AutoCloner

Multiple sequence alignment - TraesCS5A01G237000

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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	TraesCS5A01G237000	chr5A	100.000	2630	0	0	1	2630	452269304	452266675	0.000000e+00	4857
1	TraesCS5A01G237000	chr5A	91.431	1377	96	14	1129	2497	452211098	452209736	0.000000e+00	1869
2	TraesCS5A01G237000	chr5A	86.432	1533	165	26	902	2422	454346519	454348020	0.000000e+00	1639
3	TraesCS5A01G237000	chr5A	100.000	408	0	0	2922	3329	452266383	452265976	0.000000e+00	754
4	TraesCS5A01G237000	chr5A	89.908	218	20	1	898	1115	452211299	452211084	2.530000e-71	279
5	TraesCS5A01G237000	chr5B	93.109	1814	79	17	713	2497	416389614	416391410	0.000000e+00	2615
6	TraesCS5A01G237000	chr5B	91.489	1269	95	6	1142	2401	416418105	416419369	0.000000e+00	1733
7	TraesCS5A01G237000	chr5B	77.363	402	45	25	2922	3317	416391738	416392099	2.620000e-46	196
8	TraesCS5A01G237000	chr5D	92.566	1789	110	16	713	2493	353425305	353427078	0.000000e+00	2545
9	TraesCS5A01G237000	chr5D	91.714	1243	91	9	1129	2361	353432124	353433364	0.000000e+00	1714
10	TraesCS5A01G237000	chr5D	81.401	414	61	8	2922	3327	353427311	353427716	1.150000e-84	324
11	TraesCS5A01G237000	chr5D	88.532	218	21	2	900	1115	353431923	353432138	9.160000e-66	261
12	TraesCS5A01G237000	chr5D	91.304	115	8	1	2518	2630	353427071	353427185	4.450000e-34	156
13	TraesCS5A01G237000	chr3B	96.751	708	22	1	1	707	52749606	52748899	0.000000e+00	1179
14	TraesCS5A01G237000	chr3B	80.043	466	68	9	1793	2241	694175042	694174585	4.140000e-84	322
15	TraesCS5A01G237000	chr3B	87.273	275	33	2	1471	1744	694175470	694175197	2.490000e-81	313
16	TraesCS5A01G237000	chr3A	96.747	707	21	1	1	707	741645308	741644604	0.000000e+00	1177
17	TraesCS5A01G237000	chr3A	94.625	707	37	1	1	707	562918194	562918899	0.000000e+00	1094
18	TraesCS5A01G237000	chr3A	80.000	470	69	10	1793	2245	660053877	660053416	1.150000e-84	324
19	TraesCS5A01G237000	chr3A	86.909	275	34	2	1471	1744	660003145	660002872	1.160000e-79	307
20	TraesCS5A01G237000	chr3A	86.545	275	35	2	1471	1744	660054300	660054027	5.400000e-78	302
21	TraesCS5A01G237000	chr3A	72.368	456	101	24	1792	2236	653417480	653417039	1.620000e-23	121
22	TraesCS5A01G237000	chr1B	96.610	708	23	1	1	707	267810220	267810927	0.000000e+00	1173
23	TraesCS5A01G237000	chr4A	95.757	707	29	1	1	707	610092239	610092944	0.000000e+00	1138
24	TraesCS5A01G237000	chr4A	94.350	708	36	3	1	707	3362981	3363685	0.000000e+00	1083
25	TraesCS5A01G237000	chr6A	95.191	707	34	0	1	707	36259079	36259785	0.000000e+00	1118
