AutoCloner

Multiple sequence alignment - TraesCS2D01G311700

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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	TraesCS2D01G311700	chr2D	100.000	3656	0	0	1	3656	400510652	400514307	0.000000e+00	6752
1	TraesCS2D01G311700	chr2A	97.139	1608	35	2	1432	3029	537549955	537551561	0.000000e+00	2704
2	TraesCS2D01G311700	chr2A	94.737	665	29	3	776	1435	537549261	537549924	0.000000e+00	1029
3	TraesCS2D01G311700	chr2A	87.214	743	83	8	1	739	109631934	109631200	0.000000e+00	835
4	TraesCS2D01G311700	chr2A	86.486	740	97	2	2	739	578166194	578166932	0.000000e+00	809
5	TraesCS2D01G311700	chr2B	95.677	1064	32	4	1432	2483	474856821	474857882	0.000000e+00	1698
6	TraesCS2D01G311700	chr2B	94.769	650	25	4	791	1435	474856145	474856790	0.000000e+00	1003
7	TraesCS2D01G311700	chr2B	95.320	406	18	1	3251	3656	45698247	45698651	0.000000e+00	643
8	TraesCS2D01G311700	chr2B	97.406	347	8	1	2683	3029	474892221	474892566	1.130000e-164	590
9	TraesCS2D01G311700	chr2B	97.209	215	6	0	2480	2694	474857974	474858188	7.460000e-97	364
10	TraesCS2D01G311700	chr2B	92.857	224	12	2	3029	3250	45698064	45698285	4.550000e-84	322
11	TraesCS2D01G311700	chr3D	85.656	739	98	3	1	739	239889115	239888385	0.000000e+00	771
12	TraesCS2D01G311700	chr3D	94.828	406	20	1	3251	3656	434955569	434955165	1.850000e-177	632
13	TraesCS2D01G311700	chr3D	92.857	224	11	2	3031	3250	434955753	434955531	1.640000e-83	320
14	TraesCS2D01G311700	chr1B	85.893	638	77	9	3027	3656	252029091	252029723	0.000000e+00	667
15	TraesCS2D01G311700	chr3A	85.714	637	75	11	3030	3656	704770864	704770234	0.000000e+00	658
16	TraesCS2D01G311700	chr3A	92.273	220	13	3	3033	3250	739915744	739915527	3.550000e-80	309
17	TraesCS2D01G311700	chr3A	90.393	229	13	3	3030	3250	47265797	47266024	3.570000e-75	292
18	TraesCS2D01G311700	chr3B	94.828	406	20	1	3251	3656	428092722	428092318	1.850000e-177	632
19	TraesCS2D01G311700	chr3B	80.744	753	125	10	2	739	639624861	639625608	1.470000e-158	569
20	TraesCS2D01G311700	chr3B	84.449	463	70	1	2	462	639432021	639432483	4.300000e-124	455
21	TraesCS2D01G311700	chr7D	93.596	406	25	1	3251	3656	555056352	555055948	4.040000e-169	604
22	TraesCS2D01G311700	chr7D	89.407	236	15	2	3025	3250	555056549	555056314	4.620000e-74	289
23	TraesCS2D01G311700	chr5D	92.892	408	26	2	3251	3656	205573320	205572914	1.130000e-164	590
24	TraesCS2D01G311700	chr6B	89.263	475	31	3	1	475	14792952	14793406	8.800000e-161	577
25	TraesCS2D01G311700	chr6B	92.118	406	31	1	3251	3656	611658219	611658623	4.100000e-159	571
26	TraesCS2D01G311700	chr6A	92.118	406	31	1	3251	3656	119292045	119291641	4.100000e-159	571
