AutoCloner

Multiple sequence alignment - TraesCS6B01G279700

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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	TraesCS6B01G279700	chr6B	100.000	4876	0	0	1	4876	505804700	505799825	0.000000e+00	9005.0
1	TraesCS6B01G279700	chr6B	95.161	62	3	0	4438	4499	537553900	537553839	1.120000e-16	99.0
2	TraesCS6B01G279700	chr6D	96.636	2913	74	11	1973	4876	318346570	318349467	0.000000e+00	4815.0
3	TraesCS6B01G279700	chr6D	96.237	1196	28	8	775	1956	318345393	318346585	0.000000e+00	1943.0
4	TraesCS6B01G279700	chr6D	89.754	771	55	3	1	747	7447711	7446941	0.000000e+00	965.0
5	TraesCS6B01G279700	chr6D	88.745	773	61	7	1	748	58437313	58438084	0.000000e+00	922.0
6	TraesCS6B01G279700	chr6D	94.915	59	3	0	4445	4503	48675949	48675891	5.200000e-15	93.5
7	TraesCS6B01G279700	chr6D	96.429	56	2	0	4442	4497	426078390	426078335	5.200000e-15	93.5
8	TraesCS6B01G279700	chr6D	91.176	68	6	0	4438	4505	429020899	429020832	5.200000e-15	93.5
9	TraesCS6B01G279700	chr6D	89.041	73	7	1	4438	4510	386931412	386931483	6.720000e-14	89.8
10	TraesCS6B01G279700	chr6A	94.139	2815	123	18	2083	4876	455937938	455940731	0.000000e+00	4246.0
11	TraesCS6B01G279700	chr6A	95.953	1186	37	6	775	1953	455936552	455937733	0.000000e+00	1914.0
12	TraesCS6B01G279700	chr6A	96.226	106	4	0	1973	2078	455937721	455937826	1.800000e-39	174.0
13	TraesCS6B01G279700	chr6A	88.372	86	10	0	1176	1261	503829286	503829371	2.400000e-18	104.0
14	TraesCS6B01G279700	chr6A	88.372	86	10	0	1176	1261	602319912	602319827	2.400000e-18	104.0
15	TraesCS6B01G279700	chr5D	90.390	770	47	7	3	748	382081910	382082676	0.000000e+00	987.0
16	TraesCS6B01G279700	chr5D	77.674	215	34	8	2470	2674	498660546	498660756	8.570000e-23	119.0
17	TraesCS6B01G279700	chr2D	89.974	768	52	12	1	744	399427479	399428245	0.000000e+00	968.0
18	TraesCS6B01G279700	chr2D	93.651	63	4	0	4438	4500	445186789	445186727	1.440000e-15	95.3
19	TraesCS6B01G279700	chr2D	100.000	32	0	0	4387	4418	421794684	421794715	5.270000e-05	60.2
20	TraesCS6B01G279700	chr7D	89.373	781	56	10	1	757	635996733	635995956	0.000000e+00	957.0
21	TraesCS6B01G279700	chr7D	89.139	755	73	7	1	755	7721230	7720485	0.000000e+00	931.0
22	TraesCS6B01G279700	chr7D	88.817	769	61	4	1	745	509531109	509531876	0.000000e+00	920.0
23	TraesCS6B01G279700	chr7D	95.161	62	3	0	4439	4500	56643744	56643805	1.120000e-16	99.0
24	TraesCS6B01G279700	chr7D	95.161	62	3	0	4439	4500	573963527	573963466	1.120000e-16	99.0
