AutoCloner

Multiple sequence alignment - TraesCS6D01G204400

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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	TraesCS6D01G204400	chr6D	100.000	5005	0	0	1	5005	289632579	289627575	0.000000e+00	9243.0
1	TraesCS6D01G204400	chr6B	94.195	2515	101	13	2501	5005	450639984	450637505	0.000000e+00	3794.0
2	TraesCS6D01G204400	chr6B	93.117	1540	42	16	1011	2517	450641531	450640023	0.000000e+00	2198.0
3	TraesCS6D01G204400	chr6B	88.091	571	44	6	16	566	136791121	136790555	0.000000e+00	656.0
4	TraesCS6D01G204400	chr6B	89.002	491	48	5	295	784	134394112	134393627	1.990000e-168	603.0
5	TraesCS6D01G204400	chr6B	88.377	499	52	5	295	792	134398119	134397626	3.340000e-166	595.0
6	TraesCS6D01G204400	chr6B	89.691	194	19	1	597	790	136790565	136790373	3.870000e-61	246.0
7	TraesCS6D01G204400	chr6B	96.000	150	5	1	797	946	136790339	136790191	5.010000e-60	243.0
8	TraesCS6D01G204400	chr6B	95.620	137	5	1	808	944	134393568	134393433	8.440000e-53	219.0
9	TraesCS6D01G204400	chr6A	96.811	1662	49	3	2622	4280	435249463	435251123	0.000000e+00	2772.0
10	TraesCS6D01G204400	chr6A	93.373	1675	61	17	996	2627	435247718	435249385	0.000000e+00	2433.0
11	TraesCS6D01G204400	chr6A	94.136	631	25	7	4383	5005	435251128	435251754	0.000000e+00	950.0
12	TraesCS6D01G204400	chr6A	85.560	831	67	28	2	793	501235476	501234660	0.000000e+00	821.0
13	TraesCS6D01G204400	chr6A	90.018	571	52	5	2	568	100097331	100096762	0.000000e+00	734.0
14	TraesCS6D01G204400	chr6A	94.737	152	7	1	797	948	501234629	501234479	8.380000e-58	235.0
15	TraesCS6D01G204400	chr6A	92.667	150	6	2	797	946	52813952	52813808	1.410000e-50	211.0
16	TraesCS6D01G204400	chr1D	92.419	897	34	10	82	947	35782121	35783014	0.000000e+00	1249.0
17	TraesCS6D01G204400	chr1D	90.231	389	28	10	1	384	35782002	35782385	2.690000e-137	499.0
18	TraesCS6D01G204400	chr7B	86.867	967	81	33	2	946	725391211	725392153	0.000000e+00	1040.0
19	TraesCS6D01G204400	chr7B	85.890	489	55	13	301	779	85038587	85038103	4.470000e-140	508.0
20	TraesCS6D01G204400	chr5B	89.139	801	66	11	2	794	439323369	439322582	0.000000e+00	977.0
21	TraesCS6D01G204400	chr4B	85.584	985	73	30	16	946	622763380	622764349	0.000000e+00	968.0
22	TraesCS6D01G204400	chr4B	82.579	884	98	34	95	946	565317324	565316465	0.000000e+00	728.0
23	TraesCS6D01G204400	chr4A	85.825	776	72	16	2	753	651881497	651880736	0.000000e+00	789.0
