AutoCloner

Multiple sequence alignment - TraesCS6D01G136300

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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	TraesCS6D01G136300	chr6D	100.000	4560	0	0	1	4560	104765087	104769646	0.000000e+00	8421.0
1	TraesCS6D01G136300	chr6D	97.213	574	13	1	3990	4560	11163420	11162847	0.000000e+00	968.0
2	TraesCS6D01G136300	chr6A	95.583	2694	96	6	1317	3989	126913473	126916164	0.000000e+00	4294.0
3	TraesCS6D01G136300	chr6A	96.923	520	13	3	1	519	126912603	126913120	0.000000e+00	869.0
4	TraesCS6D01G136300	chr6A	98.056	360	7	0	902	1261	126913115	126913474	1.080000e-175	627.0
5	TraesCS6D01G136300	chr6B	95.110	1963	81	9	2033	3989	191198132	191200085	0.000000e+00	3079.0
6	TraesCS6D01G136300	chr6B	92.537	737	26	4	1317	2035	191197284	191198009	0.000000e+00	1029.0
7	TraesCS6D01G136300	chr6B	97.222	360	10	0	902	1261	191196926	191197285	1.080000e-170	610.0
8	TraesCS6D01G136300	chr6B	88.235	102	6	3	418	519	191196836	191196931	2.880000e-22	117.0
9	TraesCS6D01G136300	chr6B	94.444	36	2	0	902	937	191196804	191196839	6.370000e-04	56.5
10	TraesCS6D01G136300	chr2D	97.548	571	14	0	3990	4560	56064911	56065481	0.000000e+00	977.0
11	TraesCS6D01G136300	chr2D	97.213	574	13	1	3990	4560	505538666	505539239	0.000000e+00	968.0
12	TraesCS6D01G136300	chr2D	98.450	387	6	0	520	906	112095335	112095721	0.000000e+00	682.0
13	TraesCS6D01G136300	chr2D	98.450	387	6	0	520	906	493880229	493879843	0.000000e+00	682.0
14	TraesCS6D01G136300	chr5D	97.232	578	13	1	3986	4560	233054210	233053633	0.000000e+00	976.0
15	TraesCS6D01G136300	chr5D	97.373	571	15	0	3990	4560	32703033	32703603	0.000000e+00	972.0
16	TraesCS6D01G136300	chr5D	98.210	391	6	1	520	910	7604130	7603741	0.000000e+00	682.0
17	TraesCS6D01G136300	chr5D	86.747	83	7	3	2355	2434	45654353	45654434	6.280000e-14	89.8
18	TraesCS6D01G136300	chr5D	87.500	72	8	1	2362	2432	230024078	230024149	1.050000e-11	82.4
19	TraesCS6D01G136300	chr1D	97.373	571	15	0	3990	4560	414143816	414143246	0.000000e+00	972.0
20	TraesCS6D01G136300	chr1D	96.564	582	17	1	3982	4560	161711663	161711082	0.000000e+00	961.0
21	TraesCS6D01G136300	chr1D	83.562	73	5	6	317	387	204635076	204635009	1.370000e-05	62.1
22	TraesCS6D01G136300	chr7D	97.373	571	14	1	3990	4560	386719622	386720191	0.000000e+00	970.0
23	TraesCS6D01G136300	chr7D	98.741	397	4	1	515	910	546779076	546778680	0.000000e+00	704.0
