AutoCloner

Multiple sequence alignment - TraesCS2D01G274900

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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	TraesCS2D01G274900	chr2D	100.000	2435	0	0	1	2435	344302067	344304501	0.000000e+00	4497.0
1	TraesCS2D01G274900	chr2D	90.236	891	65	6	1567	2435	168238277	168239167	0.000000e+00	1144.0
2	TraesCS2D01G274900	chr2D	78.322	286	51	4	39	313	305932601	305932316	8.950000e-40	174.0
3	TraesCS2D01G274900	chr5A	90.230	870	65	11	1566	2420	524020650	524019786	0.000000e+00	1118.0
4	TraesCS2D01G274900	chr5A	89.089	889	72	14	1567	2435	551070185	551069302	0.000000e+00	1081.0
5	TraesCS2D01G274900	chr5D	89.527	888	72	8	1567	2435	472788281	472787396	0.000000e+00	1105.0
6	TraesCS2D01G274900	chr5D	89.273	867	68	12	1567	2414	177235825	177236685	0.000000e+00	1062.0
7	TraesCS2D01G274900	chr5D	91.184	397	23	4	1567	1951	493140385	493140781	1.660000e-146	529.0
8	TraesCS2D01G274900	chr1A	88.754	907	71	16	1547	2435	292747187	292748080	0.000000e+00	1081.0
9	TraesCS2D01G274900	chr1A	89.516	496	35	6	1567	2047	533918539	533918046	1.600000e-171	612.0
10	TraesCS2D01G274900	chr1A	88.845	502	43	4	1564	2052	534005346	534004845	2.680000e-169	604.0
11	TraesCS2D01G274900	chrUn	89.064	887	74	8	1567	2435	69453796	69452915	0.000000e+00	1079.0
12	TraesCS2D01G274900	chr1D	88.739	888	80	10	1567	2435	72956326	72955440	0.000000e+00	1068.0
13	TraesCS2D01G274900	chr1D	86.124	418	28	4	1566	1971	73050677	73050278	8.050000e-115	424.0
14	TraesCS2D01G274900	chr2A	95.502	667	28	2	868	1533	455480973	455481638	0.000000e+00	1064.0
15	TraesCS2D01G274900	chr2A	92.344	418	28	1	93	506	455479969	455480386	2.080000e-165	592.0
16	TraesCS2D01G274900	chr2A	90.637	267	19	4	553	816	455480390	455480653	1.390000e-92	350.0
17	TraesCS2D01G274900	chr2B	93.457	703	28	7	877	1564	409400366	409401065	0.000000e+00	1027.0
18	TraesCS2D01G274900	chr2B	81.713	864	90	27	1	840	409399553	409400372	0.000000e+00	658.0
19	TraesCS2D01G274900	chr2B	78.648	281	48	5	39	308	374021646	374021367	2.490000e-40	176.0
20	TraesCS2D01G274900	chr5B	88.082	881	79	16	1567	2435	494947693	494946827	0.000000e+00	1022.0
21	TraesCS2D01G274900	chr7D	90.230	696	55	5	1567	2249	22751589	22752284	0.000000e+00	896.0
22	TraesCS2D01G274900	chr7A	89.147	645	51	5	1566	2192	42693293	42693936	0.000000e+00	785.0
23	TraesCS2D01G274900	chr7A	88.929	280	18	5	1562	1829	539883300	539883578	1.400000e-87	333.0
