AutoCloner

Multiple sequence alignment - TraesCS3A01G425300

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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	TraesCS3A01G425300	chr3A	100.000	3105	0	0	1	3105	667660896	667664000	0.000000e+00	5734.0
1	TraesCS3A01G425300	chr4B	98.765	2916	33	3	1	2913	417375032	417372117	0.000000e+00	5182.0
2	TraesCS3A01G425300	chr4A	98.594	2916	39	2	1	2915	146048579	146045665	0.000000e+00	5156.0
3	TraesCS3A01G425300	chr4A	92.716	1620	99	12	1	1614	53752074	53753680	0.000000e+00	2320.0
4	TraesCS3A01G425300	chr4A	92.930	1471	91	10	1	1466	12669236	12667774	0.000000e+00	2128.0
5	TraesCS3A01G425300	chr4A	93.506	154	6	3	2526	2678	53753677	53753827	3.120000e-55	226.0
6	TraesCS3A01G425300	chr2D	91.008	2491	161	24	1	2454	299657540	299655076	0.000000e+00	3301.0
7	TraesCS3A01G425300	chr2D	90.689	2191	143	22	306	2454	327321670	327323841	0.000000e+00	2859.0
8	TraesCS3A01G425300	chr2D	88.710	124	10	1	2798	2917	299654897	299654774	6.940000e-32	148.0
9	TraesCS3A01G425300	chr2D	88.991	109	8	1	2795	2899	327324027	327324135	6.990000e-27	132.0
10	TraesCS3A01G425300	chr2D	93.151	73	5	0	2876	2948	74140844	74140772	1.180000e-19	108.0
11	TraesCS3A01G425300	chr2D	100.000	35	0	0	2756	2790	299655069	299655035	7.190000e-07	65.8
12	TraesCS3A01G425300	chr2D	95.238	42	0	2	2749	2790	327323843	327323882	7.190000e-07	65.8
13	TraesCS3A01G425300	chr2D	100.000	30	0	0	2757	2786	299655037	299655008	4.330000e-04	56.5
14	TraesCS3A01G425300	chr2D	100.000	30	0	0	2757	2786	327323880	327323909	4.330000e-04	56.5
15	TraesCS3A01G425300	chr1D	90.668	2186	147	21	306	2454	319528362	319526197	0.000000e+00	2854.0
16	TraesCS3A01G425300	chr1D	91.440	2091	99	21	1	2051	242558216	242560266	0.000000e+00	2796.0
17	TraesCS3A01G425300	chr1D	95.976	845	26	3	2053	2889	242560431	242561275	0.000000e+00	1365.0
18	TraesCS3A01G425300	chr1D	84.756	164	12	2	2798	2948	319526018	319525855	5.360000e-33	152.0
19	TraesCS3A01G425300	chr1D	100.000	35	0	0	2756	2790	319526190	319526156	7.190000e-07	65.8
20	TraesCS3A01G425300	chr1D	100.000	30	0	0	2757	2786	319526158	319526129	4.330000e-04	56.5
21	TraesCS3A01G425300	chr6A	85.175	2489	271	51	2	2416	241737621	241740085	0.000000e+00	2462.0
22	TraesCS3A01G425300	chr6A	86.683	413	27	11	2029	2414	261026800	261027211	1.710000e-117	433.0
23	TraesCS3A01G425300	chr7A	92.930	1471	90	11	1	1466	2540338	2541799	0.000000e+00	2128.0
24	TraesCS3A01G425300	chr7A	92.930	1471	91	10	1	1466	67563020	67564482	0.000000e+00	2128.0