24	TraesCS6D01G136300	chr7D	97.980	396	7	1	512	906	58150743	58150348	0.000000e+00	686.0
25	TraesCS6D01G136300	chr7D	98.458	389	6	0	520	908	554675999	554675611	0.000000e+00	686.0
26	TraesCS6D01G136300	chr7D	97.722	395	7	2	515	908	546778675	546778282	0.000000e+00	678.0
27	TraesCS6D01G136300	chr4D	97.043	575	14	1	3989	4560	183193084	183193658	0.000000e+00	965.0
28	TraesCS6D01G136300	chr1A	98.708	387	5	0	520	906	560264384	560264770	0.000000e+00	688.0
29	TraesCS6D01G136300	chr7A	98.201	389	7	0	520	908	216035246	216034858	0.000000e+00	680.0
30	TraesCS6D01G136300	chr5A	86.420	81	8	1	2359	2436	594959698	594959618	8.130000e-13	86.1
31	TraesCS6D01G136300	chr5A	87.879	66	8	0	2359	2424	680078002	680077937	1.360000e-10	78.7
32	TraesCS6D01G136300	chr5B	89.231	65	5	2	328	390	136020754	136020818	3.780000e-11	80.5
33	TraesCS6D01G136300	chr5B	89.231	65	4	2	2360	2424	453877933	453877994	1.360000e-10	78.7
34	TraesCS6D01G136300	chr3D	91.379	58	5	0	2359	2416	567408737	567408794	3.780000e-11	80.5
35	TraesCS6D01G136300	chr3B	84.416	77	11	1	2360	2436	628473027	628472952	1.760000e-09	75.0

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	TraesCS6D01G136300	chr6D	104765087	104769646	4559	False	8421.0	8421	100.0000	1	4560	1	chr6D.!!$F1	4559
1	TraesCS6D01G136300	chr6D	11162847	11163420	573	True	968.0	968	97.2130	3990	4560	1	chr6D.!!$R1	570
2	TraesCS6D01G136300	chr6A	126912603	126916164	3561	False	1930.0	4294	96.8540	1	3989	3	chr6A.!!$F1	3988
3	TraesCS6D01G136300	chr6B	191196804	191200085	3281	False	978.3	3079	93.5096	418	3989	5	chr6B.!!$F1	3571
4	TraesCS6D01G136300	chr2D	56064911	56065481	570	False	977.0	977	97.5480	3990	4560	1	chr2D.!!$F1	570
5	TraesCS6D01G136300	chr2D	505538666	505539239	573	False	968.0	968	97.2130	3990	4560	1	chr2D.!!$F3	570
6	TraesCS6D01G136300	chr5D	233053633	233054210	577	True	976.0	976	97.2320	3986	4560	1	chr5D.!!$R2	574
7	TraesCS6D01G136300	chr5D	32703033	32703603	570	False	972.0	972	97.3730	3990	4560	1	chr5D.!!$F1	570
8	TraesCS6D01G136300	chr1D	414143246	414143816	570	True	972.0	972	97.3730	3990	4560	1	chr1D.!!$R3	570
9	TraesCS6D01G136300	chr1D	161711082	161711663	581	True	961.0	961	96.5640	3982	4560	1	chr1D.!!$R1	578
10	TraesCS6D01G136300	chr7D	386719622	386720191	569	False	970.0	970	97.3730	3990	4560	1	chr7D.!!$F1	570
11	TraesCS6D01G136300	chr7D	546778282	546779076	794	True	691.0	704	98.2315	515	910	2	chr7D.!!$R3	395
