AutoCloner

Multiple sequence alignment - TraesCS2D01G529700

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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	TraesCS2D01G529700	chr2D	100.000	2597	0	0	1	2597	616756504	616753908	0.000000e+00	4796
1	TraesCS2D01G529700	chr2D	93.143	700	44	3	1899	2597	354034300	354033604	0.000000e+00	1024
2	TraesCS2D01G529700	chr2D	92.439	701	49	4	1899	2597	51510046	51509348	0.000000e+00	998
3	TraesCS2D01G529700	chr2D	96.667	90	2	1	522	611	616755852	616755764	5.790000e-32	148
4	TraesCS2D01G529700	chr2D	96.667	90	2	1	653	741	616755983	616755894	5.790000e-32	148
5	TraesCS2D01G529700	chr2B	93.739	1166	71	2	738	1902	752298874	752300038	0.000000e+00	1748
6	TraesCS2D01G529700	chr2B	87.078	681	60	5	3	663	752298181	752298853	0.000000e+00	745
7	TraesCS2D01G529700	chr2B	97.436	78	2	0	661	738	752298721	752298798	1.620000e-27	134
8	TraesCS2D01G529700	chr4B	87.066	951	115	7	738	1685	542582434	542583379	0.000000e+00	1068
9	TraesCS2D01G529700	chr4D	87.039	949	117	5	740	1685	438681245	438682190	0.000000e+00	1066
10	TraesCS2D01G529700	chr4D	86.501	363	43	5	1	359	244146309	244145949	6.740000e-106	394
11	TraesCS2D01G529700	chr4D	85.154	357	50	3	1	356	388331328	388331682	1.900000e-96	363
12	TraesCS2D01G529700	chr4A	86.301	949	124	5	740	1685	28185897	28186842	0.000000e+00	1027
13	TraesCS2D01G529700	chr4A	82.659	173	25	4	1683	1854	576219547	576219379	5.790000e-32	148
14	TraesCS2D01G529700	chr5D	92.439	701	47	5	1899	2597	301919812	301920508	0.000000e+00	996
15	TraesCS2D01G529700	chr3D	92.429	700	47	5	1899	2596	480927308	480928003	0.000000e+00	994
16	TraesCS2D01G529700	chr3D	92.000	700	54	2	1899	2597	188306586	188305888	0.000000e+00	981
17	TraesCS2D01G529700	chr6D	92.297	701	50	4	1899	2597	424222529	424221831	0.000000e+00	992
18	TraesCS2D01G529700	chr6D	88.219	365	32	7	1	356	268195994	268195632	2.390000e-115	425
19	TraesCS2D01G529700	chr1D	92.154	701	50	4	1899	2597	277330362	277331059	0.000000e+00	985
20	TraesCS2D01G529700	chr1D	92.143	700	51	4	1899	2596	316833613	316834310	0.000000e+00	985
21	TraesCS2D01G529700	chr1D	84.807	362	46	5	1	356	351433131	351432773	3.180000e-94	355
22	TraesCS2D01G529700	chr7D	92.000	700	55	1	1899	2597	202371944	202371245	0.000000e+00	981
23	TraesCS2D01G529700	chr7D	89.437	426	42	2	1263	1685	612164032	612163607	3.800000e-148	534
24	TraesCS2D01G529700	chr7D	82.486	531	85	8	738	1267	612376491	612377014	2.360000e-125	459
25	TraesCS2D01G529700	chr7D	88.056	360	38	3	1	360	269920443	269920089	3.090000e-114	422
