AutoCloner

Multiple sequence alignment - TraesCS6D01G044900

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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	TraesCS6D01G044900	chr6D	100.000	3852	0	0	1	3852	20143570	20139719	0.000000e+00	7114.0
1	TraesCS6D01G044900	chr6D	87.968	989	106	9	1	986	39098810	39099788	0.000000e+00	1155.0
2	TraesCS6D01G044900	chr6D	79.853	407	73	7	1160	1563	21904326	21904726	4.870000e-74	289.0
3	TraesCS6D01G044900	chr6A	93.927	1482	50	16	1757	3198	20203673	20202192	0.000000e+00	2202.0
4	TraesCS6D01G044900	chr6A	96.483	654	22	1	3199	3852	20201486	20200834	0.000000e+00	1079.0
5	TraesCS6D01G044900	chr6A	94.435	611	32	2	1001	1611	20204284	20203676	0.000000e+00	939.0
6	TraesCS6D01G044900	chr6A	72.903	1192	236	57	1167	2334	21306426	21307554	7.980000e-87	331.0
7	TraesCS6D01G044900	chr6B	93.974	1394	78	3	1085	2478	34194569	34193182	0.000000e+00	2104.0
8	TraesCS6D01G044900	chr6B	91.100	809	66	6	1673	2479	33846189	33845385	0.000000e+00	1090.0
9	TraesCS6D01G044900	chr6B	90.977	809	67	6	1673	2479	33884838	33884034	0.000000e+00	1085.0
10	TraesCS6D01G044900	chr6B	90.606	809	70	6	1673	2479	33829029	33828225	0.000000e+00	1068.0
11	TraesCS6D01G044900	chr6B	90.606	809	69	7	1673	2479	33901990	33901187	0.000000e+00	1066.0
12	TraesCS6D01G044900	chr6B	90.119	759	43	15	2472	3202	34193018	34192264	0.000000e+00	957.0
13	TraesCS6D01G044900	chr6B	90.249	523	39	7	3337	3852	34184042	34183525	0.000000e+00	673.0
14	TraesCS6D01G044900	chr6B	89.784	509	50	2	2075	2582	33883897	33883390	0.000000e+00	651.0
15	TraesCS6D01G044900	chr6B	89.841	502	49	2	2075	2575	33828088	33827588	0.000000e+00	643.0
16	TraesCS6D01G044900	chr6B	89.194	509	53	2	2075	2582	33845248	33844741	5.430000e-178	634.0
17	TraesCS6D01G044900	chr6B	90.217	460	35	5	2576	3026	33876600	33876142	3.310000e-165	592.0
18	TraesCS6D01G044900	chr6B	90.000	460	36	5	2576	3026	33820794	33820336	1.540000e-163	586.0
19	TraesCS6D01G044900	chr6B	89.783	460	37	5	2576	3026	33893750	33893292	7.170000e-162	580.0
20	TraesCS6D01G044900	chr6B	89.565	460	38	5	2576	3026	33837944	33837486	3.340000e-160	575.0
21	TraesCS6D01G044900	chr6B	79.115	407	76	7	1160	1563	36137725	36138125	4.900000e-69	272.0
22	TraesCS6D01G044900	chr6B	76.485	421	91	5	1158	1574	71347128	71347544	5.010000e-54	222.0
23	TraesCS6D01G044900	chr6B	93.182	44	3	0	3312	3355	34185212	34185169	8.930000e-07	65.8