26	TraesCS5A01G237000	chr6A	94.484	707	39	0	1	707	601248255	601248961	0.000000e+00	1090
27	TraesCS5A01G237000	chr1A	95.231	692	33	0	1	692	323633209	323632518	0.000000e+00	1096
28	TraesCS5A01G237000	chr3D	73.348	454	100	20	1792	2236	517812017	517811576	7.440000e-32	148

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	TraesCS5A01G237000	chr5A	452265976	452269304	3328	True	2805.500000	4857	100.000000	1	3329	2	chr5A.!!$R2	3328
1	TraesCS5A01G237000	chr5A	454346519	454348020	1501	False	1639.000000	1639	86.432000	902	2422	1	chr5A.!!$F1	1520
2	TraesCS5A01G237000	chr5A	452209736	452211299	1563	True	1074.000000	1869	90.669500	898	2497	2	chr5A.!!$R1	1599
3	TraesCS5A01G237000	chr5B	416418105	416419369	1264	False	1733.000000	1733	91.489000	1142	2401	1	chr5B.!!$F1	1259
4	TraesCS5A01G237000	chr5B	416389614	416392099	2485	False	1405.500000	2615	85.236000	713	3317	2	chr5B.!!$F2	2604
5	TraesCS5A01G237000	chr5D	353425305	353427716	2411	False	1008.333333	2545	88.423667	713	3327	3	chr5D.!!$F1	2614
6	TraesCS5A01G237000	chr5D	353431923	353433364	1441	False	987.500000	1714	90.123000	900	2361	2	chr5D.!!$F2	1461
7	TraesCS5A01G237000	chr3B	52748899	52749606	707	True	1179.000000	1179	96.751000	1	707	1	chr3B.!!$R1	706
8	TraesCS5A01G237000	chr3B	694174585	694175470	885	True	317.500000	322	83.658000	1471	2241	2	chr3B.!!$R2	770
9	TraesCS5A01G237000	chr3A	741644604	741645308	704	True	1177.000000	1177	96.747000	1	707	1	chr3A.!!$R3	706
10	TraesCS5A01G237000	chr3A	562918194	562918899	705	False	1094.000000	1094	94.625000	1	707	1	chr3A.!!$F1	706
11	TraesCS5A01G237000	chr3A	660053416	660054300	884	True	313.000000	324	83.272500	1471	2245	2	chr3A.!!$R4	774
12	TraesCS5A01G237000	chr1B	267810220	267810927	707	False	1173.000000	1173	96.610000	1	707	1	chr1B.!!$F1	706
13	TraesCS5A01G237000	chr4A	610092239	610092944	705	False	1138.000000	1138	95.757000	1	707	1	chr4A.!!$F2	706
14	TraesCS5A01G237000	chr4A	3362981	3363685	704	False	1083.000000	1083	94.350000	1	707	1	chr4A.!!$F1	706
15	TraesCS5A01G237000	chr6A	36259079	36259785	706	False	1118.000000	1118	95.191000	1	707	1	chr6A.!!$F1	706
16	TraesCS5A01G237000	chr6A	601248255	601248961	706	False	1090.000000	1090	94.484000	1	707	1	chr6A.!!$F2	706
17	TraesCS5A01G237000	chr1A	323632518	323633209	691	True	1096.000000	1096	95.231000	1	692	1	chr1A.!!$R1	691

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
566	571	0.310854	CCAAAACAGAACACCTCGCC	59.689	55.0	0.00	0.0	0.0	5.54	F
