AutoCloner

Multiple sequence alignment - TraesCS7A01G039600

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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	TraesCS7A01G039600	chr7A	100.000	3449	0	0	1	3449	17907482	17904034	0.000000e+00	6370.0
1	TraesCS7A01G039600	chr7A	89.727	2161	184	18	1103	3256	17390709	17388580	0.000000e+00	2726.0
2	TraesCS7A01G039600	chr7A	98.459	1103	14	1	1	1103	247655416	247654317	0.000000e+00	1940.0
3	TraesCS7A01G039600	chr7A	84.857	1466	166	31	1103	2541	18434014	18435450	0.000000e+00	1426.0
4	TraesCS7A01G039600	chr7A	85.947	1103	134	13	1103	2198	18053149	18052061	0.000000e+00	1158.0
5	TraesCS7A01G039600	chr7A	82.663	1194	188	12	1103	2291	18201914	18203093	0.000000e+00	1040.0
6	TraesCS7A01G039600	chr7A	82.740	1124	177	10	1103	2222	17423679	17422569	0.000000e+00	985.0
7	TraesCS7A01G039600	chr7A	82.489	1125	180	11	1103	2223	18035186	18034075	0.000000e+00	970.0
8	TraesCS7A01G039600	chr7A	79.476	229	22	7	3245	3449	17379076	17378849	4.640000e-29	139.0
9	TraesCS7A01G039600	chr7A	83.206	131	9	3	3330	3449	17795726	17795598	1.310000e-19	108.0
10	TraesCS7A01G039600	chr7A	97.778	45	1	0	2560	2604	18319355	18319399	1.030000e-10	78.7
11	TraesCS7A01G039600	chr5B	98.005	1103	16	1	1	1103	498817474	498818570	0.000000e+00	1910.0
12	TraesCS7A01G039600	chr4A	85.140	1541	175	24	1105	2623	715008461	715009969	0.000000e+00	1528.0
13	TraesCS7A01G039600	chr4A	84.525	1189	163	15	1103	2285	714432622	714433795	0.000000e+00	1157.0
14	TraesCS7A01G039600	chr4A	85.901	993	129	6	1157	2148	714731485	714732467	0.000000e+00	1048.0
15	TraesCS7A01G039600	chr4A	82.831	1194	162	23	1103	2289	715100145	715101302	0.000000e+00	1029.0
16	TraesCS7A01G039600	chr4A	85.315	715	41	19	2756	3449	715010034	715010705	0.000000e+00	680.0
17	TraesCS7A01G039600	chr4A	77.140	993	137	49	1516	2444	715240309	715241275	8.600000e-136	494.0
18	TraesCS7A01G039600	chr4A	82.185	421	63	9	1105	1522	715239724	715240135	5.480000e-93	351.0
19	TraesCS7A01G039600	chr2B	91.697	1108	66	3	1	1102	662410776	662409689	0.000000e+00	1513.0
20	TraesCS7A01G039600	chr7D	83.960	1490	172	28	1103	2537	18106323	18104846	0.000000e+00	1365.0
21	TraesCS7A01G039600	chr7D	80.053	1128	198	11	1106	2218	8190923	8189808	0.000000e+00	811.0
22	TraesCS7A01G039600	chr7D	84.014	882	100	21	1690	2530	18001474	18000593	0.000000e+00	809.0
23	TraesCS7A01G039600	chr7D	81.944	144	15	3	3317	3449	18103847	18103704	1.010000e-20	111.0
24	TraesCS7A01G039600	chr7D	89.773	88	5	1	2847	2934	18104601	18104518	3.640000e-20	110.0
