AutoCloner

Multiple sequence alignment - TraesCS2D01G376500

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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	TraesCS2D01G376500	chr2D	100.000	2693	0	0	1	2693	480772257	480769565	0.000000e+00	4974.0
1	TraesCS2D01G376500	chr2D	97.436	819	19	1	623	1441	73845028	73844212	0.000000e+00	1395.0
2	TraesCS2D01G376500	chr2D	97.194	499	14	0	1437	1935	73835464	73834966	0.000000e+00	845.0
3	TraesCS2D01G376500	chr2D	95.545	202	8	1	1735	1936	73844829	73845029	3.340000e-84	322.0
4	TraesCS2D01G376500	chr2D	95.050	202	9	1	1735	1935	480771434	480771635	1.560000e-82	316.0
5	TraesCS2D01G376500	chr2D	96.875	32	1	0	2019	2050	80107417	80107386	1.000000e-03	54.7
6	TraesCS2D01G376500	chr1D	97.563	1313	30	2	623	1935	254634661	254635971	0.000000e+00	2246.0
7	TraesCS2D01G376500	chr1D	97.358	265	7	0	358	622	416602294	416602030	4.090000e-123	451.0
8	TraesCS2D01G376500	chr1D	95.567	203	9	0	1735	1937	254634861	254634659	2.590000e-85	326.0
9	TraesCS2D01G376500	chr3D	97.180	1312	34	3	623	1934	601614756	601616064	0.000000e+00	2215.0
10	TraesCS2D01G376500	chr3D	97.378	267	7	0	356	622	40488236	40487970	3.160000e-124	455.0
11	TraesCS2D01G376500	chr3D	82.222	495	58	12	1446	1939	438468667	438469132	1.500000e-107	399.0
12	TraesCS2D01G376500	chr3D	88.785	321	31	4	623	941	438468058	438468375	3.250000e-104	388.0
13	TraesCS2D01G376500	chr3D	90.123	81	8	0	1396	1476	438468645	438468725	3.670000e-19	106.0
14	TraesCS2D01G376500	chr4A	91.629	1314	47	9	622	1935	161398340	161397090	0.000000e+00	1759.0
15	TraesCS2D01G376500	chr4A	93.235	340	16	4	939	1275	596223764	596223429	6.700000e-136	494.0
16	TraesCS2D01G376500	chr4A	97.004	267	8	0	356	622	713978254	713977988	1.470000e-122	449.0
17	TraesCS2D01G376500	chr2B	92.744	634	30	3	2075	2693	563861368	563860736	0.000000e+00	902.0
18	TraesCS2D01G376500	chr2B	87.784	352	23	12	2	340	563861877	563861533	6.990000e-106	394.0
19	TraesCS2D01G376500	chr2B	88.474	321	34	3	623	941	31069045	31068726	4.210000e-103	385.0
20	TraesCS2D01G376500	chr2A	88.188	618	55	9	1953	2555	623548456	623547842	0.000000e+00	721.0
21	TraesCS2D01G376500	chr2A	88.816	304	13	7	3	289	623548809	623548510	1.190000e-93	353.0
22	TraesCS2D01G376500	chr2A	94.483	145	7	1	2550	2693	623547785	623547641	3.490000e-54	222.0
23	TraesCS2D01G376500	chr2A	91.111	45	3	1	2020	2063	52742030	52741986	2.900000e-05	60.2
24	TraesCS2D01G376500	chr7D	84.924	524	67	12	1418	1935	139187813	139187296	1.110000e-143	520.0
25	TraesCS2D01G376500	chr7D	97.004	267	8	0	356	622	154397485	154397751	1.470000e-122	449.0
