AutoCloner

Multiple sequence alignment - TraesCS1D01G265800

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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	TraesCS1D01G265800	chr1D	100.000	2529	0	0	1	2529	361801465	361803993	0.000000e+00	4671.0
1	TraesCS1D01G265800	chr1D	82.318	509	70	17	1	497	10376995	10376495	8.360000e-115	424.0
2	TraesCS1D01G265800	chr1D	80.000	415	47	21	1288	1675	361907842	361908247	8.910000e-70	274.0
3	TraesCS1D01G265800	chr1D	87.879	231	18	7	992	1217	361907502	361907727	1.930000e-66	263.0
4	TraesCS1D01G265800	chr1A	93.196	1705	88	17	833	2527	461337376	461339062	0.000000e+00	2481.0
5	TraesCS1D01G265800	chr1A	86.928	765	91	6	30	789	461336616	461337376	0.000000e+00	850.0
6	TraesCS1D01G265800	chr1A	82.292	384	39	16	854	1217	461356541	461356915	3.160000e-79	305.0
7	TraesCS1D01G265800	chr1A	77.637	474	66	23	1281	1729	461357023	461357481	4.180000e-63	252.0
8	TraesCS1D01G265800	chr1B	89.065	1262	92	26	1271	2527	484297424	484298644	0.000000e+00	1524.0
9	TraesCS1D01G265800	chr1B	91.576	368	20	4	833	1200	484296964	484297320	4.860000e-137	497.0
10	TraesCS1D01G265800	chr1B	87.599	379	41	4	415	789	484286425	484286801	3.860000e-118	435.0
11	TraesCS1D01G265800	chr1B	84.048	420	64	3	2	419	484273280	484273698	3.920000e-108	401.0
12	TraesCS1D01G265800	chr1B	83.038	395	41	18	844	1217	484365756	484366145	4.030000e-88	335.0
13	TraesCS1D01G265800	chr1B	78.261	483	60	27	1281	1736	484366253	484366717	4.150000e-68	268.0
14	TraesCS1D01G265800	chr1B	84.914	232	31	4	1275	1503	484147212	484147442	5.440000e-57	231.0
15	TraesCS1D01G265800	chr1B	84.914	232	31	4	1275	1503	484214199	484214429	5.440000e-57	231.0
16	TraesCS1D01G265800	chr1B	86.503	163	15	4	552	709	673876157	673875997	3.340000e-39	172.0
17	TraesCS1D01G265800	chr5D	81.980	505	86	5	1	501	249880609	249881112	8.360000e-115	424.0
18	TraesCS1D01G265800	chr2D	80.680	559	87	11	2	549	50948521	50949069	5.030000e-112	414.0
19	TraesCS1D01G265800	chr2D	80.982	163	26	4	552	710	427337500	427337339	9.500000e-25	124.0
20	TraesCS1D01G265800	chr2D	97.727	44	1	0	789	832	539574545	539574502	2.700000e-10	76.8
21	TraesCS1D01G265800	chr3D	81.139	509	87	5	3	504	539924047	539924553	1.410000e-107	399.0
22	TraesCS1D01G265800	chr3D	95.556	45	2	0	788	832	239362750	239362794	3.490000e-09	73.1
23	TraesCS1D01G265800	chr2B	80.074	542	93	13	3	531	704289159	704289698	3.050000e-104	388.0
24	TraesCS1D01G265800	chr2B	78.320	512	97	11	5	505	800087422	800086914	4.060000e-83	318.0
