AutoCloner

Multiple sequence alignment - TraesCS2D01G221800

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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	TraesCS2D01G221800	chr2D	100.000	4016	0	0	1	4016	189283855	189287870	0.000000e+00	7417.0
1	TraesCS2D01G221800	chr2D	75.747	569	110	15	11	557	17619572	17619010	1.110000e-65	261.0
2	TraesCS2D01G221800	chr2D	78.141	398	63	15	11	390	17647320	17646929	8.680000e-57	231.0
3	TraesCS2D01G221800	chr2B	92.605	2975	175	23	1	2933	245296764	245299735	0.000000e+00	4233.0
4	TraesCS2D01G221800	chr2B	83.102	722	103	15	1153	1863	245129126	245129839	1.220000e-179	640.0
5	TraesCS2D01G221800	chr2B	89.228	492	36	11	3522	4008	245303433	245303912	2.070000e-167	599.0
6	TraesCS2D01G221800	chr2B	89.761	293	14	7	2930	3219	245299809	245300088	1.060000e-95	361.0
7	TraesCS2D01G221800	chr2B	83.457	405	45	9	2075	2460	245130051	245130452	1.370000e-94	357.0
8	TraesCS2D01G221800	chr2B	87.387	222	19	6	3311	3531	245302045	245302258	3.100000e-61	246.0
9	TraesCS2D01G221800	chr2B	97.727	44	1	0	3221	3264	245300203	245300246	4.300000e-10	76.8
10	TraesCS2D01G221800	chr2A	95.509	2093	59	11	772	2852	203226587	203228656	0.000000e+00	3312.0
11	TraesCS2D01G221800	chr2A	89.872	780	53	8	1	756	203194523	203195300	0.000000e+00	979.0
12	TraesCS2D01G221800	chr2A	88.652	564	22	12	2943	3483	203228696	203229240	0.000000e+00	649.0
13	TraesCS2D01G221800	chr2A	83.696	552	59	17	3467	4016	203244122	203244644	3.610000e-135	492.0
14	TraesCS2D01G221800	chr7B	79.458	1329	220	34	1153	2453	520416560	520417863	0.000000e+00	893.0
15	TraesCS2D01G221800	chr7B	82.222	180	32	0	2585	2764	520417621	520417800	5.370000e-34	156.0
16	TraesCS2D01G221800	chr4B	76.420	581	108	16	2	558	489395764	489396339	1.830000e-73	287.0
17	TraesCS2D01G221800	chr4B	78.892	379	66	9	1	366	500525638	500526015	1.110000e-60	244.0
18	TraesCS2D01G221800	chr3D	78.364	379	66	7	2	366	582747185	582747561	8.680000e-57	231.0
19	TraesCS2D01G221800	chr7D	74.903	518	104	15	68	562	329051949	329051435	3.140000e-51	213.0
20	TraesCS2D01G221800	chr7D	75.266	376	72	13	110	472	204146394	204146761	4.150000e-35	159.0
21	TraesCS2D01G221800	chr5A	81.707	246	41	4	2585	2828	546263467	546263710	6.810000e-48	202.0
22	TraesCS2D01G221800	chr5D	74.266	579	100	29	11	555	302328227	302327664	8.800000e-47	198.0
23	TraesCS2D01G221800	chr5D	97.143	35	1	0	3902	3936	536795844	536795878	4.330000e-05	60.2
