AutoCloner

Multiple sequence alignment - TraesCS4D01G315600

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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	TraesCS4D01G315600	chr4D	100.000	3673	0	0	1834	5506	481167745	481171417	0.000000e+00	6783.0
1	TraesCS4D01G315600	chr4D	100.000	1439	0	0	1	1439	481165912	481167350	0.000000e+00	2658.0
2	TraesCS4D01G315600	chr5A	95.365	3711	126	19	1834	5506	662342579	662338877	0.000000e+00	5858.0
3	TraesCS4D01G315600	chr5A	89.669	1026	70	13	424	1439	662343686	662342687	0.000000e+00	1275.0
4	TraesCS4D01G315600	chr5A	88.800	125	14	0	255	379	662343806	662343682	2.660000e-33	154.0
5	TraesCS4D01G315600	chr5A	87.097	93	7	5	89	178	222765470	222765380	3.510000e-17	100.0
6	TraesCS4D01G315600	chr5A	77.165	127	17	5	1271	1388	535668205	535668328	4.600000e-06	63.9
7	TraesCS4D01G315600	chr4B	94.804	2733	80	6	2794	5486	609497204	609499914	0.000000e+00	4204.0
8	TraesCS4D01G315600	chr4B	91.473	1466	86	22	3	1439	609494425	609495880	0.000000e+00	1978.0
9	TraesCS4D01G315600	chr4B	94.274	943	23	6	1834	2746	609495951	609496892	0.000000e+00	1413.0
10	TraesCS4D01G315600	chr4B	86.598	97	11	2	92	187	60771842	60771937	7.540000e-19	106.0
11	TraesCS4D01G315600	chr3D	81.424	2724	373	69	1983	4661	612904233	612901598	0.000000e+00	2104.0
12	TraesCS4D01G315600	chr3D	80.909	440	56	12	3198	3635	612086358	612086771	6.880000e-84	322.0
13	TraesCS4D01G315600	chr3D	82.873	181	31	0	3935	4115	612087062	612087242	4.410000e-36	163.0
14	TraesCS4D01G315600	chr3D	83.654	104	14	3	85	186	3008558	3008660	1.630000e-15	95.3
15	TraesCS4D01G315600	chr3B	81.225	2727	364	77	1983	4661	826082085	826084711	0.000000e+00	2063.0
16	TraesCS4D01G315600	chr3B	86.957	138	18	0	4122	4259	830369759	830369896	7.380000e-34	156.0
17	TraesCS4D01G315600	chr3A	82.721	1904	251	42	2782	4661	747627898	747626049	0.000000e+00	1622.0
18	TraesCS4D01G315600	chr3A	80.861	836	118	21	1983	2795	747628672	747627856	2.180000e-173	619.0
19	TraesCS4D01G315600	chr3A	80.456	307	47	8	3331	3635	747835363	747835068	7.180000e-54	222.0
20	TraesCS4D01G315600	chr3A	80.851	235	27	6	3670	3886	747830223	747829989	9.490000e-38	169.0
21	TraesCS4D01G315600	chr1B	77.778	774	157	12	3719	4483	9097961	9097194	3.890000e-126	462.0
22	TraesCS4D01G315600	chr1B	91.209	91	8	0	5031	5121	618697664	618697574	2.080000e-24	124.0