25	TraesCS3A01G425300	chr1A	92.862	1471	92	10	1	1466	502837519	502836057	0.000000e+00	2122.0
26	TraesCS3A01G425300	chr1A	89.091	55	3	3	2906	2957	459181374	459181428	7.190000e-07	65.8
27	TraesCS3A01G425300	chr5A	92.658	1471	93	11	1	1466	280764657	280766117	0.000000e+00	2104.0
28	TraesCS3A01G425300	chr5A	92.063	63	5	0	3033	3095	654150069	654150131	4.260000e-14	89.8
29	TraesCS3A01G425300	chr1B	93.151	73	4	1	2876	2948	633755949	633755878	4.230000e-19	106.0
30	TraesCS3A01G425300	chr1B	97.500	40	1	0	2906	2945	379657	379696	5.560000e-08	69.4
31	TraesCS3A01G425300	chr5B	79.856	139	22	6	2876	3010	166360379	166360515	2.550000e-16	97.1
32	TraesCS3A01G425300	chr5B	92.063	63	5	0	3033	3095	663222245	663222307	4.260000e-14	89.8
33	TraesCS3A01G425300	chr5B	89.041	73	7	1	2876	2948	697961108	697961037	4.260000e-14	89.8
34	TraesCS3A01G425300	chr3B	81.301	123	19	4	2870	2991	762387060	762387179	2.550000e-16	97.1
35	TraesCS3A01G425300	chrUn	85.882	85	3	3	2870	2945	469357148	469357232	7.140000e-12	82.4
36	TraesCS3A01G425300	chrUn	95.000	40	2	0	2906	2945	71647208	71647247	2.590000e-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	TraesCS3A01G425300	chr3A	667660896	667664000	3104	False	5734.000	5734	100.0000	1	3105	1	chr3A.!!$F1	3104
1	TraesCS3A01G425300	chr4B	417372117	417375032	2915	True	5182.000	5182	98.7650	1	2913	1	chr4B.!!$R1	2912
2	TraesCS3A01G425300	chr4A	146045665	146048579	2914	True	5156.000	5156	98.5940	1	2915	1	chr4A.!!$R2	2914
3	TraesCS3A01G425300	chr4A	12667774	12669236	1462	True	2128.000	2128	92.9300	1	1466	1	chr4A.!!$R1	1465
4	TraesCS3A01G425300	chr4A	53752074	53753827	1753	False	1273.000	2320	93.1110	1	2678	2	chr4A.!!$F1	2677
5	TraesCS3A01G425300	chr2D	299654774	299657540	2766	True	892.825	3301	94.9295	1	2917	4	chr2D.!!$R2	2916
6	TraesCS3A01G425300	chr2D	327321670	327324135	2465	False	778.325	2859	93.7295	306	2899	4	chr2D.!!$F1	2593
7	TraesCS3A01G425300	chr1D	242558216	242561275	3059	False	2080.500	2796	93.7080	1	2889	2	chr1D.!!$F1	2888
8	TraesCS3A01G425300	chr1D	319525855	319528362	2507	True	782.075	2854	93.8560	306	2948	4	chr1D.!!$R1	2642
9	TraesCS3A01G425300	chr6A	241737621	241740085	2464	False	2462.000	2462	85.1750	2	2416	1	chr6A.!!$F1	2414
10	TraesCS3A01G425300	chr7A	2540338	2541799	1461	False	2128.000	2128	92.9300	1	1466	1	chr7A.!!$F1	1465
11	TraesCS3A01G425300	chr7A	67563020	67564482	1462	False	2128.000	2128	92.9300	1	1466	1	chr7A.!!$F2	1465
12	TraesCS3A01G425300	chr1A	502836057	502837519	1462	True	2122.000	2122	92.8620	1	1466	1	chr1A.!!$R1	1465