24	TraesCS2D01G221800	chr5D	100.000	28	0	0	511	538	10763197	10763170	7.000000e-03	52.8
25	TraesCS2D01G221800	chr6D	81.221	213	35	4	2214	2422	414001421	414001632	2.480000e-37	167.0
26	TraesCS2D01G221800	chr6A	81.221	213	35	4	2214	2422	558982059	558982270	2.480000e-37	167.0
27	TraesCS2D01G221800	chr1D	79.424	243	45	5	2579	2818	481452613	481452373	2.480000e-37	167.0
28	TraesCS2D01G221800	chr1D	82.184	174	28	3	2583	2753	481552088	481552261	3.230000e-31	147.0
29	TraesCS2D01G221800	chr1D	81.714	175	29	3	2583	2754	481452350	481452176	4.180000e-30	143.0
30	TraesCS2D01G221800	chr1D	93.617	47	3	0	670	716	449286916	449286962	2.000000e-08	71.3
31	TraesCS2D01G221800	chr6B	80.660	212	38	2	2214	2422	623741034	623741245	1.160000e-35	161.0
32	TraesCS2D01G221800	chr6B	93.617	47	3	0	670	716	149150010	149149964	2.000000e-08	71.3
33	TraesCS2D01G221800	chr4A	75.493	355	71	8	11	351	101940805	101940453	4.150000e-35	159.0
34	TraesCS2D01G221800	chr1B	80.899	178	30	4	2583	2756	669924135	669924312	1.950000e-28	137.0
35	TraesCS2D01G221800	chr1B	90.909	44	4	0	673	716	51541428	51541385	4.330000e-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	TraesCS2D01G221800	chr2D	189283855	189287870	4015	False	7417.00	7417	100.0000	1	4016	1	chr2D.!!$F1	4015
1	TraesCS2D01G221800	chr2D	17619010	17619572	562	True	261.00	261	75.7470	11	557	1	chr2D.!!$R1	546
2	TraesCS2D01G221800	chr2B	245296764	245303912	7148	False	1103.16	4233	91.3416	1	4008	5	chr2B.!!$F2	4007
3	TraesCS2D01G221800	chr2B	245129126	245130452	1326	False	498.50	640	83.2795	1153	2460	2	chr2B.!!$F1	1307
4	TraesCS2D01G221800	chr2A	203226587	203229240	2653	False	1980.50	3312	92.0805	772	3483	2	chr2A.!!$F3	2711
5	TraesCS2D01G221800	chr2A	203194523	203195300	777	False	979.00	979	89.8720	1	756	1	chr2A.!!$F1	755
6	TraesCS2D01G221800	chr2A	203244122	203244644	522	False	492.00	492	83.6960	3467	4016	1	chr2A.!!$F2	549
7	TraesCS2D01G221800	chr7B	520416560	520417863	1303	False	524.50	893	80.8400	1153	2764	2	chr7B.!!$F1	1611
8	TraesCS2D01G221800	chr4B	489395764	489396339	575	False	287.00	287	76.4200	2	558	1	chr4B.!!$F1	556
9	TraesCS2D01G221800	chr7D	329051435	329051949	514	True	213.00	213	74.9030	68	562	1	chr7D.!!$R1	494

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
192	193	0.539986	GGTTGTCCTCGGCCATCTTA	59.460	55.000	2.24	0.00	2.10	F
