AutoCloner

Multiple sequence alignment - TraesCS2D01G057300

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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	TraesCS2D01G057300	chr2D	100.000	4757	0	0	1	4757	22821923	22817167	0.000000e+00	8785.0
1	TraesCS2D01G057300	chr2D	82.403	1398	235	10	1696	3086	22510456	22509063	0.000000e+00	1208.0
2	TraesCS2D01G057300	chr2D	90.646	588	55	0	3173	3760	22508973	22508386	0.000000e+00	782.0
3	TraesCS2D01G057300	chr2D	83.373	415	59	6	1424	1836	22510860	22510454	4.490000e-100	375.0
4	TraesCS2D01G057300	chr2D	81.696	224	41	0	1017	1240	22511289	22511066	2.260000e-43	187.0
5	TraesCS2D01G057300	chr2A	90.720	3416	217	32	1419	4757	24412099	24408707	0.000000e+00	4460.0
6	TraesCS2D01G057300	chr2A	82.033	1397	239	7	1696	3086	24174380	24175770	0.000000e+00	1179.0
7	TraesCS2D01G057300	chr2A	87.688	731	68	9	699	1418	24412868	24412149	0.000000e+00	832.0
8	TraesCS2D01G057300	chr2A	83.960	798	122	6	1696	2490	24308521	24307727	0.000000e+00	760.0
9	TraesCS2D01G057300	chr2A	84.124	611	94	3	3173	3780	24175851	24176461	5.300000e-164	588.0
10	TraesCS2D01G057300	chr2A	83.373	415	59	6	1424	1836	24308925	24308519	4.490000e-100	375.0
11	TraesCS2D01G057300	chr2A	80.488	246	48	0	995	1240	24309375	24309130	6.280000e-44	189.0
12	TraesCS2D01G057300	chr2A	87.425	167	11	5	260	421	24413440	24413279	2.920000e-42	183.0
13	TraesCS2D01G057300	chr2A	93.750	48	3	0	131	178	24413969	24413922	6.600000e-09	73.1
14	TraesCS2D01G057300	chr2B	90.277	3394	243	28	1419	4757	38416945	38420306	0.000000e+00	4359.0
15	TraesCS2D01G057300	chr2B	92.205	2463	169	15	1614	4061	38073989	38076443	0.000000e+00	3463.0
16	TraesCS2D01G057300	chr2B	88.864	2703	175	47	2139	4757	39087024	39089684	0.000000e+00	3208.0
17	TraesCS2D01G057300	chr2B	85.593	2353	320	13	1421	3761	37677485	37679830	0.000000e+00	2449.0
18	TraesCS2D01G057300	chr2B	85.490	2357	314	21	1419	3761	38034107	38036449	0.000000e+00	2433.0
19	TraesCS2D01G057300	chr2B	81.637	2102	348	26	1696	3780	39339823	39337743	0.000000e+00	1709.0
20	TraesCS2D01G057300	chr2B	80.817	2080	348	37	1696	3756	39184774	39186821	0.000000e+00	1583.0
21	TraesCS2D01G057300	chr2B	82.171	1391	232	10	1696	3078	49900409	49899027	0.000000e+00	1181.0
22	TraesCS2D01G057300	chr2B	92.000	700	46	3	642	1331	38416130	38416829	0.000000e+00	974.0
23	TraesCS2D01G057300	chr2B	86.395	441	59	1	974	1414	38073100	38073539	9.260000e-132	481.0
24	TraesCS2D01G057300	chr2B	85.106	470	69	1	946	1414	37676962	37677431	3.330000e-131	479.0
25	TraesCS2D01G057300	chr2B	86.036	444	55	6	974	1414	38033616	38034055	2.000000e-128	470.0
26	TraesCS2D01G057300	chr2B	92.169	166	8	1	13	178	38413775	38413935	3.700000e-56	230.0
