AutoCloner

Multiple sequence alignment - TraesCS6A01G097700

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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	TraesCS6A01G097700	chr6A	100.000	3933	0	0	1	3933	64910400	64906468	0.000000e+00	7263.0
1	TraesCS6A01G097700	chr6A	85.080	1374	194	7	1948	3319	64679630	64678266	0.000000e+00	1391.0
2	TraesCS6A01G097700	chr6A	85.251	1356	178	10	1956	3294	577723318	577721968	0.000000e+00	1376.0
3	TraesCS6A01G097700	chr6A	80.563	782	139	8	320	1095	64681318	64680544	1.220000e-164	590.0
4	TraesCS6A01G097700	chr6A	88.125	480	48	7	3418	3891	64678219	64677743	2.650000e-156	562.0
5	TraesCS6A01G097700	chr6A	78.487	674	108	18	1111	1754	64680468	64679802	1.320000e-109	407.0
6	TraesCS6A01G097700	chr6A	81.855	248	32	11	1698	1942	577723645	577723408	3.100000e-46	196.0
7	TraesCS6A01G097700	chr6D	92.630	2836	182	13	1111	3933	50178969	50181790	0.000000e+00	4054.0
8	TraesCS6A01G097700	chr6D	91.121	1115	96	3	1	1114	50177800	50178912	0.000000e+00	1507.0
9	TraesCS6A01G097700	chr6D	85.953	1374	174	14	1945	3314	49182762	49184120	0.000000e+00	1450.0
10	TraesCS6A01G097700	chr6D	85.126	1385	192	9	1937	3316	50605088	50606463	0.000000e+00	1404.0
11	TraesCS6A01G097700	chr6D	82.228	799	132	8	320	1112	49181037	49181831	0.000000e+00	680.0
12	TraesCS6A01G097700	chr6D	90.000	480	40	6	3418	3891	50606514	50606991	7.220000e-172	614.0
13	TraesCS6A01G097700	chr6D	91.209	182	11	5	148	327	301250688	301250866	3.930000e-60	243.0
14	TraesCS6A01G097700	chr6D	90.608	181	14	3	148	327	111470124	111470302	1.830000e-58	237.0
15	TraesCS6A01G097700	chr6B	92.473	2830	183	15	1111	3933	121433519	121430713	0.000000e+00	4019.0
16	TraesCS6A01G097700	chr6B	84.462	1506	196	11	1956	3428	649832557	649831057	0.000000e+00	1450.0
17	TraesCS6A01G097700	chr6B	89.205	1019	106	4	99	1114	121434593	121433576	0.000000e+00	1269.0
18	TraesCS6A01G097700	chr6B	94.643	112	6	0	1	112	526112425	526112536	1.450000e-39	174.0
19	TraesCS6A01G097700	chrUn	85.153	1374	193	7	1945	3316	277361311	277362675	0.000000e+00	1397.0
20	TraesCS6A01G097700	chrUn	86.556	543	66	3	1948	2489	373932975	373932439	3.380000e-165	592.0
21	TraesCS6A01G097700	chrUn	87.917	480	49	7	3418	3891	277362725	277363201	1.230000e-154	556.0
22	TraesCS6A01G097700	chrUn	82.869	467	73	4	320	782	71749157	71749620	2.830000e-111	412.0
23	TraesCS6A01G097700	chrUn	78.042	674	111	18	1111	1754	373933813	373933147	1.330000e-104	390.0
24	TraesCS6A01G097700	chrUn	78.836	378	54	10	1250	1602	478961325	478960949	8.500000e-57	231.0
25	TraesCS6A01G097700	chr7A	85.007	1374	178	20	1949	3316	591024224	591025575	0.000000e+00	1371.0
