AutoCloner

Multiple sequence alignment - TraesCS2A01G308000

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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	TraesCS2A01G308000	chr2A	100.000	6837	0	0	1	6837	529690628	529697464	0.000000e+00	12626.0
1	TraesCS2A01G308000	chr2A	93.393	4556	193	34	1568	6063	529792468	529796975	0.000000e+00	6647.0
2	TraesCS2A01G308000	chr2A	90.700	2699	157	39	3947	6618	528908623	528911254	0.000000e+00	3507.0
3	TraesCS2A01G308000	chr2A	88.963	2546	163	46	1504	3948	528906045	528908573	0.000000e+00	3037.0
4	TraesCS2A01G308000	chr2A	92.320	612	19	9	722	1314	529791497	529792099	0.000000e+00	845.0
5	TraesCS2A01G308000	chr2A	84.584	493	46	23	977	1457	528905569	528906043	4.830000e-126	462.0
6	TraesCS2A01G308000	chr2A	83.708	356	41	10	365	717	729580217	729579876	3.080000e-83	320.0
7	TraesCS2A01G308000	chr2A	90.066	151	11	2	6060	6208	529797007	529797155	7.000000e-45	193.0
8	TraesCS2A01G308000	chr2A	86.420	162	8	6	1370	1521	529792298	529792455	1.530000e-36	165.0
9	TraesCS2A01G308000	chr2B	95.807	4531	107	21	1574	6063	463856119	463860607	0.000000e+00	7238.0
10	TraesCS2A01G308000	chr2B	93.662	4323	170	42	1800	6063	464021537	464025814	0.000000e+00	6370.0
11	TraesCS2A01G308000	chr2B	88.832	2731	165	50	3947	6619	463769013	463771661	0.000000e+00	3225.0
12	TraesCS2A01G308000	chr2B	89.638	2538	152	43	1504	3948	463766444	463768963	0.000000e+00	3127.0
13	TraesCS2A01G308000	chr2B	90.081	988	53	20	572	1528	463855129	463856102	0.000000e+00	1240.0
14	TraesCS2A01G308000	chr2B	95.391	781	32	3	6060	6837	463860639	463861418	0.000000e+00	1240.0
15	TraesCS2A01G308000	chr2B	89.467	788	36	19	729	1494	464020300	464021062	0.000000e+00	952.0
16	TraesCS2A01G308000	chr2B	88.017	726	73	10	3	724	775849687	775848972	0.000000e+00	846.0
17	TraesCS2A01G308000	chr2B	85.976	492	42	18	974	1457	463765970	463766442	1.020000e-137	501.0
18	TraesCS2A01G308000	chr2B	89.956	229	15	2	358	586	463853584	463853804	8.680000e-74	289.0
19	TraesCS2A01G308000	chr2B	87.417	151	11	3	6060	6208	464025846	464025990	4.240000e-37	167.0
20	TraesCS2A01G308000	chr2D	92.828	4685	200	53	1634	6229	392052528	392057165	0.000000e+00	6665.0
21	TraesCS2A01G308000	chr2D	89.059	2541	165	44	1504	3948	391850643	391853166	0.000000e+00	3048.0
22	TraesCS2A01G308000	chr2D	91.592	2129	112	15	3947	6060	391853216	391855292	0.000000e+00	2878.0
23	TraesCS2A01G308000	chr2D	91.757	1286	72	14	41	1309	392051082	392052350	0.000000e+00	1757.0
24	TraesCS2A01G308000	chr2D	89.250	400	37	4	6229	6626	391863153	391863548	4.760000e-136	496.0
25	TraesCS2A01G308000	chr2D	84.318	491	52	13	974	1457	391850169	391850641	2.250000e-124	457.0
