AutoCloner

Multiple sequence alignment - TraesCS5B01G255000

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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	TraesCS5B01G255000	chr5B	100.000	2528	0	0	508	3035	437571555	437574082	0.000000e+00	4669.0
1	TraesCS5B01G255000	chr5B	96.629	2106	68	3	931	3035	437601255	437603358	0.000000e+00	3493.0
2	TraesCS5B01G255000	chr5B	92.836	1661	89	20	978	2630	437538094	437536456	0.000000e+00	2381.0
3	TraesCS5B01G255000	chr5B	92.586	1659	89	17	975	2630	437305589	437303962	0.000000e+00	2351.0
4	TraesCS5B01G255000	chr5B	90.685	1621	100	21	781	2359	437807236	437808847	0.000000e+00	2109.0
5	TraesCS5B01G255000	chr5B	89.945	1442	97	27	781	2198	437368293	437366876	0.000000e+00	1816.0
6	TraesCS5B01G255000	chr5B	100.000	259	0	0	1	259	437571048	437571306	2.120000e-131	479.0
7	TraesCS5B01G255000	chr5B	91.636	275	21	2	2762	3035	425718222	425718495	2.210000e-101	379.0
8	TraesCS5B01G255000	chr5B	90.397	302	8	4	635	935	437595842	437596123	7.940000e-101	377.0
9	TraesCS5B01G255000	chr5B	91.241	274	22	2	2762	3035	705991123	705991394	3.700000e-99	372.0
10	TraesCS5B01G255000	chr5B	91.353	266	23	0	2762	3027	166841524	166841259	6.180000e-97	364.0
11	TraesCS5B01G255000	chr5B	95.098	102	5	0	518	619	437595756	437595857	8.710000e-36	161.0
12	TraesCS5B01G255000	chr5B	100.000	38	0	0	1	38	437595294	437595331	1.510000e-08	71.3
13	TraesCS5B01G255000	chr5D	94.624	1395	47	7	634	2015	369076018	369077397	0.000000e+00	2135.0
14	TraesCS5B01G255000	chr5D	94.322	1321	61	6	975	2295	369061540	369060234	0.000000e+00	2012.0
15	TraesCS5B01G255000	chr5D	93.968	315	13	3	2043	2356	369058168	369057859	3.540000e-129	472.0
16	TraesCS5B01G255000	chr5D	92.056	214	10	7	2416	2626	369057858	369057649	8.230000e-76	294.0
17	TraesCS5B01G255000	chr5D	97.059	102	3	0	518	619	369075933	369076034	4.020000e-39	172.0
18	TraesCS5B01G255000	chr5D	83.871	124	10	3	2631	2754	369057612	369057499	3.200000e-20	110.0
19	TraesCS5B01G255000	chr5D	82.540	126	11	5	2627	2750	369058399	369058283	1.930000e-17	100.0
20	TraesCS5B01G255000	chr5D	79.085	153	9	12	781	912	369061736	369061586	1.940000e-12	84.2
21	TraesCS5B01G255000	chr5D	100.000	38	0	0	1	38	369075601	369075638	1.510000e-08	71.3
22	TraesCS5B01G255000	chr5A	89.477	1492	110	29	781	2256	470667556	470669016	0.000000e+00	1842.0
23	TraesCS5B01G255000	chr5A	89.898	1465	87	26	658	2078	471511174	471512621	0.000000e+00	1829.0
