AutoCloner

Multiple sequence alignment - TraesCS3D01G482800

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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	TraesCS3D01G482800	chr3D	100.000	3607	0	0	1	3607	580520680	580524286	0.000000e+00	6661.0
1	TraesCS3D01G482800	chr3D	83.658	257	35	6	171	421	615318825	615319080	6.020000e-58	235.0
2	TraesCS3D01G482800	chr3D	100.000	50	0	0	706	755	580521335	580521384	3.830000e-15	93.5
3	TraesCS3D01G482800	chr3D	100.000	50	0	0	656	705	580521385	580521434	3.830000e-15	93.5
4	TraesCS3D01G482800	chr3B	93.116	2237	89	29	706	2923	775735170	775737360	0.000000e+00	3217.0
5	TraesCS3D01G482800	chr3B	93.324	689	39	4	2925	3607	775737501	775738188	0.000000e+00	1011.0
6	TraesCS3D01G482800	chr3B	90.000	200	14	6	509	705	775735021	775735217	1.660000e-63	254.0
7	TraesCS3D01G482800	chr3A	95.062	1782	75	6	706	2479	715973391	715975167	0.000000e+00	2791.0
8	TraesCS3D01G482800	chr3A	92.570	646	42	4	2966	3607	715977384	715978027	0.000000e+00	922.0
9	TraesCS3D01G482800	chr3A	92.358	458	15	7	2478	2931	715975194	715975635	5.080000e-178	634.0
10	TraesCS3D01G482800	chr3A	88.416	423	46	1	2	421	715972664	715973086	1.160000e-139	507.0
11	TraesCS3D01G482800	chr3A	89.655	290	22	6	422	705	715973152	715973439	2.650000e-96	363.0
12	TraesCS3D01G482800	chr6B	89.648	1536	100	21	964	2462	498544192	498542679	0.000000e+00	1901.0
13	TraesCS3D01G482800	chr6B	79.545	660	106	22	1641	2282	498852254	498852902	9.190000e-121	444.0
14	TraesCS3D01G482800	chr6B	83.439	314	23	17	2634	2929	498542521	498542219	7.680000e-67	265.0
15	TraesCS3D01G482800	chr6B	83.398	259	33	9	171	421	675395932	675396188	7.790000e-57	231.0
16	TraesCS3D01G482800	chr6B	75.600	500	73	31	1073	1554	498851669	498852137	6.110000e-48	202.0
17	TraesCS3D01G482800	chr6B	82.022	89	13	1	50	135	498544484	498544396	5.000000e-09	73.1
18	TraesCS3D01G482800	chr6D	89.435	1505	111	18	964	2439	324783009	324784494	0.000000e+00	1855.0
19	TraesCS3D01G482800	chr6D	79.669	664	104	22	1641	2285	324598893	324598242	1.980000e-122	449.0
20	TraesCS3D01G482800	chr6D	81.734	323	29	12	2631	2929	324785012	324785328	3.600000e-60	243.0
21	TraesCS3D01G482800	chr6D	84.082	245	31	8	183	421	452312721	452312479	2.800000e-56	230.0
22	TraesCS3D01G482800	chr6D	75.654	497	76	26	1075	1554	324599437	324598969	4.720000e-49	206.0
