AutoCloner

Multiple sequence alignment - TraesCS2A01G355700

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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	TraesCS2A01G355700	chr2A	100.000	5034	0	0	1	5034	598624606	598619573	0.000000e+00	9297
1	TraesCS2A01G355700	chr2D	95.726	2597	90	13	2010	4591	450991701	450994291	0.000000e+00	4161
2	TraesCS2A01G355700	chr2D	96.141	1477	42	9	526	2001	450990192	450991654	0.000000e+00	2398
3	TraesCS2A01G355700	chr2D	87.217	1369	102	35	583	1938	82142138	82143446	0.000000e+00	1491
4	TraesCS2A01G355700	chr2D	85.505	1366	142	29	3016	4347	488553348	488552005	0.000000e+00	1375
5	TraesCS2A01G355700	chr2D	87.656	1199	117	21	3016	4203	489369524	489368346	0.000000e+00	1365
6	TraesCS2A01G355700	chr2D	85.212	1366	146	34	3016	4347	488453976	488452633	0.000000e+00	1352
7	TraesCS2A01G355700	chr2D	85.703	1315	133	28	3015	4317	82144028	82145299	0.000000e+00	1336
8	TraesCS2A01G355700	chr2D	85.027	1309	161	25	2010	3305	450983839	450985125	0.000000e+00	1299
9	TraesCS2A01G355700	chr2D	90.270	925	70	8	1017	1941	488554796	488553892	0.000000e+00	1192
10	TraesCS2A01G355700	chr2D	90.530	887	64	8	1017	1903	489370935	489370069	0.000000e+00	1155
11	TraesCS2A01G355700	chr2D	94.798	519	27	0	1	519	190995554	190995036	0.000000e+00	809
12	TraesCS2A01G355700	chr2D	87.321	560	52	8	1382	1941	488455085	488454545	1.540000e-174	623
13	TraesCS2A01G355700	chr2D	94.412	340	18	1	1018	1357	488455409	488455071	5.780000e-144	521
14	TraesCS2A01G355700	chr2D	84.211	456	47	15	2487	2932	488553824	488553384	2.170000e-113	420
15	TraesCS2A01G355700	chr2D	88.462	312	30	3	2655	2966	82143719	82144024	6.150000e-99	372
16	TraesCS2A01G355700	chr2D	83.886	422	35	17	4613	5034	450994381	450994769	6.150000e-99	372
17	TraesCS2A01G355700	chr2D	85.255	373	41	9	2577	2949	489369901	489369543	6.150000e-99	372
18	TraesCS2A01G355700	chr2D	80.730	493	55	26	2487	2949	488454477	488453995	1.040000e-91	348
19	TraesCS2A01G355700	chr2D	93.421	152	8	2	4441	4591	450987159	450987309	1.820000e-54	224
20	TraesCS2A01G355700	chr2D	78.042	378	35	20	548	903	489371348	489370997	1.430000e-45	195
21	TraesCS2A01G355700	chr2B	92.497	2399	122	29	2649	5034	531131194	531133547	0.000000e+00	3380
22	TraesCS2A01G355700	chr2B	96.286	1481	44	7	520	1996	531128994	531130467	0.000000e+00	2420
23	TraesCS2A01G355700	chr2B	85.417	1344	146	25	3015	4347	133980530	133981834	0.000000e+00	1351
24	TraesCS2A01G355700	chr2B	86.561	1198	130	23	3016	4203	572704988	572703812	0.000000e+00	1291
25	TraesCS2A01G355700	chr2B	90.811	925	65	8	1017	1941	572706435	572705531	0.000000e+00	1219
26	TraesCS2A01G355700	chr2B	85.280	1250	105	37	583	1797	133978675	133979880	0.000000e+00	1216