24	TraesCS5B01G255000	chr5A	88.684	866	60	20	804	1650	471503928	471504774	0.000000e+00	1022.0
25	TraesCS5B01G255000	chr5A	77.903	267	43	8	2116	2370	471506622	471506884	5.240000e-33	152.0
26	TraesCS5B01G255000	chr5A	89.109	101	11	0	2654	2754	470670694	470670794	3.180000e-25	126.0
27	TraesCS5B01G255000	chr5A	91.463	82	7	0	656	737	471479886	471479967	2.470000e-21	113.0
28	TraesCS5B01G255000	chr5A	92.537	67	5	0	518	584	471479782	471479848	2.490000e-16	97.1
29	TraesCS5B01G255000	chr5A	92.683	41	2	1	2108	2148	471460657	471460618	1.180000e-04	58.4
30	TraesCS5B01G255000	chr6B	94.662	281	14	1	2755	3035	508601804	508601525	4.650000e-118	435.0
31	TraesCS5B01G255000	chr6B	93.066	274	19	0	2762	3035	670908976	670908703	4.710000e-108	401.0
32	TraesCS5B01G255000	chr6B	92.308	273	21	0	2763	3035	179720219	179720491	3.670000e-104	388.0
33	TraesCS5B01G255000	chr2B	92.000	275	22	0	2761	3035	131111115	131110841	1.320000e-103	387.0
34	TraesCS5B01G255000	chr2A	91.197	284	24	1	2750	3033	630741770	630742052	4.750000e-103	385.0

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	TraesCS5B01G255000	chr5B	437571048	437574082	3034	False	2574.000000	4669	100.000000	1	3035	2	chr5B.!!$F5	3034
1	TraesCS5B01G255000	chr5B	437601255	437603358	2103	False	3493.000000	3493	96.629000	931	3035	1	chr5B.!!$F2	2104
2	TraesCS5B01G255000	chr5B	437536456	437538094	1638	True	2381.000000	2381	92.836000	978	2630	1	chr5B.!!$R4	1652
3	TraesCS5B01G255000	chr5B	437303962	437305589	1627	True	2351.000000	2351	92.586000	975	2630	1	chr5B.!!$R2	1655
4	TraesCS5B01G255000	chr5B	437807236	437808847	1611	False	2109.000000	2109	90.685000	781	2359	1	chr5B.!!$F3	1578
5	TraesCS5B01G255000	chr5B	437366876	437368293	1417	True	1816.000000	1816	89.945000	781	2198	1	chr5B.!!$R3	1417
6	TraesCS5B01G255000	chr5B	437595294	437596123	829	False	203.100000	377	95.165000	1	935	3	chr5B.!!$F6	934
7	TraesCS5B01G255000	chr5D	369075601	369077397	1796	False	792.766667	2135	97.227667	1	2015	3	chr5D.!!$F1	2014
8	TraesCS5B01G255000	chr5D	369057499	369061736	4237	True	512.033333	2012	87.640333	781	2754	6	chr5D.!!$R1	1973
9	TraesCS5B01G255000	chr5A	471511174	471512621	1447	False	1829.000000	1829	89.898000	658	2078	1	chr5A.!!$F1	1420
10	TraesCS5B01G255000	chr5A	470667556	470670794	3238	False	984.000000	1842	89.293000	781	2754	2	chr5A.!!$F2	1973