24	TraesCS6D01G204400	chr4A	94.118	153	8	1	797	949	651838161	651838010	1.080000e-56	231.0
25	TraesCS6D01G204400	chr5A	81.123	837	96	35	2	793	301369908	301369089	9.210000e-172	614.0
26	TraesCS6D01G204400	chr7D	77.954	694	86	42	244	888	579634494	579635169	6.120000e-99	372.0
27	TraesCS6D01G204400	chr2A	80.460	522	65	30	2	502	761193108	761193613	1.020000e-96	364.0
28	TraesCS6D01G204400	chr2B	100.000	33	0	0	1746	1778	797395309	797395277	1.500000e-05	62.1
29	TraesCS6D01G204400	chr2B	97.143	35	0	1	1746	1780	29628455	29628422	1.950000e-04	58.4
30	TraesCS6D01G204400	chr3A	100.000	31	0	0	1746	1776	735432283	735432313	1.950000e-04	58.4
31	TraesCS6D01G204400	chr3A	100.000	29	0	0	1748	1776	384188753	384188781	3.000000e-03	54.7
32	TraesCS6D01G204400	chr1A	100.000	29	0	0	1750	1778	491427375	491427403	3.000000e-03	54.7

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	TraesCS6D01G204400	chr6D	289627575	289632579	5004	True	9243.000000	9243	100.000000	1	5005	1	chr6D.!!$R1	5004
1	TraesCS6D01G204400	chr6B	450637505	450641531	4026	True	2996.000000	3794	93.656000	1011	5005	2	chr6B.!!$R3	3994
2	TraesCS6D01G204400	chr6B	134393433	134398119	4686	True	472.333333	603	90.999667	295	944	3	chr6B.!!$R1	649
3	TraesCS6D01G204400	chr6B	136790191	136791121	930	True	381.666667	656	91.260667	16	946	3	chr6B.!!$R2	930
4	TraesCS6D01G204400	chr6A	435247718	435251754	4036	False	2051.666667	2772	94.773333	996	5005	3	chr6A.!!$F1	4009
5	TraesCS6D01G204400	chr6A	100096762	100097331	569	True	734.000000	734	90.018000	2	568	1	chr6A.!!$R2	566
6	TraesCS6D01G204400	chr6A	501234479	501235476	997	True	528.000000	821	90.148500	2	948	2	chr6A.!!$R3	946
7	TraesCS6D01G204400	chr1D	35782002	35783014	1012	False	874.000000	1249	91.325000	1	947	2	chr1D.!!$F1	946
8	TraesCS6D01G204400	chr7B	725391211	725392153	942	False	1040.000000	1040	86.867000	2	946	1	chr7B.!!$F1	944
9	TraesCS6D01G204400	chr5B	439322582	439323369	787	True	977.000000	977	89.139000	2	794	1	chr5B.!!$R1	792
10	TraesCS6D01G204400	chr4B	622763380	622764349	969	False	968.000000	968	85.584000	16	946	1	chr4B.!!$F1	930
11	TraesCS6D01G204400	chr4B	565316465	565317324	859	True	728.000000	728	82.579000	95	946	1	chr4B.!!$R1	851
12	TraesCS6D01G204400	chr4A	651880736	651881497	761	True	789.000000	789	85.825000	2	753	1	chr4A.!!$R2	751
13	TraesCS6D01G204400	chr5A	301369089	301369908	819	True	614.000000	614	81.123000	2	793	1	chr5A.!!$R1	791