25	TraesCS6B01G279700	chr4D	89.419	775	56	8	1	750	19347236	19346463	0.000000e+00	953.0
26	TraesCS6B01G279700	chr4D	87.042	409	28	2	365	748	396744205	396744613	5.790000e-119	438.0
27	TraesCS6B01G279700	chr4D	95.161	62	3	0	4438	4499	296729487	296729548	1.120000e-16	99.0
28	TraesCS6B01G279700	chr4D	94.737	57	3	0	4438	4494	409172116	409172172	6.720000e-14	89.8
29	TraesCS6B01G279700	chr7A	89.453	768	56	3	4	747	92365507	92364741	0.000000e+00	946.0
30	TraesCS6B01G279700	chr7A	100.000	30	0	0	4389	4418	33452546	33452517	6.820000e-04	56.5
31	TraesCS6B01G279700	chr2A	90.072	695	67	2	54	746	744381876	744382570	0.000000e+00	900.0
32	TraesCS6B01G279700	chr2A	85.393	178	19	4	2200	2371	298635235	298635059	1.390000e-40	178.0
33	TraesCS6B01G279700	chr2A	93.939	66	3	1	4438	4503	628670122	628670186	1.120000e-16	99.0
34	TraesCS6B01G279700	chr2A	85.185	54	6	2	4367	4418	181007151	181007204	2.000000e-03	54.7
35	TraesCS6B01G279700	chr1D	89.922	645	40	5	1	620	461759551	461760195	0.000000e+00	808.0
36	TraesCS6B01G279700	chr1D	90.196	153	15	0	2200	2352	482899995	482899843	2.980000e-47	200.0
37	TraesCS6B01G279700	chr1D	93.443	61	4	0	4438	4498	7349796	7349856	1.870000e-14	91.6
38	TraesCS6B01G279700	chr1D	93.443	61	4	0	2035	2095	59876036	59875976	1.870000e-14	91.6
39	TraesCS6B01G279700	chr1D	94.828	58	3	0	4440	4497	81724792	81724849	1.870000e-14	91.6
40	TraesCS6B01G279700	chr1D	91.176	68	4	2	4438	4504	422057519	422057585	1.870000e-14	91.6
41	TraesCS6B01G279700	chr1D	91.803	61	4	1	4438	4497	193504443	193504383	3.130000e-12	84.2
42	TraesCS6B01G279700	chr1D	90.323	62	6	0	4438	4499	305226354	305226293	1.120000e-11	82.4
43	TraesCS6B01G279700	chr1D	90.000	60	6	0	4438	4497	246650040	246649981	1.460000e-10	78.7
44	TraesCS6B01G279700	chr1D	94.118	51	2	1	4438	4487	81742280	81742330	5.230000e-10	76.8
45	TraesCS6B01G279700	chr1D	91.228	57	3	1	4438	4494	386432051	386432105	5.230000e-10	76.8
46	TraesCS6B01G279700	chr1D	92.308	52	4	0	4443	4494	111003471	111003522	1.880000e-09	75.0
47	TraesCS6B01G279700	chr1D	90.909	55	5	0	4443	4497	379141328	379141274	1.880000e-09	75.0
48	TraesCS6B01G279700	chr1D	89.655	58	5	1	4438	4494	97556405	97556462	6.770000e-09	73.1
49	TraesCS6B01G279700	chr1D	87.500	64	7	1	4438	4500	99411021	99410958	6.770000e-09	73.1
50	TraesCS6B01G279700	chr5B	87.832	641	70	5	4	637	478673663	478673024	0.000000e+00	745.0