11	TraesCS5B01G255000	chr5A	471503928	471506884	2956	False	587.000000	1022	83.293500	804	2370	2	chr5A.!!$F4	1566

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
64	65	0.103208	GGGCTACATGTCGTCTCCAG	59.897	60.0	0.0	0.0	0.0	3.86	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2229	6201	0.81804	AACAAGGCGCCTTTTCTCGT	60.818	50.0	38.6	28.45	33.42	4.18	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
38	39	4.222847	CTCGGGGCTTAGACGGGC	62.223	72.222	0.00	0.00	0.00	6.13
39	40	4.772231	TCGGGGCTTAGACGGGCT	62.772	66.667	0.00	0.00	0.00	5.19
40	41	2.836360	CGGGGCTTAGACGGGCTA	60.836	66.667	0.00	0.00	0.00	3.93
41	42	2.820261	GGGGCTTAGACGGGCTAC	59.180	66.667	0.00	0.00	0.00	3.58
51	52	3.037428	CGGGCTACGTAGGGCTAC	58.963	66.667	23.47	6.66	37.93	3.58
52	53	1.825191	CGGGCTACGTAGGGCTACA	60.825	63.158	23.47	0.00	37.93	2.74
53	54	1.177256	CGGGCTACGTAGGGCTACAT	61.177	60.000	23.47	0.00	37.93	2.29
54	55	0.317479	GGGCTACGTAGGGCTACATG	59.683	60.000	23.47	0.00	35.87	3.21
56	57	1.000496	GGCTACGTAGGGCTACATGTC	60.000	57.143	23.47	3.11	35.87	3.06
58	59	1.945394	CTACGTAGGGCTACATGTCGT	59.055	52.381	15.07	6.68	35.87	4.34
59	60	0.737219	ACGTAGGGCTACATGTCGTC	59.263	55.000	0.00	0.00	35.87	4.20
61	62	1.002684	CGTAGGGCTACATGTCGTCTC	60.003	57.143	0.00	0.00	35.87	3.36
63	64	0.324368	AGGGCTACATGTCGTCTCCA	60.324	55.000	0.00	0.00	0.00	3.86
64	65	0.103208	GGGCTACATGTCGTCTCCAG	59.897	60.000	0.00	0.00	0.00	3.86
66	67	0.103208	GCTACATGTCGTCTCCAGGG	59.897	60.000	0.00	0.00	0.00	4.45
67	68	1.475403	CTACATGTCGTCTCCAGGGT	58.525	55.000	0.00	0.00	0.00	4.34
68	69	1.405821	CTACATGTCGTCTCCAGGGTC	59.594	57.143	0.00	0.00	0.00	4.46
70	71	0.608130	CATGTCGTCTCCAGGGTCAA	59.392	55.000	0.00	0.00	0.00	3.18
71	72	0.608640	ATGTCGTCTCCAGGGTCAAC	59.391	55.000	0.00	0.00	0.00	3.18
72	73	0.469331	TGTCGTCTCCAGGGTCAACT	60.469	55.000	0.00	0.00	0.00	3.16
73	74	1.202964	TGTCGTCTCCAGGGTCAACTA	60.203	52.381	0.00	0.00	0.00	2.24
74	75	1.201880	GTCGTCTCCAGGGTCAACTAC	59.798	57.143	0.00	0.00	0.00	2.73
82	83	3.976758	GGTCAACTACCGCAACCC	58.023	61.111	0.00	0.00	38.88	4.11
83	84	1.373812	GGTCAACTACCGCAACCCT	59.626	57.895	0.00	0.00	38.88	4.34
84	85	0.609662	GGTCAACTACCGCAACCCTA	59.390	55.000	0.00	0.00	38.88	3.53
86	87	0.244450	TCAACTACCGCAACCCTACG	59.756	55.000	0.00	0.00	0.00	3.51
89	90	1.098050	ACTACCGCAACCCTACGTAG	58.902	55.000	15.92	15.92	0.00	3.51