23	TraesCS3D01G482800	chr6D	83.832	167	24	3	7	170	324782671	324782837	4.820000e-34	156.0
24	TraesCS3D01G482800	chr6D	92.063	63	4	1	492	554	324782901	324782962	1.780000e-13	87.9
25	TraesCS3D01G482800	chr6A	89.177	1506	112	18	964	2439	462225715	462227199	0.000000e+00	1831.0
26	TraesCS3D01G482800	chr6A	84.836	488	65	5	3120	3607	462240287	462240765	1.950000e-132	483.0
27	TraesCS3D01G482800	chr6A	79.789	663	105	22	1641	2285	461987185	461986534	4.250000e-124	455.0
28	TraesCS3D01G482800	chr6A	81.056	322	29	16	2632	2929	462227391	462227704	1.010000e-55	228.0
29	TraesCS3D01G482800	chr6A	75.703	498	74	30	1075	1554	461987731	461987263	4.720000e-49	206.0
30	TraesCS3D01G482800	chr6A	83.333	210	28	7	2925	3129	462228156	462228363	1.710000e-43	187.0
31	TraesCS3D01G482800	chr7B	83.529	255	34	7	174	421	416437641	416437388	7.790000e-57	231.0
32	TraesCS3D01G482800	chr4A	83.333	258	35	7	171	421	703252787	703253043	7.790000e-57	231.0
33	TraesCS3D01G482800	chr2B	83.333	258	35	7	171	421	20072349	20072605	7.790000e-57	231.0
34	TraesCS3D01G482800	chr7D	83.268	257	34	7	171	421	73143483	73143736	1.010000e-55	228.0
35	TraesCS3D01G482800	chr4B	82.759	261	38	7	168	421	416644111	416643851	3.620000e-55	226.0
36	TraesCS3D01G482800	chr1A	88.889	54	4	2	622	673	53018035	53017982	8.360000e-07	65.8

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	TraesCS3D01G482800	chr3D	580520680	580524286	3606	False	2282.666667	6661	100.000000	1	3607	3	chr3D.!!$F2	3606
1	TraesCS3D01G482800	chr3B	775735021	775738188	3167	False	1494.000000	3217	92.146667	509	3607	3	chr3B.!!$F1	3098
2	TraesCS3D01G482800	chr3A	715972664	715978027	5363	False	1043.400000	2791	91.612200	2	3607	5	chr3A.!!$F1	3605
3	TraesCS3D01G482800	chr6B	498542219	498544484	2265	True	746.366667	1901	85.036333	50	2929	3	chr6B.!!$R1	2879
4	TraesCS3D01G482800	chr6B	498851669	498852902	1233	False	323.000000	444	77.572500	1073	2282	2	chr6B.!!$F2	1209
5	TraesCS3D01G482800	chr6D	324782671	324785328	2657	False	585.475000	1855	86.766000	7	2929	4	chr6D.!!$F1	2922
6	TraesCS3D01G482800	chr6D	324598242	324599437	1195	True	327.500000	449	77.661500	1075	2285	2	chr6D.!!$R2	1210
7	TraesCS3D01G482800	chr6A	462225715	462228363	2648	False	748.666667	1831	84.522000	964	3129	3	chr6A.!!$F2	2165
8	TraesCS3D01G482800	chr6A	461986534	461987731	1197	True	330.500000	455	77.746000	1075	2285	2	chr6A.!!$R1	1210