12	TraesCS6D01G136300	chr4D	183193084	183193658	574	False	965.0	965	97.0430	3989	4560	1	chr4D.!!$F1	571

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	Hairpin	End Stability	Orientation
358	360	0.035036	ATCATCTGATGCAGAGGCCG	59.965	55.000	12.78	44.08	6.13	F
975	977	1.000274	AGCGTGTTCATTGCCTTTTCC	60.000	47.619	0.00	0.00	3.13	F
1974	1994	1.224315	CGGGGACATGCCAGATTCA	59.776	57.895	8.20	38.95	2.57	F
3446	3687	0.608035	TTCGGTGATGGAACTTGGCC	60.608	55.000	0.00	0.00	5.36	F

Position	MSA Position	Penalty	Sequence	TM	GC	End Stability	Orientation
1956	1976	0.179009	ATGAATCTGGCATGTCCCCG	60.179	55.000	5.73	R
2114	2259	1.003545	CTTTATGCGATGCCCACGAAG	60.004	52.381	3.79	R
3469	3710	0.249868	CGAACAAGGCAGAGACCACA	60.250	55.000	4.17	R
4277	4535	0.485099	ATGGGTGCAGGGTGGTTTTA	59.515	50.000	1.52	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
158	159	3.958704	TCATGCAAGTTTTGTTGTACGG	58.041	40.909	0.00	0.00	0.00	4.02
169	170	7.081976	AGTTTTGTTGTACGGCTTATTTGATC	58.918	34.615	0.00	0.00	0.00	2.92
222	223	1.750399	GATGCTGCCCCGATGTGTT	60.750	57.895	0.00	0.00	0.00	3.32
242	243	2.454336	TCCTATGTGGATGACCTCGT	57.546	50.000	0.00	0.00	40.56	4.18
243	244	2.747177	TCCTATGTGGATGACCTCGTT	58.253	47.619	0.00	0.00	40.56	3.85
244	245	3.104512	TCCTATGTGGATGACCTCGTTT	58.895	45.455	0.00	0.00	40.56	3.60
358	360	0.035036	ATCATCTGATGCAGAGGCCG	59.965	55.000	12.78	0.00	44.08	6.13
379	381	2.904434	GGGGCTATATCCTCCTTTTCGA	59.096	50.000	0.00	0.00	0.00	3.71
380	382	3.326880	GGGGCTATATCCTCCTTTTCGAA	59.673	47.826	0.00	0.00	0.00	3.71
381	383	4.202430	GGGGCTATATCCTCCTTTTCGAAA	60.202	45.833	6.47	6.47	0.00	3.46
429	431	5.462398	CCGCTGACAGTATTTATGTTAGTCC	59.538	44.000	3.99	0.00	36.82	3.85
432	434	7.042335	GCTGACAGTATTTATGTTAGTCCTGT	58.958	38.462	3.99	0.00	36.82	4.00
534	536	1.107945	ACTTGGGGGTGTTTGTTTCG	58.892	50.000	0.00	0.00	0.00	3.46
652	654	7.162082	GGGACTAAATGAAGAAGACTCTCAAA	58.838	38.462	0.00	0.00	0.00	2.69
846	848	2.026169	CAGGGAGGGACTTTTTAGGGAC	60.026	54.545	0.00	0.00	41.55	4.46
952	954	7.351414	TGCATTTTAGCTTATCTATAGCGTG	57.649	36.000	0.00	0.00	43.37	5.34
958	960	4.724303	AGCTTATCTATAGCGTGTTAGCG	58.276	43.478	0.00	0.00	43.37	4.26
975	977	1.000274	AGCGTGTTCATTGCCTTTTCC	60.000	47.619	0.00	0.00	0.00	3.13
1104	1106	9.594478	TGCAAGAGTTCGATTAAAACATATCTA	57.406	29.630	0.00	0.00	0.00	1.98
1259	1261	7.724951	TGACTAATATGGATGCAAATTGATGGA	59.275	33.333	0.00	0.00	0.00	3.41