14	TraesCS6D01G204400	chr7D	579634494	579635169	675	False	372.000000	372	77.954000	244	888	1	chr7D.!!$F1	644
15	TraesCS6D01G204400	chr2A	761193108	761193613	505	False	364.000000	364	80.460000	2	502	1	chr2A.!!$F1	500

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
957	5366	0.108567	GAGCTCTCCCGGTTTGAGAC	60.109	60.000	16.50	9.15	35.15	3.36	F
1520	5944	0.391263	GTCTCGGCGGAAGTGGAAAT	60.391	55.000	7.21	0.00	0.00	2.17	F
2808	7420	1.378531	TGACTGTTTGCTGTCACACC	58.621	50.000	3.75	0.00	44.77	4.16	F
2852	7464	1.956477	GTTGAAGGGTCAGTGCAACAT	59.044	47.619	0.00	0.00	41.43	2.71	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
2441	6914	1.180029	GCTGGCTGAATGTTCACCAT	58.820	50.000	13.57	37.57	3.55	R
3220	7832	1.077858	CTGGGCTGCTTCCTCTTCC	60.078	63.158	0.00	0.00	3.46	R
3935	8547	0.673985	GTTGTTGTGGCCTTCTTCCC	59.326	55.000	3.32	0.00	3.97	R
4287	8902	3.439154	TGCTCCTTTTAATTCCATGCCA	58.561	40.909	0.00	0.00	4.92	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
111	120	7.150640	TCGATGAATTTCTCAGATTCGATGAT	58.849	34.615	0.00	0.00	37.88	2.45
116	125	9.170734	TGAATTTCTCAGATTCGATGATCTTTT	57.829	29.630	0.00	0.00	36.52	2.27
221	270	8.614994	TTTTTCAAACTCGATGAACTCTTTTC	57.385	30.769	0.00	0.00	36.57	2.29
242	291	9.839589	CTTTTCTCAAATTCGATGAACTTTTTG	57.160	29.630	0.00	0.00	0.00	2.44
243	292	6.991485	TCTCAAATTCGATGAACTTTTTGC	57.009	33.333	0.00	0.00	0.00	3.68
371	4699	9.319143	CAAACTCGATGACCTATTTTCTTATCT	57.681	33.333	0.00	0.00	0.00	1.98
413	4744	6.280855	AGTGGTGAACTTGTTTTAAAGCTT	57.719	33.333	3.62	0.00	34.57	3.74
954	5363	3.388841	GGAGCTCTCCCGGTTTGA	58.611	61.111	14.64	0.00	43.94	2.69
955	5364	1.219393	GGAGCTCTCCCGGTTTGAG	59.781	63.158	14.64	5.96	43.94	3.02
956	5365	1.258445	GGAGCTCTCCCGGTTTGAGA	61.258	60.000	14.64	12.69	43.94	3.27
957	5366	0.108567	GAGCTCTCCCGGTTTGAGAC	60.109	60.000	16.50	9.15	35.15	3.36
958	5367	1.446272	GCTCTCCCGGTTTGAGACG	60.446	63.158	16.50	9.34	35.15	4.18
959	5368	1.446272	CTCTCCCGGTTTGAGACGC	60.446	63.158	0.00	0.00	35.15	5.19
960	5369	2.434359	CTCCCGGTTTGAGACGCC	60.434	66.667	0.00	0.00	31.26	5.68
961	5370	3.952628	CTCCCGGTTTGAGACGCCC	62.953	68.421	0.00	0.00	31.26	6.13
963	5372	4.367023	CCGGTTTGAGACGCCCGA	62.367	66.667	0.00	0.00	43.01	5.14
964	5373	2.125673	CGGTTTGAGACGCCCGAT	60.126	61.111	0.00	0.00	43.01	4.18
965	5374	2.452813	CGGTTTGAGACGCCCGATG	61.453	63.158	0.00	0.00	43.01	3.84
966	5375	1.079405	GGTTTGAGACGCCCGATGA	60.079	57.895	0.00	0.00	0.00	2.92
