AutoCloner

Multiple sequence alignment - TraesCS5D01G436500

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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	TraesCS5D01G436500	chr5D	100.000	2037	0	0	1	2037	490974470	490972434	0.000000e+00	3762.0
1	TraesCS5D01G436500	chr5D	100.000	345	0	0	2402	2746	490972069	490971725	2.980000e-179	638.0
2	TraesCS5D01G436500	chr5D	84.615	247	38	0	1315	1561	491787088	491787334	2.110000e-61	246.0
3	TraesCS5D01G436500	chr5D	83.562	219	26	7	967	1179	491786783	491786997	2.160000e-46	196.0
4	TraesCS5D01G436500	chr5D	80.894	246	47	0	1316	1561	491679308	491679553	7.760000e-46	195.0
5	TraesCS5D01G436500	chr5D	87.857	140	5	3	1516	1649	490972889	490972756	1.320000e-33	154.0
6	TraesCS5D01G436500	chr5D	87.857	140	5	3	1582	1715	490972955	490972822	1.320000e-33	154.0
7	TraesCS5D01G436500	chr5B	93.202	1265	60	10	465	1715	605527331	605526079	0.000000e+00	1836.0
8	TraesCS5D01G436500	chr5B	93.536	526	26	3	1516	2035	605526146	605525623	0.000000e+00	776.0
9	TraesCS5D01G436500	chr5B	87.432	366	23	12	2402	2746	605525536	605525173	1.530000e-107	399.0
10	TraesCS5D01G436500	chr5B	93.204	206	8	2	1516	1715	605526212	605526007	5.750000e-77	298.0
11	TraesCS5D01G436500	chr5B	85.657	251	29	4	126	371	605527631	605527383	9.760000e-65	257.0
12	TraesCS5D01G436500	chr5B	84.000	250	37	2	1315	1561	606843418	606843667	1.270000e-58	237.0
13	TraesCS5D01G436500	chr5B	83.806	247	40	0	1315	1561	606835241	606835487	4.570000e-58	235.0
14	TraesCS5D01G436500	chr5B	81.513	238	44	0	1316	1553	606813999	606814236	2.160000e-46	196.0
15	TraesCS5D01G436500	chr5B	85.263	190	22	3	993	1179	606834949	606835135	1.000000e-44	191.0
16	TraesCS5D01G436500	chr5B	76.601	406	57	28	801	1183	606813431	606813821	3.610000e-44	189.0
17	TraesCS5D01G436500	chr5B	92.537	134	4	2	1582	1715	605526278	605526151	1.300000e-43	187.0
18	TraesCS5D01G436500	chr5B	80.995	221	30	6	967	1179	606843096	606843312	6.080000e-37	165.0
19	TraesCS5D01G436500	chr5B	88.571	140	4	2	1516	1649	605526074	605525941	2.830000e-35	159.0
20	TraesCS5D01G436500	chr5B	87.903	124	9	3	1	118	605529312	605529189	1.030000e-29	141.0
21	TraesCS5D01G436500	chr5A	85.648	1289	108	28	1	1230	613463268	613461998	0.000000e+00	1284.0
22	TraesCS5D01G436500	chr5A	94.824	425	16	1	1291	1715	613461980	613461562	0.000000e+00	658.0
23	TraesCS5D01G436500	chr5A	85.830	247	35	0	1315	1561	614359107	614359353	2.100000e-66	263.0
24	TraesCS5D01G436500	chr5A	92.442	172	7	1	1516	1687	613461689	613461524	9.830000e-60	241.0
25	TraesCS5D01G436500	chr5A	92.029	138	5	2	1578	1715	613461759	613461628	3.610000e-44	189.0
26	TraesCS5D01G436500	chr5A	80.488	246	48	0	1316	1561	614232062	614232307	3.610000e-44	189.0