27	TraesCS2D01G311700	chr6A	91.872	406	32	1	3251	3656	116958866	116958462	1.910000e-157	566
28	TraesCS2D01G311700	chr6A	87.500	432	52	1	5	434	454643376	454642945	7.050000e-137	497
29	TraesCS2D01G311700	chr5B	91.872	406	32	1	3251	3656	232634587	232634183	1.910000e-157	566
30	TraesCS2D01G311700	chr5B	86.616	396	49	3	2	394	157381699	157382093	5.610000e-118	435
31	TraesCS2D01G311700	chr4D	89.224	232	16	2	3027	3250	47323291	47323521	7.730000e-72	281
32	TraesCS2D01G311700	chr4B	89.035	228	14	3	3033	3250	646236237	646236463	4.650000e-69	272

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	TraesCS2D01G311700	chr2D	400510652	400514307	3655	False	6752.000000	6752	100.0000	1	3656	1	chr2D.!!$F1	3655
1	TraesCS2D01G311700	chr2A	537549261	537551561	2300	False	1866.500000	2704	95.9380	776	3029	2	chr2A.!!$F2	2253
2	TraesCS2D01G311700	chr2A	109631200	109631934	734	True	835.000000	835	87.2140	1	739	1	chr2A.!!$R1	738
3	TraesCS2D01G311700	chr2A	578166194	578166932	738	False	809.000000	809	86.4860	2	739	1	chr2A.!!$F1	737
4	TraesCS2D01G311700	chr2B	474856145	474858188	2043	False	1021.666667	1698	95.8850	791	2694	3	chr2B.!!$F3	1903
5	TraesCS2D01G311700	chr2B	45698064	45698651	587	False	482.500000	643	94.0885	3029	3656	2	chr2B.!!$F2	627
6	TraesCS2D01G311700	chr3D	239888385	239889115	730	True	771.000000	771	85.6560	1	739	1	chr3D.!!$R1	738
7	TraesCS2D01G311700	chr3D	434955165	434955753	588	True	476.000000	632	93.8425	3031	3656	2	chr3D.!!$R2	625
8	TraesCS2D01G311700	chr1B	252029091	252029723	632	False	667.000000	667	85.8930	3027	3656	1	chr1B.!!$F1	629
9	TraesCS2D01G311700	chr3A	704770234	704770864	630	True	658.000000	658	85.7140	3030	3656	1	chr3A.!!$R1	626
10	TraesCS2D01G311700	chr3B	639624861	639625608	747	False	569.000000	569	80.7440	2	739	1	chr3B.!!$F2	737
11	TraesCS2D01G311700	chr7D	555055948	555056549	601	True	446.500000	604	91.5015	3025	3656	2	chr7D.!!$R1	631

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
89	92	0.032130	GTGACTGAGCCACGTTCTCA	59.968	55.000	14.42	14.42	38.16	3.27	F
602	618	0.368227	GACTGCGCTGAGAATTGTCG	59.632	55.000	21.92	0.00	0.00	4.35	F
875	891	0.455972	CAAAAATCCATCGCGCCGTT	60.456	50.000	0.00	0.00	0.00	4.44	F
1194	1210	1.619332	GTCAAAGGTCCGTTCTCTCCT	59.381	52.381	0.00	0.00	0.00	3.69	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1231	1247	0.663568	CGTCTTCACCACACGAGGAC	60.664	60.000	0.00	36.44	3.85	R
1807	1896	2.732412	TCTCCTTCTTCTTGACAGCG	57.268	50.000	0.00	0.00	5.18	R
2249	2355	3.281727	AGCAACAGTCCTGAAACTCAA	57.718	42.857	0.40	0.00	3.02	R