24	TraesCS2D01G274900	chr3A	91.085	258	11	2	1567	1812	589316717	589316974	3.000000e-89	339.0
25	TraesCS2D01G274900	chr6A	79.058	191	37	3	588	776	71457182	71456993	7.070000e-26	128.0
26	TraesCS2D01G274900	chr7B	86.250	80	10	1	218	297	141955403	141955481	4.310000e-13	86.1
27	TraesCS2D01G274900	chr4B	86.842	76	10	0	700	775	103003293	103003368	4.310000e-13	86.1

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	TraesCS2D01G274900	chr2D	344302067	344304501	2434	False	4497.000000	4497	100.000000	1	2435	1	chr2D.!!$F2	2434
1	TraesCS2D01G274900	chr2D	168238277	168239167	890	False	1144.000000	1144	90.236000	1567	2435	1	chr2D.!!$F1	868
2	TraesCS2D01G274900	chr5A	524019786	524020650	864	True	1118.000000	1118	90.230000	1566	2420	1	chr5A.!!$R1	854
3	TraesCS2D01G274900	chr5A	551069302	551070185	883	True	1081.000000	1081	89.089000	1567	2435	1	chr5A.!!$R2	868
4	TraesCS2D01G274900	chr5D	472787396	472788281	885	True	1105.000000	1105	89.527000	1567	2435	1	chr5D.!!$R1	868
5	TraesCS2D01G274900	chr5D	177235825	177236685	860	False	1062.000000	1062	89.273000	1567	2414	1	chr5D.!!$F1	847
6	TraesCS2D01G274900	chr1A	292747187	292748080	893	False	1081.000000	1081	88.754000	1547	2435	1	chr1A.!!$F1	888
7	TraesCS2D01G274900	chr1A	534004845	534005346	501	True	604.000000	604	88.845000	1564	2052	1	chr1A.!!$R2	488
8	TraesCS2D01G274900	chrUn	69452915	69453796	881	True	1079.000000	1079	89.064000	1567	2435	1	chrUn.!!$R1	868
9	TraesCS2D01G274900	chr1D	72955440	72956326	886	True	1068.000000	1068	88.739000	1567	2435	1	chr1D.!!$R1	868
10	TraesCS2D01G274900	chr2A	455479969	455481638	1669	False	668.666667	1064	92.827667	93	1533	3	chr2A.!!$F1	1440
11	TraesCS2D01G274900	chr2B	409399553	409401065	1512	False	842.500000	1027	87.585000	1	1564	2	chr2B.!!$F1	1563
12	TraesCS2D01G274900	chr5B	494946827	494947693	866	True	1022.000000	1022	88.082000	1567	2435	1	chr5B.!!$R1	868
13	TraesCS2D01G274900	chr7D	22751589	22752284	695	False	896.000000	896	90.230000	1567	2249	1	chr7D.!!$F1	682
14	TraesCS2D01G274900	chr7A	42693293	42693936	643	False	785.000000	785	89.147000	1566	2192	1	chr7A.!!$F1	626

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
857	1188	0.179015	TTGCCTACTTTCACCCGCAA	60.179	50.0	0.0	0.0	34.08	4.85	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2237	2615	1.862602	GACTTGCGTTGCCGGGATTT	61.863	55.0	2.18	0.0	33.68	2.17	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