1260	1262	8.660295	ACTAATATGGATGCAAATTGATGGAT	57.340	30.769	0.00	0.00	33.70	3.41
1261	1263	9.758021	ACTAATATGGATGCAAATTGATGGATA	57.242	29.630	0.00	0.00	30.89	2.59
1266	1268	7.470935	TGGATGCAAATTGATGGATATTAGG	57.529	36.000	0.00	0.00	30.89	2.69
1267	1269	6.438108	TGGATGCAAATTGATGGATATTAGGG	59.562	38.462	0.00	0.00	30.89	3.53
1268	1270	5.726980	TGCAAATTGATGGATATTAGGGC	57.273	39.130	0.00	0.00	0.00	5.19
1269	1271	5.146298	TGCAAATTGATGGATATTAGGGCA	58.854	37.500	0.00	0.00	0.00	5.36
1270	1272	5.010922	TGCAAATTGATGGATATTAGGGCAC	59.989	40.000	0.00	0.00	0.00	5.01
1271	1273	9.152342	ATGCAAATTGATGGATATTAGGGCACC	62.152	40.741	0.00	0.00	38.11	5.01
1282	1284	2.682494	GGGCACCGTCTGACCCTA	60.682	66.667	1.55	0.00	43.57	3.53
1283	1285	2.722201	GGGCACCGTCTGACCCTAG	61.722	68.421	1.55	0.00	43.57	3.02
1284	1286	2.722201	GGCACCGTCTGACCCTAGG	61.722	68.421	0.06	0.06	0.00	3.02
1285	1287	1.982938	GCACCGTCTGACCCTAGGT	60.983	63.158	8.29	0.67	39.44	3.08
1311	1313	3.577805	GGTACCATTTAGCTCACCCAT	57.422	47.619	7.15	0.00	0.00	4.00
1312	1314	3.477530	GGTACCATTTAGCTCACCCATC	58.522	50.000	7.15	0.00	0.00	3.51
1313	1315	3.136626	GGTACCATTTAGCTCACCCATCT	59.863	47.826	7.15	0.00	0.00	2.90
1314	1316	4.347000	GGTACCATTTAGCTCACCCATCTA	59.653	45.833	7.15	0.00	0.00	1.98
1315	1317	4.423625	ACCATTTAGCTCACCCATCTAC	57.576	45.455	0.00	0.00	0.00	2.59
1344	1346	8.732746	CCTACTGGCTAATACTTGTTTTGTAT	57.267	34.615	0.00	0.00	32.60	2.29
1391	1393	4.451435	TGCATTGTTGTTGGCATAACATTG	59.549	37.500	22.31	22.31	39.39	2.82
1395	1397	5.268118	TGTTGTTGGCATAACATTGTCAA	57.732	34.783	12.15	0.00	38.80	3.18
1404	1406	9.531942	TTGGCATAACATTGTCAATTTCATATC	57.468	29.630	0.00	0.00	36.35	1.63
1415	1417	8.942338	TGTCAATTTCATATCGCTTACTAAGT	57.058	30.769	0.00	0.00	0.00	2.24
1491	1493	2.629617	CACCCCAAATGTGAAAGAAGCT	59.370	45.455	0.00	0.00	35.74	3.74
1580	1582	4.835284	ACAAATTTGGTCCAAGGTTTGT	57.165	36.364	27.65	27.65	38.20	2.83
1739	1759	5.012148	CCCTGGGTATGACCTTCTAAGTATG	59.988	48.000	3.97	0.00	38.64	2.39
1815	1835	3.273434	CTGTTGCCATGTGCTGTACTAT	58.727	45.455	7.54	0.00	42.00	2.12
1956	1976	4.635765	TGCAGATATGTACTTGTGAAAGGC	59.364	41.667	0.00	0.00	0.00	4.35
1974	1994	1.224315	CGGGGACATGCCAGATTCA	59.776	57.895	8.20	0.00	38.95	2.57
1998	2018	8.076781	TCATCAGAAGCTATTGACGTATTCTAC	58.923	37.037	2.49	0.00	0.00	2.59
2114	2259	0.741221	AGGCAAGGAATTCGTCGAGC	60.741	55.000	0.30	6.41	0.00	5.03
