AutoCloner

Multiple sequence alignment - TraesCS3D01G021000

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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	TraesCS3D01G021000	chr3D	100.000	2888	0	0	1	2888	7018184	7021071	0.000000e+00	5334.0
1	TraesCS3D01G021000	chr3D	84.962	931	108	19	995	1914	7090573	7089664	0.000000e+00	915.0
2	TraesCS3D01G021000	chr3D	90.991	111	3	5	598	705	354325115	354325221	3.000000e-30	143.0
3	TraesCS3D01G021000	chr3D	91.753	97	6	1	2613	2709	560556227	560556321	1.810000e-27	134.0
4	TraesCS3D01G021000	chr3D	94.253	87	3	1	2622	2708	497727913	497727997	6.490000e-27	132.0
5	TraesCS3D01G021000	chr3D	89.474	76	4	2	1	76	107046689	107046618	3.060000e-15	93.5
6	TraesCS3D01G021000	chr3D	95.238	42	2	0	703	744	350786221	350786180	1.860000e-07	67.6
7	TraesCS3D01G021000	chr3D	87.755	49	4	2	685	732	376819378	376819425	4.020000e-04	56.5
8	TraesCS3D01G021000	chr3B	90.492	1546	93	17	532	2029	8511698	8513237	0.000000e+00	1991.0
9	TraesCS3D01G021000	chr3B	86.638	928	102	13	995	1914	8634789	8633876	0.000000e+00	1007.0
10	TraesCS3D01G021000	chr3B	95.628	549	8	3	1	535	8509744	8510290	0.000000e+00	867.0
11	TraesCS3D01G021000	chr3B	89.542	612	49	5	1433	2029	8516238	8516849	0.000000e+00	761.0
12	TraesCS3D01G021000	chr3B	82.774	685	109	3	1185	1869	7376621	7375946	1.140000e-168	603.0
13	TraesCS3D01G021000	chr3B	80.204	490	53	18	1896	2371	8514966	8515425	7.720000e-86	327.0
14	TraesCS3D01G021000	chr3B	80.204	490	53	19	1896	2371	8518580	8519039	7.720000e-86	327.0
15	TraesCS3D01G021000	chr3B	83.516	182	30	0	2707	2888	8515642	8515823	1.380000e-38	171.0
16	TraesCS3D01G021000	chr3B	89.655	116	6	4	598	711	776519855	776519744	3.000000e-30	143.0
17	TraesCS3D01G021000	chr3B	86.598	97	9	4	610	705	825474226	825474133	1.420000e-18	104.0
18	TraesCS3D01G021000	chr3A	89.680	1531	101	26	785	2275	13376742	13375229	0.000000e+00	1899.0
19	TraesCS3D01G021000	chr3A	86.659	922	107	13	995	1914	13267233	13268140	0.000000e+00	1007.0
20	TraesCS3D01G021000	chr3A	84.515	917	116	11	995	1894	13324881	13325788	0.000000e+00	883.0
21	TraesCS3D01G021000	chr3A	86.857	350	35	5	2274	2623	13366371	13366033	5.840000e-102	381.0
22	TraesCS3D01G021000	chr3A	89.437	284	26	3	2340	2623	13375229	13374950	3.540000e-94	355.0
23	TraesCS3D01G021000	chr3A	87.912	182	20	2	2707	2888	13366034	13365855	2.250000e-51	213.0