26	TraesCS2D01G376500	chr7D	89.062	320	32	3	623	941	346098764	346098447	6.990000e-106	394.0
27	TraesCS2D01G376500	chr7D	96.875	32	1	0	2019	2050	95064743	95064774	1.000000e-03	54.7
28	TraesCS2D01G376500	chr4B	94.379	338	16	2	939	1275	13285158	13284823	1.430000e-142	516.0
29	TraesCS2D01G376500	chr4B	82.913	515	69	9	1431	1935	649179002	649179507	1.900000e-121	446.0
30	TraesCS2D01G376500	chr4B	100.000	30	0	0	2022	2051	25962542	25962571	3.750000e-04	56.5
31	TraesCS2D01G376500	chr4D	96.284	296	8	2	980	1275	7417593	7417301	1.450000e-132	483.0
32	TraesCS2D01G376500	chr4D	98.127	267	5	0	356	622	228617568	228617834	1.460000e-127	466.0
33	TraesCS2D01G376500	chrUn	98.113	265	5	0	358	622	42712376	42712640	1.890000e-126	462.0
34	TraesCS2D01G376500	chrUn	98.113	265	5	0	358	622	42713764	42714028	1.890000e-126	462.0
35	TraesCS2D01G376500	chrUn	98.113	265	5	0	358	622	329559586	329559850	1.890000e-126	462.0
36	TraesCS2D01G376500	chrUn	98.113	265	5	0	358	622	329972644	329972908	1.890000e-126	462.0
37	TraesCS2D01G376500	chrUn	100.000	30	0	0	2021	2050	92722828	92722799	3.750000e-04	56.5
38	TraesCS2D01G376500	chr7B	88.750	320	33	3	623	941	688921493	688921176	3.250000e-104	388.0
39	TraesCS2D01G376500	chr1B	88.750	320	32	4	623	941	175273531	175273215	3.250000e-104	388.0
40	TraesCS2D01G376500	chr1B	100.000	30	0	0	2021	2050	44083243	44083214	3.750000e-04	56.5
41	TraesCS2D01G376500	chr6D	86.667	60	7	1	1305	1364	2781561	2781619	6.220000e-07	65.8
42	TraesCS2D01G376500	chr6D	96.875	32	1	0	2019	2050	59626109	59626140	1.000000e-03	54.7
43	TraesCS2D01G376500	chr6A	86.667	60	7	1	1305	1364	1760307	1760365	6.220000e-07	65.8
44	TraesCS2D01G376500	chr6A	96.875	32	1	0	2019	2050	75913642	75913673	1.000000e-03	54.7
45	TraesCS2D01G376500	chr3B	100.000	30	0	0	2021	2050	667650242	667650271	3.750000e-04	56.5
46	TraesCS2D01G376500	chr3B	100.000	28	0	0	2023	2050	690878927	690878900	5.000000e-03	52.8
47	TraesCS2D01G376500	chr7A	96.875	32	1	0	2019	2050	510625413	510625382	1.000000e-03	54.7

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	TraesCS2D01G376500	chr2D	480769565	480772257	2692	True	4974.000000	4974	100.000000	1	2693	1	chr2D.!!$R4	2692
1	TraesCS2D01G376500	chr2D	73844212	73845028	816	True	1395.000000	1395	97.436000	623	1441	1	chr2D.!!$R2	818
2	TraesCS2D01G376500	chr1D	254634661	254635971	1310	False	2246.000000	2246	97.563000	623	1935	1	chr1D.!!$F1	1312
3	TraesCS2D01G376500	chr3D	601614756	601616064	1308	False	2215.000000	2215	97.180000	623	1934	1	chr3D.!!$F1	1311
4	TraesCS2D01G376500	chr3D	438468058	438469132	1074	False	297.666667	399	87.043333	623	1939	3	chr3D.!!$F2	1316
