AutoCloner

Multiple sequence alignment - TraesCS2B01G111500

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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	TraesCS2B01G111500	chr2B	100.000	5032	0	0	1	5032	73391205	73386174	0.000000e+00	9293.0
1	TraesCS2B01G111500	chr2B	75.457	929	137	43	2513	3392	34797271	34796385	7.960000e-98	368.0
2	TraesCS2B01G111500	chr2B	80.351	285	49	6	3597	3877	49979482	49979201	5.100000e-50	209.0
3	TraesCS2B01G111500	chr2B	76.378	254	49	9	3056	3300	50142879	50143130	5.290000e-25	126.0
4	TraesCS2B01G111500	chr2A	93.369	4615	218	34	3	4548	49928605	49924010	0.000000e+00	6746.0
5	TraesCS2B01G111500	chr2A	92.407	1159	62	12	2295	3439	44599002	44597856	0.000000e+00	1629.0
6	TraesCS2B01G111500	chr2A	84.893	1635	187	30	804	2411	23891495	23893096	0.000000e+00	1596.0
7	TraesCS2B01G111500	chr2A	91.107	1012	67	10	1861	2865	44647975	44646980	0.000000e+00	1349.0
8	TraesCS2B01G111500	chr2A	88.396	1060	112	3	821	1870	44649910	44648852	0.000000e+00	1266.0
9	TraesCS2B01G111500	chr2A	87.833	1052	117	3	829	1870	44626580	44625530	0.000000e+00	1223.0
10	TraesCS2B01G111500	chr2A	77.926	1350	234	42	974	2281	32497139	32498466	0.000000e+00	784.0
11	TraesCS2B01G111500	chr2A	88.676	521	23	14	4548	5032	49923967	49923447	2.000000e-168	603.0
12	TraesCS2B01G111500	chr2A	88.046	435	39	12	2497	2923	23893398	23893827	2.090000e-138	503.0
13	TraesCS2B01G111500	chr2A	85.282	496	46	14	3030	3508	23893888	23894373	2.110000e-133	486.0
14	TraesCS2B01G111500	chr2A	92.035	226	18	0	1861	2086	44624657	44624432	8.130000e-83	318.0
15	TraesCS2B01G111500	chr2A	92.697	178	12	1	2618	2794	44645967	44645790	6.460000e-64	255.0
16	TraesCS2B01G111500	chr2A	96.825	63	2	0	1863	1925	44646162	44646100	6.890000e-19	106.0
17	TraesCS2B01G111500	chr2D	91.990	2734	153	26	1	2688	46390850	46388137	0.000000e+00	3775.0
18	TraesCS2B01G111500	chr2D	95.164	1220	50	4	3331	4548	46374836	46373624	0.000000e+00	1917.0
19	TraesCS2B01G111500	chr2D	92.574	1010	53	8	1861	2865	38083031	38082039	0.000000e+00	1430.0
20	TraesCS2B01G111500	chr2D	91.683	1010	63	7	1861	2865	40167744	40166751	0.000000e+00	1380.0
21	TraesCS2B01G111500	chr2D	89.518	954	99	1	917	1870	40169570	40168618	0.000000e+00	1206.0
22	TraesCS2B01G111500	chr2D	89.925	665	67	0	1206	1870	38084569	38083905	0.000000e+00	857.0
23	TraesCS2B01G111500	chr2D	91.522	578	30	12	2721	3288	46388132	46387564	0.000000e+00	778.0
24	TraesCS2B01G111500	chr2D	91.051	514	16	8	4548	5032	46373581	46373069	0.000000e+00	667.0
