AutoCloner

Multiple sequence alignment - TraesCS5D01G022000

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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	TraesCS5D01G022000	chr5D	100.000	5252	0	0	420	5671	14964722	14969973	0.000000e+00	9699.0
1	TraesCS5D01G022000	chr5D	79.846	1042	176	23	422	1438	14927604	14928636	0.000000e+00	730.0
2	TraesCS5D01G022000	chr5D	100.000	261	0	0	1	261	14964303	14964563	3.070000e-132	483.0
3	TraesCS5D01G022000	chr5D	80.157	635	113	10	422	1047	14775321	14775951	4.000000e-126	462.0
4	TraesCS5D01G022000	chr5D	76.848	717	132	22	435	1133	14910381	14911081	1.930000e-99	374.0
5	TraesCS5D01G022000	chr5D	80.206	485	85	9	430	912	14924886	14925361	2.510000e-93	353.0
6	TraesCS5D01G022000	chr5D	89.811	265	22	4	420	683	14942797	14943057	9.100000e-88	335.0
7	TraesCS5D01G022000	chr5D	82.310	277	25	10	1	259	14926961	14927231	9.570000e-53	219.0
8	TraesCS5D01G022000	chr5D	86.000	100	13	1	1645	1743	14717018	14717117	7.770000e-19	106.0
9	TraesCS5D01G022000	chr5D	85.882	85	8	1	2863	2943	42032250	42032166	2.810000e-13	87.9
10	TraesCS5D01G022000	chr5A	96.521	4657	125	12	1038	5671	11514972	11519614	0.000000e+00	7668.0
11	TraesCS5D01G022000	chr5A	90.351	570	40	10	420	980	11513812	11514375	0.000000e+00	734.0
12	TraesCS5D01G022000	chr5A	79.899	791	133	17	425	1194	11371094	11371879	1.780000e-154	556.0
13	TraesCS5D01G022000	chr5A	83.813	278	27	6	1	261	11513451	11513727	1.220000e-61	248.0
14	TraesCS5D01G022000	chr5A	82.721	272	32	5	1	259	11507964	11508233	1.590000e-55	228.0
15	TraesCS5D01G022000	chr5A	82.833	233	35	4	464	694	11508365	11508594	2.680000e-48	204.0
16	TraesCS5D01G022000	chr5A	85.294	102	7	6	2863	2956	30409871	30409770	1.300000e-16	99.0
17	TraesCS5D01G022000	chr5B	90.499	5315	336	63	430	5671	13698457	13703675	0.000000e+00	6861.0
18	TraesCS5D01G022000	chr5B	80.902	1042	167	21	422	1438	13689309	13690343	0.000000e+00	793.0
19	TraesCS5D01G022000	chr5B	80.994	1026	164	21	430	1434	13682769	13683784	0.000000e+00	785.0
20	TraesCS5D01G022000	chr5B	79.838	987	171	18	464	1430	13695402	13696380	0.000000e+00	695.0
21	TraesCS5D01G022000	chr5B	81.905	525	69	12	897	1406	13680126	13680639	2.440000e-113	420.0
22	TraesCS5D01G022000	chr5B	78.990	495	92	10	430	922	13686599	13687083	1.520000e-85	327.0
23	TraesCS5D01G022000	chr5B	82.418	273	30	6	1	259	13688688	13688956	7.400000e-54	222.0
24	TraesCS5D01G022000	chr6D	84.951	412	54	6	3873	4283	317121265	317121669	1.470000e-110	411.0
25	TraesCS5D01G022000	chr7B	80.066	301	52	5	5202	5501	424533620	424533327	3.440000e-52	217.0