27	TraesCS2A01G355700	chr2B	93.760	657	29	8	2013	2661	531130525	531131177	0.000000e+00	976
28	TraesCS2A01G355700	chr2B	83.263	472	55	14	2487	2949	572705463	572705007	3.630000e-111	412
29	TraesCS2A01G355700	chr2B	89.831	295	27	2	2655	2949	133980221	133980512	4.760000e-100	375
30	TraesCS2A01G355700	chr2B	77.428	381	37	19	545	903	572706850	572706497	1.110000e-41	182
31	TraesCS2A01G355700	chr4D	95.367	518	24	0	1	518	9244379	9243862	0.000000e+00	824
32	TraesCS2A01G355700	chr3D	94.487	526	28	1	1	525	582096791	582096266	0.000000e+00	809
33	TraesCS2A01G355700	chr3D	76.134	507	101	19	1283	1779	390658593	390659089	1.080000e-61	248
34	TraesCS2A01G355700	chr7D	94.778	517	25	2	1	517	595675113	595674599	0.000000e+00	804
35	TraesCS2A01G355700	chr7D	94.242	521	28	2	1	521	544781589	544781071	0.000000e+00	795
36	TraesCS2A01G355700	chr5D	94.297	526	23	5	1	519	294593212	294593737	0.000000e+00	798
37	TraesCS2A01G355700	chr5A	94.380	516	29	0	1	516	71472376	71471861	0.000000e+00	793
38	TraesCS2A01G355700	chr1D	94.186	516	30	0	1	516	292525327	292525842	0.000000e+00	787
39	TraesCS2A01G355700	chr6A	93.834	519	30	2	1	518	461864868	461865385	0.000000e+00	780

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	TraesCS2A01G355700	chr2A	598619573	598624606	5033	True	9297.000000	9297	100.000000	1	5034	1	chr2A.!!$R1	5033
1	TraesCS2A01G355700	chr2D	450983839	450994769	10930	False	1690.800000	4161	90.840200	526	5034	5	chr2D.!!$F2	4508
2	TraesCS2A01G355700	chr2D	82142138	82145299	3161	False	1066.333333	1491	87.127333	583	4317	3	chr2D.!!$F1	3734
3	TraesCS2A01G355700	chr2D	488552005	488554796	2791	True	995.666667	1375	86.662000	1017	4347	3	chr2D.!!$R3	3330
4	TraesCS2A01G355700	chr2D	190995036	190995554	518	True	809.000000	809	94.798000	1	519	1	chr2D.!!$R1	518
5	TraesCS2A01G355700	chr2D	489368346	489371348	3002	True	771.750000	1365	85.370750	548	4203	4	chr2D.!!$R4	3655
6	TraesCS2A01G355700	chr2D	488452633	488455409	2776	True	711.000000	1352	86.918750	1018	4347	4	chr2D.!!$R2	3329
7	TraesCS2A01G355700	chr2B	531128994	531133547	4553	False	2258.666667	3380	94.181000	520	5034	3	chr2B.!!$F2	4514
8	TraesCS2A01G355700	chr2B	133978675	133981834	3159	False	980.666667	1351	86.842667	583	4347	3	chr2B.!!$F1	3764
9	TraesCS2A01G355700	chr2B	572703812	572706850	3038	True	776.000000	1291	84.515750	545	4203	4	chr2B.!!$R1	3658
10	TraesCS2A01G355700	chr4D	9243862	9244379	517	True	824.000000	824	95.367000	1	518	1	chr4D.!!$R1	517
11	TraesCS2A01G355700	chr3D	582096266	582096791	525	True	809.000000	809	94.487000	1	525	1	chr3D.!!$R1	524
12	TraesCS2A01G355700	chr7D	595674599	595675113	514	True	804.000000	804	94.778000	1	517	1	chr7D.!!$R2	516