25	TraesCS1D01G265800	chr4D	80.620	516	83	11	2	504	82862772	82862261	1.420000e-102	383.0
26	TraesCS1D01G265800	chr3A	83.333	174	21	6	543	710	362203842	362204013	1.210000e-33	154.0
27	TraesCS1D01G265800	chr4B	82.114	123	20	2	552	672	418365326	418365448	1.240000e-18	104.0
28	TraesCS1D01G265800	chr4B	97.674	43	1	0	790	832	22914633	22914675	9.700000e-10	75.0
29	TraesCS1D01G265800	chr7A	100.000	45	0	0	788	832	42495149	42495105	1.610000e-12	84.2
30	TraesCS1D01G265800	chr6A	97.778	45	1	0	788	832	14628422	14628466	7.500000e-11	78.7
31	TraesCS1D01G265800	chr5A	97.778	45	1	0	788	832	505641325	505641281	7.500000e-11	78.7

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	TraesCS1D01G265800	chr1D	361801465	361803993	2528	False	4671.0	4671	100.0000	1	2529	1	chr1D.!!$F1	2528
1	TraesCS1D01G265800	chr1D	10376495	10376995	500	True	424.0	424	82.3180	1	497	1	chr1D.!!$R1	496
2	TraesCS1D01G265800	chr1D	361907502	361908247	745	False	268.5	274	83.9395	992	1675	2	chr1D.!!$F2	683
3	TraesCS1D01G265800	chr1A	461336616	461339062	2446	False	1665.5	2481	90.0620	30	2527	2	chr1A.!!$F1	2497
4	TraesCS1D01G265800	chr1A	461356541	461357481	940	False	278.5	305	79.9645	854	1729	2	chr1A.!!$F2	875
5	TraesCS1D01G265800	chr1B	484296964	484298644	1680	False	1010.5	1524	90.3205	833	2527	2	chr1B.!!$F5	1694
6	TraesCS1D01G265800	chr1B	484365756	484366717	961	False	301.5	335	80.6495	844	1736	2	chr1B.!!$F6	892
7	TraesCS1D01G265800	chr5D	249880609	249881112	503	False	424.0	424	81.9800	1	501	1	chr5D.!!$F1	500
8	TraesCS1D01G265800	chr2D	50948521	50949069	548	False	414.0	414	80.6800	2	549	1	chr2D.!!$F1	547
9	TraesCS1D01G265800	chr3D	539924047	539924553	506	False	399.0	399	81.1390	3	504	1	chr3D.!!$F2	501
10	TraesCS1D01G265800	chr2B	704289159	704289698	539	False	388.0	388	80.0740	3	531	1	chr2B.!!$F1	528
11	TraesCS1D01G265800	chr2B	800086914	800087422	508	True	318.0	318	78.3200	5	505	1	chr2B.!!$R1	500
12	TraesCS1D01G265800	chr4D	82862261	82862772	511	True	383.0	383	80.6200	2	504	1	chr4D.!!$R1	502

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
264	268	0.106918	GGTTGTGTCCACCCTGAACA	60.107	55.0	0.0	0.0	0.0	3.18	F
1051	1093	0.172352	CCACACCACCACAACAACAC	59.828	55.0	0.0	0.0	0.0	3.32	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1175	1222	0.387367	CCGTTCACGTGTGAGAGGAG	60.387	60.0	16.51	0.09	41.13	3.69	R
2477	2613	0.179045	AGAGTTGACAGTGGTGCCAC	60.179	55.0	13.13	13.13	46.50	5.01	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