32	33	2.334838	CCTTTTTCTGCTGCATGAAGC	58.665	47.619	19.66	19.66	43.82	3.86
49	56	1.154654	GCAAAGTGCTACACGTCGC	60.155	57.895	0.00	0.00	40.96	5.19
67	74	1.225855	GCCCGCGTGATGATATGAAA	58.774	50.000	4.92	0.00	0.00	2.69
68	75	1.601903	GCCCGCGTGATGATATGAAAA	59.398	47.619	4.92	0.00	0.00	2.29
69	76	2.349817	GCCCGCGTGATGATATGAAAAG	60.350	50.000	4.92	0.00	0.00	2.27
70	77	3.130633	CCCGCGTGATGATATGAAAAGA	58.869	45.455	4.92	0.00	0.00	2.52
71	78	3.748048	CCCGCGTGATGATATGAAAAGAT	59.252	43.478	4.92	0.00	0.00	2.40
81	88	8.421002	TGATGATATGAAAAGATTGACCGTCTA	58.579	33.333	0.00	0.00	0.00	2.59
84	91	4.265904	TGAAAAGATTGACCGTCTAGCA	57.734	40.909	0.00	0.00	0.00	3.49
87	94	4.744795	AAAGATTGACCGTCTAGCAGAT	57.255	40.909	0.00	0.00	0.00	2.90
88	95	4.314740	AAGATTGACCGTCTAGCAGATC	57.685	45.455	0.00	0.00	0.00	2.75
119	137	6.662755	TGGATCCCATAATAATAGTCCATGC	58.337	40.000	9.90	0.00	30.10	4.06
141	159	3.146066	GAGTGCCAGTCCATGTAACAAA	58.854	45.455	0.00	0.00	0.00	2.83
171	189	2.232696	TGCGCTCATCCTACTGTAACAA	59.767	45.455	9.73	0.00	0.00	2.83
256	278	8.986477	ACACAAATATTTCCAAAACATAGCTC	57.014	30.769	0.00	0.00	0.00	4.09
351	373	0.183731	AGGCTATGGTTTAGGCTGCC	59.816	55.000	11.65	11.65	46.73	4.85
393	415	0.394762	ATCGTACGGTAGTGGAGGCA	60.395	55.000	16.52	0.00	0.00	4.75
404	426	4.436998	GGAGGCAGTCGACACCCG	62.437	72.222	19.50	4.12	40.25	5.28
467	489	5.250543	TCTTTTATCACCTGAACATCTCCCA	59.749	40.000	0.00	0.00	0.00	4.37
519	541	5.519206	CGCCCTTGTTGTAGAAACTATACTC	59.481	44.000	0.00	0.00	0.00	2.59
532	554	6.706270	AGAAACTATACTCCGCAATAACATGG	59.294	38.462	0.00	0.00	0.00	3.66
538	560	4.079253	ACTCCGCAATAACATGGTCTTTT	58.921	39.130	0.00	0.00	0.00	2.27
573	595	2.843730	AGCATGTATGTGTAAGGACCCA	59.156	45.455	0.00	0.00	0.00	4.51
582	604	8.278639	TGTATGTGTAAGGACCCAAATATTCAT	58.721	33.333	0.00	0.00	0.00	2.57
671	695	2.991250	AGTTTAGTTGGCGAGCATGAT	58.009	42.857	0.00	0.00	0.00	2.45
685	709	2.230992	AGCATGATAGATCCGACTCAGC	59.769	50.000	0.00	0.00	0.00	4.26
701	725	6.096036	CGACTCAGCTCATTTTTCTTCTAGA	58.904	40.000	0.00	0.00	0.00	2.43
717	741	1.732259	CTAGAAAATTGCCGTGCTCGT	59.268	47.619	7.47	0.00	35.01	4.18
729	753	3.123959	GCCGTGCTCGTCAACTAAATTTA	59.876	43.478	7.47	0.00	35.01	1.40
779	803	7.701501	ACCATGAAAAACATTTGATTTGTTTGC	59.298	29.630	0.00	0.61	44.32	3.68
780	804	7.096966	CCATGAAAAACATTTGATTTGTTTGCG	60.097	33.333	0.00	0.00	44.32	4.85
781	805	5.736358	TGAAAAACATTTGATTTGTTTGCGC	59.264	32.000	0.00	0.00	44.32	6.09