26	TraesCS6A01G097700	chr7A	86.398	522	57	9	3418	3932	591025626	591026140	3.430000e-155	558.0
27	TraesCS6A01G097700	chr7A	81.748	515	81	7	1436	1944	551543131	551542624	6.080000e-113	418.0
28	TraesCS6A01G097700	chr7A	85.266	319	41	5	3543	3855	616441783	616441465	1.360000e-84	324.0
29	TraesCS6A01G097700	chr7A	84.351	262	25	9	1695	1942	615785804	615786063	3.930000e-60	243.0
30	TraesCS6A01G097700	chr7A	82.625	259	28	10	1698	1942	616444037	616443782	3.080000e-51	213.0
31	TraesCS6A01G097700	chr7A	95.413	109	5	0	4	112	202998470	202998362	1.450000e-39	174.0
32	TraesCS6A01G097700	chr7D	82.195	1376	198	28	1956	3316	489301837	489300494	0.000000e+00	1140.0
33	TraesCS6A01G097700	chr7D	82.438	484	73	8	1436	1913	484072123	484071646	2.830000e-111	412.0
34	TraesCS6A01G097700	chr7D	84.639	319	46	3	320	637	489312658	489312342	8.200000e-82	315.0
35	TraesCS6A01G097700	chr7D	81.402	371	65	4	323	693	484073354	484072988	2.300000e-77	300.0
36	TraesCS6A01G097700	chr7D	85.000	260	24	8	1693	1942	535510724	535510978	2.350000e-62	250.0
37	TraesCS6A01G097700	chr7D	91.573	178	11	4	148	323	270700273	270700098	3.930000e-60	243.0
38	TraesCS6A01G097700	chr7B	82.555	321	52	4	320	638	517935512	517935194	2.990000e-71	279.0
39	TraesCS6A01G097700	chr7B	94.643	112	6	0	1	112	361166903	361167014	1.450000e-39	174.0
40	TraesCS6A01G097700	chr1A	92.179	179	11	3	148	324	91044688	91044865	2.350000e-62	250.0
41	TraesCS6A01G097700	chr1A	89.062	192	18	3	148	338	454738973	454738784	6.570000e-58	235.0
42	TraesCS6A01G097700	chr4D	91.209	182	12	4	148	327	363017289	363017110	1.090000e-60	244.0
43	TraesCS6A01G097700	chr2D	83.908	261	37	5	320	578	89439229	89438972	1.090000e-60	244.0
44	TraesCS6A01G097700	chr3A	89.785	186	15	4	144	327	425175195	425175378	6.570000e-58	235.0
45	TraesCS6A01G097700	chr5A	94.643	112	6	0	1	112	367139681	367139792	1.450000e-39	174.0
46	TraesCS6A01G097700	chr4A	95.413	109	5	0	4	112	358836173	358836065	1.450000e-39	174.0
47	TraesCS6A01G097700	chr4A	95.413	109	5	0	4	112	362096273	362096165	1.450000e-39	174.0
48	TraesCS6A01G097700	chr2A	95.413	109	5	0	4	112	369892071	369891963	1.450000e-39	174.0
49	TraesCS6A01G097700	chr1D	93.750	112	7	0	1	112	355934660	355934771	6.760000e-38	169.0
50	TraesCS6A01G097700	chr2B	84.314	102	12	4	1339	1437	142295681	142295781	3.230000e-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	TraesCS6A01G097700	chr6A	64906468	64910400	3932	True	7263.0	7263	100.00000	1	3933	1	chr6A.!!$R1	3932
1	TraesCS6A01G097700	chr6A	577721968	577723645	1677	True	786.0	1376	83.55300	1698	3294	2	chr6A.!!$R3	1596
2	TraesCS6A01G097700	chr6A	64677743	64681318	3575	True	737.5	1391	83.06375	320	3891	4	chr6A.!!$R2	3571
