AutoCloner

Multiple sequence alignment - TraesCS3D01G336400

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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	TraesCS3D01G336400	chr3D	100.000	4263	0	0	1	4263	448291764	448296026	0.000000e+00	7873.0
1	TraesCS3D01G336400	chr3D	83.988	331	46	5	3742	4068	589416224	589416551	1.150000e-80	311.0
2	TraesCS3D01G336400	chr3B	91.755	2547	135	38	892	3387	588156215	588158737	0.000000e+00	3470.0
3	TraesCS3D01G336400	chr3B	97.531	81	2	0	4183	4263	588158731	588158811	5.750000e-29	139.0
4	TraesCS3D01G336400	chr3B	90.698	43	4	0	180	222	31431673	31431715	1.660000e-04	58.4
5	TraesCS3D01G336400	chr3A	97.158	1654	39	4	1577	3222	589548058	589549711	0.000000e+00	2787.0
6	TraesCS3D01G336400	chr3A	89.386	1564	92	21	1	1516	589546524	589548061	0.000000e+00	1901.0
7	TraesCS3D01G336400	chr3A	94.196	1051	30	3	3213	4263	589560368	589561387	0.000000e+00	1574.0
8	TraesCS3D01G336400	chr3A	87.037	54	6	1	180	233	158597505	158597453	4.600000e-05	60.2
9	TraesCS3D01G336400	chr1D	88.748	711	59	7	3437	4142	62340825	62340131	0.000000e+00	850.0
10	TraesCS3D01G336400	chr1D	76.250	400	66	21	337	722	57504696	57504312	7.280000e-43	185.0
11	TraesCS3D01G336400	chr1D	88.095	84	9	1	4181	4263	484863345	484863262	9.760000e-17	99.0
12	TraesCS3D01G336400	chr6B	86.443	745	75	13	3423	4142	132149877	132150620	0.000000e+00	793.0
13	TraesCS3D01G336400	chr6B	76.557	546	99	24	124	649	538943064	538943600	5.430000e-69	272.0
14	TraesCS3D01G336400	chr2A	85.345	696	68	18	3478	4142	774917882	774917190	0.000000e+00	689.0
15	TraesCS3D01G336400	chr6A	84.949	691	72	17	3421	4080	97990987	97990298	0.000000e+00	671.0
16	TraesCS3D01G336400	chr6A	75.100	249	57	5	119	365	509287485	509287240	1.250000e-20	111.0
17	TraesCS3D01G336400	chr1A	84.211	722	75	15	3429	4142	278160096	278159406	0.000000e+00	665.0
18	TraesCS3D01G336400	chr1A	77.966	413	77	8	321	722	56625854	56625445	3.290000e-61	246.0
19	TraesCS3D01G336400	chr1A	91.667	84	6	1	4181	4263	581955507	581955424	9.690000e-22	115.0
20	TraesCS3D01G336400	chr5A	81.020	490	55	13	3616	4080	360070333	360069857	5.240000e-94	355.0
21	TraesCS3D01G336400	chr5A	88.406	276	29	3	3422	3694	461945348	461945623	3.180000e-86	329.0
22	TraesCS3D01G336400	chr7A	81.416	452	50	15	3697	4142	692468623	692469046	5.280000e-89	339.0
23	TraesCS3D01G336400	chr7A	88.571	280	29	3	3424	3701	692457726	692458004	1.900000e-88	337.0