24	TraesCS3D01G021000	chr3A	77.953	381	44	17	1938	2292	13367424	13367058	4.880000e-48	202.0
25	TraesCS3D01G021000	chr3A	92.632	95	5	1	2618	2712	707127207	707127115	5.020000e-28	135.0
26	TraesCS3D01G021000	chr3A	85.577	104	11	4	611	712	724148118	724148219	3.940000e-19	106.0
27	TraesCS3D01G021000	chr7A	91.761	352	22	5	1	348	129676132	129676480	1.560000e-132	483.0
28	TraesCS3D01G021000	chr7A	83.654	208	14	4	346	534	129684318	129684524	8.220000e-41	178.0
29	TraesCS3D01G021000	chr7A	91.667	96	6	1	2614	2709	3014001	3014094	6.490000e-27	132.0
30	TraesCS3D01G021000	chr7A	82.759	116	13	6	589	702	246260234	246260124	2.370000e-16	97.1
31	TraesCS3D01G021000	chr4A	95.402	87	2	1	2622	2708	112585044	112585128	1.400000e-28	137.0
32	TraesCS3D01G021000	chr5A	91.176	102	5	3	2607	2708	580286835	580286932	5.020000e-28	135.0
33	TraesCS3D01G021000	chr2D	92.553	94	5	1	2615	2708	648166010	648165919	1.810000e-27	134.0
34	TraesCS3D01G021000	chr5B	90.196	102	8	1	2619	2720	520899552	520899453	6.490000e-27	132.0
35	TraesCS3D01G021000	chr2A	90.099	101	8	1	2609	2709	715298805	715298903	2.340000e-26	130.0
36	TraesCS3D01G021000	chr1A	89.796	98	8	1	605	702	37489828	37489733	1.090000e-24	124.0
37	TraesCS3D01G021000	chr1A	82.114	123	14	5	589	708	386500125	386500242	6.590000e-17	99.0
38	TraesCS3D01G021000	chr7D	85.149	101	12	1	605	705	105285847	105285944	1.830000e-17	100.0
39	TraesCS3D01G021000	chr4B	90.698	43	4	0	703	745	7380618	7380660	1.120000e-04	58.4

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	TraesCS3D01G021000	chr3D	7018184	7021071	2887	False	5334.000000	5334	100.000000	1	2888	1	chr3D.!!$F1	2887
1	TraesCS3D01G021000	chr3D	7089664	7090573	909	True	915.000000	915	84.962000	995	1914	1	chr3D.!!$R1	919
2	TraesCS3D01G021000	chr3B	8633876	8634789	913	True	1007.000000	1007	86.638000	995	1914	1	chr3B.!!$R2	919
3	TraesCS3D01G021000	chr3B	8509744	8519039	9295	False	740.666667	1991	86.597667	1	2888	6	chr3B.!!$F1	2887
4	TraesCS3D01G021000	chr3B	7375946	7376621	675	True	603.000000	603	82.774000	1185	1869	1	chr3B.!!$R1	684
5	TraesCS3D01G021000	chr3A	13374950	13376742	1792	True	1127.000000	1899	89.558500	785	2623	2	chr3A.!!$R3	1838
6	TraesCS3D01G021000	chr3A	13267233	13268140	907	False	1007.000000	1007	86.659000	995	1914	1	chr3A.!!$F1	919
7	TraesCS3D01G021000	chr3A	13324881	13325788	907	False	883.000000	883	84.515000	995	1894	1	chr3A.!!$F2	899