1020	1076	0.539669	TGGAACTCACTCGCCTGAGA	60.540	55.000	14.13	45.57	3.27	F
1066	1122	1.214062	CTGCTCCTCTTCTCGCGTT	59.786	57.895	5.77	0.00	4.84	F
2478	2587	1.460273	CCTCCGCTCCTTCTCCTAGC	61.460	65.000	0.00	0.00	3.42	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1738	1802	0.527565	GGCGGAAGGTCACGTAGTTA	59.472	55.0	0.00	41.61	2.24	R
2527	2636	0.031994	ATGCAAACAAACGAGTGCCC	59.968	50.0	0.00	36.12	5.36	R
2529	2638	0.503961	GCATGCAAACAAACGAGTGC	59.496	50.0	14.21	37.51	4.40	R
3537	6836	2.715749	TGAAGATGTGGGGCTACATG	57.284	50.0	11.56	41.15	3.21	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
41	42	2.239150	ACGAGCCTACCTGTCTTCTCTA	59.761	50.000	0.00	0.00	0.00	2.43
46	47	3.572255	GCCTACCTGTCTTCTCTAGGATG	59.428	52.174	0.00	0.00	35.55	3.51
191	192	1.299976	GGTTGTCCTCGGCCATCTT	59.700	57.895	2.24	0.00	0.00	2.40
192	193	0.539986	GGTTGTCCTCGGCCATCTTA	59.460	55.000	2.24	0.00	0.00	2.10
193	194	1.653151	GTTGTCCTCGGCCATCTTAC	58.347	55.000	2.24	0.00	0.00	2.34
201	203	2.125269	GCCATCTTACCGCACCGT	60.125	61.111	0.00	0.00	0.00	4.83
392	423	2.406559	AGAGACGTAGACTAGGGCCTA	58.593	52.381	13.73	13.73	29.49	3.93
604	653	1.065272	AGAGAGGAGTAGACGGTCCAC	60.065	57.143	4.14	0.90	35.02	4.02
605	654	0.993470	AGAGGAGTAGACGGTCCACT	59.007	55.000	8.99	8.99	35.02	4.00
691	740	1.666888	GCCCAACAAGCAATTCGACTG	60.667	52.381	0.00	0.00	0.00	3.51
719	768	6.183360	CCAAAATTGGGGTTAGTCGATTAGAC	60.183	42.308	4.18	0.00	46.02	2.59
758	807	3.292460	ACAACCGAACCAAAAGAATGGA	58.708	40.909	0.00	0.00	43.54	3.41
770	819	6.494491	ACCAAAAGAATGGACATGAATCTCAA	59.506	34.615	0.00	0.00	43.54	3.02
787	836	0.725686	CAAAGCAGCATCTCGACTGG	59.274	55.000	0.00	0.00	34.38	4.00
806	855	6.432403	ACTGGCCCAAATTTAAAATTCAGA	57.568	33.333	0.00	0.00	0.00	3.27
827	876	2.143925	CGGCTTGGGTATAGCTAAAGC	58.856	52.381	23.28	23.28	41.95	3.51
850	900	5.049405	GCGAACTAATTCACATTATCCCCTG	60.049	44.000	0.00	0.00	34.14	4.45
929	979	0.760945	ACGATCCTCCATCCTGACCC	60.761	60.000	0.00	0.00	0.00	4.46
973	1024	1.534476	TACCCCTTGTGCTCGTCCA	60.534	57.895	0.00	0.00	0.00	4.02
977	1028	2.031012	CTTGTGCTCGTCCAGGCA	59.969	61.111	0.00	0.00	36.01	4.75
1020	1076	0.539669	TGGAACTCACTCGCCTGAGA	60.540	55.000	14.13	0.00	45.57	3.27
1066	1122	1.214062	CTGCTCCTCTTCTCGCGTT	59.786	57.895	5.77	0.00	0.00	4.84
1075	1131	3.512680	CTCTTCTCGCGTTCAGGTAATT	58.487	45.455	5.77	0.00	0.00	1.40
1570	1631	2.736682	GACGACCCCGATTGCGTTG	61.737	63.158	0.00	0.00	37.07	4.10