24	TraesCS6D01G044900	chr1D	94.586	979	52	1	1	979	121439457	121440434	0.000000e+00	1513.0
25	TraesCS6D01G044900	chr2D	94.320	986	55	1	1	986	309969288	309968304	0.000000e+00	1509.0
26	TraesCS6D01G044900	chr2D	88.742	986	102	5	1	984	593418658	593417680	0.000000e+00	1197.0
27	TraesCS6D01G044900	chr2D	80.628	382	60	14	1129	1503	628016271	628015897	2.270000e-72	283.0
28	TraesCS6D01G044900	chr4D	94.315	985	55	1	1	985	252822015	252822998	0.000000e+00	1507.0
29	TraesCS6D01G044900	chr3A	94.213	985	56	1	1	985	50217385	50216402	0.000000e+00	1502.0
30	TraesCS6D01G044900	chr2A	93.809	953	57	2	1	952	756428711	756429662	0.000000e+00	1432.0
31	TraesCS6D01G044900	chr2A	82.808	349	54	6	1159	1503	758526617	758526271	1.340000e-79	307.0
32	TraesCS6D01G044900	chrUn	88.765	988	102	5	1	987	24234073	24235052	0.000000e+00	1201.0
33	TraesCS6D01G044900	chrUn	88.629	985	102	6	1	983	24761177	24760201	0.000000e+00	1190.0
34	TraesCS6D01G044900	chr7D	88.641	986	103	5	1	985	521344901	521343924	0.000000e+00	1192.0
35	TraesCS6D01G044900	chr2B	82.808	349	54	6	1159	1503	771160312	771159966	1.340000e-79	307.0
36	TraesCS6D01G044900	chr7B	73.231	325	77	7	1170	1492	693657384	693657068	4.070000e-20	110.0

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	TraesCS6D01G044900	chr6D	20139719	20143570	3851	True	7114.000000	7114	100.000000	1	3852	1	chr6D.!!$R1	3851
1	TraesCS6D01G044900	chr6D	39098810	39099788	978	False	1155.000000	1155	87.968000	1	986	1	chr6D.!!$F2	985
2	TraesCS6D01G044900	chr6A	20200834	20204284	3450	True	1406.666667	2202	94.948333	1001	3852	3	chr6A.!!$R1	2851
3	TraesCS6D01G044900	chr6A	21306426	21307554	1128	False	331.000000	331	72.903000	1167	2334	1	chr6A.!!$F1	1167
4	TraesCS6D01G044900	chr6B	34192264	34194569	2305	True	1530.500000	2104	92.046500	1085	3202	2	chr6B.!!$R10	2117
5	TraesCS6D01G044900	chr6B	33901187	33901990	803	True	1066.000000	1066	90.606000	1673	2479	1	chr6B.!!$R5	806
6	TraesCS6D01G044900	chr6B	33883390	33884838	1448	True	868.000000	1085	90.380500	1673	2582	2	chr6B.!!$R8	909
7	TraesCS6D01G044900	chr6B	33844741	33846189	1448	True	862.000000	1090	90.147000	1673	2582	2	chr6B.!!$R7	909
8	TraesCS6D01G044900	chr6B	33827588	33829029	1441	True	855.500000	1068	90.223500	1673	2575	2	chr6B.!!$R6	902
9	TraesCS6D01G044900	chr6B	34183525	34185212	1687	True	369.400000	673	91.715500	3312	3852	2	chr6B.!!$R9	540
10	TraesCS6D01G044900	chr1D	121439457	121440434	977	False	1513.000000	1513	94.586000	1	979	1	chr1D.!!$F1	978