27	TraesCS2D01G057300	chr2B	87.629	97	7	2	450	541	38414326	38414422	1.810000e-19	108.0
28	TraesCS2D01G057300	chr2B	84.810	79	7	4	348	421	37768593	37768671	1.840000e-09	75.0
29	TraesCS2D01G057300	chr7B	82.449	245	42	1	995	1238	744137121	744137365	3.730000e-51	213.0
30	TraesCS2D01G057300	chr6A	100.000	31	0	0	4032	4062	20245896	20245866	1.850000e-04	58.4
31	TraesCS2D01G057300	chr6A	79.730	74	13	2	4645	4716	30727202	30727275	9.000000e-03	52.8
32	TraesCS2D01G057300	chr3D	100.000	31	0	0	4032	4062	591824198	591824228	1.850000e-04	58.4
33	TraesCS2D01G057300	chr1B	81.429	70	11	2	4649	4716	676003748	676003817	6.650000e-04	56.5
34	TraesCS2D01G057300	chr7D	100.000	28	0	0	4689	4716	572686505	572686532	9.000000e-03	52.8
35	TraesCS2D01G057300	chr4D	100.000	28	0	0	4689	4716	369890979	369890952	9.000000e-03	52.8
36	TraesCS2D01G057300	chr1D	78.161	87	16	3	4632	4716	298551562	298551647	9.000000e-03	52.8
37	TraesCS2D01G057300	chr1D	94.118	34	2	0	4689	4722	459875236	459875203	9.000000e-03	52.8

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	TraesCS2D01G057300	chr2D	22817167	22821923	4756	True	8785.000000	8785	100.00000	1	4757	1	chr2D.!!$R1	4756
1	TraesCS2D01G057300	chr2D	22508386	22511289	2903	True	638.000000	1208	84.52950	1017	3760	4	chr2D.!!$R2	2743
2	TraesCS2D01G057300	chr2A	24408707	24413969	5262	True	1387.025000	4460	89.89575	131	4757	4	chr2A.!!$R2	4626
3	TraesCS2D01G057300	chr2A	24174380	24176461	2081	False	883.500000	1179	83.07850	1696	3780	2	chr2A.!!$F1	2084
4	TraesCS2D01G057300	chr2A	24307727	24309375	1648	True	441.333333	760	82.60700	995	2490	3	chr2A.!!$R1	1495
5	TraesCS2D01G057300	chr2B	39087024	39089684	2660	False	3208.000000	3208	88.86400	2139	4757	1	chr2B.!!$F2	2618
6	TraesCS2D01G057300	chr2B	38073100	38076443	3343	False	1972.000000	3463	89.30000	974	4061	2	chr2B.!!$F6	3087
7	TraesCS2D01G057300	chr2B	39337743	39339823	2080	True	1709.000000	1709	81.63700	1696	3780	1	chr2B.!!$R1	2084
8	TraesCS2D01G057300	chr2B	39184774	39186821	2047	False	1583.000000	1583	80.81700	1696	3756	1	chr2B.!!$F3	2060
9	TraesCS2D01G057300	chr2B	37676962	37679830	2868	False	1464.000000	2449	85.34950	946	3761	2	chr2B.!!$F4	2815
10	TraesCS2D01G057300	chr2B	38033616	38036449	2833	False	1451.500000	2433	85.76300	974	3761	2	chr2B.!!$F5	2787
11	TraesCS2D01G057300	chr2B	38413775	38420306	6531	False	1417.750000	4359	90.51875	13	4757	4	chr2B.!!$F7	4744
12	TraesCS2D01G057300	chr2B	49899027	49900409	1382	True	1181.000000	1181	82.17100	1696	3078	1	chr2B.!!$R2	1382

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	Hairpin	End Stability	Orientation
413	848	0.549950	CCACATCAGGAGGCCATTCT	59.450	55.0	5.01	0.00	2.40	F