8	TraesCS3D01G021000	chr3A	13365855	13367424	1569	True	265.333333	381	84.240667	1938	2888	3	chr3A.!!$R2	950

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
535	1961	2.159627	CCTGTCCCGAAGAACGAAAATG	59.84	50.0	0.0	0.0	45.77	2.32	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2067	3608	0.109597	GTGAGAGCACCGGCAAATTG	60.11	55.0	0.0	0.0	44.61	2.32	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
63	64	6.066032	TGATGATGGATATGCAACTCACAAT	58.934	36.000	0.00	0.00	0.00	2.71
300	305	3.887621	TTCAGGACACATACAGCCTAC	57.112	47.619	0.00	0.00	0.00	3.18
415	430	4.855340	CCCACAAAACATGGTAGGAGTAT	58.145	43.478	0.00	0.00	35.23	2.12
461	476	3.684788	CAGGCACACTTTCATAGTACACC	59.315	47.826	0.00	0.00	34.56	4.16
535	1961	2.159627	CCTGTCCCGAAGAACGAAAATG	59.840	50.000	0.00	0.00	45.77	2.32
537	1963	3.468770	TGTCCCGAAGAACGAAAATGAA	58.531	40.909	0.00	0.00	45.77	2.57
552	1978	4.647424	AAATGAAAAAGGTCTTGTGCGA	57.353	36.364	0.00	0.00	0.00	5.10
649	2081	2.180862	TCGAGATCCGACGGCTCAG	61.181	63.158	19.19	12.52	43.23	3.35
708	2145	9.495754	GATGTGAAATAGCAAATCTGTTTAGAC	57.504	33.333	0.00	0.00	36.44	2.59
770	2207	5.944007	AGTTAGCACACACCCCTAATAAAAG	59.056	40.000	0.00	0.00	0.00	2.27
1095	2553	1.667724	GCAACCAGAACCTCATCATCG	59.332	52.381	0.00	0.00	0.00	3.84
1100	2558	3.129109	CCAGAACCTCATCATCGTCATG	58.871	50.000	0.00	0.00	0.00	3.07
1321	2803	1.935873	CGACGCATCAGATCAACCAAT	59.064	47.619	0.00	0.00	0.00	3.16
1537	3027	0.255318	CTTGGAAGATCTGCAGGCCT	59.745	55.000	15.13	0.00	0.00	5.19
1587	3077	2.217038	GGGCGAGGGAGGCATCATA	61.217	63.158	0.00	0.00	38.57	2.15
1699	3192	0.735471	CGACATCGAGAAGGAGCTCA	59.265	55.000	17.19	0.00	43.02	4.26
1940	3443	2.996621	CGTGGATTGGAACTTCTGACTC	59.003	50.000	0.00	0.00	0.00	3.36
1983	3487	2.819595	CCGTCCCAAGATGCACCG	60.820	66.667	0.00	0.00	0.00	4.94
1984	3488	3.499737	CGTCCCAAGATGCACCGC	61.500	66.667	0.00	0.00	0.00	5.68
1986	3490	3.329889	TCCCAAGATGCACCGCCT	61.330	61.111	0.00	0.00	0.00	5.52
1989	3493	1.097547	CCCAAGATGCACCGCCTAAG	61.098	60.000	0.00	0.00	0.00	2.18
1990	3494	0.107703	CCAAGATGCACCGCCTAAGA	60.108	55.000	0.00	0.00	0.00	2.10
2002	3515	3.967987	ACCGCCTAAGATTTAGGACTGAT	59.032	43.478	16.96	0.00	36.85	2.90
2006	3519	6.814146	CCGCCTAAGATTTAGGACTGATATTC	59.186	42.308	16.96	0.00	36.85	1.75
2033	3546	9.480053	TCTACTAAAGTTATGGTGTGTTACAAC	57.520	33.333	0.00	0.00	36.06	3.32