967	5376	1.084370	GGTTTGAGACGCCCGATGAG	61.084	60.000	0.00	0.00	0.00	2.90
968	5377	1.447838	TTTGAGACGCCCGATGAGC	60.448	57.895	0.00	0.00	0.00	4.26
969	5378	2.852495	TTTGAGACGCCCGATGAGCC	62.852	60.000	0.00	0.00	0.00	4.70
970	5379	4.593864	GAGACGCCCGATGAGCCC	62.594	72.222	0.00	0.00	0.00	5.19
991	5400	4.589675	GGCCACCGGGGTGTTTGA	62.590	66.667	16.19	0.00	44.02	2.69
992	5401	2.983592	GCCACCGGGGTGTTTGAG	60.984	66.667	16.19	2.30	44.02	3.02
993	5402	2.833227	CCACCGGGGTGTTTGAGA	59.167	61.111	16.19	0.00	44.02	3.27
994	5403	1.149627	CCACCGGGGTGTTTGAGAA	59.850	57.895	16.19	0.00	44.02	2.87
1017	5426	1.021390	AGATGCGTTTGGGCTCGAAG	61.021	55.000	0.00	0.00	0.00	3.79
1018	5427	2.583685	GATGCGTTTGGGCTCGAAGC	62.584	60.000	0.00	0.00	41.46	3.86
1073	5490	1.175983	CGCAACAAAACCCTAGCCCA	61.176	55.000	0.00	0.00	0.00	5.36
1077	5494	3.462982	CAACAAAACCCTAGCCCAAAAC	58.537	45.455	0.00	0.00	0.00	2.43
1225	5643	2.657237	GTGCCCTCGCTACACACT	59.343	61.111	0.00	0.00	34.43	3.55
1229	5647	1.682684	CCCTCGCTACACACTCCCT	60.683	63.158	0.00	0.00	0.00	4.20
1406	5830	1.493950	CGTGCTGAGATGATTCCCGC	61.494	60.000	0.00	0.00	0.00	6.13
1417	5841	2.552585	GATTCCCGCGGTCTCGTTGA	62.553	60.000	26.12	9.36	38.89	3.18
1520	5944	0.391263	GTCTCGGCGGAAGTGGAAAT	60.391	55.000	7.21	0.00	0.00	2.17
1716	6149	2.592861	GACATGGCGGCCCTCATC	60.593	66.667	17.97	5.24	0.00	2.92
1839	6296	7.285566	AGGTATTGAGATGTATCTTGTGCATT	58.714	34.615	0.00	0.00	37.25	3.56
1840	6297	7.776969	AGGTATTGAGATGTATCTTGTGCATTT	59.223	33.333	0.00	0.00	37.25	2.32
1841	6298	8.408601	GGTATTGAGATGTATCTTGTGCATTTT	58.591	33.333	0.00	0.00	37.25	1.82
1915	6376	5.348724	TCGTCTAATCAGCACAATTGACTTC	59.651	40.000	13.59	0.00	0.00	3.01
2000	6471	8.640651	TGCAGCCATATCAACAATTGTTTATAT	58.359	29.630	23.37	23.37	36.05	0.86
2119	6592	5.163953	CGGTGTTGTAGAAGTTTATGCTCAG	60.164	44.000	0.00	0.00	0.00	3.35
2188	6661	9.007901	ACCGTAGATATAATACAAGAGTACACC	57.992	37.037	0.00	0.00	31.96	4.16
2364	6837	7.482654	TTTCATCTGTAAGTCTTGTGTTGAG	57.517	36.000	0.00	0.00	33.76	3.02
2514	6987	5.435686	TGCCTGGAAAAGCTAGAAATCTA	57.564	39.130	0.00	0.00	0.00	1.98
2517	6990	7.573710	TGCCTGGAAAAGCTAGAAATCTATTA	58.426	34.615	0.00	0.00	0.00	0.98
2557	7085	8.310406	TGCACTAAGATAATTTGACCATATCG	57.690	34.615	0.00	0.00	32.55	2.92
2577	7106	2.290705	CGGTAGGTTTTGGGATTCTGGT	60.291	50.000	0.00	0.00	0.00	4.00
2672	7284	3.733337	GCATACTTCTCCTGTATGGTGG	58.267	50.000	13.48	0.00	44.24	4.61