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
853	940	0.106708	TTAGCGCATTAGGGAGCAGG	59.893	55.000	11.47	0.0	35.93	4.85	F
2451	2710	1.004560	ATGTGTGCAGTCCGTCTGG	60.005	57.895	0.00	0.0	43.78	3.86	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2555	3109	1.677052	GCCACCGGTTCAAGTTTTGTA	59.323	47.619	2.97	0.0	0.00	2.41	R
3471	6186	0.447801	GGTTGTGACCTAATGCAGCG	59.552	55.000	0.00	0.0	42.99	5.18	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
136	140	6.692681	GCGTTTATAACAGGTACACGAATAGA	59.307	38.462	7.58	0.00	0.00	1.98
139	143	9.740239	GTTTATAACAGGTACACGAATAGATCA	57.260	33.333	0.00	0.00	0.00	2.92
182	186	1.376683	TTCTCCGCAAACCATCCCG	60.377	57.895	0.00	0.00	0.00	5.14
212	216	6.493802	TGGATGGTTATAGAGACAGTGGTATC	59.506	42.308	0.00	0.00	35.48	2.24
213	217	6.722129	GGATGGTTATAGAGACAGTGGTATCT	59.278	42.308	0.00	0.00	46.69	1.98
217	221	6.207810	GGTTATAGAGACAGTGGTATCTCCAG	59.792	46.154	5.79	0.00	41.60	3.86
221	225	3.093057	AGACAGTGGTATCTCCAGTCAC	58.907	50.000	0.00	0.00	45.98	3.67
224	228	2.167281	CAGTGGTATCTCCAGTCACCAG	59.833	54.545	0.00	0.00	45.98	4.00
255	259	2.740981	CCTGATGCTCGCATTATTCCTC	59.259	50.000	5.79	0.00	36.70	3.71
267	271	8.148807	TCGCATTATTCCTCGATTTATTTCAA	57.851	30.769	0.00	0.00	0.00	2.69
275	279	6.795399	TCCTCGATTTATTTCAAGATTTGCC	58.205	36.000	0.00	0.00	0.00	4.52
276	280	6.376864	TCCTCGATTTATTTCAAGATTTGCCA	59.623	34.615	0.00	0.00	0.00	4.92
277	281	7.035004	CCTCGATTTATTTCAAGATTTGCCAA	58.965	34.615	0.00	0.00	0.00	4.52
279	283	7.035004	TCGATTTATTTCAAGATTTGCCAAGG	58.965	34.615	0.00	0.00	0.00	3.61
290	294	2.074230	TTGCCAAGGTGCGCTTTCAG	62.074	55.000	9.73	0.00	0.00	3.02
291	295	2.256461	CCAAGGTGCGCTTTCAGC	59.744	61.111	9.73	0.00	38.02	4.26
358	365	8.531146	TCATAAATCTAAGATGATATGTCGGCA	58.469	33.333	0.00	0.00	0.00	5.69
381	388	5.120830	CACGGTCTTTCAAAGGTCTTCATAG	59.879	44.000	0.00	0.00	0.00	2.23
383	390	4.944317	GGTCTTTCAAAGGTCTTCATAGGG	59.056	45.833	0.00	0.00	0.00	3.53
384	391	4.944317	GTCTTTCAAAGGTCTTCATAGGGG	59.056	45.833	0.00	0.00	0.00	4.79
399	406	2.358247	GGGTAGGGTGTGCGTGTG	60.358	66.667	0.00	0.00	0.00	3.82
423	495	7.067008	GTGTGCATTTATAAGGGTGAGTGTTAT	59.933	37.037	0.00	0.00	0.00	1.89
503	586	7.307632	GCTCATATTTGTAGGTAGTGCAGATTG	60.308	40.741	0.00	0.00	0.00	2.67
555	638	0.597637	CCAACTCGTCACGTGCTCTT	60.598	55.000	11.67	0.00	0.00	2.85