1738	1802	1.678598	CCAATGGCGCCATGGACATT	61.679	55.000	40.01	23.75	36.68	2.71
1814	1878	7.342284	GCCTCACCTACTATAGCCTATATGAAA	59.658	40.741	0.00	0.00	0.00	2.69
2478	2587	1.460273	CCTCCGCTCCTTCTCCTAGC	61.460	65.000	0.00	0.00	0.00	3.42
2517	2626	3.322254	GTCCGTCCAATACCTGATGATCT	59.678	47.826	0.00	0.00	0.00	2.75
2518	2627	3.574396	TCCGTCCAATACCTGATGATCTC	59.426	47.826	0.00	0.00	0.00	2.75
2519	2628	3.321968	CCGTCCAATACCTGATGATCTCA	59.678	47.826	0.00	0.00	0.00	3.27
2520	2629	4.302455	CGTCCAATACCTGATGATCTCAC	58.698	47.826	0.00	0.00	0.00	3.51
2521	2630	4.038522	CGTCCAATACCTGATGATCTCACT	59.961	45.833	0.00	0.00	0.00	3.41
2522	2631	5.295950	GTCCAATACCTGATGATCTCACTG	58.704	45.833	0.00	0.00	0.00	3.66
2523	2632	4.063689	CCAATACCTGATGATCTCACTGC	58.936	47.826	0.00	0.00	0.00	4.40
2524	2633	4.443881	CCAATACCTGATGATCTCACTGCA	60.444	45.833	0.00	0.00	0.00	4.41
2525	2634	2.687700	ACCTGATGATCTCACTGCAC	57.312	50.000	0.00	0.00	0.00	4.57
2526	2635	2.186243	ACCTGATGATCTCACTGCACT	58.814	47.619	0.00	0.00	0.00	4.40
2527	2636	2.093606	ACCTGATGATCTCACTGCACTG	60.094	50.000	0.00	0.00	0.00	3.66
2528	2637	2.552031	CTGATGATCTCACTGCACTGG	58.448	52.381	0.00	0.00	0.00	4.00
2529	2638	1.208776	TGATGATCTCACTGCACTGGG	59.791	52.381	0.00	0.00	0.00	4.45
2530	2639	0.107312	ATGATCTCACTGCACTGGGC	60.107	55.000	0.00	0.00	45.13	5.36
2751	2882	2.852413	CGCATTCAACGACTACTACCAG	59.148	50.000	0.00	0.00	0.00	4.00
2908	3056	4.887071	TCTTCGCATGGGCTGTTATTTAAT	59.113	37.500	4.59	0.00	38.10	1.40
2910	3058	5.181690	TCGCATGGGCTGTTATTTAATTC	57.818	39.130	4.59	0.00	38.10	2.17
2943	3168	4.669206	TGGACTGAACAATGCAATTTGT	57.331	36.364	0.00	0.00	41.49	2.83
3020	3245	1.761174	GGTCAAGGGCCTGAAGACA	59.239	57.895	25.77	0.52	0.00	3.41
3060	3299	3.891049	CAAAGACCAAAGGCTAGGCTAT	58.109	45.455	20.55	7.19	0.00	2.97
3103	3342	5.006455	TCAACGCTCTACTACTTCGTATCAG	59.994	44.000	0.00	0.00	32.71	2.90
3104	3343	4.440880	ACGCTCTACTACTTCGTATCAGT	58.559	43.478	0.00	0.00	0.00	3.41
3188	3434	3.926058	ACTAGGCGAATAAACCCATGT	57.074	42.857	0.00	0.00	0.00	3.21
3195	3441	4.157105	GGCGAATAAACCCATGTACTTTGT	59.843	41.667	0.00	0.00	0.00	2.83
3201	3447	2.985896	ACCCATGTACTTTGTGATCCG	58.014	47.619	0.00	0.00	0.00	4.18
3301	5244	0.674895	GAGCCGCCATCCACCATATC	60.675	60.000	0.00	0.00	0.00	1.63
3350	5461	1.007038	CAGGCTTGTGCGCAAACAT	60.007	52.632	14.00	4.22	40.82	2.71