782	806	4.871993	AAACATTTGATTTGTTTGCGCA	57.128	31.818	5.66	5.66	43.65	6.09
783	807	5.421212	AAACATTTGATTTGTTTGCGCAT	57.579	30.435	12.75	0.00	43.65	4.73
788	812	6.850317	ACATTTGATTTGTTTGCGCATAAAAC	59.150	30.769	12.75	14.13	37.90	2.43
803	1134	8.401709	TGCGCATAAAACAATTAACATCAGATA	58.598	29.630	5.66	0.00	0.00	1.98
831	1162	4.851558	GCAGTTCCATTTGTAATCGTTGAC	59.148	41.667	0.00	0.00	0.00	3.18
834	1165	6.359617	CAGTTCCATTTGTAATCGTTGACAAC	59.640	38.462	8.34	8.34	35.35	3.32
835	1166	5.365403	TCCATTTGTAATCGTTGACAACC	57.635	39.130	12.66	0.00	35.35	3.77
836	1167	5.067273	TCCATTTGTAATCGTTGACAACCT	58.933	37.500	12.66	0.62	35.35	3.50
837	1168	5.180492	TCCATTTGTAATCGTTGACAACCTC	59.820	40.000	12.66	0.44	35.35	3.85
838	1169	5.181245	CCATTTGTAATCGTTGACAACCTCT	59.819	40.000	12.66	0.00	35.35	3.69
839	1170	6.293955	CCATTTGTAATCGTTGACAACCTCTT	60.294	38.462	12.66	6.37	35.35	2.85
840	1171	5.666969	TTGTAATCGTTGACAACCTCTTG	57.333	39.130	12.66	0.00	30.72	3.02
841	1172	3.496884	TGTAATCGTTGACAACCTCTTGC	59.503	43.478	12.66	7.73	0.00	4.01
842	1173	1.523758	ATCGTTGACAACCTCTTGCC	58.476	50.000	12.66	0.00	0.00	4.52
843	1174	0.468226	TCGTTGACAACCTCTTGCCT	59.532	50.000	12.66	0.00	0.00	4.75
844	1175	1.689813	TCGTTGACAACCTCTTGCCTA	59.310	47.619	12.66	0.00	0.00	3.93
845	1176	1.798813	CGTTGACAACCTCTTGCCTAC	59.201	52.381	12.66	0.00	0.00	3.18
846	1177	2.548067	CGTTGACAACCTCTTGCCTACT	60.548	50.000	12.66	0.00	0.00	2.57
847	1178	3.477530	GTTGACAACCTCTTGCCTACTT	58.522	45.455	7.10	0.00	0.00	2.24
848	1179	3.857157	TGACAACCTCTTGCCTACTTT	57.143	42.857	0.00	0.00	0.00	2.66
849	1180	3.740115	TGACAACCTCTTGCCTACTTTC	58.260	45.455	0.00	0.00	0.00	2.62
850	1181	3.135712	TGACAACCTCTTGCCTACTTTCA	59.864	43.478	0.00	0.00	0.00	2.69
851	1182	3.477530	ACAACCTCTTGCCTACTTTCAC	58.522	45.455	0.00	0.00	0.00	3.18
852	1183	2.814336	CAACCTCTTGCCTACTTTCACC	59.186	50.000	0.00	0.00	0.00	4.02
853	1184	1.351350	ACCTCTTGCCTACTTTCACCC	59.649	52.381	0.00	0.00	0.00	4.61
854	1185	1.676014	CCTCTTGCCTACTTTCACCCG	60.676	57.143	0.00	0.00	0.00	5.28
855	1186	0.321298	TCTTGCCTACTTTCACCCGC	60.321	55.000	0.00	0.00	0.00	6.13
856	1187	0.605319	CTTGCCTACTTTCACCCGCA	60.605	55.000	0.00	0.00	0.00	5.69
857	1188	0.179015	TTGCCTACTTTCACCCGCAA	60.179	50.000	0.00	0.00	34.08	4.85
858	1189	0.179015	TGCCTACTTTCACCCGCAAA	60.179	50.000	0.00	0.00	0.00	3.68
859	1190	0.955905	GCCTACTTTCACCCGCAAAA	59.044	50.000	0.00	0.00	0.00	2.44