27	TraesCS5D01G436500	chr5A	98.058	103	2	0	1517	1619	613461622	613461520	2.170000e-41	180.0
28	TraesCS5D01G436500	chr5A	90.244	123	6	2	1913	2035	613461125	613461009	3.660000e-34	156.0
29	TraesCS5D01G436500	chr5A	87.654	81	9	1	2468	2547	21416736	21416656	2.910000e-15	93.5
30	TraesCS5D01G436500	chr4D	75.446	224	37	13	237	453	88516074	88516286	2.910000e-15	93.5
31	TraesCS5D01G436500	chr3A	79.612	103	19	2	2466	2567	487423505	487423404	3.790000e-09	73.1
32	TraesCS5D01G436500	chr3A	85.938	64	8	1	2481	2543	747649937	747650000	1.760000e-07	67.6
33	TraesCS5D01G436500	chr4B	85.938	64	8	1	2484	2546	662088084	662088021	1.760000e-07	67.6
34	TraesCS5D01G436500	chr2A	85.938	64	8	1	2484	2546	659909756	659909693	1.760000e-07	67.6
35	TraesCS5D01G436500	chr6A	88.679	53	6	0	2508	2560	321924895	321924843	6.350000e-07	65.8
36	TraesCS5D01G436500	chr3B	84.375	64	9	1	2484	2546	804537289	804537226	8.210000e-06	62.1
37	TraesCS5D01G436500	chr2D	85.000	60	7	2	2509	2566	11771522	11771463	2.950000e-05	60.2

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	TraesCS5D01G436500	chr5D	490971725	490974470	2745	True	1177.000000	3762	93.92850	1	2746	4	chr5D.!!$R1	2745
1	TraesCS5D01G436500	chr5D	491786783	491787334	551	False	221.000000	246	84.08850	967	1561	2	chr5D.!!$F2	594
2	TraesCS5D01G436500	chr5B	605525173	605529312	4139	True	506.625000	1836	90.25525	1	2746	8	chr5B.!!$R1	2745
3	TraesCS5D01G436500	chr5B	606834949	606835487	538	False	213.000000	235	84.53450	993	1561	2	chr5B.!!$F2	568
4	TraesCS5D01G436500	chr5B	606843096	606843667	571	False	201.000000	237	82.49750	967	1561	2	chr5B.!!$F3	594
5	TraesCS5D01G436500	chr5A	613461009	613463268	2259	True	451.333333	1284	92.20750	1	2035	6	chr5A.!!$R2	2034

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
682	2286	0.670546	GCAGGCACGTCATGTACACT	60.671	55.0	0.0	0.0	0.0	3.55	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2582	4599	0.250727	TGCTTTTTCCCGGTCTCTGG	60.251	55.0	0.0	0.0	0.0	3.86	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
109	116	6.439375	AGTTGTTTTAAAGAAAAGGGAGTGGT	59.561	34.615	0.00	0.00	35.21	4.16
118	125	4.041321	AGAAAAGGGAGTGGTTAGGTGTAC	59.959	45.833	0.00	0.00	0.00	2.90
120	127	1.203100	AGGGAGTGGTTAGGTGTACGT	60.203	52.381	0.00	0.00	0.00	3.57
121	128	1.203287	GGGAGTGGTTAGGTGTACGTC	59.797	57.143	0.00	0.00	0.00	4.34
122	129	2.165998	GGAGTGGTTAGGTGTACGTCT	58.834	52.381	0.00	0.00	0.00	4.18
123	130	2.094854	GGAGTGGTTAGGTGTACGTCTG	60.095	54.545	0.00	0.00	0.00	3.51
124	131	2.816087	GAGTGGTTAGGTGTACGTCTGA	59.184	50.000	0.00	0.00	0.00	3.27
137	1694	6.347160	GGTGTACGTCTGATGGAAACTTAAAC	60.347	42.308	2.50	0.00	0.00	2.01
148	1705	5.379187	TGGAAACTTAAACTGGGTTAGTCC	58.621	41.667	0.00	0.00	39.18	3.85