499	1068	0.684805	AGCGGACTGAGTAAGAGGGG	60.685	60.0	0.00	0.00	4.79	F
1050	3252	0.830444	TCCTGGTCCTGTGCGTAGTT	60.830	55.0	0.00	0.00	2.24	F
1386	3588	0.109781	TCTCGGCAAATTTCGCTTGC	60.110	50.0	10.88	46.82	4.01	F
2381	4981	0.320858	TGCAACATTGGCAGCATTGG	60.321	50.0	0.00	36.11	3.16	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1295	3497	1.164411	CCAGCATGCAACTTCCGTAA	58.836	50.000	21.98	31.97	3.18	R
1362	3564	2.749621	AGCGAAATTTGCCGAGAAATCT	59.250	40.909	0.83	0.00	2.40	R
2515	5117	0.877071	ATTTCTGCCGCAACTGACAG	59.123	50.000	0.00	0.00	3.51	R
2889	5499	1.003839	TGCGAACTGATTCCGGCTT	60.004	52.632	0.00	0.00	4.35	R
4089	6755	1.208052	AGCATGTCTCAACACCGCTAT	59.792	47.619	0.00	42.63	2.97	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
78	79	1.873591	CCTCATGCCGCCTGTTTATAC	59.126	52.381	0.00	0.00	0.00	1.47
123	124	1.673626	CGTTTATACACGTGCCAGGGT	60.674	52.381	17.22	0.00	35.34	4.34
208	230	2.896801	GCACACCGGAGCACTGTTG	61.897	63.158	9.46	0.00	0.00	3.33
215	502	3.286751	GAGCACTGTTGGCCGCAA	61.287	61.111	0.00	0.00	0.00	4.85
229	516	2.431683	GCAACAGACCAGGCAGGA	59.568	61.111	1.67	0.00	41.22	3.86
243	530	1.621672	GCAGGACCTCCCCTCTTCTG	61.622	65.000	0.00	0.00	33.38	3.02
246	533	2.685380	ACCTCCCCTCTTCTGCCG	60.685	66.667	0.00	0.00	0.00	5.69
247	534	3.474570	CCTCCCCTCTTCTGCCGG	61.475	72.222	0.00	0.00	0.00	6.13
248	535	2.685380	CTCCCCTCTTCTGCCGGT	60.685	66.667	1.90	0.00	0.00	5.28
249	536	2.683933	TCCCCTCTTCTGCCGGTC	60.684	66.667	1.90	0.00	0.00	4.79
251	538	2.266055	CCCTCTTCTGCCGGTCAC	59.734	66.667	1.90	0.00	0.00	3.67
252	539	2.125912	CCTCTTCTGCCGGTCACG	60.126	66.667	1.90	0.00	40.55	4.35
253	540	2.811317	CTCTTCTGCCGGTCACGC	60.811	66.667	1.90	0.00	39.22	5.34
255	542	4.379243	CTTCTGCCGGTCACGCCT	62.379	66.667	1.90	0.00	39.22	5.52
256	543	3.883744	CTTCTGCCGGTCACGCCTT	62.884	63.158	1.90	0.00	39.22	4.35
257	544	3.876589	TTCTGCCGGTCACGCCTTC	62.877	63.158	1.90	0.00	39.22	3.46
263	550	3.998672	GGTCACGCCTTCGGTCCA	61.999	66.667	0.00	0.00	40.69	4.02
360	792	2.363018	TCTCTCTCCAGTGCCCGG	60.363	66.667	0.00	0.00	0.00	5.73
410	845	2.599597	GCCACATCAGGAGGCCAT	59.400	61.111	5.01	0.00	42.58	4.40
412	847	1.105759	GCCACATCAGGAGGCCATTC	61.106	60.000	5.01	0.00	42.58	2.67
413	848	0.549950	CCACATCAGGAGGCCATTCT	59.450	55.000	5.01	0.00	0.00	2.40
414	849	1.676746	CACATCAGGAGGCCATTCTG	58.323	55.000	5.01	9.65	0.00	3.02
415	850	1.211212	CACATCAGGAGGCCATTCTGA	59.789	52.381	19.98	19.98	41.09	3.27
425	990	1.684248	GGCCATTCTGATTCTGCTGGT	60.684	52.381	0.00	0.00	0.00	4.00
446	1011	1.071471	CTAGCGCCGGGGAATTCAT	59.929	57.895	24.68	2.47	0.00	2.57
498	1067	2.889200	AGCGGACTGAGTAAGAGGG	58.111	57.895	0.00	0.00	0.00	4.30
499	1068	0.684805	AGCGGACTGAGTAAGAGGGG	60.685	60.000	0.00	0.00	0.00	4.79