3	TraesCS6A01G097700	chr6D	50177800	50181790	3990	False	2780.5	4054	91.87550	1	3933	2	chr6D.!!$F4	3932
4	TraesCS6A01G097700	chr6D	49181037	49184120	3083	False	1065.0	1450	84.09050	320	3314	2	chr6D.!!$F3	2994
5	TraesCS6A01G097700	chr6D	50605088	50606991	1903	False	1009.0	1404	87.56300	1937	3891	2	chr6D.!!$F5	1954
6	TraesCS6A01G097700	chr6B	121430713	121434593	3880	True	2644.0	4019	90.83900	99	3933	2	chr6B.!!$R2	3834
7	TraesCS6A01G097700	chr6B	649831057	649832557	1500	True	1450.0	1450	84.46200	1956	3428	1	chr6B.!!$R1	1472
8	TraesCS6A01G097700	chrUn	277361311	277363201	1890	False	976.5	1397	86.53500	1945	3891	2	chrUn.!!$F2	1946
9	TraesCS6A01G097700	chrUn	373932439	373933813	1374	True	491.0	592	82.29900	1111	2489	2	chrUn.!!$R2	1378
10	TraesCS6A01G097700	chr7A	591024224	591026140	1916	False	964.5	1371	85.70250	1949	3932	2	chr7A.!!$F2	1983
11	TraesCS6A01G097700	chr7A	551542624	551543131	507	True	418.0	418	81.74800	1436	1944	1	chr7A.!!$R2	508
12	TraesCS6A01G097700	chr7A	616441465	616444037	2572	True	268.5	324	83.94550	1698	3855	2	chr7A.!!$R3	2157
13	TraesCS6A01G097700	chr7D	489300494	489301837	1343	True	1140.0	1140	82.19500	1956	3316	1	chr7D.!!$R2	1360
14	TraesCS6A01G097700	chr7D	484071646	484073354	1708	True	356.0	412	81.92000	323	1913	2	chr7D.!!$R4	1590

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	Hairpin	End Stability	Orientation
656	663	0.114954	TTCTTGGCCTGCCTCCAAAT	59.885	50.0	9.97	42.45	2.32	F
1442	1619	0.038618	GTTTGGGCGGTGTTTGGATC	60.039	55.0	0.00	0.00	3.36	F
2569	2877	1.149101	AGGGAAGCAACTCCTTTGGA	58.851	50.0	0.00	35.51	3.53	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1592	1772	1.447838	CCACCATCGAAGGTCACGG	60.448	63.158	9.89	4.76	40.77	4.94	R
2794	3102	0.532862	CCATAAGAAGCGTCGCCCAT	60.533	55.000	14.86	0.00	0.00	4.00	R
3875	4747	0.984995	ACAGAACTAGTTGGCCCTCC	59.015	55.000	14.14	0.00	0.00	4.30	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
67	68	4.753233	ACCAGATGTGATTCTCTCTTTCG	58.247	43.478	0.00	0.00	0.00	3.46
95	96	3.181479	GGGTGTTAGCTACGATCATGTCA	60.181	47.826	0.00	0.00	0.00	3.58
120	121	0.777446	TAGAGCAAAGCCCCCACTTT	59.223	50.000	0.00	0.00	40.49	2.66
123	124	1.836604	GCAAAGCCCCCACTTTCCA	60.837	57.895	0.00	0.00	37.78	3.53
127	129	1.664956	AAGCCCCCACTTTCCAACCT	61.665	55.000	0.00	0.00	0.00	3.50
210	212	4.308899	AGTCATAACGCATCTACTGGTC	57.691	45.455	0.00	0.00	0.00	4.02
279	281	4.879545	TCAAACTTTACGAGGCTTGACTTT	59.120	37.500	9.20	0.00	30.70	2.66
283	285	5.850614	ACTTTACGAGGCTTGACTTTAGAA	58.149	37.500	9.20	0.00	0.00	2.10
404	407	2.728817	GATGGGAGGAGTACGCCG	59.271	66.667	10.22	0.00	40.42	6.46
465	468	7.510549	TCTTGAGCTAATAAATGGCATAACC	57.489	36.000	0.00	0.00	39.84	2.85
549	552	5.533154	TGGTTAAACGTTCAGTTGGATGAAT	59.467	36.000	0.00	0.00	43.37	2.57
