AutoCloner

Multiple sequence alignment - TraesCS3B01G575700

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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	TraesCS3B01G575700	chr3B	100.000	3440	0	0	1	3440	805812863	805809424	0.000000e+00	6353.0
1	TraesCS3B01G575700	chr3B	94.782	1399	60	6	733	2122	806058735	806057341	0.000000e+00	2167.0
2	TraesCS3B01G575700	chr3B	82.649	1631	217	36	967	2556	810194249	810192644	0.000000e+00	1384.0
3	TraesCS3B01G575700	chr3B	92.651	830	51	5	1211	2034	805968584	805967759	0.000000e+00	1186.0
4	TraesCS3B01G575700	chr3B	91.272	802	45	6	418	1215	805977934	805977154	0.000000e+00	1070.0
5	TraesCS3B01G575700	chr3B	94.286	665	37	1	2776	3440	40037006	40036343	0.000000e+00	1016.0
6	TraesCS3B01G575700	chr3B	94.129	528	31	0	763	1290	806003669	806003142	0.000000e+00	804.0
7	TraesCS3B01G575700	chr3B	94.987	379	19	0	2177	2555	806057342	806056964	2.290000e-166	595.0
8	TraesCS3B01G575700	chr3B	92.797	236	7	2	1	226	806016824	806016589	1.980000e-87	333.0
9	TraesCS3B01G575700	chr3B	94.706	170	9	0	671	840	806058872	806058703	7.320000e-67	265.0
10	TraesCS3B01G575700	chr3B	93.529	170	8	1	223	389	806016549	806016380	2.050000e-62	250.0
11	TraesCS3B01G575700	chr3B	86.809	235	14	8	2557	2775	805921573	805921340	2.650000e-61	246.0
12	TraesCS3B01G575700	chr3B	92.638	163	5	3	223	378	805979752	805979590	9.600000e-56	228.0
13	TraesCS3B01G575700	chr3B	95.652	138	6	0	89	226	805979929	805979792	4.470000e-54	222.0
14	TraesCS3B01G575700	chr3B	92.473	93	4	1	2030	2122	805956944	805956855	2.790000e-26	130.0
15	TraesCS3B01G575700	chr3B	98.305	59	1	0	1	59	806058983	806058925	1.690000e-18	104.0
16	TraesCS3B01G575700	chr3B	100.000	31	0	0	292	322	810195482	810195452	1.330000e-04	58.4
17	TraesCS3B01G575700	chr3D	93.451	1924	92	18	223	2122	598726871	598724958	0.000000e+00	2824.0
18	TraesCS3B01G575700	chr3D	95.263	380	18	0	2177	2556	598724959	598724580	1.370000e-168	603.0
19	TraesCS3B01G575700	chr3D	93.617	235	3	3	1	226	598727142	598726911	1.180000e-89	340.0
20	TraesCS3B01G575700	chr3D	86.920	237	12	10	2557	2775	598720882	598720647	7.370000e-62	248.0
21	TraesCS3B01G575700	chr3D	83.333	72	6	3	767	832	575774815	575774744	1.030000e-05	62.1
22	TraesCS3B01G575700	chr7A	83.673	2401	278	54	223	2548	566988884	566991245	0.000000e+00	2158.0
23	TraesCS3B01G575700	chr7A	80.478	2218	286	77	418	2556	566909837	566911986	0.000000e+00	1561.0
24	TraesCS3B01G575700	chr7A	87.222	180	18	3	227	406	566789737	566789911	2.090000e-47	200.0
25	TraesCS3B01G575700	chr7A	80.237	253	23	12	418	657	566789988	566790226	7.640000e-37	165.0
26	TraesCS3B01G575700	chr7A	91.566	83	4	1	13	92	566988205	566988287	1.010000e-20	111.0