26	TraesCS2A01G308000	chr2D	89.730	185	11	4	1350	1529	392052349	392052530	5.330000e-56	230.0
27	TraesCS2A01G308000	chr7B	86.546	721	80	14	3	717	80527420	80526711	0.000000e+00	778.0
28	TraesCS2A01G308000	chr4A	86.192	717	86	10	3	715	445811427	445812134	0.000000e+00	763.0
29	TraesCS2A01G308000	chr3B	85.970	727	85	14	1	722	722349852	722349138	0.000000e+00	761.0
30	TraesCS2A01G308000	chr3B	87.572	346	38	5	1	344	722305376	722305034	4.970000e-106	396.0
31	TraesCS2A01G308000	chr4B	85.797	690	83	11	25	705	188604685	188604002	0.000000e+00	717.0
32	TraesCS2A01G308000	chr5A	83.732	418	49	9	303	718	683278826	683278426	1.800000e-100	377.0
33	TraesCS2A01G308000	chr6B	73.996	523	104	23	4084	4602	227096126	227096620	4.210000e-42	183.0
34	TraesCS2A01G308000	chr6D	73.512	521	111	18	4084	4602	128257908	128258403	9.120000e-39	172.0
35	TraesCS2A01G308000	chr5B	85.366	82	10	1	2102	2183	62958499	62958578	4.390000e-12	84.2

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	TraesCS2A01G308000	chr2A	529690628	529697464	6836	False	12626.000000	12626	100.000000	1	6837	1	chr2A.!!$F1	6836
1	TraesCS2A01G308000	chr2A	528905569	528911254	5685	False	2335.333333	3507	88.082333	977	6618	3	chr2A.!!$F2	5641
2	TraesCS2A01G308000	chr2A	529791497	529797155	5658	False	1962.500000	6647	90.549750	722	6208	4	chr2A.!!$F3	5486
3	TraesCS2A01G308000	chr2B	463853584	463861418	7834	False	2501.750000	7238	92.808750	358	6837	4	chr2B.!!$F2	6479
4	TraesCS2A01G308000	chr2B	464020300	464025990	5690	False	2496.333333	6370	90.182000	729	6208	3	chr2B.!!$F3	5479
5	TraesCS2A01G308000	chr2B	463765970	463771661	5691	False	2284.333333	3225	88.148667	974	6619	3	chr2B.!!$F1	5645
6	TraesCS2A01G308000	chr2B	775848972	775849687	715	True	846.000000	846	88.017000	3	724	1	chr2B.!!$R1	721
7	TraesCS2A01G308000	chr2D	392051082	392057165	6083	False	2884.000000	6665	91.438333	41	6229	3	chr2D.!!$F3	6188
8	TraesCS2A01G308000	chr2D	391850169	391855292	5123	False	2127.666667	3048	88.323000	974	6060	3	chr2D.!!$F2	5086
9	TraesCS2A01G308000	chr7B	80526711	80527420	709	True	778.000000	778	86.546000	3	717	1	chr7B.!!$R1	714
10	TraesCS2A01G308000	chr4A	445811427	445812134	707	False	763.000000	763	86.192000	3	715	1	chr4A.!!$F1	712
11	TraesCS2A01G308000	chr3B	722349138	722349852	714	True	761.000000	761	85.970000	1	722	1	chr3B.!!$R2	721
12	TraesCS2A01G308000	chr4B	188604002	188604685	683	True	717.000000	717	85.797000	25	705	1	chr4B.!!$R1	680

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
607	1948	0.107945	GCGCCTCTCTTCAGGTTCAT	60.108	55.000	0.00	0.00	35.72	2.57	F