13	TraesCS2A01G355700	chr7D	544781071	544781589	518	True	795.000000	795	94.242000	1	521	1	chr7D.!!$R1	520
14	TraesCS2A01G355700	chr5D	294593212	294593737	525	False	798.000000	798	94.297000	1	519	1	chr5D.!!$F1	518
15	TraesCS2A01G355700	chr5A	71471861	71472376	515	True	793.000000	793	94.380000	1	516	1	chr5A.!!$R1	515
16	TraesCS2A01G355700	chr1D	292525327	292525842	515	False	787.000000	787	94.186000	1	516	1	chr1D.!!$F1	515
17	TraesCS2A01G355700	chr6A	461864868	461865385	517	False	780.000000	780	93.834000	1	518	1	chr6A.!!$F1	517

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
990	6889	0.249238	CAACTCCGCTAGCCTGCTAG	60.249	60.000	19.48	19.48	46.41	3.42	F
1590	7489	3.691342	CTGGCGGAGGTGGTCGAA	61.691	66.667	0.00	0.00	0.00	3.71	F
2466	8494	1.335324	GCGTGTTGAAGCAAGCTGATT	60.335	47.619	0.00	0.00	39.96	2.57	F
3531	9631	1.066787	GGTCTGCTGTCCTTGAGGTAC	60.067	57.143	0.00	0.00	36.34	3.34	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1835	7735	0.647410	GTCACATGCGATCCACGAAG	59.353	55.000	0.00	45.77	3.79	R
3341	9441	4.368315	TCATCGTCTCCAATGGTTTATCG	58.632	43.478	0.00	0.00	2.92	R
3811	9915	2.172293	AGACAATTCCTCCCTCATGAGC	59.828	50.000	17.76	0.00	4.26	R
4801	11016	0.461870	CCGTTGCTACATGCCTGCTA	60.462	55.000	0.00	42.00	3.49	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
177	178	4.162320	TGAAAACCTGCTCTATCTTCGGAT	59.838	41.667	0.00	0.00	38.39	4.18
283	292	3.781307	CCTTGGATCGGGCGGTGA	61.781	66.667	0.00	0.00	0.00	4.02
387	396	3.192001	CGGTAGTGCTAGAAGTGGTGTTA	59.808	47.826	0.00	0.00	0.00	2.41
414	423	3.722147	CTCAGCGCCTATGTATTCTGTT	58.278	45.455	2.29	0.00	0.00	3.16
419	428	3.741388	GCGCCTATGTATTCTGTTCTGGT	60.741	47.826	0.00	0.00	0.00	4.00
557	6383	4.893608	ACTAAAATGATTGGTTGTTGCCC	58.106	39.130	0.00	0.00	0.00	5.36
839	6722	3.680789	CGATTATTTTCCACGTGAAGCC	58.319	45.455	19.30	0.00	33.63	4.35
881	6767	3.903783	GCCCTTGCAAGCGATACA	58.096	55.556	21.43	0.00	37.47	2.29
933	6821	2.283298	TGATTGCCGAGAAGATCTTGC	58.717	47.619	14.00	10.58	0.00	4.01
990	6889	0.249238	CAACTCCGCTAGCCTGCTAG	60.249	60.000	19.48	19.48	46.41	3.42
1077	6976	4.792804	GCCACCCTGCTGAGCCTC	62.793	72.222	0.23	0.00	0.00	4.70
1590	7489	3.691342	CTGGCGGAGGTGGTCGAA	61.691	66.667	0.00	0.00	0.00	3.71
1809	7708	4.193826	GTGAGTGACACCTGTGATACAT	57.806	45.455	3.94	0.00	43.05	2.29
1978	7878	8.894768	ATGTTCTTTTATGCTCCTACATAGAC	57.105	34.615	0.00	0.00	34.15	2.59
2059	8003	5.693104	TGTGTTGTTATTGTCGAACCTACTC	59.307	40.000	0.00	0.00	0.00	2.59
2062	8006	3.119388	TGTTATTGTCGAACCTACTCCGG	60.119	47.826	0.00	0.00	0.00	5.14
2109	8055	4.809426	AGATAACCGCAGAAGAAATTACCG	59.191	41.667	0.00	0.00	0.00	4.02
2124	8070	2.837532	TACCGCCGTTTTTCTAAGGT	57.162	45.000	0.00	0.00	0.00	3.50