25	TraesCS7A01G039600	chr7D	95.556	45	2	0	2560	2604	18000526	18000482	4.770000e-09	73.1
26	TraesCS7A01G039600	chrUn	85.714	1190	155	9	1103	2289	89853197	89854374	0.000000e+00	1242.0
27	TraesCS7A01G039600	chrUn	86.042	1003	128	7	1150	2151	327046118	327045127	0.000000e+00	1066.0
28	TraesCS7A01G039600	chrUn	82.583	1200	190	12	1106	2300	262125312	262124127	0.000000e+00	1040.0
29	TraesCS7A01G039600	chrUn	93.333	45	3	0	2560	2604	77140090	77140134	2.220000e-07	67.6
30	TraesCS7A01G039600	chr4B	95.556	45	2	0	2560	2604	667242566	667242610	4.770000e-09	73.1
31	TraesCS7A01G039600	chr4B	93.333	45	3	0	2560	2604	367625805	367625849	2.220000e-07	67.6
32	TraesCS7A01G039600	chr3A	95.556	45	2	0	2560	2604	549232954	549232910	4.770000e-09	73.1
33	TraesCS7A01G039600	chr6D	93.333	45	3	0	2560	2604	380597243	380597199	2.220000e-07	67.6

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	TraesCS7A01G039600	chr7A	17904034	17907482	3448	True	6370.000000	6370	100.000000	1	3449	1	chr7A.!!$R5	3448
1	TraesCS7A01G039600	chr7A	17388580	17390709	2129	True	2726.000000	2726	89.727000	1103	3256	1	chr7A.!!$R2	2153
2	TraesCS7A01G039600	chr7A	247654317	247655416	1099	True	1940.000000	1940	98.459000	1	1103	1	chr7A.!!$R8	1102
3	TraesCS7A01G039600	chr7A	18434014	18435450	1436	False	1426.000000	1426	84.857000	1103	2541	1	chr7A.!!$F3	1438
4	TraesCS7A01G039600	chr7A	18052061	18053149	1088	True	1158.000000	1158	85.947000	1103	2198	1	chr7A.!!$R7	1095
5	TraesCS7A01G039600	chr7A	18201914	18203093	1179	False	1040.000000	1040	82.663000	1103	2291	1	chr7A.!!$F1	1188
6	TraesCS7A01G039600	chr7A	17422569	17423679	1110	True	985.000000	985	82.740000	1103	2222	1	chr7A.!!$R3	1119
7	TraesCS7A01G039600	chr7A	18034075	18035186	1111	True	970.000000	970	82.489000	1103	2223	1	chr7A.!!$R6	1120
8	TraesCS7A01G039600	chr5B	498817474	498818570	1096	False	1910.000000	1910	98.005000	1	1103	1	chr5B.!!$F1	1102
9	TraesCS7A01G039600	chr4A	714432622	714433795	1173	False	1157.000000	1157	84.525000	1103	2285	1	chr4A.!!$F1	1182
10	TraesCS7A01G039600	chr4A	715008461	715010705	2244	False	1104.000000	1528	85.227500	1105	3449	2	chr4A.!!$F4	2344
11	TraesCS7A01G039600	chr4A	714731485	714732467	982	False	1048.000000	1048	85.901000	1157	2148	1	chr4A.!!$F2	991
12	TraesCS7A01G039600	chr4A	715100145	715101302	1157	False	1029.000000	1029	82.831000	1103	2289	1	chr4A.!!$F3	1186
13	TraesCS7A01G039600	chr4A	715239724	715241275	1551	False	422.500000	494	79.662500	1105	2444	2	chr4A.!!$F5	1339