13	TraesCS3A01G425300	chr5A	280764657	280766117	1460	False	2104.000	2104	92.6580	1	1466	1	chr5A.!!$F1	1465

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
1483	1538	3.129287	ACTGAGTTCACTTGCAACCAAAG	59.871	43.478	0.0	0.0	0.0	2.77	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
3086	3531	1.374758	GAAGTGTGGACGCCAGGAG	60.375	63.158	0.0	0.0	32.34	3.69	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
1483	1538	3.129287	ACTGAGTTCACTTGCAACCAAAG	59.871	43.478	0.00	0.00	0.00	2.77
1495	1550	6.767423	ACTTGCAACCAAAGCATTTAAATTCT	59.233	30.769	0.00	0.00	42.33	2.40
1687	1762	0.815213	AAGCTCTGTCGCAAGCAACA	60.815	50.000	0.00	0.00	41.06	3.33
1886	1981	3.863780	GCATGCCGATCATCAGACACTAT	60.864	47.826	6.36	0.00	31.79	2.12
1959	2057	1.131638	ACATGCCATGATCTACGGGT	58.868	50.000	12.53	0.00	0.00	5.28
1988	2086	1.670087	GCTCAGCAGCGTACAAGAGAA	60.670	52.381	0.00	0.00	35.39	2.87
2051	2149	7.982919	TCTTATCGTGCTTATTTACTTGCCTTA	59.017	33.333	0.00	0.00	0.00	2.69
2728	3019	2.697751	AGCGAGGAAAGATCACTGCTAT	59.302	45.455	0.00	0.00	0.00	2.97
2730	3021	3.388308	CGAGGAAAGATCACTGCTATGG	58.612	50.000	0.00	0.00	0.00	2.74
2937	3382	3.992943	ATGGATTGACTTTGTCGGGTA	57.007	42.857	0.00	0.00	34.95	3.69
2941	3386	2.243602	TTGACTTTGTCGGGTACACC	57.756	50.000	0.00	0.00	38.00	4.16
2950	3395	2.202837	GGGTACACCGTCGCATCC	60.203	66.667	0.00	0.00	36.71	3.51
2951	3396	2.718073	GGGTACACCGTCGCATCCT	61.718	63.158	0.00	0.00	36.71	3.24
2952	3397	1.217244	GGTACACCGTCGCATCCTT	59.783	57.895	0.00	0.00	0.00	3.36
2953	3398	0.390735	GGTACACCGTCGCATCCTTT	60.391	55.000	0.00	0.00	0.00	3.11
2954	3399	1.435577	GTACACCGTCGCATCCTTTT	58.564	50.000	0.00	0.00	0.00	2.27
2955	3400	1.802365	GTACACCGTCGCATCCTTTTT	59.198	47.619	0.00	0.00	0.00	1.94
2978	3423	8.766000	TTTTTGAAAAAGTCCCTACTGTTTTC	57.234	30.769	0.00	13.21	42.18	2.29
2979	3424	7.712204	TTTGAAAAAGTCCCTACTGTTTTCT	57.288	32.000	17.04	0.00	42.18	2.52
2980	3425	8.810990	TTTGAAAAAGTCCCTACTGTTTTCTA	57.189	30.769	17.04	11.86	42.18	2.10
2981	3426	8.810990	TTGAAAAAGTCCCTACTGTTTTCTAA	57.189	30.769	17.04	11.60	42.18	2.10
2982	3427	8.810990	TGAAAAAGTCCCTACTGTTTTCTAAA	57.189	30.769	17.04	0.00	42.18	1.85
2983	3428	8.680001	TGAAAAAGTCCCTACTGTTTTCTAAAC	58.320	33.333	17.04	0.00	42.18	2.01
2984	3429	8.818622	AAAAAGTCCCTACTGTTTTCTAAACT	57.181	30.769	4.19	0.00	39.68	2.66
2985	3430	8.818622	AAAAGTCCCTACTGTTTTCTAAACTT	57.181	30.769	4.19	0.00	35.62	2.66
2986	3431	9.910267	AAAAGTCCCTACTGTTTTCTAAACTTA	57.090	29.630	4.19	0.00	35.62	2.24
2987	3432	9.910267	AAAGTCCCTACTGTTTTCTAAACTTAA	57.090	29.630	4.19	0.00	35.62	1.85