11	TraesCS6D01G044900	chr2D	309968304	309969288	984	True	1509.000000	1509	94.320000	1	986	1	chr2D.!!$R1	985
12	TraesCS6D01G044900	chr2D	593417680	593418658	978	True	1197.000000	1197	88.742000	1	984	1	chr2D.!!$R2	983
13	TraesCS6D01G044900	chr4D	252822015	252822998	983	False	1507.000000	1507	94.315000	1	985	1	chr4D.!!$F1	984
14	TraesCS6D01G044900	chr3A	50216402	50217385	983	True	1502.000000	1502	94.213000	1	985	1	chr3A.!!$R1	984
15	TraesCS6D01G044900	chr2A	756428711	756429662	951	False	1432.000000	1432	93.809000	1	952	1	chr2A.!!$F1	951
16	TraesCS6D01G044900	chrUn	24234073	24235052	979	False	1201.000000	1201	88.765000	1	987	1	chrUn.!!$F1	986
17	TraesCS6D01G044900	chrUn	24760201	24761177	976	True	1190.000000	1190	88.629000	1	983	1	chrUn.!!$R1	982
18	TraesCS6D01G044900	chr7D	521343924	521344901	977	True	1192.000000	1192	88.641000	1	985	1	chr7D.!!$R1	984

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
997	1002	0.608130	TGTAGTGAATCTGCCTGCGT	59.392	50.0	0.00	0.0	0.00	5.24	F
1471	1476	0.465824	CTATCGGGTCCAGGACGTCT	60.466	60.0	16.46	0.0	32.65	4.18	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2202	2210	0.741915	TGTCAAGCGTGAAAAACCCC	59.258	50.0	3.2	0.0	34.87	4.95	R
3273	5118	0.552848	AATTGTGGGATGGCCGAGAT	59.447	50.0	0.0	0.0	33.83	2.75	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
92	93	8.818141	TCAAAGTACATTTCTTCTCACACTAG	57.182	34.615	0.00	0.00	0.00	2.57
93	94	7.385205	TCAAAGTACATTTCTTCTCACACTAGC	59.615	37.037	0.00	0.00	0.00	3.42
142	144	9.838339	ACTTCTCTGTTATCTTTCTTTTTCAGA	57.162	29.630	0.00	0.00	0.00	3.27
157	159	8.316640	TCTTTTTCAGAGTAGCTCAAGATTTC	57.683	34.615	0.00	0.00	32.06	2.17
174	176	7.444183	TCAAGATTTCGAAAAGGACTACATTGT	59.556	33.333	15.66	0.00	0.00	2.71
184	186	1.555075	GACTACATTGTGGGAGCCAGA	59.445	52.381	5.10	0.00	32.34	3.86
686	689	2.365582	ACGGCCTATGGTGAATGAAAC	58.634	47.619	0.00	0.00	0.00	2.78
715	718	6.699204	CCTGTTAGTAGAGACGTAATACGAGA	59.301	42.308	20.34	0.00	46.05	4.04
740	743	6.542735	AGCATCTAACAGAACGACTCTACATA	59.457	38.462	0.00	0.00	31.12	2.29
743	746	8.560374	CATCTAACAGAACGACTCTACATATCA	58.440	37.037	0.00	0.00	31.12	2.15
747	750	7.575414	ACAGAACGACTCTACATATCAAGAT	57.425	36.000	0.00	0.00	31.12	2.40
764	767	3.314541	AGATACGCTTTTGAACGTCCT	57.685	42.857	0.00	0.00	42.46	3.85
828	831	3.969287	ATAGCGTCTCATGCCATGTAT	57.031	42.857	4.31	0.00	0.00	2.29
835	838	1.988467	CTCATGCCATGTATAGACGCG	59.012	52.381	3.53	3.53	0.00	6.01