1256	1271	0.035439	AATTTCGAGGGCACGGTGAT	60.035	50.0	13.29	0.0	0.0	3.06	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1666	1690	0.537828	CCGGAGAGGTAGAGGTAGCC	60.538	65.0	0.00	0.0	34.51	3.93	R
3243	3490	0.172127	TCTGAGCTAGCAGTGAAGCG	59.828	55.0	18.83	0.0	43.63	4.68	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
33	34	4.553330	ATCAGTTTGTCGGATGGTAGTT	57.447	40.909	0.00	0.00	30.34	2.24
93	94	3.456277	GGATTTGAGACCACATACCCTCT	59.544	47.826	0.00	0.00	0.00	3.69
493	498	5.418840	CCCAAGTAACTGAATGGTAAAGCAT	59.581	40.000	0.00	0.00	0.00	3.79
566	571	0.310854	CCAAAACAGAACACCTCGCC	59.689	55.000	0.00	0.00	0.00	5.54
653	658	2.493278	GTGCCTTAGCCATGTCATGTTT	59.507	45.455	11.84	2.29	38.69	2.83
709	714	3.354948	TGGACACTCCTCCATCAATTG	57.645	47.619	0.00	0.00	37.46	2.32
710	715	2.644299	TGGACACTCCTCCATCAATTGT	59.356	45.455	5.13	0.00	37.46	2.71
711	716	3.274288	GGACACTCCTCCATCAATTGTC	58.726	50.000	5.13	0.00	32.53	3.18
749	754	9.797556	AAGCTTTAAAATTCACGTTAAAACTCT	57.202	25.926	0.00	0.00	28.94	3.24
816	821	2.126071	TAGTGCTCGACGGCAAGC	60.126	61.111	11.70	0.00	44.18	4.01
883	888	1.200020	CTGCTCCCGTTTCCATTTCAC	59.800	52.381	0.00	0.00	0.00	3.18
885	890	1.886655	GCTCCCGTTTCCATTTCACCT	60.887	52.381	0.00	0.00	0.00	4.00
907	912	2.290641	CCAACCAACATAGGTAGGTGCA	60.291	50.000	0.00	0.00	42.25	4.57
980	985	1.137086	GCATCGTCAGGGAAGCTTCTA	59.863	52.381	25.05	6.81	0.00	2.10
1029	1034	2.034221	AAGCCTTTCCCTCACGGC	59.966	61.111	0.00	0.00	42.79	5.68
1065	1070	1.377987	GGCGCATCCAACCTGGTAA	60.378	57.895	10.83	0.00	39.03	2.85
1149	1157	0.248621	GATTTGATTCGGCAAGCGGG	60.249	55.000	0.00	0.00	0.00	6.13
1247	1262	0.931005	GCGACAGCTAATTTCGAGGG	59.069	55.000	9.63	0.00	41.01	4.30
1256	1271	0.035439	AATTTCGAGGGCACGGTGAT	60.035	50.000	13.29	0.00	0.00	3.06
1267	1282	4.175337	CGGTGATGGGGATGGCGT	62.175	66.667	0.00	0.00	0.00	5.68
1666	1690	4.052229	ACGGCGACCTCCTCAACG	62.052	66.667	16.62	0.00	0.00	4.10
1939	2069	4.659172	CCAAGGTGGCCGCCAAGA	62.659	66.667	36.17	0.00	34.18	3.02
2091	2236	4.302509	CGCACCGGGGTGTACACA	62.303	66.667	26.51	0.00	46.90	3.72
2272	2417	1.466360	CGATCAAAGCCGCAAAAGAGG	60.466	52.381	0.00	0.00	0.00	3.69
2353	2532	1.597663	GCCGTCCATCTACCAAATTCG	59.402	52.381	0.00	0.00	0.00	3.34
2369	2548	5.652452	CCAAATTCGACCCCTAGAAAATCTT	59.348	40.000	0.00	0.00	0.00	2.40
2389	2568	3.582998	TCTAAATCCCAAGGCCATGAG	57.417	47.619	10.18	0.00	0.00	2.90
2405	2584	2.959357	GAGTCACAAGCAGCGGCAC	61.959	63.158	12.44	0.00	44.61	5.01
2472	2656	8.696043	TTATACAGTGAACGTACCCTATATGT	57.304	34.615	0.00	0.00	0.00	2.29