23	TraesCS4D01G315600	chr1B	88.312	77	5	3	535	608	525841227	525841302	7.600000e-14	89.8
24	TraesCS4D01G315600	chr1B	77.931	145	16	10	348	484	10254218	10254354	5.910000e-10	76.8
25	TraesCS4D01G315600	chr1A	77.920	779	147	18	3719	4483	8217385	8218152	3.890000e-126	462.0
26	TraesCS4D01G315600	chrUn	78.071	757	143	16	3740	4483	329247037	329246291	1.810000e-124	457.0
27	TraesCS4D01G315600	chrUn	80.456	307	47	8	3331	3635	33651675	33651380	7.180000e-54	222.0
28	TraesCS4D01G315600	chrUn	80.456	307	47	8	3331	3635	184782160	184781865	7.180000e-54	222.0
29	TraesCS4D01G315600	chrUn	80.851	235	27	6	3670	3886	184781681	184781447	9.490000e-38	169.0
30	TraesCS4D01G315600	chrUn	80.851	235	27	6	3670	3886	398649929	398650163	9.490000e-38	169.0
31	TraesCS4D01G315600	chrUn	86.813	91	8	4	91	178	241299472	241299383	1.260000e-16	99.0
32	TraesCS4D01G315600	chrUn	86.813	91	8	4	91	178	317309706	317309617	1.260000e-16	99.0
33	TraesCS4D01G315600	chrUn	88.235	68	8	0	3670	3737	184781766	184781699	1.270000e-11	82.4
34	TraesCS4D01G315600	chr7D	91.011	89	8	0	5030	5118	121937433	121937345	2.690000e-23	121.0
35	TraesCS4D01G315600	chr7D	90.805	87	8	0	5030	5116	151326530	151326444	3.480000e-22	117.0
36	TraesCS4D01G315600	chr5B	89.888	89	9	0	5030	5118	306447598	306447510	1.250000e-21	115.0
37	TraesCS4D01G315600	chr5D	89.130	92	9	1	5031	5121	533641625	533641716	4.510000e-21	113.0
38	TraesCS4D01G315600	chr7A	88.636	88	10	0	521	608	204170569	204170482	2.100000e-19	108.0
39	TraesCS4D01G315600	chr4A	88.043	92	10	1	5031	5121	638216786	638216695	2.100000e-19	108.0
40	TraesCS4D01G315600	chr2D	86.667	90	10	2	91	178	69583088	69582999	1.260000e-16	99.0
41	TraesCS4D01G315600	chr2D	90.625	64	5	1	551	614	186777226	186777164	3.530000e-12	84.2
42	TraesCS4D01G315600	chr7B	86.364	88	12	0	521	608	158372547	158372460	4.540000e-16	97.1
43	TraesCS4D01G315600	chr6B	85.870	92	12	1	91	181	710798884	710798793	4.540000e-16	97.1
44	TraesCS4D01G315600	chr6B	85.870	92	12	1	91	181	711418637	711418728	4.540000e-16	97.1

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	TraesCS4D01G315600	chr4D	481165912	481171417	5505	False	4720.500000	6783	100.000	1	5506	2	chr4D.!!$F1	5505
1	TraesCS4D01G315600	chr5A	662338877	662343806	4929	True	2429.000000	5858	91.278	255	5506	3	chr5A.!!$R2	5251
2	TraesCS4D01G315600	chr4B	609494425	609499914	5489	False	2531.666667	4204	93.517	3	5486	3	chr4B.!!$F2	5483