2677	7289	3.846588	ACTTCTCCTGTATGGTGGTTGAT	59.153	43.478	0.00	0.00	37.07	2.57
2778	7390	2.268762	TGCAGTGTATTTCCTGTGCA	57.731	45.000	0.00	0.00	38.55	4.57
2779	7391	2.580962	TGCAGTGTATTTCCTGTGCAA	58.419	42.857	0.00	0.00	37.95	4.08
2808	7420	1.378531	TGACTGTTTGCTGTCACACC	58.621	50.000	3.75	0.00	44.77	4.16
2852	7464	1.956477	GTTGAAGGGTCAGTGCAACAT	59.044	47.619	0.00	0.00	41.43	2.71
3361	7973	3.317150	CTGATAACTCAGCACGTTCACA	58.683	45.455	0.00	0.00	42.36	3.58
3383	7995	5.975344	ACATACGAGTGTACCAATAATGACG	59.025	40.000	0.00	0.00	32.26	4.35
3684	8296	2.076100	CACAGTTTATTCCGCAGAGCA	58.924	47.619	0.00	0.00	0.00	4.26
3877	8489	2.034879	CGTCACATGGAGGTGGTGC	61.035	63.158	0.00	0.00	39.27	5.01
3905	8517	4.576053	CGTCCTATGCAATTCAATTCTGGA	59.424	41.667	0.00	0.00	0.00	3.86
3910	8522	4.771590	TGCAATTCAATTCTGGACAGTC	57.228	40.909	0.00	0.00	0.00	3.51
3935	8547	2.776913	GGGGAGCTCGTCCTTCTCG	61.777	68.421	15.11	0.00	46.06	4.04
3989	8601	0.252284	CACAGGGGAGAGGTAGTGGT	60.252	60.000	0.00	0.00	0.00	4.16
4058	8670	6.605471	TGCAGGAAGAGTTATACTTGAGAA	57.395	37.500	0.00	0.00	0.00	2.87
4074	8686	4.553330	TGAGAACAATGTAAGTCTCCCC	57.447	45.455	10.12	0.00	0.00	4.81
4156	8768	4.154737	GTGCATGTTGCTCATTACTTCTGA	59.845	41.667	0.00	0.00	45.31	3.27
4287	8902	3.081061	TGTAATTTTCTGCTGCCGTCAT	58.919	40.909	0.00	0.00	0.00	3.06
4326	8943	3.689347	AGCAATTCAGCATGGTAACTCA	58.311	40.909	0.00	0.00	36.16	3.41
4354	8971	8.634475	TCTCATTTTGATTCTGTAGTCATACG	57.366	34.615	0.00	0.00	34.39	3.06
4356	8973	8.996024	TCATTTTGATTCTGTAGTCATACGAA	57.004	30.769	0.00	0.00	34.39	3.85
4373	8990	8.728833	GTCATACGAAACTATAGTAGGTAGCAT	58.271	37.037	5.65	0.00	0.00	3.79
4407	9024	6.896021	TTGTGTTTATATGGAACCCGAAAA	57.104	33.333	0.00	0.00	0.00	2.29
4462	9080	1.066573	CCTTGATCTGTCCTTCGCTGT	60.067	52.381	0.00	0.00	0.00	4.40
4666	9287	8.251383	TCCAGTATTGATCTTTCCCTTAGTAG	57.749	38.462	0.00	0.00	0.00	2.57
4727	9348	6.331369	TCTCAGGTCTTTTAAAATGCTTGG	57.669	37.500	0.09	0.54	0.00	3.61
4734	9355	7.286775	AGGTCTTTTAAAATGCTTGGAGTTACA	59.713	33.333	0.09	0.00	0.00	2.41
4756	9377	6.179756	ACAAAACAAATCAGGAAGCCTTTTT	58.820	32.000	0.00	0.00	0.00	1.94
4828	9449	5.324832	TTTGGGAAGATCTGGAGAAGTTT	57.675	39.130	0.00	0.00	0.00	2.66
4836	9457	8.043710	GGAAGATCTGGAGAAGTTTAGATTTGA	58.956	37.037	0.00	0.00	30.49	2.69
4859	9483	6.128138	AGGAGTTAGGCTGATAAACTTGTT	57.872	37.500	0.00	0.00	33.72	2.83
4860	9484	5.940470	AGGAGTTAGGCTGATAAACTTGTTG	59.060	40.000	0.00	0.00	33.72	3.33