2497	2681	5.940192	TTGTGTGAAGTGATGGTAATGTC	57.060	39.130	0.00	0.00	0.00	3.06
2498	2682	5.227569	TGTGTGAAGTGATGGTAATGTCT	57.772	39.130	0.00	0.00	0.00	3.41
2499	2683	5.620206	TGTGTGAAGTGATGGTAATGTCTT	58.380	37.500	0.00	0.00	0.00	3.01
2500	2684	6.061441	TGTGTGAAGTGATGGTAATGTCTTT	58.939	36.000	0.00	0.00	0.00	2.52
2501	2685	6.545666	TGTGTGAAGTGATGGTAATGTCTTTT	59.454	34.615	0.00	0.00	0.00	2.27
2502	2686	7.068103	TGTGTGAAGTGATGGTAATGTCTTTTT	59.932	33.333	0.00	0.00	0.00	1.94
2522	2706	2.080654	TTTTGTTGAGGGGGTGAAGG	57.919	50.000	0.00	0.00	0.00	3.46
2523	2707	0.930726	TTTGTTGAGGGGGTGAAGGT	59.069	50.000	0.00	0.00	0.00	3.50
2524	2708	1.822425	TTGTTGAGGGGGTGAAGGTA	58.178	50.000	0.00	0.00	0.00	3.08
2525	2709	1.822425	TGTTGAGGGGGTGAAGGTAA	58.178	50.000	0.00	0.00	0.00	2.85
2526	2710	2.354328	TGTTGAGGGGGTGAAGGTAAT	58.646	47.619	0.00	0.00	0.00	1.89
2527	2711	2.041081	TGTTGAGGGGGTGAAGGTAATG	59.959	50.000	0.00	0.00	0.00	1.90
2528	2712	2.041216	GTTGAGGGGGTGAAGGTAATGT	59.959	50.000	0.00	0.00	0.00	2.71
2541	2725	3.782046	AGGTAATGTATGTGTGAGCGAC	58.218	45.455	0.00	0.00	0.00	5.19
2558	2742	3.620374	AGCGACTGTATGCATTTCTCTTG	59.380	43.478	3.54	0.00	0.00	3.02
2626	2865	5.898630	ATTTATGCGTTTGTGTTGGTTTC	57.101	34.783	0.00	0.00	0.00	2.78
2960	3199	4.799564	TGCTGGCTTGGGTTTTAATTAG	57.200	40.909	0.00	0.00	0.00	1.73
2973	3212	6.260377	GGTTTTAATTAGGTTATGTCGGTGC	58.740	40.000	0.00	0.00	0.00	5.01
2990	3229	6.202762	TGTCGGTGCTTTGTCATTCATATATC	59.797	38.462	0.00	0.00	0.00	1.63
2994	3233	6.202762	GGTGCTTTGTCATTCATATATCGTGA	59.797	38.462	0.00	0.00	0.00	4.35
3025	3264	7.337938	TGCTGTTGGAGATGATATTTGTTCTA	58.662	34.615	0.00	0.00	0.00	2.10
3046	3285	8.917655	GTTCTAAGAGAAGAGTGATGTTGTTAC	58.082	37.037	0.00	0.00	34.42	2.50
3047	3286	7.603651	TCTAAGAGAAGAGTGATGTTGTTACC	58.396	38.462	0.00	0.00	0.00	2.85
3048	3287	6.426646	AAGAGAAGAGTGATGTTGTTACCT	57.573	37.500	0.00	0.00	0.00	3.08
3050	3289	6.926313	AGAGAAGAGTGATGTTGTTACCTAC	58.074	40.000	0.00	0.00	0.00	3.18
3054	3296	5.734720	AGAGTGATGTTGTTACCTACATGG	58.265	41.667	0.00	0.00	37.20	3.66
3082	3324	1.002792	GTCCTTGCACGTTTTGGTCTC	60.003	52.381	0.00	0.00	0.00	3.36
3083	3325	1.021202	CCTTGCACGTTTTGGTCTCA	58.979	50.000	0.00	0.00	0.00	3.27
3090	3332	3.713288	CACGTTTTGGTCTCAGTGTCTA	58.287	45.455	0.00	0.00	0.00	2.59
3092	3334	3.383825	ACGTTTTGGTCTCAGTGTCTACT	59.616	43.478	0.00	0.00	37.75	2.57
3113	3355	0.250901	GTGGTGATTGTGTGAGCCCT	60.251	55.000	0.00	0.00	0.00	5.19
3123	3365	0.183492	TGTGAGCCCTTTGTGAGCTT	59.817	50.000	0.00	0.00	36.87	3.74
3127	3369	2.884639	TGAGCCCTTTGTGAGCTTTTAC	59.115	45.455	0.00	0.00	36.87	2.01