26	TraesCS5D01G022000	chr7A	76.101	477	70	21	5202	5671	694881624	694881185	5.760000e-50	209.0
27	TraesCS5D01G022000	chr7A	75.891	477	71	19	5202	5671	695149800	695149361	2.680000e-48	204.0
28	TraesCS5D01G022000	chr7A	75.472	477	73	23	5202	5671	695035046	695034607	5.800000e-45	193.0
29	TraesCS5D01G022000	chrUn	75.472	477	73	20	5202	5671	83176270	83176709	5.800000e-45	193.0
30	TraesCS5D01G022000	chrUn	77.855	289	35	8	5202	5487	444449041	444448779	9.840000e-33	152.0
31	TraesCS5D01G022000	chr7D	80.000	265	49	2	5226	5489	411021054	411021315	5.800000e-45	193.0
32	TraesCS5D01G022000	chr3B	88.000	100	12	0	3174	3273	142244695	142244596	9.980000e-23	119.0

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	TraesCS5D01G022000	chr5D	14964303	14969973	5670	False	5091.000000	9699	100.000000	1	5671	2	chr5D.!!$F6	5670
1	TraesCS5D01G022000	chr5D	14775321	14775951	630	False	462.000000	462	80.157000	422	1047	1	chr5D.!!$F2	625
2	TraesCS5D01G022000	chr5D	14924886	14928636	3750	False	434.000000	730	80.787333	1	1438	3	chr5D.!!$F5	1437
3	TraesCS5D01G022000	chr5D	14910381	14911081	700	False	374.000000	374	76.848000	435	1133	1	chr5D.!!$F3	698
4	TraesCS5D01G022000	chr5A	11513451	11519614	6163	False	2883.333333	7668	90.228333	1	5671	3	chr5A.!!$F3	5670
5	TraesCS5D01G022000	chr5A	11371094	11371879	785	False	556.000000	556	79.899000	425	1194	1	chr5A.!!$F1	769
6	TraesCS5D01G022000	chr5A	11507964	11508594	630	False	216.000000	228	82.777000	1	694	2	chr5A.!!$F2	693
7	TraesCS5D01G022000	chr5B	13695402	13703675	8273	False	3778.000000	6861	85.168500	430	5671	2	chr5B.!!$F2	5241
8	TraesCS5D01G022000	chr5B	13680126	13690343	10217	False	509.400000	793	81.041800	1	1438	5	chr5B.!!$F1	1437

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
889	8191	0.883833	ACACTGCAAATGTAGCCAGC	59.116	50.000	1.43	0.00	0.00	4.85	F
1251	15680	0.108041	GGGAGCGAAATCCGTGGTTA	60.108	55.000	0.00	0.00	40.56	2.85	F
1760	16234	0.178955	TGAGGGTACTTGTCGGACCA	60.179	55.000	5.55	0.00	34.73	4.02	F
1900	16374	1.153568	CAATCCGAGCGCTGAGGAA	60.154	57.895	28.18	15.74	37.62	3.36	F
3212	17691	1.165907	TTTCGGCTGGTGAGTGCAAG	61.166	55.000	0.00	0.00	0.00	4.01	F
3857	18338	0.820871	CAGACTACTGGGCAGACTCC	59.179	60.000	0.00	0.00	40.14	3.85	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1743	16217	0.113776	TCTGGTCCGACAAGTACCCT	59.886	55.000	2.74	0.00	31.97	4.34	R
2224	16698	0.245539	CCTTCTGCAATGCCACCAAG	59.754	55.000	1.53	0.00	0.00	3.61	R
3666	18145	1.134220	ACAAGAAACGACCAGAAGGCA	60.134	47.619	0.00	0.00	39.06	4.75	R
3674	18155	3.469739	TGAGGGTTAACAAGAAACGACC	58.530	45.455	8.10	0.00	0.00	4.79	R
4259	18740	0.320374	GGTCCTTCATGGTGTCGACA	59.680	55.000	15.76	15.76	37.07	4.35	R