25	TraesCS2B01G111500	chr2D	81.227	277	50	2	3611	3886	30480754	30481029	6.560000e-54	222.0
26	TraesCS2B01G111500	chr2D	82.609	69	12	0	119	187	431002207	431002275	1.510000e-05	62.1
27	TraesCS2B01G111500	chrUn	87.736	954	82	16	2001	2941	12660826	12661757	0.000000e+00	1081.0
28	TraesCS2B01G111500	chrUn	84.615	1066	128	13	938	1986	331381187	331380141	0.000000e+00	1027.0
29	TraesCS2B01G111500	chrUn	85.888	411	53	5	3597	4005	331379000	331378593	2.780000e-117	433.0
30	TraesCS2B01G111500	chrUn	88.782	312	29	3	3555	3864	12662100	12662407	1.320000e-100	377.0
31	TraesCS2B01G111500	chrUn	89.352	216	15	2	1902	2109	12660602	12660817	1.070000e-66	265.0
32	TraesCS2B01G111500	chrUn	88.785	214	24	0	3930	4143	12662407	12662620	3.860000e-66	263.0
33	TraesCS2B01G111500	chrUn	74.795	730	108	37	2709	3392	318351848	318351149	5.000000e-65	259.0
34	TraesCS2B01G111500	chrUn	89.815	108	6	3	4215	4320	12662652	12662756	3.160000e-27	134.0
35	TraesCS2B01G111500	chrUn	86.239	109	13	2	3898	4005	342412488	342412595	3.180000e-22	117.0
36	TraesCS2B01G111500	chrUn	86.239	109	13	2	3898	4005	342414971	342415078	3.180000e-22	117.0
37	TraesCS2B01G111500	chr7D	82.222	1170	175	20	1157	2311	153640358	153639207	0.000000e+00	977.0
38	TraesCS2B01G111500	chr7D	100.000	28	0	0	4199	4226	53063015	53063042	9.000000e-03	52.8
39	TraesCS2B01G111500	chr7B	82.155	1132	171	17	1195	2311	115410330	115409215	0.000000e+00	942.0
40	TraesCS2B01G111500	chr1A	75.194	387	87	8	3622	4005	555126123	555126503	1.860000e-39	174.0
41	TraesCS2B01G111500	chr4D	91.935	62	5	0	2629	2690	3887335	3887274	2.500000e-13	87.9
42	TraesCS2B01G111500	chr5A	100.000	31	0	0	4196	4226	705599792	705599822	1.960000e-04	58.4
43	TraesCS2B01G111500	chr5A	100.000	28	0	0	4199	4226	560580374	560580401	9.000000e-03	52.8
44	TraesCS2B01G111500	chr4A	100.000	31	0	0	4199	4229	603333836	603333866	1.960000e-04	58.4
45	TraesCS2B01G111500	chr5D	100.000	28	0	0	4199	4226	444034625	444034652	9.000000e-03	52.8
46	TraesCS2B01G111500	chr1D	100.000	28	0	0	4199	4226	25101606	25101633	9.000000e-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	TraesCS2B01G111500	chr2B	73386174	73391205	5031	True	9293.000000	9293	100.000000	1	5032	1	chr2B.!!$R3	5031
1	TraesCS2B01G111500	chr2B	34796385	34797271	886	True	368.000000	368	75.457000	2513	3392	1	chr2B.!!$R1	879
2	TraesCS2B01G111500	chr2A	49923447	49928605	5158	True	3674.500000	6746	91.022500	3	5032	2	chr2A.!!$R4	5029