3384	5495	0.242017	GCAGCCTCCACAACATTCAC	59.758	55.000	0.00	0.00	0.00	3.18
3388	5499	2.107204	AGCCTCCACAACATTCACTCTT	59.893	45.455	0.00	0.00	0.00	2.85
3428	5543	9.389755	GCTTCAAATTTATAGGGGCAATTTAAA	57.610	29.630	0.00	0.00	30.60	1.52
3468	5583	8.964420	ACCAAACATTGAATAAACACGATAAG	57.036	30.769	0.00	0.00	0.00	1.73
3475	5590	9.221775	CATTGAATAAACACGATAAGTTAAGGC	57.778	33.333	0.00	0.00	0.00	4.35
3520	5635	5.054390	GAATTTTAATTCAGGGCACGTCA	57.946	39.130	9.70	0.00	43.29	4.35
3537	6836	3.064931	CGTCACTTTCCTTTACTCCACC	58.935	50.000	0.00	0.00	0.00	4.61
3736	7035	9.321562	GTGTCTAACGAATAATGAATTAAGGGA	57.678	33.333	0.00	0.00	0.00	4.20
3755	7054	5.963214	GGGAGTTGGTATTACCCTAAAGA	57.037	43.478	10.37	0.00	37.50	2.52
3757	7056	6.354938	GGGAGTTGGTATTACCCTAAAGAAG	58.645	44.000	10.37	0.00	37.50	2.85
3817	7118	6.101332	TGCATAGAAATTGCAATGTTTCTCC	58.899	36.000	24.34	16.64	46.48	3.71
3829	7130	8.755696	TGCAATGTTTCTCCATATAAAAACAC	57.244	30.769	2.01	0.00	42.47	3.32
3897	7200	7.334421	ACGCATATATAGCATAAAACTTGAGGG	59.666	37.037	7.58	0.00	0.00	4.30
3899	7202	8.454106	GCATATATAGCATAAAACTTGAGGGTG	58.546	37.037	0.00	0.00	0.00	4.61
3905	7208	4.792704	GCATAAAACTTGAGGGTGTGTGTG	60.793	45.833	0.00	0.00	0.00	3.82
3907	7210	2.038387	AACTTGAGGGTGTGTGTGTC	57.962	50.000	0.00	0.00	0.00	3.67
3908	7211	1.204146	ACTTGAGGGTGTGTGTGTCT	58.796	50.000	0.00	0.00	0.00	3.41
3909	7212	2.394632	ACTTGAGGGTGTGTGTGTCTA	58.605	47.619	0.00	0.00	0.00	2.59
3910	7213	2.972713	ACTTGAGGGTGTGTGTGTCTAT	59.027	45.455	0.00	0.00	0.00	1.98
3911	7214	4.157246	ACTTGAGGGTGTGTGTGTCTATA	58.843	43.478	0.00	0.00	0.00	1.31
3912	7215	4.777896	ACTTGAGGGTGTGTGTGTCTATAT	59.222	41.667	0.00	0.00	0.00	0.86
3913	7216	5.248477	ACTTGAGGGTGTGTGTGTCTATATT	59.752	40.000	0.00	0.00	0.00	1.28
3992	7300	7.019774	TGCATCTCACAAGATTAAATAGTGC	57.980	36.000	0.00	0.00	40.38	4.40
3996	7304	5.580691	TCTCACAAGATTAAATAGTGCCACG	59.419	40.000	0.00	0.00	0.00	4.94
4002	7310	4.745125	AGATTAAATAGTGCCACGTGATCG	59.255	41.667	19.30	0.72	43.34	3.69

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
41	42	2.752030	TCATCTCGGGTTCTTCATCCT	58.248	47.619	0.00	0.00	0.00	3.24
46	47	2.315925	TGCATCATCTCGGGTTCTTC	57.684	50.000	0.00	0.00	0.00	2.87
196	197	3.414700	GTCGAAGGCAGCACGGTG	61.415	66.667	3.15	3.15	0.00	4.94
261	274	3.235481	TCCCCGTCGAAGGTGCAA	61.235	61.111	16.46	0.00	0.00	4.08
326	355	2.666862	CCACGCGTGCCCAAAGTA	60.667	61.111	33.17	0.00	0.00	2.24