146	147	1.871077	GGTTTCCACGCGGGTTTAG	59.129	57.895	12.47	0.00	38.11	1.85
242	246	0.874390	TTCAATTGCGGAGACAGTGC	59.126	50.000	0.00	0.00	0.00	4.40
248	252	2.651361	CGGAGACAGTGCGAGGTT	59.349	61.111	0.00	0.00	44.08	3.50
262	266	0.472471	GAGGTTGTGTCCACCCTGAA	59.528	55.000	0.66	0.00	0.00	3.02
264	268	0.106918	GGTTGTGTCCACCCTGAACA	60.107	55.000	0.00	0.00	0.00	3.18
518	543	2.159382	GACAACATGGTTCGGGATTGT	58.841	47.619	0.00	0.00	33.15	2.71
537	562	0.471211	TGGGAGGTTTGAGAGTCGGT	60.471	55.000	0.00	0.00	0.00	4.69
542	567	1.760613	AGGTTTGAGAGTCGGTGTTGA	59.239	47.619	0.00	0.00	0.00	3.18
544	569	2.940410	GGTTTGAGAGTCGGTGTTGAAA	59.060	45.455	0.00	0.00	0.00	2.69
556	581	5.000591	TCGGTGTTGAAAATGCTCTTATGA	58.999	37.500	0.00	0.00	0.00	2.15
583	608	7.952671	TCTAAATTAGCATCACTAGATCCGTT	58.047	34.615	0.00	0.00	30.20	4.44
586	611	8.958119	AAATTAGCATCACTAGATCCGTTTTA	57.042	30.769	0.00	0.00	30.20	1.52
713	738	9.353431	TGTACAATTATACACGGAAGGAGTATA	57.647	33.333	0.00	0.00	37.52	1.47
714	739	9.837525	GTACAATTATACACGGAAGGAGTATAG	57.162	37.037	0.00	0.00	38.76	1.31
740	765	6.818644	AGTGTGAAATTATATCTGCTGTCGTT	59.181	34.615	0.00	0.00	0.00	3.85
776	801	0.897621	ACGTGATCTGATGTGCTGGA	59.102	50.000	0.00	0.00	0.00	3.86
788	813	4.102054	TGATGTGCTGGACATGAGTGATAT	59.898	41.667	19.78	0.00	45.90	1.63
789	814	4.063998	TGTGCTGGACATGAGTGATATC	57.936	45.455	0.00	0.00	0.00	1.63
790	815	3.055591	GTGCTGGACATGAGTGATATCG	58.944	50.000	0.00	0.00	0.00	2.92
791	816	2.958355	TGCTGGACATGAGTGATATCGA	59.042	45.455	0.00	0.00	0.00	3.59
792	817	3.575687	TGCTGGACATGAGTGATATCGAT	59.424	43.478	2.16	2.16	0.00	3.59
793	818	4.039609	TGCTGGACATGAGTGATATCGATT	59.960	41.667	1.71	0.00	0.00	3.34
794	819	4.624882	GCTGGACATGAGTGATATCGATTC	59.375	45.833	1.71	1.87	0.00	2.52
795	820	4.798574	TGGACATGAGTGATATCGATTCG	58.201	43.478	1.71	0.00	0.00	3.34
796	821	4.518970	TGGACATGAGTGATATCGATTCGA	59.481	41.667	11.73	11.73	41.13	3.71
798	823	5.741510	GGACATGAGTGATATCGATTCGATC	59.258	44.000	23.82	13.03	43.45	3.69
806	831	3.531829	CGATTCGATCGCTCCAGC	58.468	61.111	11.09	0.00	46.55	4.85
826	851	2.583593	GCGATCGCGAAGGAGCTT	60.584	61.111	26.12	0.00	40.82	3.74
827	852	2.167861	GCGATCGCGAAGGAGCTTT	61.168	57.895	26.12	0.00	40.82	3.51
828	853	1.696832	GCGATCGCGAAGGAGCTTTT	61.697	55.000	26.12	0.00	40.82	2.27
829	854	0.299003	CGATCGCGAAGGAGCTTTTC	59.701	55.000	15.24	0.95	40.82	2.29