2034	3547	7.500720	ACTAAAGTTATGGTGTGTTACAACC	57.499	36.000	8.90	8.90	34.14	3.77
2044	3585	5.186021	TGGTGTGTTACAACCAAAAGATGTT	59.814	36.000	13.94	0.00	34.14	2.71
2052	3593	6.767524	ACAACCAAAAGATGTTAAGTGACA	57.232	33.333	0.00	0.00	0.00	3.58
2059	3600	8.971321	CCAAAAGATGTTAAGTGACAAAATGAG	58.029	33.333	0.00	0.00	32.47	2.90
2067	3608	4.574599	AGTGACAAAATGAGCCAAACTC	57.425	40.909	0.00	0.00	46.45	3.01
2154	3703	9.088987	AGTCTTTAAATTTGTGGAATACATGGT	57.911	29.630	0.00	0.00	39.48	3.55
2218	5585	2.813474	CGGCGAAGGTCGATTGCA	60.813	61.111	0.00	0.00	46.20	4.08
2281	5648	8.204160	CCTACTCAACATACATCCTATCAACAA	58.796	37.037	0.00	0.00	0.00	2.83
2283	5650	8.268850	ACTCAACATACATCCTATCAACAAAC	57.731	34.615	0.00	0.00	0.00	2.93
2304	6376	1.283736	GGAGTTTGTCGTGTGTCGTT	58.716	50.000	0.00	0.00	40.80	3.85
2327	6399	4.683432	GCACTCGGCAAAGTCTCT	57.317	55.556	0.00	0.00	43.97	3.10
2328	6400	2.157421	GCACTCGGCAAAGTCTCTG	58.843	57.895	0.00	0.00	43.97	3.35
2329	6401	1.905922	GCACTCGGCAAAGTCTCTGC	61.906	60.000	0.00	0.00	43.97	4.26
2330	6402	0.320247	CACTCGGCAAAGTCTCTGCT	60.320	55.000	0.00	0.00	39.82	4.24
2331	6403	0.320247	ACTCGGCAAAGTCTCTGCTG	60.320	55.000	0.02	0.02	45.79	4.41
2334	6406	3.621953	GGCAAAGTCTCTGCTGAGT	57.378	52.632	18.82	0.00	40.98	3.41
2335	6407	1.889545	GGCAAAGTCTCTGCTGAGTT	58.110	50.000	18.82	5.68	40.98	3.01
2336	6408	3.045601	GGCAAAGTCTCTGCTGAGTTA	57.954	47.619	18.82	0.00	40.98	2.24
2337	6409	3.403038	GGCAAAGTCTCTGCTGAGTTAA	58.597	45.455	18.82	0.00	40.98	2.01
2338	6410	3.815401	GGCAAAGTCTCTGCTGAGTTAAA	59.185	43.478	18.82	0.00	40.98	1.52
2371	6444	2.312390	GACAAACAAAAGGGGTAGGCA	58.688	47.619	0.00	0.00	0.00	4.75
2376	6449	1.497286	ACAAAAGGGGTAGGCAGAACA	59.503	47.619	0.00	0.00	0.00	3.18
2457	6530	5.890334	ACACTCGACAAACATTTTGAACAT	58.110	33.333	5.67	0.00	0.00	2.71
2507	6581	0.389948	CTACTGTGGCGGAGGTGAAC	60.390	60.000	0.00	0.00	0.00	3.18
2574	6649	3.918253	GACAACATGGCGGGCTGGA	62.918	63.158	2.38	0.00	0.00	3.86
2607	6682	2.126071	CGTCGTCGATGGTGGCTT	60.126	61.111	6.56	0.00	39.71	4.35
2623	6698	0.179137	GCTTCGCCCTTGCCAAATAC	60.179	55.000	0.00	0.00	0.00	1.89
2624	6699	1.463674	CTTCGCCCTTGCCAAATACT	58.536	50.000	0.00	0.00	0.00	2.12
2625	6700	1.401905	CTTCGCCCTTGCCAAATACTC	59.598	52.381	0.00	0.00	0.00	2.59
2626	6701	0.393808	TCGCCCTTGCCAAATACTCC	60.394	55.000	0.00	0.00	0.00	3.85