3133	3375	3.882888	CCTTTGTGAGCTTTTACTCCACA	59.117	43.478	0.00	0.00	35.72	4.17
3136	3378	6.206634	CCTTTGTGAGCTTTTACTCCACATTA	59.793	38.462	3.32	0.00	35.72	1.90
3141	3383	8.637986	TGTGAGCTTTTACTCCACATTAAAATT	58.362	29.630	0.00	0.00	35.72	1.82
3172	3419	4.415150	CACTCACATGGGCCGGCT	62.415	66.667	28.56	2.77	0.00	5.52
3196	3443	1.449246	GCTCTGCCTCGCTCAACAT	60.449	57.895	0.00	0.00	0.00	2.71
3198	3445	0.108472	CTCTGCCTCGCTCAACATGA	60.108	55.000	0.00	0.00	0.00	3.07
3203	3450	0.534412	CCTCGCTCAACATGACTCCT	59.466	55.000	0.00	0.00	0.00	3.69
3205	3452	2.166459	CCTCGCTCAACATGACTCCTTA	59.834	50.000	0.00	0.00	0.00	2.69
3208	3455	4.832248	TCGCTCAACATGACTCCTTATTT	58.168	39.130	0.00	0.00	0.00	1.40
3209	3456	5.245531	TCGCTCAACATGACTCCTTATTTT	58.754	37.500	0.00	0.00	0.00	1.82
3212	3459	6.568462	CGCTCAACATGACTCCTTATTTTGTT	60.568	38.462	0.00	0.00	0.00	2.83
3213	3460	6.803807	GCTCAACATGACTCCTTATTTTGTTC	59.196	38.462	0.00	0.00	0.00	3.18
3214	3461	7.522073	GCTCAACATGACTCCTTATTTTGTTCA	60.522	37.037	0.00	0.00	0.00	3.18
3218	3465	8.553459	ACATGACTCCTTATTTTGTTCACTAG	57.447	34.615	0.00	0.00	0.00	2.57
3219	3466	7.119846	ACATGACTCCTTATTTTGTTCACTAGC	59.880	37.037	0.00	0.00	0.00	3.42
3221	3468	7.224297	TGACTCCTTATTTTGTTCACTAGCTT	58.776	34.615	0.00	0.00	0.00	3.74
3223	3470	8.779354	ACTCCTTATTTTGTTCACTAGCTTAG	57.221	34.615	0.00	0.00	0.00	2.18
3224	3471	8.376270	ACTCCTTATTTTGTTCACTAGCTTAGT	58.624	33.333	0.00	0.00	40.28	2.24
3225	3472	8.773404	TCCTTATTTTGTTCACTAGCTTAGTC	57.227	34.615	0.00	0.00	36.76	2.59
3226	3473	7.822822	TCCTTATTTTGTTCACTAGCTTAGTCC	59.177	37.037	0.00	0.00	36.76	3.85
3228	3475	8.773404	TTATTTTGTTCACTAGCTTAGTCCTC	57.227	34.615	0.00	0.00	36.76	3.71
3230	3477	5.646577	TTGTTCACTAGCTTAGTCCTCTC	57.353	43.478	0.00	0.00	36.76	3.20
3231	3478	4.017808	TGTTCACTAGCTTAGTCCTCTCC	58.982	47.826	0.00	0.00	36.76	3.71
3232	3479	3.300239	TCACTAGCTTAGTCCTCTCCC	57.700	52.381	0.00	0.00	36.76	4.30
3233	3480	2.091775	TCACTAGCTTAGTCCTCTCCCC	60.092	54.545	0.00	0.00	36.76	4.81
3234	3481	1.218450	ACTAGCTTAGTCCTCTCCCCC	59.782	57.143	0.00	0.00	32.47	5.40
3256	3503	1.875813	CCGCTCGCTTCACTGCTAG	60.876	63.158	0.00	0.00	0.00	3.42
3262	3509	0.172127	CGCTTCACTGCTAGCTCAGA	59.828	55.000	17.23	7.83	37.51	3.27
3263	3510	1.403382	CGCTTCACTGCTAGCTCAGAA	60.403	52.381	17.23	14.69	37.51	3.02

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
19	20	0.035820	GCCCAAACTACCATCCGACA	60.036	55.000	0.00	0.00	0.00	4.35
33	34	0.034337	ACTCGAAAACGCTAGCCCAA	59.966	50.000	9.66	0.00	0.00	4.12