2232	8182	4.707934	TGTAACGATCAATGACCTACAGGA	59.292	41.667	1.29	0.00	38.94	3.86
2312	8265	6.112058	TCCTTTGCATTAAAATAATGGGCAC	58.888	36.000	11.02	0.00	0.00	5.01
2326	8279	3.403057	GCACGACACGCACACGAT	61.403	61.111	0.00	0.00	43.93	3.73
2333	8286	1.736282	CACGCACACGATAGCACCA	60.736	57.895	0.00	0.00	43.93	4.17
2454	8482	1.403323	TCAATGTTGCTTGCGTGTTGA	59.597	42.857	0.00	0.00	0.00	3.18
2466	8494	1.335324	GCGTGTTGAAGCAAGCTGATT	60.335	47.619	0.00	0.00	39.96	2.57
2467	8495	2.313234	CGTGTTGAAGCAAGCTGATTG	58.687	47.619	0.40	0.40	42.20	2.67
2577	8606	7.064229	ACTTTACAGACCCTTTGGAAACATTA	58.936	34.615	0.00	0.00	42.32	1.90
2795	8892	3.960102	TCTTGAGCCCTCACAAATTTGTT	59.040	39.130	21.10	5.86	39.91	2.83
2997	9094	7.774134	TGTGTTGTGTACCATATATAGTTCGT	58.226	34.615	0.00	0.00	0.00	3.85
3006	9103	7.241042	ACCATATATAGTTCGTGGTATTGCT	57.759	36.000	3.57	0.00	41.15	3.91
3305	9402	4.289245	TCTACCCATCAGTGATCATGACA	58.711	43.478	1.56	0.00	0.00	3.58
3341	9441	1.538687	ATTTTGGTGAGCCTGGCTGC	61.539	55.000	28.82	18.01	39.88	5.25
3531	9631	1.066787	GGTCTGCTGTCCTTGAGGTAC	60.067	57.143	0.00	0.00	36.34	3.34
3700	9804	6.302535	TCCACGGAGGAGTTTAAATTCATA	57.697	37.500	12.19	0.00	43.07	2.15
3811	9915	2.550830	AACAGGCAGTCAAGTACCAG	57.449	50.000	0.00	0.00	0.00	4.00
3931	10035	7.672983	TCATAAGAAGTTCCAAAGCTACTTG	57.327	36.000	3.57	0.00	32.58	3.16
4140	10250	2.190578	GCGGTGATAAGCTGCCCT	59.809	61.111	0.00	0.00	32.41	5.19
4158	10268	6.681865	GCTGCCCTTTTAACACACTAGAAAAA	60.682	38.462	0.00	0.00	0.00	1.94
4313	10452	3.915437	AAAAGGCTATGTTTCGGTGTG	57.085	42.857	0.00	0.00	0.00	3.82
4351	10490	5.455392	TCGAGATTTTCTTTCTTACGACGT	58.545	37.500	5.52	5.52	0.00	4.34
4352	10491	6.602179	TCGAGATTTTCTTTCTTACGACGTA	58.398	36.000	2.97	2.97	0.00	3.57
4353	10492	6.740002	TCGAGATTTTCTTTCTTACGACGTAG	59.260	38.462	7.89	3.31	0.00	3.51
4548	10695	3.248602	GCAATGATCGCGACCTAAGAATT	59.751	43.478	12.93	0.00	0.00	2.17
4591	10738	7.864379	AGGCTATCGAAATTTGATTTTGCATAG	59.136	33.333	0.45	0.00	34.35	2.23
4592	10739	7.115378	GGCTATCGAAATTTGATTTTGCATAGG	59.885	37.037	0.45	0.00	34.35	2.57
4634	10849	3.181510	GGTCGATTTTCCGAATGGTCAAG	60.182	47.826	0.00	0.00	40.51	3.02
4642	10857	3.732212	TCCGAATGGTCAAGCATGATAG	58.268	45.455	0.00	0.00	38.01	2.08
4643	10858	3.134623	TCCGAATGGTCAAGCATGATAGT	59.865	43.478	0.00	0.00	38.01	2.12
4644	10859	4.343814	TCCGAATGGTCAAGCATGATAGTA	59.656	41.667	0.00	0.00	38.01	1.82
4650	10865	5.988287	TGGTCAAGCATGATAGTACATTGA	58.012	37.500	0.00	0.00	38.01	2.57
4660	10875	9.591792	GCATGATAGTACATTGATAGATAAGCA	57.408	33.333	0.00	0.00	0.00	3.91
4666	10881	7.219322	AGTACATTGATAGATAAGCATGCACA	58.781	34.615	21.98	7.13	0.00	4.57
4670	10885	7.229907	ACATTGATAGATAAGCATGCACATTGA	59.770	33.333	21.98	0.72	0.00	2.57