3	TraesCS2B01G111500	chr2A	44597856	44599002	1146	True	1629.000000	1629	92.407000	2295	3439	1	chr2A.!!$R1	1144
4	TraesCS2B01G111500	chr2A	23891495	23894373	2878	False	861.666667	1596	86.073667	804	3508	3	chr2A.!!$F2	2704
5	TraesCS2B01G111500	chr2A	32497139	32498466	1327	False	784.000000	784	77.926000	974	2281	1	chr2A.!!$F1	1307
6	TraesCS2B01G111500	chr2A	44624432	44626580	2148	True	770.500000	1223	89.934000	829	2086	2	chr2A.!!$R2	1257
7	TraesCS2B01G111500	chr2A	44645790	44649910	4120	True	744.000000	1349	92.256250	821	2865	4	chr2A.!!$R3	2044
8	TraesCS2B01G111500	chr2D	46387564	46390850	3286	True	2276.500000	3775	91.756000	1	3288	2	chr2D.!!$R4	3287
9	TraesCS2B01G111500	chr2D	40166751	40169570	2819	True	1293.000000	1380	90.600500	917	2865	2	chr2D.!!$R2	1948
10	TraesCS2B01G111500	chr2D	46373069	46374836	1767	True	1292.000000	1917	93.107500	3331	5032	2	chr2D.!!$R3	1701
11	TraesCS2B01G111500	chr2D	38082039	38084569	2530	True	1143.500000	1430	91.249500	1206	2865	2	chr2D.!!$R1	1659
12	TraesCS2B01G111500	chrUn	331378593	331381187	2594	True	730.000000	1027	85.251500	938	4005	2	chrUn.!!$R2	3067
13	TraesCS2B01G111500	chrUn	12660602	12662756	2154	False	424.000000	1081	88.894000	1902	4320	5	chrUn.!!$F1	2418
14	TraesCS2B01G111500	chrUn	318351149	318351848	699	True	259.000000	259	74.795000	2709	3392	1	chrUn.!!$R1	683
15	TraesCS2B01G111500	chr7D	153639207	153640358	1151	True	977.000000	977	82.222000	1157	2311	1	chr7D.!!$R1	1154
16	TraesCS2B01G111500	chr7B	115409215	115410330	1115	True	942.000000	942	82.155000	1195	2311	1	chr7B.!!$R1	1116

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
591	600	0.250793	ACCTCAACGTTGGTGTGACA	59.749	50.000	27.02	5.95	34.90	3.58	F
733	742	1.394917	CCTTGTAGTGCAGCGATCAAC	59.605	52.381	0.00	0.00	0.00	3.18	F
1904	3766	0.962855	CTCTCTGGCAGAGTCGGTCA	60.963	60.000	36.22	19.85	43.61	4.02	F
2003	3887	1.268625	GGTTGGGAAAACGGTCATCAC	59.731	52.381	0.00	0.00	0.00	3.06	F
2437	4680	1.677576	CTGCACAATGGATTATGCCGT	59.322	47.619	0.34	0.00	37.26	5.68	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1573	1660	0.108898	CTGACGCTGAAGAGAGTGGG	60.109	60.000	0.00	31.49	4.61	R
2220	4264	0.534203	TCTCCACGTTGGGAAAGCAC	60.534	55.000	0.00	38.32	4.40	R
2772	5506	1.002033	GTGAGGCTGCAAACTTCAGTG	60.002	52.381	0.50	34.21	3.66	R
3810	7163	2.127271	TTGGCCATCACGATGAATGT	57.873	45.000	6.09	41.20	2.71	R
4045	7401	1.099689	ACGAAAACACAACACCCCAG	58.900	50.000	0.00	0.00	4.45	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