561	1351	6.018994	CACCACCTTGCTAAGATCGTTATTAC	60.019	42.308	0.00	0.00	0.00	1.89
569	1359	3.795623	AGATCGTTATTACCGTGCTGT	57.204	42.857	0.00	0.00	0.00	4.40
572	1362	2.871133	TCGTTATTACCGTGCTGTCTG	58.129	47.619	0.00	0.00	0.00	3.51
583	1373	4.518970	ACCGTGCTGTCTGAATTATTTTGT	59.481	37.500	0.00	0.00	0.00	2.83
585	1375	6.021596	CCGTGCTGTCTGAATTATTTTGTAC	58.978	40.000	0.00	0.00	0.00	2.90
588	1378	7.359595	GTGCTGTCTGAATTATTTTGTACACA	58.640	34.615	0.00	0.00	0.00	3.72
604	1398	2.750948	ACACACAGTAAGTTAGCCACG	58.249	47.619	0.00	0.00	0.00	4.94
618	1412	1.063649	CCACGCTCATGCATTCAGC	59.936	57.895	14.99	14.99	45.96	4.26
638	1432	6.239396	TCAGCACCTAGTATATCCTACTGAC	58.761	44.000	0.00	0.00	0.00	3.51
639	1433	5.122554	CAGCACCTAGTATATCCTACTGACG	59.877	48.000	0.00	0.00	0.00	4.35
640	1434	5.012871	AGCACCTAGTATATCCTACTGACGA	59.987	44.000	0.00	0.00	0.00	4.20
647	2838	7.274603	AGTATATCCTACTGACGAAGAAACC	57.725	40.000	0.00	0.00	0.00	3.27
655	2846	4.451900	ACTGACGAAGAAACCTTCACATT	58.548	39.130	0.00	0.00	39.93	2.71
718	2909	2.418692	TCCAAAATAGCGCGTTTCTGA	58.581	42.857	8.43	10.09	0.00	3.27
756	2947	3.763360	TCCATGGTCCATGTTTTGTCATC	59.237	43.478	26.73	0.00	39.94	2.92
913	3107	5.472137	ACCAAGCAAGTGTATTGTATTTCGT	59.528	36.000	0.00	0.00	0.00	3.85
994	3196	9.825109	ACAAAGATATAGTAGAAGCTTTTCTCC	57.175	33.333	0.00	0.00	32.72	3.71
1050	3252	0.830444	TCCTGGTCCTGTGCGTAGTT	60.830	55.000	0.00	0.00	0.00	2.24
1186	3388	1.216444	GATGACTGCTGCTCGTGGA	59.784	57.895	0.00	0.00	0.00	4.02
1190	3392	0.944386	GACTGCTGCTCGTGGAAAAA	59.056	50.000	0.00	0.00	0.00	1.94
1206	3408	3.975035	GGAAAAAGATCACTTGCGACAAC	59.025	43.478	0.00	0.00	36.39	3.32
1208	3410	4.836125	AAAAGATCACTTGCGACAACAT	57.164	36.364	0.00	0.00	36.39	2.71
1291	3493	4.305539	AGTGATGGTTCCATGTCAATCA	57.694	40.909	9.21	0.00	0.00	2.57
1295	3497	6.211986	AGTGATGGTTCCATGTCAATCAAATT	59.788	34.615	9.21	0.00	0.00	1.82
1341	3543	6.830838	ACCTCAACTTGACAATCTTTTCTTCT	59.169	34.615	0.00	0.00	0.00	2.85
1371	3573	2.539274	GCTTCAGCTGCTAGATTTCTCG	59.461	50.000	9.47	0.00	38.21	4.04
1386	3588	0.109781	TCTCGGCAAATTTCGCTTGC	60.110	50.000	10.88	0.00	46.82	4.01
1415	3617	2.642139	TTCGACGGTATGTGACTTCC	57.358	50.000	0.00	0.00	0.00	3.46
1800	4259	5.066913	ACCTGGATCTTTCAGAAAACCTT	57.933	39.130	0.00	0.00	34.36	3.50
2155	4753	3.624326	TTCTGTTCACAAATGAAGCGG	57.376	42.857	0.00	0.00	45.58	5.52
2187	4785	5.774498	ACCTGGATCTTTCAAACAACTTC	57.226	39.130	0.00	0.00	0.00	3.01
2258	4856	5.008331	ACTAGTGAACGTATCTCTGAACCA	58.992	41.667	0.00	0.00	33.97	3.67
2381	4981	0.320858	TGCAACATTGGCAGCATTGG	60.321	50.000	0.00	0.00	36.11	3.16
2500	5102	1.784358	CCTCGGGGGTGTAATACTCA	58.216	55.000	0.00	0.00	0.00	3.41