564	567	5.828299	GGATGAATCCGTCAAATAAACCA	57.172	39.130	0.00	0.00	40.50	3.67
586	589	3.468063	GGGGAGTGTCCGACAGTT	58.532	61.111	10.25	0.00	37.43	3.16
645	652	6.699575	TTCTTGAGCTAATAATTCTTGGCC	57.300	37.500	8.07	0.00	33.48	5.36
656	663	0.114954	TTCTTGGCCTGCCTCCAAAT	59.885	50.000	9.97	0.00	42.45	2.32
658	665	1.570501	TCTTGGCCTGCCTCCAAATAT	59.429	47.619	9.97	0.00	42.45	1.28
668	675	5.762218	CCTGCCTCCAAATATAGAAAGTCAG	59.238	44.000	0.00	0.00	0.00	3.51
739	746	3.353836	CCAAGGGTCCAACACGCG	61.354	66.667	3.53	3.53	42.88	6.01
760	767	4.454504	GCGAAATTTCCCTGAGTAGAAACA	59.545	41.667	12.54	0.00	34.97	2.83
777	786	2.936919	ACACTCATTCAGAACCTGCA	57.063	45.000	0.00	0.00	0.00	4.41
799	808	3.127533	GCCTTCCATTCGCAGCGT	61.128	61.111	15.93	0.00	0.00	5.07
802	811	1.741401	CTTCCATTCGCAGCGTGGA	60.741	57.895	20.33	20.33	38.59	4.02
816	825	2.523168	TGGACCCTCGCTGACACA	60.523	61.111	0.00	0.00	0.00	3.72
949	958	1.272760	TGCCCCATTTACCAATTCCGT	60.273	47.619	0.00	0.00	0.00	4.69
1046	1058	1.337823	CCTCGAGGTTTCAACGGTGAT	60.338	52.381	24.04	0.00	32.48	3.06
1088	1100	1.549170	TCTACGGCCCAAGAAGAAGAC	59.451	52.381	0.00	0.00	0.00	3.01
1097	1109	2.125633	GAAGAAGACGCCCCGACC	60.126	66.667	0.00	0.00	0.00	4.79
1132	1204	3.596214	GACTTTGAGGCCGACTATGAAA	58.404	45.455	0.00	0.00	0.00	2.69
1200	1272	2.061061	GGGGTGGATGAGAAGGATGAT	58.939	52.381	0.00	0.00	0.00	2.45
1247	1319	3.485431	CGCTGCTGTCAAGAGGCG	61.485	66.667	0.00	0.00	38.70	5.52
1315	1388	8.934023	TTTGAATCTGTGTATCCTTACCTTTT	57.066	30.769	0.00	0.00	0.00	2.27
1362	1449	6.263392	TGATTGTTTGATTGGTTCGGAAACTA	59.737	34.615	7.38	0.00	35.61	2.24
1370	1457	3.414269	TGGTTCGGAAACTATTTGGTCC	58.586	45.455	7.38	0.00	35.61	4.46
1388	1475	2.622064	CCTTCGATTGGGTAGGAAGG	57.378	55.000	4.46	4.46	46.67	3.46
1442	1619	0.038618	GTTTGGGCGGTGTTTGGATC	60.039	55.000	0.00	0.00	0.00	3.36
1468	1646	6.261603	GGATGTGCTATCATGAAGTGATTTGA	59.738	38.462	0.00	0.00	45.25	2.69
1497	1677	5.550403	AGGGTTAGGTTCTTCCATTTGTCTA	59.450	40.000	0.00	0.00	39.02	2.59
1505	1685	9.533831	AGGTTCTTCCATTTGTCTATTGTATTT	57.466	29.630	0.00	0.00	39.02	1.40
1551	1731	3.117888	TGTCCCTTTCTTTCACAGAAGCT	60.118	43.478	0.00	0.00	42.76	3.74
1565	1745	7.759489	TCACAGAAGCTATTTTGGTTGTTAT	57.241	32.000	0.00	0.00	0.00	1.89
1685	1865	5.408604	TCTGATTTCTCCGTTTTGCTTAGAC	59.591	40.000	0.00	0.00	0.00	2.59
1687	1867	2.806608	TCTCCGTTTTGCTTAGACGT	57.193	45.000	0.00	0.00	35.17	4.34
1688	1868	3.921119	TCTCCGTTTTGCTTAGACGTA	57.079	42.857	0.00	0.00	35.17	3.57
1689	1869	4.445452	TCTCCGTTTTGCTTAGACGTAT	57.555	40.909	0.00	0.00	35.17	3.06
1690	1870	4.813027	TCTCCGTTTTGCTTAGACGTATT	58.187	39.130	0.00	0.00	35.17	1.89