1393	2956	0.039708	GTTTCCTGCTGCTGAAGTGC	60.040	55.000	8.20	0.00	0.00	4.40	F
1606	3205	0.391597	GAAGTTGGTCTCACGGGTGA	59.608	55.000	1.05	1.05	38.06	4.02	F
2294	4150	0.674895	ATGAACTCCGACAAGCAGCC	60.675	55.000	0.00	0.00	0.00	4.85	F
2769	4637	1.134729	GCCAAGAGGAAGAGAGCTGAG	60.135	57.143	0.00	0.00	36.89	3.35	F
3735	5632	1.656095	GAAGCAGGTTTCTGACGATCG	59.344	52.381	14.88	14.88	43.49	3.69	F
3921	5818	2.038863	TCTGGAAAGCTCCCACCTTA	57.961	50.000	3.86	0.00	41.64	2.69	F
3998	5946	3.391965	CCTACAGAGAATGAGCAGATGC	58.608	50.000	0.00	0.00	42.49	3.91	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1486	3067	0.324943	ACATACCCGCAGCTTTCACT	59.675	50.000	0.00	0.00	0.00	3.41	R
2353	4209	1.006102	CCTGCCGAACACGAGTCTT	60.006	57.895	0.00	0.00	0.00	3.01	R
3114	4989	1.048601	TGAACTTGCCTCTCGAACCT	58.951	50.000	0.00	0.00	0.00	3.50	R
3604	5501	1.065126	GCAGCCCTAACAAGATCACCT	60.065	52.381	0.00	0.00	0.00	4.00	R
4139	6087	2.329379	GCTGTAGTCAGGTTTGTCTCG	58.671	52.381	0.00	0.00	41.57	4.04	R
5065	7050	2.072298	CTGAAGGTACAGCAGCTGTTC	58.928	52.381	32.64	26.37	42.59	3.18	R
5743	7730	1.227527	CTTCACCACACGGTCAGCA	60.228	57.895	0.00	0.00	44.71	4.41	R
5953	7943	6.958192	TCCTGAACTACTAATTTCTGTACCCT	59.042	38.462	0.00	0.00	0.00	4.34	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
106	108	1.001406	GCTCTACCTGCTCCGCAATAT	59.999	52.381	0.00	0.00	38.41	1.28
131	133	0.813610	CTGGCGACACAACAAGACCA	60.814	55.000	0.00	0.00	35.60	4.02
137	139	3.243068	GCGACACAACAAGACCAATCTTT	60.243	43.478	0.00	0.00	42.91	2.52
177	179	2.203084	TGTGACGCGGCTTGGAAA	60.203	55.556	15.80	0.00	0.00	3.13
432	434	0.750249	TCCGTCTTCAACACTGCAGA	59.250	50.000	23.35	0.00	0.00	4.26
506	508	4.907269	TCCATCCAACCAGAATAGCTCATA	59.093	41.667	0.00	0.00	0.00	2.15
515	517	7.618019	ACCAGAATAGCTCATATTAACAGGA	57.382	36.000	0.00	0.00	34.10	3.86
523	525	5.415415	CTCATATTAACAGGAGCAAGTGC	57.585	43.478	0.00	0.00	42.49	4.40
549	551	3.708403	TGTTCATCATCAGGCTCAGTT	57.292	42.857	0.00	0.00	0.00	3.16
550	552	4.824479	TGTTCATCATCAGGCTCAGTTA	57.176	40.909	0.00	0.00	0.00	2.24
589	1930	6.399639	AGTCTAGATCTTTAGCTGTTAGGC	57.600	41.667	0.00	0.00	0.00	3.93
607	1948	0.107945	GCGCCTCTCTTCAGGTTCAT	60.108	55.000	0.00	0.00	35.72	2.57
645	1990	3.944015	GAGATGTTCTCCCATTGTTCAGG	59.056	47.826	0.00	0.00	37.55	3.86
746	2098	4.670735	CGCCGTGAAAATAACCGAAATCTT	60.671	41.667	0.00	0.00	0.00	2.40
868	2231	4.130281	GACGGCGCGGAAGAAACG	62.130	66.667	22.76	9.49	0.00	3.60
1247	2617	0.533032	CCTTCTTCCTCCTCACGGTC	59.467	60.000	0.00	0.00	0.00	4.79
1385	2948	0.804989	ATAGTTGCGTTTCCTGCTGC	59.195	50.000	0.00	0.00	0.00	5.25
1393	2956	0.039708	GTTTCCTGCTGCTGAAGTGC	60.040	55.000	8.20	0.00	0.00	4.40