2988	3433	8.899427	AGTCCCTACTGTTTTCTAAACTTAAC	57.101	34.615	4.19	0.00	33.57	2.01
2989	3434	7.935755	AGTCCCTACTGTTTTCTAAACTTAACC	59.064	37.037	4.19	0.00	33.57	2.85
2990	3435	7.173907	GTCCCTACTGTTTTCTAAACTTAACCC	59.826	40.741	4.19	0.00	0.00	4.11
2991	3436	6.999871	CCCTACTGTTTTCTAAACTTAACCCA	59.000	38.462	4.19	0.00	0.00	4.51
2992	3437	7.040892	CCCTACTGTTTTCTAAACTTAACCCAC	60.041	40.741	4.19	0.00	0.00	4.61
2993	3438	7.499895	CCTACTGTTTTCTAAACTTAACCCACA	59.500	37.037	4.19	0.00	0.00	4.17
2994	3439	7.092137	ACTGTTTTCTAAACTTAACCCACAC	57.908	36.000	4.19	0.00	0.00	3.82
2995	3440	6.888088	ACTGTTTTCTAAACTTAACCCACACT	59.112	34.615	4.19	0.00	0.00	3.55
2996	3441	7.066645	ACTGTTTTCTAAACTTAACCCACACTC	59.933	37.037	4.19	0.00	0.00	3.51
2997	3442	6.319405	TGTTTTCTAAACTTAACCCACACTCC	59.681	38.462	4.19	0.00	0.00	3.85
2998	3443	5.633655	TTCTAAACTTAACCCACACTCCA	57.366	39.130	0.00	0.00	0.00	3.86
2999	3444	5.836024	TCTAAACTTAACCCACACTCCAT	57.164	39.130	0.00	0.00	0.00	3.41
3000	3445	5.556915	TCTAAACTTAACCCACACTCCATG	58.443	41.667	0.00	0.00	0.00	3.66
3001	3446	3.876309	AACTTAACCCACACTCCATGT	57.124	42.857	0.00	0.00	44.81	3.21
3002	3447	3.876309	ACTTAACCCACACTCCATGTT	57.124	42.857	0.00	0.00	40.64	2.71
3003	3448	4.178956	ACTTAACCCACACTCCATGTTT	57.821	40.909	0.00	0.00	40.64	2.83
3004	3449	5.313280	ACTTAACCCACACTCCATGTTTA	57.687	39.130	0.00	0.00	40.64	2.01
3005	3450	5.697067	ACTTAACCCACACTCCATGTTTAA	58.303	37.500	0.00	0.00	40.64	1.52
3006	3451	5.768164	ACTTAACCCACACTCCATGTTTAAG	59.232	40.000	7.63	7.63	40.64	1.85
3007	3452	3.876309	ACCCACACTCCATGTTTAAGT	57.124	42.857	0.00	0.00	40.64	2.24
3008	3453	3.751518	ACCCACACTCCATGTTTAAGTC	58.248	45.455	0.00	0.00	40.64	3.01
3009	3454	3.137544	ACCCACACTCCATGTTTAAGTCA	59.862	43.478	0.00	0.00	40.64	3.41
3010	3455	4.202567	ACCCACACTCCATGTTTAAGTCAT	60.203	41.667	0.00	0.00	40.64	3.06
3011	3456	5.013704	ACCCACACTCCATGTTTAAGTCATA	59.986	40.000	0.00	0.00	40.64	2.15
3012	3457	5.354234	CCCACACTCCATGTTTAAGTCATAC	59.646	44.000	0.00	0.00	40.64	2.39
3013	3458	5.937540	CCACACTCCATGTTTAAGTCATACA	59.062	40.000	0.00	0.00	40.64	2.29
3014	3459	6.429692	CCACACTCCATGTTTAAGTCATACAA	59.570	38.462	0.00	0.00	40.64	2.41
3015	3460	7.040755	CCACACTCCATGTTTAAGTCATACAAA	60.041	37.037	0.00	0.00	40.64	2.83
3016	3461	8.349245	CACACTCCATGTTTAAGTCATACAAAA	58.651	33.333	0.00	0.00	40.64	2.44
3017	3462	8.908903	ACACTCCATGTTTAAGTCATACAAAAA	58.091	29.630	0.00	0.00	38.98	1.94
3032	3477	2.279186	AAAAACTTGGCCGCACGC	60.279	55.556	0.00	0.00	0.00	5.34