26	TraesCS2D01G529700	chr7D	87.584	298	34	3	359	656	612376169	612376463	2.470000e-90	342
27	TraesCS2D01G529700	chr6A	87.328	363	36	4	1	356	301670137	301670496	8.650000e-110	407
28	TraesCS2D01G529700	chr3A	85.246	366	44	9	1	356	622261419	622261784	4.080000e-98	368
29	TraesCS2D01G529700	chr7B	84.958	359	47	6	1	356	728796875	728796521	8.840000e-95	357
30	TraesCS2D01G529700	chr7B	82.249	169	27	3	1688	1855	614664488	614664654	2.690000e-30	143
31	TraesCS2D01G529700	chr1B	85.154	357	39	10	1	354	141622372	141622717	1.140000e-93	353
32	TraesCS2D01G529700	chr3B	80.711	197	37	1	1687	1883	639369044	639368849	4.480000e-33	152
33	TraesCS2D01G529700	chr5B	83.117	154	24	1	1687	1840	283629200	283629351	3.480000e-29	139

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	TraesCS2D01G529700	chr2D	616753908	616756504	2596	True	1697.333333	4796	97.778	1	2597	3	chr2D.!!$R3	2596
1	TraesCS2D01G529700	chr2D	354033604	354034300	696	True	1024.000000	1024	93.143	1899	2597	1	chr2D.!!$R2	698
2	TraesCS2D01G529700	chr2D	51509348	51510046	698	True	998.000000	998	92.439	1899	2597	1	chr2D.!!$R1	698
3	TraesCS2D01G529700	chr2B	752298181	752300038	1857	False	875.666667	1748	92.751	3	1902	3	chr2B.!!$F1	1899
4	TraesCS2D01G529700	chr4B	542582434	542583379	945	False	1068.000000	1068	87.066	738	1685	1	chr4B.!!$F1	947
5	TraesCS2D01G529700	chr4D	438681245	438682190	945	False	1066.000000	1066	87.039	740	1685	1	chr4D.!!$F2	945
6	TraesCS2D01G529700	chr4A	28185897	28186842	945	False	1027.000000	1027	86.301	740	1685	1	chr4A.!!$F1	945
7	TraesCS2D01G529700	chr5D	301919812	301920508	696	False	996.000000	996	92.439	1899	2597	1	chr5D.!!$F1	698
8	TraesCS2D01G529700	chr3D	480927308	480928003	695	False	994.000000	994	92.429	1899	2596	1	chr3D.!!$F1	697
9	TraesCS2D01G529700	chr3D	188305888	188306586	698	True	981.000000	981	92.000	1899	2597	1	chr3D.!!$R1	698
10	TraesCS2D01G529700	chr6D	424221831	424222529	698	True	992.000000	992	92.297	1899	2597	1	chr6D.!!$R2	698
11	TraesCS2D01G529700	chr1D	277330362	277331059	697	False	985.000000	985	92.154	1899	2597	1	chr1D.!!$F1	698
12	TraesCS2D01G529700	chr1D	316833613	316834310	697	False	985.000000	985	92.143	1899	2596	1	chr1D.!!$F2	697
13	TraesCS2D01G529700	chr7D	202371245	202371944	699	True	981.000000	981	92.000	1899	2597	1	chr7D.!!$R1	698
14	TraesCS2D01G529700	chr7D	612376169	612377014	845	False	400.500000	459	85.035	359	1267	2	chr7D.!!$F1	908

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