3	TraesCS4D01G315600	chr3D	612901598	612904233	2635	True	2104.000000	2104	81.424	1983	4661	1	chr3D.!!$R1	2678
4	TraesCS4D01G315600	chr3D	612086358	612087242	884	False	242.500000	322	81.891	3198	4115	2	chr3D.!!$F2	917
5	TraesCS4D01G315600	chr3B	826082085	826084711	2626	False	2063.000000	2063	81.225	1983	4661	1	chr3B.!!$F1	2678
6	TraesCS4D01G315600	chr3A	747626049	747628672	2623	True	1120.500000	1622	81.791	1983	4661	2	chr3A.!!$R3	2678
7	TraesCS4D01G315600	chr1B	9097194	9097961	767	True	462.000000	462	77.778	3719	4483	1	chr1B.!!$R1	764
8	TraesCS4D01G315600	chr1A	8217385	8218152	767	False	462.000000	462	77.920	3719	4483	1	chr1A.!!$F1	764
9	TraesCS4D01G315600	chrUn	329246291	329247037	746	True	457.000000	457	78.071	3740	4483	1	chrUn.!!$R4	743

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	Hairpin	End Stability	Orientation
511	537	0.035056	AAAGCTTCATCCACCCCTCG	60.035	55.000	0.00	0.00	4.63	F
1287	1324	1.375908	GTGCAGATTCGGTGCTCCA	60.376	57.895	5.52	41.78	3.86	F
2564	2659	0.321564	TGGTTCAAGAGGCATGGACG	60.322	55.000	0.00	0.00	4.79	F
3305	3676	0.323633	TGGGTGATGTTGCATCTGGG	60.324	55.000	10.02	0.00	4.45	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2209	2304	0.320771	GCACTCCATTCCGTCACAGT	60.321	55.000	0.00	0.00	0.00	3.55	R
3032	3403	0.592637	TTGCATCTTCAGTTGCACCG	59.407	50.000	11.32	0.00	46.59	4.94	R
3700	4071	0.464870	CTCCTCTGGATCAGCACAGG	59.535	60.000	0.00	0.00	35.47	4.00	R
5302	5883	2.360726	TAGACCGCGGCTGTGAGA	60.361	61.111	28.58	4.94	0.00	3.27	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
35	36	2.064581	ATGGTAGGGAGACGTGGGC	61.065	63.158	0.00	0.00	0.00	5.36
48	49	3.002583	TGGGCTCGACCATGCTCA	61.003	61.111	0.00	0.00	42.05	4.26
66	67	3.681897	GCTCAGAGTCGACAACAATTCAT	59.318	43.478	19.50	0.00	0.00	2.57
67	68	4.435253	GCTCAGAGTCGACAACAATTCATG	60.435	45.833	19.50	5.97	0.00	3.07
73	74	2.935849	TCGACAACAATTCATGATCCGG	59.064	45.455	0.00	0.00	0.00	5.14
80	81	0.752658	ATTCATGATCCGGCGTCTCA	59.247	50.000	6.01	8.69	0.00	3.27
81	82	0.752658	TTCATGATCCGGCGTCTCAT	59.247	50.000	13.61	13.61	0.00	2.90
83	84	1.960689	TCATGATCCGGCGTCTCATAA	59.039	47.619	17.47	4.76	0.00	1.90
93	117	6.460781	TCCGGCGTCTCATAATGTAATTAAT	58.539	36.000	6.01	0.00	42.96	1.40
97	121	8.166706	CGGCGTCTCATAATGTAATTAATTACC	58.833	37.037	27.56	14.89	42.96	2.85