2627	6702	1.384222	CGCCCTTGCCAAATACTCCC	61.384	60.000	0.00	0.00	0.00	4.30
2628	6703	0.033109	GCCCTTGCCAAATACTCCCT	60.033	55.000	0.00	0.00	0.00	4.20
2629	6704	2.024306	GCCCTTGCCAAATACTCCCTC	61.024	57.143	0.00	0.00	0.00	4.30
2630	6705	1.410224	CCCTTGCCAAATACTCCCTCC	60.410	57.143	0.00	0.00	0.00	4.30
2631	6706	1.668419	CTTGCCAAATACTCCCTCCG	58.332	55.000	0.00	0.00	0.00	4.63
2632	6707	0.988832	TTGCCAAATACTCCCTCCGT	59.011	50.000	0.00	0.00	0.00	4.69
2633	6708	1.868713	TGCCAAATACTCCCTCCGTA	58.131	50.000	0.00	0.00	0.00	4.02
2634	6709	2.189676	TGCCAAATACTCCCTCCGTAA	58.810	47.619	0.00	0.00	0.00	3.18
2635	6710	2.572556	TGCCAAATACTCCCTCCGTAAA	59.427	45.455	0.00	0.00	0.00	2.01
2636	6711	2.941064	GCCAAATACTCCCTCCGTAAAC	59.059	50.000	0.00	0.00	0.00	2.01
2637	6712	3.370209	GCCAAATACTCCCTCCGTAAACT	60.370	47.826	0.00	0.00	0.00	2.66
2638	6713	4.141869	GCCAAATACTCCCTCCGTAAACTA	60.142	45.833	0.00	0.00	0.00	2.24
2639	6714	5.627503	GCCAAATACTCCCTCCGTAAACTAA	60.628	44.000	0.00	0.00	0.00	2.24
2640	6715	6.589135	CCAAATACTCCCTCCGTAAACTAAT	58.411	40.000	0.00	0.00	0.00	1.73
2641	6716	7.687592	GCCAAATACTCCCTCCGTAAACTAATA	60.688	40.741	0.00	0.00	0.00	0.98
2642	6717	8.373220	CCAAATACTCCCTCCGTAAACTAATAT	58.627	37.037	0.00	0.00	0.00	1.28
2647	6722	8.406730	ACTCCCTCCGTAAACTAATATAAGAG	57.593	38.462	0.00	0.00	0.00	2.85
2648	6723	7.039853	ACTCCCTCCGTAAACTAATATAAGAGC	60.040	40.741	0.00	0.00	0.00	4.09
2649	6724	6.072286	TCCCTCCGTAAACTAATATAAGAGCG	60.072	42.308	0.00	0.00	0.00	5.03
2650	6725	6.294397	CCCTCCGTAAACTAATATAAGAGCGT	60.294	42.308	0.00	0.00	0.00	5.07
2651	6726	7.144000	CCTCCGTAAACTAATATAAGAGCGTT	58.856	38.462	0.00	0.00	0.00	4.84
2652	6727	7.650903	CCTCCGTAAACTAATATAAGAGCGTTT	59.349	37.037	0.00	0.00	0.00	3.60
2653	6728	9.669353	CTCCGTAAACTAATATAAGAGCGTTTA	57.331	33.333	0.00	0.00	0.00	2.01
2702	6777	9.530633	AAACGCTCTTATATTAGTTTACAGAGG	57.469	33.333	0.00	0.00	31.14	3.69
2703	6778	7.659186	ACGCTCTTATATTAGTTTACAGAGGG	58.341	38.462	8.36	8.36	42.53	4.30
2704	6779	7.504911	ACGCTCTTATATTAGTTTACAGAGGGA	59.495	37.037	14.96	0.00	40.49	4.20
2705	6780	8.024285	CGCTCTTATATTAGTTTACAGAGGGAG	58.976	40.741	4.76	0.00	40.49	4.30
2706	6781	8.862085	GCTCTTATATTAGTTTACAGAGGGAGT	58.138	37.037	0.00	0.00	0.00	3.85
2725	6800	2.725203	TAGAAGGCAAAGGCACGCGT	62.725	55.000	5.58	5.58	43.71	6.01
2748	6823	2.048603	GCTTGACTGGGCCATGGTC	61.049	63.158	14.67	16.75	0.00	4.02
