AutoCloner

Multiple sequence alignment - TraesCS5A01G463700

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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	TraesCS5A01G463700	chr5A	100.000	3386	0	0	1	3386	643628332	643624947	0.000000e+00	6253.0
1	TraesCS5A01G463700	chr5A	84.033	1453	192	20	954	2378	643578543	643577103	0.000000e+00	1362.0
2	TraesCS5A01G463700	chr5A	85.312	817	117	3	1562	2378	643453170	643452357	0.000000e+00	841.0
3	TraesCS5A01G463700	chr5A	82.114	984	152	17	1411	2379	643734545	643733571	0.000000e+00	821.0
4	TraesCS5A01G463700	chr5A	83.852	867	128	8	1505	2362	643854910	643854047	0.000000e+00	815.0
5	TraesCS5A01G463700	chr5A	86.897	435	44	2	986	1408	643855541	643855108	3.060000e-130	475.0
6	TraesCS5A01G463700	chr5B	88.783	2630	174	44	69	2634	648146806	648144234	0.000000e+00	3110.0
7	TraesCS5A01G463700	chr5B	85.371	1415	175	18	978	2370	648135996	648134592	0.000000e+00	1437.0
8	TraesCS5A01G463700	chr5B	84.298	968	143	5	1406	2370	648122857	648123818	0.000000e+00	937.0
9	TraesCS5A01G463700	chr5B	83.588	981	141	16	1406	2373	648180353	648179380	0.000000e+00	902.0
10	TraesCS5A01G463700	chr5B	83.163	980	136	19	1406	2367	648260039	648259071	0.000000e+00	869.0
11	TraesCS5A01G463700	chr5B	84.896	821	106	7	1559	2378	647993859	647993056	0.000000e+00	813.0
12	TraesCS5A01G463700	chr5B	87.126	435	44	1	986	1408	648260585	648260151	1.830000e-132	483.0
13	TraesCS5A01G463700	chr5B	89.305	374	32	4	2777	3143	648143931	648143559	2.380000e-126	462.0
14	TraesCS5A01G463700	chr5B	90.351	342	17	7	3060	3386	648143560	648143220	5.190000e-118	435.0
15	TraesCS5A01G463700	chr5B	75.449	167	33	6	149	311	54700502	54700340	1.300000e-09	75.0
16	TraesCS5A01G463700	chr5D	92.606	1961	109	19	687	2643	515412649	515410721	0.000000e+00	2785.0
17	TraesCS5A01G463700	chr5D	83.546	863	127	13	1505	2356	515568273	515567415	0.000000e+00	793.0
18	TraesCS5A01G463700	chr5D	82.957	886	136	13	1505	2379	551243502	551242621	0.000000e+00	785.0
19	TraesCS5A01G463700	chr5D	89.576	566	27	15	1	549	515413199	515412649	0.000000e+00	689.0
20	TraesCS5A01G463700	chr5D	83.558	742	81	19	948	1670	515339061	515338342	0.000000e+00	656.0
21	TraesCS5A01G463700	chr5D	87.788	434	42	7	986	1408	515568864	515568431	6.520000e-137	497.0
22	TraesCS5A01G463700	chr5D	86.636	434	46	7	986	1407	551244094	551243661	1.420000e-128	470.0
23	TraesCS5A01G463700	chr5D	86.009	436	47	3	986	1408	515466254	515465820	3.980000e-124	455.0