27	TraesCS3B01G575700	chr3A	81.563	2137	275	65	484	2556	732405048	732402967	0.000000e+00	1653.0
28	TraesCS3B01G575700	chr3A	93.204	1030	57	7	1103	2123	728915280	728914255	0.000000e+00	1502.0
29	TraesCS3B01G575700	chr3A	96.042	379	15	0	2178	2556	728914257	728913879	4.880000e-173	617.0
30	TraesCS3B01G575700	chr3A	91.034	435	31	1	671	1105	728925372	728924946	6.400000e-162	580.0
31	TraesCS3B01G575700	chr3A	90.265	226	10	5	13	226	728930994	728930769	5.620000e-73	285.0
32	TraesCS3B01G575700	chr3A	84.167	240	16	10	2557	2775	728913041	728912803	2.690000e-51	213.0
33	TraesCS3B01G575700	chrUn	84.400	1641	197	33	940	2545	86612092	86613708	0.000000e+00	1557.0
34	TraesCS3B01G575700	chrUn	88.655	238	23	4	422	656	86611614	86611850	1.560000e-73	287.0
35	TraesCS3B01G575700	chrUn	94.444	36	2	0	223	258	86611349	86611384	4.800000e-04	56.5
36	TraesCS3B01G575700	chr7D	82.975	1815	219	56	788	2548	500776011	500777789	0.000000e+00	1557.0
37	TraesCS3B01G575700	chr7D	78.390	236	20	16	423	636	500775649	500775875	1.300000e-24	124.0
38	TraesCS3B01G575700	chr7B	82.977	1592	204	47	993	2551	528873876	528875433	0.000000e+00	1376.0
39	TraesCS3B01G575700	chr7B	83.443	1522	193	34	1054	2549	73176697	73178185	0.000000e+00	1360.0
40	TraesCS3B01G575700	chr7B	82.516	1590	227	34	993	2556	664398858	664397294	0.000000e+00	1349.0
41	TraesCS3B01G575700	chr7B	94.153	667	37	2	2774	3440	602559314	602559978	0.000000e+00	1014.0
42	TraesCS3B01G575700	chr7B	83.317	1001	135	20	1572	2556	528876727	528877711	0.000000e+00	894.0
43	TraesCS3B01G575700	chr7B	78.421	380	44	21	228	583	528873137	528873502	2.690000e-51	213.0
44	TraesCS3B01G575700	chr6B	95.188	665	30	1	2776	3440	646920182	646920844	0.000000e+00	1050.0
45	TraesCS3B01G575700	chr6B	94.444	666	35	2	2775	3440	94238775	94238112	0.000000e+00	1024.0
46	TraesCS3B01G575700	chr5B	94.737	665	34	1	2776	3440	534452955	534453618	0.000000e+00	1033.0
47	TraesCS3B01G575700	chr5B	94.286	665	36	2	2776	3440	463926251	463926913	0.000000e+00	1016.0
48	TraesCS3B01G575700	chr2B	94.864	662	32	2	2779	3440	13327781	13328440	0.000000e+00	1033.0
49	TraesCS3B01G575700	chr2B	94.453	667	36	1	2774	3440	702902632	702903297	0.000000e+00	1026.0
50	TraesCS3B01G575700	chr4B	94.461	668	32	5	2776	3440	650941150	650941815	0.000000e+00	1024.0
51	TraesCS3B01G575700	chr5D	82.927	902	129	18	1653	2547	483769579	483768696	0.000000e+00	789.0

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	TraesCS3B01G575700	chr3B	805809424	805812863	3439	True	6353.000000	6353	100.000000	1	3440	1	chr3B.!!$R2	3439
1	TraesCS3B01G575700	chr3B	805967759	805968584	825	True	1186.000000	1186	92.651000	1211	2034	1	chr3B.!!$R5	823