3033	3478	2.781158	AAAAACTTGGCCGCACGCT	61.781	52.632	0.00	0.00	37.74	5.07
3034	3479	2.677573	AAAAACTTGGCCGCACGCTC	62.678	55.000	0.00	0.00	37.74	5.03
3044	3489	4.070552	GCACGCTCCTCTTCCGGT	62.071	66.667	0.00	0.00	0.00	5.28
3045	3490	2.182030	CACGCTCCTCTTCCGGTC	59.818	66.667	0.00	0.00	0.00	4.79
3046	3491	3.069318	ACGCTCCTCTTCCGGTCC	61.069	66.667	0.00	0.00	0.00	4.46
3047	3492	3.839432	CGCTCCTCTTCCGGTCCC	61.839	72.222	0.00	0.00	0.00	4.46
3048	3493	2.364448	GCTCCTCTTCCGGTCCCT	60.364	66.667	0.00	0.00	0.00	4.20
3049	3494	2.428085	GCTCCTCTTCCGGTCCCTC	61.428	68.421	0.00	0.00	0.00	4.30
3050	3495	1.758906	CTCCTCTTCCGGTCCCTCC	60.759	68.421	0.00	0.00	0.00	4.30
3051	3496	2.038975	CCTCTTCCGGTCCCTCCA	59.961	66.667	0.00	0.00	35.57	3.86
3052	3497	1.383248	CCTCTTCCGGTCCCTCCAT	60.383	63.158	0.00	0.00	35.57	3.41
3053	3498	1.690219	CCTCTTCCGGTCCCTCCATG	61.690	65.000	0.00	0.00	35.57	3.66
3054	3499	2.190578	CTTCCGGTCCCTCCATGC	59.809	66.667	0.00	0.00	35.57	4.06
3055	3500	3.406595	CTTCCGGTCCCTCCATGCC	62.407	68.421	0.00	0.00	35.57	4.40
3056	3501	3.943137	TTCCGGTCCCTCCATGCCT	62.943	63.158	0.00	0.00	35.57	4.75
3057	3502	3.866582	CCGGTCCCTCCATGCCTC	61.867	72.222	0.00	0.00	35.57	4.70
3058	3503	4.227134	CGGTCCCTCCATGCCTCG	62.227	72.222	0.00	0.00	35.57	4.63
3059	3504	4.554036	GGTCCCTCCATGCCTCGC	62.554	72.222	0.00	0.00	35.97	5.03
3060	3505	4.554036	GTCCCTCCATGCCTCGCC	62.554	72.222	0.00	0.00	0.00	5.54
3062	3507	3.882326	CCCTCCATGCCTCGCCAT	61.882	66.667	0.00	0.00	0.00	4.40
3063	3508	2.281345	CCTCCATGCCTCGCCATC	60.281	66.667	0.00	0.00	0.00	3.51
3064	3509	2.281345	CTCCATGCCTCGCCATCC	60.281	66.667	0.00	0.00	0.00	3.51
3065	3510	3.839353	CTCCATGCCTCGCCATCCC	62.839	68.421	0.00	0.00	0.00	3.85
3066	3511	4.962836	CCATGCCTCGCCATCCCC	62.963	72.222	0.00	0.00	0.00	4.81
3088	3533	3.787001	CCCCCGCACTTCTCCCTC	61.787	72.222	0.00	0.00	0.00	4.30
3089	3534	3.787001	CCCCGCACTTCTCCCTCC	61.787	72.222	0.00	0.00	0.00	4.30
3090	3535	2.685380	CCCGCACTTCTCCCTCCT	60.685	66.667	0.00	0.00	0.00	3.69
3091	3536	2.581354	CCGCACTTCTCCCTCCTG	59.419	66.667	0.00	0.00	0.00	3.86
3092	3537	2.581354	CGCACTTCTCCCTCCTGG	59.419	66.667	0.00	0.00	0.00	4.45
3093	3538	2.270527	GCACTTCTCCCTCCTGGC	59.729	66.667	0.00	0.00	0.00	4.85
3094	3539	2.581354	CACTTCTCCCTCCTGGCG	59.419	66.667	0.00	0.00	0.00	5.69
3095	3540	2.120718	ACTTCTCCCTCCTGGCGT	59.879	61.111	0.00	0.00	0.00	5.68
3096	3541	1.985116	ACTTCTCCCTCCTGGCGTC	60.985	63.158	0.00	0.00	0.00	5.19
3097	3542	2.683933	TTCTCCCTCCTGGCGTCC	60.684	66.667	0.00	0.00	0.00	4.79
3098	3543	3.539593	TTCTCCCTCCTGGCGTCCA	62.540	63.158	0.00	0.00	0.00	4.02