99	100	0.251341	ATGTGGGTTGTGCTTCCCTC	60.251	55.0	0.0	0.0	43.74	4.3	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1699	1723	0.108138	CTAAGGAACCGAGGGCACAG	60.108	60.0	0.0	0.0	0.0	3.66	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
99	100	0.251341	ATGTGGGTTGTGCTTCCCTC	60.251	55.000	0.00	0.00	43.74	4.30
100	101	1.966451	GTGGGTTGTGCTTCCCTCG	60.966	63.158	0.00	0.00	43.74	4.63
137	138	1.497286	ACTTCTTTGGCCCAACAGGTA	59.503	47.619	0.00	0.00	38.26	3.08
139	140	2.507407	TCTTTGGCCCAACAGGTATC	57.493	50.000	0.00	0.00	38.26	2.24
144	145	2.840511	TGGCCCAACAGGTATCTTCTA	58.159	47.619	0.00	0.00	38.26	2.10
147	148	3.181464	GGCCCAACAGGTATCTTCTAGTC	60.181	52.174	0.00	0.00	38.26	2.59
187	188	4.222124	AGTTTCACTGTGTTTGGACTCT	57.778	40.909	7.79	0.00	0.00	3.24
188	189	3.941483	AGTTTCACTGTGTTTGGACTCTG	59.059	43.478	7.79	0.00	0.00	3.35
193	194	3.016736	ACTGTGTTTGGACTCTGTTTGG	58.983	45.455	0.00	0.00	30.47	3.28
204	205	7.214467	TGGACTCTGTTTGGTATTGATTTTC	57.786	36.000	0.00	0.00	0.00	2.29
207	208	6.681777	ACTCTGTTTGGTATTGATTTTCTGC	58.318	36.000	0.00	0.00	0.00	4.26
209	210	5.471797	TCTGTTTGGTATTGATTTTCTGCGA	59.528	36.000	0.00	0.00	0.00	5.10
210	211	6.016693	TCTGTTTGGTATTGATTTTCTGCGAA	60.017	34.615	0.00	0.00	0.00	4.70
211	212	6.148948	TGTTTGGTATTGATTTTCTGCGAAG	58.851	36.000	0.00	0.00	0.00	3.79
212	213	5.957842	TTGGTATTGATTTTCTGCGAAGT	57.042	34.783	0.00	0.00	0.00	3.01
373	394	7.545489	AGACGTATTAGTTAGTCCCTCAAAAG	58.455	38.462	0.00	0.00	34.41	2.27
526	547	7.809665	TCGGTTGGTAAAAGCTAATCTTAAAC	58.190	34.615	0.00	0.00	33.88	2.01
636	657	7.283127	TCTCAAAAGCTTGTTAATCTGTCTGTT	59.717	33.333	0.00	0.00	33.94	3.16
673	694	9.184523	TGTAATTAAGCTAGTTTTATGTGGCAT	57.815	29.630	0.00	0.00	0.00	4.40
674	695	9.665264	GTAATTAAGCTAGTTTTATGTGGCATC	57.335	33.333	0.00	0.00	0.00	3.91
676	697	7.553881	TTAAGCTAGTTTTATGTGGCATCTC	57.446	36.000	0.00	0.00	0.00	2.75
677	698	5.102953	AGCTAGTTTTATGTGGCATCTCA	57.897	39.130	0.00	0.00	0.00	3.27
678	699	4.878397	AGCTAGTTTTATGTGGCATCTCAC	59.122	41.667	0.00	0.00	38.09	3.51
681	702	4.655963	AGTTTTATGTGGCATCTCACTGT	58.344	39.130	0.00	0.00	38.40	3.55
682	703	5.072741	AGTTTTATGTGGCATCTCACTGTT	58.927	37.500	0.00	0.00	38.40	3.16
683	704	6.237901	AGTTTTATGTGGCATCTCACTGTTA	58.762	36.000	0.00	0.00	38.40	2.41
684	705	6.714810	AGTTTTATGTGGCATCTCACTGTTAA	59.285	34.615	0.00	0.00	38.40	2.01
685	706	7.394359	AGTTTTATGTGGCATCTCACTGTTAAT	59.606	33.333	0.00	0.00	38.40	1.40
686	707	8.673711	GTTTTATGTGGCATCTCACTGTTAATA	58.326	33.333	0.00	0.00	38.40	0.98