51	TraesCS6B01G279700	chr7B	83.146	623	58	22	1	620	357638034	357638612	4.320000e-145	525.0
52	TraesCS6B01G279700	chr4A	82.600	477	76	7	275	746	531236260	531235786	9.760000e-112	414.0
53	TraesCS6B01G279700	chr4A	79.679	187	29	6	2459	2638	713895273	713895089	5.120000e-25	126.0
54	TraesCS6B01G279700	chr3D	90.795	239	20	1	519	757	500652766	500652530	7.880000e-83	318.0
55	TraesCS6B01G279700	chr3D	93.939	66	4	0	2030	2095	324311174	324311109	3.110000e-17	100.0
56	TraesCS6B01G279700	chr3D	95.161	62	3	0	4439	4500	610340259	610340198	1.120000e-16	99.0
57	TraesCS6B01G279700	chr3A	92.424	66	5	0	2030	2095	397141363	397141428	1.440000e-15	95.3
58	TraesCS6B01G279700	chrUn	91.176	68	6	0	4438	4505	126680571	126680638	5.200000e-15	93.5
59	TraesCS6B01G279700	chrUn	94.737	57	3	0	4438	4494	50619932	50619988	6.720000e-14	89.8
60	TraesCS6B01G279700	chr5A	93.548	62	3	1	2037	2097	48921388	48921449	1.870000e-14	91.6
61	TraesCS6B01G279700	chr3B	89.189	74	5	3	2022	2095	73692412	73692342	6.720000e-14	89.8
62	TraesCS6B01G279700	chr3B	90.909	66	6	0	2030	2095	394954539	394954604	6.720000e-14	89.8
63	TraesCS6B01G279700	chr1A	90.141	71	3	4	2022	2089	296939066	296939135	6.720000e-14	89.8

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	TraesCS6B01G279700	chr6B	505799825	505804700	4875	True	9005.000000	9005	100.000000	1	4876	1	chr6B.!!$R1	4875
1	TraesCS6B01G279700	chr6D	318345393	318349467	4074	False	3379.000000	4815	96.436500	775	4876	2	chr6D.!!$F3	4101
2	TraesCS6B01G279700	chr6D	7446941	7447711	770	True	965.000000	965	89.754000	1	747	1	chr6D.!!$R1	746
3	TraesCS6B01G279700	chr6D	58437313	58438084	771	False	922.000000	922	88.745000	1	748	1	chr6D.!!$F1	747
4	TraesCS6B01G279700	chr6A	455936552	455940731	4179	False	2111.333333	4246	95.439333	775	4876	3	chr6A.!!$F2	4101
5	TraesCS6B01G279700	chr5D	382081910	382082676	766	False	987.000000	987	90.390000	3	748	1	chr5D.!!$F1	745
6	TraesCS6B01G279700	chr2D	399427479	399428245	766	False	968.000000	968	89.974000	1	744	1	chr2D.!!$F1	743
7	TraesCS6B01G279700	chr7D	635995956	635996733	777	True	957.000000	957	89.373000	1	757	1	chr7D.!!$R3	756
8	TraesCS6B01G279700	chr7D	7720485	7721230	745	True	931.000000	931	89.139000	1	755	1	chr7D.!!$R1	754
9	TraesCS6B01G279700	chr7D	509531109	509531876	767	False	920.000000	920	88.817000	1	745	1	chr7D.!!$F2	744
10	TraesCS6B01G279700	chr4D	19346463	19347236	773	True	953.000000	953	89.419000	1	750	1	chr4D.!!$R1	749