3099	3544	3.775654	CTCCCTCCTGGCGTCCAC	61.776	72.222	0.00	0.00	0.00	4.02
3100	3545	4.631740	TCCCTCCTGGCGTCCACA	62.632	66.667	0.00	0.00	0.00	4.17
3101	3546	4.394712	CCCTCCTGGCGTCCACAC	62.395	72.222	0.00	0.00	0.00	3.82
3102	3547	3.314331	CCTCCTGGCGTCCACACT	61.314	66.667	0.00	0.00	0.00	3.55
3103	3548	2.743718	CTCCTGGCGTCCACACTT	59.256	61.111	0.00	0.00	0.00	3.16
3104	3549	1.374758	CTCCTGGCGTCCACACTTC	60.375	63.158	0.00	0.00	0.00	3.01

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
1483	1538	8.924691	TGCAATGTTGAACTAGAATTTAAATGC	58.075	29.630	0.39	0.00	0.00	3.56
1633	1692	5.263185	CAGAATTTTGTCGTCGTTGTTCTT	58.737	37.500	0.00	0.00	0.00	2.52
1860	1955	1.904537	TCTGATGATCGGCATGCCTAT	59.095	47.619	33.07	28.07	37.34	2.57
2051	2149	2.223595	CGCTCCTTCTCGTCACACATAT	60.224	50.000	0.00	0.00	0.00	1.78
2260	2543	5.153513	GCTTCTTTGAACATCGCATTGTTA	58.846	37.500	1.55	0.00	39.85	2.41
2400	2688	2.425668	CGGGGCTTCCAATAATTCGTTT	59.574	45.455	0.00	0.00	34.36	3.60
2916	3361	3.992943	ACCCGACAAAGTCAATCCATA	57.007	42.857	0.00	0.00	32.09	2.74
2918	3363	2.369203	TGTACCCGACAAAGTCAATCCA	59.631	45.455	0.00	0.00	34.15	3.41
2937	3382	3.015516	AAAAAGGATGCGACGGTGT	57.984	47.368	0.00	0.00	0.00	4.16
2953	3398	8.590204	AGAAAACAGTAGGGACTTTTTCAAAAA	58.410	29.630	17.61	0.00	40.50	1.94
2954	3399	8.129496	AGAAAACAGTAGGGACTTTTTCAAAA	57.871	30.769	17.61	0.00	40.50	2.44
2955	3400	7.712204	AGAAAACAGTAGGGACTTTTTCAAA	57.288	32.000	17.61	0.00	40.50	2.69
2956	3401	8.810990	TTAGAAAACAGTAGGGACTTTTTCAA	57.189	30.769	17.61	11.74	40.50	2.69
2957	3402	8.680001	GTTTAGAAAACAGTAGGGACTTTTTCA	58.320	33.333	17.61	8.77	40.50	2.69
2958	3403	8.900781	AGTTTAGAAAACAGTAGGGACTTTTTC	58.099	33.333	5.42	12.50	41.75	2.29
2959	3404	8.818622	AGTTTAGAAAACAGTAGGGACTTTTT	57.181	30.769	5.42	0.00	41.75	1.94
2960	3405	8.818622	AAGTTTAGAAAACAGTAGGGACTTTT	57.181	30.769	5.42	0.00	41.75	2.27
2961	3406	9.910267	TTAAGTTTAGAAAACAGTAGGGACTTT	57.090	29.630	5.42	0.00	41.75	2.66
2962	3407	9.334947	GTTAAGTTTAGAAAACAGTAGGGACTT	57.665	33.333	5.42	0.00	41.75	3.01
2963	3408	7.935755	GGTTAAGTTTAGAAAACAGTAGGGACT	59.064	37.037	5.42	0.00	46.37	3.85
2964	3409	7.173907	GGGTTAAGTTTAGAAAACAGTAGGGAC	59.826	40.741	5.42	0.00	0.00	4.46
2965	3410	7.147337	TGGGTTAAGTTTAGAAAACAGTAGGGA	60.147	37.037	5.42	0.00	0.00	4.20
2966	3411	6.999871	TGGGTTAAGTTTAGAAAACAGTAGGG	59.000	38.462	5.42	0.00	0.00	3.53
2967	3412	7.499895	TGTGGGTTAAGTTTAGAAAACAGTAGG	59.500	37.037	5.42	0.00	0.00	3.18
2968	3413	8.340443	GTGTGGGTTAAGTTTAGAAAACAGTAG	58.660	37.037	5.42	0.00	0.00	2.57