24	TraesCS3D01G336400	chr7A	86.641	262	29	2	3887	4142	692459890	692460151	6.980000e-73	285.0
25	TraesCS3D01G336400	chr6D	78.505	535	96	14	47	564	357341766	357342298	2.460000e-87	333.0
26	TraesCS3D01G336400	chr6D	79.620	368	65	8	3714	4076	421471730	421471368	5.470000e-64	255.0
27	TraesCS3D01G336400	chr4A	76.696	575	119	12	2	564	578217677	578218248	5.360000e-79	305.0
28	TraesCS3D01G336400	chr4A	76.829	328	68	5	52	376	222565904	222565582	1.220000e-40	178.0
29	TraesCS3D01G336400	chr7B	73.848	738	149	29	3	722	60612426	60613137	1.970000e-63	254.0
30	TraesCS3D01G336400	chr5D	86.190	210	19	8	3502	3705	43133815	43134020	7.180000e-53	219.0
31	TraesCS3D01G336400	chr7D	73.509	721	126	39	1	706	305119965	305119295	3.340000e-51	213.0
32	TraesCS3D01G336400	chr7D	90.476	84	7	1	4181	4263	211874818	211874901	4.510000e-20	110.0
33	TraesCS3D01G336400	chr4D	76.451	293	55	12	9	294	84257254	84256969	3.430000e-31	147.0
34	TraesCS3D01G336400	chr1B	77.778	189	31	8	349	529	92881097	92880912	5.830000e-19	106.0
35	TraesCS3D01G336400	chr2D	88.889	81	8	1	4181	4260	619468921	619469001	9.760000e-17	99.0
36	TraesCS3D01G336400	chr2B	88.235	85	6	3	4181	4263	14433126	14433044	9.760000e-17	99.0
37	TraesCS3D01G336400	chr2B	88.235	85	6	3	4181	4263	14458719	14458637	9.760000e-17	99.0
38	TraesCS3D01G336400	chr2B	88.235	85	6	3	4181	4263	14487515	14487433	9.760000e-17	99.0

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	TraesCS3D01G336400	chr3D	448291764	448296026	4262	False	7873.0	7873	100.000	1	4263	1	chr3D.!!$F1	4262
1	TraesCS3D01G336400	chr3B	588156215	588158811	2596	False	1804.5	3470	94.643	892	4263	2	chr3B.!!$F2	3371
2	TraesCS3D01G336400	chr3A	589546524	589549711	3187	False	2344.0	2787	93.272	1	3222	2	chr3A.!!$F2	3221
3	TraesCS3D01G336400	chr3A	589560368	589561387	1019	False	1574.0	1574	94.196	3213	4263	1	chr3A.!!$F1	1050
4	TraesCS3D01G336400	chr1D	62340131	62340825	694	True	850.0	850	88.748	3437	4142	1	chr1D.!!$R2	705
5	TraesCS3D01G336400	chr6B	132149877	132150620	743	False	793.0	793	86.443	3423	4142	1	chr6B.!!$F1	719
6	TraesCS3D01G336400	chr6B	538943064	538943600	536	False	272.0	272	76.557	124	649	1	chr6B.!!$F2	525
7	TraesCS3D01G336400	chr2A	774917190	774917882	692	True	689.0	689	85.345	3478	4142	1	chr2A.!!$R1	664
8	TraesCS3D01G336400	chr6A	97990298	97990987	689	True	671.0	671	84.949	3421	4080	1	chr6A.!!$R1	659