3187	3402	0.739462	CGAGGCCTAATGTCGTTGCA	60.739	55.000	4.42	0.00	4.08	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
87	90	0.681733	ATGTGACTGAGCCACGTTCT	59.318	50.000	0.00	0.00	37.34	3.01
89	92	0.032130	GTGACTGAGCCACGTTCTCA	59.968	55.000	14.42	14.42	38.16	3.27
223	226	3.838244	TCCATAGCACCAGTGTTATCC	57.162	47.619	4.39	0.00	35.29	2.59
279	282	1.877637	TGAGTGTTGTCCACCATTCG	58.122	50.000	0.00	0.00	45.74	3.34
324	327	0.623324	TCCAATCCGGTCTTCCCCAT	60.623	55.000	0.00	0.00	35.57	4.00
422	425	4.003788	ACAGAAGGGACACGCCGG	62.004	66.667	0.00	0.00	37.63	6.13
451	454	1.067416	AGCTGTCGTCGTTGAAGCA	59.933	52.632	11.60	0.00	36.32	3.91
510	513	6.572519	CCATATGAAAAACTTACATGTGGGG	58.427	40.000	9.11	0.73	44.04	4.96
537	553	2.349590	CGACATCTCCAAATCTGCACA	58.650	47.619	0.00	0.00	0.00	4.57
552	568	4.070552	ACAGCTCCCGCGTTCTCC	62.071	66.667	4.92	0.00	42.32	3.71
602	618	0.368227	GACTGCGCTGAGAATTGTCG	59.632	55.000	21.92	0.00	0.00	4.35
735	751	1.064017	GGGGACATATCTTGCCACCAA	60.064	52.381	0.00	0.00	0.00	3.67
736	752	2.424812	GGGGACATATCTTGCCACCAAT	60.425	50.000	0.00	0.00	0.00	3.16
738	754	2.887152	GGACATATCTTGCCACCAATCC	59.113	50.000	0.00	0.00	0.00	3.01
739	755	2.887152	GACATATCTTGCCACCAATCCC	59.113	50.000	0.00	0.00	0.00	3.85
740	756	1.881973	CATATCTTGCCACCAATCCCG	59.118	52.381	0.00	0.00	0.00	5.14
741	757	0.465460	TATCTTGCCACCAATCCCGC	60.465	55.000	0.00	0.00	0.00	6.13
742	758	3.451894	CTTGCCACCAATCCCGCC	61.452	66.667	0.00	0.00	0.00	6.13
743	759	3.944250	CTTGCCACCAATCCCGCCT	62.944	63.158	0.00	0.00	0.00	5.52
744	760	4.738998	TGCCACCAATCCCGCCTG	62.739	66.667	0.00	0.00	0.00	4.85
781	797	5.712752	TGTATACAGCCTACCAAGGTCTAT	58.287	41.667	0.08	0.00	45.64	1.98
782	798	6.141083	TGTATACAGCCTACCAAGGTCTATT	58.859	40.000	0.08	0.00	45.64	1.73
784	800	6.919775	ATACAGCCTACCAAGGTCTATTAG	57.080	41.667	0.00	0.00	45.64	1.73
815	831	1.406903	CCCAAATCTGCCATTCTCCC	58.593	55.000	0.00	0.00	0.00	4.30
816	832	1.063417	CCCAAATCTGCCATTCTCCCT	60.063	52.381	0.00	0.00	0.00	4.20
817	833	2.175499	CCCAAATCTGCCATTCTCCCTA	59.825	50.000	0.00	0.00	0.00	3.53
818	834	3.217626	CCAAATCTGCCATTCTCCCTAC	58.782	50.000	0.00	0.00	0.00	3.18
819	835	2.874701	CAAATCTGCCATTCTCCCTACG	59.125	50.000	0.00	0.00	0.00	3.51
830	846	1.207089	TCTCCCTACGCTCCATTGTTG	59.793	52.381	0.00	0.00	0.00	3.33
853	869	1.664151	GAAAGTAGTCCGCCCAAATCG	59.336	52.381	0.00	0.00	0.00	3.34
875	891	0.455972	CAAAAATCCATCGCGCCGTT	60.456	50.000	0.00	0.00	0.00	4.44
879	895	2.298158	AATCCATCGCGCCGTTCTCT	62.298	55.000	0.00	0.00	0.00	3.10
1194	1210	1.619332	GTCAAAGGTCCGTTCTCTCCT	59.381	52.381	0.00	0.00	0.00	3.69
1225	1241	4.097286	TGAGATTCCGATTCATGTCGTGTA	59.903	41.667	5.17	0.00	39.89	2.90
