AutoCloner

Multiple sequence alignment - TraesCS5A01G024800

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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	TraesCS5A01G024800	chr5A	100.000	1730	0	0	1	1730	19252819	19254548	0.000000e+00	3195.0
1	TraesCS5A01G024800	chr5A	100.000	1682	0	0	2258	3939	19255076	19256757	0.000000e+00	3107.0
2	TraesCS5A01G024800	chr6D	99.626	803	3	0	1	803	124513564	124512762	0.000000e+00	1467.0
3	TraesCS5A01G024800	chr7D	99.502	803	4	0	1	803	381977722	381978524	0.000000e+00	1461.0
4	TraesCS5A01G024800	chr7D	99.253	803	6	0	1	803	203496039	203495237	0.000000e+00	1450.0
5	TraesCS5A01G024800	chr7D	99.253	803	6	0	1	803	381916018	381915216	0.000000e+00	1450.0
6	TraesCS5A01G024800	chr7D	96.040	101	2	2	3174	3273	405908646	405908547	3.150000e-36	163.0
7	TraesCS5A01G024800	chr7B	99.502	803	4	0	1	803	716882751	716883553	0.000000e+00	1461.0
8	TraesCS5A01G024800	chr7B	99.502	803	4	0	1	803	742985474	742984672	0.000000e+00	1461.0
9	TraesCS5A01G024800	chr7B	99.377	803	5	0	1	803	716842510	716843312	0.000000e+00	1456.0
10	TraesCS5A01G024800	chr7B	93.269	104	6	1	3168	3271	40180635	40180737	6.820000e-33	152.0
11	TraesCS5A01G024800	chr7B	100.000	28	0	0	1593	1620	711556020	711556047	7.000000e-03	52.8
12	TraesCS5A01G024800	chr7A	99.378	804	4	1	1	803	120845121	120845924	0.000000e+00	1456.0
13	TraesCS5A01G024800	chr2B	99.253	803	6	0	1	803	112837066	112836264	0.000000e+00	1450.0
14	TraesCS5A01G024800	chr2B	97.872	94	1	1	3181	3274	704294224	704294316	1.130000e-35	161.0
15	TraesCS5A01G024800	chr2B	93.333	105	4	3	3185	3288	738486661	738486763	6.820000e-33	152.0
16	TraesCS5A01G024800	chr5D	92.777	803	44	5	2280	3075	28640076	28640871	0.000000e+00	1149.0
17	TraesCS5A01G024800	chr5D	89.753	849	41	16	873	1702	28639053	28639874	0.000000e+00	1044.0
18	TraesCS5A01G024800	chr5D	90.173	692	47	12	3269	3939	28643756	28644447	0.000000e+00	881.0
19	TraesCS5A01G024800	chr5D	95.098	102	3	2	3068	3169	28640948	28641047	4.070000e-35	159.0
20	TraesCS5A01G024800	chr5D	96.842	95	3	0	3178	3272	364250315	364250221	4.070000e-35	159.0
21	TraesCS5A01G024800	chr5D	88.991	109	10	2	1595	1702	28639878	28639985	2.470000e-27	134.0
22	TraesCS5A01G024800	chr5D	100.000	29	0	0	2972	3000	28640840	28640868	2.000000e-03	54.7
23	TraesCS5A01G024800	chr5B	90.110	910	49	17	812	1702	21152086	21152973	0.000000e+00	1144.0