902	907	5.516996	GCTCCAAAAACGCTTTACTAAGTT	58.483	37.500	0.00	0.00	33.74	2.66
926	931	3.900601	ACTCTATGGTTGCCTAGAGATGG	59.099	47.826	19.08	0.00	42.29	3.51
948	953	6.124340	TGGAATAACACGTCTCTACCTATGA	58.876	40.000	0.00	0.00	0.00	2.15
970	975	5.069119	TGAAATATGACGTCTCTACAGGCAT	59.931	40.000	17.92	1.38	0.00	4.40
987	992	5.536161	ACAGGCATGTTTTCTTGTAGTGAAT	59.464	36.000	0.00	0.00	35.63	2.57
988	993	6.088824	CAGGCATGTTTTCTTGTAGTGAATC	58.911	40.000	0.00	0.00	0.00	2.52
989	994	6.006449	AGGCATGTTTTCTTGTAGTGAATCT	58.994	36.000	0.00	0.00	0.00	2.40
990	995	6.072286	AGGCATGTTTTCTTGTAGTGAATCTG	60.072	38.462	0.00	0.00	0.00	2.90
991	996	5.570589	GCATGTTTTCTTGTAGTGAATCTGC	59.429	40.000	0.00	0.00	0.00	4.26
992	997	5.689383	TGTTTTCTTGTAGTGAATCTGCC	57.311	39.130	0.00	0.00	0.00	4.85
993	998	5.376625	TGTTTTCTTGTAGTGAATCTGCCT	58.623	37.500	0.00	0.00	0.00	4.75
994	999	5.239306	TGTTTTCTTGTAGTGAATCTGCCTG	59.761	40.000	0.00	0.00	0.00	4.85
995	1000	2.977914	TCTTGTAGTGAATCTGCCTGC	58.022	47.619	0.00	0.00	0.00	4.85
996	1001	1.662629	CTTGTAGTGAATCTGCCTGCG	59.337	52.381	0.00	0.00	0.00	5.18
997	1002	0.608130	TGTAGTGAATCTGCCTGCGT	59.392	50.000	0.00	0.00	0.00	5.24
998	1003	1.001974	TGTAGTGAATCTGCCTGCGTT	59.998	47.619	0.00	0.00	0.00	4.84
999	1004	1.394917	GTAGTGAATCTGCCTGCGTTG	59.605	52.381	0.00	0.00	0.00	4.10
1007	1012	3.060736	TCTGCCTGCGTTGGTATTTTA	57.939	42.857	0.00	0.00	0.00	1.52
1125	1130	2.604174	CCGCCACGAACAACCAGTC	61.604	63.158	0.00	0.00	0.00	3.51
1290	1295	1.004918	CACCGACCGCTCCTTTCTT	60.005	57.895	0.00	0.00	0.00	2.52
1291	1296	1.004918	ACCGACCGCTCCTTTCTTG	60.005	57.895	0.00	0.00	0.00	3.02
1363	1368	1.604378	CGAATCTTCCACCCAGCCT	59.396	57.895	0.00	0.00	0.00	4.58
1471	1476	0.465824	CTATCGGGTCCAGGACGTCT	60.466	60.000	16.46	0.00	32.65	4.18
1476	1481	3.681835	GTCCAGGACGTCTGCGGT	61.682	66.667	16.46	0.00	42.05	5.68
1655	1660	3.465403	CCTCGTCCCTCCTGGCAG	61.465	72.222	7.75	7.75	0.00	4.85
1665	1670	1.364626	CTCCTGGCAGCGACAATGAC	61.365	60.000	9.56	0.00	0.00	3.06
1666	1671	2.743752	CCTGGCAGCGACAATGACG	61.744	63.158	9.56	0.02	0.00	4.35
1804	1809	5.450137	CCATCTCAGAGTTGGAATGATTTGC	60.450	44.000	19.53	0.00	37.27	3.68
1807	1812	4.012374	TCAGAGTTGGAATGATTTGCCTC	58.988	43.478	0.00	0.00	0.00	4.70
1891	1896	6.258160	CGCTTTTACTGGATAATGAAGTTGG	58.742	40.000	0.00	0.00	0.00	3.77
1896	1901	5.104259	ACTGGATAATGAAGTTGGAGGAC	57.896	43.478	0.00	0.00	0.00	3.85