4673	10888	7.813645	TGATAGATAAGCATGCACATTGATTC	58.186	34.615	21.98	8.13	0.00	2.52
4676	10891	6.447162	AGATAAGCATGCACATTGATTCATG	58.553	36.000	21.98	10.74	39.29	3.07
4688	10903	7.875327	ACATTGATTCATGTGATCATTCAGA	57.125	32.000	12.88	0.00	30.85	3.27
4689	10904	7.931275	ACATTGATTCATGTGATCATTCAGAG	58.069	34.615	12.88	0.00	30.85	3.35
4690	10905	6.373186	TTGATTCATGTGATCATTCAGAGC	57.627	37.500	12.88	0.00	30.85	4.09
4691	10906	4.820173	TGATTCATGTGATCATTCAGAGCC	59.180	41.667	0.00	0.00	30.85	4.70
4723	10938	3.240899	GCGACACGAACAAATTAATTGCG	60.241	43.478	0.39	6.48	43.13	4.85
4747	10962	1.299648	CTTGCCGGAATGGACCTGA	59.700	57.895	5.05	0.00	42.00	3.86
4753	10968	1.644786	CGGAATGGACCTGAAACGGC	61.645	60.000	0.00	0.00	0.00	5.68
4761	10976	2.331893	CCTGAAACGGCGCATCCAA	61.332	57.895	10.83	0.00	34.01	3.53
4762	10977	1.578926	CTGAAACGGCGCATCCAAA	59.421	52.632	10.83	0.00	34.01	3.28
4763	10978	0.454957	CTGAAACGGCGCATCCAAAG	60.455	55.000	10.83	0.00	34.01	2.77
4771	10986	3.243068	ACGGCGCATCCAAAGAATAAATC	60.243	43.478	10.83	0.00	34.01	2.17
4780	10995	3.384467	CCAAAGAATAAATCCCGGTGCAT	59.616	43.478	0.00	0.00	0.00	3.96
4782	10997	5.507315	CCAAAGAATAAATCCCGGTGCATAC	60.507	44.000	0.00	0.00	0.00	2.39
4783	10998	4.431416	AGAATAAATCCCGGTGCATACA	57.569	40.909	0.00	0.00	0.00	2.29
4785	11000	1.961793	TAAATCCCGGTGCATACAGC	58.038	50.000	0.00	0.00	45.96	4.40
4796	11011	1.668419	GCATACAGCGAAAGGGATGT	58.332	50.000	0.00	0.00	40.15	3.06
4797	11012	2.833794	GCATACAGCGAAAGGGATGTA	58.166	47.619	0.00	0.00	42.29	2.29
4798	11013	2.544267	GCATACAGCGAAAGGGATGTAC	59.456	50.000	0.00	0.00	41.08	2.90
4799	11014	3.741388	GCATACAGCGAAAGGGATGTACT	60.741	47.826	0.00	0.00	41.08	2.73
4800	11015	2.386661	ACAGCGAAAGGGATGTACTG	57.613	50.000	0.00	0.00	34.26	2.74
4801	11016	1.623811	ACAGCGAAAGGGATGTACTGT	59.376	47.619	0.00	0.00	34.26	3.55
4802	11017	2.829720	ACAGCGAAAGGGATGTACTGTA	59.170	45.455	0.00	0.00	34.26	2.74
4803	11018	3.119101	ACAGCGAAAGGGATGTACTGTAG	60.119	47.826	0.00	0.00	34.26	2.74
4804	11019	2.159085	AGCGAAAGGGATGTACTGTAGC	60.159	50.000	0.00	0.00	0.00	3.58
4808	11023	1.123928	AGGGATGTACTGTAGCAGGC	58.876	55.000	0.00	0.00	35.51	4.85
4809	11024	0.830648	GGGATGTACTGTAGCAGGCA	59.169	55.000	0.00	0.50	35.51	4.75
4827	11042	1.655484	CATGTAGCAACGGAGCATCA	58.345	50.000	4.18	3.21	36.25	3.07
4828	11043	2.216046	CATGTAGCAACGGAGCATCAT	58.784	47.619	4.18	5.16	36.25	2.45
4847	11062	3.506067	TCATCTCTGACAGCTTACGTTCA	59.494	43.478	0.00	0.00	0.00	3.18
4855	11070	4.688879	TGACAGCTTACGTTCATTGGTTAG	59.311	41.667	0.00	0.00	0.00	2.34
4857	11072	3.007635	AGCTTACGTTCATTGGTTAGCC	58.992	45.455	0.00	0.00	39.04	3.93
4931	11146	5.163864	TGCGATATGAATTATGAATGCGACC	60.164	40.000	0.00	0.00	0.00	4.79