2149	2294	2.264005	TAAAGACCCGCAACACACAT	57.736	45.000	0.00	0.00	0.00	3.21
2182	2327	4.133078	GCACTTTAGCCTCATCTATTGCT	58.867	43.478	0.00	0.00	37.84	3.91
2235	2380	5.301551	TGAATGCTGTTCAGGTTTGTGTTAT	59.698	36.000	1.97	0.00	0.00	1.89
2304	2449	3.130693	ACAAGTTCTCCCGTATAGTGAGC	59.869	47.826	0.00	0.00	0.00	4.26
2379	2524	5.614324	TGTACTCCCTCTGTTCCATATTG	57.386	43.478	0.00	0.00	0.00	1.90
2416	2561	4.690748	CAGCGACAATTAATATGGATCGGT	59.309	41.667	0.00	0.00	39.16	4.69
2419	2564	5.614668	GCGACAATTAATATGGATCGGTGTG	60.615	44.000	0.00	0.00	0.00	3.82
2420	2565	5.694458	CGACAATTAATATGGATCGGTGTGA	59.306	40.000	0.00	0.00	0.00	3.58
2524	2669	4.627035	GCATGTCTGTTTTGGCCTATTTTC	59.373	41.667	3.32	0.00	0.00	2.29
2611	2756	7.554835	TGTTCTTAGAACTTAGTTTTTGCCTGA	59.445	33.333	23.27	0.00	0.00	3.86
2789	2934	1.202806	TGACCACCTTTTCAGGCTCAG	60.203	52.381	0.00	0.00	45.56	3.35
3052	3197	4.697352	AGAGAAAAGGACATTGAATCACGG	59.303	41.667	0.00	0.00	0.00	4.94
3446	3687	0.608035	TTCGGTGATGGAACTTGGCC	60.608	55.000	0.00	0.00	0.00	5.36
3469	3710	1.611673	CCCAATCTCAAAGGTGTCGCT	60.612	52.381	0.00	0.00	0.00	4.93
3481	3722	2.433318	GTCGCTGTGGTCTCTGCC	60.433	66.667	0.00	0.00	0.00	4.85
3547	3788	0.388520	CCATCTTGACGAGTGTGCGA	60.389	55.000	0.00	0.00	34.83	5.10
3556	3797	3.372676	GAGTGTGCGATGCTTGGCG	62.373	63.158	2.26	0.00	0.00	5.69
3602	3843	4.503714	TCTCTTGTTTTGTCAAGGGAGT	57.496	40.909	5.10	0.00	46.08	3.85
3603	3844	4.199310	TCTCTTGTTTTGTCAAGGGAGTG	58.801	43.478	5.10	0.00	46.08	3.51
3675	3916	1.029408	TGATTACATGGTGCGGTGGC	61.029	55.000	0.00	0.00	40.52	5.01
3688	3929	0.588730	CGGTGGCACGAATATTTGCG	60.589	55.000	12.17	2.03	39.81	4.85
3831	4072	4.360889	ACTCTCCATGACATCTTCCTCTT	58.639	43.478	0.00	0.00	0.00	2.85
3835	4076	7.038017	ACTCTCCATGACATCTTCCTCTTTTTA	60.038	37.037	0.00	0.00	0.00	1.52
3899	4143	4.921470	AATTCCGCCGATATAAACGATG	57.079	40.909	0.00	0.00	0.00	3.84
3957	4206	5.064441	AGCATTGCCAGACTAATTTTGTC	57.936	39.130	4.70	3.19	34.88	3.18
4043	4292	5.061721	AGTCCAAGTCAATTTTGTACCCT	57.938	39.130	0.00	0.00	0.00	4.34
4046	4295	7.238710	AGTCCAAGTCAATTTTGTACCCTTAT	58.761	34.615	0.00	0.00	0.00	1.73
4063	4312	4.189231	CCTTATCCCAAGTCGGTTTGTAG	58.811	47.826	0.00	0.00	0.00	2.74
4277	4535	1.422161	GGCCCTCACCATAGCTCCAT	61.422	60.000	0.00	0.00	0.00	3.41
4283	4541	4.137543	CCTCACCATAGCTCCATAAAACC	58.862	47.826	0.00	0.00	0.00	3.27