24	TraesCS5A01G463700	chr5D	86.500	400	41	7	2642	3030	515410578	515410181	8.680000e-116	427.0
25	TraesCS5A01G463700	chr5D	86.297	343	34	7	2681	3012	393679320	393679660	8.930000e-96	361.0
26	TraesCS5A01G463700	chr1B	86.486	407	47	7	1038	1437	136921882	136922287	1.120000e-119	440.0
27	TraesCS5A01G463700	chr4D	86.589	343	33	7	2681	3012	495759269	495759609	1.920000e-97	366.0
28	TraesCS5A01G463700	chr1D	86.589	343	33	7	2681	3012	45886262	45886602	1.920000e-97	366.0
29	TraesCS5A01G463700	chr1D	86.006	343	34	8	2681	3012	5239351	5239012	4.160000e-94	355.0
30	TraesCS5A01G463700	chr1D	86.006	343	35	7	2681	3012	481233302	481232962	4.160000e-94	355.0
31	TraesCS5A01G463700	chr1D	89.362	47	5	0	1376	1422	83902761	83902807	3.650000e-05	60.2
32	TraesCS5A01G463700	chr2D	86.217	341	34	7	2681	3010	4963262	4962924	1.160000e-94	357.0
33	TraesCS5A01G463700	chr7D	85.965	342	36	7	2681	3012	603069434	603069095	4.160000e-94	355.0
34	TraesCS5A01G463700	chr2A	79.114	158	27	4	145	302	737302793	737302642	1.660000e-18	104.0
35	TraesCS5A01G463700	chr6B	73.529	204	47	6	112	312	140672638	140672439	1.690000e-08	71.3
36	TraesCS5A01G463700	chr4B	74.257	202	35	10	74	271	16053578	16053766	6.060000e-08	69.4
37	TraesCS5A01G463700	chr6A	90.000	50	4	1	142	191	554824654	554824606	2.820000e-06	63.9

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	TraesCS5A01G463700	chr5A	643624947	643628332	3385	True	6253.000000	6253	100.000000	1	3386	1	chr5A.!!$R3	3385
1	TraesCS5A01G463700	chr5A	643577103	643578543	1440	True	1362.000000	1362	84.033000	954	2378	1	chr5A.!!$R2	1424
2	TraesCS5A01G463700	chr5A	643452357	643453170	813	True	841.000000	841	85.312000	1562	2378	1	chr5A.!!$R1	816
3	TraesCS5A01G463700	chr5A	643733571	643734545	974	True	821.000000	821	82.114000	1411	2379	1	chr5A.!!$R4	968
4	TraesCS5A01G463700	chr5A	643854047	643855541	1494	True	645.000000	815	85.374500	986	2362	2	chr5A.!!$R5	1376
5	TraesCS5A01G463700	chr5B	648134592	648135996	1404	True	1437.000000	1437	85.371000	978	2370	1	chr5B.!!$R3	1392
6	TraesCS5A01G463700	chr5B	648143220	648146806	3586	True	1335.666667	3110	89.479667	69	3386	3	chr5B.!!$R5	3317
7	TraesCS5A01G463700	chr5B	648122857	648123818	961	False	937.000000	937	84.298000	1406	2370	1	chr5B.!!$F1	964
8	TraesCS5A01G463700	chr5B	648179380	648180353	973	True	902.000000	902	83.588000	1406	2373	1	chr5B.!!$R4	967
9	TraesCS5A01G463700	chr5B	647993056	647993859	803	True	813.000000	813	84.896000	1559	2378	1	chr5B.!!$R2	819