2780	6855	3.857854	CTTGCTAGCAGCCACGCG	61.858	66.667	18.45	3.53	41.51	6.01
2801	6876	2.617215	GGTGATTGGGGGAGGGGT	60.617	66.667	0.00	0.00	0.00	4.95
2848	6923	1.133575	CATGCATGGGAAGGATGAGGT	60.134	52.381	19.40	0.00	37.02	3.85

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
90	91	9.994432	TTTTCGTGTTTAAATTCATGCATTTTT	57.006	22.222	8.62	0.22	0.00	1.94
91	92	9.649024	CTTTTCGTGTTTAAATTCATGCATTTT	57.351	25.926	8.62	0.00	0.00	1.82
300	305	4.563184	GTGTGCCTCTATCTTTTGTCTACG	59.437	45.833	0.00	0.00	0.00	3.51
415	430	4.041567	ACCATGTCAGGTGAATAGTCAACA	59.958	41.667	11.32	4.45	44.63	3.33
461	476	2.740447	CACCACTCACACATCATGTCAG	59.260	50.000	0.00	0.00	40.64	3.51
492	507	1.646189	GTTGGAGAGCGGATTGTCTC	58.354	55.000	0.00	0.00	38.84	3.36
528	543	4.085619	CGCACAAGACCTTTTTCATTTTCG	60.086	41.667	0.00	0.00	0.00	3.46
535	1961	2.612212	TGTCTCGCACAAGACCTTTTTC	59.388	45.455	8.05	0.00	44.17	2.29
537	1963	2.325583	TGTCTCGCACAAGACCTTTT	57.674	45.000	8.05	0.00	44.17	2.27
563	1989	2.987282	TTTTCTGGCTGTCGCGCTCA	62.987	55.000	5.56	3.71	36.88	4.26
572	2004	2.680913	CCCGCTCGTTTTCTGGCTG	61.681	63.158	0.00	0.00	0.00	4.85
607	2039	5.288712	ACTCTATGTAAGATTCGTGCAAACG	59.711	40.000	0.00	0.00	32.41	3.60
729	2166	0.408700	ACTCGTACTCCCCCTGTCTT	59.591	55.000	0.00	0.00	0.00	3.01
730	2167	0.408700	AACTCGTACTCCCCCTGTCT	59.591	55.000	0.00	0.00	0.00	3.41
734	2171	0.333993	TGCTAACTCGTACTCCCCCT	59.666	55.000	0.00	0.00	0.00	4.79
736	2173	1.135170	GTGTGCTAACTCGTACTCCCC	60.135	57.143	0.00	0.00	0.00	4.81
770	2207	1.084289	GTGTAGCCATCCAAACCGAC	58.916	55.000	0.00	0.00	0.00	4.79
833	2270	8.168725	TCGACTAATATATAGACCCAAAGAGGT	58.831	37.037	0.00	0.00	45.12	3.85
1095	2553	2.690778	GGACGGCTTGGTGCATGAC	61.691	63.158	0.00	0.00	45.15	3.06
1321	2803	0.391528	TCGATGTCGACGTAGGTCCA	60.392	55.000	10.95	3.77	44.22	4.02
1537	3027	0.682852	ACGTCACCCGAGGATTTCAA	59.317	50.000	0.00	0.00	40.70	2.69
1587	3077	3.049674	TCGTCGTTCGGGTACGCT	61.050	61.111	8.43	0.00	41.16	5.07
1699	3192	3.007973	GCCTCTCGCCGTTCTTCCT	62.008	63.158	0.00	0.00	0.00	3.36
1807	3300	1.673665	GCTTGGTCCTGCTGGTGAG	60.674	63.158	9.73	5.03	34.23	3.51
1983	3487	8.811994	AGAGAATATCAGTCCTAAATCTTAGGC	58.188	37.037	7.48	3.92	34.74	3.93
2006	3519	9.701098	TTGTAACACACCATAACTTTAGTAGAG	57.299	33.333	0.00	0.00	0.00	2.43
2010	3523	7.055378	TGGTTGTAACACACCATAACTTTAGT	58.945	34.615	0.00	0.00	28.95	2.24