1691	1871	5.232463	TCTCCGTTTTGCTTAGACGTATTT	58.768	37.500	0.00	0.00	35.17	1.40
1692	1872	5.346822	TCTCCGTTTTGCTTAGACGTATTTC	59.653	40.000	0.00	0.00	35.17	2.17
1696	1882	6.529125	CCGTTTTGCTTAGACGTATTTCTCTA	59.471	38.462	0.00	0.00	35.17	2.43
1721	1909	6.232581	TGAATTGTTTCCTTGTGATGGTTT	57.767	33.333	0.00	0.00	0.00	3.27
1929	2133	8.175716	CCTCGATTTTCCTTATTAAGTTGTGAC	58.824	37.037	2.88	0.00	0.00	3.67
2041	2328	2.290896	TGTTGGTCCCTCTTAGCATTGG	60.291	50.000	0.00	0.00	0.00	3.16
2055	2348	3.101437	AGCATTGGCATTGATCTTCCAA	58.899	40.909	13.23	9.68	44.61	3.53
2072	2371	7.019774	TCTTCCAATTCTGATGATTTAAGCG	57.980	36.000	0.00	0.00	0.00	4.68
2221	2529	4.675671	CGTGTTTGGCTTGGTACTTTCAAA	60.676	41.667	0.00	0.00	0.00	2.69
2365	2673	2.026262	TCCTAAAGCACCCAAGCTAAGG	60.026	50.000	9.70	9.70	45.89	2.69
2569	2877	1.149101	AGGGAAGCAACTCCTTTGGA	58.851	50.000	0.00	0.00	35.51	3.53
2624	2932	7.617329	CCAAGACTCCAGATATATCATCCACTA	59.383	40.741	15.08	0.00	0.00	2.74
2751	3059	4.989168	CCAGAGTAACACCTACAACTCAAC	59.011	45.833	4.35	0.00	40.65	3.18
2752	3060	5.452776	CCAGAGTAACACCTACAACTCAACA	60.453	44.000	4.35	0.00	40.65	3.33
2794	3102	5.072040	ACAATGATATCGATATCGTGGCA	57.928	39.130	31.25	19.33	41.55	4.92
2802	3110	1.291877	GATATCGTGGCATGGGCGAC	61.292	60.000	6.90	0.00	44.31	5.19
2828	3136	1.127343	TATGGATGATGGCGTGGTCA	58.873	50.000	0.00	0.00	0.00	4.02
2846	3154	3.281727	TCAAGCCGATTGATAGCCTTT	57.718	42.857	0.00	0.00	43.09	3.11
2869	3177	3.507233	TGAATTTTGATGTGCCTCAGGAC	59.493	43.478	0.00	0.00	0.00	3.85
2874	3182	0.459237	GATGTGCCTCAGGACGTCAG	60.459	60.000	18.91	9.45	0.00	3.51
2970	3280	8.984112	TTATATATAGGGACAAAGGGTAAGCT	57.016	34.615	0.00	0.00	0.00	3.74
2996	3306	5.409643	GCATATTGCACGTTTAGTCTGAT	57.590	39.130	0.00	0.00	44.26	2.90
3109	3420	4.761739	GGCTAGCATATGCCTATGTTCAAA	59.238	41.667	23.96	0.00	45.26	2.69
3117	3428	8.233190	GCATATGCCTATGTTCAAACTTAGATC	58.767	37.037	17.26	8.27	38.32	2.75
3394	3736	3.951563	ATGGATTTGCCTGGCTACTTA	57.048	42.857	21.03	0.00	37.63	2.24
3438	3783	2.159503	TGGTAAATTATGGTTGTGCGCG	60.160	45.455	0.00	0.00	0.00	6.86
3509	3855	2.294074	GTGTGTTAAGCCAACCTGTCA	58.706	47.619	0.00	0.00	36.20	3.58
3685	4548	4.088634	TGAGTGGAGGGATTTTCCATTTG	58.911	43.478	0.00	0.00	45.85	2.32
3773	4643	8.474025	TGAACCACATACTTTTCACTTGATTTT	58.526	29.630	0.00	0.00	0.00	1.82

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
12	13	1.544724	GGCCAACACTATTGCCAGAA	58.455	50.000	0.00	0.00	43.46	3.02
67	68	3.863142	TCGTAGCTAACACCCTCTTTC	57.137	47.619	0.00	0.00	0.00	2.62
120	121	9.169592	GTATAATTTTAGCAAGTGTAGGTTGGA	57.830	33.333	0.00	0.00	0.00	3.53
181	183	8.058328	CAGTAGATGCGTTATGACTTAACATTG	58.942	37.037	10.76	0.00	40.25	2.82