5524	20019	0.173481	TTGTTCTCATCGGAGCGGAG	59.827	55.000	0.00	0.00	41.13	4.63	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
21	3986	4.078639	CAACTCCCAAGATTAGCTAGGG	57.921	50.000	8.43	8.43	40.98	3.53
41	4006	6.742559	AGGGTATACTCAACGGTCAATAAT	57.257	37.500	5.34	0.00	0.00	1.28
42	4007	6.756221	AGGGTATACTCAACGGTCAATAATC	58.244	40.000	5.34	0.00	0.00	1.75
56	4021	8.262227	ACGGTCAATAATCCATTTCTAACACTA	58.738	33.333	0.00	0.00	0.00	2.74
75	4040	3.249189	GTCTGGGCCCCACTCACA	61.249	66.667	22.27	0.00	0.00	3.58
113	4085	6.721571	TGACTAAACTTGAATCTAAAGCCG	57.278	37.500	0.00	0.00	0.00	5.52
114	4086	6.228258	TGACTAAACTTGAATCTAAAGCCGT	58.772	36.000	0.00	0.00	0.00	5.68
135	4120	7.042658	AGCCGTCTTAAGTCGATTCATAATTTC	60.043	37.037	21.19	0.00	0.00	2.17
174	4162	3.328931	AGCTTTCATATCATCCGACCCAT	59.671	43.478	0.00	0.00	0.00	4.00
200	4188	7.259088	AGAGGACTAACCACATAACAAGATT	57.741	36.000	0.00	0.00	42.04	2.40
448	4654	2.226437	AGTCCAATCACATTTCGTGCAC	59.774	45.455	6.82	6.82	45.92	4.57
457	4663	2.360483	ACATTTCGTGCACCATTTGTCA	59.640	40.909	12.15	0.00	0.00	3.58
460	4666	1.889545	TCGTGCACCATTTGTCATGA	58.110	45.000	12.15	0.00	0.00	3.07
461	4667	2.435422	TCGTGCACCATTTGTCATGAT	58.565	42.857	12.15	0.00	0.00	2.45
462	4668	2.162008	TCGTGCACCATTTGTCATGATG	59.838	45.455	12.15	0.00	0.00	3.07
501	4707	8.162878	ACATGAATCTTATAGACAAAGGCATG	57.837	34.615	0.00	0.00	36.12	4.06
607	4818	3.164269	ACCATGGCGCCCTCCTAG	61.164	66.667	26.77	9.25	0.00	3.02
648	7949	3.711704	CTCCCACCATAATGTCTACTGGT	59.288	47.826	0.00	0.00	42.66	4.00
710	8011	3.116300	CACTCGTAAATCATCTCGGTGG	58.884	50.000	0.00	0.00	0.00	4.61
735	8036	2.101249	GACAATATTACCCCGACGGTCA	59.899	50.000	13.94	0.00	43.58	4.02
737	8038	3.243975	ACAATATTACCCCGACGGTCATC	60.244	47.826	13.94	0.00	43.58	2.92
790	8091	4.038763	TCTCTCAAGTTTCGTTTAGCTGGA	59.961	41.667	0.00	0.00	0.00	3.86
793	8094	6.460781	TCTCAAGTTTCGTTTAGCTGGATAA	58.539	36.000	0.00	0.00	0.00	1.75
889	8191	0.883833	ACACTGCAAATGTAGCCAGC	59.116	50.000	1.43	0.00	0.00	4.85
985	14856	1.807142	GCTTTAACTGCACTCCACCTC	59.193	52.381	0.00	0.00	0.00	3.85
1251	15680	0.108041	GGGAGCGAAATCCGTGGTTA	60.108	55.000	0.00	0.00	40.56	2.85
1346	15789	4.695455	TCTTTTGCCTACTCTGAATTTCGG	59.305	41.667	0.00	0.00	0.00	4.30
1454	15897	0.742635	GCTTCTCTCTGGGGCTTTCG	60.743	60.000	0.00	0.00	0.00	3.46
1603	16064	2.288025	GGGCTCCAACGTCTGGGTA	61.288	63.158	14.23	0.00	46.44	3.69
1604	16065	1.218316	GGCTCCAACGTCTGGGTAG	59.782	63.158	14.23	8.30	46.44	3.18
1708	16169	1.328279	TCTCCGTCAACTTCTGAGCA	58.672	50.000	0.00	0.00	33.60	4.26