27	29	6.316390	ACAACCTTTCAACTTCAGTAACTCTG	59.684	38.462	0.00	0.00	44.85	3.35
67	69	6.375174	TCACATTCTTCGATCAAAACCATCAT	59.625	34.615	0.00	0.00	0.00	2.45
73	75	5.880164	TCGATCAAAACCATCATACCCTA	57.120	39.130	0.00	0.00	0.00	3.53
84	86	6.605119	ACCATCATACCCTAGAAAATCCTTG	58.395	40.000	0.00	0.00	0.00	3.61
110	112	5.419542	CCCTACGACATCATCTTTTTCAGA	58.580	41.667	0.00	0.00	35.33	3.27
196	198	2.664568	CGCAAGACTCCATGCAAATTTG	59.335	45.455	14.03	14.03	42.68	2.32
249	251	2.198406	CTTGTTCGTGTTGACCTTCGA	58.802	47.619	0.00	0.00	0.00	3.71
283	291	0.990818	GCTCCAATCTCCCCCTCCTT	60.991	60.000	0.00	0.00	0.00	3.36
337	345	4.543689	AGATTCATGTTCCTCATTGCCAT	58.456	39.130	0.00	0.00	34.09	4.40
341	349	5.486735	TCATGTTCCTCATTGCCATTTTT	57.513	34.783	0.00	0.00	34.09	1.94
351	359	6.127253	CCTCATTGCCATTTTTAGTCTTCCAT	60.127	38.462	0.00	0.00	0.00	3.41
354	362	6.916360	TTGCCATTTTTAGTCTTCCATTCT	57.084	33.333	0.00	0.00	0.00	2.40
389	397	0.902531	TGCCTTCTTACCCTTCTCCG	59.097	55.000	0.00	0.00	0.00	4.63
408	416	1.409427	CGCCTCCCTAAAGTTCGATCT	59.591	52.381	0.00	0.00	0.00	2.75
425	433	2.061509	TCTCGTCGACCCCATGATTA	57.938	50.000	10.58	0.00	0.00	1.75
446	455	3.620488	ACCGCTTCACAATCCAATATGT	58.380	40.909	0.00	0.00	0.00	2.29
457	466	5.129485	ACAATCCAATATGTCCTCTCTCGTT	59.871	40.000	0.00	0.00	0.00	3.85
468	477	3.377485	TCCTCTCTCGTTTGATCTTACCG	59.623	47.826	0.00	0.00	0.00	4.02
587	596	1.065709	ACAAGACCTCAACGTTGGTGT	60.066	47.619	27.02	22.61	36.59	4.16
591	600	0.250793	ACCTCAACGTTGGTGTGACA	59.749	50.000	27.02	5.95	34.90	3.58
596	605	1.798223	CAACGTTGGTGTGACATCGAT	59.202	47.619	20.71	0.00	37.11	3.59
609	618	4.572389	GTGACATCGATGGAGTAAGCAAAT	59.428	41.667	28.09	3.39	0.00	2.32
611	620	4.769688	ACATCGATGGAGTAAGCAAATCA	58.230	39.130	28.09	0.00	0.00	2.57
634	643	1.400494	GCCGCCTATCGTGAAAAACAT	59.600	47.619	0.00	0.00	36.19	2.71
672	681	5.865085	TGCAGGTACTAAGTGAAAGATGTT	58.135	37.500	0.00	0.00	36.02	2.71
673	682	5.932303	TGCAGGTACTAAGTGAAAGATGTTC	59.068	40.000	0.00	0.00	36.02	3.18
723	732	5.093849	TCATACTAAACCCCTTGTAGTGC	57.906	43.478	0.00	0.00	30.81	4.40
724	733	4.532916	TCATACTAAACCCCTTGTAGTGCA	59.467	41.667	0.00	0.00	30.81	4.57
733	742	1.394917	CCTTGTAGTGCAGCGATCAAC	59.605	52.381	0.00	0.00	0.00	3.18
790	809	7.697691	TCTGAGACATGAAAGAAAGAAACAAC	58.302	34.615	0.00	0.00	0.00	3.32
876	904	3.215975	TGGCCCAACTAAGTAACAACAC	58.784	45.455	0.00	0.00	0.00	3.32
911	964	3.064408	GCTTCGGTCCCTTTATAAAACGG	59.936	47.826	0.00	2.40	0.00	4.44