297	299	3.181426	ACTCCCCCGGTCATTTTTAGTTT	60.181	43.478	0.00	0.00	0.00	2.66
404	407	6.095160	ACTTGTAGTATGACTGTGCTACTACC	59.905	42.308	21.73	12.01	43.51	3.18
465	468	7.218145	GATTTTTGCAAATCACTCATAGCTG	57.782	36.000	13.65	0.00	45.45	4.24
521	524	6.210287	TCCAACTGAACGTTTAACCAAAAT	57.790	33.333	0.46	0.00	32.27	1.82
549	552	2.690786	CGTCCTGGTTTATTTGACGGA	58.309	47.619	0.00	0.00	43.60	4.69
555	558	1.990327	ACTCCCCGTCCTGGTTTATTT	59.010	47.619	0.00	0.00	35.15	1.40
639	646	2.077687	ATATTTGGAGGCAGGCCAAG	57.922	50.000	13.63	0.00	45.39	3.61
645	652	6.481644	GTCTGACTTTCTATATTTGGAGGCAG	59.518	42.308	0.00	0.00	0.00	4.85
656	663	8.577296	GGCTGTATGTATGTCTGACTTTCTATA	58.423	37.037	9.51	0.00	0.00	1.31
658	665	6.379988	TGGCTGTATGTATGTCTGACTTTCTA	59.620	38.462	9.51	0.00	0.00	2.10
668	675	5.182001	GGGAATGAATGGCTGTATGTATGTC	59.818	44.000	0.00	0.00	0.00	3.06
677	684	1.620524	CCTTGGGGAATGAATGGCTGT	60.621	52.381	0.00	0.00	33.58	4.40
739	746	7.135089	GAGTGTTTCTACTCAGGGAAATTTC	57.865	40.000	9.83	9.83	45.03	2.17
760	767	2.027745	ACGATGCAGGTTCTGAATGAGT	60.028	45.455	0.00	0.00	28.32	3.41
777	786	1.078497	TGCGAATGGAAGGCACGAT	60.078	52.632	0.00	0.00	0.00	3.73
799	808	1.913262	ATGTGTCAGCGAGGGTCCA	60.913	57.895	0.00	0.00	0.00	4.02
802	811	2.665000	CCATGTGTCAGCGAGGGT	59.335	61.111	0.00	0.00	0.00	4.34
816	825	2.360191	GCATGTGGTGGGACCCAT	59.640	61.111	18.51	0.00	37.50	4.00
968	980	1.726791	GTACCTCGTCGTAGTCGTCAA	59.273	52.381	0.00	0.00	40.43	3.18
1036	1048	1.375396	CCTTCCGCATCACCGTTGA	60.375	57.895	0.00	0.00	35.73	3.18
1038	1050	1.671054	CACCTTCCGCATCACCGTT	60.671	57.895	0.00	0.00	0.00	4.44
1046	1058	1.823295	GCCTCTATCACCTTCCGCA	59.177	57.895	0.00	0.00	0.00	5.69
1072	1084	2.391389	GCGTCTTCTTCTTGGGCCG	61.391	63.158	0.00	0.00	0.00	6.13
1127	1199	3.927555	TCGGCCTCGAAGTTTTCAT	57.072	47.368	0.00	0.00	43.03	2.57
1200	1272	1.541379	TTTCGATGACCTCCTCGTCA	58.459	50.000	0.00	0.00	46.36	4.35
1247	1319	1.344087	TGATACCTTGGGAGAGGGACC	60.344	57.143	0.00	0.00	41.31	4.46
1315	1388	2.535012	TGGTACAACACTCAATCGCA	57.465	45.000	0.00	0.00	31.92	5.10
1362	1449	2.899303	ACCCAATCGAAGGACCAAAT	57.101	45.000	8.71	0.00	0.00	2.32
1370	1457	2.500098	TGTCCTTCCTACCCAATCGAAG	59.500	50.000	0.00	0.00	33.11	3.79
1388	1475	2.698274	AGGAACCCCAACACAATTTGTC	59.302	45.455	0.00	0.00	37.51	3.18
1442	1619	3.721035	TCACTTCATGATAGCACATCCG	58.279	45.455	0.00	0.00	29.99	4.18
1468	1646	5.536497	ATGGAAGAACCTAACCCTTCATT	57.464	39.130	0.00	0.00	38.35	2.57
1497	1677	7.093509	GGAAACATCCTACCAACCAAATACAAT	60.094	37.037	0.00	0.00	0.00	2.71
1505	1685	3.885976	TTGGAAACATCCTACCAACCA	57.114	42.857	0.00	0.00	42.32	3.67
1578	1758	6.311935	CGAAGGTCACGGAAAGTATAAATCAA	59.688	38.462	0.00	0.00	0.00	2.57