101	125	8.943002	GTCTCATAATGTAATTAATTACCCCCG	58.057	37.037	27.56	16.10	42.96	5.73
102	126	8.662255	TCTCATAATGTAATTAATTACCCCCGT	58.338	33.333	27.56	14.73	42.96	5.28
103	127	8.851541	TCATAATGTAATTAATTACCCCCGTC	57.148	34.615	27.56	8.72	42.96	4.79
104	128	7.603404	TCATAATGTAATTAATTACCCCCGTCG	59.397	37.037	27.56	14.51	42.96	5.12
107	131	2.916702	ATTAATTACCCCCGTCGTCC	57.083	50.000	0.00	0.00	0.00	4.79
121	145	3.181484	CCGTCGTCCCATAATGTAAGACA	60.181	47.826	0.00	0.00	0.00	3.41
182	207	8.418662	ACATTATAGCACGAATGGAGTACTAAA	58.581	33.333	0.00	0.00	37.37	1.85
191	216	9.931210	CACGAATGGAGTACTAAATAAATTTCC	57.069	33.333	0.00	0.00	0.00	3.13
207	232	0.108207	TTCCGTTCCTAACCGGCAAA	59.892	50.000	0.00	0.00	43.87	3.68
232	258	2.472695	ACACACGCATGACATAGGTT	57.527	45.000	0.00	0.00	0.00	3.50
271	297	2.345880	AAACACGACACGAGCGAGGT	62.346	55.000	0.00	0.00	0.00	3.85
379	405	5.522460	CGTTGTTCAGTTAAACCTTCTCTCA	59.478	40.000	0.00	0.00	0.00	3.27
406	432	4.325344	GGATTGAAGAGGATTGAAGGGGAA	60.325	45.833	0.00	0.00	0.00	3.97
423	449	7.071321	TGAAGGGGAATTAGAGAGATTTAGACC	59.929	40.741	0.00	0.00	0.00	3.85
426	452	6.785466	GGGGAATTAGAGAGATTTAGACCTCT	59.215	42.308	0.00	0.00	42.01	3.69
448	474	7.562821	CCTCTTGGGATTTAATTCCTCTCAATT	59.437	37.037	14.46	0.00	37.23	2.32
469	495	2.716424	TCCCTTCAAATCCACCTCAACT	59.284	45.455	0.00	0.00	0.00	3.16
472	498	3.755378	CCTTCAAATCCACCTCAACTGAG	59.245	47.826	0.00	0.00	41.71	3.35
477	503	1.423584	TCCACCTCAACTGAGCAAGA	58.576	50.000	0.89	0.00	40.75	3.02
478	504	1.980765	TCCACCTCAACTGAGCAAGAT	59.019	47.619	0.89	0.00	40.75	2.40
506	532	3.636153	AGGTCTAAAGCTTCATCCACC	57.364	47.619	0.00	2.17	0.00	4.61
510	536	2.505819	TCTAAAGCTTCATCCACCCCTC	59.494	50.000	0.00	0.00	0.00	4.30
511	537	0.035056	AAAGCTTCATCCACCCCTCG	60.035	55.000	0.00	0.00	0.00	4.63
626	657	2.862674	TAACAAGCTAAGGCCGGCGG	62.863	60.000	24.35	24.35	39.73	6.13
646	678	2.049767	GTTATGCGGTTGGTGGGGG	61.050	63.158	0.00	0.00	0.00	5.40
676	708	1.676006	CAAGGGCGTTTCAGTCTTTGT	59.324	47.619	0.00	0.00	29.75	2.83
683	715	4.386652	GGCGTTTCAGTCTTTGTATACGAA	59.613	41.667	5.43	5.43	32.14	3.85
743	775	2.537625	GCATCTGAATCCGACGAAGAAG	59.462	50.000	0.00	0.00	0.00	2.85
768	802	2.437413	GCTAGGACAAAAAGGGGACAG	58.563	52.381	0.00	0.00	0.00	3.51
797	831	8.196771	GCATTTTGGTCTTTACATATGGAATCA	58.803	33.333	7.80	0.00	0.00	2.57
1207	1244	4.373116	CTACCGCCGCCGCCATAT	62.373	66.667	0.00	0.00	0.00	1.78