1441	3012	6.314917	AGTGGTATTGTTCCTGGAAGATTTT	58.685	36.000	9.92	0.00	34.07	1.82
1521	3102	5.183140	CGGGTATGTGAAAGAATTCCTTTGT	59.817	40.000	0.65	0.00	44.63	2.83
1536	3117	2.287009	CCTTTGTTTGAGCCTGTTCGTC	60.287	50.000	0.00	0.00	0.00	4.20
1545	3126	2.572284	CTGTTCGTCGGGGAGTCC	59.428	66.667	0.00	0.00	0.00	3.85
1548	3129	1.368579	GTTCGTCGGGGAGTCCAAA	59.631	57.895	12.30	0.00	34.36	3.28
1606	3205	0.391597	GAAGTTGGTCTCACGGGTGA	59.608	55.000	1.05	1.05	38.06	4.02
1623	3222	3.500680	GGGTGACACGAATTGCTTTTCTA	59.499	43.478	0.00	0.00	0.00	2.10
1693	3299	3.383185	TGTTTGATTGAAGCGTTTTCCCT	59.617	39.130	0.00	0.00	0.00	4.20
1735	3341	5.759506	TTTTATCTGCAGTTCGGTGAAAA	57.240	34.783	14.67	6.02	0.00	2.29
1759	3365	6.996509	ACGTAAACAGGGACAATTAGAGTAA	58.003	36.000	0.00	0.00	0.00	2.24
1762	3368	9.590451	CGTAAACAGGGACAATTAGAGTAATTA	57.410	33.333	0.00	0.00	36.29	1.40
1791	3609	9.433153	GTAACTAACTATTGCCTGTAGAAAAGT	57.567	33.333	0.00	0.00	0.00	2.66
1792	3610	8.919777	AACTAACTATTGCCTGTAGAAAAGTT	57.080	30.769	0.00	0.00	0.00	2.66
1947	3772	4.593634	ACTTGGTCTGGCTTAGAAGTAACT	59.406	41.667	0.00	0.00	37.12	2.24
2014	3843	5.491982	AGTCTGTTGGTTGATGTAATCCTC	58.508	41.667	0.00	0.00	44.73	3.71
2018	3847	5.416083	TGTTGGTTGATGTAATCCTCGTAG	58.584	41.667	0.00	0.00	44.73	3.51
2294	4150	0.674895	ATGAACTCCGACAAGCAGCC	60.675	55.000	0.00	0.00	0.00	4.85
2300	4156	1.270550	CTCCGACAAGCAGCCAAAAAT	59.729	47.619	0.00	0.00	0.00	1.82
2694	4561	6.983890	TGTGTTGTCATACATACGCTGATTAT	59.016	34.615	0.00	0.00	0.00	1.28
2698	4565	8.851416	GTTGTCATACATACGCTGATTATAGTC	58.149	37.037	0.00	0.00	0.00	2.59
2769	4637	1.134729	GCCAAGAGGAAGAGAGCTGAG	60.135	57.143	0.00	0.00	36.89	3.35
2949	4824	8.950208	AAGTTTTCTTCTCATATACTGTAGGC	57.050	34.615	0.00	0.00	34.76	3.93
2950	4825	8.079211	AGTTTTCTTCTCATATACTGTAGGCA	57.921	34.615	0.00	0.00	0.00	4.75
3243	5140	1.675219	CAGCAAAAAGGCCAGCCAT	59.325	52.632	12.03	0.00	38.92	4.40
3403	5300	2.147150	GTCAGGGAGTTTGAGCTGTTC	58.853	52.381	0.00	0.00	0.00	3.18
3601	5498	9.241919	TGGAAAGTAAAAGATGCAAGATCATTA	57.758	29.630	0.00	0.00	0.00	1.90
3735	5632	1.656095	GAAGCAGGTTTCTGACGATCG	59.344	52.381	14.88	14.88	43.49	3.69
3916	5813	3.744940	AATTCATCTGGAAAGCTCCCA	57.255	42.857	7.48	7.48	41.64	4.37
3921	5818	2.038863	TCTGGAAAGCTCCCACCTTA	57.961	50.000	3.86	0.00	41.64	2.69
3998	5946	3.391965	CCTACAGAGAATGAGCAGATGC	58.608	50.000	0.00	0.00	42.49	3.91
4139	6087	4.883083	TGTGGTTACTGACTCAATGAGAC	58.117	43.478	18.20	11.65	33.32	3.36
4291	6239	5.701290	GGTAAGATCCCAGTGTTATGCATAC	59.299	44.000	5.74	0.00	0.00	2.39
4300	6248	7.831690	TCCCAGTGTTATGCATACAGAAATTTA	59.168	33.333	5.74	0.00	0.00	1.40