9	TraesCS3D01G336400	chr1A	278159406	278160096	690	True	665.0	665	84.211	3429	4142	1	chr1A.!!$R2	713
10	TraesCS3D01G336400	chr7A	692457726	692460151	2425	False	311.0	337	87.606	3424	4142	2	chr7A.!!$F2	718
11	TraesCS3D01G336400	chr6D	357341766	357342298	532	False	333.0	333	78.505	47	564	1	chr6D.!!$F1	517
12	TraesCS3D01G336400	chr4A	578217677	578218248	571	False	305.0	305	76.696	2	564	1	chr4A.!!$F1	562
13	TraesCS3D01G336400	chr7B	60612426	60613137	711	False	254.0	254	73.848	3	722	1	chr7B.!!$F1	719
14	TraesCS3D01G336400	chr7D	305119295	305119965	670	True	213.0	213	73.509	1	706	1	chr7D.!!$R1	705

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
826	849	0.383590	TGGTTCAATGCACGTGGTTG	59.616	50.0	18.88	0.0	0.00	3.77	F
1520	1592	0.245266	CACATGCCAGATGCTTTGCA	59.755	50.0	0.00	0.0	44.86	4.08	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2509	2587	2.347697	TCCACGAAGACAATGACGAG	57.652	50.000	0.00	0.0	0.00	4.18	R
3509	3593	4.275689	TGCAATAGTCACTGTTGTTTCTGG	59.724	41.667	15.04	0.0	35.51	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
45	50	7.604164	AGGATAAAATAGTCATTGTATGCCGAG	59.396	37.037	0.00	0.00	34.67	4.63
50	55	0.809636	TCATTGTATGCCGAGCACCG	60.810	55.000	0.50	0.00	43.04	4.94
71	76	1.990799	TGTAGAGGCGATTGAACACG	58.009	50.000	0.00	0.00	0.00	4.49
138	143	2.233922	ACATCGGGGACAAAGTAGTCAG	59.766	50.000	0.00	0.00	40.29	3.51
157	162	2.095415	CAGCCATCAACATCATATGCCG	60.095	50.000	0.00	0.00	0.00	5.69
194	199	3.517296	TTCAACACTCAATGCCCCTTA	57.483	42.857	0.00	0.00	0.00	2.69
222	227	3.511146	TCCCTTGAAATTGAGAACATGCC	59.489	43.478	0.00	0.00	0.00	4.40
223	228	3.258872	CCCTTGAAATTGAGAACATGCCA	59.741	43.478	0.00	0.00	0.00	4.92
253	259	1.891933	TGGGCATCATAGGGAACTGA	58.108	50.000	0.00	0.00	43.88	3.41
344	351	3.203716	GAAGTATTCCGAGGCCGAATTT	58.796	45.455	9.30	0.25	39.83	1.82
415	431	1.511850	CATTTGGCAGTGTCGAGTGA	58.488	50.000	1.25	0.00	0.00	3.41
421	437	1.583054	GCAGTGTCGAGTGAGGTTTT	58.417	50.000	0.00	0.00	0.00	2.43
423	439	2.821546	CAGTGTCGAGTGAGGTTTTCA	58.178	47.619	0.00	0.00	0.00	2.69
746	769	5.831997	AGCGTTCAAATTTGCTTCTAGTTT	58.168	33.333	13.54	0.00	32.89	2.66
772	795	5.441709	AAAATTCAAACATACGAACGGGT	57.558	34.783	0.00	0.00	0.00	5.28
812	835	2.021457	CCGGACATTTATGGGTGGTTC	58.979	52.381	0.00	0.00	0.00	3.62
813	836	2.619332	CCGGACATTTATGGGTGGTTCA	60.619	50.000	0.00	0.00	0.00	3.18
826	849	0.383590	TGGTTCAATGCACGTGGTTG	59.616	50.000	18.88	0.00	0.00	3.77