2033	3546	8.870160	TCATTTTGTCACTTAACATCTTTTGG	57.130	30.769	0.00	0.00	0.00	3.28
2034	3547	8.482429	GCTCATTTTGTCACTTAACATCTTTTG	58.518	33.333	0.00	0.00	0.00	2.44
2044	3585	6.072112	GAGTTTGGCTCATTTTGTCACTTA	57.928	37.500	0.00	0.00	43.58	2.24
2067	3608	0.109597	GTGAGAGCACCGGCAAATTG	60.110	55.000	0.00	0.00	44.61	2.32
2075	3616	2.654749	TGTAATCAGTGAGAGCACCG	57.345	50.000	0.00	0.00	46.32	4.94
2170	5537	5.220491	CGGCATCTAAGCTCTTTCTTGTAAC	60.220	44.000	0.00	0.00	34.17	2.50
2171	5538	4.870426	CGGCATCTAAGCTCTTTCTTGTAA	59.130	41.667	0.00	0.00	34.17	2.41
2246	5613	4.517453	TGTATGTTGAGTAGGTTTTGCCAC	59.483	41.667	0.00	0.00	40.61	5.01
2281	5648	2.277084	GACACACGACAAACTCCAGTT	58.723	47.619	0.00	0.00	40.50	3.16
2283	5650	0.852777	CGACACACGACAAACTCCAG	59.147	55.000	0.00	0.00	45.77	3.86
2293	6365	2.232296	GCCGACAAACGACACACGA	61.232	57.895	0.00	0.00	45.77	4.35
2295	6367	3.401095	TGCCGACAAACGACACAC	58.599	55.556	0.00	0.00	45.77	3.82
2304	6376	2.203084	TTTGCCGAGTGCCGACAA	60.203	55.556	0.00	0.00	38.83	3.18
2312	6384	0.320247	CAGCAGAGACTTTGCCGAGT	60.320	55.000	14.01	0.00	42.48	4.18
2371	6444	0.250901	AGCATTGTTCGCCCTGTTCT	60.251	50.000	0.00	0.00	0.00	3.01
2376	6449	1.973281	CACCAGCATTGTTCGCCCT	60.973	57.895	0.00	0.00	0.00	5.19
2403	6476	1.538047	CACTTGGCATAACACCAGCT	58.462	50.000	0.00	0.00	38.73	4.24
2425	6498	3.997681	TGTTTGTCGAGTGTCAAAGAACA	59.002	39.130	0.00	0.00	34.56	3.18
2489	6563	1.669440	GTTCACCTCCGCCACAGTA	59.331	57.895	0.00	0.00	0.00	2.74
2490	6564	2.426023	GTTCACCTCCGCCACAGT	59.574	61.111	0.00	0.00	0.00	3.55
2507	6581	0.461961	CTCTTGCTACTTCGGGAGGG	59.538	60.000	0.00	0.00	0.00	4.30
2555	6630	2.672651	CAGCCCGCCATGTTGTCA	60.673	61.111	0.00	0.00	0.00	3.58
2592	6667	2.180769	CGAAGCCACCATCGACGA	59.819	61.111	0.00	0.00	41.43	4.20
2607	6682	0.393808	GGAGTATTTGGCAAGGGCGA	60.394	55.000	0.00	0.00	42.47	5.54
2623	6698	7.314393	GCTCTTATATTAGTTTACGGAGGGAG	58.686	42.308	0.00	0.00	0.00	4.30
2624	6699	6.072286	CGCTCTTATATTAGTTTACGGAGGGA	60.072	42.308	0.00	0.00	34.63	4.20
2625	6700	6.091437	CGCTCTTATATTAGTTTACGGAGGG	58.909	44.000	0.00	0.00	0.00	4.30
2626	6701	6.675987	ACGCTCTTATATTAGTTTACGGAGG	58.324	40.000	0.00	0.00	0.00	4.30
2627	6702	8.571461	AAACGCTCTTATATTAGTTTACGGAG	57.429	34.615	0.00	0.00	31.14	4.63
2676	6751	9.530633	CCTCTGTAAACTAATATAAGAGCGTTT	57.469	33.333	0.00	0.00	0.00	3.60