1229	1245	4.499037	TCCGATTCATGTCGTGTATAGG	57.501	45.455	5.17	4.93	39.89	2.57
1231	1247	4.215613	TCCGATTCATGTCGTGTATAGGAG	59.784	45.833	8.74	0.00	35.51	3.69
1303	1324	4.749245	AGACTGGCAATTTTTGAGTACG	57.251	40.909	0.00	0.00	0.00	3.67
1559	1648	7.116736	ACTCCTTCAAGGAAAAGTTAGACAAA	58.883	34.615	7.78	0.00	45.28	2.83
1601	1690	2.802247	TGATGAAGAACTGAACACGCTG	59.198	45.455	0.00	0.00	0.00	5.18
1777	1866	2.100916	TGAGCTTGATAACCTAGACCGC	59.899	50.000	0.00	0.00	0.00	5.68
2011	2107	5.310451	GTTGTCCATCCCAACAGTAAGTTA	58.690	41.667	0.00	0.00	41.40	2.24
2224	2330	5.705609	ACACTGGTTGGAATGTAAATGAC	57.294	39.130	0.00	0.00	0.00	3.06
2249	2355	5.964477	TGGTTCCTCCTAATTCAGTATGAGT	59.036	40.000	0.00	0.00	41.44	3.41
2441	2547	6.329496	TGTTTTGGCTTCTTTTCTTGTACTG	58.671	36.000	0.00	0.00	0.00	2.74
2770	2971	2.557920	AACTCTCCCAGTTGCTTCAG	57.442	50.000	0.00	0.00	44.28	3.02
2889	3090	9.443283	CATTTCACTCACTTTTAGTTTGAGAAG	57.557	33.333	4.88	0.00	39.36	2.85
3004	3205	8.931775	GTTGGATGTTTTTGTCACTTTTACTTT	58.068	29.630	0.00	0.00	0.00	2.66
3079	3280	6.312426	ACTTTGCGTTTCATTTCATTGAACAA	59.688	30.769	0.00	0.00	35.42	2.83
3085	3286	7.043458	GCGTTTCATTTCATTGAACAAGAAGAA	60.043	33.333	0.00	0.00	35.42	2.52
3100	3301	2.910977	AGAAGAAATCGGGGGTACAACT	59.089	45.455	0.00	0.00	0.00	3.16
3126	3327	1.140312	AAGGAGGGACACACACACAT	58.860	50.000	0.00	0.00	0.00	3.21
3138	3353	0.386352	ACACACATACACGACCGTCG	60.386	55.000	19.24	19.24	46.93	5.12
3187	3402	1.279271	GGTGCCCTCAACTACAGACAT	59.721	52.381	0.00	0.00	0.00	3.06
3225	3484	3.052082	CCAGCAGGGCAACGTCAG	61.052	66.667	0.00	0.00	37.60	3.51
3226	3485	2.281070	CAGCAGGGCAACGTCAGT	60.281	61.111	0.00	0.00	37.60	3.41
3227	3486	2.281070	AGCAGGGCAACGTCAGTG	60.281	61.111	0.00	0.00	37.60	3.66
3228	3487	4.030452	GCAGGGCAACGTCAGTGC	62.030	66.667	2.01	2.01	37.60	4.40
3229	3488	3.357079	CAGGGCAACGTCAGTGCC	61.357	66.667	19.39	19.39	41.01	5.01
3230	3489	3.872603	AGGGCAACGTCAGTGCCA	61.873	61.111	26.49	0.00	42.42	4.92
3231	3490	2.672996	GGGCAACGTCAGTGCCAT	60.673	61.111	26.49	0.00	42.42	4.40
3232	3491	2.268076	GGGCAACGTCAGTGCCATT	61.268	57.895	26.49	0.00	42.42	3.16
3233	3492	1.081242	GGCAACGTCAGTGCCATTG	60.081	57.895	21.97	0.00	41.22	2.82
3234	3493	1.730547	GCAACGTCAGTGCCATTGC	60.731	57.895	0.00	8.63	38.93	3.56
3235	3494	1.081242	CAACGTCAGTGCCATTGCC	60.081	57.895	0.00	0.00	36.33	4.52
3236	3495	1.528076	AACGTCAGTGCCATTGCCA	60.528	52.632	0.00	0.00	36.33	4.92
3237	3496	1.106351	AACGTCAGTGCCATTGCCAA	61.106	50.000	0.00	0.00	36.33	4.52
3238	3497	1.106351	ACGTCAGTGCCATTGCCAAA	61.106	50.000	0.00	0.00	36.33	3.28