970	997	1.723608	CTTTCAACGCCAGTGCACCA	61.724	55.000	14.63	0.00	37.32	4.17
1248	1281	3.051392	GCTTTGGGATCCGCGTTGG	62.051	63.158	4.92	0.00	40.09	3.77
1260	1293	1.535462	CCGCGTTGGAGAACAGAAAAT	59.465	47.619	4.92	0.00	42.00	1.82
1261	1294	2.412847	CCGCGTTGGAGAACAGAAAATC	60.413	50.000	4.92	0.00	42.00	2.17
1268	1301	6.801862	CGTTGGAGAACAGAAAATCAAATACC	59.198	38.462	0.00	0.00	31.78	2.73
1270	1303	5.714806	TGGAGAACAGAAAATCAAATACCCC	59.285	40.000	0.00	0.00	0.00	4.95
1275	1308	2.943033	AGAAAATCAAATACCCCGAGCG	59.057	45.455	0.00	0.00	0.00	5.03
1295	1333	3.611517	CGATTTTATCTTTGCTCTGCCG	58.388	45.455	0.00	0.00	0.00	5.69
1343	1405	5.615289	AGGAATCCGATACTGAGAATTTGG	58.385	41.667	0.00	0.00	0.00	3.28
1345	1407	4.696479	ATCCGATACTGAGAATTTGGCT	57.304	40.909	0.00	0.00	0.00	4.75
1367	1429	1.202486	GCATCGATCGAGGTAAACCCA	60.202	52.381	28.10	0.00	36.42	4.51
1369	1431	1.843368	TCGATCGAGGTAAACCCACT	58.157	50.000	15.15	0.00	36.42	4.00
1388	1450	2.237392	ACTATCAGTTCTTGGTCCTGCC	59.763	50.000	0.00	0.00	37.90	4.85
1424	1486	2.431057	CTGTTCTTGCCGACTAGGGTAT	59.569	50.000	0.00	0.00	41.48	2.73
1519	1591	0.459585	CCACATGCCAGATGCTTTGC	60.460	55.000	0.00	0.00	42.00	3.68
1520	1592	0.245266	CACATGCCAGATGCTTTGCA	59.755	50.000	0.00	0.00	44.86	4.08
1521	1593	0.530744	ACATGCCAGATGCTTTGCAG	59.469	50.000	0.00	0.00	43.65	4.41
1522	1594	0.530744	CATGCCAGATGCTTTGCAGT	59.469	50.000	0.00	0.00	43.65	4.40
1524	1596	1.214589	GCCAGATGCTTTGCAGTGG	59.785	57.895	15.38	15.38	43.65	4.00
1525	1597	1.530013	GCCAGATGCTTTGCAGTGGT	61.530	55.000	18.74	0.00	43.99	4.16
1538	1611	2.375174	TGCAGTGGTGGAGGACTAATTT	59.625	45.455	0.00	0.00	0.00	1.82
1545	1618	4.223032	TGGTGGAGGACTAATTTGAGAGAC	59.777	45.833	0.00	0.00	0.00	3.36
1546	1619	4.425520	GTGGAGGACTAATTTGAGAGACG	58.574	47.826	0.00	0.00	0.00	4.18
1554	1627	4.469945	ACTAATTTGAGAGACGAATCCCCA	59.530	41.667	0.00	0.00	31.98	4.96
1558	1631	1.762957	TGAGAGACGAATCCCCAATCC	59.237	52.381	0.00	0.00	0.00	3.01
1561	1634	2.092914	AGAGACGAATCCCCAATCCAAC	60.093	50.000	0.00	0.00	0.00	3.77
1581	1654	1.056700	ACGGAGGAGGGCATTGCTAT	61.057	55.000	8.82	0.00	0.00	2.97
1585	1658	2.659428	GAGGAGGGCATTGCTATTTGT	58.341	47.619	8.82	0.00	0.00	2.83
1610	1683	1.608025	CCAACTCGTTTCCTGCAGCTA	60.608	52.381	8.66	0.00	0.00	3.32
1611	1684	1.461127	CAACTCGTTTCCTGCAGCTAC	59.539	52.381	8.66	4.63	0.00	3.58
1879	1957	2.124570	CCCAATGGCGGAGACCTG	60.125	66.667	0.00	0.00	25.51	4.00