10	TraesCS5A01G463700	chr5B	648259071	648260585	1514	True	676.000000	869	85.144500	986	2367	2	chr5B.!!$R6	1381
11	TraesCS5A01G463700	chr5D	515410181	515413199	3018	True	1300.333333	2785	89.560667	1	3030	3	chr5D.!!$R3	3029
12	TraesCS5A01G463700	chr5D	515338342	515339061	719	True	656.000000	656	83.558000	948	1670	1	chr5D.!!$R1	722
13	TraesCS5A01G463700	chr5D	515567415	515568864	1449	True	645.000000	793	85.667000	986	2356	2	chr5D.!!$R4	1370
14	TraesCS5A01G463700	chr5D	551242621	551244094	1473	True	627.500000	785	84.796500	986	2379	2	chr5D.!!$R5	1393

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
928	1006	0.31904	GCACTGAGCACGAACAGAGA	60.319	55.0	0.0	0.0	44.79	3.1	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2736	3185	0.321653	GAGGATTGTTGGTCACCGCT	60.322	55.0	0.0	0.0	0.0	5.52	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
343	363	1.500108	CATGCGCTCCTCATTCTCTC	58.500	55.000	9.73	0.00	0.00	3.20
344	364	1.068895	CATGCGCTCCTCATTCTCTCT	59.931	52.381	9.73	0.00	0.00	3.10
345	365	1.189752	TGCGCTCCTCATTCTCTCTT	58.810	50.000	9.73	0.00	0.00	2.85
346	366	1.135915	TGCGCTCCTCATTCTCTCTTC	59.864	52.381	9.73	0.00	0.00	2.87
347	367	1.408702	GCGCTCCTCATTCTCTCTTCT	59.591	52.381	0.00	0.00	0.00	2.85
348	368	2.543653	GCGCTCCTCATTCTCTCTTCTC	60.544	54.545	0.00	0.00	0.00	2.87
349	369	2.951642	CGCTCCTCATTCTCTCTTCTCT	59.048	50.000	0.00	0.00	0.00	3.10
383	410	5.937975	ATCCACCATTTTATTCCACCTTG	57.062	39.130	0.00	0.00	0.00	3.61
437	464	8.801882	ACCCATATTTTGATTTCTCGAACTTA	57.198	30.769	0.00	0.00	0.00	2.24
469	497	3.824414	AATTCCTCGCGTAAAAACCTG	57.176	42.857	5.77	0.00	0.00	4.00
567	598	8.822652	ATCAGTTTTTGGAATGAGTGAATTTC	57.177	30.769	0.00	0.00	0.00	2.17
605	648	9.657419	AGAGTGAAATCAGTGAAATTTGTTTTT	57.343	25.926	0.00	0.00	0.00	1.94
611	654	9.540431	AAATCAGTGAAATTTGTTTTTGAAACG	57.460	25.926	0.00	0.00	0.00	3.60
614	657	7.596995	TCAGTGAAATTTGTTTTTGAAACGAGT	59.403	29.630	0.00	0.00	0.00	4.18
625	668	3.961477	TGAAACGAGTGAAACCATGTG	57.039	42.857	0.00	0.00	37.80	3.21
696	770	5.796350	AATGACTAACAATAACACCTCGC	57.204	39.130	0.00	0.00	0.00	5.03
701	775	2.094762	ACAATAACACCTCGCAGTCC	57.905	50.000	0.00	0.00	0.00	3.85
711	785	1.268539	CCTCGCAGTCCACAAAAACAC	60.269	52.381	0.00	0.00	0.00	3.32
715	789	2.024414	GCAGTCCACAAAAACACCTCT	58.976	47.619	0.00	0.00	0.00	3.69
716	790	2.427095	GCAGTCCACAAAAACACCTCTT	59.573	45.455	0.00	0.00	0.00	2.85
719	793	4.035675	CAGTCCACAAAAACACCTCTTCTC	59.964	45.833	0.00	0.00	0.00	2.87