3239	3498	0.664166	CGTCAGTGCCATTGCCAAAC	60.664	55.000	0.00	0.00	36.33	2.93
3240	3499	0.664166	GTCAGTGCCATTGCCAAACG	60.664	55.000	0.00	0.00	36.33	3.60
3241	3500	2.023223	CAGTGCCATTGCCAAACGC	61.023	57.895	0.00	0.00	36.33	4.84
3242	3501	2.738139	GTGCCATTGCCAAACGCC	60.738	61.111	0.00	0.00	36.24	5.68
3243	3502	2.916703	TGCCATTGCCAAACGCCT	60.917	55.556	0.00	0.00	36.24	5.52
3244	3503	2.125952	GCCATTGCCAAACGCCTC	60.126	61.111	0.00	0.00	36.24	4.70
3245	3504	2.639327	GCCATTGCCAAACGCCTCT	61.639	57.895	0.00	0.00	36.24	3.69
3246	3505	1.312371	GCCATTGCCAAACGCCTCTA	61.312	55.000	0.00	0.00	36.24	2.43
3247	3506	0.734889	CCATTGCCAAACGCCTCTAG	59.265	55.000	0.00	0.00	36.24	2.43
3248	3507	0.734889	CATTGCCAAACGCCTCTAGG	59.265	55.000	0.00	0.00	36.24	3.02
3249	3508	0.394352	ATTGCCAAACGCCTCTAGGG	60.394	55.000	0.00	0.00	36.24	3.53
3301	3560	2.825836	CCAGGGACGATTGCAGCC	60.826	66.667	0.00	0.00	0.00	4.85
3305	3564	2.124151	GGACGATTGCAGCCCCAT	60.124	61.111	0.00	0.00	0.00	4.00
3381	3640	1.303561	GCAGGGCCTGACATGAACA	60.304	57.895	37.07	0.00	32.44	3.18
3451	3710	2.035632	GCTCCCTGTGTAGCAGTCTAT	58.964	52.381	0.00	0.00	43.55	1.98

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
87	90	2.046314	GCGGCTGGCCTACTTTGA	60.046	61.111	3.32	0.00	34.80	2.69
113	116	2.103373	AGATTGAGTTAGAGGCGCAGA	58.897	47.619	10.83	0.00	0.00	4.26
223	226	2.266055	GAAGGAGGCGTGGACAGG	59.734	66.667	0.00	0.00	0.00	4.00
279	282	4.082571	CCATCCACAGATTCAAACCTTGTC	60.083	45.833	0.00	0.00	0.00	3.18
324	327	1.075212	TGGGCCAAGATCATGAACACA	59.925	47.619	2.13	0.00	0.00	3.72
431	434	1.891060	GCTTCAACGACGACAGCTGG	61.891	60.000	19.93	3.21	0.00	4.85
451	454	2.435805	ACAGATGTTGGACAGCGGATAT	59.564	45.455	3.66	0.00	39.90	1.63
552	568	1.574428	CCACTTTGCGGGAAGAACG	59.426	57.895	1.86	0.00	0.00	3.95
585	601	0.094216	CACGACAATTCTCAGCGCAG	59.906	55.000	11.47	0.00	0.00	5.18
713	729	1.148273	TGGCAAGATATGTCCCCGC	59.852	57.895	0.00	0.00	30.45	6.13
757	773	3.961408	AGACCTTGGTAGGCTGTATACAG	59.039	47.826	25.68	25.68	46.22	2.74
758	774	3.990369	AGACCTTGGTAGGCTGTATACA	58.010	45.455	5.25	5.25	46.22	2.29
759	775	6.667558	AATAGACCTTGGTAGGCTGTATAC	57.332	41.667	0.00	0.00	46.22	1.47
760	776	6.952358	CCTAATAGACCTTGGTAGGCTGTATA	59.048	42.308	0.00	0.00	46.22	1.47
761	777	5.780793	CCTAATAGACCTTGGTAGGCTGTAT	59.219	44.000	0.00	0.00	46.22	2.29
762	778	5.103387	TCCTAATAGACCTTGGTAGGCTGTA	60.103	44.000	0.00	0.00	46.22	2.74
763	779	3.967987	CCTAATAGACCTTGGTAGGCTGT	59.032	47.826	0.00	0.00	46.22	4.40
764	780	4.223953	TCCTAATAGACCTTGGTAGGCTG	58.776	47.826	0.00	0.00	46.22	4.85
765	781	4.554553	TCCTAATAGACCTTGGTAGGCT	57.445	45.455	0.00	0.00	46.22	4.58