90	91	1.340017	ACTACCGCAACCCTACGTAGA	60.340	52.381	24.15	0.00	0.00	2.59
91	92	1.745087	CTACCGCAACCCTACGTAGAA	59.255	52.381	24.15	0.00	0.00	2.10
92	93	1.188863	ACCGCAACCCTACGTAGAAT	58.811	50.000	24.15	8.40	0.00	2.40
93	94	1.551883	ACCGCAACCCTACGTAGAATT	59.448	47.619	24.15	13.91	0.00	2.17
94	95	2.027837	ACCGCAACCCTACGTAGAATTT	60.028	45.455	24.15	10.35	0.00	1.82
104	151	0.450184	CGTAGAATTTTGGGGGTGCG	59.550	55.000	0.00	0.00	0.00	5.34
108	155	1.203075	AGAATTTTGGGGGTGCGGTAA	60.203	47.619	0.00	0.00	0.00	2.85
109	156	1.828595	GAATTTTGGGGGTGCGGTAAT	59.171	47.619	0.00	0.00	0.00	1.89
157	204	2.113433	GCCGCCGAGACAGTAGAGA	61.113	63.158	0.00	0.00	0.00	3.10
158	205	1.654954	GCCGCCGAGACAGTAGAGAA	61.655	60.000	0.00	0.00	0.00	2.87
179	234	0.373024	GCAACTCGAGCAAGATGAGC	59.627	55.000	13.61	1.41	32.98	4.26
180	235	1.005340	CAACTCGAGCAAGATGAGCC	58.995	55.000	13.61	0.00	32.98	4.70
188	243	2.510238	AAGATGAGCCGTGCGAGC	60.510	61.111	0.00	0.00	0.00	5.03
214	313	4.589908	GGGTCACAAAGATCAGTGGTTAT	58.410	43.478	11.46	0.00	36.43	1.89
218	317	4.012374	CACAAAGATCAGTGGTTATGCCT	58.988	43.478	0.00	0.00	38.35	4.75
219	318	5.045942	TCACAAAGATCAGTGGTTATGCCTA	60.046	40.000	11.46	0.00	38.35	3.93
221	320	5.185454	CAAAGATCAGTGGTTATGCCTACA	58.815	41.667	0.00	0.00	38.35	2.74
222	321	5.636903	AAGATCAGTGGTTATGCCTACAT	57.363	39.130	0.00	0.00	40.49	2.29
223	322	5.636903	AGATCAGTGGTTATGCCTACATT	57.363	39.130	0.00	0.00	37.74	2.71
224	323	5.371526	AGATCAGTGGTTATGCCTACATTG	58.628	41.667	0.00	0.00	37.74	2.82
225	324	3.884895	TCAGTGGTTATGCCTACATTGG	58.115	45.455	0.00	0.00	37.74	3.16
226	325	3.521531	TCAGTGGTTATGCCTACATTGGA	59.478	43.478	0.00	0.00	37.74	3.53
229	328	3.118038	GTGGTTATGCCTACATTGGAGGA	60.118	47.826	19.75	4.39	37.74	3.71
230	329	3.525609	TGGTTATGCCTACATTGGAGGAA	59.474	43.478	19.75	8.93	37.74	3.36
231	330	4.137543	GGTTATGCCTACATTGGAGGAAG	58.862	47.826	19.75	0.00	37.74	3.46
232	331	4.137543	GTTATGCCTACATTGGAGGAAGG	58.862	47.826	19.75	3.35	37.74	3.46
233	332	1.668826	TGCCTACATTGGAGGAAGGT	58.331	50.000	19.75	0.00	35.99	3.50
234	333	1.992557	TGCCTACATTGGAGGAAGGTT	59.007	47.619	19.75	0.00	35.99	3.50
235	334	2.378547	TGCCTACATTGGAGGAAGGTTT	59.621	45.455	19.75	0.00	35.99	3.27
236	335	3.181423	TGCCTACATTGGAGGAAGGTTTT	60.181	43.478	19.75	0.00	35.99	2.43
237	336	3.193479	GCCTACATTGGAGGAAGGTTTTG	59.807	47.826	19.75	0.00	35.99	2.44
238	337	3.193479	CCTACATTGGAGGAAGGTTTTGC	59.807	47.826	9.58	0.00	35.99	3.68