54	55	6.494842	TCAAATCCTGCGCAATAAGTATTTC	58.505	36.000	13.05	0.00	0.00	2.17
93	94	0.178903	ACAGGTTAGGGACAGAGCCA	60.179	55.000	0.00	0.00	0.00	4.75
462	467	5.014755	ACCATTCAGTTACTTGGGTATTCCA	59.985	40.000	6.54	0.00	45.43	3.53
493	498	7.599621	CAGACAATTGTTTGGATGCAAATTAGA	59.400	33.333	18.89	3.13	37.15	2.10
500	505	5.301551	ACTTACAGACAATTGTTTGGATGCA	59.698	36.000	27.18	8.62	37.15	3.96
566	571	8.010733	TGGCTTAAAGATCAATTTCCATAAGG	57.989	34.615	0.00	0.00	0.00	2.69
653	658	6.880529	TGCTGATGACACTATTCTTTTCATGA	59.119	34.615	0.00	0.00	0.00	3.07
707	712	2.639065	AGCTTCGGTTTGAACAGACAA	58.361	42.857	0.00	0.00	32.93	3.18
708	713	2.325583	AGCTTCGGTTTGAACAGACA	57.674	45.000	0.00	0.00	32.93	3.41
709	714	3.692791	AAAGCTTCGGTTTGAACAGAC	57.307	42.857	0.00	0.00	32.93	3.51
710	715	5.821516	TTTAAAGCTTCGGTTTGAACAGA	57.178	34.783	0.00	0.00	34.94	3.41
711	716	7.221838	TGAATTTTAAAGCTTCGGTTTGAACAG	59.778	33.333	0.00	0.00	34.94	3.16
765	770	9.566432	GACCAGTGAGGAAATCTAAATTCATAT	57.434	33.333	0.00	0.00	41.22	1.78
810	815	0.897401	AAGAGGCCTCAAAGCTTGCC	60.897	55.000	33.90	15.88	44.35	4.52
816	821	6.183360	CGTAATTTGACTAAGAGGCCTCAAAG	60.183	42.308	33.90	28.92	36.37	2.77
932	937	3.499737	GCAACGTGATGAGCCCCG	61.500	66.667	0.00	0.00	0.00	5.73
980	985	1.141657	TCTTCTCAGTGCTGCAAAGGT	59.858	47.619	2.77	0.00	0.00	3.50
1065	1070	1.826096	GGGGAAGAGAGCTTTCGTACT	59.174	52.381	2.50	0.00	33.61	2.73
1112	1120	0.391130	TCGCACACCTAGTTGGATGC	60.391	55.000	12.19	12.19	43.26	3.91
1149	1157	2.032799	TGCACAAACGATTCCACTTCAC	59.967	45.455	0.00	0.00	0.00	3.18
1209	1224	2.985847	GTGACCTTGCAGGCCCAC	60.986	66.667	0.00	0.00	39.63	4.61
1247	1262	2.516930	CCATCCCCATCACCGTGC	60.517	66.667	0.00	0.00	0.00	5.34
1256	1271	4.776322	CTTGCGACGCCATCCCCA	62.776	66.667	18.69	0.00	0.00	4.96
1488	1512	3.233980	AGGCAGACCAGCACGTCA	61.234	61.111	6.04	0.00	39.06	4.35
1666	1690	0.537828	CCGGAGAGGTAGAGGTAGCC	60.538	65.000	0.00	0.00	34.51	3.93
2091	2236	2.678934	TCGCCGTAGTCCCTTGCT	60.679	61.111	0.00	0.00	0.00	3.91
2272	2417	1.901650	CTGAACCTTGCGAACTCGGC	61.902	60.000	0.69	0.00	40.23	5.54
2353	2532	6.999272	GGGATTTAGAAGATTTTCTAGGGGTC	59.001	42.308	5.90	4.11	44.46	4.46
2369	2548	2.852449	ACTCATGGCCTTGGGATTTAGA	59.148	45.455	24.61	0.00	0.00	2.10
2389	2568	4.030452	GGTGCCGCTGCTTGTGAC	62.030	66.667	0.70	0.00	38.71	3.67
2405	2584	4.607293	TTTATGACGATCCTCATCCTGG	57.393	45.455	10.06	0.00	32.86	4.45
2472	2656	7.068103	AGACATTACCATCACTTCACACAAAAA	59.932	33.333	0.00	0.00	0.00	1.94
2502	2686	2.292587	ACCTTCACCCCCTCAACAAAAA	60.293	45.455	0.00	0.00	0.00	1.94