2563	5171	5.022282	AGACAACAACAAATTTGAAGGGG	57.978	39.130	24.64	12.49	0.00	4.79
2656	5264	9.123902	CACTGGACATTTCATTATGGAATCTTA	57.876	33.333	0.00	0.00	0.00	2.10
2722	5330	5.865552	GGTGACATTCATCCAGAAATTTGTG	59.134	40.000	8.32	8.32	40.22	3.33
2889	5499	6.560003	TCCTTCATTACAGCTTTGGATCTA	57.440	37.500	0.00	0.00	0.00	1.98
3053	5663	5.713389	TCTCTCATAACAAACTCTCGGGTTA	59.287	40.000	0.00	0.00	0.00	2.85
3116	5738	6.715264	GCTTATACATTTTACTGGCCCAGTAT	59.285	38.462	23.77	11.40	44.85	2.12
3119	5741	4.929479	ACATTTTACTGGCCCAGTATCAA	58.071	39.130	23.77	18.75	44.85	2.57
3121	5743	3.359695	TTTACTGGCCCAGTATCAACC	57.640	47.619	23.77	0.00	44.85	3.77
3122	5744	1.959710	TACTGGCCCAGTATCAACCA	58.040	50.000	19.72	0.00	43.46	3.67
3139	5761	4.352595	TCAACCATAACTCTTTTGGAGGGA	59.647	41.667	0.00	0.00	45.83	4.20
3140	5762	5.076873	CAACCATAACTCTTTTGGAGGGAA	58.923	41.667	0.00	0.00	45.83	3.97
3141	5763	4.663334	ACCATAACTCTTTTGGAGGGAAC	58.337	43.478	0.00	0.00	45.83	3.62
3186	5808	9.726438	ATGGGCTTCTTATATAACAGTGATTAC	57.274	33.333	0.00	0.00	0.00	1.89
3204	5826	0.468226	ACGAACTCCAAGGCTTCACA	59.532	50.000	0.00	0.00	0.00	3.58
3207	5829	2.554032	CGAACTCCAAGGCTTCACATTT	59.446	45.455	0.00	0.00	0.00	2.32
3811	6441	2.670905	TGAATGGCGACGATTTACACAG	59.329	45.455	0.00	0.00	0.00	3.66
3854	6484	6.455360	TGCTTTAATAATCTGCTTTCCTGG	57.545	37.500	0.00	0.00	0.00	4.45
3890	6520	9.740239	AACTATGCTATCATTTGTTGCTTTATG	57.260	29.630	0.00	0.00	34.22	1.90
4062	6705	5.012664	TGTTTGGTAGCATTCTCAACCTAGA	59.987	40.000	0.00	0.00	32.99	2.43
4064	6707	5.755409	TGGTAGCATTCTCAACCTAGAAA	57.245	39.130	0.00	0.00	38.90	2.52
4065	6708	6.121776	TGGTAGCATTCTCAACCTAGAAAA	57.878	37.500	0.00	0.00	38.90	2.29
4070	6736	6.538263	AGCATTCTCAACCTAGAAAAGAACT	58.462	36.000	0.00	0.00	38.90	3.01
4089	6755	4.717233	ACTTGCATTTGTTGTTGTCTGA	57.283	36.364	0.00	0.00	0.00	3.27
4113	6779	1.606480	CGGTGTTGAGACATGCTGAGT	60.606	52.381	0.00	0.00	38.23	3.41
4133	6799	4.013728	AGTTGACACTTTGTTTGGTAGCA	58.986	39.130	0.00	0.00	0.00	3.49
4146	6812	7.372451	TGTTTGGTAGCATGTATCTGTTTAC	57.628	36.000	0.00	0.00	0.00	2.01
4162	6828	6.207928	TCTGTTTACACATGCTGAACAATTG	58.792	36.000	3.24	3.24	30.72	2.32
4175	6844	5.526846	GCTGAACAATTGTGAATTCCCAAAA	59.473	36.000	12.82	0.00	0.00	2.44
4176	6845	6.205270	GCTGAACAATTGTGAATTCCCAAAAT	59.795	34.615	12.82	0.00	0.00	1.82
4440	7167	7.223777	TGGAAATTCCGAACAGTTTTGAAAATC	59.776	33.333	7.60	4.93	40.17	2.17
4442	7169	7.698836	AATTCCGAACAGTTTTGAAAATCTG	57.301	32.000	14.35	14.35	40.08	2.90
4447	7174	8.073768	TCCGAACAGTTTTGAAAATCTGAATAC	58.926	33.333	19.55	10.65	38.48	1.89
4448	7175	8.076178	CCGAACAGTTTTGAAAATCTGAATACT	58.924	33.333	19.55	0.00	38.48	2.12
4600	7335	0.679960	GGCTATTGGCGTGTTCCCTT	60.680	55.000	0.00	0.00	42.94	3.95