4978	11193	2.198406	GTGAGGTTTTTCCGGCAAAAC	58.802	47.619	27.72	27.72	43.26	2.43
4980	11195	0.818938	AGGTTTTTCCGGCAAAACGT	59.181	45.000	28.15	26.68	44.41	3.99
4986	11201	0.382515	TTCCGGCAAAACGTTCAAGG	59.617	50.000	0.00	1.53	0.00	3.61

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
33	34	3.357079	GCACCGCTCAACCACCAG	61.357	66.667	0.00	0.00	0.00	4.00
126	127	1.946768	CAATATTCACCGCCACCGAAT	59.053	47.619	0.00	0.00	36.29	3.34
177	178	1.143838	CTTCATCATCGCCGGTCCA	59.856	57.895	1.90	0.00	0.00	4.02
187	188	5.104776	TCAAGAAGGGAACGATCTTCATCAT	60.105	40.000	0.00	0.00	41.16	2.45
338	347	6.350864	CCCGAAGAGATGAAGCTACATATGAT	60.351	42.308	10.38	0.00	0.00	2.45
409	418	0.107897	ACGCACACAACCAGAACAGA	60.108	50.000	0.00	0.00	0.00	3.41
414	423	0.675208	AACACACGCACACAACCAGA	60.675	50.000	0.00	0.00	0.00	3.86
419	428	2.099254	CGCAACACACGCACACAA	59.901	55.556	0.00	0.00	0.00	3.33
532	4241	6.931840	GGGCAACAACCAATCATTTTAGTTTA	59.068	34.615	0.00	0.00	39.74	2.01
536	4245	3.925913	CGGGCAACAACCAATCATTTTAG	59.074	43.478	0.00	0.00	39.74	1.85
880	6766	2.632028	TGGGAAATGGTTTGGATGTGTG	59.368	45.455	0.00	0.00	0.00	3.82
881	6767	2.969628	TGGGAAATGGTTTGGATGTGT	58.030	42.857	0.00	0.00	0.00	3.72
933	6821	0.751277	TAGTGGCAAATGGCGATGGG	60.751	55.000	2.36	0.00	46.16	4.00
990	6889	1.689273	AGAGACGGCATTGAGTATCCC	59.311	52.381	0.00	0.00	29.64	3.85
994	6893	0.175760	GGCAGAGACGGCATTGAGTA	59.824	55.000	0.00	0.00	0.00	2.59
1764	7663	3.403057	GCGAAGTCGAAGCACGCA	61.403	61.111	17.72	0.00	46.75	5.24
1794	7693	6.238211	GCAAGTATCAATGTATCACAGGTGTC	60.238	42.308	0.00	0.00	0.00	3.67
1835	7735	0.647410	GTCACATGCGATCCACGAAG	59.353	55.000	0.00	0.00	45.77	3.79
1963	7863	7.805083	ATTTATCCAGTCTATGTAGGAGCAT	57.195	36.000	0.00	0.00	32.91	3.79
2109	8055	3.935315	AGGACTACCTTAGAAAAACGGC	58.065	45.455	0.00	0.00	45.36	5.68
2232	8182	3.945285	AGTGTGACCAACGTTCAAGAAAT	59.055	39.130	0.00	0.00	0.00	2.17
2312	8265	1.799916	TGCTATCGTGTGCGTGTCG	60.800	57.895	0.00	0.00	39.49	4.35
2326	8279	3.072330	TGTTTGGATCAGTTCTGGTGCTA	59.928	43.478	6.20	0.00	0.00	3.49
2333	8286	6.174720	TGAACTAGTGTTTGGATCAGTTCT	57.825	37.500	15.30	1.51	41.42	3.01
2523	8552	7.886629	ATATTTTGTTGTCATGGTGCTCTAT	57.113	32.000	0.00	0.00	0.00	1.98
2577	8606	8.713971	TCAACATGGTAAGACAATAGGATATGT	58.286	33.333	0.00	0.00	0.00	2.29
2596	8636	5.569059	GCCGACAAGTTAGAAATTCAACATG	59.431	40.000	0.00	4.32	31.48	3.21
3305	9402	6.428771	CACCAAAATCATCAAATGGCTTCTTT	59.571	34.615	0.00	0.00	34.45	2.52
3341	9441	4.368315	TCATCGTCTCCAATGGTTTATCG	58.632	43.478	0.00	0.00	0.00	2.92
3531	9631	6.980593	TGACCATTCATTCTAAAGTTTGTGG	58.019	36.000	0.00	0.00	0.00	4.17
3700	9804	2.839486	TGAACTCGATGGCTGAAAGT	57.161	45.000	0.00	0.00	35.30	2.66