24	TraesCS5A01G024800	chr5B	91.299	793	44	11	2258	3045	21153168	21153940	0.000000e+00	1059.0
25	TraesCS5A01G024800	chr5B	92.926	311	20	1	3269	3577	21154863	21155173	6.000000e-123	451.0
26	TraesCS5A01G024800	chr5B	86.638	232	22	6	3041	3270	21153869	21154093	8.450000e-62	248.0
27	TraesCS5A01G024800	chr5B	88.073	109	11	2	1595	1702	21152977	21153084	1.150000e-25	128.0
28	TraesCS5A01G024800	chr3A	98.913	92	1	0	3182	3273	476568313	476568404	8.760000e-37	165.0
29	TraesCS5A01G024800	chrUn	98.889	90	1	0	3184	3273	2693229	2693318	1.130000e-35	161.0
30	TraesCS5A01G024800	chr2A	94.118	102	4	2	3181	3280	177665197	177665298	1.900000e-33	154.0
31	TraesCS5A01G024800	chr2A	87.302	126	11	4	3175	3299	755454548	755454669	5.310000e-29	139.0
32	TraesCS5A01G024800	chr6B	100.000	28	0	0	1593	1620	84146168	84146195	7.000000e-03	52.8
33	TraesCS5A01G024800	chr4D	96.875	32	0	1	1590	1621	353425546	353425516	7.000000e-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	TraesCS5A01G024800	chr5A	19252819	19256757	3938	False	3151.000000	3195	100.000000	1	3939	2	chr5A.!!$F1	3938
1	TraesCS5A01G024800	chr6D	124512762	124513564	802	True	1467.000000	1467	99.626000	1	803	1	chr6D.!!$R1	802
2	TraesCS5A01G024800	chr7D	381977722	381978524	802	False	1461.000000	1461	99.502000	1	803	1	chr7D.!!$F1	802
3	TraesCS5A01G024800	chr7D	203495237	203496039	802	True	1450.000000	1450	99.253000	1	803	1	chr7D.!!$R1	802
4	TraesCS5A01G024800	chr7D	381915216	381916018	802	True	1450.000000	1450	99.253000	1	803	1	chr7D.!!$R2	802
5	TraesCS5A01G024800	chr7B	716882751	716883553	802	False	1461.000000	1461	99.502000	1	803	1	chr7B.!!$F4	802
6	TraesCS5A01G024800	chr7B	742984672	742985474	802	True	1461.000000	1461	99.502000	1	803	1	chr7B.!!$R1	802
7	TraesCS5A01G024800	chr7B	716842510	716843312	802	False	1456.000000	1456	99.377000	1	803	1	chr7B.!!$F3	802
8	TraesCS5A01G024800	chr7A	120845121	120845924	803	False	1456.000000	1456	99.378000	1	803	1	chr7A.!!$F1	802
9	TraesCS5A01G024800	chr2B	112836264	112837066	802	True	1450.000000	1450	99.253000	1	803	1	chr2B.!!$R1	802
10	TraesCS5A01G024800	chr5D	28639053	28644447	5394	False	570.283333	1149	92.798667	873	3939	6	chr5D.!!$F1	3066
11	TraesCS5A01G024800	chr5B	21152086	21155173	3087	False	606.000000	1144	89.809200	812	3577	5	chr5B.!!$F1	2765

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
895	911	0.736636	CCTCGATGCCACGTACACTA	59.263	55.0	0.0	0.0	34.7	2.74	F