4442	6393	6.897966	AGTACTCTCTGGATATGGTCAGAAAA	59.102	38.462	0.00	0.00	39.23	2.29
4534	6485	8.347771	TGCAAGTTCTGAAGATAATGATAATGC	58.652	33.333	0.00	0.00	0.00	3.56
4544	6495	8.631480	AAGATAATGATAATGCAATCAGCTCA	57.369	30.769	7.15	0.00	45.94	4.26
4676	6641	6.913170	TCTGCAGTGGAATTCTAACATTTTC	58.087	36.000	14.67	0.00	0.00	2.29
4679	6644	6.267471	TGCAGTGGAATTCTAACATTTTCCTT	59.733	34.615	5.23	0.00	38.73	3.36
4680	6645	7.154656	GCAGTGGAATTCTAACATTTTCCTTT	58.845	34.615	5.23	0.00	38.73	3.11
5065	7050	4.172512	AGCTGGCCATGGAGCTCG	62.173	66.667	19.69	2.88	41.94	5.03
5232	7217	6.467677	CACCTTAACTTTCTGAGATTGAGGA	58.532	40.000	10.86	0.00	0.00	3.71
5724	7711	3.866582	GGATGCAGCCCTACGCCT	61.867	66.667	10.76	0.00	38.78	5.52
5789	7776	3.731728	TGCTCATCAGGGTGGCCC	61.732	66.667	0.00	0.00	45.90	5.80
5961	7951	9.886132	ACAGAAATTAATTACTACAGGGTACAG	57.114	33.333	0.01	0.00	0.00	2.74
6063	8063	0.682209	GCTCAATGGCACCTGGTGAT	60.682	55.000	30.23	12.91	35.23	3.06
6064	8064	1.408683	GCTCAATGGCACCTGGTGATA	60.409	52.381	30.23	17.35	35.23	2.15
6065	8065	2.569059	CTCAATGGCACCTGGTGATAG	58.431	52.381	30.23	13.71	35.23	2.08
6158	8194	6.430925	TGGATGTTAAACTCTTGAATCACTGG	59.569	38.462	0.00	0.00	0.00	4.00
6172	8208	4.713792	ATCACTGGTTCTGAAAAGGAGT	57.286	40.909	0.00	0.00	0.00	3.85
6316	8368	7.338710	CCAAAGTAATCAGGAATTCAGGAGTA	58.661	38.462	7.93	4.87	0.00	2.59
6338	8390	4.317530	AAACTCCCAGGGTTTCTTATCC	57.682	45.455	5.01	0.00	32.26	2.59
6400	8453	5.935945	TCACACTTCAAAGGAGTGGATAAA	58.064	37.500	10.02	0.00	37.03	1.40
6401	8454	6.361433	TCACACTTCAAAGGAGTGGATAAAA	58.639	36.000	10.02	0.00	37.03	1.52
6463	8516	6.595326	CCAACAATGTCTCTGCTTCATTACTA	59.405	38.462	0.00	0.00	31.76	1.82
6556	8611	2.994143	CTTGCAGTGTGCTTGCACCG	62.994	60.000	21.01	11.67	45.31	4.94
6638	8693	1.619807	TACAGCCCTCGGTAAAGCCC	61.620	60.000	0.00	0.00	0.00	5.19
6665	8720	4.039852	TGGCTGTCGGCATAGAAACATATA	59.960	41.667	5.89	0.00	44.01	0.86
6693	8748	0.391597	TTTCTCGAGCCACCGTTTCT	59.608	50.000	7.81	0.00	0.00	2.52
6723	8778	2.477176	GCACTGCCGTTTGGACACA	61.477	57.895	0.00	0.00	37.49	3.72
6734	8789	2.268762	TTGGACACATGCTAGCAACA	57.731	45.000	23.54	11.02	0.00	3.33
6772	8827	2.134789	ACCTATGCCTCCAAGCTTTG	57.865	50.000	0.00	0.00	0.00	2.77
6778	8833	2.680913	CCTCCAAGCTTTGCCGTCG	61.681	63.158	0.00	0.00	0.00	5.12
6800	8855	0.744874	ATAGCTATGCCACGTGTCGT	59.255	50.000	15.65	5.52	42.36	4.34
6801	8856	0.528924	TAGCTATGCCACGTGTCGTT	59.471	50.000	15.65	0.00	38.32	3.85
6807	8862	4.012895	CCACGTGTCGTTGCCTGC	62.013	66.667	15.65	0.00	38.32	4.85

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