11	TraesCS6B01G279700	chr7A	92364741	92365507	766	True	946.000000	946	89.453000	4	747	1	chr7A.!!$R2	743
12	TraesCS6B01G279700	chr2A	744381876	744382570	694	False	900.000000	900	90.072000	54	746	1	chr2A.!!$F3	692
13	TraesCS6B01G279700	chr1D	461759551	461760195	644	False	808.000000	808	89.922000	1	620	1	chr1D.!!$F8	619
14	TraesCS6B01G279700	chr5B	478673024	478673663	639	True	745.000000	745	87.832000	4	637	1	chr5B.!!$R1	633
15	TraesCS6B01G279700	chr7B	357638034	357638612	578	False	525.000000	525	83.146000	1	620	1	chr7B.!!$F1	619

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	End Stability	Orientation
889	927	1.203313	AGAGTCAGCCCAGTTCCCTAA	60.203	52.381	2.69	F
1489	1535	1.078759	CCTGCCGAGACTTTGTAGCG	61.079	60.000	4.26	F
1985	2031	0.247736	GCGGGGATAGTCTATGGCTG	59.752	60.000	4.85	F

Position	MSA Position	Penalty	Sequence	TM	GC	End Stability	Orientation
1965	2011	0.178932	AGCCATAGACTATCCCCGCA	60.179	55.000	5.69	R
3237	3402	3.679502	GGATTGGGAAAATTGCGTGAAAG	59.320	43.478	2.62	R
3920	4087	7.507277	ACTCTAGTTGGACAGCTATGATATGAA	59.493	37.037	2.57	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
26	27	2.066262	CACACGCCCAACAAGTACTAG	58.934	52.381	0.00	0.00	0.00	2.57
128	129	3.055458	TGACGATTTAGTTGCCATCCTGA	60.055	43.478	0.00	0.00	0.00	3.86
171	172	5.120208	CGGGATGACAAGTGTAGTTGTAAAG	59.880	44.000	5.15	0.00	40.83	1.85
176	177	6.526526	TGACAAGTGTAGTTGTAAAGGCATA	58.473	36.000	5.15	0.00	40.83	3.14
234	235	7.282224	GCCATGTCTAATTTATGGTAGTTGTCA	59.718	37.037	0.00	0.00	42.60	3.58
252	253	4.366586	TGTCACGTGTAATCAAACCGTAA	58.633	39.130	16.51	0.00	0.00	3.18
507	510	3.390135	CACAACATAGGAGTGTCGTGTT	58.610	45.455	0.00	0.00	33.46	3.32
655	689	3.006752	GGCACACCAAATCCATCTTTTCA	59.993	43.478	0.00	0.00	35.26	2.69
657	691	5.105392	GGCACACCAAATCCATCTTTTCATA	60.105	40.000	0.00	0.00	35.26	2.15
696	730	1.611977	ACAGTGAACGACGATTCAGGA	59.388	47.619	0.00	0.00	39.25	3.86
738	772	1.477030	CCATACGTGTCCGCGTTAGC	61.477	60.000	11.40	0.00	43.04	3.09
754	788	3.969981	CGTTAGCGTTTCCGTTGATTTTT	59.030	39.130	0.00	0.00	36.15	1.94
813	851	3.161866	GCCACATCTTGGGGAAAAACTA	58.838	45.455	0.00	0.00	46.22	2.24
815	853	4.953579	GCCACATCTTGGGGAAAAACTATA	59.046	41.667	0.00	0.00	46.22	1.31
889	927	1.203313	AGAGTCAGCCCAGTTCCCTAA	60.203	52.381	0.00	0.00	0.00	2.69
1289	1330	3.502595	GTCTGTACTCTGTAGTCTGCACA	59.497	47.826	0.00	0.00	37.15	4.57
1330	1376	3.994392	TCCATTCCGTCTCTTTTTCGAAG	59.006	43.478	0.00	0.00	0.00	3.79