3811	9915	2.172293	AGACAATTCCTCCCTCATGAGC	59.828	50.000	17.76	0.00	0.00	4.26
3931	10035	2.297033	TGCAATTTTCTTGGCACTCTCC	59.703	45.455	0.00	0.00	0.00	3.71
4093	10197	4.390297	GGCTAATGCTCGGATATCAAGAAC	59.610	45.833	4.83	0.00	39.59	3.01
4313	10452	3.004024	TCTCGAGTTACCGTGTGAAAC	57.996	47.619	13.13	0.00	37.35	2.78
4351	10490	5.125739	CCCGCAAAATGGTAAAATGGTACTA	59.874	40.000	0.00	0.00	0.00	1.82
4352	10491	4.081917	CCCGCAAAATGGTAAAATGGTACT	60.082	41.667	0.00	0.00	0.00	2.73
4353	10492	4.177783	CCCGCAAAATGGTAAAATGGTAC	58.822	43.478	0.00	0.00	0.00	3.34
4603	10750	2.374877	GAAAATCGACCGGCCATCGC	62.375	60.000	19.19	3.85	39.46	4.58
4604	10751	1.641677	GAAAATCGACCGGCCATCG	59.358	57.895	18.17	18.17	41.00	3.84
4607	10822	2.435234	CGGAAAATCGACCGGCCA	60.435	61.111	0.00	0.00	44.59	5.36
4619	10834	2.789213	TCATGCTTGACCATTCGGAAA	58.211	42.857	0.00	0.00	35.59	3.13
4634	10849	9.591792	TGCTTATCTATCAATGTACTATCATGC	57.408	33.333	0.00	0.00	0.00	4.06
4642	10857	7.425577	TGTGCATGCTTATCTATCAATGTAC	57.574	36.000	20.33	2.96	0.00	2.90
4643	10858	8.508875	CAATGTGCATGCTTATCTATCAATGTA	58.491	33.333	20.33	0.00	0.00	2.29
4644	10859	7.229907	TCAATGTGCATGCTTATCTATCAATGT	59.770	33.333	20.33	0.00	0.00	2.71
4650	10865	7.754851	TGAATCAATGTGCATGCTTATCTAT	57.245	32.000	20.33	7.42	0.00	1.98
4666	10881	6.016192	GGCTCTGAATGATCACATGAATCAAT	60.016	38.462	15.90	10.11	36.79	2.57
4670	10885	4.788679	TGGCTCTGAATGATCACATGAAT	58.211	39.130	0.00	0.00	36.79	2.57
4673	10888	3.945921	AGTTGGCTCTGAATGATCACATG	59.054	43.478	0.00	0.00	36.79	3.21
4676	10891	3.603532	TCAGTTGGCTCTGAATGATCAC	58.396	45.455	0.00	0.00	40.82	3.06
4684	10899	0.601046	CGCTGTTCAGTTGGCTCTGA	60.601	55.000	8.41	8.41	41.85	3.27
4685	10900	0.601046	TCGCTGTTCAGTTGGCTCTG	60.601	55.000	1.78	4.40	36.85	3.35
4686	10901	0.601311	GTCGCTGTTCAGTTGGCTCT	60.601	55.000	1.78	0.00	0.00	4.09
4687	10902	0.880278	TGTCGCTGTTCAGTTGGCTC	60.880	55.000	1.78	0.00	0.00	4.70
4688	10903	1.146041	TGTCGCTGTTCAGTTGGCT	59.854	52.632	1.78	0.00	0.00	4.75
4689	10904	1.279840	GTGTCGCTGTTCAGTTGGC	59.720	57.895	1.78	0.00	0.00	4.52
4690	10905	0.874175	TCGTGTCGCTGTTCAGTTGG	60.874	55.000	1.78	0.00	0.00	3.77
4691	10906	0.927537	TTCGTGTCGCTGTTCAGTTG	59.072	50.000	1.78	0.00	0.00	3.16
4747	10962	0.887933	ATTCTTTGGATGCGCCGTTT	59.112	45.000	4.18	0.00	40.66	3.60
4753	10968	3.304659	CCGGGATTTATTCTTTGGATGCG	60.305	47.826	0.00	0.00	0.00	4.73
4761	10976	4.787551	TGTATGCACCGGGATTTATTCTT	58.212	39.130	6.32	0.00	0.00	2.52
4762	10977	4.389374	CTGTATGCACCGGGATTTATTCT	58.611	43.478	6.32	0.00	0.00	2.40
4763	10978	3.058224	GCTGTATGCACCGGGATTTATTC	60.058	47.826	6.32	0.00	42.31	1.75
4771	10986	1.705337	CTTTCGCTGTATGCACCGGG	61.705	60.000	6.32	0.00	43.06	5.73