726	801	7.416213	CCACAAAAACACCTCTTCTCAAACATA	60.416	37.037	0.00	0.00	0.00	2.29
729	804	7.881775	AAAACACCTCTTCTCAAACATAGTT	57.118	32.000	0.00	0.00	0.00	2.24
774	849	7.899178	TCAAGTAAAATGCGAGAACAAGATA	57.101	32.000	0.00	0.00	0.00	1.98
775	850	7.739295	TCAAGTAAAATGCGAGAACAAGATAC	58.261	34.615	0.00	0.00	0.00	2.24
820	896	2.868044	GCACAGTCCTACTTGACCACTG	60.868	54.545	0.00	0.00	40.33	3.66
840	916	2.818274	GCCGGGCGTGGAAGTAAG	60.818	66.667	1.81	0.00	0.00	2.34
841	917	2.818274	CCGGGCGTGGAAGTAAGC	60.818	66.667	0.00	0.00	0.00	3.09
842	918	3.186047	CGGGCGTGGAAGTAAGCG	61.186	66.667	0.00	0.00	0.00	4.68
843	919	2.047560	GGGCGTGGAAGTAAGCGT	60.048	61.111	0.00	0.00	0.00	5.07
844	920	2.098831	GGGCGTGGAAGTAAGCGTC	61.099	63.158	0.00	0.00	0.00	5.19
845	921	2.442188	GGCGTGGAAGTAAGCGTCG	61.442	63.158	0.00	0.00	0.00	5.12
846	922	1.443194	GCGTGGAAGTAAGCGTCGA	60.443	57.895	0.00	0.00	0.00	4.20
847	923	1.671880	GCGTGGAAGTAAGCGTCGAC	61.672	60.000	5.18	5.18	0.00	4.20
848	924	0.386352	CGTGGAAGTAAGCGTCGACA	60.386	55.000	17.16	0.00	33.14	4.35
849	925	1.058404	GTGGAAGTAAGCGTCGACAC	58.942	55.000	17.16	5.80	33.59	3.67
889	965	1.338674	ACACGGAATCTCATTTCGCCA	60.339	47.619	0.00	0.00	45.00	5.69
928	1006	0.319040	GCACTGAGCACGAACAGAGA	60.319	55.000	0.00	0.00	44.79	3.10
929	1007	1.695813	CACTGAGCACGAACAGAGAG	58.304	55.000	0.00	0.00	37.54	3.20
950	1028	1.201429	ACCACCAAGCTCCCGATTCT	61.201	55.000	0.00	0.00	0.00	2.40
982	1060	1.591703	CCAAGTGGACGAGCTAGCA	59.408	57.895	18.83	0.00	37.39	3.49
1081	1164	3.702048	GCCACCTGCTCCCGTACA	61.702	66.667	0.00	0.00	36.87	2.90
1256	1370	4.953868	CAACGACGTCCCGGCACA	62.954	66.667	10.58	0.00	32.52	4.57
1512	1752	3.912907	CGCGCTCCTCCCCGTTAT	61.913	66.667	5.56	0.00	0.00	1.89
1912	2158	2.282180	TCAGAAAACCCAGCGGCC	60.282	61.111	0.00	0.00	0.00	6.13
1955	2204	0.543749	GACATCCTCCCTCCTGGTTG	59.456	60.000	0.00	0.00	34.77	3.77
2109	2366	2.887568	CACCCGCTCGTCATGCTC	60.888	66.667	0.00	0.00	0.00	4.26
2112	2369	4.147449	CCGCTCGTCATGCTCCCA	62.147	66.667	0.00	0.00	0.00	4.37
2388	2645	1.511850	CAGGTGCAACGAACTGATGA	58.488	50.000	0.00	0.00	38.12	2.92
2410	2667	6.908825	TGACAATTTCACTACTGCCAAATAC	58.091	36.000	0.00	0.00	0.00	1.89
2411	2668	6.714810	TGACAATTTCACTACTGCCAAATACT	59.285	34.615	0.00	0.00	0.00	2.12
2412	2669	7.880713	TGACAATTTCACTACTGCCAAATACTA	59.119	33.333	0.00	0.00	0.00	1.82
2413	2670	8.630054	ACAATTTCACTACTGCCAAATACTAA	57.370	30.769	0.00	0.00	0.00	2.24