934	987	3.055719	CCACCATCGCCACACACC	61.056	66.667	0.00	0.00	0.00	4.16
1422	1509	2.963854	CGCATCCTCGAAGCGCAT	60.964	61.111	11.47	0.00	42.32	4.73
1478	1565	2.726821	CCACATGAATGGCTACCTTGT	58.273	47.619	0.00	0.00	31.52	3.16
1561	1648	4.980805	GACCGTGGCCGCAAGACA	62.981	66.667	18.18	0.00	43.02	3.41
1573	1660	3.023735	AAGACATGCCCCTCCCCC	61.024	66.667	0.00	0.00	0.00	5.40
1904	3766	0.962855	CTCTCTGGCAGAGTCGGTCA	60.963	60.000	36.22	19.85	43.61	4.02
1929	3807	2.373169	TGCCTTCAGAGTCAGGATTGTT	59.627	45.455	0.00	0.00	30.81	2.83
2003	3887	1.268625	GGTTGGGAAAACGGTCATCAC	59.731	52.381	0.00	0.00	0.00	3.06
2178	4222	2.618241	TCTGAGCTTGAATGTGCGTTTT	59.382	40.909	0.00	0.00	0.00	2.43
2197	4241	2.338984	GGGTTCGCAGTGACGTCT	59.661	61.111	17.92	0.00	0.00	4.18
2258	4302	5.221521	TGGAGAGACTGCACATTATGGTATC	60.222	44.000	0.00	0.00	0.00	2.24
2427	4668	2.228138	AGTGTTTTGCTGCACAATGG	57.772	45.000	0.00	0.00	38.31	3.16
2437	4680	1.677576	CTGCACAATGGATTATGCCGT	59.322	47.619	0.34	0.00	37.26	5.68
2468	4719	8.932945	TGATTTATAGTGTTCTGCTTCTGTAG	57.067	34.615	0.00	0.00	0.00	2.74
2469	4720	7.981789	TGATTTATAGTGTTCTGCTTCTGTAGG	59.018	37.037	0.00	0.00	0.00	3.18
2470	4721	6.852420	TTATAGTGTTCTGCTTCTGTAGGT	57.148	37.500	0.00	0.00	0.00	3.08
2471	4722	7.949690	TTATAGTGTTCTGCTTCTGTAGGTA	57.050	36.000	0.00	0.00	0.00	3.08
2472	4723	8.534954	TTATAGTGTTCTGCTTCTGTAGGTAT	57.465	34.615	0.00	0.00	0.00	2.73
2473	4724	9.636789	TTATAGTGTTCTGCTTCTGTAGGTATA	57.363	33.333	0.00	0.00	0.00	1.47
2570	4875	8.668353	CACATAGTAAACTAGCACATTCATGTT	58.332	33.333	0.00	0.00	39.39	2.71
2657	5373	6.648725	GCTAGTTTGATCATATCAGGACCTTC	59.351	42.308	0.00	0.00	40.94	3.46
2772	5506	2.749621	AGACCAAAATCGTCCATTCTGC	59.250	45.455	0.00	0.00	0.00	4.26
2906	5721	5.235305	AGGCTATTTCGTAATTTGCAGTG	57.765	39.130	11.98	0.00	0.00	3.66
2987	5824	7.604164	CAGCATTTAGTTATGGACCAGTATAGG	59.396	40.741	0.00	0.00	0.00	2.57
3128	5980	3.297134	ACCTTTTTCTTCCTGACAGCA	57.703	42.857	0.00	0.00	0.00	4.41
3513	6789	2.029020	TCTCAACAATCAGGTCGTCTGG	60.029	50.000	8.24	0.00	43.53	3.86
3812	7165	4.662961	CGCTCGCTGTGGTCCACA	62.663	66.667	23.38	23.38	42.45	4.17
4045	7401	2.104170	AGCTTAGCCTCTGTGGAGTAC	58.896	52.381	0.00	0.00	37.86	2.73
4121	7477	2.043980	CCGCGGCCTTATGTTGGTT	61.044	57.895	14.67	0.00	0.00	3.67
4160	7516	2.494059	GTGTGTGGTGCTATCAACTGT	58.506	47.619	0.00	0.00	0.00	3.55
4340	7714	4.951715	TTCCATCTCTTGAATGGAACATGG	59.048	41.667	12.37	0.00	46.16	3.66
4422	7796	3.370840	AGCATTACATTTGAGGCAGGA	57.629	42.857	0.00	0.00	0.00	3.86