4384	4642	1.686325	ATCTCGCCGCCCACAACTAT	61.686	55.000	0.00	0.00	0.00	2.12
4504	4762	2.561733	TGAAAGACGATCTCGCGATT	57.438	45.000	10.36	0.00	44.43	3.34

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
158	159	2.945668	AGTTGAGGCCGATCAAATAAGC	59.054	45.455	8.89	0.00	40.72	3.09
169	170	2.076863	CAAAACCTAGAGTTGAGGCCG	58.923	52.381	0.00	0.00	39.19	6.13
267	269	1.998315	CTGAGGCTGATCAAAGTGACG	59.002	52.381	0.00	0.00	0.00	4.35
358	360	2.904434	TCGAAAAGGAGGATATAGCCCC	59.096	50.000	2.64	4.93	0.00	5.80
429	431	4.997395	ACTACTTTAATGCACAGTCCACAG	59.003	41.667	0.00	0.00	0.00	3.66
432	434	6.952773	AAAACTACTTTAATGCACAGTCCA	57.047	33.333	0.00	0.00	0.00	4.02
652	654	5.360999	CCAAAAAGTCCCAAAAAGACTCTCT	59.639	40.000	0.00	0.00	43.77	3.10
817	819	2.658807	AGTCCCTCCCTGTTTGTTTC	57.341	50.000	0.00	0.00	0.00	2.78
846	848	5.500546	AGTCCCAACTAAAAAGTCCCTAG	57.499	43.478	0.00	0.00	32.59	3.02
952	954	2.989422	AAGGCAATGAACACGCTAAC	57.011	45.000	0.00	0.00	0.00	2.34
958	960	4.525912	ATCAGGAAAAGGCAATGAACAC	57.474	40.909	0.00	0.00	0.00	3.32
1104	1106	7.616528	ATTAAGTAAATAAATGGGCTGCCAT	57.383	32.000	22.05	9.32	0.00	4.40
1259	1261	1.692519	GGTCAGACGGTGCCCTAATAT	59.307	52.381	0.00	0.00	0.00	1.28
1260	1262	1.117150	GGTCAGACGGTGCCCTAATA	58.883	55.000	0.00	0.00	0.00	0.98
1261	1263	1.623542	GGGTCAGACGGTGCCCTAAT	61.624	60.000	10.38	0.00	38.70	1.73
1262	1264	2.288025	GGGTCAGACGGTGCCCTAA	61.288	63.158	10.38	0.00	38.70	2.69
1263	1265	1.866483	TAGGGTCAGACGGTGCCCTA	61.866	60.000	17.59	17.59	45.76	3.53
1264	1266	4.640690	AGGGTCAGACGGTGCCCT	62.641	66.667	13.01	13.01	43.96	5.19
1265	1267	2.682494	TAGGGTCAGACGGTGCCC	60.682	66.667	9.90	9.90	40.84	5.36
1266	1268	2.722201	CCTAGGGTCAGACGGTGCC	61.722	68.421	0.00	0.00	0.00	5.01
1267	1269	1.982938	ACCTAGGGTCAGACGGTGC	60.983	63.158	14.81	0.00	0.00	5.01
1268	1270	4.436368	ACCTAGGGTCAGACGGTG	57.564	61.111	14.81	0.00	0.00	4.94
1279	1281	0.187851	ATGGTACCCTCCGACCTAGG	59.812	60.000	10.07	7.41	36.62	3.02
1280	1282	2.083628	AATGGTACCCTCCGACCTAG	57.916	55.000	10.07	0.00	36.62	3.02
1281	1283	2.555732	AAATGGTACCCTCCGACCTA	57.444	50.000	10.07	0.00	36.62	3.08
1282	1284	2.395619	CTAAATGGTACCCTCCGACCT	58.604	52.381	10.07	0.00	36.62	3.85
1283	1285	1.202615	GCTAAATGGTACCCTCCGACC	60.203	57.143	10.07	0.00	36.17	4.79
1284	1286	1.761198	AGCTAAATGGTACCCTCCGAC	59.239	52.381	10.07	0.00	0.00	4.79
1285	1287	2.037144	GAGCTAAATGGTACCCTCCGA	58.963	52.381	10.07	0.00	0.00	4.55