2332	2410	4.200283	GTCGAGGAGCCGCTCAGG	62.200	72.222	21.76	10.01	44.97	3.86
3118	3198	3.055167	TCTGATTCTTTTGGGCGATGAGA	60.055	43.478	0.00	0.00	0.00	3.27
3297	3380	3.966006	CCCCTTTTAGGTACTCCCTCTAC	59.034	52.174	0.00	0.00	44.81	2.59
3353	3436	4.619628	GCTAATTCTTTTGGGCGGCTTTAA	60.620	41.667	9.56	0.00	0.00	1.52
3418	3501	4.832608	GTCGGCCGGCGGATCTTT	62.833	66.667	35.32	0.00	0.00	2.52
3419	3502	3.148963	TCGGCCGGCGGATCTTTA	61.149	61.111	33.44	9.64	0.00	1.85
3420	3503	2.202960	CGGCCGGCGGATCTTTAA	60.203	61.111	33.44	0.00	0.00	1.52
3421	3504	2.244651	CGGCCGGCGGATCTTTAAG	61.245	63.158	33.44	6.56	0.00	1.85
3422	3505	2.543802	GGCCGGCGGATCTTTAAGC	61.544	63.158	33.44	10.58	0.00	3.09
3423	3506	2.882366	GCCGGCGGATCTTTAAGCG	61.882	63.158	33.44	0.00	0.00	4.68
3424	3507	2.244651	CCGGCGGATCTTTAAGCGG	61.245	63.158	24.41	0.00	0.00	5.52
3425	3508	1.227147	CGGCGGATCTTTAAGCGGA	60.227	57.895	0.00	0.00	32.72	5.54
3426	3509	0.600255	CGGCGGATCTTTAAGCGGAT	60.600	55.000	0.00	0.00	32.72	4.18
3427	3510	1.149148	GGCGGATCTTTAAGCGGATC	58.851	55.000	0.00	0.00	38.01	3.36
3583	3669	5.008613	AGTGACGATTGCAAAAAGAGCTTTA	59.991	36.000	1.71	0.00	31.63	1.85
3693	3780	4.994852	ACTATCGCAACAAGAGCTTTGTTA	59.005	37.500	19.63	10.32	40.30	2.41
3773	5644	4.778143	GCTCGCCGTCAACCCCAT	62.778	66.667	0.00	0.00	0.00	4.00
3861	5734	1.100510	TCGAATCCGACAAGATCCGT	58.899	50.000	0.00	0.00	40.30	4.69
3976	5849	1.257743	TCGGATCCGATGAGATTCCC	58.742	55.000	32.59	0.00	44.01	3.97
3986	5859	0.105194	TGAGATTCCCCGCCTCCATA	60.105	55.000	0.00	0.00	0.00	2.74

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
35	39	1.739929	CAACGGTGCTCGGCATACA	60.740	57.895	1.90	0.00	41.91	2.29
36	40	0.458889	TACAACGGTGCTCGGCATAC	60.459	55.000	0.00	0.00	41.91	2.39
45	50	0.739813	AATCGCCTCTACAACGGTGC	60.740	55.000	0.00	0.00	0.00	5.01
50	55	2.092211	CGTGTTCAATCGCCTCTACAAC	59.908	50.000	0.00	0.00	0.00	3.32
138	143	2.153645	TCGGCATATGATGTTGATGGC	58.846	47.619	6.97	0.00	41.42	4.40
157	162	3.425577	TGAATTGAAAGATGGCGCATC	57.574	42.857	10.83	10.70	40.80	3.91
194	199	7.543359	TGTTCTCAATTTCAAGGGATCAATT	57.457	32.000	0.00	0.00	0.00	2.32
253	259	3.624861	GGATGAAACGATGATGAAGCACT	59.375	43.478	0.00	0.00	0.00	4.40
344	351	9.724839	GTTGTTTACTTTGAAGCAAACACTATA	57.275	29.630	17.46	5.21	46.39	1.31
421	437	1.539388	GCACATTTCCGACCATGTTGA	59.461	47.619	0.00	0.00	30.90	3.18
423	439	1.614996	TGCACATTTCCGACCATGTT	58.385	45.000	0.00	0.00	30.90	2.71
