.804933	GCTCGATCTCCCACCATTTCTC	60.805	54.545	0.00	0.00	0.00	2.87
600	605	1.139853	GCTCGATCTCCCACCATTTCT	59.860	52.381	0.00	0.00	0.00	2.52
601	606	1.134401	TGCTCGATCTCCCACCATTTC	60.134	52.381	0.00	0.00	0.00	2.17
602	607	0.911769	TGCTCGATCTCCCACCATTT	59.088	50.000	0.00	0.00	0.00	2.32
603	608	0.467384	CTGCTCGATCTCCCACCATT	59.533	55.000	0.00	0.00	0.00	3.16
604	609	2.037620	GCTGCTCGATCTCCCACCAT	62.038	60.000	0.00	0.00	0.00	3.55
605	610	2.725312	GCTGCTCGATCTCCCACCA	61.725	63.158	0.00	0.00	0.00	4.17
606	611	2.107953	GCTGCTCGATCTCCCACC	59.892	66.667	0.00	0.00	0.00	4.61
607	612	1.520342	GTGCTGCTCGATCTCCCAC	60.520	63.158	0.00	0.00	0.00	4.61
608	613	2.725312	GGTGCTGCTCGATCTCCCA	61.725	63.158	0.00	0.00	0.00	4.37
609	614	2.107953	GGTGCTGCTCGATCTCCC	59.892	66.667	0.00	0.00	0.00	4.30
610	615	1.067250	GAGGTGCTGCTCGATCTCC	59.933	63.158	0.00	0.00	0.00	3.71
611	616	0.248990	CAGAGGTGCTGCTCGATCTC	60.249	60.000	0.00	0.00	37.90	2.75
612	617	1.815196	CAGAGGTGCTGCTCGATCT	59.185	57.895	0.00	1.86	37.90	2.75
613	618	4.416533	CAGAGGTGCTGCTCGATC	57.583	61.111	0.00	0.00	37.90	3.69
623	628	1.004044	ACCAAGAATCCAGCAGAGGTG	59.996	52.381	0.00	0.00	0.00	4.00
624	629	1.280421	GACCAAGAATCCAGCAGAGGT	59.720	52.381	0.00	0.00	0.00	3.85
625	630	1.280133	TGACCAAGAATCCAGCAGAGG	59.720	52.381	0.00	0.00	0.00	3.69
672	677	6.202379	ACATCAGATCAATCTATGCTTGAACG	59.798	38.462	0.00	0.00	36.30	3.95
707	712	7.224753	ACGGCAGGATCAAATTAATATATAGCG	59.775	37.037	0.00	0.00	0.00	4.26
746	765	0.103208	GACAGCCTGCTACGCATACT	59.897	55.000	0.00	0.00	38.13	2.12
795	819	6.267817	CAAGTCTTTGTGAATTGTGATGTGT	58.732	36.000	0.00	0.00	43.36	3.72
804	828	6.486993	GGTCTAGGAACAAGTCTTTGTGAATT	59.513	38.462	0.00	0.00	46.54	2.17
805	829	5.998363	GGTCTAGGAACAAGTCTTTGTGAAT	59.002	40.000	0.00	0.00	46.54	2.57
806	830	5.365619	GGTCTAGGAACAAGTCTTTGTGAA	58.634	41.667	0.00	0.00	46.54	3.18
849	875	6.636454	ACGTATATGTATCCCATTTCCCAT	57.364	37.500	0.00	0.00	34.86	4.00
850	876	6.350361	CGTACGTATATGTATCCCATTTCCCA	60.350	42.308	7.22	0.00	34.86	4.37
851	877	6.038356	CGTACGTATATGTATCCCATTTCCC	58.962	44.000	7.22	0.00	34.86	3.97
852	878	6.038356	CCGTACGTATATGTATCCCATTTCC	58.962	44.000	15.21	0.00	34.86	3.13
853	879	5.517770	GCCGTACGTATATGTATCCCATTTC	59.482	44.000	15.21	0.00	34.86	2.17
854	880	5.047164	TGCCGTACGTATATGTATCCCATTT	60.047	40.000	15.21	0.00	34.86	2.32