1343	1389	5.467399	TCTTTTTCGAAGGCGTAGAATTGAA	59.533	36.000	0.00	0.00	38.98	2.69
1361	1407	2.094675	GAACCTTGCATGCCAGTATGT	58.905	47.619	16.68	4.27	0.00	2.29
1489	1535	1.078759	CCTGCCGAGACTTTGTAGCG	61.079	60.000	0.00	0.00	0.00	4.26
1774	1820	8.725148	CATACTTTCTTTCATACAAGCAACTCT	58.275	33.333	0.00	0.00	0.00	3.24
1888	1934	5.372343	AGGAACTGCATGATGGTGTAATA	57.628	39.130	0.00	0.00	37.18	0.98
1956	2002	6.318913	AGGATTACATAGTCTATGGCTGTCT	58.681	40.000	21.32	11.39	40.47	3.41
1958	2004	7.291182	AGGATTACATAGTCTATGGCTGTCTTT	59.709	37.037	21.32	3.34	40.47	2.52
1959	2005	7.934120	GGATTACATAGTCTATGGCTGTCTTTT	59.066	37.037	21.32	2.72	40.47	2.27
1960	2006	9.331282	GATTACATAGTCTATGGCTGTCTTTTT	57.669	33.333	21.32	2.09	40.47	1.94
1985	2031	0.247736	GCGGGGATAGTCTATGGCTG	59.752	60.000	0.00	0.00	0.00	4.85
1998	2044	2.409948	ATGGCTGTCAGCTTCCTTAC	57.590	50.000	23.68	6.43	41.99	2.34
2006	2052	6.261118	GCTGTCAGCTTCCTTACAAATAATG	58.739	40.000	17.89	0.00	38.45	1.90
3256	3421	2.159043	TGCTTTCACGCAATTTTCCCAA	60.159	40.909	0.00	0.00	36.89	4.12
3270	3435	5.620738	TTTTCCCAATCCACAACATTTCA	57.379	34.783	0.00	0.00	0.00	2.69
3408	3573	9.153721	CAATGCAGTAATGTGTTATCCAAATTT	57.846	29.630	0.00	0.00	32.99	1.82
3459	3624	4.636249	TGGGTCATATTTTTGCACCAAAC	58.364	39.130	0.00	0.00	32.79	2.93
3920	4087	4.470602	CCTTGGAAGAGTAGGTTGGTTTT	58.529	43.478	0.00	0.00	0.00	2.43
4079	4249	9.976776	TGGTATTTGTATATTTTGTGACCCTTA	57.023	29.630	0.00	0.00	0.00	2.69
4148	4318	6.963796	AGTGACACATTTGAGACTGATTTTC	58.036	36.000	8.59	0.00	0.00	2.29
4151	4321	7.917505	GTGACACATTTGAGACTGATTTTCTTT	59.082	33.333	0.00	0.00	0.00	2.52
4154	4324	9.305925	ACACATTTGAGACTGATTTTCTTTTTC	57.694	29.630	0.00	0.00	0.00	2.29
4277	4447	1.401552	TGCTTCGCTTCCATTGCATAC	59.598	47.619	0.00	0.00	0.00	2.39
4343	4514	5.055144	TGATTCTCAGAGATACATTGCAGC	58.945	41.667	0.00	0.00	0.00	5.25
4354	4525	6.351711	AGATACATTGCAGCACAGATAAGAA	58.648	36.000	0.00	0.00	0.00	2.52
4411	4585	8.012957	ACTACTCCCTCTGTTCACAAATATAG	57.987	38.462	0.00	0.00	0.00	1.31
4412	4586	6.240549	ACTCCCTCTGTTCACAAATATAGG	57.759	41.667	0.00	0.00	0.00	2.57
4413	4587	5.964477	ACTCCCTCTGTTCACAAATATAGGA	59.036	40.000	0.00	0.00	0.00	2.94
4414	4588	6.617371	ACTCCCTCTGTTCACAAATATAGGAT	59.383	38.462	0.00	0.00	0.00	3.24
4415	4589	6.830912	TCCCTCTGTTCACAAATATAGGATG	58.169	40.000	0.00	0.00	0.00	3.51
4416	4590	6.386927	TCCCTCTGTTCACAAATATAGGATGT	59.613	38.462	0.00	0.00	0.00	3.06