4662	7401	0.978667	TCCCGTGCAGGCTACCAATA	60.979	55.000	0.00	0.00	39.21	1.90
4671	7410	4.345257	TGCAGGCTACCAATAAACCAAAAA	59.655	37.500	0.00	0.00	0.00	1.94
4675	7414	5.782845	AGGCTACCAATAAACCAAAAATGGA	59.217	36.000	1.10	0.00	0.00	3.41
4717	7459	1.614996	TGCACCCTACCAAACACATG	58.385	50.000	0.00	0.00	0.00	3.21
4734	7476	3.310774	CACATGCTAACTATCACTGGTGC	59.689	47.826	0.00	0.00	0.00	5.01
4741	7483	2.384828	ACTATCACTGGTGCGGATGTA	58.615	47.619	0.00	0.00	0.00	2.29

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
89	90	6.347563	CGTGTATAAACGGGCTTGTCTAAAAA	60.348	38.462	7.61	0.00	39.89	1.94
90	91	5.120519	CGTGTATAAACGGGCTTGTCTAAAA	59.879	40.000	7.61	0.00	39.89	1.52
91	92	4.626604	CGTGTATAAACGGGCTTGTCTAAA	59.373	41.667	7.61	0.00	39.89	1.85
92	93	4.175516	CGTGTATAAACGGGCTTGTCTAA	58.824	43.478	7.61	0.00	39.89	2.10
93	94	3.772932	CGTGTATAAACGGGCTTGTCTA	58.227	45.455	7.61	0.00	39.89	2.59
229	516	2.685380	CGGCAGAAGAGGGGAGGT	60.685	66.667	0.00	0.00	0.00	3.85
259	546	4.489771	CCACCCCGGATGCTGGAC	62.490	72.222	0.73	0.00	36.56	4.02
333	759	3.223589	GAGAGAGAGGGCGAGGGC	61.224	72.222	0.00	0.00	38.90	5.19
334	760	2.520741	GGAGAGAGAGGGCGAGGG	60.521	72.222	0.00	0.00	0.00	4.30
337	763	1.379176	CACTGGAGAGAGAGGGCGA	60.379	63.158	0.00	0.00	0.00	5.54
338	764	3.074999	GCACTGGAGAGAGAGGGCG	62.075	68.421	0.00	0.00	0.00	6.13
339	765	2.730524	GGCACTGGAGAGAGAGGGC	61.731	68.421	0.00	0.00	0.00	5.19
340	766	2.063378	GGGCACTGGAGAGAGAGGG	61.063	68.421	0.00	0.00	0.00	4.30
341	767	2.422231	CGGGCACTGGAGAGAGAGG	61.422	68.421	0.00	0.00	0.00	3.69
360	792	2.352915	CGCGAGAGACGATGAGGC	60.353	66.667	0.00	0.00	45.77	4.70
407	842	1.938577	CGACCAGCAGAATCAGAATGG	59.061	52.381	0.00	0.00	36.16	3.16
440	1005	0.249120	TCAGTCGACCGCCATGAATT	59.751	50.000	13.01	0.00	0.00	2.17
446	1011	2.765250	GAAGCTTCAGTCGACCGCCA	62.765	60.000	21.67	0.00	0.00	5.69
491	1060	0.546598	GCTAAGCAAGCCCCCTCTTA	59.453	55.000	0.00	0.00	46.25	2.10
493	1062	3.002371	GCTAAGCAAGCCCCCTCT	58.998	61.111	0.00	0.00	46.25	3.69
511	1081	0.912486	GAGGTGGAAGTGGCATACCT	59.088	55.000	9.17	9.17	44.04	3.08
561	1351	5.046910	ACAAAATAATTCAGACAGCACGG	57.953	39.130	0.00	0.00	0.00	4.94
583	1373	3.858129	GCGTGGCTAACTTACTGTGTGTA	60.858	47.826	0.00	0.00	0.00	2.90
585	1375	1.459592	GCGTGGCTAACTTACTGTGTG	59.540	52.381	0.00	0.00	0.00	3.82
588	1378	1.616865	TGAGCGTGGCTAACTTACTGT	59.383	47.619	0.00	0.00	39.88	3.55
618	1412	7.160049	TCTTCGTCAGTAGGATATACTAGGTG	58.840	42.308	0.00	0.00	0.00	4.00
619	1413	7.313740	TCTTCGTCAGTAGGATATACTAGGT	57.686	40.000	0.00	0.00	0.00	3.08
620	1414	8.505625	GTTTCTTCGTCAGTAGGATATACTAGG	58.494	40.741	0.00	0.00	0.00	3.02
628	1422	5.074584	GAAGGTTTCTTCGTCAGTAGGAT	57.925	43.478	0.00	0.00	39.82	3.24