2	TraesCS3B01G575700	chr3B	40036343	40037006	663	True	1016.000000	1016	94.286000	2776	3440	1	chr3B.!!$R1	664
3	TraesCS3B01G575700	chr3B	806003142	806003669	527	True	804.000000	804	94.129000	763	1290	1	chr3B.!!$R6	527
4	TraesCS3B01G575700	chr3B	806056964	806058983	2019	True	782.750000	2167	95.695000	1	2555	4	chr3B.!!$R9	2554
5	TraesCS3B01G575700	chr3B	810192644	810195482	2838	True	721.200000	1384	91.324500	292	2556	2	chr3B.!!$R10	2264
6	TraesCS3B01G575700	chr3B	805977154	805979929	2775	True	506.666667	1070	93.187333	89	1215	3	chr3B.!!$R7	1126
7	TraesCS3B01G575700	chr3D	598720647	598727142	6495	True	1003.750000	2824	92.312750	1	2775	4	chr3D.!!$R2	2774
8	TraesCS3B01G575700	chr7A	566909837	566911986	2149	False	1561.000000	1561	80.478000	418	2556	1	chr7A.!!$F1	2138
9	TraesCS3B01G575700	chr7A	566988205	566991245	3040	False	1134.500000	2158	87.619500	13	2548	2	chr7A.!!$F3	2535
10	TraesCS3B01G575700	chr3A	732402967	732405048	2081	True	1653.000000	1653	81.563000	484	2556	1	chr3A.!!$R3	2072
11	TraesCS3B01G575700	chr3A	728912803	728915280	2477	True	777.333333	1502	91.137667	1103	2775	3	chr3A.!!$R4	1672
12	TraesCS3B01G575700	chrUn	86611349	86613708	2359	False	633.500000	1557	89.166333	223	2545	3	chrUn.!!$F1	2322
13	TraesCS3B01G575700	chr7D	500775649	500777789	2140	False	840.500000	1557	80.682500	423	2548	2	chr7D.!!$F1	2125
14	TraesCS3B01G575700	chr7B	73176697	73178185	1488	False	1360.000000	1360	83.443000	1054	2549	1	chr7B.!!$F1	1495
15	TraesCS3B01G575700	chr7B	664397294	664398858	1564	True	1349.000000	1349	82.516000	993	2556	1	chr7B.!!$R1	1563
16	TraesCS3B01G575700	chr7B	602559314	602559978	664	False	1014.000000	1014	94.153000	2774	3440	1	chr7B.!!$F2	666
17	TraesCS3B01G575700	chr7B	528873137	528877711	4574	False	827.666667	1376	81.571667	228	2556	3	chr7B.!!$F3	2328
18	TraesCS3B01G575700	chr6B	646920182	646920844	662	False	1050.000000	1050	95.188000	2776	3440	1	chr6B.!!$F1	664
19	TraesCS3B01G575700	chr6B	94238112	94238775	663	True	1024.000000	1024	94.444000	2775	3440	1	chr6B.!!$R1	665
20	TraesCS3B01G575700	chr5B	534452955	534453618	663	False	1033.000000	1033	94.737000	2776	3440	1	chr5B.!!$F2	664
21	TraesCS3B01G575700	chr5B	463926251	463926913	662	False	1016.000000	1016	94.286000	2776	3440	1	chr5B.!!$F1	664
22	TraesCS3B01G575700	chr2B	13327781	13328440	659	False	1033.000000	1033	94.864000	2779	3440	1	chr2B.!!$F1	661
23	TraesCS3B01G575700	chr2B	702902632	702903297	665	False	1026.000000	1026	94.453000	2774	3440	1	chr2B.!!$F2	666
24	TraesCS3B01G575700	chr4B	650941150	650941815	665	False	1024.000000	1024	94.461000	2776	3440	1	chr4B.!!$F1	664