1709	16170	1.270826	TCTCCGTCAACTTCTGAGCAG	59.729	52.381	0.00	0.00	33.60	4.24
1725	16186	2.002127	CAGGAATCTCGCGCTGTTC	58.998	57.895	5.56	4.90	0.00	3.18
1742	16216	2.162681	GTTCCTGATTCCCAACCTGTG	58.837	52.381	0.00	0.00	0.00	3.66
1743	16217	1.741028	TCCTGATTCCCAACCTGTGA	58.259	50.000	0.00	0.00	0.00	3.58
1745	16219	1.340405	CCTGATTCCCAACCTGTGAGG	60.340	57.143	0.00	0.00	42.49	3.86
1747	16221	0.698818	GATTCCCAACCTGTGAGGGT	59.301	55.000	7.66	0.00	43.31	4.34
1749	16223	1.061546	TTCCCAACCTGTGAGGGTAC	58.938	55.000	7.66	0.00	43.31	3.34
1750	16224	0.192566	TCCCAACCTGTGAGGGTACT	59.807	55.000	7.66	0.00	43.31	2.73
1752	16226	1.271379	CCCAACCTGTGAGGGTACTTG	60.271	57.143	0.00	0.00	40.58	3.16
1753	16227	1.420138	CCAACCTGTGAGGGTACTTGT	59.580	52.381	0.00	0.00	40.58	3.16
1754	16228	2.550208	CCAACCTGTGAGGGTACTTGTC	60.550	54.545	0.00	0.00	40.58	3.18
1755	16229	0.966920	ACCTGTGAGGGTACTTGTCG	59.033	55.000	0.00	0.00	40.58	4.35
1756	16230	0.246635	CCTGTGAGGGTACTTGTCGG	59.753	60.000	0.00	0.00	0.00	4.79
1757	16231	1.254026	CTGTGAGGGTACTTGTCGGA	58.746	55.000	0.00	0.00	0.00	4.55
1758	16232	0.963962	TGTGAGGGTACTTGTCGGAC	59.036	55.000	0.00	0.00	0.00	4.79
1759	16233	0.245813	GTGAGGGTACTTGTCGGACC	59.754	60.000	5.55	0.00	0.00	4.46
1760	16234	0.178955	TGAGGGTACTTGTCGGACCA	60.179	55.000	5.55	0.00	34.73	4.02
1768	16242	1.899814	ACTTGTCGGACCAGATTGCTA	59.100	47.619	15.37	0.00	0.00	3.49
1778	16252	4.202567	GGACCAGATTGCTATAATTGGGGA	60.203	45.833	9.45	0.00	0.00	4.81
1864	16338	1.969923	GAGGAGAGGCTGTATGATGCT	59.030	52.381	0.00	0.00	0.00	3.79
1900	16374	1.153568	CAATCCGAGCGCTGAGGAA	60.154	57.895	28.18	15.74	37.62	3.36
1921	16395	2.817396	GCTGGCAACTCGAGAGGC	60.817	66.667	21.68	22.05	37.61	4.70
2224	16698	1.527844	GGCACTCATGGATGGCCTC	60.528	63.158	3.32	0.00	41.39	4.70
2260	16734	2.717639	AGGGCATACGCAAGATCTTT	57.282	45.000	4.86	0.00	41.24	2.52
2337	16811	5.915758	GCAGTAGATGTTCTATACTGGTTCG	59.084	44.000	12.14	0.00	44.21	3.95
2347	16821	6.323203	TCTATACTGGTTCGTATAACTGGC	57.677	41.667	0.00	0.00	33.33	4.85
2356	16830	6.757947	TGGTTCGTATAACTGGCTACATTAAC	59.242	38.462	0.00	0.00	0.00	2.01
2566	17042	8.884323	TCTGGATAACCATAAGCTAATTCTGAT	58.116	33.333	0.00	0.00	45.87	2.90
2669	17148	6.244654	TGGTGAAATGTGAATATGGAGTGAA	58.755	36.000	0.00	0.00	0.00	3.18
2673	17152	8.246180	GTGAAATGTGAATATGGAGTGAATGTT	58.754	33.333	0.00	0.00	0.00	2.71
2978	17457	3.758554	GCTTTGAACTTGAGAGGCCATTA	59.241	43.478	5.01	0.00	0.00	1.90
3209	17688	1.331756	CATATTTCGGCTGGTGAGTGC	59.668	52.381	0.00	0.00	0.00	4.40
3212	17691	1.165907	TTTCGGCTGGTGAGTGCAAG	61.166	55.000	0.00	0.00	0.00	4.01
3666	18145	5.107607	CGTAGCTTGAATTTGTCGTGTAGTT	60.108	40.000	0.00	0.00	0.00	2.24