106	108	0.179070	TGTTGTGTCGCCAGTTGCTA	60.179	50.000	0.00	0.00	38.05	3.49
131	133	5.381757	TGGCAGTACCTACAACAAAAGATT	58.618	37.500	0.00	0.00	40.22	2.40
137	139	5.240623	CAGAAAATGGCAGTACCTACAACAA	59.759	40.000	0.00	0.00	40.22	2.83
177	179	5.246656	TGCTGAATCAATGTCCCTTTCAATT	59.753	36.000	0.00	0.00	0.00	2.32
210	212	5.356190	TCAGTTTTGATGATGATTCCTCTGC	59.644	40.000	0.00	0.00	0.00	4.26
381	383	2.167693	ACCTTCGAAGCCAATATCACGA	59.832	45.455	19.99	0.00	0.00	4.35
515	517	4.219944	ATGATGAACATTGAAGCACTTGCT	59.780	37.500	0.00	0.00	44.79	3.91
518	520	5.105877	CCTGATGATGAACATTGAAGCACTT	60.106	40.000	0.00	0.00	39.56	3.16
519	521	4.398358	CCTGATGATGAACATTGAAGCACT	59.602	41.667	0.00	0.00	39.56	4.40
520	522	4.669318	CCTGATGATGAACATTGAAGCAC	58.331	43.478	0.00	0.00	39.56	4.40
521	523	3.129813	GCCTGATGATGAACATTGAAGCA	59.870	43.478	0.00	0.00	39.56	3.91
522	524	3.380637	AGCCTGATGATGAACATTGAAGC	59.619	43.478	0.00	0.00	39.56	3.86
523	525	4.638865	TGAGCCTGATGATGAACATTGAAG	59.361	41.667	0.00	0.00	39.56	3.02
524	526	4.591929	TGAGCCTGATGATGAACATTGAA	58.408	39.130	0.00	0.00	39.56	2.69
526	528	3.945921	ACTGAGCCTGATGATGAACATTG	59.054	43.478	0.00	0.00	39.56	2.82
529	531	3.708403	AACTGAGCCTGATGATGAACA	57.292	42.857	0.00	0.00	0.00	3.18
589	1930	1.066573	ACATGAACCTGAAGAGAGGCG	60.067	52.381	0.00	0.00	36.46	5.52
607	1948	2.325661	TCTCTCCCTGGACATTGACA	57.674	50.000	0.00	0.00	0.00	3.58
645	1990	1.694696	AGAAGTGTGAAGGGACTCACC	59.305	52.381	1.54	0.00	38.49	4.02
718	2065	2.653113	CGGTTATTTTCACGGCGTTTTC	59.347	45.455	11.19	0.00	0.00	2.29
868	2231	1.343465	TCCACTTGTTTCTCGAGTCCC	59.657	52.381	13.13	1.77	38.62	4.46
869	2232	2.036089	ACTCCACTTGTTTCTCGAGTCC	59.964	50.000	13.13	2.14	38.62	3.85
870	2233	3.372660	ACTCCACTTGTTTCTCGAGTC	57.627	47.619	13.13	5.30	38.62	3.36
971	2338	1.305297	ATCAGACTGCCCTCCGTGA	60.305	57.895	0.00	0.00	0.00	4.35
972	2339	1.142748	GATCAGACTGCCCTCCGTG	59.857	63.158	0.00	0.00	0.00	4.94
973	2340	2.418910	CGATCAGACTGCCCTCCGT	61.419	63.158	0.00	0.00	0.00	4.69
974	2341	2.415010	CGATCAGACTGCCCTCCG	59.585	66.667	0.00	0.00	0.00	4.63
975	2342	2.060980	ACCGATCAGACTGCCCTCC	61.061	63.158	0.00	0.00	0.00	4.30
976	2343	1.142748	CACCGATCAGACTGCCCTC	59.857	63.158	0.00	0.00	0.00	4.30
977	2344	3.023949	GCACCGATCAGACTGCCCT	62.024	63.158	0.00	0.00	0.00	5.19
978	2345	2.512515	GCACCGATCAGACTGCCC	60.513	66.667	0.00	0.00	0.00	5.36
979	2346	2.887568	CGCACCGATCAGACTGCC	60.888	66.667	0.00	0.00	0.00	4.85
980	2347	2.887568	CCGCACCGATCAGACTGC	60.888	66.667	0.00	0.00	0.00	4.40
981	2348	1.807165	CACCGCACCGATCAGACTG	60.807	63.158	0.00	0.00	0.00	3.51