239	338	1.613437	ACATTGGAGGAAGGTTTTGCG	59.387	47.619	0.00	0.00	0.00	4.85
240	339	1.067635	CATTGGAGGAAGGTTTTGCGG	60.068	52.381	0.00	0.00	0.00	5.69
241	340	0.825840	TTGGAGGAAGGTTTTGCGGG	60.826	55.000	0.00	0.00	0.00	6.13
242	341	1.977009	GGAGGAAGGTTTTGCGGGG	60.977	63.158	0.00	0.00	0.00	5.73
243	342	2.600470	AGGAAGGTTTTGCGGGGC	60.600	61.111	0.00	0.00	0.00	5.80
249	348	2.503382	GGTTTTGCGGGGCAGGAAA	61.503	57.895	0.00	0.00	40.61	3.13
563	690	2.098117	CCGATCCAAAACAAGAGCATCC	59.902	50.000	0.00	0.00	33.66	3.51
593	720	3.128415	TGGCACATAATGAAACACGATGG	59.872	43.478	0.00	0.00	0.00	3.51
617	744	9.906660	TGGTACACATTGAAATAAAGAATGAAC	57.093	29.630	0.00	0.00	32.47	3.18
618	745	9.906660	GGTACACATTGAAATAAAGAATGAACA	57.093	29.630	0.00	0.00	32.47	3.18
620	747	8.816640	ACACATTGAAATAAAGAATGAACACC	57.183	30.769	0.00	0.00	32.47	4.16
621	748	7.872483	ACACATTGAAATAAAGAATGAACACCC	59.128	33.333	0.00	0.00	32.47	4.61
622	749	7.331687	CACATTGAAATAAAGAATGAACACCCC	59.668	37.037	0.00	0.00	32.47	4.95
623	750	7.235399	ACATTGAAATAAAGAATGAACACCCCT	59.765	33.333	0.00	0.00	32.47	4.79
624	751	8.748412	CATTGAAATAAAGAATGAACACCCCTA	58.252	33.333	0.00	0.00	30.03	3.53
625	752	8.713708	TTGAAATAAAGAATGAACACCCCTAA	57.286	30.769	0.00	0.00	0.00	2.69
626	753	8.713708	TGAAATAAAGAATGAACACCCCTAAA	57.286	30.769	0.00	0.00	0.00	1.85
627	754	9.148879	TGAAATAAAGAATGAACACCCCTAAAA	57.851	29.630	0.00	0.00	0.00	1.52
628	755	9.990360	GAAATAAAGAATGAACACCCCTAAAAA	57.010	29.630	0.00	0.00	0.00	1.94
701	828	9.180678	ACAAAAACAATTAGCGTGAATCTTAAG	57.819	29.630	0.00	0.00	0.00	1.85
835	991	2.167398	TACAGTCTCGCCCAAGCCAC	62.167	60.000	0.00	0.00	34.57	5.01
836	992	4.379243	AGTCTCGCCCAAGCCACG	62.379	66.667	0.00	0.00	34.57	4.94
1008	1224	1.536418	CTCCTCCCCGATGGCCATA	60.536	63.158	20.84	0.64	0.00	2.74
1010	1226	1.127567	TCCTCCCCGATGGCCATAAG	61.128	60.000	20.84	15.83	0.00	1.73
1705	2727	3.682292	GACATGTGGTCCCTCGGCC	62.682	68.421	1.15	0.00	40.83	6.13
2229	6201	4.838046	TTCGCAGTTGACCACGAA	57.162	50.000	0.00	5.15	41.76	3.85
2414	6389	3.483869	GGGGAGAGCAGGGCGAAT	61.484	66.667	0.00	0.00	0.00	3.34
2453	6428	6.200808	GTGGCATTTGTTCATTTTCCTTTTG	58.799	36.000	0.00	0.00	0.00	2.44
2791	8148	5.405331	AAAGCTAAAACGTCAGTTGACTC	57.595	39.130	10.27	0.00	42.66	3.36
2821	8178	4.823276	GCGCTAGCATGTCTGACT	57.177	55.556	16.45	0.00	44.35	3.41