2503	2687	1.289530	ACCTTCACCCCCTCAACAAAA	59.710	47.619	0.00	0.00	0.00	2.44
2504	2688	0.930726	ACCTTCACCCCCTCAACAAA	59.069	50.000	0.00	0.00	0.00	2.83
2505	2689	1.822425	TACCTTCACCCCCTCAACAA	58.178	50.000	0.00	0.00	0.00	2.83
2506	2690	1.822425	TTACCTTCACCCCCTCAACA	58.178	50.000	0.00	0.00	0.00	3.33
2507	2691	2.041216	ACATTACCTTCACCCCCTCAAC	59.959	50.000	0.00	0.00	0.00	3.18
2508	2692	2.354328	ACATTACCTTCACCCCCTCAA	58.646	47.619	0.00	0.00	0.00	3.02
2509	2693	2.053747	ACATTACCTTCACCCCCTCA	57.946	50.000	0.00	0.00	0.00	3.86
2510	2694	3.458487	ACATACATTACCTTCACCCCCTC	59.542	47.826	0.00	0.00	0.00	4.30
2511	2695	3.202151	CACATACATTACCTTCACCCCCT	59.798	47.826	0.00	0.00	0.00	4.79
2512	2696	3.053917	ACACATACATTACCTTCACCCCC	60.054	47.826	0.00	0.00	0.00	5.40
2513	2697	3.945285	CACACATACATTACCTTCACCCC	59.055	47.826	0.00	0.00	0.00	4.95
2514	2698	4.839121	TCACACATACATTACCTTCACCC	58.161	43.478	0.00	0.00	0.00	4.61
2515	2699	4.332819	GCTCACACATACATTACCTTCACC	59.667	45.833	0.00	0.00	0.00	4.02
2516	2700	4.032900	CGCTCACACATACATTACCTTCAC	59.967	45.833	0.00	0.00	0.00	3.18
2517	2701	4.081917	TCGCTCACACATACATTACCTTCA	60.082	41.667	0.00	0.00	0.00	3.02
2518	2702	4.267928	GTCGCTCACACATACATTACCTTC	59.732	45.833	0.00	0.00	0.00	3.46
2519	2703	4.081642	AGTCGCTCACACATACATTACCTT	60.082	41.667	0.00	0.00	0.00	3.50
2520	2704	3.447586	AGTCGCTCACACATACATTACCT	59.552	43.478	0.00	0.00	0.00	3.08
2521	2705	3.551890	CAGTCGCTCACACATACATTACC	59.448	47.826	0.00	0.00	0.00	2.85
2522	2706	4.174009	ACAGTCGCTCACACATACATTAC	58.826	43.478	0.00	0.00	0.00	1.89
2523	2707	4.450082	ACAGTCGCTCACACATACATTA	57.550	40.909	0.00	0.00	0.00	1.90
2524	2708	3.319137	ACAGTCGCTCACACATACATT	57.681	42.857	0.00	0.00	0.00	2.71
2525	2709	4.363138	CATACAGTCGCTCACACATACAT	58.637	43.478	0.00	0.00	0.00	2.29
2526	2710	3.769536	CATACAGTCGCTCACACATACA	58.230	45.455	0.00	0.00	0.00	2.29
2527	2711	2.535984	GCATACAGTCGCTCACACATAC	59.464	50.000	0.00	0.00	0.00	2.39
2528	2712	2.165437	TGCATACAGTCGCTCACACATA	59.835	45.455	0.00	0.00	0.00	2.29
2541	2725	5.049198	ACACACACAAGAGAAATGCATACAG	60.049	40.000	0.00	0.00	0.00	2.74
2558	2742	2.033299	AGTTTGCTGCACATACACACAC	59.967	45.455	0.00	0.00	33.10	3.82
2960	3199	2.147958	TGACAAAGCACCGACATAACC	58.852	47.619	0.00	0.00	0.00	2.85
2973	3212	8.315391	ACCATCACGATATATGAATGACAAAG	57.685	34.615	0.00	0.00	0.00	2.77
2990	3229	0.320683	TCCAACAGCAGACCATCACG	60.321	55.000	0.00	0.00	0.00	4.35
2994	3233	1.911357	TCATCTCCAACAGCAGACCAT	59.089	47.619	0.00	0.00	0.00	3.55