14	TraesCS7A01G039600	chr2B	662409689	662410776	1087	True	1513.000000	1513	91.697000	1	1102	1	chr2B.!!$R1	1101
15	TraesCS7A01G039600	chr7D	8189808	8190923	1115	True	811.000000	811	80.053000	1106	2218	1	chr7D.!!$R1	1112
16	TraesCS7A01G039600	chr7D	18103704	18106323	2619	True	528.666667	1365	85.225667	1103	3449	3	chr7D.!!$R3	2346
17	TraesCS7A01G039600	chr7D	18000482	18001474	992	True	441.050000	809	89.785000	1690	2604	2	chr7D.!!$R2	914
18	TraesCS7A01G039600	chrUn	89853197	89854374	1177	False	1242.000000	1242	85.714000	1103	2289	1	chrUn.!!$F2	1186
19	TraesCS7A01G039600	chrUn	327045127	327046118	991	True	1066.000000	1066	86.042000	1150	2151	1	chrUn.!!$R2	1001
20	TraesCS7A01G039600	chrUn	262124127	262125312	1185	True	1040.000000	1040	82.583000	1106	2300	1	chrUn.!!$R1	1194

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
752	753	2.372688	GGAGGGGATCTGGGTCCA	59.627	66.667	2.12	0.0	40.17	4.02	F
1423	1451	0.320374	CACCAAGGTAGTTGCCGAGA	59.680	55.000	0.00	0.0	34.45	4.04	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2297	2557	0.031585	TGACCTGAGGTTTGTCGTCG	59.968	55.0	5.21	0.0	35.25	5.12	R
3151	3947	0.095417	GAAGAACTGATTGTCGGCGC	59.905	55.0	0.00	0.0	0.00	6.53	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
167	168	4.993028	AGCCACAATTAAACCACCTCTAA	58.007	39.130	0.00	0.00	0.00	2.10
398	399	5.584649	AGAACTCAATCGACAGAAAACAACA	59.415	36.000	0.00	0.00	0.00	3.33
399	400	5.811399	ACTCAATCGACAGAAAACAACAA	57.189	34.783	0.00	0.00	0.00	2.83
400	401	5.569413	ACTCAATCGACAGAAAACAACAAC	58.431	37.500	0.00	0.00	0.00	3.32
583	584	3.329889	TCCAGGCTCGGCAATGGT	61.330	61.111	14.52	0.00	37.90	3.55
752	753	2.372688	GGAGGGGATCTGGGTCCA	59.627	66.667	2.12	0.00	40.17	4.02
1116	1123	6.406849	GGCATCCAAAAAGCAACATAGGATTA	60.407	38.462	0.00	0.00	0.00	1.75
1139	1146	1.394917	GCGCCACTTGAAGTATGTGAG	59.605	52.381	0.00	0.00	36.76	3.51
1153	1160	9.219603	TGAAGTATGTGAGTTTTTCTAATCCTG	57.780	33.333	0.00	0.00	0.00	3.86
1234	1241	6.790825	GCGTACTTTGAACATAAGAAACAGTC	59.209	38.462	0.00	0.00	0.00	3.51
1244	1251	9.922305	GAACATAAGAAACAGTCATATTACAGC	57.078	33.333	0.00	0.00	0.00	4.40
1251	1258	6.546428	AACAGTCATATTACAGCACTACCT	57.454	37.500	0.00	0.00	0.00	3.08
1256	1263	8.144478	CAGTCATATTACAGCACTACCTATTGT	58.856	37.037	0.00	0.00	0.00	2.71
1298	1305	0.753867	TGCAGTCTCCGTTGTACCAA	59.246	50.000	0.00	0.00	0.00	3.67
1301	1308	2.812011	GCAGTCTCCGTTGTACCAAAAT	59.188	45.455	0.00	0.00	0.00	1.82
1305	1312	5.121768	CAGTCTCCGTTGTACCAAAATTAGG	59.878	44.000	0.00	0.00	0.00	2.69