1247	2617	2.890474	CCCCCGACTTCGCAATCG	60.890	66.667	0.00	0.00	38.18	3.34
1486	3067	0.324943	ACATACCCGCAGCTTTCACT	59.675	50.000	0.00	0.00	0.00	3.41
1494	3075	3.065371	GGAATTCTTTCACATACCCGCAG	59.935	47.826	5.23	0.00	33.23	5.18
1521	3102	1.301401	CCCGACGAACAGGCTCAAA	60.301	57.895	0.00	0.00	0.00	2.69
1536	3117	3.886123	AGAATGTTATTTGGACTCCCCG	58.114	45.455	0.00	0.00	37.93	5.73
1545	3126	6.697019	CCGCTATTCCCAAAGAATGTTATTTG	59.303	38.462	6.00	6.00	45.11	2.32
1548	3129	5.445964	ACCGCTATTCCCAAAGAATGTTAT	58.554	37.500	0.00	0.00	45.11	1.89
1566	3155	1.375098	GCTCACGACTACCTACCGCT	61.375	60.000	0.00	0.00	0.00	5.52
1606	3205	5.957842	TCCAATAGAAAAGCAATTCGTGT	57.042	34.783	0.00	0.00	34.46	4.49
1623	3222	2.162319	AAAACGCGGCAAAATCCAAT	57.838	40.000	12.47	0.00	0.00	3.16
1651	3256	1.202964	ACCGGAAAACCCCAAACTAGG	60.203	52.381	9.46	0.00	0.00	3.02
1735	3341	5.479124	ACTCTAATTGTCCCTGTTTACGT	57.521	39.130	0.00	0.00	0.00	3.57
1762	3368	7.713734	TCTACAGGCAATAGTTAGTTACTGT	57.286	36.000	0.00	0.00	40.59	3.55
1848	3670	4.261994	CCGAAACAACCTGAAATCAATGGT	60.262	41.667	0.00	0.00	0.00	3.55
1931	3756	5.351740	GCAAGGTAAGTTACTTCTAAGCCAG	59.648	44.000	12.65	0.00	0.00	4.85
1947	3772	3.138304	CAGCAGTACAAGTGCAAGGTAA	58.862	45.455	9.25	0.00	46.65	2.85
2014	3843	3.387050	AGTTGTTTCTATAGCCCCCTACG	59.613	47.826	0.00	0.00	0.00	3.51
2018	3847	5.691896	ACATTAGTTGTTTCTATAGCCCCC	58.308	41.667	0.00	0.00	33.74	5.40
2294	4150	4.689812	TCCGCATTTCCACATCAATTTTTG	59.310	37.500	0.00	0.00	0.00	2.44
2300	4156	3.087781	TCAATCCGCATTTCCACATCAA	58.912	40.909	0.00	0.00	0.00	2.57
2353	4209	1.006102	CCTGCCGAACACGAGTCTT	60.006	57.895	0.00	0.00	0.00	3.01
2694	4561	9.026121	AGAAGCAGAACATTAGAACTAAGACTA	57.974	33.333	0.00	0.00	0.00	2.59
2707	4574	8.345724	ACAAATCAGATAAGAAGCAGAACATT	57.654	30.769	0.00	0.00	0.00	2.71
2769	4637	1.936547	CCTCCTCGCTGCTTCAAATAC	59.063	52.381	0.00	0.00	0.00	1.89
2937	4810	5.459505	ACTTCTCCAGTGCCTACAGTATAT	58.540	41.667	0.00	0.00	32.83	0.86
2949	4824	4.035675	GGACTTCACAAAACTTCTCCAGTG	59.964	45.833	0.00	0.00	35.12	3.66
2950	4825	4.200092	GGACTTCACAAAACTTCTCCAGT	58.800	43.478	0.00	0.00	37.30	4.00
3114	4989	1.048601	TGAACTTGCCTCTCGAACCT	58.951	50.000	0.00	0.00	0.00	3.50
3243	5140	4.947388	ACAACCTGCTTGTTTCAGAAGTTA	59.053	37.500	0.00	0.00	40.45	2.24
3403	5300	4.349501	GTCCCTCGAGTATTGTCTTAACG	58.650	47.826	12.31	0.00	0.00	3.18
3601	5498	3.054802	CAGCCCTAACAAGATCACCTTCT	60.055	47.826	0.00	0.00	31.42	2.85
3604	5501	1.065126	GCAGCCCTAACAAGATCACCT	60.065	52.381	0.00	0.00	0.00	4.00
3874	5771	8.484214	AATTAATGCTCAGAGGAGTAGATACA	57.516	34.615	0.00	0.00	43.37	2.29
3921	5818	6.938030	TGTTTCGGAACTAACATTAACCTCAT	59.062	34.615	8.32	0.00	36.70	2.90