1725	1871	0.036732	AATCCACTGCTTTCGAGCCA	59.963	50.0	0.0	0.0	0.0	4.75	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2387	2533	0.179137	GCGGGAGGCTTTGTTAATGC	60.179	55.0	0.0	0.0	39.11	3.56	R
3615	6611	0.252197	AACTATGGTTGGAGGCGGAC	59.748	55.0	0.0	0.0	33.96	4.79	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
803	805	9.822727	TGTTCTACATATATCAACAGATAGGGA	57.177	33.333	0.00	0.00	0.00	4.20
808	810	8.833231	ACATATATCAACAGATAGGGAAAACG	57.167	34.615	0.00	0.00	0.00	3.60
809	811	7.878127	ACATATATCAACAGATAGGGAAAACGG	59.122	37.037	0.00	0.00	0.00	4.44
810	812	2.706890	TCAACAGATAGGGAAAACGGC	58.293	47.619	0.00	0.00	0.00	5.68
843	845	0.827507	TGTCCTTGCTTTCTTGCCCC	60.828	55.000	0.00	0.00	0.00	5.80
844	846	1.228862	TCCTTGCTTTCTTGCCCCC	60.229	57.895	0.00	0.00	0.00	5.40
845	847	1.533753	CCTTGCTTTCTTGCCCCCA	60.534	57.895	0.00	0.00	0.00	4.96
846	848	1.120795	CCTTGCTTTCTTGCCCCCAA	61.121	55.000	0.00	0.00	0.00	4.12
866	868	4.754618	CCAAGGCAAAAGGAAAAATACCAC	59.245	41.667	0.00	0.00	0.00	4.16
894	910	1.248785	ACCTCGATGCCACGTACACT	61.249	55.000	0.00	0.00	34.70	3.55
895	911	0.736636	CCTCGATGCCACGTACACTA	59.263	55.000	0.00	0.00	34.70	2.74
896	912	1.533338	CCTCGATGCCACGTACACTAC	60.533	57.143	0.00	0.00	34.70	2.73
897	913	1.131693	CTCGATGCCACGTACACTACA	59.868	52.381	0.00	0.00	34.70	2.74
898	914	1.135603	TCGATGCCACGTACACTACAC	60.136	52.381	0.00	0.00	34.70	2.90
903	919	1.738030	GCCACGTACACTACACCCATC	60.738	57.143	0.00	0.00	0.00	3.51
910	926	1.136305	ACACTACACCCATCGATTCCG	59.864	52.381	0.00	0.00	37.07	4.30
982	999	1.069090	ATACACGGCGGCATACCAG	59.931	57.895	13.24	0.00	34.57	4.00
1038	1055	4.208686	GCGTACGGGGAGGAGCAG	62.209	72.222	18.39	0.00	0.00	4.24
1039	1056	3.528370	CGTACGGGGAGGAGCAGG	61.528	72.222	7.57	0.00	0.00	4.85
1040	1057	2.043248	GTACGGGGAGGAGCAGGA	60.043	66.667	0.00	0.00	0.00	3.86
1041	1058	2.128507	GTACGGGGAGGAGCAGGAG	61.129	68.421	0.00	0.00	0.00	3.69
1452	1481	2.510238	CCCAGCTTCTTCGAGCCG	60.510	66.667	0.00	0.00	43.74	5.52
1554	1586	2.561373	GTTTCCGAGCCAAAGCCG	59.439	61.111	0.00	0.00	41.25	5.52
1601	1636	4.699522	AAAGCTCCGACCGCCACC	62.700	66.667	0.00	0.00	0.00	4.61
1653	1688	1.672854	TATCACGCCCACTTCCTCCG	61.673	60.000	0.00	0.00	0.00	4.63
1664	1699	2.096174	CACTTCCTCCGTTCTCGTCTAG	59.904	54.545	0.00	0.00	35.01	2.43
1715	1861	4.179579	GCCGGCGAAATCCACTGC	62.180	66.667	12.58	0.00	0.00	4.40
1716	1862	2.436646	CCGGCGAAATCCACTGCT	60.437	61.111	9.30	0.00	0.00	4.24