1212	1249	2.672996	GCCGCCGCCATATCCATT	60.673	61.111	0.00	0.00	0.00	3.16
1246	1283	2.344950	CTCTTCAGCGTCTGCAGATTT	58.655	47.619	21.47	5.70	46.23	2.17
1287	1324	1.375908	GTGCAGATTCGGTGCTCCA	60.376	57.895	5.52	0.00	41.78	3.86
1939	2015	8.370940	TGTATCTTCAGTTGATCCTTCATATCC	58.629	37.037	0.00	0.00	0.00	2.59
1965	2043	1.476891	GTCGTTCATGCACTCTAGGGA	59.523	52.381	0.00	0.00	0.00	4.20
1975	2053	1.978580	CACTCTAGGGAGGTGTTTGGT	59.021	52.381	0.00	0.00	43.46	3.67
2025	2108	4.894784	TGGAGAGGACTGTATTTGTCAAC	58.105	43.478	0.00	0.00	36.26	3.18
2205	2300	3.372060	GTGGCTGCTGTTTGTACTTTTC	58.628	45.455	0.00	0.00	0.00	2.29
2209	2304	4.202010	GGCTGCTGTTTGTACTTTTCTGAA	60.202	41.667	0.00	0.00	0.00	3.02
2492	2587	2.417719	CAGTACAGGAAGTTGGTGCTC	58.582	52.381	0.00	0.00	0.00	4.26
2564	2659	0.321564	TGGTTCAAGAGGCATGGACG	60.322	55.000	0.00	0.00	0.00	4.79
3032	3403	2.671396	AGTACGTGATTCAAACATCCGC	59.329	45.455	0.00	0.00	0.00	5.54
3305	3676	0.323633	TGGGTGATGTTGCATCTGGG	60.324	55.000	10.02	0.00	0.00	4.45
3329	3700	6.264518	GGAAGAAGATGAAAACTGTGGGTAAA	59.735	38.462	0.00	0.00	0.00	2.01
3366	3737	3.102972	TCTTCCTCCATTCTCTCAGGTG	58.897	50.000	0.00	0.00	0.00	4.00
3563	3934	4.825422	ACAAGATGAAGAGCGATTTGAGA	58.175	39.130	0.00	0.00	0.00	3.27
3572	3943	3.119173	AGAGCGATTTGAGAGAGAAGGTG	60.119	47.826	0.00	0.00	0.00	4.00
3594	3965	6.819146	GGTGAAGGAGATAAGAAGTAAACCAG	59.181	42.308	0.00	0.00	0.00	4.00
3664	4035	6.748132	ACAAACATGTTGAGGGTAATGAAAG	58.252	36.000	12.82	0.00	0.00	2.62
3700	4071	5.702865	TGATTCTACTGCAAACAAAGATGC	58.297	37.500	0.00	0.00	42.86	3.91
3782	4309	6.688578	TGACAACACTTTCTCCTATACTGTC	58.311	40.000	0.00	0.00	0.00	3.51
3968	4498	2.791560	CGCATCGAGGACAAATAGTGAG	59.208	50.000	0.00	0.00	0.00	3.51
3978	4508	4.215613	GGACAAATAGTGAGTTTGGACCAC	59.784	45.833	0.00	0.00	40.08	4.16
4168	4698	2.834638	AATTGGTCCCCTGATTGGAG	57.165	50.000	0.00	0.00	38.35	3.86
4404	4934	2.291217	GGGGAAGAAGCTCCAAATGTCT	60.291	50.000	0.00	0.00	37.20	3.41
4550	5087	0.469705	ATGCCTTTGTTGACCTGCCA	60.470	50.000	0.00	0.00	0.00	4.92
4603	5143	7.149307	GCTAGTTTCTATAGTTTCCTAGCCTG	58.851	42.308	20.45	3.69	39.80	4.85
4665	5205	2.517980	TGGGGCTAGCCATTCCTAAATT	59.482	45.455	34.09	0.00	37.98	1.82
4723	5263	6.959361	TCTCAAAACTTAAACAGTGATGCTC	58.041	36.000	0.00	0.00	35.12	4.26
4820	5360	7.981789	TGTTGTTTTATCTCTAGCTGTATGAGG	59.018	37.037	0.00	0.00	0.00	3.86