217	1793	2.352032	CCTCCCGACGGCTTCTTCT	61.352	63.158	8.86	0.00	0.00	2.85
225	1801	2.391389	CGGCTTCTTCTCCAACCGC	61.391	63.158	0.00	0.00	33.46	5.68
324	1902	1.541310	CCTCCACTCAACCGCTACCA	61.541	60.000	0.00	0.00	0.00	3.25
361	1939	1.074775	CCCCCGACCATCCCTCTAA	60.075	63.158	0.00	0.00	0.00	2.10
368	1946	1.384082	CCATCCCTCTAACCCCGGT	60.384	63.158	0.00	0.00	0.00	5.28
374	1952	1.146263	CTCTAACCCCGGTGATGGC	59.854	63.158	0.00	0.00	0.00	4.40
375	1953	2.192175	CTAACCCCGGTGATGGCC	59.808	66.667	0.00	0.00	0.00	5.36
405	1984	2.917227	CAAACCTGCACCACCCCC	60.917	66.667	0.00	0.00	0.00	5.40
433	2012	4.142271	GCCCTAAGATAGATGATGGAGTCG	60.142	50.000	0.00	0.00	0.00	4.18
478	2057	3.452786	CTTCTCCGGCGAGCTCCA	61.453	66.667	9.30	0.00	35.94	3.86
484	2063	2.279784	CGGCGAGCTCCATCCTTC	60.280	66.667	8.47	0.00	0.00	3.46
485	2064	2.790791	CGGCGAGCTCCATCCTTCT	61.791	63.158	8.47	0.00	0.00	2.85
486	2065	1.524482	GGCGAGCTCCATCCTTCTT	59.476	57.895	8.47	0.00	0.00	2.52
492	2093	1.064832	AGCTCCATCCTTCTTTCTGGC	60.065	52.381	0.00	0.00	0.00	4.85
506	2107	2.743636	TCTGGCTGTTAGTTCCTTCG	57.256	50.000	0.00	0.00	0.00	3.79
541	2144	9.527157	TTGACTGACCCAAATTATAAATTCAGA	57.473	29.630	6.87	0.00	34.58	3.27
544	2147	9.308000	ACTGACCCAAATTATAAATTCAGACAA	57.692	29.630	6.87	0.00	34.58	3.18
547	2150	8.980143	ACCCAAATTATAAATTCAGACAAACG	57.020	30.769	0.00	0.00	0.00	3.60
561	2164	6.495706	TCAGACAAACGTACATCTAGCTATG	58.504	40.000	0.00	0.00	0.00	2.23
570	2174	6.150318	CGTACATCTAGCTATGGTGTAAAGG	58.850	44.000	14.16	6.87	0.00	3.11
589	2193	9.567776	TGTAAAGGAAAAACAGAGATGATAACA	57.432	29.630	0.00	0.00	0.00	2.41
617	2221	7.147742	TGGAGATTATACTCAACATGTAGTGCA	60.148	37.037	10.89	0.00	38.51	4.57
682	2286	0.670546	GCAGGCACGTCATGTACACT	60.671	55.000	0.00	0.00	0.00	3.55
686	2290	1.278238	GCACGTCATGTACACTAGCC	58.722	55.000	0.00	0.00	0.00	3.93
751	2355	4.082354	AGACCGCGTCAGACTAAACTAAAT	60.082	41.667	4.92	0.00	34.60	1.40
757	2361	6.534934	GCGTCAGACTAAACTAAATTTCCTG	58.465	40.000	0.00	0.00	0.00	3.86
762	2366	9.449719	TCAGACTAAACTAAATTTCCTGAATCC	57.550	33.333	0.00	0.00	32.79	3.01
1064	2680	4.803908	CGCCTTCCTCCCCTTGCC	62.804	72.222	0.00	0.00	0.00	4.52
1212	2831	3.566351	TCTCCTTCGGATTCATGCTCTA	58.434	45.455	0.00	0.00	0.00	2.43
1226	2845	2.509569	TGCTCTATTTGCCCACGAAAA	58.490	42.857	0.00	0.00	0.00	2.29
1228	2847	3.128589	TGCTCTATTTGCCCACGAAAATC	59.871	43.478	0.00	0.00	0.00	2.17
1241	2860	3.430218	CACGAAAATCTGACCTGTCACTC	59.570	47.826	0.00	0.00	35.46	3.51
1269	2888	6.035112	CACAACTAAGCTTAGAGAATCGTTCC	59.965	42.308	34.65	0.00	42.67	3.62
1272	2891	6.508777	ACTAAGCTTAGAGAATCGTTCCATC	58.491	40.000	34.65	0.00	42.67	3.51
1436	3125	2.202987	GGCAGCGATCAGGTCCAG	60.203	66.667	0.00	0.00	0.00	3.86