1717	1863	2.040544	CCGGCGAAATCCACTGCTT	61.041	57.895	9.30	0.00	0.00	3.91
1718	1864	1.586154	CCGGCGAAATCCACTGCTTT	61.586	55.000	9.30	0.00	0.00	3.51
1719	1865	0.179189	CGGCGAAATCCACTGCTTTC	60.179	55.000	0.00	0.00	0.00	2.62
1725	1871	0.036732	AATCCACTGCTTTCGAGCCA	59.963	50.000	0.00	0.00	0.00	4.75
1726	1872	0.036732	ATCCACTGCTTTCGAGCCAA	59.963	50.000	0.00	0.00	0.00	4.52
1727	1873	0.179032	TCCACTGCTTTCGAGCCAAA	60.179	50.000	0.00	0.00	0.00	3.28
1728	1874	0.239347	CCACTGCTTTCGAGCCAAAG	59.761	55.000	0.00	0.00	36.58	2.77
2302	2448	3.700350	CCACCCCCTCCTCCTCCT	61.700	72.222	0.00	0.00	0.00	3.69
2303	2449	2.041405	CACCCCCTCCTCCTCCTC	60.041	72.222	0.00	0.00	0.00	3.71
2304	2450	3.369388	ACCCCCTCCTCCTCCTCC	61.369	72.222	0.00	0.00	0.00	4.30
2310	2456	4.507916	TCCTCCTCCTCCGGCGAG	62.508	72.222	9.30	10.56	35.72	5.03
2401	2547	0.611896	AGCCCGCATTAACAAAGCCT	60.612	50.000	0.00	0.00	0.00	4.58
2402	2548	0.179137	GCCCGCATTAACAAAGCCTC	60.179	55.000	0.00	0.00	0.00	4.70
2429	2575	3.702048	CCGAACGGAAGCCCTGGA	61.702	66.667	7.53	0.00	37.50	3.86
2430	2576	2.584608	CGAACGGAAGCCCTGGAT	59.415	61.111	0.00	0.00	0.00	3.41
2523	2669	4.921834	GAGTACAGCCACTCTGCC	57.078	61.111	0.00	0.00	46.76	4.85
2530	2676	3.715097	GCCACTCTGCCTCAGCCT	61.715	66.667	0.00	0.00	38.69	4.58
2705	2854	1.708993	AAGGTTGCCACTGCTGGAGA	61.709	55.000	2.24	0.00	40.55	3.71
2730	2879	4.533919	TGAAGAAGCAAGAGGAGAAGAG	57.466	45.455	0.00	0.00	0.00	2.85
2739	2888	2.222271	AGAGGAGAAGAGGATGGAGGA	58.778	52.381	0.00	0.00	0.00	3.71
2780	2929	2.430382	GAACGGTGGAAGACAGCCGA	62.430	60.000	8.87	0.00	44.62	5.54
2792	2941	3.753434	AGCCGACTGAGCACGAGG	61.753	66.667	0.00	0.00	0.00	4.63
2795	2944	1.513158	CCGACTGAGCACGAGGATT	59.487	57.895	0.00	0.00	0.00	3.01
2796	2945	0.803768	CCGACTGAGCACGAGGATTG	60.804	60.000	0.00	0.00	0.00	2.67
2800	2949	0.460987	CTGAGCACGAGGATTGGGAC	60.461	60.000	0.00	0.00	0.00	4.46
2875	3024	3.027170	GCTGGTGACGAACATGGCG	62.027	63.158	8.44	8.44	0.00	5.69
2935	3084	4.175489	CGCACCATGAGCAGCAGC	62.175	66.667	10.12	0.00	42.56	5.25
2972	3125	3.054434	ACCATAAGGCTAATGAGTGCACA	60.054	43.478	21.04	0.00	39.06	4.57
2973	3126	3.313526	CCATAAGGCTAATGAGTGCACAC	59.686	47.826	21.04	14.15	0.00	3.82
3060	3213	3.242739	CCGTGCACTGTTAATTATCTGCC	60.243	47.826	16.19	0.00	0.00	4.85
3061	3214	3.242739	CGTGCACTGTTAATTATCTGCCC	60.243	47.826	16.19	0.00	0.00	5.36