5	TraesCS2D01G376500	chr4A	161397090	161398340	1250	True	1759.000000	1759	91.629000	622	1935	1	chr4A.!!$R1	1313
6	TraesCS2D01G376500	chr2B	563860736	563861877	1141	True	648.000000	902	90.264000	2	2693	2	chr2B.!!$R2	2691
7	TraesCS2D01G376500	chr2A	623547641	623548809	1168	True	432.000000	721	90.495667	3	2693	3	chr2A.!!$R2	2690
8	TraesCS2D01G376500	chr7D	139187296	139187813	517	True	520.000000	520	84.924000	1418	1935	1	chr7D.!!$R1	517
9	TraesCS2D01G376500	chr4B	649179002	649179507	505	False	446.000000	446	82.913000	1431	1935	1	chr4B.!!$F2	504
10	TraesCS2D01G376500	chrUn	42712376	42714028	1652	False	462.000000	462	98.113000	358	622	2	chrUn.!!$F3	264

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
294	329	0.17668	GCATCATCCACGGTCTCTGT	59.823	55.0	0.0	0.0	0.0	3.41	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1760	2709	0.165944	GTCCAGATTTTGCCGACGTG	59.834	55.0	0.0	0.0	0.0	4.49	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
22	23	1.986882	CTTGTTTGTCAAGGCCTCCT	58.013	50.000	5.23	0.00	46.85	3.69
23	24	1.882623	CTTGTTTGTCAAGGCCTCCTC	59.117	52.381	5.23	0.00	46.85	3.71
24	25	0.250295	TGTTTGTCAAGGCCTCCTCG	60.250	55.000	5.23	0.00	30.89	4.63
25	26	1.302511	TTTGTCAAGGCCTCCTCGC	60.303	57.895	5.23	0.00	30.89	5.03
104	119	2.425124	CACCGTCTTTTGTGCGCG	60.425	61.111	0.00	0.00	0.00	6.86
163	188	0.754587	ACGTATCCTCGGTTCCCTCC	60.755	60.000	0.00	0.00	34.94	4.30
206	232	4.987285	CAGTCAATCTCTGGATTATGGACG	59.013	45.833	0.00	0.00	39.87	4.79
229	264	9.507280	GACGTGTATAATTTGTTACTACTGCTA	57.493	33.333	0.00	0.00	0.00	3.49
254	289	3.443681	ACTGCATTATTCGTCCTTTTGGG	59.556	43.478	0.00	0.00	40.87	4.12
286	321	1.300465	CCTCGGAGCATCATCCACG	60.300	63.158	0.00	0.00	39.53	4.94
289	324	1.592669	CGGAGCATCATCCACGGTC	60.593	63.158	0.00	0.00	39.53	4.79
290	325	1.826024	GGAGCATCATCCACGGTCT	59.174	57.895	0.00	0.00	39.34	3.85
292	327	0.749649	GAGCATCATCCACGGTCTCT	59.250	55.000	0.00	0.00	33.17	3.10
293	328	0.463204	AGCATCATCCACGGTCTCTG	59.537	55.000	0.00	0.00	0.00	3.35
294	329	0.176680	GCATCATCCACGGTCTCTGT	59.823	55.000	0.00	0.00	0.00	3.41
295	330	1.931906	CATCATCCACGGTCTCTGTG	58.068	55.000	2.15	2.15	37.09	3.66
305	340	3.125316	CACGGTCTCTGTGAAAAATAGCC	59.875	47.826	2.94	0.00	39.73	3.93
307	342	3.372206	CGGTCTCTGTGAAAAATAGCCTG	59.628	47.826	0.00	0.00	0.00	4.85
350	385	9.213777	ACAAGTAAATATGAATGAGAGGGAGTA	57.786	33.333	0.00	0.00	0.00	2.59
377	412	1.303561	GCTGGTCACAATGGGCAGA	60.304	57.895	0.00	0.00	0.00	4.26
410	445	5.402997	AGTAACCTACACAGTTTCCTAGC	57.597	43.478	0.00	0.00	0.00	3.42
516	551	1.044611	TGGAGTGTGTGATGTTCCGA	58.955	50.000	0.00	0.00	0.00	4.55
543	578	3.268023	AGCTAGTTATCACAAGCACCC	57.732	47.619	0.00	0.00	37.44	4.61