4864	5404	4.041075	TCTGGTTGCTCAACATACCACTTA	59.959	41.667	13.89	0.00	42.85	2.24
5051	5611	7.568738	TCTTTTACTCCCTCTGATCCATATTGA	59.431	37.037	0.00	0.00	0.00	2.57
5216	5795	0.179100	CAGGTATGCGGACTGTCCAG	60.179	60.000	25.42	18.30	35.91	3.86
5302	5883	4.922206	TGTACAGATTGCCTTTTCTGGAT	58.078	39.130	0.00	0.00	42.93	3.41

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
1	2	7.492552	TCCCTACCATGACCCTAATATATTGA	58.507	38.462	8.28	0.00	0.00	2.57
10	11	1.133575	CGTCTCCCTACCATGACCCTA	60.134	57.143	0.00	0.00	0.00	3.53
17	18	2.064581	GCCCACGTCTCCCTACCAT	61.065	63.158	0.00	0.00	0.00	3.55
35	36	3.639162	GACTCTGAGCATGGTCGAG	57.361	57.895	28.72	28.72	0.00	4.04
48	49	4.872691	GGATCATGAATTGTTGTCGACTCT	59.127	41.667	17.92	0.00	0.00	3.24
55	56	1.401552	CGCCGGATCATGAATTGTTGT	59.598	47.619	5.05	0.00	0.00	3.32
66	67	1.686587	ACATTATGAGACGCCGGATCA	59.313	47.619	5.05	3.21	0.00	2.92
67	68	2.440539	ACATTATGAGACGCCGGATC	57.559	50.000	5.05	0.64	0.00	3.36
73	74	8.448615	GGGGTAATTAATTACATTATGAGACGC	58.551	37.037	30.11	17.81	43.33	5.19
80	81	7.452562	ACGACGGGGGTAATTAATTACATTAT	58.547	34.615	30.11	16.50	43.33	1.28
81	82	6.825610	ACGACGGGGGTAATTAATTACATTA	58.174	36.000	30.11	2.52	43.33	1.90
83	84	5.294734	ACGACGGGGGTAATTAATTACAT	57.705	39.130	30.11	15.41	43.33	2.29
93	117	0.325110	TTATGGGACGACGGGGGTAA	60.325	55.000	0.00	0.00	0.00	2.85
97	121	1.042229	TACATTATGGGACGACGGGG	58.958	55.000	0.00	0.00	0.00	5.73
150	175	6.811954	TCCATTCGTGCTATAATGTAAGACA	58.188	36.000	0.00	0.00	32.34	3.41
154	179	7.948357	AGTACTCCATTCGTGCTATAATGTAA	58.052	34.615	0.00	0.00	32.34	2.41
165	190	9.931210	GGAAATTTATTTAGTACTCCATTCGTG	57.069	33.333	0.00	0.00	0.00	4.35
207	232	5.414454	ACCTATGTCATGCGTGTGTTATTTT	59.586	36.000	5.68	0.00	0.00	1.82
215	240	3.002791	CTCAAACCTATGTCATGCGTGT	58.997	45.455	5.68	0.00	0.00	4.49
292	318	0.031994	AAAAGTGGTTCATGCGTGCC	59.968	50.000	0.00	0.00	0.00	5.01
333	359	5.830991	ACGCCTACAAGAGATTCTCTTCTAT	59.169	40.000	23.11	14.98	46.42	1.98
335	361	4.020543	ACGCCTACAAGAGATTCTCTTCT	58.979	43.478	23.11	15.82	46.42	2.85
346	372	2.902705	ACTGAACAACGCCTACAAGA	57.097	45.000	0.00	0.00	0.00	3.02
379	405	4.325658	CCTTCAATCCTCTTCAATCCCCTT	60.326	45.833	0.00	0.00	0.00	3.95
393	419	5.896073	TCTCTCTAATTCCCCTTCAATCC	57.104	43.478	0.00	0.00	0.00	3.01
406	432	7.366226	TCCCAAGAGGTCTAAATCTCTCTAAT	58.634	38.462	0.00	0.00	39.22	1.73