1306	1313	5.012354	AGTCTCCGTTGTACCAAAATTAGGA	59.988	40.000	4.01	0.00	0.00	2.94
1313	1320	4.009675	TGTACCAAAATTAGGAGCTGCAG	58.990	43.478	10.11	10.11	0.00	4.41
1396	1412	3.593442	TCACACCTTTGGTTGATCCTT	57.407	42.857	0.00	0.00	31.02	3.36
1423	1451	0.320374	CACCAAGGTAGTTGCCGAGA	59.680	55.000	0.00	0.00	34.45	4.04
1432	1460	3.430374	GGTAGTTGCCGAGATACACATGT	60.430	47.826	0.00	0.00	0.00	3.21
1460	1488	2.604174	GCCGTTGGTCCGTGTCAAG	61.604	63.158	0.00	0.00	0.00	3.02
1558	1766	4.022068	CCAGTGGCAAAGCAATTAAAGAGA	60.022	41.667	0.00	0.00	0.00	3.10
1595	1803	2.039480	AGCTGAGAAAACTGAGCATGGA	59.961	45.455	10.70	0.00	33.67	3.41
1596	1804	2.816087	GCTGAGAAAACTGAGCATGGAA	59.184	45.455	0.00	0.00	0.00	3.53
1597	1805	3.119919	GCTGAGAAAACTGAGCATGGAAG	60.120	47.826	0.00	0.00	0.00	3.46
1598	1806	2.816087	TGAGAAAACTGAGCATGGAAGC	59.184	45.455	0.00	0.00	0.00	3.86
1599	1807	2.163211	GAGAAAACTGAGCATGGAAGCC	59.837	50.000	0.00	0.00	34.23	4.35
1600	1808	1.888512	GAAAACTGAGCATGGAAGCCA	59.111	47.619	0.00	0.00	38.19	4.75
1601	1809	2.226962	AAACTGAGCATGGAAGCCAT	57.773	45.000	0.00	0.00	46.37	4.40
2078	2320	3.225104	TGGCATCAGGAATTATTGGAGC	58.775	45.455	0.00	0.00	0.00	4.70
2117	2359	3.768757	CTCAAGGAGATCTCACTTGGTCT	59.231	47.826	31.82	16.93	37.90	3.85
2119	2361	1.830477	AGGAGATCTCACTTGGTCTGC	59.170	52.381	23.85	2.84	0.00	4.26
2218	2460	2.994995	ACCGGAGCCATCACGACA	60.995	61.111	9.46	0.00	0.00	4.35
2252	2494	2.224523	TCGTCCAAGTGGAAGAAGCAAT	60.225	45.455	12.80	0.00	46.91	3.56
2297	2557	3.198489	GCCTGAAGCAGCGGTAGC	61.198	66.667	0.00	0.00	42.97	3.58
2391	2671	6.983890	TGCGATGTGCTAATTAATCTGAACTA	59.016	34.615	0.00	0.00	46.63	2.24
2396	2676	8.352752	TGTGCTAATTAATCTGAACTATGTCG	57.647	34.615	0.00	0.00	0.00	4.35
2462	2791	2.203470	TGCTGACTGAATCATGCCAA	57.797	45.000	0.00	0.00	36.48	4.52
2630	3005	4.079253	GCCAGACACTTGGATTTAAGGAA	58.921	43.478	0.00	0.00	40.87	3.36
2666	3041	8.367660	AGAGATCATACTTCAAAGTGGTTAGA	57.632	34.615	5.66	0.00	40.07	2.10
2706	3081	7.766738	TCTCGTTTTGTTTATGTAGCCATCATA	59.233	33.333	0.00	0.00	32.29	2.15
2733	3108	6.996509	ACATTTTCGGTACTTACAGTTCCTA	58.003	36.000	0.00	0.00	33.97	2.94
2761	3136	3.713858	TTTCAAGCCTGTGAACACATG	57.286	42.857	8.09	6.94	41.01	3.21
2943	3363	3.126831	CAAGAGACGCCACAATATCCTC	58.873	50.000	0.00	0.00	0.00	3.71
2944	3364	1.689273	AGAGACGCCACAATATCCTCC	59.311	52.381	0.00	0.00	0.00	4.30
2945	3365	1.412710	GAGACGCCACAATATCCTCCA	59.587	52.381	0.00	0.00	0.00	3.86
2946	3366	2.037772	GAGACGCCACAATATCCTCCAT	59.962	50.000	0.00	0.00	0.00	3.41