1953	1958	4.622701	GGAATTCTCCATTCTTGAACCG	57.377	45.455	5.23	0.00	41.22	4.44
1972	1978	1.377229	CCACCCGAAGCCAAAGGTA	59.623	57.895	0.00	0.00	0.00	3.08
2170	2178	1.471684	CATTGGAGAGCAGCTTGTTCC	59.528	52.381	12.43	12.43	0.00	3.62
2271	2279	1.186200	CTCTTGACATCTCCGACCCA	58.814	55.000	0.00	0.00	0.00	4.51
2657	3768	3.821033	GGAACTGCTTGTTATGGTCAGTT	59.179	43.478	5.72	5.72	46.75	3.16
2813	3925	7.756722	CAGGAATTTCTTGTTTGGTAATAGCTG	59.243	37.037	0.00	0.00	0.00	4.24
2898	4010	8.090214	GCTTGGTATGGTTGCAAATAATATCAT	58.910	33.333	0.00	0.00	0.00	2.45
2958	4071	4.253685	ACCATGTAGATTTTCCTCGTGTG	58.746	43.478	0.00	0.00	0.00	3.82
2981	4094	7.503230	TGTGATCAGATTACCATTGCATATTGT	59.497	33.333	0.00	0.00	0.00	2.71
3026	4140	7.780745	TGGTTACAAGGGAAAACATTTCTAGAA	59.219	33.333	0.00	0.00	0.00	2.10
3030	4144	8.581253	ACAAGGGAAAACATTTCTAGAATAGG	57.419	34.615	5.89	1.71	39.78	2.57
3031	4145	7.615757	ACAAGGGAAAACATTTCTAGAATAGGG	59.384	37.037	5.89	0.00	39.78	3.53
3032	4146	6.129874	AGGGAAAACATTTCTAGAATAGGGC	58.870	40.000	5.89	0.00	39.78	5.19
3033	4147	6.068794	AGGGAAAACATTTCTAGAATAGGGCT	60.069	38.462	5.89	0.00	39.78	5.19
3035	4149	7.445707	GGGAAAACATTTCTAGAATAGGGCTAG	59.554	40.741	5.89	0.00	39.78	3.42
3080	4219	7.612065	TGAATTAGAATAGGGCTAGCAACTA	57.388	36.000	18.24	17.73	0.00	2.24
3273	5118	2.413351	GCGACGCAGCAGATCCTA	59.587	61.111	16.42	0.00	37.05	2.94
3475	6467	9.480433	ACGGAAGTTTCAGAATGATATGCAAGC	62.480	40.741	0.00	0.00	46.40	4.01
3528	6520	2.095617	CAGCATCGTCTTGTTCAATGCA	60.096	45.455	8.19	0.00	43.96	3.96
3540	6532	5.070770	TGTTCAATGCAACTTCTTGTGTT	57.929	34.783	0.00	0.00	0.00	3.32
3732	6724	3.118000	AGTCCGTCCCAACTTCTTTTCTT	60.118	43.478	0.00	0.00	0.00	2.52
3791	6783	1.156034	ATGCATCATCCGTGAGTGCG	61.156	55.000	0.00	0.00	39.55	5.34
3796	6793	0.172578	TCATCCGTGAGTGCGTTAGG	59.827	55.000	0.00	0.00	0.00	2.69
3838	6835	4.320935	GGCATTCCGAACAATAGTTTGTGT	60.321	41.667	0.00	0.00	45.30	3.72

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
12	13	2.767505	GAGGTTGTGTAGGAGTGGTTG	58.232	52.381	0.00	0.00	0.00	3.77
58	59	9.725019	AGAAGAAATGTACTTTGATGATGTACA	57.275	29.630	0.00	0.00	46.53	2.90
142	144	5.639931	GTCCTTTTCGAAATCTTGAGCTACT	59.360	40.000	12.12	0.00	0.00	2.57
157	159	3.670625	TCCCACAATGTAGTCCTTTTCG	58.329	45.455	0.00	0.00	0.00	3.46
174	176	1.289160	ATAGTTGCTTCTGGCTCCCA	58.711	50.000	0.00	0.00	42.39	4.37
337	339	7.236019	TCAATTAGTAGGAACAACCACCTTAGA	59.764	37.037	0.00	0.00	42.04	2.10