708	795	9.435688	AAAAACTTGCAATTTGAAGTAGACTTT	57.564	25.926	0.00	3.10	36.11	2.66
709	796	8.634475	AAACTTGCAATTTGAAGTAGACTTTC	57.366	30.769	0.00	0.00	36.11	2.62
710	797	7.333528	ACTTGCAATTTGAAGTAGACTTTCA	57.666	32.000	0.00	0.00	36.11	2.69
711	798	7.771183	ACTTGCAATTTGAAGTAGACTTTCAA	58.229	30.769	0.00	0.00	36.11	2.69
712	799	8.416329	ACTTGCAATTTGAAGTAGACTTTCAAT	58.584	29.630	0.00	0.00	36.11	2.57
713	800	9.897744	CTTGCAATTTGAAGTAGACTTTCAATA	57.102	29.630	0.00	0.00	36.11	1.90
714	801	9.677567	TTGCAATTTGAAGTAGACTTTCAATAC	57.322	29.630	0.00	0.00	36.11	1.89
715	802	8.845227	TGCAATTTGAAGTAGACTTTCAATACA	58.155	29.630	0.00	0.00	36.11	2.29
716	803	9.846248	GCAATTTGAAGTAGACTTTCAATACAT	57.154	29.630	0.00	0.00	36.11	2.29
792	879	9.878667	TTTTCTCATAACACGGTAATCAAGATA	57.121	29.630	0.00	0.00	0.00	1.98
853	940	0.106708	TTAGCGCATTAGGGAGCAGG	59.893	55.000	11.47	0.00	35.93	4.85
868	955	5.193728	AGGGAGCAGGGTAATTAAAGATGAA	59.806	40.000	0.00	0.00	0.00	2.57
875	962	7.121315	GCAGGGTAATTAAAGATGAAAGAGTGT	59.879	37.037	0.00	0.00	0.00	3.55
1236	1343	1.106944	AGGGCCACAAAAACCAGACG	61.107	55.000	6.18	0.00	0.00	4.18
1554	1688	4.433413	CGCGTGCTATGATGTAAGCATAAG	60.433	45.833	0.00	0.00	43.92	1.73
1892	2113	6.126409	AGGATCCTCTTCAGTCTACAGTTAG	58.874	44.000	9.02	0.00	0.00	2.34
2282	2529	4.559153	GGTGAACTACCGCTAAGTTACAA	58.441	43.478	0.00	0.00	40.26	2.41
2451	2710	1.004560	ATGTGTGCAGTCCGTCTGG	60.005	57.895	0.00	0.00	43.78	3.86
2483	2868	8.880878	TTTTCTTTACAATAGGAAAACTTGCC	57.119	30.769	0.00	0.00	34.24	4.52
2487	2872	3.081804	ACAATAGGAAAACTTGCCTCCG	58.918	45.455	0.00	0.00	35.73	4.63
2501	2886	5.941647	ACTTGCCTCCGCTTACTAAAATTTA	59.058	36.000	0.00	0.00	35.36	1.40
2506	2891	6.674760	GCCTCCGCTTACTAAAATTTACACTG	60.675	42.308	0.00	0.00	0.00	3.66
2543	3097	6.940298	ACTCCGAAATGAAGTTCTTCCAATAA	59.060	34.615	4.17	0.00	0.00	1.40
2545	3099	7.165485	TCCGAAATGAAGTTCTTCCAATAAGA	58.835	34.615	4.17	0.00	0.00	2.10
2734	3358	2.360350	CTGCCCTGTCATGCCGTT	60.360	61.111	0.00	0.00	0.00	4.44
2824	3472	8.450578	TGATTGCCCTACTCAATTATTAACAG	57.549	34.615	0.00	0.00	34.59	3.16
2843	3491	4.737054	ACAGAAGCTGTTTGTTGAAAGTG	58.263	39.130	0.00	0.00	42.59	3.16
2976	5685	6.721571	AATAATTGAAGGTCGTGTGTACTG	57.278	37.500	0.00	0.00	0.00	2.74
3070	5779	5.923684	ACAACATTTTACCCAAACTATTGCG	59.076	36.000	0.00	0.00	35.10	4.85