855	881	4.463539	TGCCGTACGTATATGTATCCCATT	59.536	41.667	15.21	0.00	34.86	3.16
856	882	4.018490	TGCCGTACGTATATGTATCCCAT	58.982	43.478	15.21	0.00	37.58	4.00
857	883	3.419943	TGCCGTACGTATATGTATCCCA	58.580	45.455	15.21	3.50	0.00	4.37
858	884	3.181493	CCTGCCGTACGTATATGTATCCC	60.181	52.174	15.21	1.21	0.00	3.85
859	885	3.691118	TCCTGCCGTACGTATATGTATCC	59.309	47.826	15.21	1.52	0.00	2.59
860	886	4.952262	TCCTGCCGTACGTATATGTATC	57.048	45.455	15.21	2.31	0.00	2.24
870	896	0.536687	TAGGGAGATCCTGCCGTACG	60.537	60.000	8.69	8.69	46.84	3.67
879	905	6.477901	AGGAGGCTATATATAGGGAGATCC	57.522	45.833	19.19	11.42	0.00	3.36
925	954	0.376152	CGGTTGCTATGCTGCTTGAG	59.624	55.000	0.00	0.00	0.00	3.02
969	1004	5.710984	TGTTTTCTCCTCGCTAGAGTAAAG	58.289	41.667	0.00	0.00	42.86	1.85
1193	1245	2.424601	CTGCATGGGTCAATTCATTCGT	59.575	45.455	0.00	0.00	0.00	3.85
1194	1246	2.424601	ACTGCATGGGTCAATTCATTCG	59.575	45.455	0.00	0.00	0.00	3.34
1200	1252	2.083774	CACGTACTGCATGGGTCAATT	58.916	47.619	0.00	0.00	0.00	2.32
1204	1256	0.037697	TGACACGTACTGCATGGGTC	60.038	55.000	0.00	0.00	45.48	4.46
1643	1695	1.649815	CAAACACCGCGTTGGCTAA	59.350	52.632	8.96	0.00	43.94	3.09
1773	1834	7.762615	CCAAATAGTACTGGTCGATTCTTACAA	59.237	37.037	5.39	0.00	0.00	2.41
1775	1840	7.222224	CACCAAATAGTACTGGTCGATTCTTAC	59.778	40.741	5.39	0.00	44.30	2.34
1776	1841	7.093640	ACACCAAATAGTACTGGTCGATTCTTA	60.094	37.037	5.39	0.00	44.30	2.10
1777	1842	6.106673	CACCAAATAGTACTGGTCGATTCTT	58.893	40.000	5.39	0.00	44.30	2.52
1912	7887	3.469863	TTGTGTCCCACGAGGCCAC	62.470	63.158	5.01	11.28	37.14	5.01
1913	7888	3.164977	TTGTGTCCCACGAGGCCA	61.165	61.111	5.01	0.00	37.14	5.36
1914	7889	2.668550	GTTGTGTCCCACGAGGCC	60.669	66.667	0.00	0.00	37.14	5.19
1915	7890	2.668550	GGTTGTGTCCCACGAGGC	60.669	66.667	0.00	0.00	37.14	4.70
1916	7891	2.032071	GGGTTGTGTCCCACGAGG	59.968	66.667	0.00	0.00	46.30	4.63
1962	7938	9.793252	ACATCAATATTACACAAGAAAGCATTC	57.207	29.630	0.00	0.00	35.70	2.67
1963	7939	9.577110	CACATCAATATTACACAAGAAAGCATT	57.423	29.630	0.00	0.00	0.00	3.56
1964	7940	8.742777	ACACATCAATATTACACAAGAAAGCAT	58.257	29.630	0.00	0.00	0.00	3.79
1965	7941	8.109705	ACACATCAATATTACACAAGAAAGCA	57.890	30.769	0.00	0.00	0.00	3.91
1966	7942	8.853345	CAACACATCAATATTACACAAGAAAGC	58.147	33.333	0.00	0.00	0.00	3.51