3069	3222	8.184192	CACTGTTAATTATCTGCCCAAGTTAAG	58.816	37.037	0.00	0.00	0.00	1.85
3135	3371	8.124823	ACATGCAATCGTTTATATCAGACTTTG	58.875	33.333	0.00	0.00	0.00	2.77
3183	3427	8.237267	AGTTTAACACTCAGCATTGCTATTTAC	58.763	33.333	11.55	1.10	36.40	2.01
3184	3428	7.921786	TTAACACTCAGCATTGCTATTTACT	57.078	32.000	11.55	0.00	36.40	2.24
3193	3437	4.998033	GCATTGCTATTTACTACTCCCTCC	59.002	45.833	0.16	0.00	0.00	4.30
3199	3443	6.183360	TGCTATTTACTACTCCCTCCGTAAAC	60.183	42.308	0.00	0.00	35.45	2.01
3200	3444	6.040278	GCTATTTACTACTCCCTCCGTAAACT	59.960	42.308	0.00	0.00	35.45	2.66
3212	3456	6.779049	TCCCTCCGTAAACTAATATAAGAGCA	59.221	38.462	0.00	0.00	0.00	4.26
3310	6304	3.311091	ACTAACATGGACCGGCCTATAA	58.689	45.455	14.76	0.00	37.63	0.98
3320	6314	5.067954	GGACCGGCCTATAATGTTGTAAAT	58.932	41.667	0.00	0.00	0.00	1.40
3327	6321	8.007716	CGGCCTATAATGTTGTAAATAAACTCG	58.992	37.037	0.00	0.00	0.00	4.18
3341	6335	9.719206	GTAAATAAACTCGAAAGTTAGTCGTTC	57.281	33.333	0.00	0.00	45.07	3.95
3437	6433	1.960689	GCCACTTCCAGTTGCCTAAAA	59.039	47.619	0.00	0.00	31.35	1.52
3461	6457	5.895636	TTCGGCAAGTGATCAACATAAAT	57.104	34.783	0.00	0.00	0.00	1.40
3619	6621	2.125350	GCAGCTCCAGAAGGTCCG	60.125	66.667	0.00	0.00	31.91	4.79
3648	6650	6.620877	AACCATAGTTGATAGTCTGTCCAA	57.379	37.500	0.00	0.00	33.97	3.53
3649	6651	6.814954	ACCATAGTTGATAGTCTGTCCAAT	57.185	37.500	0.00	0.00	0.00	3.16
3660	6665	8.258007	TGATAGTCTGTCCAATAAGAAATTCGT	58.742	33.333	0.00	0.00	0.00	3.85
3755	6772	1.770518	CCCTAGGGTAGGCAAGGGG	60.771	68.421	20.88	0.00	44.32	4.79
3761	6778	4.822628	GTAGGCAAGGGGGCAGGC	62.823	72.222	0.00	0.00	46.44	4.85
3765	6782	3.698820	GCAAGGGGGCAGGCAAAG	61.699	66.667	0.00	0.00	0.00	2.77
3775	6792	1.283793	CAGGCAAAGGCACAACTCG	59.716	57.895	0.00	0.00	43.71	4.18
3780	6797	1.522668	CAAAGGCACAACTCGATCCA	58.477	50.000	0.00	0.00	0.00	3.41
3783	6800	1.742761	AGGCACAACTCGATCCAATG	58.257	50.000	0.00	0.00	0.00	2.82
3784	6801	0.099436	GGCACAACTCGATCCAATGC	59.901	55.000	0.00	0.00	0.00	3.56
3802	6819	2.281070	ACTTGCTGGTGTGGCTCG	60.281	61.111	0.00	0.00	0.00	5.03
3808	6825	1.812922	CTGGTGTGGCTCGCAGATC	60.813	63.158	2.30	0.00	33.89	2.75
3809	6826	2.512515	GGTGTGGCTCGCAGATCC	60.513	66.667	2.30	0.00	44.26	3.36
3857	6874	0.454600	GCCATGAGACAGCCAACATG	59.545	55.000	0.00	0.00	39.51	3.21
3910	6927	4.688021	AGCTATCTAACCTTCTTTGCTCG	58.312	43.478	0.00	0.00	0.00	5.03
3924	6941	4.277174	TCTTTGCTCGCAAAAGTAAATCCA	59.723	37.500	16.72	0.00	44.07	3.41