25	TraesCS3B01G575700	chr5D	483768696	483769579	883	True	789.000000	789	82.927000	1653	2547	1	chr5D.!!$R1	894

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
265	735	0.519519	TTTCAAGGCAATACACCGCG	59.480	50.000	0.00	0.00	0.0	6.46	F
712	3068	1.378250	GAGCAGCTGGCCAGTGAAT	60.378	57.895	32.81	19.85	46.5	2.57	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1113	4188	0.875059	CGAAGACAAAGAAGGTGGCC	59.125	55.0	0.00	0.0	0.0	5.36	R
2631	11736	0.108138	GCTTAGGTCGCAGTGGACAT	60.108	55.0	12.09	8.5	38.7	3.06	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
265	735	0.519519	TTTCAAGGCAATACACCGCG	59.480	50.000	0.00	0.00	0.00	6.46
348	913	9.063615	GGTTCTACTTTGTCTGAGGAAAATTAA	57.936	33.333	0.00	0.00	0.00	1.40
352	917	7.208225	ACTTTGTCTGAGGAAAATTAAGCTC	57.792	36.000	0.00	0.00	0.00	4.09
378	2559	1.831736	CCAATACGACCCAAGTCCTCT	59.168	52.381	0.00	0.00	40.12	3.69
420	2650	1.865725	GCATGAGCGTTTTCGTGTAC	58.134	50.000	0.00	0.00	46.03	2.90
457	2699	1.960689	GAGCCCCTTTGCAACTGTTAA	59.039	47.619	0.00	0.00	0.00	2.01
497	2739	1.961277	CGAGGCCAACGTTGAGCTT	60.961	57.895	29.35	24.25	0.00	3.74
517	2770	4.275936	GCTTCTACAAAGGCTCAAAGACAA	59.724	41.667	0.00	0.00	0.00	3.18
668	2969	1.758514	GAGGAGGTCTGATGGCCGA	60.759	63.158	0.00	0.00	0.00	5.54
712	3068	1.378250	GAGCAGCTGGCCAGTGAAT	60.378	57.895	32.81	19.85	46.50	2.57
832	3267	2.287308	CCCGATTTCGACTTGTTTTGCA	60.287	45.455	0.67	0.00	43.02	4.08
955	3426	1.738346	CTGGGCGATCGTGATCCTCA	61.738	60.000	17.81	4.47	34.40	3.86
990	4056	3.402681	CCATCCGCCTCCACACCT	61.403	66.667	0.00	0.00	0.00	4.00
991	4057	2.671070	CATCCGCCTCCACACCTT	59.329	61.111	0.00	0.00	0.00	3.50
1113	4188	2.165234	TCATGAGAAGAAGCTGTCGAGG	59.835	50.000	0.00	0.00	0.00	4.63
1177	4252	2.284405	TCCCTCTGACCGAACCCC	60.284	66.667	0.00	0.00	0.00	4.95
1207	4282	3.130819	CGCGGCAATGGGCTTACA	61.131	61.111	0.00	0.00	44.01	2.41
1291	4366	4.633565	GCTTCTCAAACTACAAGATCCAGG	59.366	45.833	0.00	0.00	0.00	4.45
1293	4368	3.582647	TCTCAAACTACAAGATCCAGGCA	59.417	43.478	0.00	0.00	0.00	4.75
1518	4628	3.894947	GGTGGCGCAACCGTGTTT	61.895	61.111	20.41	0.00	43.94	2.83
1559	4669	1.497286	TCCCACCTTTACCAAGCAAGT	59.503	47.619	0.00	0.00	0.00	3.16
1560	4670	2.712087	TCCCACCTTTACCAAGCAAGTA	59.288	45.455	0.00	0.00	0.00	2.24
1561	4671	3.138653	TCCCACCTTTACCAAGCAAGTAA	59.861	43.478	0.00	0.00	0.00	2.24
1562	4672	3.506067	CCCACCTTTACCAAGCAAGTAAG	59.494	47.826	0.00	0.00	31.66	2.34
1810	7199	8.922237	TGCAGATTAATGCTTATATTGGGAAAA	58.078	29.630	0.00	0.00	46.63	2.29
1862	7251	2.260844	TTGTTGAAGCTCTGGGTGAG	57.739	50.000	0.00	0.00	45.33	3.51
1939	7328	2.101917	ACTAACAACTACACCACGTGCT	59.898	45.455	10.91	0.00	36.98	4.40
2017	7406	3.817647	GACAGCAAAGAAGAATGTCCACT	59.182	43.478	0.00	0.00	35.37	4.00