4591	8008	2.494870	GAGCATGTGGAAGCAAAGGAAT	59.505	45.455	0.00	0.00	0.00	3.01
4633	8051	4.766632	GGCTGCTGGGGAAAGGGG	62.767	72.222	0.00	0.00	0.00	4.79
4667	8085	9.887629	TGCCATTTGTTTAAAATCATGATGTAT	57.112	25.926	9.46	1.21	0.00	2.29
4791	8312	1.063266	ACAACCTGGTGAACAATGGGT	60.063	47.619	0.00	0.00	0.00	4.51
4802	8323	1.172180	ACAATGGGTGTTCGCCACAG	61.172	55.000	4.78	0.00	46.44	3.66
4812	8333	0.821301	TTCGCCACAGCCAATCAACA	60.821	50.000	0.00	0.00	34.57	3.33
4832	8379	5.913137	ACATTGACAAGGACTGAAAAACA	57.087	34.783	6.88	0.00	0.00	2.83
4908	8464	1.989864	TGTTGCATTACTAGCACGACG	59.010	47.619	0.00	0.00	42.54	5.12
4920	8476	1.004595	GCACGACGATAAACCCCTTC	58.995	55.000	0.00	0.00	0.00	3.46

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
21	23	1.985159	TGATAGGGTTGCACCAGAGTT	59.015	47.619	7.49	0.00	41.02	3.01
27	29	2.418368	TGTGATGATAGGGTTGCACC	57.582	50.000	0.00	0.00	37.60	5.01
67	69	3.784202	GGGGTCAAGGATTTTCTAGGGTA	59.216	47.826	0.00	0.00	0.00	3.69
73	75	3.055312	GTCGTAGGGGTCAAGGATTTTCT	60.055	47.826	0.00	0.00	0.00	2.52
84	86	3.821421	AAAGATGATGTCGTAGGGGTC	57.179	47.619	0.00	0.00	0.00	4.46
110	112	6.933521	GTCATTCAGATGTATTGTCTAGGCAT	59.066	38.462	0.00	0.00	34.77	4.40
115	117	7.996385	TCTTCGTCATTCAGATGTATTGTCTA	58.004	34.615	0.00	0.00	34.73	2.59
122	124	5.047306	ACAACCTCTTCGTCATTCAGATGTA	60.047	40.000	0.00	0.00	34.73	2.29
302	310	6.347061	AACATGAATCTAAAAGAGGGGGAT	57.653	37.500	0.00	0.00	0.00	3.85
337	345	8.884124	ATGATGGAAGAATGGAAGACTAAAAA	57.116	30.769	0.00	0.00	0.00	1.94
341	349	6.408548	GGTGATGATGGAAGAATGGAAGACTA	60.409	42.308	0.00	0.00	0.00	2.59
389	397	2.544069	CGAGATCGAACTTTAGGGAGGC	60.544	54.545	0.00	0.00	43.02	4.70
408	416	0.748450	GGTAATCATGGGGTCGACGA	59.252	55.000	9.92	0.54	0.00	4.20
425	433	3.620488	ACATATTGGATTGTGAAGCGGT	58.380	40.909	0.00	0.00	0.00	5.68
446	455	3.377485	CGGTAAGATCAAACGAGAGAGGA	59.623	47.826	0.00	0.00	0.00	3.71
457	466	2.037902	TGGTGTTCTGCGGTAAGATCAA	59.962	45.455	0.00	0.00	29.87	2.57
468	477	2.281484	TCGCCCTTGGTGTTCTGC	60.281	61.111	0.00	0.00	34.40	4.26
508	517	1.300620	CAGACGCTCGGGTTGACAA	60.301	57.895	0.00	0.00	0.00	3.18
509	518	2.338620	CAGACGCTCGGGTTGACA	59.661	61.111	0.00	0.00	0.00	3.58
587	596	3.885724	TTGCTTACTCCATCGATGTCA	57.114	42.857	23.27	9.16	0.00	3.58
591	600	5.641209	GCTATGATTTGCTTACTCCATCGAT	59.359	40.000	0.00	0.00	0.00	3.59
596	605	3.466836	CGGCTATGATTTGCTTACTCCA	58.533	45.455	0.00	0.00	0.00	3.86