2853	8210	1.507140	CCAGCCACCTAGGGATTGTA	58.493	55.000	14.81	0.00	38.09	2.41
2902	8259	7.964666	AGTTCTAAAGAATGTCTAGCTACCT	57.035	36.000	0.00	0.00	36.33	3.08
2913	8270	0.041238	TAGCTACCTGGTGAGCCACT	59.959	55.000	10.23	2.40	40.46	4.00
2960	8317	4.703093	CCGTAGCTTAAATCCCTGGAAAAA	59.297	41.667	0.00	0.00	0.00	1.94
3024	8381	0.321653	ATTTCTGCGGTGACTCCCAC	60.322	55.000	0.00	0.00	44.95	4.61

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
38	39	1.945394	ACGACATGTAGCCCTACGTAG	59.055	52.381	15.92	15.92	38.85	3.51
39	40	1.942657	GACGACATGTAGCCCTACGTA	59.057	52.381	5.81	0.00	38.85	3.57
40	41	0.737219	GACGACATGTAGCCCTACGT	59.263	55.000	5.81	6.04	38.85	3.57
41	42	1.002684	GAGACGACATGTAGCCCTACG	60.003	57.143	5.81	2.60	38.85	3.51
42	43	1.337387	GGAGACGACATGTAGCCCTAC	59.663	57.143	5.81	1.00	36.63	3.18
43	44	1.064240	TGGAGACGACATGTAGCCCTA	60.064	52.381	5.81	0.00	0.00	3.53
44	45	0.324368	TGGAGACGACATGTAGCCCT	60.324	55.000	5.81	3.68	0.00	5.19
46	47	0.103208	CCTGGAGACGACATGTAGCC	59.897	60.000	5.81	0.24	0.00	3.93
48	49	1.405821	GACCCTGGAGACGACATGTAG	59.594	57.143	0.00	0.00	0.00	2.74
49	50	1.272258	TGACCCTGGAGACGACATGTA	60.272	52.381	0.00	0.00	0.00	2.29
50	51	0.541998	TGACCCTGGAGACGACATGT	60.542	55.000	0.00	0.00	0.00	3.21
51	52	0.608130	TTGACCCTGGAGACGACATG	59.392	55.000	0.00	0.00	0.00	3.21
52	53	0.608640	GTTGACCCTGGAGACGACAT	59.391	55.000	0.00	0.00	0.00	3.06
53	54	0.469331	AGTTGACCCTGGAGACGACA	60.469	55.000	0.00	0.00	0.00	4.35
54	55	1.201880	GTAGTTGACCCTGGAGACGAC	59.798	57.143	0.00	0.00	0.00	4.34
56	57	0.531200	GGTAGTTGACCCTGGAGACG	59.469	60.000	0.00	0.00	43.25	4.18
58	59	1.255667	GCGGTAGTTGACCCTGGAGA	61.256	60.000	0.00	0.00	46.81	3.71
59	60	1.218316	GCGGTAGTTGACCCTGGAG	59.782	63.158	0.00	0.00	46.81	3.86
61	62	0.953960	GTTGCGGTAGTTGACCCTGG	60.954	60.000	0.00	0.00	46.81	4.45
63	64	1.373812	GGTTGCGGTAGTTGACCCT	59.626	57.895	0.00	0.00	46.81	4.34
64	65	1.673337	GGGTTGCGGTAGTTGACCC	60.673	63.158	0.00	0.00	46.81	4.46
66	67	1.718396	GTAGGGTTGCGGTAGTTGAC	58.282	55.000	0.00	0.00	0.00	3.18
67	68	0.244450	CGTAGGGTTGCGGTAGTTGA	59.756	55.000	0.00	0.00	0.00	3.18
68	69	0.037975	ACGTAGGGTTGCGGTAGTTG	60.038	55.000	0.00	0.00	36.68	3.16
70	71	1.098050	CTACGTAGGGTTGCGGTAGT	58.902	55.000	15.07	0.00	36.68	2.73
71	72	1.382522	TCTACGTAGGGTTGCGGTAG	58.617	55.000	22.01	0.00	36.68	3.18
72	73	1.832883	TTCTACGTAGGGTTGCGGTA	58.167	50.000	22.01	0.00	36.68	4.02