687	708	8.437360	TTTATGTGGCATCTCACTGTTAATAG	57.563	34.615	0.00	0.00	38.40	1.73
688	709	5.675684	TGTGGCATCTCACTGTTAATAGA	57.324	39.130	6.19	0.00	38.40	1.98
689	710	6.048732	TGTGGCATCTCACTGTTAATAGAA	57.951	37.500	6.19	0.00	38.40	2.10
690	711	6.653020	TGTGGCATCTCACTGTTAATAGAAT	58.347	36.000	6.19	0.00	38.40	2.40
691	712	7.112122	TGTGGCATCTCACTGTTAATAGAATT	58.888	34.615	6.19	0.00	38.40	2.17
692	713	8.264347	TGTGGCATCTCACTGTTAATAGAATTA	58.736	33.333	6.19	0.00	38.40	1.40
693	714	8.552034	GTGGCATCTCACTGTTAATAGAATTAC	58.448	37.037	6.19	0.00	34.98	1.89
694	715	8.264347	TGGCATCTCACTGTTAATAGAATTACA	58.736	33.333	6.19	0.00	0.00	2.41
695	716	9.109393	GGCATCTCACTGTTAATAGAATTACAA	57.891	33.333	6.19	0.00	0.00	2.41
717	738	8.871686	ACAAACATTTGGACATTCTTTCTTAC	57.128	30.769	9.09	0.00	42.34	2.34
718	739	7.926018	ACAAACATTTGGACATTCTTTCTTACC	59.074	33.333	9.09	0.00	42.34	2.85
719	740	7.839680	AACATTTGGACATTCTTTCTTACCT	57.160	32.000	0.00	0.00	0.00	3.08
720	741	8.934023	AACATTTGGACATTCTTTCTTACCTA	57.066	30.769	0.00	0.00	0.00	3.08
721	742	8.934023	ACATTTGGACATTCTTTCTTACCTAA	57.066	30.769	0.00	0.00	0.00	2.69
722	743	9.533831	ACATTTGGACATTCTTTCTTACCTAAT	57.466	29.630	0.00	0.00	0.00	1.73
793	814	9.376075	CTTATCCGATGATCTATGTTTAGCAAT	57.624	33.333	0.00	0.00	32.18	3.56
831	852	8.487313	TCATTGTCGTGTAGCATATTTTTAGT	57.513	30.769	0.00	0.00	0.00	2.24
863	884	9.618890	ATTGAAATGCTCTAACTGTGTACATAT	57.381	29.630	0.00	0.00	0.00	1.78
900	922	5.472301	AATTGGAGGTGTCCTTATCCATT	57.528	39.130	0.00	0.00	44.30	3.16
914	936	6.069088	TCCTTATCCATTGTCCTATGTTTGGT	60.069	38.462	0.00	0.00	0.00	3.67
939	961	9.931710	GTAAATAATTACAATTGTCGTTGTTGC	57.068	29.630	15.85	9.45	42.08	4.17
1021	1043	5.995565	TCTATATAAAGGGTCACCATCCG	57.004	43.478	0.00	0.00	40.13	4.18
1028	1050	0.834612	GGGTCACCATCCGGTCATTA	59.165	55.000	0.00	0.00	44.71	1.90
1066	1088	5.446143	TCTTTCTCGAGAGCAATATCTCC	57.554	43.478	15.94	0.00	42.34	3.71
1067	1089	5.136828	TCTTTCTCGAGAGCAATATCTCCT	58.863	41.667	15.94	0.00	42.34	3.69
1070	1092	4.661222	TCTCGAGAGCAATATCTCCTGAT	58.339	43.478	12.08	0.00	42.34	2.90
1076	1098	8.217111	TCGAGAGCAATATCTCCTGATAGATAT	58.783	37.037	0.00	0.00	46.47	1.63
1130	1152	3.118261	TCATCTCCACTTTGAGTATGCCC	60.118	47.826	0.00	0.00	33.93	5.36
1199	1221	6.093495	CGAAGAAGGTAAGGATTGCATTGTTA	59.907	38.462	0.00	0.00	37.98	2.41
1206	1228	8.088365	AGGTAAGGATTGCATTGTTAAAAGAAC	58.912	33.333	0.00	0.00	29.70	3.01
1236	1258	1.351153	GTTAGAGAGAGTGGTTGCGC	58.649	55.000	0.00	0.00	0.00	6.09