860	1191	1.338655	GCCTACTTTCACCCGCAAAAA	59.661	47.619	0.00	0.00	0.00	1.94
1017	1370	0.035439	AAATGGCTACCTCCACCACG	60.035	55.000	0.00	0.00	39.25	4.94
1059	1412	2.434884	CTCGCCACGCTCACCATT	60.435	61.111	0.00	0.00	0.00	3.16
1075	1428	1.134753	CCATTGCCGCTGCTGAAATAA	59.865	47.619	0.70	0.00	38.71	1.40
1503	1857	1.329292	TGTGCTGTTGTTGTTACTCGC	59.671	47.619	0.00	0.00	0.00	5.03
1506	1860	1.597663	GCTGTTGTTGTTACTCGCTGT	59.402	47.619	0.00	0.00	0.00	4.40
1515	1869	6.884187	TGTTGTTACTCGCTGTATTTTTCTC	58.116	36.000	0.00	0.00	0.00	2.87
1522	1876	2.093783	CGCTGTATTTTTCTCCGTCACC	59.906	50.000	0.00	0.00	0.00	4.02
1529	1883	3.655276	TTTTCTCCGTCACCTGAGTAC	57.345	47.619	0.00	0.00	0.00	2.73
1564	1918	6.237313	ACTACAAAATAAAGAGCGTGGTTC	57.763	37.500	0.00	0.00	0.00	3.62
1608	1962	8.852135	ACTTTTCCAATTAAACTTATCCACGAA	58.148	29.630	0.00	0.00	0.00	3.85
1636	1990	5.357032	ACAGTAAGCATGGCATAAAAGGTAC	59.643	40.000	0.00	0.00	0.00	3.34
1641	1995	3.490761	GCATGGCATAAAAGGTACGCATT	60.491	43.478	0.00	0.00	0.00	3.56
1675	2029	4.201990	ACCTAAGCATACTAGCACGTACAC	60.202	45.833	0.00	0.00	36.85	2.90
1682	2048	3.396260	ACTAGCACGTACACAACCATT	57.604	42.857	0.00	0.00	0.00	3.16
1736	2102	3.194968	ACGAGTAAACGAGGGATGAACAT	59.805	43.478	0.00	0.00	37.03	2.71
2100	2475	2.557490	GTGAACCGAACTAGGTCACTCT	59.443	50.000	8.85	0.00	45.21	3.24
2373	2755	3.599285	TTCGGCTCGTTCCCGCAAT	62.599	57.895	6.34	0.00	45.19	3.56

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
11	12	2.929592	GCTTCATGCAGCAGAAAAAGGG	60.930	50.000	12.75	0.00	42.31	3.95
32	33	1.491563	GGCGACGTGTAGCACTTTG	59.508	57.895	7.39	0.00	32.66	2.77
35	36	4.415332	CGGGCGACGTGTAGCACT	62.415	66.667	5.82	0.00	37.93	4.40
49	56	3.130633	TCTTTTCATATCATCACGCGGG	58.869	45.455	12.47	6.51	0.00	6.13
53	60	6.018751	ACGGTCAATCTTTTCATATCATCACG	60.019	38.462	0.00	0.00	0.00	4.35
54	61	7.225538	AGACGGTCAATCTTTTCATATCATCAC	59.774	37.037	11.27	0.00	0.00	3.06
67	74	3.243234	CGATCTGCTAGACGGTCAATCTT	60.243	47.826	11.27	0.00	0.00	2.40
68	75	2.292016	CGATCTGCTAGACGGTCAATCT	59.708	50.000	11.27	0.00	0.00	2.40
69	76	2.033550	ACGATCTGCTAGACGGTCAATC	59.966	50.000	11.27	0.00	0.00	2.67
70	77	2.025155	ACGATCTGCTAGACGGTCAAT	58.975	47.619	11.27	0.00	0.00	2.57
71	78	1.460504	ACGATCTGCTAGACGGTCAA	58.539	50.000	11.27	0.00	0.00	3.18
81	88	1.071385	GGATCCATCCAACGATCTGCT	59.929	52.381	6.95	0.00	46.38	4.24
119	137	1.337728	TGTTACATGGACTGGCACTCG	60.338	52.381	0.00	0.00	0.00	4.18