830	855	2.971920	CGATCGCGAAGGAGCTTTTCC	61.972	57.143	15.24	0.00	42.80	3.13
842	867	3.303132	GGAGCTTTTCCGTATACAATGCG	60.303	47.826	3.32	0.00	35.91	4.73
999	1041	4.325204	TCAATCAAGTTACGAAATCGACGG	59.675	41.667	10.16	0.00	43.02	4.79
1051	1093	0.172352	CCACACCACCACAACAACAC	59.828	55.000	0.00	0.00	0.00	3.32
1104	1151	2.032178	AGTGAGAGCTTTGCACGAAAAC	59.968	45.455	8.33	0.00	37.60	2.43
1113	1160	4.789481	GCTTTGCACGAAAACTTCATCAGA	60.789	41.667	0.00	0.00	0.00	3.27
1175	1222	2.584608	CCGTCCTGGTCATGGGAC	59.415	66.667	8.40	8.40	46.00	4.46
1201	1248	1.144969	CACACGTGAACGGTAAGCAT	58.855	50.000	25.01	0.00	44.95	3.79
1246	1306	1.521423	GTAGTTCGATCGATTTGGGCG	59.479	52.381	20.18	0.00	0.00	6.13
1260	1349	3.469008	TTGGGCGGTCATATCTTGTAG	57.531	47.619	0.00	0.00	0.00	2.74
1261	1354	1.070134	TGGGCGGTCATATCTTGTAGC	59.930	52.381	0.00	0.00	0.00	3.58
1384	1491	3.979497	CCCACCCCAAGTGTCCCC	61.979	72.222	0.00	0.00	45.74	4.81
1531	1649	5.414454	GGCATGATATGTTCCGCCTAAAATA	59.586	40.000	0.00	0.00	38.36	1.40
1546	1664	7.435192	CCGCCTAAAATAAAATAAAAGCTCAGG	59.565	37.037	0.00	0.00	0.00	3.86
1596	1726	0.459078	TGTGTGTGTGGCCAACAATG	59.541	50.000	7.24	0.00	41.57	2.82
1597	1727	0.875474	GTGTGTGTGGCCAACAATGC	60.875	55.000	7.24	3.80	41.57	3.56
1598	1728	1.042003	TGTGTGTGGCCAACAATGCT	61.042	50.000	7.24	0.00	41.57	3.79
1615	1746	5.983720	ACAATGCTTATACCAGTATGTCGTC	59.016	40.000	0.45	0.00	0.00	4.20
1700	1831	6.787085	GGAATATCCTCCGTGAATAAACAG	57.213	41.667	0.00	0.00	32.53	3.16
1751	1884	0.750249	TGAGTTCTCTTGTCCACGCA	59.250	50.000	1.53	0.00	0.00	5.24
1840	1976	9.555727	GTATGTTAGATGCTAGGTTATTTTCCA	57.444	33.333	0.00	0.00	0.00	3.53
1843	1979	8.764558	TGTTAGATGCTAGGTTATTTTCCACTA	58.235	33.333	0.00	0.00	0.00	2.74
1844	1980	9.043079	GTTAGATGCTAGGTTATTTTCCACTAC	57.957	37.037	0.00	0.00	0.00	2.73
1914	2050	9.383519	ACACTAAATCTATTCATCAAACATCGT	57.616	29.630	0.00	0.00	0.00	3.73
1939	2075	7.033530	AGCAGTACTAGCTTAGTTATCACAG	57.966	40.000	12.32	0.00	39.87	3.66
1959	2095	1.188219	ACTCACACGAGCTGATGGGT	61.188	55.000	0.00	0.00	43.66	4.51
1974	2110	5.068987	GCTGATGGGTGGCTATTTGAAATTA	59.931	40.000	0.00	0.00	0.00	1.40
2019	2155	7.230913	ACATACAATAACTATCCTACGCACTCT	59.769	37.037	0.00	0.00	0.00	3.24
2057	2193	0.179156	GCATGCCACACCTTTCATCG	60.179	55.000	6.36	0.00	0.00	3.84
2139	2275	6.412653	CGTTTGACAATTTTGTGTACCTGTAC	59.587	38.462	0.00	0.45	42.43	2.90
2167	2303	2.880963	TGGCTACAAACCAAACTTGC	57.119	45.000	0.00	0.00	33.12	4.01