73	74	1.188863	ATTCTACGTAGGGTTGCGGT	58.811	50.000	22.01	0.00	36.68	5.68
74	75	2.304751	AATTCTACGTAGGGTTGCGG	57.695	50.000	22.01	0.00	36.68	5.69
78	79	3.308617	CCCCCAAAATTCTACGTAGGGTT	60.309	47.826	22.01	13.84	32.90	4.11
80	81	2.240414	ACCCCCAAAATTCTACGTAGGG	59.760	50.000	22.01	14.84	38.04	3.53
81	82	3.275999	CACCCCCAAAATTCTACGTAGG	58.724	50.000	22.01	5.31	0.00	3.18
82	83	2.681344	GCACCCCCAAAATTCTACGTAG	59.319	50.000	16.73	16.73	0.00	3.51
83	84	2.713877	GCACCCCCAAAATTCTACGTA	58.286	47.619	0.00	0.00	0.00	3.57
84	85	1.541379	GCACCCCCAAAATTCTACGT	58.459	50.000	0.00	0.00	0.00	3.57
86	87	0.815095	CCGCACCCCCAAAATTCTAC	59.185	55.000	0.00	0.00	0.00	2.59
89	90	1.258676	TTACCGCACCCCCAAAATTC	58.741	50.000	0.00	0.00	0.00	2.17
90	91	1.945580	ATTACCGCACCCCCAAAATT	58.054	45.000	0.00	0.00	0.00	1.82
91	92	1.552792	CAATTACCGCACCCCCAAAAT	59.447	47.619	0.00	0.00	0.00	1.82
92	93	0.969894	CAATTACCGCACCCCCAAAA	59.030	50.000	0.00	0.00	0.00	2.44
93	94	0.112606	TCAATTACCGCACCCCCAAA	59.887	50.000	0.00	0.00	0.00	3.28
94	95	0.609681	GTCAATTACCGCACCCCCAA	60.610	55.000	0.00	0.00	0.00	4.12
108	155	2.285368	TCCGCCTCCAGGGTCAAT	60.285	61.111	0.00	0.00	37.43	2.57
109	156	3.319198	GTCCGCCTCCAGGGTCAA	61.319	66.667	0.00	0.00	37.43	3.18
143	190	1.464734	TGCCTTCTCTACTGTCTCGG	58.535	55.000	0.00	0.00	0.00	4.63
145	192	3.426963	CGAGTTGCCTTCTCTACTGTCTC	60.427	52.174	0.00	0.00	0.00	3.36
157	204	1.002430	TCATCTTGCTCGAGTTGCCTT	59.998	47.619	15.13	0.00	0.00	4.35
158	205	0.610174	TCATCTTGCTCGAGTTGCCT	59.390	50.000	15.13	0.00	0.00	4.75
188	243	1.361668	CTGATCTTTGTGACCCGCGG	61.362	60.000	21.04	21.04	0.00	6.46
190	245	0.798776	CACTGATCTTTGTGACCCGC	59.201	55.000	7.86	0.00	36.38	6.13
191	246	1.270839	ACCACTGATCTTTGTGACCCG	60.271	52.381	13.06	2.79	36.38	5.28
192	247	2.568623	ACCACTGATCTTTGTGACCC	57.431	50.000	13.06	0.00	36.38	4.46
194	249	4.142600	GGCATAACCACTGATCTTTGTGAC	60.143	45.833	13.06	0.00	38.86	3.67
195	250	4.009675	GGCATAACCACTGATCTTTGTGA	58.990	43.478	13.06	0.00	38.86	3.58
196	251	4.012374	AGGCATAACCACTGATCTTTGTG	58.988	43.478	0.00	0.89	43.14	3.33
214	313	1.668826	ACCTTCCTCCAATGTAGGCA	58.331	50.000	0.00	0.00	33.84	4.75
218	317	2.817258	CGCAAAACCTTCCTCCAATGTA	59.183	45.455	0.00	0.00	0.00	2.29
219	318	1.613437	CGCAAAACCTTCCTCCAATGT	59.387	47.619	0.00	0.00	0.00	2.71
221	320	1.256812	CCGCAAAACCTTCCTCCAAT	58.743	50.000	0.00	0.00	0.00	3.16