4417	4591	7.056635	CCCTCTGTTCACAAATATAGGATGTT	58.943	38.462	0.00	0.00	0.00	2.71
4501	4675	3.670625	TGTGAACGGAGGGAATACTTTG	58.329	45.455	0.00	0.00	0.00	2.77
4502	4676	3.071892	TGTGAACGGAGGGAATACTTTGT	59.928	43.478	0.00	0.00	0.00	2.83
4514	4688	5.394115	GGGAATACTTTGTAAGTTGCATGGG	60.394	44.000	0.00	0.00	42.81	4.00
4549	4723	6.038161	CGATTTCATTATGGGCAAGAACTGTA	59.962	38.462	0.00	0.00	0.00	2.74
4650	4824	1.269778	GGTTTTCTGCAAGCCCACTTC	60.270	52.381	0.00	0.00	32.29	3.01
4652	4826	1.321474	TTTCTGCAAGCCCACTTCAG	58.679	50.000	0.00	0.00	32.29	3.02
4751	4925	2.295909	GCTCACAAACCAGGCATTGTTA	59.704	45.455	8.23	1.49	37.66	2.41
4757	4931	2.364972	ACCAGGCATTGTTATAGGCC	57.635	50.000	0.00	0.00	46.77	5.19

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
26	27	2.456119	CGCGCAGGGTGAAGATGAC	61.456	63.158	8.75	0.00	34.98	3.06
128	129	2.224606	CGGATAACTGCATCTGCCAAT	58.775	47.619	0.00	0.00	41.18	3.16
139	140	3.198068	CACTTGTCATCCCGGATAACTG	58.802	50.000	0.73	0.00	0.00	3.16
187	188	7.584122	TGGCAACTATAGTTAACCAAAACAA	57.416	32.000	26.14	10.70	39.20	2.83
234	235	4.378666	GGCAATTACGGTTTGATTACACGT	60.379	41.667	0.00	0.00	41.10	4.49
252	253	4.575885	AGTAGTTAATCACACACGGCAAT	58.424	39.130	0.00	0.00	0.00	3.56
343	344	7.482743	GCAACTGTGATTAACAATACATGTCAG	59.517	37.037	0.00	1.15	42.99	3.51
346	347	6.208402	TGGCAACTGTGATTAACAATACATGT	59.792	34.615	2.69	2.69	38.67	3.21
492	495	0.108804	CGCCAACACGACACTCCTAT	60.109	55.000	0.00	0.00	34.06	2.57
507	510	2.192861	CACCACCTGCTTTTCGCCA	61.193	57.895	0.00	0.00	38.05	5.69
526	554	1.072331	ACTAGTTTCTGCCCACACAGG	59.928	52.381	0.00	0.00	38.26	4.00
655	689	8.188799	CACTGTCTTTTGCATGAATCTTGATAT	58.811	33.333	0.00	0.00	0.00	1.63
657	691	6.208007	TCACTGTCTTTTGCATGAATCTTGAT	59.792	34.615	0.00	0.00	0.00	2.57
696	730	0.834687	TTCCCCAACTCGCCTACACT	60.835	55.000	0.00	0.00	0.00	3.55
755	789	3.954904	TCAATGGAAACGACCCTCAAAAA	59.045	39.130	0.00	0.00	0.00	1.94
756	790	3.556999	TCAATGGAAACGACCCTCAAAA	58.443	40.909	0.00	0.00	0.00	2.44
757	791	3.216187	TCAATGGAAACGACCCTCAAA	57.784	42.857	0.00	0.00	0.00	2.69
758	792	2.940994	TCAATGGAAACGACCCTCAA	57.059	45.000	0.00	0.00	0.00	3.02
759	793	3.433306	AATCAATGGAAACGACCCTCA	57.567	42.857	0.00	0.00	0.00	3.86
760	794	4.217550	TCAAAATCAATGGAAACGACCCTC	59.782	41.667	0.00	0.00	0.00	4.30
761	795	4.148838	TCAAAATCAATGGAAACGACCCT	58.851	39.130	0.00	0.00	0.00	4.34
762	796	4.513198	TCAAAATCAATGGAAACGACCC	57.487	40.909	0.00	0.00	0.00	4.46