3998	5946	4.512198	GTCCTCATGAAGCATCTCATTGAG	59.488	45.833	7.38	7.38	33.66	3.02
4064	6012	6.129179	TCACTTTGTCTTGGAAATCCTTCTT	58.871	36.000	0.44	0.00	36.82	2.52
4139	6087	2.329379	GCTGTAGTCAGGTTTGTCTCG	58.671	52.381	0.00	0.00	41.57	4.04
4291	6239	9.512435	AAGAAGCAATTCGATGATAAATTTCTG	57.488	29.630	0.00	0.00	0.00	3.02
4466	6417	2.606725	GTCATGACTTGCCTTCATCTCG	59.393	50.000	18.83	0.00	30.98	4.04
4534	6485	4.744570	AGCAATGACAAATGAGCTGATTG	58.255	39.130	0.00	0.15	0.00	2.67
4544	6495	4.081862	CCCTTGATGACAGCAATGACAAAT	60.082	41.667	6.59	0.00	0.00	2.32
4653	6618	6.071728	AGGAAAATGTTAGAATTCCACTGCAG	60.072	38.462	13.48	13.48	43.03	4.41
4676	6641	6.701400	ACTTGCAGTTGCTGTTTATAAAAAGG	59.299	34.615	15.71	1.83	42.66	3.11
4679	6644	8.160521	TCTACTTGCAGTTGCTGTTTATAAAA	57.839	30.769	5.62	0.00	42.66	1.52
4680	6645	7.737972	TCTACTTGCAGTTGCTGTTTATAAA	57.262	32.000	5.62	0.00	42.66	1.40
5065	7050	2.072298	CTGAAGGTACAGCAGCTGTTC	58.928	52.381	32.64	26.37	42.59	3.18
5232	7217	2.203625	AAATTGGCCCTGCACGGT	60.204	55.556	0.00	0.00	0.00	4.83
5743	7730	1.227527	CTTCACCACACGGTCAGCA	60.228	57.895	0.00	0.00	44.71	4.41
5953	7943	6.958192	TCCTGAACTACTAATTTCTGTACCCT	59.042	38.462	0.00	0.00	0.00	4.34
5954	7944	7.179076	TCCTGAACTACTAATTTCTGTACCC	57.821	40.000	0.00	0.00	0.00	3.69
5955	7945	8.258708	ACATCCTGAACTACTAATTTCTGTACC	58.741	37.037	0.00	0.00	0.00	3.34
5956	7946	9.654663	AACATCCTGAACTACTAATTTCTGTAC	57.345	33.333	0.00	0.00	0.00	2.90
5968	7958	9.626045	CCAAGAATTTTTAACATCCTGAACTAC	57.374	33.333	0.00	0.00	0.00	2.73
6316	8368	4.673968	GGATAAGAAACCCTGGGAGTTTT	58.326	43.478	22.23	9.82	37.55	2.43
6400	8453	5.806654	AAAATAGTGTTGTCCTGCCATTT	57.193	34.783	0.00	0.00	0.00	2.32
6401	8454	5.070313	ACAAAAATAGTGTTGTCCTGCCATT	59.930	36.000	0.00	0.00	32.52	3.16
6463	8516	5.486419	AGGCAAATTTCTCCCAAAATCAGAT	59.514	36.000	3.09	0.00	0.00	2.90
6556	8611	0.168128	GCATACACACCGTTTCCTGC	59.832	55.000	0.00	0.00	0.00	4.85
6638	8693	1.665916	CTATGCCGACAGCCATCCG	60.666	63.158	0.00	0.00	42.71	4.18
6639	8694	0.106708	TTCTATGCCGACAGCCATCC	59.893	55.000	0.00	0.00	42.71	3.51
6665	8720	1.372623	GCTCGAGAAAACCGTCGGT	60.373	57.895	18.75	12.23	37.65	4.69
6716	8771	1.812235	CTGTTGCTAGCATGTGTCCA	58.188	50.000	20.13	7.74	0.00	4.02
6723	8778	2.743752	CGCACGCTGTTGCTAGCAT	61.744	57.895	20.13	0.00	43.87	3.79
6772	8827	1.009389	GGCATAGCTATGACGACGGC	61.009	60.000	33.10	17.64	35.75	5.68
6778	8833	2.128035	GACACGTGGCATAGCTATGAC	58.872	52.381	33.10	31.37	42.14	3.06
6807	8862	2.859273	GATGACCACCAGGAGCACCG	62.859	65.000	0.00	0.00	41.83	4.94

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.