423	449	8.530804	AATTGAGAGGAATTAAATCCCAAGAG	57.469	34.615	5.92	0.00	40.59	2.85
426	452	6.611236	GGGAATTGAGAGGAATTAAATCCCAA	59.389	38.462	5.92	4.36	40.59	4.12
448	474	2.716424	AGTTGAGGTGGATTTGAAGGGA	59.284	45.455	0.00	0.00	0.00	4.20
469	495	7.482169	TTAGACCTTCTTAAGATCTTGCTCA	57.518	36.000	18.47	0.00	0.00	4.26
472	498	6.821160	AGCTTTAGACCTTCTTAAGATCTTGC	59.179	38.462	18.47	12.52	35.74	4.01
477	503	7.990314	GGATGAAGCTTTAGACCTTCTTAAGAT	59.010	37.037	5.89	0.00	35.74	2.40
478	504	7.038302	TGGATGAAGCTTTAGACCTTCTTAAGA	60.038	37.037	0.00	0.00	35.74	2.10
495	521	2.190578	CCGAGGGGTGGATGAAGC	59.809	66.667	0.00	0.00	0.00	3.86
506	532	4.498894	AAAGTTTAATACTCCCCGAGGG	57.501	45.455	0.00	0.00	46.11	4.30
510	536	5.005094	TGGTGAAAAGTTTAATACTCCCCG	58.995	41.667	0.00	0.00	35.54	5.73
511	537	5.184479	GGTGGTGAAAAGTTTAATACTCCCC	59.816	44.000	0.00	0.00	35.54	4.81
513	539	7.881751	ACTAGGTGGTGAAAAGTTTAATACTCC	59.118	37.037	0.00	0.00	35.54	3.85
514	540	8.843885	ACTAGGTGGTGAAAAGTTTAATACTC	57.156	34.615	0.00	0.00	35.54	2.59
626	657	1.591504	CCCCACCAACCGCATAACAC	61.592	60.000	0.00	0.00	0.00	3.32
646	678	4.785453	CGCCCTTGCCCTCTCACC	62.785	72.222	0.00	0.00	0.00	4.02
676	708	2.841881	AGCTTTCTTGGGGGTTCGTATA	59.158	45.455	0.00	0.00	0.00	1.47
743	775	2.826128	CCCCTTTTTGTCCTAGCCTTTC	59.174	50.000	0.00	0.00	0.00	2.62
768	802	5.453198	CCATATGTAAAGACCAAAATGCCCC	60.453	44.000	1.24	0.00	0.00	5.80
797	831	2.552373	CCTTGCCCTAGGTTTTCTCGTT	60.552	50.000	8.29	0.00	0.00	3.85
799	833	1.679032	CCCTTGCCCTAGGTTTTCTCG	60.679	57.143	8.29	0.00	33.17	4.04
889	923	3.073144	TGCCTTCGTTTACTTTGCAAC	57.927	42.857	0.00	0.00	0.00	4.17
1110	1147	4.944372	CGCCCGCGACAGATACCC	62.944	72.222	8.23	0.00	42.83	3.69
1163	1200	1.675116	GGAAGCACGGAAAGGGTAGAC	60.675	57.143	0.00	0.00	0.00	2.59
1191	1228	4.367023	GATATGGCGGCGGCGGTA	62.367	66.667	33.02	22.51	41.24	4.02
1207	1244	1.511305	GTCCGTCGCTCTGAATGGA	59.489	57.895	0.00	0.00	32.50	3.41
1212	1249	1.303398	AAGAGGTCCGTCGCTCTGA	60.303	57.895	2.21	0.00	0.00	3.27
1246	1283	2.516227	ATCACACCGAGAGAGGAAGA	57.484	50.000	0.00	0.00	34.73	2.87
1287	1324	3.074412	CGGGAAATCAAACTAGCACTGT	58.926	45.455	0.00	0.00	0.00	3.55
1934	2010	4.572389	GTGCATGAACGACAAAGAGGATAT	59.428	41.667	0.00	0.00	0.00	1.63
1939	2015	3.062763	AGAGTGCATGAACGACAAAGAG	58.937	45.455	0.00	0.00	0.00	2.85
1965	2043	8.522542	TTATAACTACACAAAACCAAACACCT	57.477	30.769	0.00	0.00	0.00	4.00