1573	3262	1.134901	CACCGTCCTCGTCTTCTCG	59.865	63.158	0.00	0.00	35.01	4.04
1687	3514	3.951769	CTCCTTGGCTTGCCCCTGG	62.952	68.421	9.35	8.48	0.00	4.45
1789	3616	3.930848	CCAAGTACCGACTATGTTGTTCC	59.069	47.826	0.00	0.00	33.58	3.62
1814	3641	0.937699	TTGCTAGTCACGTCGTGCAC	60.938	55.000	20.56	17.64	32.98	4.57
1824	3651	2.048597	TCGTGCACGGTGTGATCC	60.049	61.111	36.41	0.00	40.29	3.36
1825	3652	2.356913	CGTGCACGGTGTGATCCA	60.357	61.111	31.15	0.00	35.23	3.41
1838	3665	0.530288	TGATCCATCGCACTGTTCGA	59.470	50.000	4.82	4.82	40.45	3.71
1848	3675	2.880822	CACTGTTCGATTCGTGCATT	57.119	45.000	5.89	0.00	0.00	3.56
1900	3727	2.223782	TGCTGTCCAACACAAGCAATTC	60.224	45.455	0.00	0.00	36.68	2.17
1907	3734	7.215789	TGTCCAACACAAGCAATTCATTATTT	58.784	30.769	0.00	0.00	29.30	1.40
1938	3938	3.853330	CACGCAGTCGATTGGCCG	61.853	66.667	10.16	8.08	41.61	6.13
1950	3950	3.126171	TCGATTGGCCGTTTTAGATGTTG	59.874	43.478	0.00	0.00	0.00	3.33
1959	3959	4.979815	CCGTTTTAGATGTTGGTTGTTTCC	59.020	41.667	0.00	0.00	0.00	3.13
2035	4035	3.127030	GCATCACAGTTTAACCAGCCTAC	59.873	47.826	0.00	0.00	0.00	3.18
2469	4469	6.759827	ACAAATATAACCGTGTGTCTACATCC	59.240	38.462	0.00	0.00	39.39	3.51
2477	4477	3.060761	CGTGTGTCTACATCCAAATCACG	59.939	47.826	0.00	0.00	39.39	4.35
2486	4486	5.059404	ACATCCAAATCACGAACCATTTC	57.941	39.130	0.00	0.00	0.00	2.17
2490	4490	3.574614	CAAATCACGAACCATTTCCACC	58.425	45.455	0.00	0.00	0.00	4.61
2534	4535	8.356657	AGATCTTCGAAACTAGATCCTATGTTG	58.643	37.037	17.33	0.00	45.05	3.33
2585	4602	5.931441	AAACTGAATCGAGAAAAGACCAG	57.069	39.130	0.00	0.00	0.00	4.00
2593	4610	0.977395	AGAAAAGACCAGAGACCGGG	59.023	55.000	6.32	0.00	0.00	5.73
2651	4669	3.429684	GGAAAACCGAAAACAAGGAAGCA	60.430	43.478	0.00	0.00	0.00	3.91
2659	4677	5.285651	CGAAAACAAGGAAGCATGGTTTTA	58.714	37.500	12.13	0.00	40.55	1.52
2661	4679	5.869649	AAACAAGGAAGCATGGTTTTACT	57.130	34.783	12.13	7.97	0.00	2.24
2662	4680	5.869649	AACAAGGAAGCATGGTTTTACTT	57.130	34.783	12.13	13.17	0.00	2.24
2665	4683	6.280643	ACAAGGAAGCATGGTTTTACTTTTC	58.719	36.000	12.13	0.00	0.00	2.29
2666	4684	6.127196	ACAAGGAAGCATGGTTTTACTTTTCA	60.127	34.615	12.13	0.00	0.00	2.69
2667	4685	5.842907	AGGAAGCATGGTTTTACTTTTCAC	58.157	37.500	12.13	0.00	0.00	3.18
2669	4687	5.221441	GGAAGCATGGTTTTACTTTTCACCT	60.221	40.000	12.13	0.00	0.00	4.00
2702	4720	3.070429	CACACAGGTGCTTTCACTTTC	57.930	47.619	0.00	0.00	42.72	2.62
2713	4731	1.593196	TTCACTTTCGGGAAGCACAG	58.407	50.000	0.00	0.00	39.04	3.66
2722	4740	1.944024	CGGGAAGCACAGTTGTGTTTA	59.056	47.619	13.20	0.00	46.83	2.01
2724	4742	3.548014	CGGGAAGCACAGTTGTGTTTAAG	60.548	47.826	13.20	5.63	46.83	1.85
2742	4760	2.450609	AGCGTAAAGTACACCTGTGG	57.549	50.000	1.91	0.00	34.19	4.17