2466	2724	8.260818	TGGAAACCACACATTCAAAGAATTAAA	58.739	29.630	0.00	0.00	0.00	1.52
2467	2725	9.271828	GGAAACCACACATTCAAAGAATTAAAT	57.728	29.630	0.00	0.00	0.00	1.40
2470	2728	7.090173	ACCACACATTCAAAGAATTAAATCGG	58.910	34.615	0.00	0.00	0.00	4.18
2471	2729	7.090173	CCACACATTCAAAGAATTAAATCGGT	58.910	34.615	0.00	0.00	0.00	4.69
2474	2732	7.090173	CACATTCAAAGAATTAAATCGGTGGT	58.910	34.615	0.00	0.00	0.00	4.16
2552	2810	7.362574	GCATCTTACTCAAGTTGTCTCTAGTCT	60.363	40.741	2.11	0.00	35.01	3.24
2554	2812	8.466617	TCTTACTCAAGTTGTCTCTAGTCTTT	57.533	34.615	2.11	0.00	33.20	2.52
2640	2899	3.707102	ACAACAGGAAGGTAGAGATAGGC	59.293	47.826	0.00	0.00	0.00	3.93
2644	3086	4.202588	ACAGGAAGGTAGAGATAGGCGTAT	60.203	45.833	0.00	0.00	0.00	3.06
2659	3101	1.738030	GCGTATAGTTGACTTGGCGGT	60.738	52.381	0.00	0.00	0.00	5.68
2671	3113	0.037326	TTGGCGGTCATCTGAGACAC	60.037	55.000	8.71	0.00	40.29	3.67
2725	3174	2.308570	TGATACAAGTCCCATTGCTGGT	59.691	45.455	0.00	0.00	41.37	4.00
2736	3185	1.962807	CATTGCTGGTTGACCAAAGGA	59.037	47.619	4.18	0.00	46.97	3.36
2737	3186	1.691196	TTGCTGGTTGACCAAAGGAG	58.309	50.000	4.18	0.00	46.97	3.69
2747	3200	1.228124	CCAAAGGAGCGGTGACCAA	60.228	57.895	1.11	0.00	0.00	3.67
2753	3206	1.305930	GGAGCGGTGACCAACAATCC	61.306	60.000	1.11	0.00	0.00	3.01
2786	3249	2.420129	GGTCATGTTACCTTCCAGCGAT	60.420	50.000	0.00	0.00	36.53	4.58
2795	3258	3.853207	ACCTTCCAGCGATACCCTAATA	58.147	45.455	0.00	0.00	0.00	0.98
2855	3318	6.751514	TGAAAGAAGCACAAGTGTCTTTAA	57.248	33.333	14.81	8.29	36.59	1.52
2892	3355	7.006865	TGGGTTTAGTATTTGCTACTGTACA	57.993	36.000	0.00	0.00	40.94	2.90
2893	3356	7.451732	TGGGTTTAGTATTTGCTACTGTACAA	58.548	34.615	0.00	0.00	40.94	2.41
2895	3358	8.953313	GGGTTTAGTATTTGCTACTGTACAAAT	58.047	33.333	21.00	21.00	45.73	2.32
2948	3412	0.542467	TTCCACATGCAGTTGGCCAT	60.542	50.000	6.09	0.00	43.89	4.40
3030	3499	2.959707	AGGGATACTCGCTAAACAGGAG	59.040	50.000	0.00	0.00	37.94	3.69
3032	3501	3.887716	GGGATACTCGCTAAACAGGAGTA	59.112	47.826	2.97	2.97	44.64	2.59
3067	3536	7.303634	TGACAAAGTTCAGTCTAAACAAGTC	57.696	36.000	9.12	0.00	35.81	3.01
3103	3658	2.094906	CCCAAGCAATCACTGTGACATG	60.095	50.000	13.50	15.54	0.00	3.21
3111	3666	5.680408	GCAATCACTGTGACATGCCATATTT	60.680	40.000	27.28	8.92	36.88	1.40
3169	3728	3.055530	TGGAGCTCCATCAGAAGAAGAAC	60.056	47.826	32.00	0.00	42.01	3.01
3188	3747	6.892310	AGAACAAAAAGCAACATCTTTCAC	57.108	33.333	0.00	0.00	35.41	3.18
3223	3782	5.075493	AGAAAGGTGCATCAAGTGAATTCT	58.925	37.500	7.05	0.00	0.00	2.40