222	321	0.825840	CCCGCAAAACCTTCCTCCAA	60.826	55.000	0.00	0.00	0.00	3.53
223	322	1.228429	CCCGCAAAACCTTCCTCCA	60.228	57.895	0.00	0.00	0.00	3.86
224	323	1.977009	CCCCGCAAAACCTTCCTCC	60.977	63.158	0.00	0.00	0.00	4.30
225	324	2.636412	GCCCCGCAAAACCTTCCTC	61.636	63.158	0.00	0.00	0.00	3.71
226	325	2.600470	GCCCCGCAAAACCTTCCT	60.600	61.111	0.00	0.00	0.00	3.36
229	328	2.917227	CCTGCCCCGCAAAACCTT	60.917	61.111	0.00	0.00	38.41	3.50
230	329	2.937959	TTTCCTGCCCCGCAAAACCT	62.938	55.000	0.00	0.00	38.41	3.50
231	330	2.034048	TTTTCCTGCCCCGCAAAACC	62.034	55.000	0.00	0.00	38.41	3.27
232	331	0.034756	ATTTTCCTGCCCCGCAAAAC	59.965	50.000	0.00	0.00	38.41	2.43
233	332	0.034616	CATTTTCCTGCCCCGCAAAA	59.965	50.000	0.00	0.00	38.41	2.44
234	333	0.829602	TCATTTTCCTGCCCCGCAAA	60.830	50.000	0.00	0.00	38.41	3.68
235	334	0.829602	TTCATTTTCCTGCCCCGCAA	60.830	50.000	0.00	0.00	38.41	4.85
236	335	0.614415	ATTCATTTTCCTGCCCCGCA	60.614	50.000	0.00	0.00	36.92	5.69
237	336	0.179103	CATTCATTTTCCTGCCCCGC	60.179	55.000	0.00	0.00	0.00	6.13
238	337	0.461135	CCATTCATTTTCCTGCCCCG	59.539	55.000	0.00	0.00	0.00	5.73
239	338	1.571955	ACCATTCATTTTCCTGCCCC	58.428	50.000	0.00	0.00	0.00	5.80
563	690	8.161610	CGTGTTTCATTATGTGCCAATAAAAAG	58.838	33.333	0.00	0.00	0.00	2.27
682	809	5.484173	TGCCTTAAGATTCACGCTAATTG	57.516	39.130	3.36	0.00	0.00	2.32
701	828	1.610522	GCATGGATATCTGTGGTTGCC	59.389	52.381	2.05	0.00	0.00	4.52
752	895	1.676006	CAAAGGAACTGCGGTCACTTT	59.324	47.619	17.23	17.23	40.86	2.66
2229	6201	0.818040	AACAAGGCGCCTTTTCTCGT	60.818	50.000	38.60	28.45	33.42	4.18
2267	6239	2.034066	CACGTGCATGGGGTCCTT	59.966	61.111	11.36	0.00	0.00	3.36
2414	6389	1.382146	CCACGGGCCCTAAGGTAGA	60.382	63.158	22.43	0.00	34.57	2.59
2453	6428	8.023706	GGATGTTCATTTTCTAGGAAGTTCAAC	58.976	37.037	5.01	0.00	0.00	3.18
2644	6691	4.736793	GCAACTTTCAGAAATGTGTGTCTG	59.263	41.667	0.00	0.00	42.23	3.51
2781	8138	6.348458	CGCCAAATGAATAAAGAGTCAACTGA	60.348	38.462	0.00	0.00	32.51	3.41
2788	8145	4.035675	GCTAGCGCCAAATGAATAAAGAGT	59.964	41.667	2.29	0.00	0.00	3.24
2791	8148	4.291540	TGCTAGCGCCAAATGAATAAAG	57.708	40.909	10.77	0.00	34.43	1.85
2821	8178	1.208052	GTGGCTGGCTGATTCTCTACA	59.792	52.381	2.00	0.00	0.00	2.74
2902	8259	4.260985	CATTGTAATACAGTGGCTCACCA	58.739	43.478	7.88	0.00	46.51	4.17
2937	8294	3.553828	TTCCAGGGATTTAAGCTACGG	57.446	47.619	0.00	0.00	0.00	4.02

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.