1969	7945	8.296000	CCACAACACATCAATATTACACAAGAA	58.704	33.333	0.00	0.00	0.00	2.52
2022	8001	9.005777	AGTTACGCAGGAAAAGAACAATTTATA	57.994	29.630	0.00	0.00	0.00	0.98
2023	8002	7.882179	AGTTACGCAGGAAAAGAACAATTTAT	58.118	30.769	0.00	0.00	0.00	1.40
2079	8058	9.030301	CCAACAATTTCAAAAGAATAAAGACGT	57.970	29.630	0.00	0.00	0.00	4.34
2090	8069	9.108284	ACACTATTTTCCCAACAATTTCAAAAG	57.892	29.630	0.00	0.00	0.00	2.27
2093	8074	9.454859	AAAACACTATTTTCCCAACAATTTCAA	57.545	25.926	0.00	0.00	0.00	2.69
2113	8094	9.065871	GCATTGTCACTAGAATATCAAAAACAC	57.934	33.333	0.00	0.00	0.00	3.32
2199	8180	9.195411	TGAACTTGCATCAAATTCTTATGTTTC	57.805	29.630	0.00	0.00	31.94	2.78
2229	8211	2.727123	TTGTGCTTTTCCAGTCCTCA	57.273	45.000	0.00	0.00	0.00	3.86
2242	8224	7.547227	GGAACAAATGGAGTAATTATTGTGCT	58.453	34.615	5.67	0.00	31.90	4.40
2243	8225	6.472163	CGGAACAAATGGAGTAATTATTGTGC	59.528	38.462	1.67	0.22	31.90	4.57
2244	8226	6.972328	CCGGAACAAATGGAGTAATTATTGTG	59.028	38.462	0.00	0.00	31.90	3.33
2245	8227	6.887545	TCCGGAACAAATGGAGTAATTATTGT	59.112	34.615	0.00	0.00	32.78	2.71
2246	8228	7.328277	TCCGGAACAAATGGAGTAATTATTG	57.672	36.000	0.00	0.00	0.00	1.90
2253	8276	7.174253	GCAATATATTCCGGAACAAATGGAGTA	59.826	37.037	21.56	4.82	32.39	2.59
2267	8299	7.857389	CCAAAATCCGATATGCAATATATTCCG	59.143	37.037	0.00	0.00	40.26	4.30
2269	8301	8.190122	TGCCAAAATCCGATATGCAATATATTC	58.810	33.333	0.00	0.00	40.26	1.75
2337	8370	6.487331	TGGTTTGGTATTGTAGACGTTGAAAT	59.513	34.615	0.00	0.00	0.00	2.17
2339	8372	5.366460	TGGTTTGGTATTGTAGACGTTGAA	58.634	37.500	0.00	0.00	0.00	2.69
2345	8378	5.250200	TGGTGATGGTTTGGTATTGTAGAC	58.750	41.667	0.00	0.00	0.00	2.59
2437	8470	8.168626	GTGATTTGGTTTTCTCAAAAAGTCAAC	58.831	33.333	0.00	0.00	37.60	3.18
2447	8480	3.283751	ACCGTGTGATTTGGTTTTCTCA	58.716	40.909	0.00	0.00	29.87	3.27
2448	8481	3.982576	ACCGTGTGATTTGGTTTTCTC	57.017	42.857	0.00	0.00	29.87	2.87
2449	8482	7.362574	CCATAATACCGTGTGATTTGGTTTTCT	60.363	37.037	0.00	0.00	37.20	2.52
2466	8516	7.042797	TGTACTTACTCCGTTCCATAATACC	57.957	40.000	0.00	0.00	0.00	2.73
2467	8517	9.538508	AATTGTACTTACTCCGTTCCATAATAC	57.461	33.333	0.00	0.00	0.00	1.89
2602	8653	7.383300	CACGAAAAGACATGATATGAGAGCATA	59.617	37.037	0.00	0.00	41.00	3.14
2612	8663	3.937814	AGGTGCACGAAAAGACATGATA	58.062	40.909	11.45	0.00	0.00	2.15

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.