3282	3841	8.970859	AAGTCTTCTTTAAGGGATGATATGTG	57.029	34.615	0.00	0.00	33.22	3.21
3300	3859	2.170397	TGTGAGGTCTGTTCTCAAAGCA	59.830	45.455	0.00	0.00	42.13	3.91
3322	3890	6.656693	AGCAAACAAGATAATCAGTTGCTACT	59.343	34.615	6.22	0.00	31.54	2.57
3366	3934	2.578021	ACATTACAAGGCCCTCATGTCT	59.422	45.455	0.00	0.00	0.00	3.41
3367	3935	3.209410	CATTACAAGGCCCTCATGTCTC	58.791	50.000	0.00	0.00	0.00	3.36
3368	3936	0.824109	TACAAGGCCCTCATGTCTCG	59.176	55.000	0.00	0.00	0.00	4.04
3382	3950	4.827284	TCATGTCTCGCTAGTTCATGGATA	59.173	41.667	17.94	5.10	37.08	2.59
3383	3951	4.837896	TGTCTCGCTAGTTCATGGATAG	57.162	45.455	0.00	0.00	0.00	2.08

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
126	127	9.883142	AAAAAGTCTTATGATGTGAACCAAAAA	57.117	25.926	0.00	0.00	0.00	1.94
271	274	6.115448	AGGAATTTCATAGGATAGGGTTCG	57.885	41.667	0.00	0.00	0.00	3.95
272	275	7.974504	TGTAGGAATTTCATAGGATAGGGTTC	58.025	38.462	0.00	0.00	0.00	3.62
343	363	5.048434	GGTGGATTTGTTTGGAAGAGAGAAG	60.048	44.000	0.00	0.00	0.00	2.85
344	364	4.827284	GGTGGATTTGTTTGGAAGAGAGAA	59.173	41.667	0.00	0.00	0.00	2.87
345	365	4.141274	TGGTGGATTTGTTTGGAAGAGAGA	60.141	41.667	0.00	0.00	0.00	3.10
346	366	4.144297	TGGTGGATTTGTTTGGAAGAGAG	58.856	43.478	0.00	0.00	0.00	3.20
347	367	4.177537	TGGTGGATTTGTTTGGAAGAGA	57.822	40.909	0.00	0.00	0.00	3.10
348	368	5.473066	AATGGTGGATTTGTTTGGAAGAG	57.527	39.130	0.00	0.00	0.00	2.85
349	369	5.885449	AAATGGTGGATTTGTTTGGAAGA	57.115	34.783	0.00	0.00	32.69	2.87
383	410	7.793927	AAGACATAGCTGATTTAAGTTAGGC	57.206	36.000	0.00	0.00	0.00	3.93
437	464	8.836268	TTACGCGAGGAATTTGGTTATATAAT	57.164	30.769	15.93	0.00	0.00	1.28
535	566	9.185192	CACTCATTCCAAAAACTGATTTTACTC	57.815	33.333	0.00	0.00	39.20	2.59
605	648	3.275143	ACACATGGTTTCACTCGTTTCA	58.725	40.909	0.00	0.00	0.00	2.69
611	654	7.973944	ACTCTTTTTAAACACATGGTTTCACTC	59.026	33.333	13.43	0.00	46.61	3.51
614	657	7.831753	TCACTCTTTTTAAACACATGGTTTCA	58.168	30.769	13.43	3.49	46.61	2.69
670	713	7.572353	GCGAGGTGTTATTGTTAGTCATTTCAA	60.572	37.037	0.00	0.00	0.00	2.69
681	724	2.224426	TGGACTGCGAGGTGTTATTGTT	60.224	45.455	0.00	0.00	0.00	2.83
696	770	3.947834	AGAAGAGGTGTTTTTGTGGACTG	59.052	43.478	0.00	0.00	0.00	3.51
701	775	5.708948	TGTTTGAGAAGAGGTGTTTTTGTG	58.291	37.500	0.00	0.00	0.00	3.33
711	785	8.383318	TCTTTTCAACTATGTTTGAGAAGAGG	57.617	34.615	14.90	0.00	45.11	3.69
751	826	7.478667	GTGTATCTTGTTCTCGCATTTTACTTG	59.521	37.037	0.00	0.00	0.00	3.16
844	920	0.594602	TTGGGTAGTGTCGAGTGTCG	59.405	55.000	0.00	0.00	42.10	4.35