3674	18155	2.148916	TGTCGTGTAGTTGCCTTCTG	57.851	50.000	0.00	0.00	0.00	3.02
3857	18338	0.820871	CAGACTACTGGGCAGACTCC	59.179	60.000	0.00	0.00	40.14	3.85
4259	18740	2.202703	GCGGCGGACTCGTACATT	60.203	61.111	9.78	0.00	38.89	2.71
4487	18969	3.255642	CACCCTGTCGAAAATTGGTTGAT	59.744	43.478	0.00	0.00	0.00	2.57
4534	19016	5.823045	TCCACCTTTGTTTGTTTGTTTGTTT	59.177	32.000	0.00	0.00	0.00	2.83
4535	19017	5.911838	CCACCTTTGTTTGTTTGTTTGTTTG	59.088	36.000	0.00	0.00	0.00	2.93
4740	19232	6.620678	TGATGTGAAAAGTAAGGCATAAAGC	58.379	36.000	0.00	0.00	44.65	3.51
4887	19379	8.943002	ACTAAAATAGGAACAAACAGGATTACG	58.057	33.333	0.00	0.00	0.00	3.18
4984	19476	3.392616	AGTAATATCCAGACTTGGCCCTG	59.607	47.826	0.00	0.00	44.63	4.45
5016	19508	7.602753	ACATGGAAATTTCTAGTAGCAAAACC	58.397	34.615	17.42	0.00	0.00	3.27
5147	19642	5.960202	AGGCATGAATTTTCCAAGATAAGGT	59.040	36.000	0.00	0.00	0.00	3.50
5200	19695	4.582656	ACTGATGCACTTCTAGTAGCTAGG	59.417	45.833	0.00	0.00	35.03	3.02
5261	19756	2.994995	ATCCCACCGCTCGTGTCA	60.995	61.111	0.80	0.00	41.26	3.58
5520	20015	2.489938	TAAGCAATCCAAGTCGGCTT	57.510	45.000	0.00	0.00	45.78	4.35
5524	20019	2.945668	AGCAATCCAAGTCGGCTTATTC	59.054	45.455	0.00	0.00	32.87	1.75
5586	20082	5.582269	TGTGAGAACAGAACAGAACAGAAAG	59.418	40.000	0.00	0.00	0.00	2.62

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
21	3986	8.603242	AATGGATTATTGACCGTTGAGTATAC	57.397	34.615	0.00	0.00	34.60	1.47
41	4006	4.469945	CCCAGACCTAGTGTTAGAAATGGA	59.530	45.833	0.00	0.00	30.30	3.41
42	4007	4.770795	CCCAGACCTAGTGTTAGAAATGG	58.229	47.826	0.00	0.00	0.00	3.16
56	4021	4.270153	TGAGTGGGGCCCAGACCT	62.270	66.667	29.66	20.75	32.34	3.85
75	4040	8.559536	CAAGTTTAGTCATGTGTATGAAACTGT	58.440	33.333	6.61	0.00	44.49	3.55
142	4127	8.344831	CGGATGATATGAAAGCTTTGTCAAATA	58.655	33.333	18.30	6.96	0.00	1.40
143	4128	7.067372	TCGGATGATATGAAAGCTTTGTCAAAT	59.933	33.333	18.30	3.09	0.00	2.32
162	4150	2.091278	AGTCCTCTAATGGGTCGGATGA	60.091	50.000	0.00	0.00	0.00	2.92
174	4162	7.786046	TCTTGTTATGTGGTTAGTCCTCTAA	57.214	36.000	0.00	0.00	37.07	2.10
448	4654	4.109766	GTGTGCATCATCATGACAAATGG	58.890	43.478	0.00	0.00	30.57	3.16
457	4663	2.773661	TGTCCCTAGTGTGCATCATCAT	59.226	45.455	0.00	0.00	0.00	2.45
460	4666	2.773661	TCATGTCCCTAGTGTGCATCAT	59.226	45.455	0.00	0.00	0.00	2.45
461	4667	2.187100	TCATGTCCCTAGTGTGCATCA	58.813	47.619	0.00	0.00	0.00	3.07
462	4668	2.988010	TCATGTCCCTAGTGTGCATC	57.012	50.000	0.00	0.00	0.00	3.91
501	4707	1.749258	GTGATTCCCGGTGCCTTCC	60.749	63.158	0.00	0.00	0.00	3.46
607	4818	4.039852	GGGAGAATGGTAGAGAGAATGGAC	59.960	50.000	0.00	0.00	0.00	4.02