4861	9485	5.705905	GGAGTTAGGCTGATAAACTTGTTGT	59.294	40.000	0.00	0.00	33.72	3.32
4898	9522	0.957888	GAGGGACTTGCTGCTTGGTC	60.958	60.000	0.00	6.45	41.55	4.02
4934	9559	3.181511	TGTGAGAGTTGTTTCAGTTTGCG	60.182	43.478	0.00	0.00	0.00	4.85
4960	9588	0.310854	CGACAAGGAAAAGCACACCC	59.689	55.000	0.00	0.00	0.00	4.61
4972	9600	2.357034	ACACCCGCACGACATGTC	60.357	61.111	16.21	16.21	0.00	3.06

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
118	127	9.434420	AGTTTCAAAAATGTTCATCAAGTTTGA	57.566	25.926	0.00	0.00	39.18	2.69
119	128	9.693157	GAGTTTCAAAAATGTTCATCAAGTTTG	57.307	29.630	0.00	0.00	36.28	2.93
120	129	8.594687	CGAGTTTCAAAAATGTTCATCAAGTTT	58.405	29.630	0.00	0.00	0.00	2.66
121	130	7.973388	TCGAGTTTCAAAAATGTTCATCAAGTT	59.027	29.630	0.00	0.00	0.00	2.66
122	131	7.479980	TCGAGTTTCAAAAATGTTCATCAAGT	58.520	30.769	0.00	0.00	0.00	3.16
123	132	7.912949	TCGAGTTTCAAAAATGTTCATCAAG	57.087	32.000	0.00	0.00	0.00	3.02
124	133	8.134261	TCATCGAGTTTCAAAAATGTTCATCAA	58.866	29.630	0.00	0.00	0.00	2.57
125	134	7.647228	TCATCGAGTTTCAAAAATGTTCATCA	58.353	30.769	0.00	0.00	0.00	3.07
126	135	8.420189	GTTCATCGAGTTTCAAAAATGTTCATC	58.580	33.333	0.00	0.00	0.00	2.92
127	136	8.137437	AGTTCATCGAGTTTCAAAAATGTTCAT	58.863	29.630	0.00	0.00	0.00	2.57
128	137	7.479980	AGTTCATCGAGTTTCAAAAATGTTCA	58.520	30.769	0.00	0.00	0.00	3.18
129	138	7.914537	AGTTCATCGAGTTTCAAAAATGTTC	57.085	32.000	0.00	0.00	0.00	3.18
130	139	8.702163	AAAGTTCATCGAGTTTCAAAAATGTT	57.298	26.923	0.00	0.00	0.00	2.71
131	140	8.702163	AAAAGTTCATCGAGTTTCAAAAATGT	57.298	26.923	0.00	0.00	0.00	2.71
215	264	9.801873	AAAAAGTTCATCGAATTTGAGAAAAGA	57.198	25.926	1.10	0.00	0.00	2.52
221	270	6.752335	TGCAAAAAGTTCATCGAATTTGAG	57.248	33.333	1.10	0.00	31.23	3.02
948	5357	1.079405	TCATCGGGCGTCTCAAACC	60.079	57.895	0.00	0.00	0.00	3.27
949	5358	1.696832	GCTCATCGGGCGTCTCAAAC	61.697	60.000	0.00	0.00	0.00	2.93
950	5359	1.447838	GCTCATCGGGCGTCTCAAA	60.448	57.895	0.00	0.00	0.00	2.69
951	5360	2.184322	GCTCATCGGGCGTCTCAA	59.816	61.111	0.00	0.00	0.00	3.02
952	5361	3.838271	GGCTCATCGGGCGTCTCA	61.838	66.667	0.00	0.00	0.00	3.27
953	5362	4.593864	GGGCTCATCGGGCGTCTC	62.594	72.222	0.00	0.00	0.00	3.36
978	5387	1.144093	TCAATTCTCAAACACCCCGGT	59.856	47.619	0.00	0.00	0.00	5.28
979	5388	1.812571	CTCAATTCTCAAACACCCCGG	59.187	52.381	0.00	0.00	0.00	5.73
980	5389	2.778299	TCTCAATTCTCAAACACCCCG	58.222	47.619	0.00	0.00	0.00	5.73