553	574	2.044650	TCGCCGCTGTACTACCCT	60.045	61.111	0.00	0.00	0.00	4.34
581	603	1.202440	TGTTGTATACCGGCGTGATCC	60.202	52.381	6.01	0.00	0.00	3.36
690	713	3.733960	GAAGGTTTGCGGGCGTCC	61.734	66.667	0.00	0.00	0.00	4.79
746	769	5.174035	CCGTTCGTATGTTTGAATTTTTGCA	59.826	36.000	0.00	0.00	0.00	4.08
751	774	4.276431	ACACCCGTTCGTATGTTTGAATTT	59.724	37.500	0.00	0.00	0.00	1.82
766	789	0.475044	TAAGCCCTTCAACACCCGTT	59.525	50.000	0.00	0.00	35.01	4.44
772	795	3.219281	GGACACTTTAAGCCCTTCAACA	58.781	45.455	0.00	0.00	0.00	3.33
812	835	0.733566	GCATCCAACCACGTGCATTG	60.734	55.000	18.80	18.80	37.52	2.82
813	836	1.586028	GCATCCAACCACGTGCATT	59.414	52.632	10.91	3.51	37.52	3.56
826	849	1.527370	GGTACAGACCAGGGCATCC	59.473	63.158	0.00	0.00	46.12	3.51
970	997	3.124636	GCAACGAGTGAATTCATACGGTT	59.875	43.478	27.51	19.26	33.91	4.44
1248	1281	5.646360	TCGGGGTATTTGATTTTCTGTTCTC	59.354	40.000	0.00	0.00	0.00	2.87
1249	1282	5.566469	TCGGGGTATTTGATTTTCTGTTCT	58.434	37.500	0.00	0.00	0.00	3.01
1250	1283	5.676331	GCTCGGGGTATTTGATTTTCTGTTC	60.676	44.000	0.00	0.00	0.00	3.18
1251	1284	4.157840	GCTCGGGGTATTTGATTTTCTGTT	59.842	41.667	0.00	0.00	0.00	3.16
1252	1285	3.694566	GCTCGGGGTATTTGATTTTCTGT	59.305	43.478	0.00	0.00	0.00	3.41
1260	1293	2.702592	AAATCGCTCGGGGTATTTGA	57.297	45.000	0.00	0.00	0.00	2.69
1261	1294	4.755123	AGATAAAATCGCTCGGGGTATTTG	59.245	41.667	0.00	0.00	0.00	2.32
1268	1301	2.614057	AGCAAAGATAAAATCGCTCGGG	59.386	45.455	0.00	0.00	0.00	5.14
1275	1308	3.378427	ACCGGCAGAGCAAAGATAAAATC	59.622	43.478	0.00	0.00	0.00	2.17
1312	1374	4.040095	TCAGTATCGGATTCCTCGTCTCTA	59.960	45.833	0.30	0.00	0.00	2.43
1327	1389	2.289002	GCCAGCCAAATTCTCAGTATCG	59.711	50.000	0.00	0.00	0.00	2.92
1330	1392	2.877097	TGCCAGCCAAATTCTCAGTA	57.123	45.000	0.00	0.00	0.00	2.74
1343	1405	0.032130	TTACCTCGATCGATGCCAGC	59.968	55.000	19.78	0.00	0.00	4.85
1345	1407	1.202486	GGTTTACCTCGATCGATGCCA	60.202	52.381	19.78	4.76	0.00	4.92
1367	1429	2.237392	GGCAGGACCAAGAACTGATAGT	59.763	50.000	0.00	0.00	38.86	2.12
1369	1431	1.559682	GGGCAGGACCAAGAACTGATA	59.440	52.381	0.00	0.00	42.05	2.15
1388	1450	1.672881	GAACAGGGCGAGAATTCATGG	59.327	52.381	8.44	0.00	0.00	3.66
1424	1486	1.403647	CGCGTCCTCTGTTATCCAACA	60.404	52.381	0.00	0.00	42.39	3.33
1519	1591	4.020218	TCTCAAATTAGTCCTCCACCACTG	60.020	45.833	0.00	0.00	0.00	3.66
1520	1592	4.168101	TCTCAAATTAGTCCTCCACCACT	58.832	43.478	0.00	0.00	0.00	4.00