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
83	90	7.616542	ACCACTCCCTTTTCTTTAAAACAACTA	59.383	33.333	0.00	0.00	31.37	2.24
109	116	4.525487	AGTTTCCATCAGACGTACACCTAA	59.475	41.667	0.00	0.00	0.00	2.69
118	125	4.154195	CCCAGTTTAAGTTTCCATCAGACG	59.846	45.833	0.00	0.00	0.00	4.18
120	127	5.319043	ACCCAGTTTAAGTTTCCATCAGA	57.681	39.130	0.00	0.00	0.00	3.27
121	128	6.715264	ACTAACCCAGTTTAAGTTTCCATCAG	59.285	38.462	0.00	0.00	31.59	2.90
122	129	6.607019	ACTAACCCAGTTTAAGTTTCCATCA	58.393	36.000	0.00	0.00	31.59	3.07
123	130	6.150641	GGACTAACCCAGTTTAAGTTTCCATC	59.849	42.308	0.00	0.00	37.72	3.51
124	131	6.008331	GGACTAACCCAGTTTAAGTTTCCAT	58.992	40.000	0.00	0.00	37.72	3.41
137	1694	4.265073	CTGGAAAGAATGGACTAACCCAG	58.735	47.826	0.00	0.00	39.97	4.45
148	1705	0.391130	TCCGACGGCTGGAAAGAATG	60.391	55.000	9.66	0.00	30.98	2.67
225	1801	2.519302	GCCATTGATCCGTGGGGG	60.519	66.667	13.54	0.00	36.00	5.40
299	1875	2.266055	GTTGAGTGGAGGGCGGAG	59.734	66.667	0.00	0.00	0.00	4.63
300	1876	3.319198	GGTTGAGTGGAGGGCGGA	61.319	66.667	0.00	0.00	0.00	5.54
310	1888	0.250166	GTGGTTGGTAGCGGTTGAGT	60.250	55.000	0.00	0.00	0.00	3.41
402	1981	1.059913	CTATCTTAGGGCTGTGGGGG	58.940	60.000	0.00	0.00	0.00	5.40
404	1983	3.242867	TCATCTATCTTAGGGCTGTGGG	58.757	50.000	0.00	0.00	0.00	4.61
405	1984	4.323333	CCATCATCTATCTTAGGGCTGTGG	60.323	50.000	0.00	0.00	0.00	4.17
410	1989	4.142271	CGACTCCATCATCTATCTTAGGGC	60.142	50.000	0.00	0.00	0.00	5.19
433	2012	2.485657	GGTCTATCTTAAGGTGGCAGGC	60.486	54.545	1.85	0.00	0.00	4.85
443	2022	2.769602	AGCCTCCGGGTCTATCTTAA	57.230	50.000	0.00	0.00	34.45	1.85
478	2057	4.917906	ACTAACAGCCAGAAAGAAGGAT	57.082	40.909	0.00	0.00	0.00	3.24
484	2063	3.433615	CGAAGGAACTAACAGCCAGAAAG	59.566	47.826	0.00	0.00	38.49	2.62
485	2064	3.399330	CGAAGGAACTAACAGCCAGAAA	58.601	45.455	0.00	0.00	38.49	2.52
486	2065	2.870435	GCGAAGGAACTAACAGCCAGAA	60.870	50.000	0.00	0.00	38.49	3.02
492	2093	2.631418	TCGAGCGAAGGAACTAACAG	57.369	50.000	0.00	0.00	38.49	3.16
506	2107	2.151202	TGGGTCAGTCAAATTTCGAGC	58.849	47.619	0.00	0.00	0.00	5.03
541	2144	5.105473	ACACCATAGCTAGATGTACGTTTGT	60.105	40.000	0.00	0.00	0.00	2.83
544	2147	6.704289	TTACACCATAGCTAGATGTACGTT	57.296	37.500	11.93	0.00	0.00	3.99
547	2150	7.286215	TCCTTTACACCATAGCTAGATGTAC	57.714	40.000	11.93	0.00	0.00	2.90
561	2164	6.877611	TCATCTCTGTTTTTCCTTTACACC	57.122	37.500	0.00	0.00	0.00	4.16
570	2174	8.950210	TCTCCATTGTTATCATCTCTGTTTTTC	58.050	33.333	0.00	0.00	0.00	2.29
589	2193	9.770097	CACTACATGTTGAGTATAATCTCCATT	57.230	33.333	14.37	0.00	33.93	3.16
591	2195	7.147742	TGCACTACATGTTGAGTATAATCTCCA	60.148	37.037	14.37	0.00	33.93	3.86
682	2286	1.229177	TCCACCTGTGCTCTGGCTA	60.229	57.895	11.20	0.00	39.59	3.93