2098	7495	5.463286	TGCATGCATTCAAAAGTGTCTTAG	58.537	37.500	18.46	0.00	0.00	2.18
2102	7502	7.568134	GCATGCATTCAAAAGTGTCTTAGTTTG	60.568	37.037	14.21	0.00	32.34	2.93
2155	7558	4.433022	CGATCGTGTGCTTCAACTACTTTC	60.433	45.833	7.03	0.00	0.00	2.62
2156	7559	3.787785	TCGTGTGCTTCAACTACTTTCA	58.212	40.909	0.00	0.00	0.00	2.69
2158	7561	5.534407	TCGTGTGCTTCAACTACTTTCATA	58.466	37.500	0.00	0.00	0.00	2.15
2160	7563	6.145534	TCGTGTGCTTCAACTACTTTCATAAG	59.854	38.462	0.00	0.00	37.40	1.73
2161	7564	6.073765	CGTGTGCTTCAACTACTTTCATAAGT	60.074	38.462	0.00	0.00	46.18	2.24
2162	7565	7.518370	CGTGTGCTTCAACTACTTTCATAAGTT	60.518	37.037	0.00	0.00	41.85	2.66
2163	7566	7.798982	GTGTGCTTCAACTACTTTCATAAGTTC	59.201	37.037	0.00	0.00	41.85	3.01
2164	7567	7.497579	TGTGCTTCAACTACTTTCATAAGTTCA	59.502	33.333	0.00	0.00	41.85	3.18
2165	7568	8.507249	GTGCTTCAACTACTTTCATAAGTTCAT	58.493	33.333	0.00	0.00	41.85	2.57
2166	7569	9.719355	TGCTTCAACTACTTTCATAAGTTCATA	57.281	29.630	0.00	0.00	41.85	2.15
2283	7686	2.236395	AGATTCGAAGGGTTACTGTGGG	59.764	50.000	3.35	0.00	0.00	4.61
2315	7718	3.209410	AGTTGTCCACAGAGCTTCTTTG	58.791	45.455	0.00	0.00	0.00	2.77
2319	7722	1.134128	TCCACAGAGCTTCTTTGCACA	60.134	47.619	0.00	0.00	34.99	4.57
2467	7870	7.717568	AGTCAGCTTTCATATATCGTTGTAGT	58.282	34.615	0.00	0.00	0.00	2.73
2595	11700	9.466497	AATTGCTCAAAAATAAGAGACTATCCA	57.534	29.630	0.00	0.00	33.74	3.41
2631	11736	0.671251	GTGAACATTCGGGTTTGGCA	59.329	50.000	0.00	0.00	0.00	4.92
2634	11739	1.272212	GAACATTCGGGTTTGGCATGT	59.728	47.619	0.00	0.00	0.00	3.21
2640	11745	1.865788	CGGGTTTGGCATGTCCACTG	61.866	60.000	8.18	0.49	46.55	3.66
2641	11746	1.290009	GGTTTGGCATGTCCACTGC	59.710	57.895	8.18	2.97	46.55	4.40
2642	11747	1.081242	GTTTGGCATGTCCACTGCG	60.081	57.895	8.18	0.00	46.55	5.18
2643	11748	1.228094	TTTGGCATGTCCACTGCGA	60.228	52.632	8.18	0.00	46.55	5.10
2646	11751	2.046892	GCATGTCCACTGCGACCT	60.047	61.111	0.00	0.00	31.35	3.85
2650	11755	0.108138	ATGTCCACTGCGACCTAAGC	60.108	55.000	0.00	0.00	31.35	3.09
2651	11756	1.448013	GTCCACTGCGACCTAAGCC	60.448	63.158	0.00	0.00	0.00	4.35
2652	11757	2.125106	CCACTGCGACCTAAGCCC	60.125	66.667	0.00	0.00	0.00	5.19
2674	11799	2.681778	CCTCCTCGAGGCCAGTGT	60.682	66.667	27.39	0.00	43.29	3.55
2676	11801	3.057547	CTCCTCGAGGCCAGTGTCG	62.058	68.421	27.39	5.48	37.54	4.35
2700	11825	1.890876	CACTGGGTGGTCGATTTCAA	58.109	50.000	0.00	0.00	0.00	2.69
2702	11827	0.796312	CTGGGTGGTCGATTTCAACG	59.204	55.000	0.00	0.00	0.00	4.10
2733	11858	1.405463	CAAAAAGAATCCGGCTAGGCC	59.595	52.381	11.22	0.00	46.75	5.19
2788	11913	7.398024	AGGAGATTGCAACACTAGTAGAAAAT	58.602	34.615	0.00	0.00	0.00	1.82