3928	6945	3.057526	GCTCGCAAAAGTAAATCCACCTT	60.058	43.478	0.00	0.00	0.00	3.50

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
803	805	2.104170	TGGTTCCTTTCTTGCCGTTTT	58.896	42.857	0.00	0.00	0.00	2.43
804	806	1.770294	TGGTTCCTTTCTTGCCGTTT	58.230	45.000	0.00	0.00	0.00	3.60
805	807	1.613437	CATGGTTCCTTTCTTGCCGTT	59.387	47.619	0.00	0.00	0.00	4.44
806	808	1.247567	CATGGTTCCTTTCTTGCCGT	58.752	50.000	0.00	0.00	0.00	5.68
807	809	1.200020	GACATGGTTCCTTTCTTGCCG	59.800	52.381	0.00	0.00	0.00	5.69
808	810	1.546029	GGACATGGTTCCTTTCTTGCC	59.454	52.381	0.00	0.00	32.24	4.52
809	811	2.519013	AGGACATGGTTCCTTTCTTGC	58.481	47.619	0.00	0.00	44.22	4.01
843	845	4.754618	GTGGTATTTTTCCTTTTGCCTTGG	59.245	41.667	0.00	0.00	0.00	3.61
844	846	5.610398	AGTGGTATTTTTCCTTTTGCCTTG	58.390	37.500	0.00	0.00	0.00	3.61
845	847	5.602561	AGAGTGGTATTTTTCCTTTTGCCTT	59.397	36.000	0.00	0.00	0.00	4.35
846	848	5.147767	AGAGTGGTATTTTTCCTTTTGCCT	58.852	37.500	0.00	0.00	0.00	4.75
866	868	0.872021	GGCATCGAGGTTGCGTAGAG	60.872	60.000	0.00	0.00	41.07	2.43
910	926	6.711277	TGCAGATATATGTATTCCAAGGGTC	58.289	40.000	0.00	0.00	0.00	4.46
1036	1053	2.063378	GGTCCAGCTCCTCCTCCTG	61.063	68.421	0.00	0.00	0.00	3.86
1037	1054	2.366570	GGTCCAGCTCCTCCTCCT	59.633	66.667	0.00	0.00	0.00	3.69
1038	1055	2.766229	GGGTCCAGCTCCTCCTCC	60.766	72.222	0.00	0.00	0.00	4.30
1039	1056	3.151022	CGGGTCCAGCTCCTCCTC	61.151	72.222	0.00	0.00	0.00	3.71
1040	1057	4.787280	CCGGGTCCAGCTCCTCCT	62.787	72.222	0.00	0.00	0.00	3.69
1146	1163	2.048503	AGCACGCCGTAGTTGTCC	60.049	61.111	0.00	0.00	0.00	4.02
1204	1221	1.671379	GGTCCTTGGTGAAGCGGAC	60.671	63.158	0.00	0.00	44.00	4.79
1260	1277	3.685214	CTCGTCCTCGAACCTGGCG	62.685	68.421	0.00	0.00	45.61	5.69
1494	1526	1.282930	GAGGAAGTGGACGTGAACGC	61.283	60.000	2.11	0.00	44.43	4.84
1497	1529	1.111116	ACGGAGGAAGTGGACGTGAA	61.111	55.000	0.00	0.00	36.32	3.18
1536	1568	2.962569	GGCTTTGGCTCGGAAACC	59.037	61.111	0.00	0.00	38.73	3.27
1609	1644	4.838152	CGGTGATGGAGGCGGTGG	62.838	72.222	0.00	0.00	0.00	4.61
1653	1688	3.218227	GGGGGCCTAGACGAGAAC	58.782	66.667	0.84	0.00	0.00	3.01
2257	2403	1.153127	TGGTGGTGGTGGAAACGAC	60.153	57.895	0.00	0.00	0.00	4.34
2258	2404	1.153127	GTGGTGGTGGTGGAAACGA	60.153	57.895	0.00	0.00	0.00	3.85
2259	2405	2.190841	GGTGGTGGTGGTGGAAACG	61.191	63.158	0.00	0.00	0.00	3.60
2260	2406	1.076632	TGGTGGTGGTGGTGGAAAC	60.077	57.895	0.00	0.00	0.00	2.78