1422	1444	3.992260	ATCGATTGTCCTTAGAGTCCG	57.008	47.619	0.00	0.00	0.00	4.79
1444	1466	1.962144	GCTCAAATGTGCCAGCACT	59.038	52.632	22.29	6.62	46.30	4.40
1575	1599	4.006989	TGTTGTCGTGAGGAAATAATGGG	58.993	43.478	0.00	0.00	0.00	4.00
1576	1600	4.258543	GTTGTCGTGAGGAAATAATGGGA	58.741	43.478	0.00	0.00	0.00	4.37
1659	1683	9.588096	AATTATCCAAGGAAAGAGTTGTAGTTT	57.412	29.630	0.00	0.00	0.00	2.66
1708	1732	3.885901	GGGATTTCTATTTCTGTGCCCTC	59.114	47.826	0.00	0.00	0.00	4.30
1721	1745	1.141234	GCCCTCGGTTCCTTAGTCG	59.859	63.158	0.00	0.00	0.00	4.18
1726	1750	0.524862	TCGGTTCCTTAGTCGTGCTC	59.475	55.000	0.00	0.00	0.00	4.26
1738	1762	1.880027	GTCGTGCTCAGTTTTTCCCAT	59.120	47.619	0.00	0.00	0.00	4.00
1748	1772	4.462483	TCAGTTTTTCCCATGGCATCTAAC	59.538	41.667	6.09	6.55	0.00	2.34
1784	1808	0.967380	CTCCACCACTTGCCCCATTC	60.967	60.000	0.00	0.00	0.00	2.67
1793	1817	3.007182	CACTTGCCCCATTCTCACAAAAT	59.993	43.478	0.00	0.00	0.00	1.82
1802	1826	4.022416	CCATTCTCACAAAATCCCAAACGA	60.022	41.667	0.00	0.00	0.00	3.85
1809	1833	3.059166	CAAAATCCCAAACGAAGCCTTG	58.941	45.455	0.00	0.00	0.00	3.61
1810	1834	1.995376	AATCCCAAACGAAGCCTTGT	58.005	45.000	0.00	0.00	0.00	3.16
1812	1836	1.028905	TCCCAAACGAAGCCTTGTTG	58.971	50.000	0.00	0.00	0.00	3.33
1814	1838	1.136110	CCCAAACGAAGCCTTGTTGTT	59.864	47.619	0.00	0.00	0.00	2.83
1840	1864	1.531149	CAAGCAGTTGACCGTTACCTG	59.469	52.381	0.00	0.00	35.46	4.00
1859	1883	1.208358	CTCGGTTACTGACGCGTCA	59.792	57.895	36.96	36.96	38.06	4.35
1883	1907	1.139058	CGGGGATCTTAAGACAGGTGG	59.861	57.143	7.48	0.00	0.00	4.61
1928	1953	5.099042	AGAACCGTTCTTACCTATGCATT	57.901	39.130	3.54	0.00	36.36	3.56
2073	2100	0.602638	GCATGTCTGTCGGTGGAACA	60.603	55.000	0.00	0.00	39.98	3.18
2091	2118	0.738762	CAGGTCTCATGTGCGTGGAG	60.739	60.000	0.00	0.00	0.00	3.86
2303	2332	2.810274	ACACGCAATGATCTATCCATGC	59.190	45.455	0.00	6.89	35.39	4.06
2305	2334	3.439129	CACGCAATGATCTATCCATGCAT	59.561	43.478	13.91	0.00	37.28	3.96
2322	2352	3.293311	GCATATGCATAGCAACAAGGG	57.707	47.619	22.84	0.00	43.62	3.95
2334	2364	0.474184	AACAAGGGGGAGAGTGTGTG	59.526	55.000	0.00	0.00	0.00	3.82
2392	2422	1.710013	ACGCGGTTGATGTAGTTGAG	58.290	50.000	12.47	0.00	0.00	3.02
2512	2542	5.048364	GCAAGATGTCGAGGTAGTAGATGAT	60.048	44.000	0.00	0.00	0.00	2.45

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	3.107601	AGCACCACCTCTTTGCTCTATA	58.892	45.455	0.00	0.00	43.14	1.31
1	2	1.912043	AGCACCACCTCTTTGCTCTAT	59.088	47.619	0.00	0.00	43.14	1.98
88	89	3.706373	GGCTCCGAGGGAAGCACA	61.706	66.667	5.39	0.00	31.05	4.57