763	797	5.102313	GGATCAAAATCAATGGAAACGACC	58.898	41.667	0.00	0.00	33.21	4.79
764	798	4.793216	CGGATCAAAATCAATGGAAACGAC	59.207	41.667	0.00	0.00	33.21	4.34
765	799	4.697828	TCGGATCAAAATCAATGGAAACGA	59.302	37.500	0.00	0.00	33.21	3.85
766	800	4.980590	TCGGATCAAAATCAATGGAAACG	58.019	39.130	0.00	0.00	33.21	3.60
767	801	6.256321	CCAATCGGATCAAAATCAATGGAAAC	59.744	38.462	0.00	0.00	33.21	2.78
768	802	6.339730	CCAATCGGATCAAAATCAATGGAAA	58.660	36.000	0.00	0.00	33.21	3.13
769	803	5.681954	GCCAATCGGATCAAAATCAATGGAA	60.682	40.000	4.23	0.00	33.21	3.53
770	804	4.202141	GCCAATCGGATCAAAATCAATGGA	60.202	41.667	4.23	0.00	33.21	3.41
771	805	4.053295	GCCAATCGGATCAAAATCAATGG	58.947	43.478	0.00	0.00	33.21	3.16
772	806	4.053295	GGCCAATCGGATCAAAATCAATG	58.947	43.478	0.00	0.00	33.21	2.82
773	807	3.705579	TGGCCAATCGGATCAAAATCAAT	59.294	39.130	0.61	0.00	33.21	2.57
813	851	6.890814	GCCCAGTACCATATACAGTAGAGTAT	59.109	42.308	0.00	0.00	38.24	2.12
815	853	5.078256	GCCCAGTACCATATACAGTAGAGT	58.922	45.833	0.00	0.00	0.00	3.24
904	942	5.760743	TCTCTGTCGAGTCAATCTTCGATAT	59.239	40.000	0.00	0.00	38.45	1.63
914	952	5.690409	GTGTGTAATTTCTCTGTCGAGTCAA	59.310	40.000	0.00	0.00	38.45	3.18
1289	1330	2.617532	GGACACGGACTACTACTCCAGT	60.618	54.545	0.00	0.00	41.62	4.00
1330	1376	1.810151	TGCAAGGTTCAATTCTACGCC	59.190	47.619	0.00	0.00	0.00	5.68
1343	1389	1.466856	CACATACTGGCATGCAAGGT	58.533	50.000	25.83	18.43	0.00	3.50
1361	1407	4.547671	TGGATTTTTACTTCCCAACACCA	58.452	39.130	0.00	0.00	0.00	4.17
1489	1535	7.648142	TCAACAAATGTAATTCACAGAAGGAC	58.352	34.615	0.00	0.00	41.51	3.85
1583	1629	7.661536	TGGCTAAATCTGTCAGATAGTTAGT	57.338	36.000	23.34	6.45	32.89	2.24
1774	1820	6.665992	ATATTCGGGCTTTGTCATACTAGA	57.334	37.500	0.00	0.00	0.00	2.43
1888	1934	8.169977	TCAAGTTCAATGATCAAAAGCTAAGT	57.830	30.769	0.00	0.00	0.00	2.24
1961	2007	3.815809	CCATAGACTATCCCCGCAAAAA	58.184	45.455	0.00	0.00	0.00	1.94
1962	2008	2.486548	GCCATAGACTATCCCCGCAAAA	60.487	50.000	0.00	0.00	0.00	2.44
1963	2009	1.071699	GCCATAGACTATCCCCGCAAA	59.928	52.381	0.00	0.00	0.00	3.68
1964	2010	0.685097	GCCATAGACTATCCCCGCAA	59.315	55.000	0.00	0.00	0.00	4.85
1965	2011	0.178932	AGCCATAGACTATCCCCGCA	60.179	55.000	0.00	0.00	0.00	5.69
1966	2012	0.247736	CAGCCATAGACTATCCCCGC	59.752	60.000	0.00	0.00	0.00	6.13
1967	2013	1.546476	GACAGCCATAGACTATCCCCG	59.454	57.143	0.00	0.00	0.00	5.73
1968	2014	2.564947	CTGACAGCCATAGACTATCCCC	59.435	54.545	0.00	0.00	0.00	4.81