351	380	2.456577	TGCAGTATGAGTGCTAGTCCA	58.543	47.619	7.73	0.00	44.61	4.02
438	472	0.533491	GTGCACATGGATGGCAATGT	59.467	50.000	13.17	0.00	37.50	2.71
441	475	2.979058	ATGTGCACATGGATGGCAA	58.021	47.368	30.92	0.00	36.33	4.52
559	607	6.535865	TCGCGAGTTATATATTCTCTCCTCTC	59.464	42.308	3.71	0.00	0.00	3.20
566	614	6.535865	TCCTCTCTCGCGAGTTATATATTCTC	59.464	42.308	33.33	0.00	38.45	2.87
571	619	5.149973	ACTCCTCTCTCGCGAGTTATATA	57.850	43.478	33.33	14.05	38.45	0.86
642	691	1.224592	CGCCTGTTAGCCTCCCAAT	59.775	57.895	0.00	0.00	0.00	3.16
644	693	2.284331	TCGCCTGTTAGCCTCCCA	60.284	61.111	0.00	0.00	0.00	4.37
719	768	6.036735	TCGGTTGTTTTCTCTGTTAGACTTTG	59.963	38.462	0.00	0.00	32.51	2.77
720	769	6.110707	TCGGTTGTTTTCTCTGTTAGACTTT	58.889	36.000	0.00	0.00	32.51	2.66
724	773	4.812626	GGTTCGGTTGTTTTCTCTGTTAGA	59.187	41.667	0.00	0.00	0.00	2.10
726	775	4.515361	TGGTTCGGTTGTTTTCTCTGTTA	58.485	39.130	0.00	0.00	0.00	2.41
758	807	4.270834	AGATGCTGCTTTGAGATTCATGT	58.729	39.130	0.00	0.00	0.00	3.21
770	819	1.449246	GCCAGTCGAGATGCTGCTT	60.449	57.895	0.00	0.00	0.00	3.91
787	836	4.092821	GCCGTCTGAATTTTAAATTTGGGC	59.907	41.667	4.32	9.09	0.00	5.36
806	855	2.484947	GCTTTAGCTATACCCAAGCCGT	60.485	50.000	13.79	0.00	41.02	5.68
827	876	5.049405	GCAGGGGATAATGTGAATTAGTTCG	60.049	44.000	0.00	0.00	37.15	3.95
850	900	2.104928	GCTTAAATGGCCGCCAGC	59.895	61.111	18.96	11.49	36.75	4.85
881	931	1.902918	TGGCACACCCTCACATTGC	60.903	57.895	0.00	0.00	33.59	3.56
973	1024	2.959030	TCTATTGCGTATCAGAGTGCCT	59.041	45.455	0.00	0.00	0.00	4.75
977	1028	4.142160	TGCTGTTCTATTGCGTATCAGAGT	60.142	41.667	0.00	0.00	0.00	3.24
1020	1076	2.408241	GGCGCAGAGTAGGACGAGT	61.408	63.158	10.83	0.00	0.00	4.18
1075	1131	7.458397	ACACCAACCTCAAGTCTATTTGATTA	58.542	34.615	0.00	0.00	36.55	1.75
1570	1631	2.456119	CGACACCTTCAGCGCATCC	61.456	63.158	11.47	0.00	0.00	3.51
1738	1802	0.527565	GGCGGAAGGTCACGTAGTTA	59.472	55.000	0.00	0.00	41.61	2.24
1784	1848	0.889306	CTATAGTAGGTGAGGCCGGC	59.111	60.000	21.18	21.18	43.70	6.13
2478	2587	5.418310	ACGGACAACAACTTAATTGACTG	57.582	39.130	0.00	0.00	41.23	3.51
2522	2631	1.724582	AACAAACGAGTGCCCAGTGC	61.725	55.000	0.00	0.00	41.77	4.40
2523	2632	0.738389	AAACAAACGAGTGCCCAGTG	59.262	50.000	0.00	0.00	0.00	3.66
2524	2633	0.738389	CAAACAAACGAGTGCCCAGT	59.262	50.000	0.00	0.00	0.00	4.00
2525	2634	0.594796	GCAAACAAACGAGTGCCCAG	60.595	55.000	0.00	0.00	0.00	4.45