682	1303	6.735130	GTTTGCAGAAAACACTAGGTTACAT	58.265	36.000	0.00	0.00	46.30	2.29
737	1358	4.217754	TCTTGTTGCAAATAACACCGAC	57.782	40.909	0.00	0.00	40.04	4.79
811	1432	0.179181	GACGTGGCATAACGACTCGA	60.179	55.000	5.20	0.00	46.49	4.04
945	1568	3.706373	ACGCGAGCAGAACCCCAT	61.706	61.111	15.93	0.00	0.00	4.00
1378	2302	0.867086	CAAGGCGGGCAACAATTTTG	59.133	50.000	3.78	0.00	39.74	2.44
1379	2303	0.755686	AAGGCGGGCAACAATTTTGA	59.244	45.000	3.78	0.00	39.74	2.69
1388	2312	4.749598	GGGCAACAATTTTGATTTCGAACT	59.250	37.500	0.00	0.00	39.74	3.01
1664	2596	1.542108	CCATGAGAAAGGGGATCGAGC	60.542	57.143	0.00	0.00	0.00	5.03
1673	2605	1.566231	AGGGGATCGAGCAGGAATTTT	59.434	47.619	1.84	0.00	0.00	1.82
1676	2608	2.550978	GGATCGAGCAGGAATTTTCGA	58.449	47.619	1.84	0.00	44.88	3.71
1757	2706	1.726265	GTCTCGGCCGAGTCGTTAT	59.274	57.895	44.61	0.00	42.49	1.89
1758	2707	0.591741	GTCTCGGCCGAGTCGTTATG	60.592	60.000	44.61	24.92	42.49	1.90
1759	2708	1.944676	CTCGGCCGAGTCGTTATGC	60.945	63.158	40.77	7.37	37.47	3.14
1760	2709	2.960129	CGGCCGAGTCGTTATGCC	60.960	66.667	24.07	17.51	38.74	4.40
1761	2710	2.185867	GGCCGAGTCGTTATGCCA	59.814	61.111	21.15	0.00	41.76	4.92
1762	2711	2.171725	GGCCGAGTCGTTATGCCAC	61.172	63.158	21.15	0.10	41.76	5.01
1763	2712	2.514013	GCCGAGTCGTTATGCCACG	61.514	63.158	12.31	0.00	41.78	4.94
1764	2713	1.153901	CCGAGTCGTTATGCCACGT	60.154	57.895	12.31	0.00	41.16	4.49
1765	2714	1.138047	CCGAGTCGTTATGCCACGTC	61.138	60.000	12.31	0.00	41.16	4.34
1766	2715	1.461317	CGAGTCGTTATGCCACGTCG	61.461	60.000	3.82	0.00	41.16	5.12
1767	2716	1.138047	GAGTCGTTATGCCACGTCGG	61.138	60.000	0.00	0.00	41.16	4.79
1855	2804	4.520111	TGCAACAAGATTACACAAGATGCT	59.480	37.500	0.00	0.00	0.00	3.79
1865	2814	8.531982	AGATTACACAAGATGCTGTACTTTCTA	58.468	33.333	0.00	0.00	0.00	2.10
1940	2889	3.153369	TCTTGCAATTTACTCTGCCCA	57.847	42.857	0.00	0.00	37.79	5.36
1941	2890	3.700538	TCTTGCAATTTACTCTGCCCAT	58.299	40.909	0.00	0.00	37.79	4.00
1942	2891	4.088634	TCTTGCAATTTACTCTGCCCATT	58.911	39.130	0.00	0.00	37.79	3.16
1943	2892	3.872511	TGCAATTTACTCTGCCCATTG	57.127	42.857	0.00	0.00	37.79	2.82
1944	2893	3.164268	TGCAATTTACTCTGCCCATTGT	58.836	40.909	0.00	0.00	37.79	2.71
1945	2894	3.056678	TGCAATTTACTCTGCCCATTGTG	60.057	43.478	0.00	0.00	37.79	3.33
1946	2895	3.193267	GCAATTTACTCTGCCCATTGTGA	59.807	43.478	0.00	0.00	32.18	3.58
1947	2896	4.737054	CAATTTACTCTGCCCATTGTGAC	58.263	43.478	0.00	0.00	0.00	3.67
1948	2897	2.489938	TTACTCTGCCCATTGTGACC	57.510	50.000	0.00	0.00	0.00	4.02
1949	2898	1.357137	TACTCTGCCCATTGTGACCA	58.643	50.000	0.00	0.00	0.00	4.02
1950	2899	0.037303	ACTCTGCCCATTGTGACCAG	59.963	55.000	0.00	0.00	0.00	4.00