141	159	1.276421	AGGATGAGCGCAACACTAACT	59.724	47.619	11.47	3.59	0.00	2.24
171	189	3.136626	AGGGTGTTTTGTAGCAAGACTCT	59.863	43.478	4.60	0.00	0.00	3.24
205	223	3.018149	GCAATGGTTTATAACGGGGTGA	58.982	45.455	0.00	0.00	0.00	4.02
216	234	8.668510	AATATTTGTGTTGTTGCAATGGTTTA	57.331	26.923	0.59	0.00	0.00	2.01
351	373	1.623081	CGTTGATTGGACGACCCACG	61.623	60.000	0.34	0.00	46.62	4.94
369	391	0.042708	CCACTACCGTACGATCGTCG	60.043	60.000	26.48	24.80	46.93	5.12
393	415	2.979197	CTCTTCGCGGGTGTCGACT	61.979	63.158	17.92	0.00	42.43	4.18
404	426	0.809241	CACCTGGCTGATCTCTTCGC	60.809	60.000	0.00	0.00	0.00	4.70
538	560	7.119116	ACACATACATGCTATTGTTCTTCGAAA	59.881	33.333	0.00	0.00	0.00	3.46
582	604	7.778083	TCTATGTCTAAAAATCTTACGCTGGA	58.222	34.615	0.00	0.00	0.00	3.86
625	647	7.163441	TGTTATCCTCGGCTAATAATTTACCC	58.837	38.462	0.00	0.00	0.00	3.69
671	695	5.127845	AGAAAAATGAGCTGAGTCGGATCTA	59.872	40.000	17.69	5.45	0.00	1.98
717	741	6.260050	GGCGTGAGGATGATAAATTTAGTTGA	59.740	38.462	3.94	0.00	0.00	3.18
729	753	7.336931	GGTAATTTATATTGGCGTGAGGATGAT	59.663	37.037	0.00	0.00	0.00	2.45
776	800	7.087007	TCTGATGTTAATTGTTTTATGCGCAA	58.913	30.769	17.11	0.11	0.00	4.85
777	801	6.616017	TCTGATGTTAATTGTTTTATGCGCA	58.384	32.000	14.96	14.96	0.00	6.09
778	802	7.684062	ATCTGATGTTAATTGTTTTATGCGC	57.316	32.000	0.00	0.00	0.00	6.09
803	1134	7.391148	ACGATTACAAATGGAACTGCTAAAT	57.609	32.000	0.00	0.00	0.00	1.40
811	1142	5.627780	GGTTGTCAACGATTACAAATGGAAC	59.372	40.000	9.57	0.00	37.35	3.62
831	1162	2.814336	GGTGAAAGTAGGCAAGAGGTTG	59.186	50.000	0.00	0.00	36.67	3.77
834	1165	1.676014	CGGGTGAAAGTAGGCAAGAGG	60.676	57.143	0.00	0.00	0.00	3.69
835	1166	1.726853	CGGGTGAAAGTAGGCAAGAG	58.273	55.000	0.00	0.00	0.00	2.85
836	1167	0.321298	GCGGGTGAAAGTAGGCAAGA	60.321	55.000	0.00	0.00	0.00	3.02
837	1168	0.605319	TGCGGGTGAAAGTAGGCAAG	60.605	55.000	0.00	0.00	0.00	4.01
838	1169	0.179015	TTGCGGGTGAAAGTAGGCAA	60.179	50.000	0.00	0.00	37.98	4.52
839	1170	0.179015	TTTGCGGGTGAAAGTAGGCA	60.179	50.000	0.00	0.00	0.00	4.75
840	1171	0.955905	TTTTGCGGGTGAAAGTAGGC	59.044	50.000	0.00	0.00	0.00	3.93
864	1195	6.075315	ACCATTAAGTAGGCAAGAGGTTTTT	58.925	36.000	0.00	0.00	0.00	1.94
865	1196	5.641155	ACCATTAAGTAGGCAAGAGGTTTT	58.359	37.500	0.00	0.00	0.00	2.43
866	1197	5.256806	ACCATTAAGTAGGCAAGAGGTTT	57.743	39.130	0.00	0.00	0.00	3.27
867	1198	4.929146	ACCATTAAGTAGGCAAGAGGTT	57.071	40.909	0.00	0.00	0.00	3.50
868	1199	5.030820	AGTACCATTAAGTAGGCAAGAGGT	58.969	41.667	0.00	0.00	0.00	3.85