1521	1593	4.223032	TCTCTCAAATTAGTCCTCCACCAC	59.777	45.833	0.00	0.00	0.00	4.16
1522	1594	4.223032	GTCTCTCAAATTAGTCCTCCACCA	59.777	45.833	0.00	0.00	0.00	4.17
1524	1596	4.158025	TCGTCTCTCAAATTAGTCCTCCAC	59.842	45.833	0.00	0.00	0.00	4.02
1525	1597	4.341487	TCGTCTCTCAAATTAGTCCTCCA	58.659	43.478	0.00	0.00	0.00	3.86
1538	1611	1.762957	GGATTGGGGATTCGTCTCTCA	59.237	52.381	0.00	0.00	0.00	3.27
1545	1618	0.732571	CGTGTTGGATTGGGGATTCG	59.267	55.000	0.00	0.00	0.00	3.34
1546	1619	1.102978	CCGTGTTGGATTGGGGATTC	58.897	55.000	0.00	0.00	42.00	2.52
1558	1631	1.002134	AATGCCCTCCTCCGTGTTG	60.002	57.895	0.00	0.00	0.00	3.33
1561	1634	1.971505	TAGCAATGCCCTCCTCCGTG	61.972	60.000	0.00	0.00	0.00	4.94
1571	1644	4.464069	TGGGTTAACAAATAGCAATGCC	57.536	40.909	8.10	0.00	0.00	4.40
1581	1654	4.096682	CAGGAAACGAGTTGGGTTAACAAA	59.903	41.667	8.10	0.00	41.88	2.83
1585	1658	2.223745	GCAGGAAACGAGTTGGGTTAA	58.776	47.619	0.00	0.00	0.00	2.01
1610	1683	1.684049	CCGGCCTCCTCTTCTCAGT	60.684	63.158	0.00	0.00	0.00	3.41
1611	1684	1.380515	TCCGGCCTCCTCTTCTCAG	60.381	63.158	0.00	0.00	0.00	3.35
2172	2250	2.811317	CGTCCAGTTCCTGCGAGC	60.811	66.667	0.00	0.00	0.00	5.03
2199	2277	4.506255	GTCCATCCCCCGCCAAGG	62.506	72.222	0.00	0.00	40.63	3.61
2489	2567	4.740822	GGTGGTGGGCTTGCCGAT	62.741	66.667	5.49	0.00	0.00	4.18
2509	2587	2.347697	TCCACGAAGACAATGACGAG	57.652	50.000	0.00	0.00	0.00	4.18
3118	3198	8.201242	AGAAGAGAGAAAAACTACTCATCCTT	57.799	34.615	0.00	0.00	35.83	3.36
3297	3380	6.560251	GCTCTAAAACGTTCTGCATTTGTTTG	60.560	38.462	0.00	0.00	33.42	2.93
3353	3436	8.457238	AAGCTGAAGAGAGACAACTTATTTTT	57.543	30.769	0.00	0.00	0.00	1.94
3427	3510	4.435651	GCGAGACGGTGGATCTTTAAAAAG	60.436	45.833	0.00	0.00	37.36	2.27
3509	3593	4.275689	TGCAATAGTCACTGTTGTTTCTGG	59.724	41.667	15.04	0.00	35.51	3.86
3583	3669	6.738114	ACAACGTCATCAATGTTTCTGAAAT	58.262	32.000	6.06	0.00	34.80	2.17
3693	3780	3.255149	CCTTCAGCAGAGCATGTTTTCTT	59.745	43.478	0.00	0.00	0.00	2.52
3841	5714	1.681793	ACGGATCTTGTCGGATTCGAT	59.318	47.619	0.00	0.00	44.78	3.59
3861	5734	1.043116	ACGATGGCGAGGATTCCAGA	61.043	55.000	5.29	0.00	41.64	3.86
4030	5925	3.502211	TCGGAAAGGAGAATTTGCAACTC	59.498	43.478	0.00	2.42	31.47	3.01
4149	6044	1.079127	CCTTCAACCAGCGGATCGT	60.079	57.895	1.50	0.00	0.00	3.73
4158	6053	3.117284	AGGGAAAAGCTTACCTTCAACCA	60.117	43.478	18.01	0.00	44.35	3.67

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.