4780	10995	2.829720	ACAGTACATCCCTTTCGCTGTA	59.170	45.455	0.00	0.00	34.47	2.74
4782	10997	2.386661	ACAGTACATCCCTTTCGCTG	57.613	50.000	0.00	0.00	0.00	5.18
4783	10998	2.159085	GCTACAGTACATCCCTTTCGCT	60.159	50.000	0.00	0.00	0.00	4.93
4785	11000	3.448686	CTGCTACAGTACATCCCTTTCG	58.551	50.000	0.00	0.00	0.00	3.46
4786	11001	3.798202	CCTGCTACAGTACATCCCTTTC	58.202	50.000	0.00	0.00	0.00	2.62
4787	11002	2.092914	GCCTGCTACAGTACATCCCTTT	60.093	50.000	0.00	0.00	0.00	3.11
4788	11003	1.486726	GCCTGCTACAGTACATCCCTT	59.513	52.381	0.00	0.00	0.00	3.95
4789	11004	1.123928	GCCTGCTACAGTACATCCCT	58.876	55.000	0.00	0.00	0.00	4.20
4790	11005	0.830648	TGCCTGCTACAGTACATCCC	59.169	55.000	0.00	0.00	0.00	3.85
4791	11006	2.158900	ACATGCCTGCTACAGTACATCC	60.159	50.000	0.00	0.00	28.42	3.51
4792	11007	3.185246	ACATGCCTGCTACAGTACATC	57.815	47.619	0.00	0.00	28.42	3.06
4793	11008	3.493350	GCTACATGCCTGCTACAGTACAT	60.493	47.826	0.00	0.00	35.15	2.29
4794	11009	2.159099	GCTACATGCCTGCTACAGTACA	60.159	50.000	0.00	0.00	35.15	2.90
4795	11010	2.159099	TGCTACATGCCTGCTACAGTAC	60.159	50.000	0.00	0.00	42.00	2.73
4796	11011	2.107366	TGCTACATGCCTGCTACAGTA	58.893	47.619	0.00	0.00	42.00	2.74
4797	11012	0.904649	TGCTACATGCCTGCTACAGT	59.095	50.000	0.00	0.00	42.00	3.55
4798	11013	1.667724	GTTGCTACATGCCTGCTACAG	59.332	52.381	12.16	0.00	42.00	2.74
4799	11014	1.737838	GTTGCTACATGCCTGCTACA	58.262	50.000	12.16	0.00	42.00	2.74
4800	11015	0.652592	CGTTGCTACATGCCTGCTAC	59.347	55.000	0.00	1.32	42.00	3.58
4801	11016	0.461870	CCGTTGCTACATGCCTGCTA	60.462	55.000	0.00	0.00	42.00	3.49
4802	11017	1.746615	CCGTTGCTACATGCCTGCT	60.747	57.895	0.00	0.00	42.00	4.24
4803	11018	1.709147	CTCCGTTGCTACATGCCTGC	61.709	60.000	0.00	0.00	42.00	4.85
4804	11019	1.709147	GCTCCGTTGCTACATGCCTG	61.709	60.000	0.00	0.00	42.00	4.85
4808	11023	1.655484	TGATGCTCCGTTGCTACATG	58.345	50.000	0.00	0.00	0.00	3.21
4809	11024	2.103771	AGATGATGCTCCGTTGCTACAT	59.896	45.455	0.00	0.00	34.46	2.29
4827	11042	4.727507	ATGAACGTAAGCTGTCAGAGAT	57.272	40.909	3.32	0.00	45.62	2.75
4828	11043	4.237724	CAATGAACGTAAGCTGTCAGAGA	58.762	43.478	3.32	0.00	45.62	3.10
4847	11062	4.629779	CCGTTCCGGCTAACCAAT	57.370	55.556	0.00	0.00	41.17	3.16
4881	11096	1.375268	GGCAGAGGAGTGTGCAGAC	60.375	63.158	5.72	5.72	44.89	3.51
4931	11146	3.371097	ATCCTGTACCCGCAGCACG	62.371	63.158	0.00	0.00	43.15	5.34
4947	11162	5.617751	CGGAAAAACCTCACATTCTGTCATC	60.618	44.000	0.00	0.00	36.31	2.92
4962	11177	1.589320	GAACGTTTTGCCGGAAAAACC	59.411	47.619	34.96	22.37	43.86	3.27
4978	11193	1.860950	CACTATCGCATCCCTTGAACG	59.139	52.381	0.00	0.00	0.00	3.95
4980	11195	3.995199	GATCACTATCGCATCCCTTGAA	58.005	45.455	0.00	0.00	0.00	2.69

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.