1592	1772	1.447838	CCACCATCGAAGGTCACGG	60.448	63.158	9.89	4.76	40.77	4.94
1688	1868	9.918630	CACAAGGAAACAATTCAATAGAGAAAT	57.081	29.630	0.00	0.00	37.29	2.17
1689	1869	9.130661	TCACAAGGAAACAATTCAATAGAGAAA	57.869	29.630	0.00	0.00	37.29	2.52
1690	1870	8.690203	TCACAAGGAAACAATTCAATAGAGAA	57.310	30.769	0.00	0.00	37.29	2.87
1691	1871	8.733458	CATCACAAGGAAACAATTCAATAGAGA	58.267	33.333	0.00	0.00	37.29	3.10
1692	1872	7.972277	CCATCACAAGGAAACAATTCAATAGAG	59.028	37.037	0.00	0.00	37.29	2.43
1696	1882	6.423776	ACCATCACAAGGAAACAATTCAAT	57.576	33.333	0.00	0.00	37.29	2.57
1721	1909	4.102524	AGAACAATCCTCACACACACCTAA	59.897	41.667	0.00	0.00	0.00	2.69
2041	2328	6.387041	TCATCAGAATTGGAAGATCAATGC	57.613	37.500	0.00	0.00	37.42	3.56
2055	2348	6.488006	AGTTATGGCGCTTAAATCATCAGAAT	59.512	34.615	7.64	0.00	0.00	2.40
2221	2529	3.360340	GCAGCAGCTTCGGCACTT	61.360	61.111	3.32	0.00	44.74	3.16
2284	2592	6.133356	TGGTTCCTCTGGAAAGTTAACATTT	58.867	36.000	8.61	5.65	43.86	2.32
2365	2673	1.972872	CAGTAGGTTCCCATGATGCC	58.027	55.000	0.00	0.00	0.00	4.40
2569	2877	5.520748	AATTCCAACCCAAGTCAGAGTAT	57.479	39.130	0.00	0.00	0.00	2.12
2624	2932	3.197766	TCAGCGATGGTAGAAATTGGAGT	59.802	43.478	0.00	0.00	0.00	3.85
2794	3102	0.532862	CCATAAGAAGCGTCGCCCAT	60.533	55.000	14.86	0.00	0.00	4.00
2802	3110	1.462283	CGCCATCATCCATAAGAAGCG	59.538	52.381	0.00	0.00	35.38	4.68
2828	3136	3.620488	TCAAAAGGCTATCAATCGGCTT	58.380	40.909	0.00	0.00	46.36	4.35
2846	3154	4.022068	GTCCTGAGGCACATCAAAATTCAA	60.022	41.667	0.00	0.00	0.00	2.69
2869	3177	0.884259	TGTCCATGTTGCCACTGACG	60.884	55.000	0.00	0.00	30.70	4.35
2874	3182	1.617850	TCCAAATGTCCATGTTGCCAC	59.382	47.619	0.00	0.00	0.00	5.01
3109	3420	8.636213	CAGGATGCAATATTTTTGGATCTAAGT	58.364	33.333	16.58	2.69	43.76	2.24
3117	3428	6.127535	ACAGACTCAGGATGCAATATTTTTGG	60.128	38.462	0.00	0.00	34.76	3.28
3124	3435	5.316167	ACAAAACAGACTCAGGATGCAATA	58.684	37.500	0.00	0.00	34.76	1.90
3219	3536	8.873215	ATGGTAGTGACGATATAAAAGTTGAG	57.127	34.615	0.00	0.00	0.00	3.02
3394	3736	5.296780	CACACCTCTACAACAGAAATTGTGT	59.703	40.000	1.46	0.00	42.74	3.72
3438	3783	1.065126	GCCCCTGCATCCATAGGATAC	60.065	57.143	0.00	0.00	40.98	2.24
3568	4428	5.911838	CCATATGATCACGCATCTAGTATCG	59.088	44.000	3.65	0.00	31.92	2.92
3652	4513	2.441001	CCCTCCACTCATGAATTAGCCT	59.559	50.000	0.00	0.00	0.00	4.58
3654	4515	3.845781	TCCCTCCACTCATGAATTAGC	57.154	47.619	0.00	0.00	0.00	3.09
3685	4548	9.525409	AAAATGCATTTCTATAAGAATGCACTC	57.475	29.630	25.62	0.00	43.88	3.51
3773	4643	5.069781	CCAATTTGGTGAAGGTTCTGGTAAA	59.930	40.000	7.31	0.00	31.35	2.01
3875	4747	0.984995	ACAGAACTAGTTGGCCCTCC	59.015	55.000	14.14	0.00	0.00	4.30

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.