108	109	1.340114	GGCCAAAGAAGTACCAGAGGG	60.340	57.143	0.00	0.00	41.29	4.30
109	110	1.340114	GGGCCAAAGAAGTACCAGAGG	60.340	57.143	4.39	0.00	0.00	3.69
110	111	1.351017	TGGGCCAAAGAAGTACCAGAG	59.649	52.381	2.13	0.00	0.00	3.35
111	112	1.440618	TGGGCCAAAGAAGTACCAGA	58.559	50.000	2.13	0.00	0.00	3.86
112	113	1.886542	GTTGGGCCAAAGAAGTACCAG	59.113	52.381	22.82	0.00	0.00	4.00
187	188	5.697473	TCGCAGAAAATCAATACCAAACA	57.303	34.783	0.00	0.00	0.00	2.83
188	189	6.149633	ACTTCGCAGAAAATCAATACCAAAC	58.850	36.000	0.00	0.00	45.90	2.93
226	231	2.100749	GCCCAGTGTTAGTTGCTGTTTT	59.899	45.455	0.00	0.00	0.00	2.43
232	237	0.875059	GAGTGCCCAGTGTTAGTTGC	59.125	55.000	0.00	0.00	0.00	4.17
502	523	7.813645	AGTTTAAGATTAGCTTTTACCAACCG	58.186	34.615	0.00	0.00	38.05	4.44
526	547	6.317140	ACAGTGAGATGCCACATAAAACATAG	59.683	38.462	0.00	0.00	39.42	2.23
663	684	7.791029	TCTATTAACAGTGAGATGCCACATAA	58.209	34.615	0.00	0.00	39.42	1.90
664	685	7.360113	TCTATTAACAGTGAGATGCCACATA	57.640	36.000	0.00	0.00	39.42	2.29
669	690	8.662781	TGTAATTCTATTAACAGTGAGATGCC	57.337	34.615	0.00	0.00	0.00	4.40
691	712	9.959749	GTAAGAAAGAATGTCCAAATGTTTGTA	57.040	29.630	4.92	0.00	36.45	2.41
692	713	7.926018	GGTAAGAAAGAATGTCCAAATGTTTGT	59.074	33.333	4.92	0.00	36.45	2.83
693	714	8.143835	AGGTAAGAAAGAATGTCCAAATGTTTG	58.856	33.333	0.00	0.00	37.90	2.93
694	715	8.250143	AGGTAAGAAAGAATGTCCAAATGTTT	57.750	30.769	0.00	0.00	0.00	2.83
695	716	7.839680	AGGTAAGAAAGAATGTCCAAATGTT	57.160	32.000	0.00	0.00	0.00	2.71
696	717	8.934023	TTAGGTAAGAAAGAATGTCCAAATGT	57.066	30.769	0.00	0.00	0.00	2.71
727	748	9.965902	AATCATGGAGAAAAGTACACTCTTTAT	57.034	29.630	0.00	0.00	36.75	1.40
729	750	9.793259	TTAATCATGGAGAAAAGTACACTCTTT	57.207	29.630	0.00	0.00	39.00	2.52
730	751	9.965902	ATTAATCATGGAGAAAAGTACACTCTT	57.034	29.630	0.00	0.00	0.00	2.85
731	752	9.965902	AATTAATCATGGAGAAAAGTACACTCT	57.034	29.630	0.00	0.00	0.00	3.24
793	814	7.915293	ACACGACAATGAAGGTCATAATTAA	57.085	32.000	0.00	0.00	35.76	1.40
831	852	8.196771	ACACAGTTAGAGCATTTCAATTTTTGA	58.803	29.630	0.00	0.00	38.04	2.69
914	936	8.841822	CGCAACAACGACAATTGTAATTATTTA	58.158	29.630	11.95	0.00	42.01	1.40
939	961	8.420374	TGTCCTCTAAAGAAAAATATGCTACG	57.580	34.615	0.00	0.00	0.00	3.51
1028	1050	8.378172	TCGAGAAAGATATGAGTTGTGTTTTT	57.622	30.769	0.00	0.00	0.00	1.94
1130	1152	0.901124	CAGACCACCTCCCTCTCTTG	59.099	60.000	0.00	0.00	0.00	3.02
1199	1221	0.769247	ACCGGGCTACCTGTTCTTTT	59.231	50.000	6.32	0.00	28.79	2.27