1951	2900	1.303561	TCTGCCCATTGTGACCAGC	60.304	57.895	0.00	0.00	0.00	4.85
1952	2901	2.283101	TGCCCATTGTGACCAGCC	60.283	61.111	0.00	0.00	0.00	4.85
1953	2902	2.036256	GCCCATTGTGACCAGCCT	59.964	61.111	0.00	0.00	0.00	4.58
1954	2903	1.302949	GCCCATTGTGACCAGCCTA	59.697	57.895	0.00	0.00	0.00	3.93
1955	2904	0.323360	GCCCATTGTGACCAGCCTAA	60.323	55.000	0.00	0.00	0.00	2.69
1956	2905	1.686115	GCCCATTGTGACCAGCCTAAT	60.686	52.381	0.00	0.00	0.00	1.73
1957	2906	2.422803	GCCCATTGTGACCAGCCTAATA	60.423	50.000	0.00	0.00	0.00	0.98
1958	2907	3.214328	CCCATTGTGACCAGCCTAATAC	58.786	50.000	0.00	0.00	0.00	1.89
1959	2908	3.371487	CCCATTGTGACCAGCCTAATACA	60.371	47.826	0.00	0.00	0.00	2.29
1971	2920	3.895656	AGCCTAATACAGCGTTCCAGATA	59.104	43.478	0.00	0.00	0.00	1.98
1989	2938	6.498651	TCCAGATAAAGGTCTTCAGACTTCTT	59.501	38.462	6.91	0.53	44.20	2.52
1998	2947	6.070309	AGGTCTTCAGACTTCTTTATGAGCAT	60.070	38.462	6.91	0.00	44.20	3.79
2008	2957	0.599991	TTATGAGCATGCGGCCTACG	60.600	55.000	13.01	0.00	46.50	3.51
2023	2972	0.454600	CTACGCTTCGGCAGGACTTA	59.545	55.000	0.00	0.00	41.88	2.24
2024	2973	1.067212	CTACGCTTCGGCAGGACTTAT	59.933	52.381	0.00	0.00	41.88	1.73
2025	2974	1.108776	ACGCTTCGGCAGGACTTATA	58.891	50.000	0.00	0.00	41.88	0.98
2026	2975	1.202382	ACGCTTCGGCAGGACTTATAC	60.202	52.381	0.00	0.00	41.88	1.47
2028	2977	2.745102	GCTTCGGCAGGACTTATACTC	58.255	52.381	0.00	0.00	41.33	2.59
2030	2979	1.700955	TCGGCAGGACTTATACTCCC	58.299	55.000	0.00	0.00	0.00	4.30
2032	2981	1.614413	CGGCAGGACTTATACTCCCTC	59.386	57.143	0.00	0.00	0.00	4.30
2033	2982	1.972075	GGCAGGACTTATACTCCCTCC	59.028	57.143	0.00	0.00	0.00	4.30
2034	2983	1.614413	GCAGGACTTATACTCCCTCCG	59.386	57.143	0.00	0.00	0.00	4.63
2035	2984	2.946785	CAGGACTTATACTCCCTCCGT	58.053	52.381	0.00	0.00	0.00	4.69
2036	2985	2.885894	CAGGACTTATACTCCCTCCGTC	59.114	54.545	0.00	0.00	0.00	4.79
2037	2986	2.158490	AGGACTTATACTCCCTCCGTCC	60.158	54.545	0.00	0.00	39.68	4.79
2038	2987	2.237643	GACTTATACTCCCTCCGTCCC	58.762	57.143	0.00	0.00	0.00	4.46
2039	2988	1.572415	ACTTATACTCCCTCCGTCCCA	59.428	52.381	0.00	0.00	0.00	4.37
2043	2992	1.961133	TACTCCCTCCGTCCCAAAAT	58.039	50.000	0.00	0.00	0.00	1.82
2044	2993	1.961133	ACTCCCTCCGTCCCAAAATA	58.039	50.000	0.00	0.00	0.00	1.40
2046	2995	2.645797	ACTCCCTCCGTCCCAAAATAAA	59.354	45.455	0.00	0.00	0.00	1.40
2049	2998	3.010808	TCCCTCCGTCCCAAAATAAATGT	59.989	43.478	0.00	0.00	0.00	2.71
2069	3022	7.588497	AATGTTATTTTAGGATGGAGGAAGC	57.412	36.000	0.00	0.00	0.00	3.86
2118	3111	6.761714	TCTTGTTTCTTCAGAACTTCAGGTAC	59.238	38.462	0.00	0.00	33.13	3.34
2147	3140	4.225942	TCCTATCAGAAGCATTGGTTGAGT	59.774	41.667	5.71	0.00	0.00	3.41