2952	3372	2.423231	CCACAATATCCTCCATGGTGCA	60.423	50.000	12.58	0.00	37.07	4.57
2970	3390	4.280929	GGTGCATGTTTCCTTTTAACCTCT	59.719	41.667	0.00	0.00	0.00	3.69
3110	3906	1.278985	TCAATGCTCCCGTGATCTTGT	59.721	47.619	0.00	0.00	0.00	3.16
3118	3914	1.009829	CCGTGATCTTGTAGCAAGCC	58.990	55.000	4.16	0.50	0.00	4.35
3135	3931	0.240945	GCCACAACGTCATTTCCAGG	59.759	55.000	0.00	0.00	0.00	4.45
3171	3967	1.714794	CGCCGACAATCAGTTCTTCT	58.285	50.000	0.00	0.00	0.00	2.85
3172	3968	2.069273	CGCCGACAATCAGTTCTTCTT	58.931	47.619	0.00	0.00	0.00	2.52
3173	3969	2.092838	CGCCGACAATCAGTTCTTCTTC	59.907	50.000	0.00	0.00	0.00	2.87
3174	3970	3.067106	GCCGACAATCAGTTCTTCTTCA	58.933	45.455	0.00	0.00	0.00	3.02
3182	3978	4.008074	TCAGTTCTTCTTCACCATGGAC	57.992	45.455	21.47	2.07	0.00	4.02
3218	4014	7.628366	GCGATGTCAAATCCTATTTTCTTGGAA	60.628	37.037	0.00	0.00	32.26	3.53
3256	4052	3.028850	CCCAGCTGGAACATCAATTGAT	58.971	45.455	34.91	15.36	38.20	2.57
3257	4053	3.449737	CCCAGCTGGAACATCAATTGATT	59.550	43.478	34.91	6.09	38.20	2.57
3279	4075	1.743958	GCATCTTGCAATGCTCAGAGT	59.256	47.619	16.07	0.00	46.81	3.24
3280	4076	2.478031	GCATCTTGCAATGCTCAGAGTG	60.478	50.000	16.07	9.13	46.81	3.51
3288	4084	5.673514	TGCAATGCTCAGAGTGTAATCATA	58.326	37.500	6.82	0.00	0.00	2.15
3296	4092	7.871463	TGCTCAGAGTGTAATCATAATGATCTG	59.129	37.037	0.00	0.00	35.76	2.90
3312	4118	5.818136	TGATCTGTTGCTAATTACTTGCC	57.182	39.130	0.00	0.00	0.00	4.52
3327	4133	3.989787	GCCTTGTTTGCCCGTGGG	61.990	66.667	0.00	0.00	38.57	4.61
3344	4150	4.253685	CGTGGGTCTCTGTTTGTATGATT	58.746	43.478	0.00	0.00	0.00	2.57
3393	4210	4.142534	TGACGACACCTGCTTACTGTATAC	60.143	45.833	0.00	0.00	0.00	1.47
3414	4231	4.511527	ACGATTGTGCTCTGAAGAATGAT	58.488	39.130	0.00	0.00	0.00	2.45
3416	4233	4.260661	CGATTGTGCTCTGAAGAATGATGG	60.261	45.833	0.00	0.00	0.00	3.51
3417	4234	3.708403	TGTGCTCTGAAGAATGATGGT	57.292	42.857	0.00	0.00	0.00	3.55
3424	4241	1.003003	TGAAGAATGATGGTGCCGACA	59.997	47.619	0.00	0.00	0.00	4.35
3432	4249	0.537143	ATGGTGCCGACAAAGAGCAA	60.537	50.000	0.00	0.00	38.45	3.91

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
19	20	4.404073	ACAGTCTATGGACCTCAATCTGAC	59.596	45.833	5.47	0.00	43.05	3.51
25	26	3.779444	AGTCACAGTCTATGGACCTCAA	58.221	45.455	5.47	0.00	43.05	3.02
167	168	0.618458	TTCGAGCCTGCTTTGGGTAT	59.382	50.000	0.00	0.00	38.02	2.73
398	399	5.837437	TCTGTTTCTGTTGTTGTTGTTGTT	58.163	33.333	0.00	0.00	0.00	2.83
399	400	5.446143	TCTGTTTCTGTTGTTGTTGTTGT	57.554	34.783	0.00	0.00	0.00	3.32