2797	11922	7.633116	GCAACACTAGTAGAAAATAGGGCTACT	60.633	40.741	3.59	0.00	44.90	2.57
2880	12005	4.323477	CCCGGTTCGTGAGCCCAA	62.323	66.667	0.00	0.00	0.00	4.12
2974	12099	4.522971	GACCAATGGTCCTCGCTC	57.477	61.111	21.30	0.00	46.19	5.03
3016	12141	1.285950	GTTCTTGGCTTGAACCGGC	59.714	57.895	0.00	0.00	38.19	6.13
3050	12175	0.034863	TTTAGTCCCGGTTCATGCCC	60.035	55.000	0.00	0.00	0.00	5.36
3096	12221	5.891980	TATATATACCCCATCGCCGCGGA	62.892	52.174	33.48	9.86	0.00	5.54
3208	12334	0.524862	GAAATGCCTGAGCCACACTG	59.475	55.000	0.00	0.00	38.69	3.66
3220	12346	1.953686	GCCACACTGGTTAAGCTTTCA	59.046	47.619	3.20	0.23	40.46	2.69
3257	12383	2.426522	CTCCGAGCTCCATTTTCAACA	58.573	47.619	8.47	0.00	0.00	3.33
3278	12404	6.351327	ACAAGATTTGTCTAGATTTAGCGC	57.649	37.500	0.00	0.00	40.56	5.92
3286	12412	2.290916	TCTAGATTTAGCGCTCCGTCAG	59.709	50.000	16.34	5.81	0.00	3.51
3296	12422	4.414956	TCCGTCAGGCCCCATCCT	62.415	66.667	0.00	0.00	37.47	3.24
3298	12424	2.765807	CGTCAGGCCCCATCCTCT	60.766	66.667	0.00	0.00	33.25	3.69

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
348	913	3.199071	TGGGTCGTATTGGTAAATGAGCT	59.801	43.478	0.00	0.00	0.00	4.09
352	917	4.334481	GGACTTGGGTCGTATTGGTAAATG	59.666	45.833	0.00	0.00	42.97	2.32
378	2559	6.542005	TGCTCATAAGAAACTGTGTTTCTCAA	59.458	34.615	21.15	14.72	37.75	3.02
415	2601	3.691049	TCAAAACAGCAGCTTGTACAC	57.309	42.857	0.00	0.00	0.00	2.90
420	2650	2.391879	GCTCTTCAAAACAGCAGCTTG	58.608	47.619	0.00	0.00	33.06	4.01
457	2699	0.036010	CTTGGGTGTCGCCTTCTCAT	60.036	55.000	1.66	0.00	37.43	2.90
497	2739	4.776349	TGTTGTCTTTGAGCCTTTGTAGA	58.224	39.130	0.00	0.00	0.00	2.59
668	2969	1.931007	GCATGCCCTCTTCCCCTCTT	61.931	60.000	6.36	0.00	0.00	2.85
832	3267	6.761242	TCTTCAATTTATGGAATCATCGACGT	59.239	34.615	0.00	0.00	34.96	4.34
903	3370	5.975693	TTCGCCAACTAAAAATCAGGAAT	57.024	34.783	0.00	0.00	0.00	3.01
955	3426	1.328430	GGTTCTACTACTGCCGGCCT	61.328	60.000	26.77	11.92	0.00	5.19
1087	4162	1.998315	CAGCTTCTTCTCATGACCACG	59.002	52.381	0.00	0.00	0.00	4.94
1113	4188	0.875059	CGAAGACAAAGAAGGTGGCC	59.125	55.000	0.00	0.00	0.00	5.36
1177	4252	2.278206	CCGCGACATCTCGGTGAG	60.278	66.667	8.23	0.00	39.22	3.51
1239	4314	2.531376	GGTATTCGGCCGCGGAAAG	61.531	63.158	33.48	19.09	0.00	2.62
1291	4366	7.438459	ACAATAGTACTTACCGATGAAATCTGC	59.562	37.037	0.00	0.00	42.58	4.26
1444	4554	2.434185	CGCTGTACGGGCATGTGT	60.434	61.111	3.34	0.00	38.44	3.72
1518	4628	6.161855	GGAACCTCATGTGATGTACTATCA	57.838	41.667	0.00	0.00	0.00	2.15
1559	4669	8.840200	ACCATCTTCCTGAAAGTATCTACTTA	57.160	34.615	3.16	0.00	45.17	2.24
1561	4671	6.897966	TGACCATCTTCCTGAAAGTATCTACT	59.102	38.462	0.00	0.00	38.39	2.57
1562	4672	7.113658	TGACCATCTTCCTGAAAGTATCTAC	57.886	40.000	0.00	0.00	36.31	2.59