766	782	5.625568	TTTCCTAATAGACCTTGGTAGGC	57.374	43.478	0.00	0.00	46.22	3.93
768	784	8.272173	TCCAATTTTCCTAATAGACCTTGGTAG	58.728	37.037	0.00	0.00	33.87	3.18
769	785	8.165267	TCCAATTTTCCTAATAGACCTTGGTA	57.835	34.615	0.00	0.00	33.87	3.25
770	786	7.039722	TCCAATTTTCCTAATAGACCTTGGT	57.960	36.000	0.00	0.00	33.87	3.67
771	787	6.039829	GCTCCAATTTTCCTAATAGACCTTGG	59.960	42.308	0.00	0.00	33.54	3.61
772	788	6.039829	GGCTCCAATTTTCCTAATAGACCTTG	59.960	42.308	0.00	0.00	0.00	3.61
773	789	6.129874	GGCTCCAATTTTCCTAATAGACCTT	58.870	40.000	0.00	0.00	0.00	3.50
774	790	5.399152	GGGCTCCAATTTTCCTAATAGACCT	60.399	44.000	0.00	0.00	0.00	3.85
781	797	5.187576	CAGATTTGGGCTCCAATTTTCCTAA	59.812	40.000	7.39	0.00	43.55	2.69
782	798	4.711355	CAGATTTGGGCTCCAATTTTCCTA	59.289	41.667	7.39	0.00	43.55	2.94
784	800	3.865446	CAGATTTGGGCTCCAATTTTCC	58.135	45.455	7.39	0.00	43.55	3.13
830	846	0.611714	TTGGGCGGACTACTTTCTCC	59.388	55.000	0.00	0.00	0.00	3.71
853	869	1.758783	GGCGCGATGGATTTTTGATC	58.241	50.000	12.10	0.00	0.00	2.92
1152	1168	4.824515	AGCTCGAGGTCCCCGGAG	62.825	72.222	12.24	0.00	33.99	4.63
1194	1210	3.055891	TGAATCGGAATCTCAACAGAGCA	60.056	43.478	0.00	0.00	29.82	4.26
1225	1241	1.005569	TCACCACACGAGGACTCCTAT	59.994	52.381	0.00	0.00	31.76	2.57
1229	1245	0.959553	TCTTCACCACACGAGGACTC	59.040	55.000	0.00	0.00	0.00	3.36
1231	1247	0.663568	CGTCTTCACCACACGAGGAC	60.664	60.000	0.00	0.00	36.44	3.85
1303	1324	3.733443	AAGCAGGATTTTCAACCACAC	57.267	42.857	0.00	0.00	0.00	3.82
1487	1576	3.492011	CACAAAAAGAAGCATGCCACTTC	59.508	43.478	21.48	16.01	43.16	3.01
1506	1595	4.350368	TTTCCTGATACTCTGTTGCACA	57.650	40.909	0.00	0.00	0.00	4.57
1559	1648	4.640201	TCAGTAACTGTTTCAGCTTTTGCT	59.360	37.500	0.00	0.00	43.96	3.91
1601	1690	2.898729	TCTCCTCCATCTCATTTCGC	57.101	50.000	0.00	0.00	0.00	4.70
1755	1844	3.797184	GCGGTCTAGGTTATCAAGCTCAG	60.797	52.174	0.00	0.00	40.27	3.35
1807	1896	2.732412	TCTCCTTCTTCTTGACAGCG	57.268	50.000	0.00	0.00	0.00	5.18
2011	2107	7.445402	GTGAATATCAAACAGGCCACTACATAT	59.555	37.037	5.01	0.00	0.00	1.78
2224	2330	6.098982	ACTCATACTGAATTAGGAGGAACCAG	59.901	42.308	0.00	0.00	42.04	4.00
2249	2355	3.281727	AGCAACAGTCCTGAAACTCAA	57.718	42.857	0.40	0.00	0.00	3.02
2441	2547	6.098409	TCCATAGGTAGAAACTGATGTCCTTC	59.902	42.308	0.00	0.00	0.00	3.46
2510	2711	7.862372	CACACAAGTTTTGTTTGCTGTAGATAT	59.138	33.333	0.00	0.00	43.23	1.63
2574	2775	7.876936	TTCGAACTTATCTAGCTTCTTCCTA	57.123	36.000	0.00	0.00	0.00	2.94
2770	2971	4.040952	AGGATGCCATACAACTAGGTCATC	59.959	45.833	0.00	0.00	36.30	2.92
2870	3071	6.377327	TTGGCTTCTCAAACTAAAAGTGAG	57.623	37.500	0.00	0.00	40.15	3.51