869	1200	5.615925	AGTACCATTAAGTAGGCAAGAGG	57.384	43.478	0.00	0.00	0.00	3.69
870	1201	6.985059	GGTTAGTACCATTAAGTAGGCAAGAG	59.015	42.308	0.00	0.00	44.36	2.85
871	1202	6.406177	CGGTTAGTACCATTAAGTAGGCAAGA	60.406	42.308	0.00	0.00	45.31	3.02
872	1203	5.751990	CGGTTAGTACCATTAAGTAGGCAAG	59.248	44.000	0.00	0.00	45.31	4.01
873	1204	5.187576	ACGGTTAGTACCATTAAGTAGGCAA	59.812	40.000	0.00	0.00	45.31	4.52
874	1205	4.711355	ACGGTTAGTACCATTAAGTAGGCA	59.289	41.667	0.00	0.00	45.31	4.75
875	1206	5.268118	ACGGTTAGTACCATTAAGTAGGC	57.732	43.478	0.00	0.00	45.31	3.93
1017	1370	3.453070	GAGACAGGAGATGGCGGCC	62.453	68.421	13.32	13.32	44.27	6.13
1027	1380	1.610327	CGAGGAGGAGGAGACAGGA	59.390	63.158	0.00	0.00	0.00	3.86
1059	1412	1.656818	GCCTTATTTCAGCAGCGGCA	61.657	55.000	12.44	0.00	44.61	5.69
1188	1541	4.988598	CTGAGGCGGCGGTTGTGT	62.989	66.667	9.78	0.00	0.00	3.72
1243	1596	0.249911	GTGAACACGAGCTGGACCTT	60.250	55.000	1.44	0.00	0.00	3.50
1281	1634	4.394712	CCGGAGGCGACCTGCTTT	62.395	66.667	13.64	0.00	46.14	3.51
1453	1806	1.469126	GGAGCGCACATACGTACACG	61.469	60.000	11.47	0.00	46.33	4.49
1503	1857	4.566004	TCAGGTGACGGAGAAAAATACAG	58.434	43.478	0.00	0.00	0.00	2.74
1515	1869	1.446907	AGTACGTACTCAGGTGACGG	58.553	55.000	22.45	0.00	40.84	4.79
1522	1876	4.681835	AGTTGCACTAGTACGTACTCAG	57.318	45.455	30.53	24.60	37.73	3.35
1529	1883	8.918658	TCTTTATTTTGTAGTTGCACTAGTACG	58.081	33.333	0.00	0.00	30.12	3.67
1545	1899	5.460646	ACATGAACCACGCTCTTTATTTTG	58.539	37.500	0.00	0.00	0.00	2.44
1546	1900	5.705609	ACATGAACCACGCTCTTTATTTT	57.294	34.783	0.00	0.00	0.00	1.82
1554	1908	1.234821	TTCCAACATGAACCACGCTC	58.765	50.000	0.00	0.00	0.00	5.03
1564	1918	8.411318	GGAAAAGTGCTAATATTTCCAACATG	57.589	34.615	10.41	0.00	46.43	3.21
1595	1949	7.604927	TGCTTACTGTTTATTCGTGGATAAGTT	59.395	33.333	0.00	0.00	0.00	2.66
1608	1962	7.124147	ACCTTTTATGCCATGCTTACTGTTTAT	59.876	33.333	0.00	0.00	0.00	1.40
1641	1995	6.401047	AGTATGCTTAGGTATCGCTACAAA	57.599	37.500	0.00	0.00	0.00	2.83
1675	2029	3.853831	TGTGCTGCTCATAAATGGTTG	57.146	42.857	0.00	0.00	0.00	3.77
1682	2048	3.006859	AGCCGTATATGTGCTGCTCATAA	59.993	43.478	23.26	12.83	33.23	1.90
2033	2408	3.193691	CCGTCATCTACTGTTCCTCACTT	59.806	47.826	0.00	0.00	0.00	3.16
2237	2615	1.862602	GACTTGCGTTGCCGGGATTT	61.863	55.000	2.18	0.00	33.68	2.17
2386	2771	4.379143	CGCCTCGTCACGACACGA	62.379	66.667	10.83	11.95	46.42	4.35

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.