3025	3264	6.426646	AGGTAACAACATCACTCTTCTCTT	57.573	37.500	0.00	0.00	41.41	2.85
3046	3285	1.275291	AGGACACGACAACCATGTAGG	59.725	52.381	0.00	0.00	40.74	3.18
3047	3286	2.736721	CAAGGACACGACAACCATGTAG	59.263	50.000	0.00	0.00	40.74	2.74
3048	3287	2.761559	CAAGGACACGACAACCATGTA	58.238	47.619	0.00	0.00	40.74	2.29
3050	3289	0.238289	GCAAGGACACGACAACCATG	59.762	55.000	0.00	0.00	0.00	3.66
3060	3302	0.454196	ACCAAAACGTGCAAGGACAC	59.546	50.000	4.26	0.00	37.19	3.67
3083	3325	2.972713	ACAATCACCACCAGTAGACACT	59.027	45.455	0.00	0.00	34.42	3.55
3090	3332	1.815408	GCTCACACAATCACCACCAGT	60.815	52.381	0.00	0.00	0.00	4.00
3092	3334	0.537143	GGCTCACACAATCACCACCA	60.537	55.000	0.00	0.00	0.00	4.17
3113	3355	7.575414	TTAATGTGGAGTAAAAGCTCACAAA	57.425	32.000	6.28	0.00	37.24	2.83
3136	3378	9.733556	TGTGAGTGTTGTAGTATCCATAATTTT	57.266	29.630	0.00	0.00	0.00	1.82
3141	3383	6.183360	CCCATGTGAGTGTTGTAGTATCCATA	60.183	42.308	0.00	0.00	0.00	2.74
3147	3389	2.027561	GGCCCATGTGAGTGTTGTAGTA	60.028	50.000	0.00	0.00	0.00	1.82
3148	3390	1.271379	GGCCCATGTGAGTGTTGTAGT	60.271	52.381	0.00	0.00	0.00	2.73
3150	3392	0.321210	CGGCCCATGTGAGTGTTGTA	60.321	55.000	0.00	0.00	0.00	2.41
3151	3393	1.600636	CGGCCCATGTGAGTGTTGT	60.601	57.895	0.00	0.00	0.00	3.32
3152	3394	2.334946	CCGGCCCATGTGAGTGTTG	61.335	63.158	0.00	0.00	0.00	3.33
3172	3419	0.316522	GAGCGAGGCAGAGCATCATA	59.683	55.000	4.51	0.00	39.45	2.15
3196	3443	6.769512	AGCTAGTGAACAAAATAAGGAGTCA	58.230	36.000	0.00	0.00	0.00	3.41
3198	3445	8.376270	ACTAAGCTAGTGAACAAAATAAGGAGT	58.624	33.333	0.00	0.00	37.69	3.85
3203	3450	8.594550	AGAGGACTAAGCTAGTGAACAAAATAA	58.405	33.333	0.00	0.00	39.59	1.40
3205	3452	7.010339	AGAGGACTAAGCTAGTGAACAAAAT	57.990	36.000	0.00	0.00	39.59	1.82
3208	3455	4.463186	GGAGAGGACTAAGCTAGTGAACAA	59.537	45.833	0.00	0.00	39.59	2.83
3209	3456	4.017808	GGAGAGGACTAAGCTAGTGAACA	58.982	47.826	0.00	0.00	39.59	3.18
3212	3459	2.091775	GGGGAGAGGACTAAGCTAGTGA	60.092	54.545	0.00	0.00	39.59	3.41
3213	3460	2.312390	GGGGAGAGGACTAAGCTAGTG	58.688	57.143	0.00	0.00	39.59	2.74
3214	3461	1.218450	GGGGGAGAGGACTAAGCTAGT	59.782	57.143	0.00	0.00	42.86	2.57
3233	3480	4.821589	GTGAAGCGAGCGGAGGGG	62.822	72.222	0.00	0.00	0.00	4.79
3234	3481	3.764466	AGTGAAGCGAGCGGAGGG	61.764	66.667	0.00	0.00	0.00	4.30
3235	3482	2.507992	CAGTGAAGCGAGCGGAGG	60.508	66.667	0.00	0.00	0.00	4.30
3237	3484	2.271607	CTAGCAGTGAAGCGAGCGGA	62.272	60.000	0.00	0.00	40.15	5.54
3243	3490	0.172127	TCTGAGCTAGCAGTGAAGCG	59.828	55.000	18.83	0.00	43.63	4.68

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.