400	401	4.324402	GCTCTGTTTCTGTTGTTGTTGTTG	59.676	41.667	0.00	0.00	0.00	3.33
503	504	3.055240	CCTTCAAGAAGCCTCTGACTGAT	60.055	47.826	4.30	0.00	37.11	2.90
583	584	0.541998	TGTCGGAAAGAGAGGGCTCA	60.542	55.000	0.00	0.00	43.81	4.26
752	753	2.697147	TTTCAGGGCCGCTTCTTGCT	62.697	55.000	0.00	0.00	40.11	3.91
1116	1123	2.162208	CACATACTTCAAGTGGCGCAAT	59.838	45.455	10.83	0.00	0.00	3.56
1234	1241	9.494271	AATCACAATAGGTAGTGCTGTAATATG	57.506	33.333	0.00	0.00	35.76	1.78
1256	1263	8.749354	TGCATAGACTCTTGAGTTTACTAATCA	58.251	33.333	4.67	2.94	0.00	2.57
1279	1286	2.432119	TGGTACAACGGAGACTGCA	58.568	52.632	0.00	0.00	31.92	4.41
1298	1305	3.659183	ACCATCTGCAGCTCCTAATTT	57.341	42.857	9.47	0.00	0.00	1.82
1301	1308	2.305635	TCAAACCATCTGCAGCTCCTAA	59.694	45.455	9.47	0.00	0.00	2.69
1305	1312	1.818642	AGTCAAACCATCTGCAGCTC	58.181	50.000	9.47	0.00	0.00	4.09
1306	1313	1.884579	CAAGTCAAACCATCTGCAGCT	59.115	47.619	9.47	0.00	0.00	4.24
1313	1320	4.082125	AGGTTCATCCAAGTCAAACCATC	58.918	43.478	5.47	0.00	41.46	3.51
1396	1412	1.005037	CTACCTTGGTGCGCTCACA	60.005	57.895	9.73	1.44	44.87	3.58
1423	1451	2.700897	GGCTAGACCAGGACATGTGTAT	59.299	50.000	1.15	0.00	38.86	2.29
1432	1460	1.229082	ACCAACGGCTAGACCAGGA	60.229	57.895	0.00	0.00	39.03	3.86
1460	1488	1.886542	CTTTTGGCACCCTAACACCTC	59.113	52.381	0.00	0.00	0.00	3.85
1595	1803	2.754186	GCCCATTCTGTATCCATGGCTT	60.754	50.000	6.96	0.00	36.83	4.35
1596	1804	1.202976	GCCCATTCTGTATCCATGGCT	60.203	52.381	6.96	0.00	36.83	4.75
1597	1805	1.251251	GCCCATTCTGTATCCATGGC	58.749	55.000	6.96	0.00	36.83	4.40
1598	1806	1.145531	TGGCCCATTCTGTATCCATGG	59.854	52.381	4.97	4.97	37.76	3.66
1599	1807	2.233271	GTGGCCCATTCTGTATCCATG	58.767	52.381	0.00	0.00	0.00	3.66
1600	1808	1.145738	GGTGGCCCATTCTGTATCCAT	59.854	52.381	0.00	0.00	0.00	3.41
1601	1809	0.550914	GGTGGCCCATTCTGTATCCA	59.449	55.000	0.00	0.00	0.00	3.41
1602	1810	0.550914	TGGTGGCCCATTCTGTATCC	59.449	55.000	0.00	0.00	35.17	2.59
1603	1811	2.301346	CTTGGTGGCCCATTCTGTATC	58.699	52.381	0.00	0.00	41.49	2.24
1604	1812	1.686115	GCTTGGTGGCCCATTCTGTAT	60.686	52.381	0.00	0.00	41.49	2.29
1612	1820	1.155859	ATTTCTGCTTGGTGGCCCA	59.844	52.632	0.00	0.00	39.65	5.36
2022	2264	5.012871	ACTGATATCTATCATTGCCAGCTGT	59.987	40.000	13.81	0.00	41.46	4.40
2229	2471	1.797025	CTTCTTCCACTTGGACGACC	58.203	55.000	4.00	0.00	45.39	4.79
2252	2494	1.414158	GGGAGATGACGATTCCTCCA	58.586	55.000	16.07	0.00	45.26	3.86
2297	2557	0.031585	TGACCTGAGGTTTGTCGTCG	59.968	55.000	5.21	0.00	35.25	5.12
2462	2791	2.639839	AGAGTGTAGCTTGTGGTGGAAT	59.360	45.455	0.00	0.00	0.00	3.01