1286	1288	1.760613	TGAGCTAAATGGTACCCTCCG	59.239	52.381	10.07	0.00	0.00	4.63
1287	1289	2.158798	GGTGAGCTAAATGGTACCCTCC	60.159	54.545	10.07	0.00	0.00	4.30
1288	1290	2.158798	GGGTGAGCTAAATGGTACCCTC	60.159	54.545	10.07	8.01	43.43	4.30
1289	1291	1.844497	GGGTGAGCTAAATGGTACCCT	59.156	52.381	10.07	0.00	43.43	4.34
1290	1292	1.562475	TGGGTGAGCTAAATGGTACCC	59.438	52.381	10.07	0.00	46.23	3.69
1291	1293	3.136626	AGATGGGTGAGCTAAATGGTACC	59.863	47.826	4.43	4.43	0.00	3.34
1292	1294	4.423625	AGATGGGTGAGCTAAATGGTAC	57.576	45.455	0.00	0.00	0.00	3.34
1293	1295	4.966168	TGTAGATGGGTGAGCTAAATGGTA	59.034	41.667	0.00	0.00	0.00	3.25
1294	1296	3.780294	TGTAGATGGGTGAGCTAAATGGT	59.220	43.478	0.00	0.00	0.00	3.55
1295	1297	4.422073	TGTAGATGGGTGAGCTAAATGG	57.578	45.455	0.00	0.00	0.00	3.16
1296	1298	4.214971	GCATGTAGATGGGTGAGCTAAATG	59.785	45.833	1.57	0.00	40.15	2.32
1297	1299	4.392940	GCATGTAGATGGGTGAGCTAAAT	58.607	43.478	1.57	0.00	0.00	1.40
1298	1300	3.433598	GGCATGTAGATGGGTGAGCTAAA	60.434	47.826	1.57	0.00	0.00	1.85
1299	1301	2.104792	GGCATGTAGATGGGTGAGCTAA	59.895	50.000	1.57	0.00	0.00	3.09
1300	1302	1.694150	GGCATGTAGATGGGTGAGCTA	59.306	52.381	1.57	0.00	0.00	3.32
1301	1303	0.471617	GGCATGTAGATGGGTGAGCT	59.528	55.000	1.57	0.00	0.00	4.09
1302	1304	0.471617	AGGCATGTAGATGGGTGAGC	59.528	55.000	1.57	0.00	0.00	4.26
1303	1305	2.968574	AGTAGGCATGTAGATGGGTGAG	59.031	50.000	1.57	0.00	0.00	3.51
1304	1306	2.700371	CAGTAGGCATGTAGATGGGTGA	59.300	50.000	1.57	0.00	0.00	4.02
1305	1307	2.224378	CCAGTAGGCATGTAGATGGGTG	60.224	54.545	1.57	0.00	0.00	4.61
1306	1308	2.050144	CCAGTAGGCATGTAGATGGGT	58.950	52.381	1.57	0.00	0.00	4.51
1307	1309	2.847327	CCAGTAGGCATGTAGATGGG	57.153	55.000	1.57	0.00	0.00	4.00
1344	1346	7.973388	GCAACCAGAACTTATAAATGCACATAA	59.027	33.333	0.00	0.00	0.00	1.90
1404	1406	7.686938	GCAATTGTAACAGTAACTTAGTAAGCG	59.313	37.037	9.92	0.00	0.00	4.68
1491	1493	6.315714	TGATACACCCCCAAGTAATTTTGAA	58.684	36.000	0.00	0.00	0.00	2.69
1739	1759	3.782889	AACCAGTTTGCTTCAACAGAC	57.217	42.857	0.00	0.00	0.00	3.51
1956	1976	0.179009	ATGAATCTGGCATGTCCCCG	60.179	55.000	0.00	0.00	0.00	5.73
1998	2018	9.645059	AAGATAATCATAGAACACATACCATCG	57.355	33.333	0.00	0.00	0.00	3.84
2114	2259	1.003545	CTTTATGCGATGCCCACGAAG	60.004	52.381	0.00	0.00	0.00	3.79
2149	2294	1.953686	GCTAAAGTGCAACCAGTTCCA	59.046	47.619	0.00	0.00	37.80	3.53