2261	2407	1.076632	GTGGTGGTGGTGGTGGAAA	60.077	57.895	0.00	0.00	0.00	3.13
2262	2408	2.598467	GTGGTGGTGGTGGTGGAA	59.402	61.111	0.00	0.00	0.00	3.53
2263	2409	3.494254	GGTGGTGGTGGTGGTGGA	61.494	66.667	0.00	0.00	0.00	4.02
2264	2410	3.814906	TGGTGGTGGTGGTGGTGG	61.815	66.667	0.00	0.00	0.00	4.61
2265	2411	2.518349	GTGGTGGTGGTGGTGGTG	60.518	66.667	0.00	0.00	0.00	4.17
2266	2412	3.816090	GGTGGTGGTGGTGGTGGT	61.816	66.667	0.00	0.00	0.00	4.16
2267	2413	3.814906	TGGTGGTGGTGGTGGTGG	61.815	66.667	0.00	0.00	0.00	4.61
2268	2414	2.518349	GTGGTGGTGGTGGTGGTG	60.518	66.667	0.00	0.00	0.00	4.17
2310	2456	1.674651	GGGTCGAAGAAAGTGGGCC	60.675	63.158	0.00	0.00	39.69	5.80
2387	2533	0.179137	GCGGGAGGCTTTGTTAATGC	60.179	55.000	0.00	0.00	39.11	3.56
2523	2669	1.908483	GGGGGTGACTTAGGCTGAG	59.092	63.158	4.52	4.52	0.00	3.35
2530	2676	1.534476	TGACAGCGGGGGTGACTTA	60.534	57.895	1.38	0.00	34.87	2.24
2640	2789	1.067565	TGCGATGCTTCTTCTTCGTCT	60.068	47.619	0.00	0.00	36.43	4.18
2696	2845	2.937799	GCTTCTTCATCTTCTCCAGCAG	59.062	50.000	0.00	0.00	0.00	4.24
2705	2854	5.248020	TCTTCTCCTCTTGCTTCTTCATCTT	59.752	40.000	0.00	0.00	0.00	2.40
2730	2879	1.066143	TCGCTTTCTTGTCCTCCATCC	60.066	52.381	0.00	0.00	0.00	3.51
2739	2888	1.003233	GCCTCCCTCGCTTTCTTGT	60.003	57.895	0.00	0.00	0.00	3.16
2780	2929	0.904865	TCCCAATCCTCGTGCTCAGT	60.905	55.000	0.00	0.00	0.00	3.41
2792	2941	1.535462	CTTTGGTGACACGTCCCAATC	59.465	52.381	16.08	0.00	42.67	2.67
2795	2944	1.525077	GCTTTGGTGACACGTCCCA	60.525	57.895	0.00	3.99	42.67	4.37
2796	2945	1.227853	AGCTTTGGTGACACGTCCC	60.228	57.895	0.00	0.00	42.67	4.46
2800	2949	1.280746	CAGCAGCTTTGGTGACACG	59.719	57.895	0.00	0.00	42.67	4.49
2848	2997	2.126424	GTCACCAGCTCCGTCGTC	60.126	66.667	0.00	0.00	0.00	4.20
2956	3109	1.349026	ACAGTGTGCACTCATTAGCCT	59.651	47.619	19.41	0.00	40.20	4.58
3035	3188	5.064198	GCAGATAATTAACAGTGCACGGTTA	59.936	40.000	30.56	30.56	35.89	2.85
3037	3190	3.374058	GCAGATAATTAACAGTGCACGGT	59.626	43.478	17.33	17.33	0.00	4.83
3039	3192	3.242739	GGGCAGATAATTAACAGTGCACG	60.243	47.826	12.01	9.15	32.42	5.34
3099	3335	6.846870	AAACGATTGCATGTGTTATTTACG	57.153	33.333	0.00	0.00	0.00	3.18
3135	3371	7.138692	ACTTTATGTCTCTTGCAGATCAAAC	57.861	36.000	0.00	0.00	33.65	2.93
3183	3427	9.512588	TCTTATATTAGTTTACGGAGGGAGTAG	57.487	37.037	0.00	0.00	0.00	2.57
3184	3428	9.512588	CTCTTATATTAGTTTACGGAGGGAGTA	57.487	37.037	0.00	0.00	0.00	2.59