2174	2310	5.458779	GCTACAAACCAAACTTGCTGTTAAG	59.541	40.000	0.00	0.00	38.03	1.85
2183	2319	6.642540	CCAAACTTGCTGTTAAGAGAAATTCC	59.357	38.462	3.33	0.00	38.03	3.01
2185	2321	6.809630	ACTTGCTGTTAAGAGAAATTCCTC	57.190	37.500	3.33	0.00	0.00	3.71
2242	2378	6.073819	GGTTTGACTTGAATGCAAATGGTAAC	60.074	38.462	0.00	0.00	34.47	2.50
2295	2431	1.071385	AGCATAATCAGGCTTCGAGGG	59.929	52.381	0.00	0.00	39.13	4.30
2352	2488	8.641499	AAATGACAAAAGAATTCGTAAAAGCA	57.359	26.923	0.00	0.00	0.00	3.91
2360	2496	6.759497	AGAATTCGTAAAAGCAGCCTAATT	57.241	33.333	0.00	0.00	0.00	1.40
2361	2497	7.859325	AGAATTCGTAAAAGCAGCCTAATTA	57.141	32.000	0.00	0.00	0.00	1.40
2367	2503	5.507315	CGTAAAAGCAGCCTAATTAATGGGG	60.507	44.000	9.03	6.31	0.00	4.96
2387	2523	7.633193	TGGGGATGTTATATTGTTGTACAAC	57.367	36.000	28.13	28.13	41.40	3.32
2407	2543	5.065218	ACAACGAGATCATGCAATTAGGAAC	59.935	40.000	0.00	0.00	0.00	3.62
2409	2545	5.431765	ACGAGATCATGCAATTAGGAACTT	58.568	37.500	0.00	0.00	41.75	2.66

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
11	12	3.458872	CAGACGCTGGGCAAGAATA	57.541	52.632	0.00	0.00	0.00	1.75
146	147	1.154225	CGCATTCAAACGCCTCCAC	60.154	57.895	0.00	0.00	0.00	4.02
222	225	1.470098	GCACTGTCTCCGCAATTGAAT	59.530	47.619	10.34	0.00	0.00	2.57
248	252	1.148273	GCTGTTCAGGGTGGACACA	59.852	57.895	4.69	0.00	0.00	3.72
262	266	0.957395	CGCTCCACATTGAAGGCTGT	60.957	55.000	0.00	0.00	0.00	4.40
264	268	1.377725	CCGCTCCACATTGAAGGCT	60.378	57.895	0.00	0.00	0.00	4.58
298	302	2.420568	CCAGCTGCCCGCATTCATT	61.421	57.895	8.66	0.00	42.61	2.57
398	415	2.258726	AAACGCGAGGAGGTTTGCC	61.259	57.895	15.93	0.00	35.21	4.52
468	489	0.252197	AAGCTATCCAACACGGTCCC	59.748	55.000	0.00	0.00	35.57	4.46
505	528	1.682849	CTCCCACAATCCCGAACCA	59.317	57.895	0.00	0.00	0.00	3.67
518	543	0.471211	ACCGACTCTCAAACCTCCCA	60.471	55.000	0.00	0.00	0.00	4.37
537	562	8.846943	TTAGAGTCATAAGAGCATTTTCAACA	57.153	30.769	0.00	0.00	0.00	3.33
544	569	9.790344	ATGCTAATTTAGAGTCATAAGAGCATT	57.210	29.630	7.63	7.52	42.61	3.56
556	581	7.231722	ACGGATCTAGTGATGCTAATTTAGAGT	59.768	37.037	7.63	0.00	38.64	3.24
642	667	9.683651	CAAAGTTTTAAAATTTCGGTCAACTTC	57.316	29.630	8.89	0.00	33.21	3.01
650	675	7.673810	ACGAGTCAAAGTTTTAAAATTTCGG	57.326	32.000	8.89	5.59	0.00	4.30
713	738	6.699204	CGACAGCAGATATAATTTCACACTCT	59.301	38.462	0.00	0.00	0.00	3.24
714	739	6.477033	ACGACAGCAGATATAATTTCACACTC	59.523	38.462	0.00	0.00	0.00	3.51
740	765	1.269883	ACGTGCACACCGATTTAGACA	60.270	47.619	18.64	0.00	0.00	3.41