609	618	1.324383	TTCACGATAGGCGGCTATGA	58.676	50.000	33.47	23.52	46.49	2.15
611	620	2.870411	GTTTTTCACGATAGGCGGCTAT	59.130	45.455	29.55	29.55	46.49	2.97
634	643	2.118313	CTGCATGTGGAGGATTGTCA	57.882	50.000	0.00	0.00	0.00	3.58
672	681	5.808540	CGTTCACTTATCCCGTCATAAAAGA	59.191	40.000	0.00	0.00	0.00	2.52
673	682	5.808540	TCGTTCACTTATCCCGTCATAAAAG	59.191	40.000	0.00	0.00	0.00	2.27
678	687	2.479049	CGTCGTTCACTTATCCCGTCAT	60.479	50.000	0.00	0.00	0.00	3.06
723	732	0.656259	CTGAGCCATGTTGATCGCTG	59.344	55.000	0.00	0.00	0.00	5.18
724	733	1.094073	GCTGAGCCATGTTGATCGCT	61.094	55.000	0.00	0.00	0.00	4.93
733	742	3.374220	TGTTTCTTTTGCTGAGCCATG	57.626	42.857	0.23	0.00	0.00	3.66
768	777	8.917415	AAAGTTGTTTCTTTCTTTCATGTCTC	57.083	30.769	0.00	0.00	33.05	3.36
769	778	9.710900	AAAAAGTTGTTTCTTTCTTTCATGTCT	57.289	25.926	0.00	0.00	36.75	3.41
864	892	6.016192	CAGTCTCTCTGGAGTGTTGTTACTTA	60.016	42.308	0.00	0.00	40.23	2.24
876	904	0.455410	CCGAAGCAGTCTCTCTGGAG	59.545	60.000	0.00	0.00	43.78	3.86
934	987	2.750350	GACTGGGTGTGGGTGGAG	59.250	66.667	0.00	0.00	0.00	3.86
994	1050	1.976132	CTCGGGTCAGCCATGGTCAT	61.976	60.000	14.67	0.00	36.17	3.06
1060	1116	3.434319	GTGCGGGTCACAGCCATG	61.434	66.667	0.00	0.00	44.98	3.66
1573	1660	0.108898	CTGACGCTGAAGAGAGTGGG	60.109	60.000	0.00	0.00	31.49	4.61
1651	1738	2.359975	GTGGGGAAAGGAGGCACG	60.360	66.667	0.00	0.00	0.00	5.34
1739	1826	2.837947	TGTTGAGGATCTCCAGGACAT	58.162	47.619	0.00	0.00	38.89	3.06
1904	3766	0.617413	CCTGACTCTGAAGGCACCAT	59.383	55.000	0.00	0.00	34.81	3.55
1929	3807	3.982111	TGCAGCTTGGGGGCATCA	61.982	61.111	0.00	0.00	31.58	3.07
2178	4222	3.509137	GACGTCACTGCGAACCCCA	62.509	63.158	11.55	0.00	35.59	4.96
2220	4264	0.534203	TCTCCACGTTGGGAAAGCAC	60.534	55.000	0.00	0.00	38.32	4.40
2258	4302	6.446781	AAGCAGAATATGAATTGGTGACAG	57.553	37.500	0.00	0.00	44.54	3.51
2427	4668	9.155975	ACTATAAATCAAGATGACGGCATAATC	57.844	33.333	2.12	0.00	34.11	1.75
2437	4680	9.102757	GAAGCAGAACACTATAAATCAAGATGA	57.897	33.333	0.00	0.00	0.00	2.92
2468	4719	9.274206	GAAAGAAAATCTGGACATACCTATACC	57.726	37.037	0.00	0.00	39.86	2.73
2471	4722	8.552296	ACAGAAAGAAAATCTGGACATACCTAT	58.448	33.333	8.26	0.00	46.81	2.57
2472	4723	7.918076	ACAGAAAGAAAATCTGGACATACCTA	58.082	34.615	8.26	0.00	46.81	3.08
2473	4724	6.784031	ACAGAAAGAAAATCTGGACATACCT	58.216	36.000	8.26	0.00	46.81	3.08
2570	4875	1.040646	AACAGCCTCGAGAACTGTCA	58.959	50.000	29.45	0.00	43.63	3.58
2772	5506	1.002033	GTGAGGCTGCAAACTTCAGTG	60.002	52.381	0.50	0.00	34.21	3.66