2969	3414	8.048514	AGTGTGGGTTAAGTTTAGAAAACAGTA	58.951	33.333	5.42	0.00	0.00	2.74
2970	3415	6.888088	AGTGTGGGTTAAGTTTAGAAAACAGT	59.112	34.615	5.42	0.00	0.00	3.55
2971	3416	7.329588	AGTGTGGGTTAAGTTTAGAAAACAG	57.670	36.000	5.42	0.00	0.00	3.16
2972	3417	6.319405	GGAGTGTGGGTTAAGTTTAGAAAACA	59.681	38.462	5.42	0.00	0.00	2.83
2973	3418	6.319405	TGGAGTGTGGGTTAAGTTTAGAAAAC	59.681	38.462	0.00	0.00	0.00	2.43
2974	3419	6.424883	TGGAGTGTGGGTTAAGTTTAGAAAA	58.575	36.000	0.00	0.00	0.00	2.29
2975	3420	6.003859	TGGAGTGTGGGTTAAGTTTAGAAA	57.996	37.500	0.00	0.00	0.00	2.52
2976	3421	5.633655	TGGAGTGTGGGTTAAGTTTAGAA	57.366	39.130	0.00	0.00	0.00	2.10
2977	3422	5.072600	ACATGGAGTGTGGGTTAAGTTTAGA	59.927	40.000	0.00	0.00	40.28	2.10
2978	3423	5.313712	ACATGGAGTGTGGGTTAAGTTTAG	58.686	41.667	0.00	0.00	40.28	1.85
2979	3424	5.313280	ACATGGAGTGTGGGTTAAGTTTA	57.687	39.130	0.00	0.00	40.28	2.01
2980	3425	4.178956	ACATGGAGTGTGGGTTAAGTTT	57.821	40.909	0.00	0.00	40.28	2.66
2981	3426	3.876309	ACATGGAGTGTGGGTTAAGTT	57.124	42.857	0.00	0.00	40.28	2.66
2982	3427	3.876309	AACATGGAGTGTGGGTTAAGT	57.124	42.857	0.00	0.00	41.14	2.24
2983	3428	5.768164	ACTTAAACATGGAGTGTGGGTTAAG	59.232	40.000	0.00	0.00	41.14	1.85
2984	3429	5.697067	ACTTAAACATGGAGTGTGGGTTAA	58.303	37.500	0.00	0.00	41.14	2.01
2985	3430	5.163184	TGACTTAAACATGGAGTGTGGGTTA	60.163	40.000	0.00	0.00	41.14	2.85
2986	3431	4.142038	GACTTAAACATGGAGTGTGGGTT	58.858	43.478	0.00	0.00	41.14	4.11
2987	3432	3.137544	TGACTTAAACATGGAGTGTGGGT	59.862	43.478	0.00	0.00	41.14	4.51
2988	3433	3.750371	TGACTTAAACATGGAGTGTGGG	58.250	45.455	0.00	0.00	41.14	4.61
2989	3434	5.937540	TGTATGACTTAAACATGGAGTGTGG	59.062	40.000	0.00	0.00	41.14	4.17
2990	3435	7.433708	TTGTATGACTTAAACATGGAGTGTG	57.566	36.000	0.00	0.00	41.14	3.82
2991	3436	8.458573	TTTTGTATGACTTAAACATGGAGTGT	57.541	30.769	0.00	0.00	44.84	3.55
3015	3460	2.279186	GCGTGCGGCCAAGTTTTT	60.279	55.556	2.24	0.00	34.80	1.94
3016	3461	3.194272	GAGCGTGCGGCCAAGTTTT	62.194	57.895	2.24	0.00	45.17	2.43
3017	3462	3.660111	GAGCGTGCGGCCAAGTTT	61.660	61.111	2.24	0.00	45.17	2.66
3027	3472	3.991536	GACCGGAAGAGGAGCGTGC	62.992	68.421	9.46	0.00	34.73	5.34
3028	3473	2.182030	GACCGGAAGAGGAGCGTG	59.818	66.667	9.46	0.00	34.73	5.34
3029	3474	3.069318	GGACCGGAAGAGGAGCGT	61.069	66.667	9.46	0.00	34.73	5.07
3030	3475	3.839432	GGGACCGGAAGAGGAGCG	61.839	72.222	9.46	0.00	34.73	5.03
3031	3476	2.364448	AGGGACCGGAAGAGGAGC	60.364	66.667	9.46	0.00	34.73	4.70
3032	3477	1.758906	GGAGGGACCGGAAGAGGAG	60.759	68.421	9.46	0.00	34.73	3.69