346	348	9.180678	CACACAATTTCAATTAGTAGGAACAAC	57.819	33.333	0.00	0.00	0.00	3.32
686	689	0.381089	CGTCTCTACTAACAGGGCCG	59.619	60.000	0.00	0.00	0.00	6.13
715	718	4.700692	TGTAGAGTCGTTCTGTTAGATGCT	59.299	41.667	3.06	0.00	36.61	3.79
740	743	4.092968	GGACGTTCAAAAGCGTATCTTGAT	59.907	41.667	0.00	0.00	41.70	2.57
743	746	3.660865	AGGACGTTCAAAAGCGTATCTT	58.339	40.909	0.00	0.00	41.70	2.40
747	750	6.418819	GCTATATTAGGACGTTCAAAAGCGTA	59.581	38.462	0.00	0.00	41.70	4.42
764	767	9.032420	CGTCTCTAGATATGACACGCTATATTA	57.968	37.037	10.29	0.00	0.00	0.98
804	807	3.513119	ACATGGCATGAGACGCTATATCT	59.487	43.478	32.74	3.47	0.00	1.98
805	808	3.854666	ACATGGCATGAGACGCTATATC	58.145	45.455	32.74	0.00	0.00	1.63
835	838	1.871080	AATATAGACACGCTGGCTGC	58.129	50.000	6.26	6.26	35.73	5.25
887	892	6.812160	CCATAGAGTCAACTTAGTAAAGCGTT	59.188	38.462	0.00	0.00	36.05	4.84
902	907	4.251103	TCTCTAGGCAACCATAGAGTCA	57.749	45.455	10.88	0.00	43.60	3.41
948	953	5.163405	ACATGCCTGTAGAGACGTCATATTT	60.163	40.000	19.50	0.00	32.49	1.40
970	975	5.239306	CAGGCAGATTCACTACAAGAAAACA	59.761	40.000	0.00	0.00	0.00	2.83
987	992	1.904287	AAAATACCAACGCAGGCAGA	58.096	45.000	0.00	0.00	0.00	4.26
988	993	3.057876	TGTTAAAATACCAACGCAGGCAG	60.058	43.478	0.00	0.00	0.00	4.85
989	994	2.885266	TGTTAAAATACCAACGCAGGCA	59.115	40.909	0.00	0.00	0.00	4.75
990	995	3.498082	CTGTTAAAATACCAACGCAGGC	58.502	45.455	0.00	0.00	0.00	4.85
991	996	3.504520	ACCTGTTAAAATACCAACGCAGG	59.495	43.478	0.00	0.00	45.43	4.85
992	997	4.454504	AGACCTGTTAAAATACCAACGCAG	59.545	41.667	0.00	0.00	0.00	5.18
993	998	4.391155	AGACCTGTTAAAATACCAACGCA	58.609	39.130	0.00	0.00	0.00	5.24
994	999	5.446875	GCTAGACCTGTTAAAATACCAACGC	60.447	44.000	0.00	0.00	0.00	4.84
995	1000	5.873164	AGCTAGACCTGTTAAAATACCAACG	59.127	40.000	0.00	0.00	0.00	4.10
996	1001	7.174426	ACAAGCTAGACCTGTTAAAATACCAAC	59.826	37.037	0.00	0.00	0.00	3.77
997	1002	7.228590	ACAAGCTAGACCTGTTAAAATACCAA	58.771	34.615	0.00	0.00	0.00	3.67
998	1003	6.775708	ACAAGCTAGACCTGTTAAAATACCA	58.224	36.000	0.00	0.00	0.00	3.25
999	1004	8.827677	CATACAAGCTAGACCTGTTAAAATACC	58.172	37.037	0.00	0.00	0.00	2.73
1007	1012	5.482908	CTGAACATACAAGCTAGACCTGTT	58.517	41.667	0.00	0.00	0.00	3.16
1112	1117	1.885850	GCGTGGACTGGTTGTTCGT	60.886	57.895	0.00	0.00	0.00	3.85
1264	1269	4.451150	GCGGTCGGTGATGAGGCA	62.451	66.667	0.00	0.00	0.00	4.75
1326	1331	0.458669	GGTCGTAATCGAGGAAGCCA	59.541	55.000	0.00	0.00	46.96	4.75
1628	1633	1.671379	GGGACGAGGAAGGTGTTGC	60.671	63.158	0.00	0.00	0.00	4.17