3105	5814	5.595542	CCCTGCCTGAATTTGATCTCATTTA	59.404	40.000	0.00	0.00	0.00	1.40
3107	5816	7.201974	CCCTGCCTGAATTTGATCTCATTTAAT	60.202	37.037	0.00	0.00	0.00	1.40
3185	5898	3.498777	GGCTCTGTTTACGAGAAAAAGCT	59.501	43.478	0.00	0.00	0.00	3.74
3231	5944	0.937304	CCTTGTCGACCACACAACAG	59.063	55.000	14.12	0.00	33.41	3.16
3280	5995	0.468400	GCTAGGATCCGGAGACACCT	60.468	60.000	20.43	20.43	36.50	4.00
3281	5996	2.030045	GCTAGGATCCGGAGACACCTT	61.030	57.143	21.35	0.00	34.96	3.50
3452	6167	1.843368	TCAGATCGTTTCTACCGGGT	58.157	50.000	6.32	4.46	31.77	5.28
3454	6169	1.109609	AGATCGTTTCTACCGGGTCC	58.890	55.000	6.32	0.00	30.96	4.46
3457	6172	1.444895	CGTTTCTACCGGGTCCACG	60.445	63.158	6.32	4.44	0.00	4.94
3471	6186	1.201880	GTCCACGAACTCACTACCCTC	59.798	57.143	0.00	0.00	0.00	4.30
3502	6217	1.408702	GTCACAACCCATGCAACACTT	59.591	47.619	0.00	0.00	0.00	3.16
3533	6248	2.093106	CTACACCCTAGAGTTGTCGCT	58.907	52.381	0.00	0.00	0.00	4.93
3553	6268	1.554617	TGCACCTCCATTCGAGATTGA	59.445	47.619	0.00	0.00	41.63	2.57
3602	6317	4.147449	TCGCTCCGGCATCCACAG	62.147	66.667	0.00	0.00	38.60	3.66

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
158	162	0.107410	TGGTTTGCGGAGAACACACT	60.107	50.000	4.88	0.00	0.00	3.55
168	172	3.439540	CCACGGGATGGTTTGCGG	61.440	66.667	0.00	0.00	44.46	5.69
182	186	5.104900	ACTGTCTCTATAACCATCCAACCAC	60.105	44.000	0.00	0.00	0.00	4.16
217	221	0.765510	AGGACTTGAACCCTGGTGAC	59.234	55.000	0.00	0.00	0.00	3.67
218	222	0.764890	CAGGACTTGAACCCTGGTGA	59.235	55.000	0.00	0.00	44.68	4.02
224	228	1.743996	GAGCATCAGGACTTGAACCC	58.256	55.000	0.00	0.00	39.77	4.11
240	244	5.786401	ATAAATCGAGGAATAATGCGAGC	57.214	39.130	0.00	0.00	36.12	5.03
255	259	6.813152	ACCTTGGCAAATCTTGAAATAAATCG	59.187	34.615	0.00	0.00	0.00	3.34
267	271	1.181098	AAGCGCACCTTGGCAAATCT	61.181	50.000	11.47	0.00	30.99	2.40
270	274	1.067250	GAAAGCGCACCTTGGCAAA	59.933	52.632	11.47	0.00	33.01	3.68
290	294	0.036388	TTGACCAGAACATCTCCCGC	60.036	55.000	0.00	0.00	0.00	6.13
291	295	1.726853	GTTGACCAGAACATCTCCCG	58.273	55.000	0.00	0.00	0.00	5.14
294	298	1.986378	CGTCGTTGACCAGAACATCTC	59.014	52.381	0.00	0.00	0.00	2.75
303	310	3.547249	GACGCCTCGTCGTTGACCA	62.547	63.158	3.54	0.00	46.56	4.02
320	327	4.471904	AGATTTATGAAGTCACCGCAGA	57.528	40.909	0.00	0.00	0.00	4.26
323	330	6.701841	TCATCTTAGATTTATGAAGTCACCGC	59.298	38.462	0.00	0.00	0.00	5.68