2189	3191	3.245300	TGAGGAGCTACTGTACCTGTCTT	60.245	47.826	0.99	0.00	32.53	3.01
2293	3295	2.002586	CATGATCGAGCCGACACTTTT	58.997	47.619	0.00	0.00	39.18	2.27
2352	3361	1.342174	TCAGACACGGGACCAAACTAC	59.658	52.381	0.00	0.00	0.00	2.73
2396	3405	2.621338	TCGACAATGCAGAATGTCTCC	58.379	47.619	20.89	3.90	42.93	3.71
2443	3452	5.414454	TGCCTCCATAAGTAACATCAAACAC	59.586	40.000	0.00	0.00	0.00	3.32
2453	3462	4.431416	AACATCAAACACCACCTGTCTA	57.569	40.909	0.00	0.00	30.29	2.59
2503	3512	1.790755	TTCGACATCAAACAGACCGG	58.209	50.000	0.00	0.00	0.00	5.28
2529	3538	7.201496	GCCATTCATTCATCAGACACATTTTTC	60.201	37.037	0.00	0.00	0.00	2.29
2602	3674	5.533533	ACGAATAGCTAGATACAGCGTAG	57.466	43.478	9.10	0.00	46.52	3.51

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
84	95	1.772063	GCGCACAAAAGACGGTGAGT	61.772	55.000	0.30	0.00	37.19	3.41
229	264	5.354234	CCAAAAGGACGAATAATGCAGTAGT	59.646	40.000	0.00	0.00	0.00	2.73
254	289	3.120165	GCTCCGAGGAAACAACTCAAATC	60.120	47.826	0.00	0.00	34.66	2.17
286	321	4.327680	ACAGGCTATTTTTCACAGAGACC	58.672	43.478	0.00	0.00	0.00	3.85
289	324	7.173218	TGTTTAGACAGGCTATTTTTCACAGAG	59.827	37.037	0.00	0.00	0.00	3.35
290	325	6.995686	TGTTTAGACAGGCTATTTTTCACAGA	59.004	34.615	0.00	0.00	0.00	3.41
292	327	7.575414	TTGTTTAGACAGGCTATTTTTCACA	57.425	32.000	0.00	0.00	37.04	3.58
293	328	9.476202	AATTTGTTTAGACAGGCTATTTTTCAC	57.524	29.630	0.00	0.00	37.04	3.18
332	367	5.401750	AGCAGTACTCCCTCTCATTCATAT	58.598	41.667	0.00	0.00	0.00	1.78
333	368	4.809193	AGCAGTACTCCCTCTCATTCATA	58.191	43.478	0.00	0.00	0.00	2.15
337	372	3.964031	CCTTAGCAGTACTCCCTCTCATT	59.036	47.826	0.00	0.00	0.00	2.57
340	375	1.684450	GCCTTAGCAGTACTCCCTCTC	59.316	57.143	0.00	0.00	39.53	3.20
341	376	1.289530	AGCCTTAGCAGTACTCCCTCT	59.710	52.381	0.00	0.00	43.56	3.69
350	385	0.764890	TTGTGACCAGCCTTAGCAGT	59.235	50.000	0.00	0.00	43.56	4.40
377	412	7.904205	ACTGTGTAGGTTACTAGCTTATGTTT	58.096	34.615	0.00	0.00	33.36	2.83
410	445	5.480772	CCCACTATGGAGGTAGTAACATAGG	59.519	48.000	13.22	4.60	44.29	2.57
532	567	0.687354	GAAGAGAGGGGTGCTTGTGA	59.313	55.000	0.00	0.00	0.00	3.58
543	578	6.543465	TGTGGCACATATTTAATGAAGAGAGG	59.457	38.462	17.96	0.00	44.52	3.69
811	1432	0.456221	CCATCTAACGCCGTCTCAGT	59.544	55.000	0.00	0.00	0.00	3.41
945	1568	3.916544	CGCTGGATCTGGCGGCTA	61.917	66.667	19.49	0.00	46.42	3.93
1378	2302	3.751621	CTGCCACATCAAGTTCGAAATC	58.248	45.455	0.00	0.00	0.00	2.17
1379	2303	2.095059	GCTGCCACATCAAGTTCGAAAT	60.095	45.455	0.00	0.00	0.00	2.17
1388	2312	3.364441	GCCACGCTGCCACATCAA	61.364	61.111	0.00	0.00	0.00	2.57
1425	2349	4.373116	GGACGAGCGCCAAGGACA	62.373	66.667	2.29	0.00	0.00	4.02