1969	2015	2.028567	GCTGACAGCCATAGACTATCCC	60.029	54.545	17.01	0.00	34.48	3.85
1970	2016	2.896685	AGCTGACAGCCATAGACTATCC	59.103	50.000	23.74	0.00	43.77	2.59
1971	2017	4.555262	GAAGCTGACAGCCATAGACTATC	58.445	47.826	23.74	5.20	43.77	2.08
1985	2031	8.263940	TGTACATTATTTGTAAGGAAGCTGAC	57.736	34.615	0.00	0.00	42.37	3.51
2198	2351	9.997172	TCCTCTATATATCTGCAGGAAAAGATA	57.003	33.333	15.13	3.62	39.18	1.98
2417	2570	4.022416	CACAATAAGCAGGCTTTTGTACCA	60.022	41.667	22.12	4.33	36.51	3.25
3237	3402	3.679502	GGATTGGGAAAATTGCGTGAAAG	59.320	43.478	0.00	0.00	0.00	2.62
3920	4087	7.507277	ACTCTAGTTGGACAGCTATGATATGAA	59.493	37.037	0.00	0.00	0.00	2.57
4148	4318	5.471456	TGCTCTAGCCAAGAAGAAGAAAAAG	59.529	40.000	0.00	0.00	41.18	2.27
4151	4321	4.623932	TGCTCTAGCCAAGAAGAAGAAA	57.376	40.909	0.00	0.00	41.18	2.52
4154	4324	4.405116	AGATGCTCTAGCCAAGAAGAAG	57.595	45.455	0.00	0.00	41.18	2.85
4277	4447	4.399303	AGAAGTTGTGTTTCCACTCCTTTG	59.601	41.667	0.00	0.00	42.34	2.77
4384	4558	6.875972	ATTTGTGAACAGAGGGAGTAGTAT	57.124	37.500	0.00	0.00	0.00	2.12
4385	4559	7.973048	ATATTTGTGAACAGAGGGAGTAGTA	57.027	36.000	0.00	0.00	0.00	1.82
4411	4585	7.548196	TCGTATTGAAGTATCCAAAACATCC	57.452	36.000	0.00	0.00	0.00	3.51
4412	4586	8.665685	AGTTCGTATTGAAGTATCCAAAACATC	58.334	33.333	0.00	0.00	38.49	3.06
4413	4587	8.561738	AGTTCGTATTGAAGTATCCAAAACAT	57.438	30.769	0.00	0.00	38.49	2.71
4414	4588	7.972832	AGTTCGTATTGAAGTATCCAAAACA	57.027	32.000	0.00	0.00	38.49	2.83
4415	4589	8.928733	TGTAGTTCGTATTGAAGTATCCAAAAC	58.071	33.333	0.00	0.00	42.82	2.43
4416	4590	9.661563	ATGTAGTTCGTATTGAAGTATCCAAAA	57.338	29.630	0.00	0.00	42.82	2.44
4425	4599	7.136772	TCGGATGTATGTAGTTCGTATTGAAG	58.863	38.462	0.00	0.00	37.23	3.02
4501	4675	2.409948	AGAGCTCCCATGCAACTTAC	57.590	50.000	10.93	0.00	34.99	2.34
4502	4676	3.107601	AGTAGAGCTCCCATGCAACTTA	58.892	45.455	10.93	0.00	34.99	2.24
4514	4688	5.866633	CCCATAATGAAATCGAGTAGAGCTC	59.133	44.000	5.27	5.27	40.77	4.09
4526	4700	7.716799	TTACAGTTCTTGCCCATAATGAAAT	57.283	32.000	0.00	0.00	0.00	2.17
4530	4704	6.753279	CACATTTACAGTTCTTGCCCATAATG	59.247	38.462	0.00	0.00	0.00	1.90
4534	4708	4.151883	ACACATTTACAGTTCTTGCCCAT	58.848	39.130	0.00	0.00	0.00	4.00
4652	4826	7.145932	AGTGAAATACCAAAGCAGTTGATAC	57.854	36.000	1.93	0.00	39.87	2.24
4751	4925	4.570663	GCACTCGTCGCGGCCTAT	62.571	66.667	4.51	0.00	0.00	2.57

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.