352	359	0.234884	CTTTGAAAGACCGTGCCGAC	59.765	55.000	0.00	0.00	0.00	4.79
355	362	0.591659	GACCTTTGAAAGACCGTGCC	59.408	55.000	6.49	0.00	0.00	5.01
358	365	3.553828	TGAAGACCTTTGAAAGACCGT	57.446	42.857	6.49	0.00	0.00	4.83
365	372	4.473559	CCTACCCCTATGAAGACCTTTGAA	59.526	45.833	0.00	0.00	0.00	2.69
381	388	3.633116	ACACGCACACCCTACCCC	61.633	66.667	0.00	0.00	0.00	4.95
383	390	1.959226	CACACACGCACACCCTACC	60.959	63.158	0.00	0.00	0.00	3.18
384	391	2.604174	GCACACACGCACACCCTAC	61.604	63.158	0.00	0.00	0.00	3.18
399	406	5.897377	AACACTCACCCTTATAAATGCAC	57.103	39.130	0.00	0.00	0.00	4.57
433	513	5.643379	AATGAGCCAACATCGTGTAAAAT	57.357	34.783	0.00	0.00	0.00	1.82
459	542	0.869730	GCCAAAGTCGAGCCGTAAAA	59.130	50.000	0.00	0.00	0.00	1.52
682	769	9.435688	AAAGTCTACTTCAAATTGCAAGTTTTT	57.564	25.926	9.83	0.00	34.61	1.94
683	770	9.087424	GAAAGTCTACTTCAAATTGCAAGTTTT	57.913	29.630	9.83	0.29	34.61	2.43
684	771	8.250332	TGAAAGTCTACTTCAAATTGCAAGTTT	58.750	29.630	9.83	5.32	34.61	2.66
685	772	7.771183	TGAAAGTCTACTTCAAATTGCAAGTT	58.229	30.769	6.26	6.26	34.61	2.66
686	773	7.333528	TGAAAGTCTACTTCAAATTGCAAGT	57.666	32.000	4.94	0.00	34.61	3.16
687	774	8.807667	ATTGAAAGTCTACTTCAAATTGCAAG	57.192	30.769	4.94	0.00	34.61	4.01
688	775	9.677567	GTATTGAAAGTCTACTTCAAATTGCAA	57.322	29.630	0.00	0.00	34.61	4.08
689	776	8.845227	TGTATTGAAAGTCTACTTCAAATTGCA	58.155	29.630	4.26	0.00	34.61	4.08
690	777	9.846248	ATGTATTGAAAGTCTACTTCAAATTGC	57.154	29.630	4.26	0.00	34.61	3.56
767	854	9.878667	TTATCTTGATTACCGTGTTATGAGAAA	57.121	29.630	0.00	0.00	0.00	2.52
768	855	9.878667	TTTATCTTGATTACCGTGTTATGAGAA	57.121	29.630	0.00	0.00	0.00	2.87
818	905	4.155826	TGCGCTAAGTGCATGTAGAAATTT	59.844	37.500	9.73	0.00	44.36	1.82
853	940	7.755373	GCCAACACTCTTTCATCTTTAATTACC	59.245	37.037	0.00	0.00	0.00	2.85
868	955	2.632987	AACGGTAAGCCAACACTCTT	57.367	45.000	0.00	0.00	34.09	2.85
875	962	1.957177	TGCATTGAAACGGTAAGCCAA	59.043	42.857	0.00	0.00	34.09	4.52
936	1023	7.072202	ACTTCCTCCATCTGATGAGAAATGTAT	59.928	37.037	18.92	0.00	0.00	2.29
1196	1303	2.126417	GACTGCAGCAGGCTTGTGTG	62.126	60.000	26.38	0.00	45.15	3.82
1197	1304	1.895707	GACTGCAGCAGGCTTGTGT	60.896	57.895	26.38	3.97	45.15	3.72
1236	1343	0.455005	CGGACGAAGAGGGGTTAGTC	59.545	60.000	0.00	0.00	32.86	2.59
1554	1688	2.206576	AATGGAAGGAGCTTGGTGAC	57.793	50.000	0.00	0.00	0.00	3.67