2677	6752	8.142551	CCCTCTGTAAACTAATATAAGAGCGTT	58.857	37.037	0.00	0.00	0.00	4.84
2678	6753	7.504911	TCCCTCTGTAAACTAATATAAGAGCGT	59.495	37.037	0.00	0.00	0.00	5.07
2679	6754	7.883217	TCCCTCTGTAAACTAATATAAGAGCG	58.117	38.462	0.00	0.00	0.00	5.03
2680	6755	8.862085	ACTCCCTCTGTAAACTAATATAAGAGC	58.138	37.037	0.00	0.00	0.00	4.09
2686	6761	9.369672	CCTTCTACTCCCTCTGTAAACTAATAT	57.630	37.037	0.00	0.00	0.00	1.28
2687	6762	7.287235	GCCTTCTACTCCCTCTGTAAACTAATA	59.713	40.741	0.00	0.00	0.00	0.98
2688	6763	6.098552	GCCTTCTACTCCCTCTGTAAACTAAT	59.901	42.308	0.00	0.00	0.00	1.73
2689	6764	5.421374	GCCTTCTACTCCCTCTGTAAACTAA	59.579	44.000	0.00	0.00	0.00	2.24
2690	6765	4.954826	GCCTTCTACTCCCTCTGTAAACTA	59.045	45.833	0.00	0.00	0.00	2.24
2691	6766	3.770388	GCCTTCTACTCCCTCTGTAAACT	59.230	47.826	0.00	0.00	0.00	2.66
2692	6767	3.514309	TGCCTTCTACTCCCTCTGTAAAC	59.486	47.826	0.00	0.00	0.00	2.01
2693	6768	3.786553	TGCCTTCTACTCCCTCTGTAAA	58.213	45.455	0.00	0.00	0.00	2.01
2694	6769	3.468071	TGCCTTCTACTCCCTCTGTAA	57.532	47.619	0.00	0.00	0.00	2.41
2695	6770	3.468071	TTGCCTTCTACTCCCTCTGTA	57.532	47.619	0.00	0.00	0.00	2.74
2696	6771	2.327325	TTGCCTTCTACTCCCTCTGT	57.673	50.000	0.00	0.00	0.00	3.41
2697	6772	2.093235	CCTTTGCCTTCTACTCCCTCTG	60.093	54.545	0.00	0.00	0.00	3.35
2698	6773	2.192263	CCTTTGCCTTCTACTCCCTCT	58.808	52.381	0.00	0.00	0.00	3.69
2699	6774	1.407575	GCCTTTGCCTTCTACTCCCTC	60.408	57.143	0.00	0.00	0.00	4.30
2700	6775	0.621082	GCCTTTGCCTTCTACTCCCT	59.379	55.000	0.00	0.00	0.00	4.20
2701	6776	0.328258	TGCCTTTGCCTTCTACTCCC	59.672	55.000	0.00	0.00	36.33	4.30
2702	6777	1.454201	GTGCCTTTGCCTTCTACTCC	58.546	55.000	0.00	0.00	36.33	3.85
2703	6778	1.079503	CGTGCCTTTGCCTTCTACTC	58.920	55.000	0.00	0.00	36.33	2.59
2704	6779	0.955919	GCGTGCCTTTGCCTTCTACT	60.956	55.000	0.00	0.00	36.33	2.57
2705	6780	1.502190	GCGTGCCTTTGCCTTCTAC	59.498	57.895	0.00	0.00	36.33	2.59
2706	6781	2.032634	CGCGTGCCTTTGCCTTCTA	61.033	57.895	0.00	0.00	36.33	2.10
2707	6782	3.357079	CGCGTGCCTTTGCCTTCT	61.357	61.111	0.00	0.00	36.33	2.85
2732	6807	2.350895	CGACCATGGCCCAGTCAA	59.649	61.111	13.04	0.00	0.00	3.18
2780	6855	2.438434	CTCCCCCAATCACCACGC	60.438	66.667	0.00	0.00	0.00	5.34
2810	6885	4.003788	CCACGGAACCCTGTCGCT	62.004	66.667	0.00	0.00	0.00	4.93
2818	6893	2.491152	CATGCATGCCACGGAACC	59.509	61.111	14.93	0.00	0.00	3.62

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.