2000	2079	3.177228	ACAAATACAGTCCTCTCCAGCT	58.823	45.455	0.00	0.00	0.00	4.24
2025	2108	8.470040	ACAACTAATTGCAGCATAAAGATTTG	57.530	30.769	0.00	0.00	39.66	2.32
2205	2300	2.289072	ACTCCATTCCGTCACAGTTCAG	60.289	50.000	0.00	0.00	0.00	3.02
2209	2304	0.320771	GCACTCCATTCCGTCACAGT	60.321	55.000	0.00	0.00	0.00	3.55
2492	2587	1.153289	CTTGTCGGGATGGAGCTGG	60.153	63.158	0.00	0.00	0.00	4.85
2564	2659	1.098712	TGGTTTTGTCGGACAGCACC	61.099	55.000	23.95	23.95	34.38	5.01
2813	3184	4.161295	TGATGGCGAGGAAGCGGG	62.161	66.667	0.00	0.00	38.18	6.13
3032	3403	0.592637	TTGCATCTTCAGTTGCACCG	59.407	50.000	11.32	0.00	46.59	4.94
3305	3676	6.877611	TTACCCACAGTTTTCATCTTCTTC	57.122	37.500	0.00	0.00	0.00	2.87
3329	3700	2.290577	GGAAGAACCAACTCCAGCATCT	60.291	50.000	0.00	0.00	38.79	2.90
3366	3737	1.761784	TCCAACATAATTGGCCCATGC	59.238	47.619	0.00	0.00	39.38	4.06
3563	3934	6.260663	ACTTCTTATCTCCTTCACCTTCTCT	58.739	40.000	0.00	0.00	0.00	3.10
3572	3943	7.042950	GGACTGGTTTACTTCTTATCTCCTTC	58.957	42.308	0.00	0.00	0.00	3.46
3594	3965	6.861572	GCTTTTCCATTAACTGTAACTTGGAC	59.138	38.462	0.00	0.00	31.10	4.02
3664	4035	5.050227	GCAGTAGAATCATCTGATGCAAGAC	60.050	44.000	12.78	7.01	42.99	3.01
3700	4071	0.464870	CTCCTCTGGATCAGCACAGG	59.535	60.000	0.00	0.00	35.47	4.00
3782	4309	3.870538	TCATGGAAATCAGGATCAGGG	57.129	47.619	0.00	0.00	30.49	4.45
3968	4498	1.000843	GCCCAATTCAGTGGTCCAAAC	59.999	52.381	0.00	0.00	36.90	2.93
3978	4508	1.098050	CCGGAAGAAGCCCAATTCAG	58.902	55.000	0.00	0.00	0.00	3.02
4186	4716	5.124457	ACCAGATCATAAACATGAAGCACAC	59.876	40.000	0.00	0.00	33.83	3.82
4404	4934	6.665680	GGATCTACCTCATAGCTATCTTTGGA	59.334	42.308	2.34	0.00	35.41	3.53
4603	5143	8.828688	ACAAAGGTGATAGTCAAAAGTAGTAC	57.171	34.615	0.00	0.00	0.00	2.73
4665	5205	2.710471	TGCCCAGATGCCATACAAGATA	59.290	45.455	0.00	0.00	0.00	1.98
4688	5228	8.397906	TGTTTAAGTTTTGAGATGACAAGACAG	58.602	33.333	0.00	0.00	37.35	3.51
4820	5360	8.470002	ACCAGATAAAATAGCAAAACCTTCATC	58.530	33.333	0.00	0.00	0.00	2.92
4995	5555	4.665833	AAAACTCCGGAAAAGGGAAAAG	57.334	40.909	5.23	0.00	32.02	2.27
5039	5599	3.499537	GCTGCGACAATCAATATGGATCA	59.500	43.478	0.00	0.00	0.00	2.92
5051	5611	4.315803	AGTTGTACTAAAGCTGCGACAAT	58.684	39.130	0.00	0.00	0.00	2.71
5302	5883	2.360726	TAGACCGCGGCTGTGAGA	60.361	61.111	28.58	4.94	0.00	3.27

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.