640	1434	6.715347	AAGTTGCTAATGTGAAGGTTTCTT	57.285	33.333	0.00	0.00	35.62	2.52
647	2838	8.633075	TGAAAAGAAAAGTTGCTAATGTGAAG	57.367	30.769	0.00	0.00	0.00	3.02
655	2846	7.066887	TGTCAGTCATGAAAAGAAAAGTTGCTA	59.933	33.333	0.00	0.00	37.14	3.49
756	2947	5.009010	GTGGGTAGCCATAGACATCAAATTG	59.991	44.000	18.29	0.00	0.00	2.32
836	3027	3.904136	CTTGGACAGCAACTTTACCTG	57.096	47.619	0.00	0.00	0.00	4.00
864	3055	2.819608	CAAAGTTGTGGTCCATGGTAGG	59.180	50.000	12.58	0.00	0.00	3.18
913	3107	6.075315	TCTGCTCCTTTATACACCTGCTATA	58.925	40.000	0.00	0.00	0.00	1.31
994	3196	0.890683	AAGAAGCGGCCCATTTGAAG	59.109	50.000	0.00	0.00	0.00	3.02
1050	3252	0.976641	AACTCGGAAGCATGGAGTGA	59.023	50.000	2.80	0.00	40.67	3.41
1186	3388	4.630894	TGTTGTCGCAAGTGATCTTTTT	57.369	36.364	0.00	0.00	39.48	1.94
1190	3392	2.738846	GTGATGTTGTCGCAAGTGATCT	59.261	45.455	0.00	0.00	37.30	2.75
1206	3408	2.281498	ACGCAATATTCGTCGTGTGATG	59.719	45.455	7.00	0.00	34.84	3.07
1208	3410	1.915350	GACGCAATATTCGTCGTGTGA	59.085	47.619	18.12	0.00	45.19	3.58
1291	3493	4.236935	CAGCATGCAACTTCCGTAAATTT	58.763	39.130	21.98	0.00	0.00	1.82
1295	3497	1.164411	CCAGCATGCAACTTCCGTAA	58.836	50.000	21.98	0.00	31.97	3.18
1320	3522	7.166473	CGGAAAGAAGAAAAGATTGTCAAGTTG	59.834	37.037	0.00	0.00	0.00	3.16
1362	3564	2.749621	AGCGAAATTTGCCGAGAAATCT	59.250	40.909	0.83	0.00	0.00	2.40
1386	3588	6.735063	GTCACATACCGTCGAAATTTTGTAAG	59.265	38.462	5.33	0.00	0.00	2.34
1415	3617	7.394870	TGCTCGATTCAGAATAAGATTTACG	57.605	36.000	8.58	1.07	0.00	3.18
1465	3720	4.825422	TGAGGTTGAGATACTTGAGCTTG	58.175	43.478	0.00	0.00	0.00	4.01
1663	4121	8.588290	TTTTCTAAACCTGCCATGTATACATT	57.412	30.769	15.85	2.71	33.61	2.71
1944	4542	8.515414	GCTAGAACAACCAAATCAGTATTTCTT	58.485	33.333	0.00	0.00	32.87	2.52
1947	4545	6.653320	TCGCTAGAACAACCAAATCAGTATTT	59.347	34.615	0.00	0.00	35.65	1.40
2155	4753	5.488341	TGAAAGATCCAGGTAAACTAGTGC	58.512	41.667	0.00	0.00	0.00	4.40
2187	4785	8.796475	CAAATGGGGTATAATGATCCAACTAAG	58.204	37.037	0.00	0.00	0.00	2.18
2258	4856	2.928334	CTGGCAGCTGTCCTTCAATAT	58.072	47.619	17.28	0.00	0.00	1.28
2515	5117	0.877071	ATTTCTGCCGCAACTGACAG	59.123	50.000	0.00	0.00	0.00	3.51
2563	5171	4.647399	ACCAGACAGATTTCTAGGTAGAGC	59.353	45.833	0.00	0.00	33.21	4.09
2617	5225	2.169144	TGTCCAGTGCTCCTGACATATG	59.831	50.000	0.00	0.00	44.49	1.78
2656	5264	1.602311	CTCAAAGCTGCCAGTGAAGT	58.398	50.000	0.00	0.00	0.00	3.01
2816	5424	6.521427	GCCTGACAGTGAATTCCCAGATATAT	60.521	42.308	2.27	0.00	0.00	0.86
2889	5499	1.003839	TGCGAACTGATTCCGGCTT	60.004	52.632	0.00	0.00	0.00	4.35
3053	5663	2.355310	CCACCAATACACCGTGGTACAT	60.355	50.000	3.03	0.00	46.61	2.29
3114	5736	6.216662	TCCCTCCAAAAGAGTTATGGTTGATA	59.783	38.462	0.00	0.00	41.47	2.15