686	2290	1.202687	TCTTTGTCCACCTGTGCTCTG	60.203	52.381	0.00	0.00	0.00	3.35
751	2355	3.181429	ACAAAGCAGGAGGATTCAGGAAA	60.181	43.478	0.00	0.00	0.00	3.13
757	2361	4.442706	TCGATAACAAAGCAGGAGGATTC	58.557	43.478	0.00	0.00	0.00	2.52
762	2366	3.706698	TCGATCGATAACAAAGCAGGAG	58.293	45.455	15.15	0.00	0.00	3.69
975	2584	3.743396	AGATCGAGCAACTCAAACTGAAC	59.257	43.478	2.38	0.00	0.00	3.18
1045	2661	2.269241	CAAGGGGAGGAAGGCGAC	59.731	66.667	0.00	0.00	0.00	5.19
1167	2786	5.878406	ATGGAGTTGATTGAGTACCTAGG	57.122	43.478	7.41	7.41	0.00	3.02
1212	2831	2.231235	GGTCAGATTTTCGTGGGCAAAT	59.769	45.455	0.00	0.00	0.00	2.32
1226	2845	0.900182	TGCGGAGTGACAGGTCAGAT	60.900	55.000	1.66	0.00	40.75	2.90
1228	2847	1.373497	GTGCGGAGTGACAGGTCAG	60.373	63.158	1.66	0.00	40.75	3.51
1241	2860	3.232213	TCTCTAAGCTTAGTTGTGCGG	57.768	47.619	28.31	13.33	32.61	5.69
1451	3140	1.374758	GCAGACGAACCACCTCCTG	60.375	63.158	0.00	0.00	0.00	3.86
1489	3178	2.016318	CGTTGAGCTTCATGCCCATAA	58.984	47.619	0.00	0.00	44.23	1.90
1573	3262	1.279840	GCGGCGAGGATTGTATTGC	59.720	57.895	12.98	0.00	0.00	3.56
1762	3589	4.978083	ACATAGTCGGTACTTGGTACAG	57.022	45.455	9.56	6.03	42.39	2.74
1763	3590	4.523943	ACAACATAGTCGGTACTTGGTACA	59.476	41.667	9.56	0.00	40.41	2.90
1789	3616	1.125021	CGACGTGACTAGCAAAAGCAG	59.875	52.381	0.00	0.00	0.00	4.24
1814	3641	1.153568	AGTGCGATGGATCACACCG	60.154	57.895	4.52	0.00	39.90	4.94
1824	3651	0.992072	ACGAATCGAACAGTGCGATG	59.008	50.000	17.62	8.36	46.67	3.84
1907	3734	4.150980	CGACTGCGTGTGGTAATTCTAAAA	59.849	41.667	0.00	0.00	0.00	1.52
1916	3916	0.389296	CCAATCGACTGCGTGTGGTA	60.389	55.000	0.00	0.00	37.58	3.25
1938	3938	8.192110	TGTAAGGAAACAACCAACATCTAAAAC	58.808	33.333	0.00	0.00	0.00	2.43
1950	3950	6.084326	ACACATGAATGTAAGGAAACAACC	57.916	37.500	0.00	0.00	39.39	3.77
2433	4433	8.202137	ACACGGTTATATTTGTGCTATAAGACT	58.798	33.333	0.00	0.00	35.79	3.24
2445	4445	6.759356	TGGATGTAGACACACGGTTATATTTG	59.241	38.462	0.00	0.00	37.54	2.32
2469	4469	3.005261	TGGTGGAAATGGTTCGTGATTTG	59.995	43.478	0.00	0.00	34.28	2.32
2490	4490	0.523072	CTCAACGCAGGAACCCAATG	59.477	55.000	0.00	0.00	0.00	2.82
2534	4535	8.575649	TGGAAAAAGAATGGTCTAAACCTATC	57.424	34.615	0.00	0.00	46.60	2.08
2573	4590	1.066787	CCCGGTCTCTGGTCTTTTCTC	60.067	57.143	0.00	0.00	0.00	2.87
2582	4599	0.250727	TGCTTTTTCCCGGTCTCTGG	60.251	55.000	0.00	0.00	0.00	3.86
2585	4602	3.120792	GTTTTTGCTTTTTCCCGGTCTC	58.879	45.455	0.00	0.00	0.00	3.36
2713	4731	5.903530	GGTGTACTTTACGCTTAAACACAAC	59.096	40.000	14.62	10.14	39.11	3.32
2722	4740	2.103601	ACCACAGGTGTACTTTACGCTT	59.896	45.455	0.00	0.00	39.11	4.68
2724	4742	2.159327	ACCACAGGTGTACTTTACGC	57.841	50.000	0.00	0.00	32.98	4.42

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.