1664	2596	6.072508	TCCTTGTTTCTCATCGAAAATTCCTG	60.073	38.462	0.00	0.00	42.87	3.86
1673	2605	4.805719	CGATTCATCCTTGTTTCTCATCGA	59.194	41.667	0.00	0.00	0.00	3.59
1676	2608	6.409704	TCTTCGATTCATCCTTGTTTCTCAT	58.590	36.000	0.00	0.00	0.00	2.90
1759	2708	0.953471	TCCAGATTTTGCCGACGTGG	60.953	55.000	0.00	0.00	42.50	4.94
1760	2709	0.165944	GTCCAGATTTTGCCGACGTG	59.834	55.000	0.00	0.00	0.00	4.49
1761	2710	0.953960	GGTCCAGATTTTGCCGACGT	60.954	55.000	0.00	0.00	0.00	4.34
1762	2711	1.644786	GGGTCCAGATTTTGCCGACG	61.645	60.000	0.00	0.00	0.00	5.12
1763	2712	0.608035	TGGGTCCAGATTTTGCCGAC	60.608	55.000	0.00	0.00	0.00	4.79
1764	2713	0.608035	GTGGGTCCAGATTTTGCCGA	60.608	55.000	0.00	0.00	0.00	5.54
1765	2714	1.595093	GGTGGGTCCAGATTTTGCCG	61.595	60.000	0.00	0.00	35.97	5.69
1766	2715	0.251787	AGGTGGGTCCAGATTTTGCC	60.252	55.000	0.00	0.00	39.02	4.52
1767	2716	0.890683	CAGGTGGGTCCAGATTTTGC	59.109	55.000	0.00	0.00	39.02	3.68
1768	2717	2.162681	GACAGGTGGGTCCAGATTTTG	58.837	52.381	0.00	0.00	39.02	2.44
1769	2718	1.780309	TGACAGGTGGGTCCAGATTTT	59.220	47.619	0.00	0.00	36.97	1.82
1770	2719	1.073923	GTGACAGGTGGGTCCAGATTT	59.926	52.381	0.00	0.00	36.97	2.17
1771	2720	0.693049	GTGACAGGTGGGTCCAGATT	59.307	55.000	0.00	0.00	36.97	2.40
1940	2889	3.545703	GCTGTATTAGGCTGGTCACAAT	58.454	45.455	0.00	0.00	0.00	2.71
1941	2890	2.676750	CGCTGTATTAGGCTGGTCACAA	60.677	50.000	0.00	0.00	0.00	3.33
1942	2891	1.134818	CGCTGTATTAGGCTGGTCACA	60.135	52.381	0.00	0.00	0.00	3.58
1943	2892	1.134788	ACGCTGTATTAGGCTGGTCAC	60.135	52.381	0.00	0.00	0.00	3.67
1944	2893	1.191535	ACGCTGTATTAGGCTGGTCA	58.808	50.000	0.00	0.00	0.00	4.02
1945	2894	2.202566	GAACGCTGTATTAGGCTGGTC	58.797	52.381	0.00	0.00	0.00	4.02
1946	2895	1.134491	GGAACGCTGTATTAGGCTGGT	60.134	52.381	0.00	0.00	0.00	4.00
1947	2896	1.134521	TGGAACGCTGTATTAGGCTGG	60.135	52.381	0.00	0.00	0.00	4.85
1948	2897	2.159099	TCTGGAACGCTGTATTAGGCTG	60.159	50.000	0.00	0.00	0.00	4.85
1949	2898	2.108168	TCTGGAACGCTGTATTAGGCT	58.892	47.619	0.00	0.00	0.00	4.58
1950	2899	2.596904	TCTGGAACGCTGTATTAGGC	57.403	50.000	0.00	0.00	0.00	3.93
1951	2900	5.696724	CCTTTATCTGGAACGCTGTATTAGG	59.303	44.000	0.00	0.00	0.00	2.69
1952	2901	6.281405	ACCTTTATCTGGAACGCTGTATTAG	58.719	40.000	0.00	0.00	0.00	1.73
1953	2902	6.097839	AGACCTTTATCTGGAACGCTGTATTA	59.902	38.462	0.00	0.00	0.00	0.98
1954	2903	5.099042	ACCTTTATCTGGAACGCTGTATT	57.901	39.130	0.00	0.00	0.00	1.89
1955	2904	4.406003	AGACCTTTATCTGGAACGCTGTAT	59.594	41.667	0.00	0.00	0.00	2.29
1956	2905	3.767673	AGACCTTTATCTGGAACGCTGTA	59.232	43.478	0.00	0.00	0.00	2.74
1957	2906	2.567615	AGACCTTTATCTGGAACGCTGT	59.432	45.455	0.00	0.00	0.00	4.40