2182	2327	1.877443	GAACCTTTTGCTAACTCGGCA	59.123	47.619	0.00	0.00	37.97	5.69
2235	2380	8.843308	AAGGTATATGTGGGTACAAAGTACTA	57.157	34.615	0.00	0.00	40.84	1.82
2304	2449	5.592054	TCTAGTGATGCACTATTTTCCGAG	58.408	41.667	7.65	0.00	44.49	4.63
2379	2524	9.982291	TTAATTGTCGCTGATTTAGTACAAATC	57.018	29.630	17.04	17.04	37.68	2.17
2416	2561	5.356882	GCAACAAAAGTATGCTACTCACA	57.643	39.130	0.00	0.00	38.26	3.58
2524	2669	6.308371	TGCATGATACATGTAGCAATTCTG	57.692	37.500	26.09	19.91	34.93	3.02
2657	2802	9.979578	TTCACATATACAGCAAAAGAAACAAAT	57.020	25.926	0.00	0.00	0.00	2.32
2789	2934	5.304686	TCCAATATTGTATGGAGGACACC	57.695	43.478	14.25	0.00	40.74	4.16
2991	3136	6.365247	ACACGAAGTACATCAGTGAAATACAC	59.635	38.462	21.25	10.07	45.18	2.90
3052	3197	3.435186	GCAGCCTCCAAGAACGCC	61.435	66.667	0.00	0.00	0.00	5.68
3093	3238	4.057428	GCGGCACTCCACTCGACT	62.057	66.667	0.00	0.00	0.00	4.18
3274	3515	4.057943	AGGTAGTCCGCCCCGTCT	62.058	66.667	0.00	0.00	39.05	4.18
3446	3687	2.716217	GACACCTTTGAGATTGGGGAG	58.284	52.381	0.00	0.00	0.00	4.30
3469	3710	0.249868	CGAACAAGGCAGAGACCACA	60.250	55.000	0.00	0.00	0.00	4.17
3481	3722	1.390123	ACGCATTCACGATCGAACAAG	59.610	47.619	24.34	9.53	36.70	3.16
3547	3788	2.560542	CTCTAGGATCTACGCCAAGCAT	59.439	50.000	0.00	0.00	0.00	3.79
3556	3797	5.768164	AGTGAAAGCTAGCTCTAGGATCTAC	59.232	44.000	19.65	7.34	33.87	2.59
3602	3843	7.037438	ACACTCGACTGAAGTAAAAACTTACA	58.963	34.615	0.00	0.00	0.00	2.41
3603	3844	7.460751	ACACTCGACTGAAGTAAAAACTTAC	57.539	36.000	0.00	0.00	0.00	2.34
3675	3916	1.267334	CCGTGGACGCAAATATTCGTG	60.267	52.381	6.90	0.00	39.22	4.35
3688	3929	1.997606	CTTCCGTATCAAACCGTGGAC	59.002	52.381	0.00	0.00	0.00	4.02
3771	4012	5.106038	GGGCCAACAAATTAGTAGTACAACC	60.106	44.000	4.39	0.00	0.00	3.77
3899	4143	1.478510	ACAGATGGAGTCGGTCATCAC	59.521	52.381	9.61	0.00	41.45	3.06
3957	4206	7.857734	TTGAGAGAGATAGTACACTTCAGAG	57.142	40.000	0.00	0.00	0.00	3.35
4043	4292	3.602483	GCTACAAACCGACTTGGGATAA	58.398	45.455	0.00	0.00	44.64	1.75
4046	4295	0.035739	GGCTACAAACCGACTTGGGA	59.964	55.000	0.00	0.00	44.64	4.37
4063	4312	5.980116	CGGCATACAAGAGTATATATGAGGC	59.020	44.000	0.00	0.00	38.88	4.70
4277	4535	0.485099	ATGGGTGCAGGGTGGTTTTA	59.515	50.000	0.00	0.00	0.00	1.52
4283	4541	2.273449	GAGGATGGGTGCAGGGTG	59.727	66.667	0.00	0.00	0.00	4.61
4384	4642	4.709886	TCGAAGAGATGTCTCCAATGGTAA	59.290	41.667	6.41	0.00	43.88	2.85

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.