648	7949	5.172934	GGAGTGAAACGGTACAATGATGTA	58.827	41.667	0.00	0.00	45.86	2.29
667	7968	0.696501	GTGTATGGGGTTGGTGGAGT	59.303	55.000	0.00	0.00	0.00	3.85
710	8011	0.393820	TCGGGGTAATATTGTCGGGC	59.606	55.000	0.00	0.00	0.00	6.13
790	8091	4.917415	GCTCATGTTTTTCACTGCGTTTAT	59.083	37.500	0.00	0.00	0.00	1.40
793	8094	2.731217	GCTCATGTTTTTCACTGCGTT	58.269	42.857	0.00	0.00	0.00	4.84
800	8101	1.896220	AGGCTCGCTCATGTTTTTCA	58.104	45.000	0.00	0.00	0.00	2.69
902	8213	8.913487	AAATGATTTGCTTCCATTTCTTCTTT	57.087	26.923	0.00	0.00	36.17	2.52
912	8224	2.352617	GCGTGGAAATGATTTGCTTCCA	60.353	45.455	10.69	1.77	44.95	3.53
913	8225	2.262211	GCGTGGAAATGATTTGCTTCC	58.738	47.619	10.69	0.00	39.31	3.46
943	14813	5.949952	AGCAAGAACCCTAATAATTCCGTTT	59.050	36.000	0.00	0.00	0.00	3.60
985	14856	1.347062	GGCAGAGAGATAGAAGGGGG	58.653	60.000	0.00	0.00	0.00	5.40
1251	15680	0.983378	CAAGGAGGAGGTCGGGGATT	60.983	60.000	0.00	0.00	0.00	3.01
1346	15789	1.737735	GCAACAAATTCCGGCAGCC	60.738	57.895	0.00	0.00	0.00	4.85
1497	15945	4.320421	CGAATCTGCAGGACAAAAATCACA	60.320	41.667	15.13	0.00	0.00	3.58
1567	16028	2.108168	CCCTCCACGAATCTCCAGTTA	58.892	52.381	0.00	0.00	0.00	2.24
1569	16030	1.617947	GCCCTCCACGAATCTCCAGT	61.618	60.000	0.00	0.00	0.00	4.00
1603	16064	2.355115	GGGACCGCCACCAAATCT	59.645	61.111	0.00	0.00	35.15	2.40
1604	16065	3.131478	CGGGACCGCCACCAAATC	61.131	66.667	0.00	0.00	35.15	2.17
1708	16169	1.153549	GGAACAGCGCGAGATTCCT	60.154	57.895	21.56	2.57	36.67	3.36
1709	16170	1.153549	AGGAACAGCGCGAGATTCC	60.154	57.895	21.40	21.40	38.61	3.01
1725	16186	1.340405	CCTCACAGGTTGGGAATCAGG	60.340	57.143	0.00	0.00	0.00	3.86
1742	16216	0.531200	CTGGTCCGACAAGTACCCTC	59.469	60.000	0.00	0.00	31.97	4.30
1743	16217	0.113776	TCTGGTCCGACAAGTACCCT	59.886	55.000	2.74	0.00	31.97	4.34
1745	16219	2.618053	CAATCTGGTCCGACAAGTACC	58.382	52.381	2.74	0.00	0.00	3.34
1747	16221	1.899814	AGCAATCTGGTCCGACAAGTA	59.100	47.619	2.74	0.00	0.00	2.24
1749	16223	2.672961	TAGCAATCTGGTCCGACAAG	57.327	50.000	0.00	0.00	0.00	3.16
1750	16224	4.746535	TTATAGCAATCTGGTCCGACAA	57.253	40.909	0.00	0.00	0.00	3.18
1752	16226	4.452455	CCAATTATAGCAATCTGGTCCGAC	59.548	45.833	0.00	0.00	0.00	4.79
1753	16227	4.504864	CCCAATTATAGCAATCTGGTCCGA	60.505	45.833	0.00	0.00	0.00	4.55
1754	16228	3.753272	CCCAATTATAGCAATCTGGTCCG	59.247	47.826	0.00	0.00	0.00	4.79
1755	16229	4.082125	CCCCAATTATAGCAATCTGGTCC	58.918	47.826	0.00	0.00	0.00	4.46
1756	16230	4.985538	TCCCCAATTATAGCAATCTGGTC	58.014	43.478	0.00	0.00	0.00	4.02
1757	16231	5.074929	TCATCCCCAATTATAGCAATCTGGT	59.925	40.000	0.00	0.00	0.00	4.00