807	832	2.945398	AAGCTCCTTCGCGATCGCTC	62.945	60.000	34.69	15.63	39.32	5.03
808	833	2.564553	AAAGCTCCTTCGCGATCGCT	62.565	55.000	34.69	13.33	39.32	4.93
809	834	1.696832	AAAAGCTCCTTCGCGATCGC	61.697	55.000	29.80	29.80	35.26	4.58
810	835	0.299003	GAAAAGCTCCTTCGCGATCG	59.701	55.000	10.88	11.69	34.40	3.69
811	836	0.653114	GGAAAAGCTCCTTCGCGATC	59.347	55.000	10.88	0.00	41.61	3.69
812	837	1.084370	CGGAAAAGCTCCTTCGCGAT	61.084	55.000	10.88	0.00	42.85	4.58
813	838	1.736645	CGGAAAAGCTCCTTCGCGA	60.737	57.895	3.71	3.71	42.85	5.87
814	839	0.734942	TACGGAAAAGCTCCTTCGCG	60.735	55.000	0.00	0.00	42.85	5.87
815	840	1.653151	ATACGGAAAAGCTCCTTCGC	58.347	50.000	0.00	0.00	42.85	4.70
816	841	3.777478	TGTATACGGAAAAGCTCCTTCG	58.223	45.455	0.00	0.00	42.85	3.79
817	842	5.504173	GCATTGTATACGGAAAAGCTCCTTC	60.504	44.000	0.00	0.00	42.85	3.46
818	843	4.335594	GCATTGTATACGGAAAAGCTCCTT	59.664	41.667	0.00	0.00	42.85	3.36
819	844	3.877508	GCATTGTATACGGAAAAGCTCCT	59.122	43.478	0.00	0.00	42.85	3.69
820	845	3.303132	CGCATTGTATACGGAAAAGCTCC	60.303	47.826	0.00	0.00	41.40	4.70
821	846	3.308866	ACGCATTGTATACGGAAAAGCTC	59.691	43.478	0.00	0.00	0.00	4.09
822	847	3.063452	CACGCATTGTATACGGAAAAGCT	59.937	43.478	0.00	0.00	0.00	3.74
823	848	3.181514	ACACGCATTGTATACGGAAAAGC	60.182	43.478	0.00	0.00	36.32	3.51
824	849	4.092237	TGACACGCATTGTATACGGAAAAG	59.908	41.667	0.00	0.00	39.17	2.27
825	850	3.995048	TGACACGCATTGTATACGGAAAA	59.005	39.130	0.00	0.00	39.17	2.29
826	851	3.586892	TGACACGCATTGTATACGGAAA	58.413	40.909	0.00	0.00	39.17	3.13
827	852	3.233684	TGACACGCATTGTATACGGAA	57.766	42.857	0.00	0.00	39.17	4.30
828	853	2.943449	TGACACGCATTGTATACGGA	57.057	45.000	0.00	0.00	39.17	4.69
829	854	3.123790	TGTTTGACACGCATTGTATACGG	59.876	43.478	0.00	0.00	39.17	4.02
830	855	4.314948	TGTTTGACACGCATTGTATACG	57.685	40.909	0.00	0.00	39.17	3.06
831	856	5.737290	GGATTGTTTGACACGCATTGTATAC	59.263	40.000	0.00	0.00	39.17	1.47
842	867	0.385473	CGGCGTGGATTGTTTGACAC	60.385	55.000	0.00	0.00	0.00	3.67
967	1007	4.935205	TCGTAACTTGATTGACAATCCTGG	59.065	41.667	22.44	15.07	37.88	4.45
999	1041	3.019933	GCGGGCAGCTCTATATATAGC	57.980	52.381	14.03	11.23	44.04	2.97
1051	1093	0.108186	TGCGGTGGTAGAATGCTCTG	60.108	55.000	0.00	0.00	32.70	3.35
1113	1160	1.341080	CTTGGTGCCCTTCATGGTTT	58.659	50.000	0.00	0.00	0.00	3.27
1175	1222	0.387367	CCGTTCACGTGTGAGAGGAG	60.387	60.000	16.51	0.09	41.13	3.69
1201	1248	2.703416	AGAACGATTGAGCATGAGCAA	58.297	42.857	0.00	0.00	45.49	3.91