3241	3487	9.939424	ACTCCCTCTGTAAACTAATATAAGAGT	57.061	33.333	0.00	0.00	0.00	3.24
3252	3498	4.097418	AGCATGTACTCCCTCTGTAAACT	58.903	43.478	0.00	0.00	0.00	2.66
3253	3499	4.473477	AGCATGTACTCCCTCTGTAAAC	57.527	45.455	0.00	0.00	0.00	2.01
3320	6314	6.498304	AGTGAACGACTAACTTTCGAGTTTA	58.502	36.000	0.00	0.00	39.83	2.01
3327	6321	7.621633	GCAGGAATAAGTGAACGACTAACTTTC	60.622	40.741	0.00	0.00	35.77	2.62
3331	6325	5.169295	AGCAGGAATAAGTGAACGACTAAC	58.831	41.667	0.00	0.00	33.09	2.34
3341	6335	7.775120	ACCAATGAAATTAGCAGGAATAAGTG	58.225	34.615	0.00	0.00	32.46	3.16
3437	6433	5.895636	TTATGTTGATCACTTGCCGAAAT	57.104	34.783	0.00	0.00	0.00	2.17
3461	6457	7.872881	TGTTGCGGTTAATTCTAACAAATGTA	58.127	30.769	0.00	0.00	39.43	2.29
3600	6596	1.078567	GGACCTTCTGGAGCTGCAG	60.079	63.158	27.83	27.83	37.04	4.41
3614	6610	1.146263	CTATGGTTGGAGGCGGACC	59.854	63.158	0.00	0.00	0.00	4.46
3615	6611	0.252197	AACTATGGTTGGAGGCGGAC	59.748	55.000	0.00	0.00	33.96	4.79
3643	6645	7.562454	TTATCCCACGAATTTCTTATTGGAC	57.438	36.000	0.00	0.00	0.00	4.02
3699	6704	9.082313	AGAGCCCATTATCAAAAGGTATTATTG	57.918	33.333	0.00	0.00	0.00	1.90
3705	6722	5.073144	CCCTAGAGCCCATTATCAAAAGGTA	59.927	44.000	0.00	0.00	0.00	3.08
3711	6728	4.476846	TGAAACCCTAGAGCCCATTATCAA	59.523	41.667	0.00	0.00	0.00	2.57
3719	6736	1.133761	GGGAATGAAACCCTAGAGCCC	60.134	57.143	0.00	0.00	43.65	5.19
3755	6772	2.029518	GTTGTGCCTTTGCCTGCC	59.970	61.111	0.00	0.00	36.33	4.85
3761	6778	1.522668	TGGATCGAGTTGTGCCTTTG	58.477	50.000	0.00	0.00	0.00	2.77
3762	6779	2.270352	TTGGATCGAGTTGTGCCTTT	57.730	45.000	0.00	0.00	0.00	3.11
3765	6782	0.099436	GCATTGGATCGAGTTGTGCC	59.901	55.000	0.00	0.00	0.00	5.01
3775	6792	1.135199	CACCAGCAAGTGCATTGGATC	60.135	52.381	16.15	0.00	45.16	3.36
3780	6797	2.043625	CCACACCAGCAAGTGCATT	58.956	52.632	6.00	0.00	45.16	3.56
3783	6800	2.908940	AGCCACACCAGCAAGTGC	60.909	61.111	6.08	0.00	41.67	4.40
3784	6801	2.610694	CGAGCCACACCAGCAAGTG	61.611	63.158	4.71	4.71	43.65	3.16
3802	6819	0.254178	TCCAAGCAAGGAGGATCTGC	59.746	55.000	0.00	0.00	32.77	4.26
3808	6825	1.280457	AGTAGGTCCAAGCAAGGAGG	58.720	55.000	0.00	0.00	38.64	4.30
3809	6826	2.832129	TGTAGTAGGTCCAAGCAAGGAG	59.168	50.000	0.00	0.00	38.64	3.69
3885	6902	6.092807	CGAGCAAAGAAGGTTAGATAGCTTTT	59.907	38.462	0.00	0.00	44.30	2.27
3889	6906	3.246463	GCGAGCAAAGAAGGTTAGATAGC	59.754	47.826	0.00	0.00	0.00	2.97

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.