1689	7065	7.562454	TGTTGATATAGTACTCACATCGTCA	57.438	36.000	0.00	2.22	0.00	4.35
1690	7066	9.762062	CTATGTTGATATAGTACTCACATCGTC	57.238	37.037	0.00	0.00	0.00	4.20
1759	7143	9.801873	CACCCCATACAAGAAAATTAAGTTATG	57.198	33.333	0.00	0.00	0.00	1.90
1774	7161	3.636300	GCATTAATCTGCACCCCATACAA	59.364	43.478	0.00	0.00	41.87	2.41
1781	7168	6.350445	CCCAATATAAGCATTAATCTGCACCC	60.350	42.308	4.00	0.00	44.77	4.61
1810	7199	7.002879	ACATTAGCTGCCATCTCTTTTATCAT	58.997	34.615	0.00	0.00	0.00	2.45
1814	7203	4.883585	CCACATTAGCTGCCATCTCTTTTA	59.116	41.667	0.00	0.00	0.00	1.52
1855	7244	2.507886	TGACAAGAACCTTTCTCACCCA	59.492	45.455	0.00	0.00	39.61	4.51
1862	7251	4.562789	GCAAGTTGTTGACAAGAACCTTTC	59.437	41.667	21.02	8.64	35.43	2.62
1939	7328	7.875554	GGAAGCACCCAAGTTTTCAAAAATATA	59.124	33.333	0.00	0.00	0.00	0.86
2017	7406	1.881324	TGTGGTGTACAGATCGACGAA	59.119	47.619	0.00	0.00	33.42	3.85
2126	7528	2.564553	GAAGCACACGATCGAGCCCT	62.565	60.000	24.34	10.77	0.00	5.19
2130	7533	1.702886	AGTTGAAGCACACGATCGAG	58.297	50.000	24.34	17.42	0.00	4.04
2132	7535	2.596452	AGTAGTTGAAGCACACGATCG	58.404	47.619	14.88	14.88	0.00	3.69
2283	7686	0.819259	TGGACAACTCACCTTGCTGC	60.819	55.000	0.00	0.00	0.00	5.25
2319	7722	5.789643	ATTTATTGGACTTGTTGCACACT	57.210	34.783	0.00	0.00	0.00	3.55
2595	11700	2.231380	ACCCCATTTCCCACTCGCT	61.231	57.895	0.00	0.00	0.00	4.93
2631	11736	0.108138	GCTTAGGTCGCAGTGGACAT	60.108	55.000	12.09	8.50	38.70	3.06
2634	11739	2.656069	GGGCTTAGGTCGCAGTGGA	61.656	63.158	0.00	0.00	0.00	4.02
2660	11765	4.803426	GCGACACTGGCCTCGAGG	62.803	72.222	27.83	27.83	38.53	4.63
2700	11825	2.650322	TCTTTTTGCCTCCTTGTTCGT	58.350	42.857	0.00	0.00	0.00	3.85
2702	11827	4.560128	GGATTCTTTTTGCCTCCTTGTTC	58.440	43.478	0.00	0.00	0.00	3.18
2733	11858	1.136336	GCTCCTAAAAATATCGGCGCG	60.136	52.381	0.00	0.00	0.00	6.86
2737	11862	5.308825	ACATCCAGCTCCTAAAAATATCGG	58.691	41.667	0.00	0.00	0.00	4.18
2739	11864	7.040823	CCTCAACATCCAGCTCCTAAAAATATC	60.041	40.741	0.00	0.00	0.00	1.63
2788	11913	3.625099	GGCCGAACAGTAGCCCTA	58.375	61.111	0.00	0.00	41.00	3.53
2859	11984	2.126031	GCTCACGAACCGGGTCTC	60.126	66.667	19.34	4.04	0.00	3.36
2974	12099	2.285024	CCAATGGTTGTGGGCCAGG	61.285	63.158	6.40	0.00	39.65	4.45
3016	12141	1.073923	ACTAAAGCCACCCCTTCTGTG	59.926	52.381	0.00	0.00	0.00	3.66
3050	12175	2.160813	CAAGTTATTTGTCCCGGTTCGG	59.839	50.000	0.00	0.00	38.14	4.30
3257	12383	5.755861	GGAGCGCTAAATCTAGACAAATCTT	59.244	40.000	11.50	0.00	36.29	2.40
3278	12404	3.866582	GGATGGGGCCTGACGGAG	61.867	72.222	0.84	0.00	0.00	4.63
3296	12422	3.379445	GCGGTGAAGACGGGGAGA	61.379	66.667	0.00	0.00	0.00	3.71

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.