2526	2635	1.315981	TGCAAACAAACGAGTGCCCA	61.316	50.000	0.00	0.00	36.12	5.36
2527	2636	0.031994	ATGCAAACAAACGAGTGCCC	59.968	50.000	0.00	0.00	36.12	5.36
2528	2637	1.130955	CATGCAAACAAACGAGTGCC	58.869	50.000	0.00	0.00	36.12	5.01
2529	2638	0.503961	GCATGCAAACAAACGAGTGC	59.496	50.000	14.21	0.00	37.51	4.40
2530	2639	1.837648	TGCATGCAAACAAACGAGTG	58.162	45.000	20.30	0.00	0.00	3.51
2531	2640	2.396601	CATGCATGCAAACAAACGAGT	58.603	42.857	26.68	0.00	0.00	4.18
2908	3056	6.227522	TGTTCAGTCCAAATACGAGAATGAA	58.772	36.000	0.00	0.00	40.93	2.57
2910	3058	6.480524	TTGTTCAGTCCAAATACGAGAATG	57.519	37.500	0.00	0.00	0.00	2.67
3003	3228	1.003580	TCATGTCTTCAGGCCCTTGAC	59.996	52.381	0.00	3.84	0.00	3.18
3020	3245	1.346395	TGCTACCAGTTGTCGGTTCAT	59.654	47.619	0.00	0.00	37.99	2.57
3060	3299	6.403200	GCGTTGAGTTCATTATTCCAAGCTAA	60.403	38.462	0.00	0.00	0.00	3.09
3188	3434	2.165167	AGACCGACGGATCACAAAGTA	58.835	47.619	23.38	0.00	0.00	2.24
3201	3447	5.076106	GCGTTATATAAGACGTAGACCGAC	58.924	45.833	8.37	0.00	41.10	4.79
3343	5454	3.119779	CCATTTGGCATTTCCATGTTTGC	60.120	43.478	0.00	0.00	46.04	3.68
3428	5543	8.584157	TCAATGTTTGGTTAGATTAAGCATTGT	58.416	29.630	18.40	0.00	45.25	2.71
3514	5629	3.493503	GTGGAGTAAAGGAAAGTGACGTG	59.506	47.826	0.00	0.00	0.00	4.49
3515	5630	3.493873	GGTGGAGTAAAGGAAAGTGACGT	60.494	47.826	0.00	0.00	0.00	4.34
3519	5634	4.398319	ACATGGTGGAGTAAAGGAAAGTG	58.602	43.478	0.00	0.00	0.00	3.16
3520	5635	4.724279	ACATGGTGGAGTAAAGGAAAGT	57.276	40.909	0.00	0.00	0.00	2.66
3537	6836	2.715749	TGAAGATGTGGGGCTACATG	57.284	50.000	11.56	0.00	41.15	3.21
3722	7021	9.856162	GGTAATACCAACTCCCTTAATTCATTA	57.144	33.333	4.24	0.00	38.42	1.90
3736	7035	7.460082	TCTTCCTTCTTTAGGGTAATACCAACT	59.540	37.037	12.03	2.72	44.86	3.16
3846	7147	9.813080	GTGTAAGTTGTATTGTCTTCTGAAATC	57.187	33.333	0.00	0.00	0.00	2.17
3851	7154	5.176774	TGCGTGTAAGTTGTATTGTCTTCTG	59.823	40.000	0.00	0.00	0.00	3.02
3853	7156	5.585500	TGCGTGTAAGTTGTATTGTCTTC	57.415	39.130	0.00	0.00	0.00	2.87
3881	7184	3.569701	CACACACCCTCAAGTTTTATGCT	59.430	43.478	0.00	0.00	0.00	3.79
3882	7185	3.317993	ACACACACCCTCAAGTTTTATGC	59.682	43.478	0.00	0.00	0.00	3.14
3897	7200	9.894783	CACTAGGTATAATATAGACACACACAC	57.105	37.037	0.00	0.00	0.00	3.82
3943	7251	8.971321	CATTTCATTTTTGTTTTGTCGAGAGAT	58.029	29.630	0.00	0.00	45.19	2.75

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.