845	921	1.338973	TGTTGGGTAGTGTCGAGTGTC	59.661	52.381	0.00	0.00	0.00	3.67
846	922	1.405872	TGTTGGGTAGTGTCGAGTGT	58.594	50.000	0.00	0.00	0.00	3.55
847	923	2.519377	TTGTTGGGTAGTGTCGAGTG	57.481	50.000	0.00	0.00	0.00	3.51
848	924	3.764237	ATTTGTTGGGTAGTGTCGAGT	57.236	42.857	0.00	0.00	0.00	4.18
849	925	4.387862	GTGTATTTGTTGGGTAGTGTCGAG	59.612	45.833	0.00	0.00	0.00	4.04
889	965	3.865929	CTGCTCACGCGGTGGACTT	62.866	63.158	12.47	0.00	39.65	3.01
928	1006	4.335647	CGGGAGCTTGGTGGTGCT	62.336	66.667	0.00	0.00	42.82	4.40
929	1007	3.628646	ATCGGGAGCTTGGTGGTGC	62.629	63.158	0.00	0.00	0.00	5.01
982	1060	1.134280	CATGGCGAAGATCAGGAGGTT	60.134	52.381	0.00	0.00	0.00	3.50
1014	1097	1.005275	CAGCGGCGAGGATGATGAT	60.005	57.895	12.98	0.00	0.00	2.45
1119	1202	2.552802	CGTGGAGACGTAGGACACT	58.447	57.895	0.00	0.00	40.91	3.55
1346	1460	2.202797	CGATGACCCAGTGAGGCG	60.203	66.667	0.00	0.00	35.39	5.52
1512	1752	1.160870	TTCCCTCCCCTCTTGCTCA	59.839	57.895	0.00	0.00	0.00	4.26
1620	1860	2.360726	TCCCACTCGACGCAGCTA	60.361	61.111	0.00	0.00	0.00	3.32
2109	2366	1.815421	CTGGTCGCCGAAGATTGGG	60.815	63.158	0.00	0.00	0.00	4.12
2112	2369	2.584608	CCCTGGTCGCCGAAGATT	59.415	61.111	0.00	0.00	0.00	2.40
2388	2645	8.630054	TTAGTATTTGGCAGTAGTGAAATTGT	57.370	30.769	0.42	0.00	0.00	2.71
2412	2669	9.449719	AGTAATCTGGAACGATTTTACTGATTT	57.550	29.630	6.65	0.00	34.58	2.17
2413	2670	9.449719	AAGTAATCTGGAACGATTTTACTGATT	57.550	29.630	6.59	6.59	34.58	2.57
2415	2672	8.717821	CAAAGTAATCTGGAACGATTTTACTGA	58.282	33.333	0.00	0.00	34.58	3.41
2416	2673	7.962918	CCAAAGTAATCTGGAACGATTTTACTG	59.037	37.037	0.00	0.00	34.58	2.74
2466	2724	2.303022	ACTTGAATCAGTGACCACCGAT	59.697	45.455	0.00	0.00	30.22	4.18
2467	2725	1.691976	ACTTGAATCAGTGACCACCGA	59.308	47.619	0.00	0.00	0.00	4.69
2468	2726	2.169832	ACTTGAATCAGTGACCACCG	57.830	50.000	0.00	0.00	0.00	4.94
2470	2728	7.602644	TGTATAAGAACTTGAATCAGTGACCAC	59.397	37.037	0.00	0.00	0.00	4.16
2471	2729	7.676004	TGTATAAGAACTTGAATCAGTGACCA	58.324	34.615	0.00	0.00	0.00	4.02
2474	2732	8.134202	TCCTGTATAAGAACTTGAATCAGTGA	57.866	34.615	0.00	0.00	0.00	3.41
2556	2814	7.454380	TCCCATGGTTGTTTTCTCAGAATAAAT	59.546	33.333	11.73	0.00	0.00	1.40
2589	2847	5.066913	ACTGAAAATCCCTCCTGAACTTT	57.933	39.130	0.00	0.00	0.00	2.66
2595	2854	5.789643	TTTGAAACTGAAAATCCCTCCTG	57.210	39.130	0.00	0.00	0.00	3.86
2640	2899	2.190981	GACCGCCAAGTCAACTATACG	58.809	52.381	0.00	0.00	36.73	3.06
2659	3101	5.130705	ACTATACAGGGTGTCTCAGATGA	57.869	43.478	0.00	0.00	0.00	2.92