3033	3478	1.886730	ATGGAGGGACCGGAAGAGGA	61.887	60.000	9.46	0.00	42.61	3.71
3034	3479	1.383248	ATGGAGGGACCGGAAGAGG	60.383	63.158	9.46	0.00	42.61	3.69
3035	3480	1.826024	CATGGAGGGACCGGAAGAG	59.174	63.158	9.46	0.00	42.61	2.85
3036	3481	2.367202	GCATGGAGGGACCGGAAGA	61.367	63.158	9.46	0.00	42.61	2.87
3037	3482	2.190578	GCATGGAGGGACCGGAAG	59.809	66.667	9.46	0.00	42.61	3.46
3038	3483	3.407967	GGCATGGAGGGACCGGAA	61.408	66.667	9.46	0.00	42.61	4.30
3039	3484	4.414956	AGGCATGGAGGGACCGGA	62.415	66.667	9.46	0.00	42.61	5.14
3040	3485	3.866582	GAGGCATGGAGGGACCGG	61.867	72.222	0.00	0.00	42.61	5.28
3041	3486	4.227134	CGAGGCATGGAGGGACCG	62.227	72.222	0.00	0.00	42.61	4.79
3042	3487	4.554036	GCGAGGCATGGAGGGACC	62.554	72.222	0.00	0.00	39.54	4.46
3043	3488	4.554036	GGCGAGGCATGGAGGGAC	62.554	72.222	0.00	0.00	0.00	4.46
3045	3490	3.839353	GATGGCGAGGCATGGAGGG	62.839	68.421	16.91	0.00	0.00	4.30
3046	3491	2.281345	GATGGCGAGGCATGGAGG	60.281	66.667	16.91	0.00	0.00	4.30
3047	3492	2.281345	GGATGGCGAGGCATGGAG	60.281	66.667	16.91	0.00	0.00	3.86
3048	3493	3.877450	GGGATGGCGAGGCATGGA	61.877	66.667	16.91	0.00	0.00	3.41
3049	3494	4.962836	GGGGATGGCGAGGCATGG	62.963	72.222	16.91	0.00	0.00	3.66
3071	3516	3.787001	GAGGGAGAAGTGCGGGGG	61.787	72.222	0.00	0.00	0.00	5.40
3072	3517	3.787001	GGAGGGAGAAGTGCGGGG	61.787	72.222	0.00	0.00	0.00	5.73
3073	3518	2.685380	AGGAGGGAGAAGTGCGGG	60.685	66.667	0.00	0.00	0.00	6.13
3074	3519	2.581354	CAGGAGGGAGAAGTGCGG	59.419	66.667	0.00	0.00	0.00	5.69
3075	3520	2.581354	CCAGGAGGGAGAAGTGCG	59.419	66.667	0.00	0.00	40.01	5.34
3076	3521	2.270527	GCCAGGAGGGAGAAGTGC	59.729	66.667	0.00	0.00	40.01	4.40
3077	3522	2.232298	GACGCCAGGAGGGAGAAGTG	62.232	65.000	0.00	0.00	39.08	3.16
3078	3523	1.985116	GACGCCAGGAGGGAGAAGT	60.985	63.158	0.00	0.00	39.08	3.01
3079	3524	2.726351	GGACGCCAGGAGGGAGAAG	61.726	68.421	0.00	0.00	39.08	2.85
3080	3525	2.683933	GGACGCCAGGAGGGAGAA	60.684	66.667	0.00	0.00	39.08	2.87
3081	3526	3.992641	TGGACGCCAGGAGGGAGA	61.993	66.667	0.00	0.00	39.08	3.71
3082	3527	3.775654	GTGGACGCCAGGAGGGAG	61.776	72.222	0.00	0.00	43.05	4.30
3083	3528	4.631740	TGTGGACGCCAGGAGGGA	62.632	66.667	0.00	0.00	40.01	4.20
3084	3529	4.394712	GTGTGGACGCCAGGAGGG	62.395	72.222	0.00	0.00	40.85	4.30
3085	3530	2.788191	GAAGTGTGGACGCCAGGAGG	62.788	65.000	0.00	0.00	32.34	4.30
3086	3531	1.374758	GAAGTGTGGACGCCAGGAG	60.375	63.158	0.00	0.00	32.34	3.69
3087	3532	2.741092	GAAGTGTGGACGCCAGGA	59.259	61.111	0.00	0.00	32.34	3.86

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.