981	5390	3.119352	GCATCTCAATTCTCAAACACCCC	60.119	47.826	0.00	0.00	0.00	4.95
982	5391	3.426695	CGCATCTCAATTCTCAAACACCC	60.427	47.826	0.00	0.00	0.00	4.61
983	5392	3.189287	ACGCATCTCAATTCTCAAACACC	59.811	43.478	0.00	0.00	0.00	4.16
984	5393	4.410492	ACGCATCTCAATTCTCAAACAC	57.590	40.909	0.00	0.00	0.00	3.32
985	5394	5.214417	CAAACGCATCTCAATTCTCAAACA	58.786	37.500	0.00	0.00	0.00	2.83
986	5395	4.618489	CCAAACGCATCTCAATTCTCAAAC	59.382	41.667	0.00	0.00	0.00	2.93
987	5396	4.321156	CCCAAACGCATCTCAATTCTCAAA	60.321	41.667	0.00	0.00	0.00	2.69
988	5397	3.191162	CCCAAACGCATCTCAATTCTCAA	59.809	43.478	0.00	0.00	0.00	3.02
989	5398	2.749076	CCCAAACGCATCTCAATTCTCA	59.251	45.455	0.00	0.00	0.00	3.27
990	5399	2.478539	GCCCAAACGCATCTCAATTCTC	60.479	50.000	0.00	0.00	0.00	2.87
991	5400	1.474077	GCCCAAACGCATCTCAATTCT	59.526	47.619	0.00	0.00	0.00	2.40
992	5401	1.474077	AGCCCAAACGCATCTCAATTC	59.526	47.619	0.00	0.00	0.00	2.17
993	5402	1.474077	GAGCCCAAACGCATCTCAATT	59.526	47.619	0.00	0.00	0.00	2.32
994	5403	1.098050	GAGCCCAAACGCATCTCAAT	58.902	50.000	0.00	0.00	0.00	2.57
1017	5426	2.273776	GGGAGCAAAGGAGAGGGC	59.726	66.667	0.00	0.00	0.00	5.19
1018	5427	3.002371	GGGGAGCAAAGGAGAGGG	58.998	66.667	0.00	0.00	0.00	4.30
1140	5557	0.103208	CGGAGTGTGATAGTGGCTCC	59.897	60.000	0.00	0.00	41.55	4.70
1406	5830	2.288273	ACTTCCTCTTTCAACGAGACCG	60.288	50.000	0.00	0.00	42.50	4.79
1417	5841	2.373502	CTCCACCTTCCACTTCCTCTTT	59.626	50.000	0.00	0.00	0.00	2.52
1520	5944	1.283029	CCTTGCTTCCTCCATTCTCCA	59.717	52.381	0.00	0.00	0.00	3.86
1716	6149	1.027357	CCATCAATTTGCCCTCCTCG	58.973	55.000	0.00	0.00	0.00	4.63
1854	6311	7.492669	GCTAGCAAATGATTCACACTCTACTAA	59.507	37.037	10.63	0.00	0.00	2.24
1915	6376	8.828688	TCATCATCTAATAGAGCTTGATTGTG	57.171	34.615	2.95	0.00	29.92	3.33
2000	6471	5.446860	AGCTGGAGTACTATTAGCACACTA	58.553	41.667	20.84	0.00	36.87	2.74
2119	6592	6.310224	ACAAGTTGTAGCAACAAATCAACAAC	59.690	34.615	6.75	7.81	46.84	3.32
2250	6723	5.545335	AGGATCTGCAAGGTATGACATATCA	59.455	40.000	8.42	0.00	39.83	2.15
2441	6914	1.180029	GCTGGCTGAATGTTCACCAT	58.820	50.000	13.57	0.00	37.57	3.55
2557	7085	3.451402	ACCAGAATCCCAAAACCTACC	57.549	47.619	0.00	0.00	0.00	3.18
2577	7106	9.733556	ATACAGGAAATATGTAAACACTGTCAA	57.266	29.630	0.00	0.00	38.67	3.18
2646	7258	6.648310	CACCATACAGGAGAAGTATGCTAATG	59.352	42.308	7.60	1.31	44.62	1.90
2687	7299	7.615403	TGACTAAATGAGAAGCACTGTCTATT	58.385	34.615	0.00	0.00	0.00	1.73