1246	1306	5.419542	TGTCACTTGCTACAAGATATGACC	58.580	41.667	18.85	8.36	35.45	4.02
1260	1349	1.672881	GGCATCAGGTATGTCACTTGC	59.327	52.381	0.00	0.00	40.14	4.01
1261	1354	1.935873	CGGCATCAGGTATGTCACTTG	59.064	52.381	0.00	0.00	40.44	3.16
1531	1649	4.943705	TCATCTCGCCTGAGCTTTTATTTT	59.056	37.500	0.00	0.00	42.26	1.82
1546	1664	1.547292	GATGACGCTGCTCATCTCGC	61.547	60.000	23.11	8.00	42.32	5.03
1596	1726	5.692613	AGAGACGACATACTGGTATAAGC	57.307	43.478	0.00	0.00	0.00	3.09
1597	1727	6.018098	ACGAAGAGACGACATACTGGTATAAG	60.018	42.308	0.00	0.00	37.03	1.73
1598	1728	5.819379	ACGAAGAGACGACATACTGGTATAA	59.181	40.000	0.00	0.00	37.03	0.98
1615	1746	2.128035	AGAAAACACAGCGACGAAGAG	58.872	47.619	0.00	0.00	0.00	2.85
1700	1831	1.795162	GCCACGCACAATCATTACAGC	60.795	52.381	0.00	0.00	0.00	4.40
1893	2029	8.437360	TGCTACGATGTTTGATGAATAGATTT	57.563	30.769	0.00	0.00	0.00	2.17
1913	2049	7.928103	TGTGATAACTAAGCTAGTACTGCTAC	58.072	38.462	16.73	10.82	40.22	3.58
1914	2050	7.991460	TCTGTGATAACTAAGCTAGTACTGCTA	59.009	37.037	16.73	5.20	40.22	3.49
1915	2051	6.829298	TCTGTGATAACTAAGCTAGTACTGCT	59.171	38.462	5.39	9.69	43.32	4.24
1917	2053	8.215926	AGTCTGTGATAACTAAGCTAGTACTG	57.784	38.462	5.39	0.00	38.26	2.74
1939	2075	0.459237	CCCATCAGCTCGTGTGAGTC	60.459	60.000	0.00	0.00	44.48	3.36
1959	2095	9.528489	ACTAGAAAGGTTAATTTCAAATAGCCA	57.472	29.630	0.00	0.00	40.86	4.75
1974	2110	5.869649	ATGTGCCAAAAACTAGAAAGGTT	57.130	34.783	0.00	0.00	32.55	3.50
2019	2155	4.822685	TGCCCGTAGTAAGATGGTAAAA	57.177	40.909	0.00	0.00	0.00	1.52
2139	2275	3.950397	TGGTTTGTAGCCATACTTCCTG	58.050	45.455	0.00	0.00	32.75	3.86
2167	2303	8.535690	AACGTTAGAGGAATTTCTCTTAACAG	57.464	34.615	21.48	17.59	43.26	3.16
2174	2310	8.928270	TTGAGATAACGTTAGAGGAATTTCTC	57.072	34.615	14.25	16.56	0.00	2.87
2242	2378	7.636150	AAACTGAGATCAAATATGGAACCTG	57.364	36.000	0.00	0.00	0.00	4.00
2285	2421	2.125766	AACCACCTTCCCTCGAAGCC	62.126	60.000	0.00	0.00	43.66	4.35
2295	2431	9.614792	AACTATATCTTATGTTGAACCACCTTC	57.385	33.333	0.00	0.00	0.00	3.46
2352	2488	9.479549	CAATATAACATCCCCATTAATTAGGCT	57.520	33.333	0.00	0.00	0.00	4.58
2360	2496	9.922477	TTGTACAACAATATAACATCCCCATTA	57.078	29.630	3.59	0.00	32.34	1.90
2361	2497	8.691797	GTTGTACAACAATATAACATCCCCATT	58.308	33.333	29.46	0.00	40.59	3.16
2387	2523	5.998454	AAGTTCCTAATTGCATGATCTCG	57.002	39.130	0.00	0.00	0.00	4.04
2477	2613	0.179045	AGAGTTGACAGTGGTGCCAC	60.179	55.000	13.13	13.13	46.50	5.01

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.