3116	5738	4.352595	TCCCTCCAAAAGAGTTATGGTTGA	59.647	41.667	0.00	0.00	41.47	3.18
3119	5741	4.354087	AGTTCCCTCCAAAAGAGTTATGGT	59.646	41.667	0.00	0.00	41.47	3.55
3121	5743	6.294731	CCAAAGTTCCCTCCAAAAGAGTTATG	60.295	42.308	0.00	0.00	41.47	1.90
3122	5744	5.775195	CCAAAGTTCCCTCCAAAAGAGTTAT	59.225	40.000	0.00	0.00	41.47	1.89
3139	5761	5.123820	CCATATCATCGAACACACCAAAGTT	59.876	40.000	0.00	0.00	0.00	2.66
3140	5762	4.635765	CCATATCATCGAACACACCAAAGT	59.364	41.667	0.00	0.00	0.00	2.66
3141	5763	4.035558	CCCATATCATCGAACACACCAAAG	59.964	45.833	0.00	0.00	0.00	2.77
3186	5808	1.813513	ATGTGAAGCCTTGGAGTTCG	58.186	50.000	0.00	0.00	0.00	3.95
3204	5826	5.546035	ATGGGTTCCCTTTAGTGGTAAAT	57.454	39.130	9.43	0.00	0.00	1.40
3207	5829	4.225717	GTGTATGGGTTCCCTTTAGTGGTA	59.774	45.833	9.43	0.00	0.00	3.25
3625	6251	3.262660	TCAGAATCATCAGCCACACTTCT	59.737	43.478	0.00	0.00	0.00	2.85
3854	6484	9.708222	CAAATGATAGCATAGTTTACAACAGAC	57.292	33.333	0.00	0.00	33.44	3.51
3890	6520	2.175878	TCTGCTGAGACAAAGCTTCC	57.824	50.000	0.00	0.00	41.42	3.46
4062	6705	6.650390	AGACAACAACAAATGCAAGTTCTTTT	59.350	30.769	0.00	0.00	0.00	2.27
4064	6707	5.577945	CAGACAACAACAAATGCAAGTTCTT	59.422	36.000	0.00	0.00	0.00	2.52
4065	6708	5.104374	CAGACAACAACAAATGCAAGTTCT	58.896	37.500	0.00	0.00	0.00	3.01
4070	6736	5.221880	GCTATCAGACAACAACAAATGCAA	58.778	37.500	0.00	0.00	0.00	4.08
4089	6755	1.208052	AGCATGTCTCAACACCGCTAT	59.792	47.619	0.00	0.00	42.63	2.97
4113	6779	4.400884	ACATGCTACCAAACAAAGTGTCAA	59.599	37.500	0.00	0.00	0.00	3.18
4133	6799	6.654582	TGTTCAGCATGTGTAAACAGATACAT	59.345	34.615	0.00	0.00	38.03	2.29
4146	6812	5.119588	GGAATTCACAATTGTTCAGCATGTG	59.880	40.000	8.77	0.00	38.68	3.21
4242	6949	9.263538	TCAGAAAATGTTCAGAATTCCAAAATG	57.736	29.630	0.65	0.00	36.09	2.32
4422	7132	8.076178	AGTATTCAGATTTTCAAAACTGTTCGG	58.924	33.333	8.81	0.00	39.14	4.30
4423	7133	9.450807	AAGTATTCAGATTTTCAAAACTGTTCG	57.549	29.630	8.81	0.00	39.14	3.95
4539	7268	2.022346	GATGCGAGCGACGACGTA	59.978	61.111	9.33	3.42	45.77	3.57
4586	7321	0.748729	ACGAAAAGGGAACACGCCAA	60.749	50.000	0.00	0.00	0.00	4.52
4590	7325	0.591170	ATGCACGAAAAGGGAACACG	59.409	50.000	0.00	0.00	0.00	4.49
4597	7332	1.061131	CTCGTAGCATGCACGAAAAGG	59.939	52.381	30.68	21.35	46.76	3.11
4600	7335	0.739462	CCCTCGTAGCATGCACGAAA	60.739	55.000	30.68	18.46	46.76	3.46
4671	7410	8.778059	TGAGGGTAAATTTACTACTCAATCCAT	58.222	33.333	31.22	14.36	40.73	3.41
4675	7414	8.052748	TGCATGAGGGTAAATTTACTACTCAAT	58.947	33.333	33.73	25.72	43.48	2.57
4717	7459	1.136305	TCCGCACCAGTGATAGTTAGC	59.864	52.381	0.99	0.00	0.00	3.09
4734	7476	5.424121	GAAATCCAACCATCTTACATCCG	57.576	43.478	0.00	0.00	0.00	4.18

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.