2759	7371	2.268762	TGCACAGGAAATACACTGCA	57.731	45.000	0.00	0.00	38.25	4.41
2760	7372	3.428045	GGATTGCACAGGAAATACACTGC	60.428	47.826	0.00	0.00	38.25	4.40
2778	7390	5.948162	ACAGCAAACAGTCAAGATATGGATT	59.052	36.000	0.00	0.00	0.00	3.01
2779	7391	5.503927	ACAGCAAACAGTCAAGATATGGAT	58.496	37.500	0.00	0.00	0.00	3.41
2808	7420	3.029570	TCACTCTCTCACCCATGATCTG	58.970	50.000	0.00	0.00	33.22	2.90
3220	7832	1.077858	CTGGGCTGCTTCCTCTTCC	60.078	63.158	0.00	0.00	0.00	3.46
3352	7964	2.912967	GGTACACTCGTATGTGAACGTG	59.087	50.000	11.46	0.00	43.31	4.49
3361	7973	4.980434	GCGTCATTATTGGTACACTCGTAT	59.020	41.667	0.00	0.00	39.29	3.06
3383	7995	1.160137	GATTCACTGTGACTGGTGGC	58.840	55.000	10.56	0.00	34.57	5.01
3572	8184	4.352893	TGGATCCACTGAGTATGTTCTGA	58.647	43.478	11.44	0.00	0.00	3.27
3684	8296	3.385755	GGCATTGGATTTACAGGCATTCT	59.614	43.478	0.00	0.00	0.00	2.40
3877	8489	2.554142	TGAATTGCATAGGACGCTGAG	58.446	47.619	0.00	0.00	0.00	3.35
3905	8517	2.393646	GAGCTCCCCTGATTAGACTGT	58.606	52.381	0.87	0.00	0.00	3.55
3910	8522	0.676736	GGACGAGCTCCCCTGATTAG	59.323	60.000	8.47	0.00	31.83	1.73
3935	8547	0.673985	GTTGTTGTGGCCTTCTTCCC	59.326	55.000	3.32	0.00	0.00	3.97
3989	8601	5.132502	CAGTTATCCTATTTGTGATGCCCA	58.867	41.667	0.00	0.00	0.00	5.36
4058	8670	5.183228	CAATTACGGGGAGACTTACATTGT	58.817	41.667	0.00	0.00	0.00	2.71
4287	8902	3.439154	TGCTCCTTTTAATTCCATGCCA	58.561	40.909	0.00	0.00	0.00	4.92
4407	9024	6.096705	TCAACCTCAAGAAAACATGTCATTGT	59.903	34.615	0.00	0.00	0.00	2.71
4619	9240	6.096282	TGGAAGACAGGTTTCCTTTTTAAGTG	59.904	38.462	5.70	0.00	43.63	3.16
4727	9348	5.920840	GGCTTCCTGATTTGTTTTGTAACTC	59.079	40.000	0.00	0.00	35.24	3.01
4734	9355	5.589855	CCAAAAAGGCTTCCTGATTTGTTTT	59.410	36.000	16.10	1.72	38.49	2.43
4756	9377	4.080186	TCAGCTTCCTGATTCATTCATCCA	60.080	41.667	0.00	0.00	42.98	3.41
4828	9449	7.914427	TTATCAGCCTAACTCCTCAAATCTA	57.086	36.000	0.00	0.00	0.00	1.98
4836	9457	5.763876	ACAAGTTTATCAGCCTAACTCCT	57.236	39.130	0.00	0.00	31.26	3.69
4861	9485	9.726794	AAGTCCCTCTTTCCGAAAACGAAAGTA	62.727	40.741	9.44	0.00	44.29	2.24
4898	9522	4.759782	ACTCTCACATTTTCAGGTATCGG	58.240	43.478	0.00	0.00	0.00	4.18
4934	9559	2.098443	TGCTTTTCCTTGTCGTCCAAAC	59.902	45.455	0.00	0.00	31.20	2.93
4960	9588	0.998669	TTGCATAGACATGTCGTGCG	59.001	50.000	33.65	21.18	43.76	5.34
4972	9600	4.199310	TCGGAAGAAAATCCCTTGCATAG	58.801	43.478	0.00	0.00	36.00	2.23

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.