2889	3090	4.457257	GTGCTGATATAAGGGAGATTTGGC	59.543	45.833	0.00	0.00	0.00	4.52
3004	3205	7.987750	TTAAACAATACAGGTGAGCAACATA	57.012	32.000	0.00	0.00	0.00	2.29
3007	3208	8.587952	AAAATTAAACAATACAGGTGAGCAAC	57.412	30.769	0.00	0.00	0.00	4.17
3037	3238	1.784525	AGTCTCTTGCGTTTTCTCGG	58.215	50.000	0.00	0.00	0.00	4.63
3079	3280	2.910977	AGTTGTACCCCCGATTTCTTCT	59.089	45.455	0.00	0.00	0.00	2.85
3085	3286	1.280998	CTGGAAGTTGTACCCCCGATT	59.719	52.381	0.00	0.00	0.00	3.34
3100	3301	1.420138	GTGTGTCCCTCCTTTCTGGAA	59.580	52.381	0.00	0.00	45.63	3.53
3138	3353	2.150397	AGTTGTAGTCGCTTGGTGAC	57.850	50.000	3.39	3.39	42.60	3.67
3187	3402	0.739462	CGAGGCCTAATGTCGTTGCA	60.739	55.000	4.42	0.00	0.00	4.08
3219	3478	1.106351	TTTGGCAATGGCACTGACGT	61.106	50.000	9.62	0.00	43.71	4.34
3220	3479	0.664166	GTTTGGCAATGGCACTGACG	60.664	55.000	9.62	0.00	43.71	4.35
3221	3480	0.664166	CGTTTGGCAATGGCACTGAC	60.664	55.000	9.62	0.00	43.71	3.51
3222	3481	1.659233	CGTTTGGCAATGGCACTGA	59.341	52.632	9.62	0.00	43.71	3.41
3223	3482	2.023223	GCGTTTGGCAATGGCACTG	61.023	57.895	9.62	3.30	43.71	3.66
3224	3483	2.339712	GCGTTTGGCAATGGCACT	59.660	55.556	9.62	0.00	43.71	4.40
3225	3484	2.738139	GGCGTTTGGCAATGGCAC	60.738	61.111	9.62	7.39	46.16	5.01
3226	3485	2.916703	AGGCGTTTGGCAATGGCA	60.917	55.556	22.42	5.05	45.11	4.92
3227	3486	1.312371	TAGAGGCGTTTGGCAATGGC	61.312	55.000	15.73	15.73	46.16	4.40
3228	3487	0.734889	CTAGAGGCGTTTGGCAATGG	59.265	55.000	0.00	0.00	46.16	3.16
3229	3488	0.734889	CCTAGAGGCGTTTGGCAATG	59.265	55.000	0.00	0.00	46.16	2.82
3230	3489	0.394352	CCCTAGAGGCGTTTGGCAAT	60.394	55.000	0.00	0.00	46.16	3.56
3231	3490	1.002624	CCCTAGAGGCGTTTGGCAA	60.003	57.895	0.00	0.00	46.16	4.52
3232	3491	2.668632	CCCTAGAGGCGTTTGGCA	59.331	61.111	0.00	0.00	46.16	4.92
3233	3492	2.124695	CCCCTAGAGGCGTTTGGC	60.125	66.667	0.00	0.00	42.51	4.52
3234	3493	2.124695	GCCCCTAGAGGCGTTTGG	60.125	66.667	0.00	0.00	44.57	3.28
3241	3500	2.759973	TGACGCTGCCCCTAGAGG	60.760	66.667	0.00	0.00	0.00	3.69
3242	3501	2.811101	CTGACGCTGCCCCTAGAG	59.189	66.667	0.00	0.00	0.00	2.43
3243	3502	3.461773	GCTGACGCTGCCCCTAGA	61.462	66.667	0.00	0.00	0.00	2.43
3244	3503	4.880537	CGCTGACGCTGCCCCTAG	62.881	72.222	0.00	0.00	0.00	3.02
3301	3560	4.828296	GGCCTGGGCAGTCATGGG	62.828	72.222	16.34	0.00	44.11	4.00
3305	3564	4.641645	CGTTGGCCTGGGCAGTCA	62.642	66.667	22.78	6.00	44.11	3.41
3376	3635	3.066064	CCAACGATTGTTTCACCTGTTCA	59.934	43.478	0.00	0.00	35.72	3.18
3381	3640	1.144093	TCCCCAACGATTGTTTCACCT	59.856	47.619	0.00	0.00	35.72	4.00
3566	3829	1.272554	GGAGAAATCCCAGGTCCGGT	61.273	60.000	0.00	0.00	0.00	5.28

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.