2725	3174	0.534203	GTCACCGCTCCTTTGGTCAA	60.534	55.000	0.00	0.00	35.96	3.18
2736	3185	0.321653	GAGGATTGTTGGTCACCGCT	60.322	55.000	0.00	0.00	0.00	5.52
2737	3186	1.305930	GGAGGATTGTTGGTCACCGC	61.306	60.000	0.00	0.00	0.00	5.68
2747	3200	4.222336	TGACCATGTTTTTGGAGGATTGT	58.778	39.130	0.00	0.00	39.25	2.71
2773	3226	3.317455	TTAGGGTATCGCTGGAAGGTA	57.683	47.619	0.00	0.00	0.00	3.08
2779	3232	4.748892	CTGTCATATTAGGGTATCGCTGG	58.251	47.826	0.00	0.00	0.00	4.85
2780	3233	4.081972	AGCTGTCATATTAGGGTATCGCTG	60.082	45.833	0.00	0.00	0.00	5.18
2786	3249	5.071788	CCTCCAAAGCTGTCATATTAGGGTA	59.928	44.000	0.00	0.00	0.00	3.69
2795	3258	1.000396	GGGCCTCCAAAGCTGTCAT	60.000	57.895	0.84	0.00	0.00	3.06
2855	3318	9.582648	AAATACTAAACCCAATGTAGTCTGTTT	57.417	29.630	0.00	0.00	30.81	2.83
2911	3374	3.835490	GGAATGATTTCGAGGGCACCAC	61.835	54.545	0.00	0.00	41.76	4.16
2948	3412	7.370383	GGCTTTAGAAATGATCAACACTCAAA	58.630	34.615	0.00	0.00	0.00	2.69
3002	3470	2.865343	AGCGAGTATCCCTGTTTACG	57.135	50.000	0.00	0.00	0.00	3.18
3030	3499	7.171678	ACTGAACTTTGTCATGCTTACTCTTAC	59.828	37.037	0.00	0.00	0.00	2.34
3032	3501	6.058183	ACTGAACTTTGTCATGCTTACTCTT	58.942	36.000	0.00	0.00	0.00	2.85
3067	3536	4.050852	GCTTGGGGAAGCAATGATTTAG	57.949	45.455	1.90	0.00	44.85	1.85
3111	3666	8.616942	GGCCTTTCTTTTATGTTTTAGCAAAAA	58.383	29.630	0.00	0.00	32.15	1.94
3115	3670	6.412362	TGGCCTTTCTTTTATGTTTTAGCA	57.588	33.333	3.32	0.00	0.00	3.49
3116	3671	7.096551	TGATGGCCTTTCTTTTATGTTTTAGC	58.903	34.615	3.32	0.00	0.00	3.09
3117	3672	9.143631	CTTGATGGCCTTTCTTTTATGTTTTAG	57.856	33.333	3.32	0.00	0.00	1.85
3118	3673	8.093927	CCTTGATGGCCTTTCTTTTATGTTTTA	58.906	33.333	3.32	0.00	0.00	1.52
3121	3676	6.041423	CCTTGATGGCCTTTCTTTTATGTT	57.959	37.500	3.32	0.00	0.00	2.71
3122	3677	5.665916	CCTTGATGGCCTTTCTTTTATGT	57.334	39.130	3.32	0.00	0.00	2.29
3169	3728	6.044682	AGGAAGTGAAAGATGTTGCTTTTTG	58.955	36.000	0.00	0.00	38.16	2.44
3259	3818	7.659390	CCTCACATATCATCCCTTAAAGAAGAC	59.341	40.741	0.00	0.00	34.25	3.01
3266	3825	5.905331	ACAGACCTCACATATCATCCCTTAA	59.095	40.000	0.00	0.00	0.00	1.85
3267	3826	5.467738	ACAGACCTCACATATCATCCCTTA	58.532	41.667	0.00	0.00	0.00	2.69
3282	3841	3.627577	TGTTTGCTTTGAGAACAGACCTC	59.372	43.478	0.00	0.00	0.00	3.85
3300	3859	8.854614	AGAAGTAGCAACTGATTATCTTGTTT	57.145	30.769	0.00	0.00	35.62	2.83
3322	3890	3.698289	ACTGAAGTGGAGGACGATAGAA	58.302	45.455	0.00	0.00	41.38	2.10

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.