1206	1228	1.033574	CTCTCTAACCGGGCTACCTG	58.966	60.000	6.32	0.00	33.28	4.00
1236	1258	4.892433	TCTTTTGCTCTCTCTTTCTCCAG	58.108	43.478	0.00	0.00	0.00	3.86
1454	1476	5.235186	AGTTTGTGATTCGACTGAAGACAAG	59.765	40.000	0.00	0.00	39.57	3.16
1699	1723	0.108138	CTAAGGAACCGAGGGCACAG	60.108	60.000	0.00	0.00	0.00	3.66
1708	1732	0.242825	TGAGCACGACTAAGGAACCG	59.757	55.000	0.00	0.00	0.00	4.44
1721	1745	1.337167	GCCATGGGAAAAACTGAGCAC	60.337	52.381	15.13	0.00	0.00	4.40
1726	1750	4.463891	AGTTAGATGCCATGGGAAAAACTG	59.536	41.667	22.14	0.00	0.00	3.16
1738	1762	6.016276	GGAAAAGTGAGAAAAGTTAGATGCCA	60.016	38.462	0.00	0.00	0.00	4.92
1748	1772	3.570125	GTGGAGGGGAAAAGTGAGAAAAG	59.430	47.826	0.00	0.00	0.00	2.27
1784	1808	3.308530	GCTTCGTTTGGGATTTTGTGAG	58.691	45.455	0.00	0.00	0.00	3.51
1793	1817	1.028905	CAACAAGGCTTCGTTTGGGA	58.971	50.000	0.00	0.00	0.00	4.37
1802	1826	1.846007	TGGACACAACAACAAGGCTT	58.154	45.000	0.00	0.00	0.00	4.35
1809	1833	2.163412	TCAACTGCTTGGACACAACAAC	59.837	45.455	0.00	0.00	32.14	3.32
1810	1834	2.163412	GTCAACTGCTTGGACACAACAA	59.837	45.455	0.00	0.00	32.14	2.83
1812	1836	1.065551	GGTCAACTGCTTGGACACAAC	59.934	52.381	0.00	0.00	32.14	3.32
1814	1838	0.813610	CGGTCAACTGCTTGGACACA	60.814	55.000	0.00	0.00	0.00	3.72
1840	1864	2.126580	ACGCGTCAGTAACCGAGC	60.127	61.111	5.58	0.00	0.00	5.03
1859	1883	0.326238	TGTCTTAAGATCCCCGGCCT	60.326	55.000	8.75	0.00	0.00	5.19
1862	1886	1.139058	CACCTGTCTTAAGATCCCCGG	59.861	57.143	8.75	4.62	0.00	5.73
1866	1890	1.134068	GGCCCACCTGTCTTAAGATCC	60.134	57.143	8.75	0.00	0.00	3.36
2073	2100	0.900182	TCTCCACGCACATGAGACCT	60.900	55.000	0.00	0.00	30.48	3.85
2091	2118	0.746923	GCCCGGACCAACCTTACATC	60.747	60.000	0.73	0.00	36.31	3.06
2272	2300	3.786516	TCATTGCGTGTCCGTAGAATA	57.213	42.857	0.00	0.00	36.15	1.75
2273	2301	2.665649	TCATTGCGTGTCCGTAGAAT	57.334	45.000	0.00	0.00	36.15	2.40
2281	2310	3.120408	GCATGGATAGATCATTGCGTGTC	60.120	47.826	0.00	0.00	0.00	3.67
2303	2332	2.559668	CCCCCTTGTTGCTATGCATATG	59.440	50.000	6.92	0.00	38.76	1.78
2305	2334	1.849692	TCCCCCTTGTTGCTATGCATA	59.150	47.619	6.20	6.20	38.76	3.14
2322	2352	1.200948	GGTACGTACACACACTCTCCC	59.799	57.143	26.02	1.43	0.00	4.30
2392	2422	4.429213	GCCGGAGCTAGAAGAAGC	57.571	61.111	5.05	0.00	43.11	3.86
2473	2503	1.352017	TCTTGCTGGATCAAGAAGGCA	59.648	47.619	0.00	0.00	46.56	4.75
2512	2542	0.948623	CACCATCGTGCTGACGGAAA	60.949	55.000	0.00	0.00	46.11	3.13
2537	2567	1.009829	GATCACTTCACCATCACCGC	58.990	55.000	0.00	0.00	0.00	5.68

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.