2630	3005	1.686355	ATGATCTCTTCCGAGTCGCT	58.314	50.000	7.12	0.00	38.45	4.93
2666	3041	0.531974	ACGAGATGTGGCGTGTTGTT	60.532	50.000	0.00	0.00	39.56	2.83
2733	3108	2.694628	TCACAGGCTTGAAAACATTGCT	59.305	40.909	1.40	0.00	0.00	3.91
2761	3136	6.162777	TGTGTAAATAGGGGTACGTGTAAAC	58.837	40.000	0.00	0.00	0.00	2.01
2943	3363	3.405823	AAAAGGAAACATGCACCATGG	57.594	42.857	11.19	11.19	45.16	3.66
2944	3364	4.690280	GGTTAAAAGGAAACATGCACCATG	59.310	41.667	3.80	3.80	46.18	3.66
2945	3365	4.592778	AGGTTAAAAGGAAACATGCACCAT	59.407	37.500	0.00	0.00	0.00	3.55
2946	3366	3.964031	AGGTTAAAAGGAAACATGCACCA	59.036	39.130	0.00	0.00	0.00	4.17
2952	3372	7.283354	GCTAGCATAGAGGTTAAAAGGAAACAT	59.717	37.037	10.63	0.00	42.77	2.71
2970	3390	8.239038	ACTCATTAAACTGTCTAGCTAGCATA	57.761	34.615	18.83	5.65	0.00	3.14
3110	3906	1.890876	AATGACGTTGTGGCTTGCTA	58.109	45.000	0.00	0.00	0.00	3.49
3118	3914	0.881118	CCCCTGGAAATGACGTTGTG	59.119	55.000	0.00	0.00	0.00	3.33
3149	3945	3.702334	GAACTGATTGTCGGCGCGC	62.702	63.158	25.94	25.94	0.00	6.86
3150	3946	1.626654	AAGAACTGATTGTCGGCGCG	61.627	55.000	0.00	0.00	0.00	6.86
3151	3947	0.095417	GAAGAACTGATTGTCGGCGC	59.905	55.000	0.00	0.00	0.00	6.53
3171	3967	3.073678	CGTTGATCAAGTCCATGGTGAA	58.926	45.455	12.58	0.00	0.00	3.18
3172	3968	2.698803	CGTTGATCAAGTCCATGGTGA	58.301	47.619	12.58	8.92	0.00	4.02
3173	3969	1.131126	GCGTTGATCAAGTCCATGGTG	59.869	52.381	12.58	2.68	0.00	4.17
3174	3970	1.453155	GCGTTGATCAAGTCCATGGT	58.547	50.000	12.58	0.00	0.00	3.55
3182	3978	3.454042	TTTGACATCGCGTTGATCAAG	57.546	42.857	23.12	4.54	34.13	3.02
3218	4014	1.081174	TGGGACTGGAAGAGGAAGGAT	59.919	52.381	0.00	0.00	37.43	3.24
3272	4068	9.761504	AACAGATCATTATGATTACACTCTGAG	57.238	33.333	21.03	2.45	37.20	3.35
3288	4084	6.604795	AGGCAAGTAATTAGCAACAGATCATT	59.395	34.615	0.00	0.00	0.00	2.57
3296	4092	5.107491	GCAAACAAGGCAAGTAATTAGCAAC	60.107	40.000	0.00	0.00	0.00	4.17
3312	4118	1.515521	GAGACCCACGGGCAAACAAG	61.516	60.000	0.69	0.00	39.32	3.16
3360	4166	3.614150	GCAGGTGTCGTCATTCTTCAGTA	60.614	47.826	0.00	0.00	0.00	2.74
3393	4210	4.260661	CCATCATTCTTCAGAGCACAATCG	60.261	45.833	0.00	0.00	0.00	3.34
3414	4231	0.749818	TTTGCTCTTTGTCGGCACCA	60.750	50.000	0.00	0.00	35.62	4.17
3416	4233	1.852280	GTTTTTGCTCTTTGTCGGCAC	59.148	47.619	0.00	0.00	35.62	5.01
3417	4234	1.474478	TGTTTTTGCTCTTTGTCGGCA	59.526	42.857	0.00	0.00	0.00	5.69
3424	4241	3.026694	AGCTGACCTGTTTTTGCTCTTT	58.973	40.909	0.00	0.00	0.00	2.52

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.