1758	16232	5.573219	TCATCCCCAATTATAGCAATCTGG	58.427	41.667	0.00	0.00	0.00	3.86
1759	16233	7.528996	TTTCATCCCCAATTATAGCAATCTG	57.471	36.000	0.00	0.00	0.00	2.90
1760	16234	7.951806	TCATTTCATCCCCAATTATAGCAATCT	59.048	33.333	0.00	0.00	0.00	2.40
1913	16387	2.818714	GACGTCCTCGCCTCTCGA	60.819	66.667	3.51	0.00	46.29	4.04
1921	16395	4.717629	TTGGCAGCGACGTCCTCG	62.718	66.667	10.58	0.00	45.97	4.63
2224	16698	0.245539	CCTTCTGCAATGCCACCAAG	59.754	55.000	1.53	0.00	0.00	3.61
2260	16734	3.861840	CTTCTCCGAATTAGTGAAGGCA	58.138	45.455	10.05	0.00	32.84	4.75
2356	16830	7.231705	CAGTGAGCTGACTGAAACTAATATG	57.768	40.000	27.04	0.00	45.39	1.78
2669	17148	2.742428	ATAGGGCACTGCATGAACAT	57.258	45.000	0.00	0.00	0.00	2.71
2673	17152	3.554934	CCTTAAATAGGGCACTGCATGA	58.445	45.455	0.00	0.00	40.67	3.07
2978	17457	3.843893	ATTGCTTCTTTGGCCAACTTT	57.156	38.095	20.35	0.00	0.00	2.66
3277	17756	3.624707	GCAATAGAACCCCTCCATGTCAA	60.625	47.826	0.00	0.00	0.00	3.18
3353	17832	1.135731	CGACTGACTGGACGAGCTC	59.864	63.158	2.73	2.73	0.00	4.09
3666	18145	1.134220	ACAAGAAACGACCAGAAGGCA	60.134	47.619	0.00	0.00	39.06	4.75
3674	18155	3.469739	TGAGGGTTAACAAGAAACGACC	58.530	45.455	8.10	0.00	0.00	4.79
3949	18430	0.250901	GAACTCATGGCCACACCTGT	60.251	55.000	8.16	0.00	40.22	4.00
4031	18512	1.301716	GGGCTCAGCGTTGTCTTCA	60.302	57.895	0.00	0.00	0.00	3.02
4259	18740	0.320374	GGTCCTTCATGGTGTCGACA	59.680	55.000	15.76	15.76	37.07	4.35
4307	18788	3.361174	TCGCTCATCACCGACACA	58.639	55.556	0.00	0.00	0.00	3.72
4487	18969	9.137459	TGGAAGTATCATTTTGTTTTTCCAGTA	57.863	29.630	0.00	0.00	38.24	2.74
4534	19016	1.754226	GAGGGACAGCCAAACAAAACA	59.246	47.619	0.00	0.00	35.15	2.83
4535	19017	1.068588	GGAGGGACAGCCAAACAAAAC	59.931	52.381	0.00	0.00	35.15	2.43
4740	19232	1.886542	GGGTTGCTTTTGTCTACCTGG	59.113	52.381	0.00	0.00	0.00	4.45
4741	19233	1.886542	GGGGTTGCTTTTGTCTACCTG	59.113	52.381	0.00	0.00	0.00	4.00
4742	19234	1.497286	TGGGGTTGCTTTTGTCTACCT	59.503	47.619	0.00	0.00	0.00	3.08
4743	19235	1.989706	TGGGGTTGCTTTTGTCTACC	58.010	50.000	0.00	0.00	0.00	3.18
4887	19379	1.311859	TGGCATTGCGATGGATTCTC	58.688	50.000	15.85	0.00	33.72	2.87
5147	19642	5.307204	ACTGGCTTTGGTTACGTTACATAA	58.693	37.500	7.05	0.00	0.00	1.90
5156	19651	5.104562	GTCAGTTAACTGGCTTTGGTTAC	57.895	43.478	28.75	15.57	44.71	2.50
5200	19695	3.190953	AGTCTTGTTAGCAGTAGTCGTCC	59.809	47.826	0.00	0.00	0.00	4.79
5261	19756	2.335369	GACGATGACGCGGGCTAT	59.665	61.111	12.47	0.00	43.96	2.97
5520	20015	2.271944	TCTCATCGGAGCGGAGAATA	57.728	50.000	4.84	0.00	41.13	1.75
5524	20019	0.173481	TTGTTCTCATCGGAGCGGAG	59.827	55.000	0.00	0.00	41.13	4.63

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.