1958	2907	3.252974	AGACCTTTATCTGGAACGCTG	57.747	47.619	0.00	0.00	0.00	5.18
1959	2908	3.260884	TGAAGACCTTTATCTGGAACGCT	59.739	43.478	0.00	0.00	0.00	5.07
1971	2920	6.652900	GCTCATAAAGAAGTCTGAAGACCTTT	59.347	38.462	14.85	14.85	45.85	3.11
1989	2938	0.599991	CGTAGGCCGCATGCTCATAA	60.600	55.000	17.13	0.00	40.92	1.90
2008	2957	2.546162	GGAGTATAAGTCCTGCCGAAGC	60.546	54.545	0.00	0.00	34.81	3.86
2009	2958	2.036089	GGGAGTATAAGTCCTGCCGAAG	59.964	54.545	1.01	0.00	37.84	3.79
2010	2959	2.037144	GGGAGTATAAGTCCTGCCGAA	58.963	52.381	1.01	0.00	37.84	4.30
2012	2961	1.614413	GAGGGAGTATAAGTCCTGCCG	59.386	57.143	1.01	0.00	43.36	5.69
2013	2962	1.972075	GGAGGGAGTATAAGTCCTGCC	59.028	57.143	1.01	0.00	37.84	4.85
2015	2964	2.885894	GACGGAGGGAGTATAAGTCCTG	59.114	54.545	1.01	0.00	37.84	3.86
2017	2966	2.237643	GGACGGAGGGAGTATAAGTCC	58.762	57.143	0.00	0.00	39.63	3.85
2018	2967	2.237643	GGGACGGAGGGAGTATAAGTC	58.762	57.143	0.00	0.00	0.00	3.01
2023	2972	1.961133	TTTTGGGACGGAGGGAGTAT	58.039	50.000	0.00	0.00	0.00	2.12
2024	2973	1.961133	ATTTTGGGACGGAGGGAGTA	58.039	50.000	0.00	0.00	0.00	2.59
2025	2974	1.961133	TATTTTGGGACGGAGGGAGT	58.039	50.000	0.00	0.00	0.00	3.85
2026	2975	3.359695	TTTATTTTGGGACGGAGGGAG	57.640	47.619	0.00	0.00	0.00	4.30
2028	2977	3.361786	ACATTTATTTTGGGACGGAGGG	58.638	45.455	0.00	0.00	0.00	4.30
2030	2979	8.996024	AAAATAACATTTATTTTGGGACGGAG	57.004	30.769	13.37	0.00	36.22	4.63
2043	2992	9.131791	GCTTCCTCCATCCTAAAATAACATTTA	57.868	33.333	0.00	0.00	0.00	1.40
2044	2993	7.619302	TGCTTCCTCCATCCTAAAATAACATTT	59.381	33.333	0.00	0.00	0.00	2.32
2046	2995	6.547510	GTGCTTCCTCCATCCTAAAATAACAT	59.452	38.462	0.00	0.00	0.00	2.71
2049	2998	6.327386	AGTGCTTCCTCCATCCTAAAATAA	57.673	37.500	0.00	0.00	0.00	1.40
2056	3009	0.539051	CGAAGTGCTTCCTCCATCCT	59.461	55.000	6.38	0.00	36.27	3.24
2118	3111	2.975732	TGCTTCTGATAGGAGTGCTG	57.024	50.000	0.00	0.00	0.00	4.41
2147	3140	2.227149	CACAAGCTTCAAGCATGCAGTA	59.773	45.455	21.98	4.89	43.10	2.74
2189	3191	0.250234	GTGCCAGCAGTAGACCATCA	59.750	55.000	0.00	0.00	0.00	3.07
2232	3234	5.254901	ACAGTTGGGTGTTAAGTGTGTTAA	58.745	37.500	0.00	0.00	39.51	2.01
2293	3295	3.808728	CTGTTCCAGTCCAAACTTGAGA	58.191	45.455	0.00	0.00	31.71	3.27
2352	3361	7.465916	CGATTTTCTGATTGGTGTGTATAGTGG	60.466	40.741	0.00	0.00	0.00	4.00
2443	3452	3.627577	GTGGTTGCAATATAGACAGGTGG	59.372	47.826	0.59	0.00	0.00	4.61
2453	3462	4.018415	AGGTTAGAGTGGTGGTTGCAATAT	60.018	41.667	0.59	0.00	0.00	1.28
2503	3512	4.913335	ATGTGTCTGATGAATGAATGGC	57.087	40.909	0.00	0.00	0.00	4.40
2660	3732	5.360591	CGCTCTTCCTGTCAATATTTAGGT	58.639	41.667	9.03	0.00	0.00	3.08

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.