2987	5824	3.253188	TGCTCAACACTAAATGCTGGAAC	59.747	43.478	0.00	0.00	0.00	3.62
3128	5980	9.901172	AGATAAATAAGTCCGTAGTTTCCATTT	57.099	29.630	0.00	0.00	0.00	2.32
3185	6053	5.955488	TGGAACAAGTTTTTCAATTGACGA	58.045	33.333	7.89	0.00	31.92	4.20
3513	6789	5.221891	ACATAAACAGATGAACATGCGTC	57.778	39.130	0.00	0.00	0.00	5.19
3570	6919	2.173569	ACCAGAAGTCAAGAGGCAAAGT	59.826	45.455	0.00	0.00	0.00	2.66
3657	7008	2.358737	CTTGCGGGTGAGGTGGTC	60.359	66.667	0.00	0.00	0.00	4.02
3804	7157	2.631267	CATCACGATGAATGTGGACCA	58.369	47.619	0.47	0.00	41.20	4.02
3810	7163	2.127271	TTGGCCATCACGATGAATGT	57.873	45.000	6.09	0.00	41.20	2.71
3812	7165	2.233271	GGATTGGCCATCACGATGAAT	58.767	47.619	6.09	0.00	41.20	2.57
3887	7240	2.618816	GGACTCAGATGCCATGTTTCCA	60.619	50.000	0.00	0.00	0.00	3.53
3951	7304	2.748465	CGGTTTTGAAGTTCCAGGGAGT	60.748	50.000	0.00	0.00	0.00	3.85
4045	7401	1.099689	ACGAAAACACAACACCCCAG	58.900	50.000	0.00	0.00	0.00	4.45
4121	7477	1.137872	ACCAAGCCGCAAATTCAACAA	59.862	42.857	0.00	0.00	0.00	2.83
4160	7516	5.642165	TGGGTTACAGGGCAAGTAAAATAA	58.358	37.500	3.09	0.00	33.64	1.40
4340	7714	9.436957	TGATTGAAAAGAACCTCAACTATCTAC	57.563	33.333	0.00	0.00	34.52	2.59
4375	7749	7.123247	TCGCTACTGTTACCCTAGTTTTTCTAT	59.877	37.037	0.00	0.00	0.00	1.98
4411	7785	1.133823	TGTTGCTTCTCCTGCCTCAAA	60.134	47.619	0.00	0.00	0.00	2.69
4422	7796	6.721318	TCCTCTATTTGGTTATGTTGCTTCT	58.279	36.000	0.00	0.00	0.00	2.85
4591	8008	4.583073	GTCCCTTTGCTTCCAAAAACTCTA	59.417	41.667	0.00	0.00	40.21	2.43
4709	8230	0.119155	TGGGTGAGAATCCACTCCCT	59.881	55.000	13.34	0.00	36.72	4.20
4732	8253	6.419791	TCTCAAAGAAACTAAGGAAACCACA	58.580	36.000	0.00	0.00	0.00	4.17
4791	8312	0.821301	TTGATTGGCTGTGGCGAACA	60.821	50.000	0.00	0.00	38.86	3.18
4802	8323	3.256631	AGTCCTTGTCAATGTTGATTGGC	59.743	43.478	0.00	0.00	43.42	4.52
4812	8333	4.956075	AGGTGTTTTTCAGTCCTTGTCAAT	59.044	37.500	0.00	0.00	0.00	2.57
4832	8379	2.301870	TCCTGTTTTGTCGATAGCAGGT	59.698	45.455	20.26	0.00	42.77	4.00
4875	8422	2.495155	TGCAACACATGGAGCATACT	57.505	45.000	0.00	0.00	31.05	2.12
4876	8423	3.788333	AATGCAACACATGGAGCATAC	57.212	42.857	14.05	0.00	46.10	2.39
4877	8424	4.525996	AGTAATGCAACACATGGAGCATA	58.474	39.130	14.05	4.15	46.10	3.14
4879	8426	2.794103	AGTAATGCAACACATGGAGCA	58.206	42.857	0.00	1.66	39.60	4.26
4908	8464	8.635765	TGCAATATTATCAGAAGGGGTTTATC	57.364	34.615	0.00	0.00	0.00	1.75
4920	8476	4.214971	GGCACTGACCTGCAATATTATCAG	59.785	45.833	8.98	8.98	39.08	2.90

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.