1579	1782	1.662876	CGACCACTTGTCCAATTTGCG	60.663	52.381	0.00	0.00	41.18	4.85
1585	1788	1.070786	GAGCCGACCACTTGTCCAA	59.929	57.895	0.00	0.00	41.18	3.53
1892	2113	6.443792	ACATTTACTTCCATTGTTTTCCGTC	58.556	36.000	0.00	0.00	0.00	4.79
2282	2529	5.819379	CACACACAGAGCAGATAAATATGGT	59.181	40.000	0.00	0.00	31.77	3.55
2299	2546	7.731882	TTTCGAGGTATAAAATTCACACACA	57.268	32.000	0.00	0.00	0.00	3.72
2483	2868	7.117236	TGACAGTGTAAATTTTAGTAAGCGGAG	59.883	37.037	0.00	0.00	0.00	4.63
2487	2872	9.946165	AACTTGACAGTGTAAATTTTAGTAAGC	57.054	29.630	0.00	0.00	31.60	3.09
2501	2886	4.038763	TCGGAGTATTGAACTTGACAGTGT	59.961	41.667	0.00	0.00	39.07	3.55
2506	2891	6.721571	TCATTTCGGAGTATTGAACTTGAC	57.278	37.500	0.00	0.00	39.07	3.18
2545	3099	8.508875	CCGGTTCAAGTTTTGTATACATAAGTT	58.491	33.333	18.11	18.11	33.00	2.66
2547	3101	7.960738	CACCGGTTCAAGTTTTGTATACATAAG	59.039	37.037	2.97	0.00	0.00	1.73
2548	3102	7.094720	CCACCGGTTCAAGTTTTGTATACATAA	60.095	37.037	2.97	5.49	0.00	1.90
2555	3109	1.677052	GCCACCGGTTCAAGTTTTGTA	59.323	47.619	2.97	0.00	0.00	2.41
2734	3358	2.618816	GGGAGAATTGCATGTGTCCTCA	60.619	50.000	11.66	0.00	0.00	3.86
2824	3472	6.466308	AAAACACTTTCAACAAACAGCTTC	57.534	33.333	0.00	0.00	0.00	3.86
2843	3491	7.015877	CGTAGAACTGAAGCTCCATTAAAAAC	58.984	38.462	0.00	0.00	0.00	2.43
2909	3572	4.807304	TGTAGAAAAGACACAACCGAAGAC	59.193	41.667	0.00	0.00	0.00	3.01
3035	5744	5.044558	GGTAAAATGTTGTCGCAGGAAAAA	58.955	37.500	0.00	0.00	0.00	1.94
3070	5779	2.114616	TCAGGCAGGGATCTTTCTCTC	58.885	52.381	0.00	0.00	26.59	3.20
3136	5849	5.607119	TGTTTAGGTTTTCGATCAGCTTC	57.393	39.130	1.79	0.00	0.00	3.86
3231	5944	6.258068	GCCTGTGTTTTATGACTATGGTCTAC	59.742	42.308	10.82	2.31	42.54	2.59
3280	5995	0.949105	GCGAGCTCGGGAAGTTGAAA	60.949	55.000	35.10	0.00	40.23	2.69
3281	5996	1.374252	GCGAGCTCGGGAAGTTGAA	60.374	57.895	35.10	0.00	40.23	2.69
3452	6167	1.542492	GAGGGTAGTGAGTTCGTGGA	58.458	55.000	0.00	0.00	0.00	4.02
3454	6169	0.456312	GCGAGGGTAGTGAGTTCGTG	60.456	60.000	0.00	0.00	34.05	4.35
3457	6172	0.458716	GCAGCGAGGGTAGTGAGTTC	60.459	60.000	0.00	0.00	0.00	3.01
3471	6186	0.447801	GGTTGTGACCTAATGCAGCG	59.552	55.000	0.00	0.00	42.99	5.18
3502	6217	1.831286	GGGTGTAGGCTAGCCGCTA	60.831	63.158	27.83	13.34	41.95	4.26
3533	6248	1.554617	TCAATCTCGAATGGAGGTGCA	59.445	47.619	0.00	0.00	43.34	4.57

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.