1655	1660	3.084579	CAGCCTCGTCATTGTCGC	58.915	61.111	0.00	0.00	0.00	5.19
1688	1693	4.142160	CCATCCAGATGACTCTAAACGACA	60.142	45.833	9.24	0.00	41.20	4.35
1804	1809	1.529309	GCCCTAAGGAGCCAAGAGG	59.471	63.158	0.00	0.00	33.47	3.69
1891	1896	3.506067	ACCAACATTTTCATTCCGTCCTC	59.494	43.478	0.00	0.00	0.00	3.71
1896	1901	3.244976	GAGCACCAACATTTTCATTCCG	58.755	45.455	0.00	0.00	0.00	4.30
1953	1958	2.757980	TACCTTTGGCTTCGGGTGGC	62.758	60.000	0.00	0.00	33.74	5.01
1972	1978	6.064060	CCATGGTCATATTAGGAATGTGTGT	58.936	40.000	2.57	0.00	32.51	3.72
2170	2178	1.132453	TGAGCTTCCATCGTCGTACAG	59.868	52.381	0.00	0.00	0.00	2.74
2197	2205	1.211709	GCGTGAAAAACCCCGGATG	59.788	57.895	0.73	0.00	0.00	3.51
2202	2210	0.741915	TGTCAAGCGTGAAAAACCCC	59.258	50.000	3.20	0.00	34.87	4.95
2271	2279	2.849943	TGGGAAGTTGCTATATGGGTGT	59.150	45.455	0.00	0.00	0.00	4.16
2368	2385	1.077212	ATCAGGCAGGCCATGTGAC	60.077	57.895	13.63	0.00	38.92	3.67
2813	3925	7.939039	TCATGAGATAAATTTATGGGTCTCACC	59.061	37.037	22.50	5.80	36.09	4.02
2898	4010	6.015095	CCATAGTGGTAGATAGCAATGACTCA	60.015	42.308	2.54	0.00	35.24	3.41
2958	4071	8.355169	ACAACAATATGCAATGGTAATCTGATC	58.645	33.333	0.00	0.00	0.00	2.92
3026	4140	7.665974	GGTTACATGCTTTTATTCTAGCCCTAT	59.334	37.037	0.00	0.00	36.56	2.57
3029	4143	5.592688	TGGTTACATGCTTTTATTCTAGCCC	59.407	40.000	0.00	0.00	36.56	5.19
3030	4144	6.693315	TGGTTACATGCTTTTATTCTAGCC	57.307	37.500	0.00	0.00	36.56	3.93
3031	4145	9.831737	CATATGGTTACATGCTTTTATTCTAGC	57.168	33.333	0.00	0.00	37.97	3.42
3088	4227	8.861033	TTATCAAATTTGATGAACTGCTATGC	57.139	30.769	33.94	0.00	46.68	3.14
3273	5118	0.552848	AATTGTGGGATGGCCGAGAT	59.447	50.000	0.00	0.00	33.83	2.75
3403	6393	0.577269	GACTGATTGCCATACGCGAC	59.423	55.000	15.93	0.00	42.08	5.19
3407	6397	1.324435	CGTGTGACTGATTGCCATACG	59.676	52.381	0.00	0.00	38.58	3.06
3475	6467	0.911769	TCCTAACAGCATGGACCCTG	59.088	55.000	0.00	0.00	43.62	4.45
3477	6469	3.478540	GTCCTAACAGCATGGACCC	57.521	57.895	0.00	0.00	43.10	4.46
3540	6532	3.390135	CAACGACTTTGACTCTTGCCTA	58.610	45.455	0.00	0.00	37.39	3.93
3732	6724	4.952071	TGATGGCATTCCTTCACAAAAA	57.048	36.364	0.00	0.00	40.40	1.94
3784	6776	0.394938	TTTCCTGCCTAACGCACTCA	59.605	50.000	0.00	0.00	44.64	3.41
3791	6783	1.886542	CCACCAGTTTTCCTGCCTAAC	59.113	52.381	0.00	0.00	40.06	2.34
3796	6793	0.310854	CGAACCACCAGTTTTCCTGC	59.689	55.000	0.00	0.00	39.40	4.85

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.