AutoCloner

Multiple sequence alignment - TraesCS4A01G176600

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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	TraesCS4A01G176600	chr4A	100.000	3950	0	0	1	3950	448102319	448106268	0.000000e+00	7295.0
1	TraesCS4A01G176600	chr4A	87.356	87	11	0	1132	1218	447777162	447777248	2.510000e-17	100.0
2	TraesCS4A01G176600	chr4A	87.037	54	7	0	1429	1482	579372436	579372383	1.190000e-05	62.1
3	TraesCS4A01G176600	chr4B	94.595	3423	107	25	135	3513	185870506	185867118	0.000000e+00	5225.0
4	TraesCS4A01G176600	chr4B	96.119	335	9	1	3616	3950	185867120	185866790	9.650000e-151	544.0
5	TraesCS4A01G176600	chr4B	95.215	209	10	0	2632	2840	131369587	131369795	8.180000e-87	331.0
6	TraesCS4A01G176600	chr4B	86.022	186	12	5	3616	3800	628068444	628068616	1.870000e-43	187.0
7	TraesCS4A01G176600	chr4B	96.296	108	4	0	3510	3617	416442599	416442706	1.130000e-40	178.0
8	TraesCS4A01G176600	chr4B	94.783	115	5	1	3508	3621	628505269	628505155	1.130000e-40	178.0
9	TraesCS4A01G176600	chr4B	86.957	161	8	7	2957	3111	628068110	628068263	6.790000e-38	169.0
10	TraesCS4A01G176600	chr4B	86.331	139	8	1	1	139	185871770	185871643	1.480000e-29	141.0
11	TraesCS4A01G176600	chr4B	93.617	94	6	0	3846	3939	628068620	628068713	1.480000e-29	141.0
12	TraesCS4A01G176600	chr4D	96.949	2917	62	8	624	3523	122259948	122257042	0.000000e+00	4868.0
13	TraesCS4A01G176600	chr4D	94.852	641	14	5	1	624	122265152	122264514	0.000000e+00	983.0
14	TraesCS4A01G176600	chr4D	94.236	347	16	1	3604	3950	122256903	122256561	9.720000e-146	527.0
15	TraesCS4A01G176600	chr4D	86.890	328	25	8	3616	3939	489728411	489728724	6.280000e-93	351.0
16	TraesCS4A01G176600	chr4D	86.585	328	27	8	3616	3939	489733687	489734001	2.920000e-91	346.0
17	TraesCS4A01G176600	chr4D	92.899	169	12	0	3345	3513	489728245	489728413	3.050000e-61	246.0
18	TraesCS4A01G176600	chr4D	86.486	148	10	6	2957	3101	489733351	489733491	1.900000e-33	154.0
19	TraesCS4A01G176600	chr7B	74.262	983	224	26	1825	2788	88246338	88247310	1.720000e-103	387.0
20	TraesCS4A01G176600	chr7B	74.040	990	229	24	1825	2794	87173309	87172328	2.880000e-101	379.0
21	TraesCS4A01G176600	chr7B	95.536	112	5	0	3506	3617	134635191	134635080	3.140000e-41	180.0
22	TraesCS4A01G176600	chr7B	87.037	54	7	0	1429	1482	87173726	87173673	1.190000e-05	62.1
23	TraesCS4A01G176600	chr7B	87.037	54	7	0	1429	1482	88245927	88245980	1.190000e-05	62.1
24	TraesCS4A01G176600	chr7A	74.522	942	215	21	1825	2749	127608376	127609309	1.720000e-103	387.0
25	TraesCS4A01G176600	chr7A	95.614	114	5	0	3509	3622	192671964	192671851	2.420000e-42	183.0
26	TraesCS4A01G176600	chr7D	73.263	1137	269	30	1825	2939	126682749	126683872	2.230000e-102	383.0
27	TraesCS4A01G176600	chr7D	73.951	906	212	20	1907	2794	126506249	126505350	1.050000e-90	344.0
28	TraesCS4A01G176600	chr7D	87.037	54	7	0	1429	1482	88363050	88362997	1.190000e-05	62.1
29	TraesCS4A01G176600	chr7D	87.037	54	7	0	1429	1482	126506745	126506692	1.190000e-05	62.1
30	TraesCS4A01G176600	chr5A	88.272	324	25	4	3616	3939	671183081	671183391	3.730000e-100	375.0
31	TraesCS4A01G176600	chr5A	86.544	327	27	7	3616	3939	671177074	671177386	1.050000e-90	344.0
32	TraesCS4A01G176600	chr5A	92.398	171	11	1	3345	3513	671176906	671177076	3.940000e-60	243.0
33	TraesCS4A01G176600	chr5A	90.643	171	11	3	3345	3513	671182916	671183083	5.140000e-54	222.0
34	TraesCS4A01G176600	chr5A	84.768	151	10	6	2957	3101	671182741	671182884	5.320000e-29	139.0
35	TraesCS4A01G176600	chr6A	95.536	112	5	0	3510	3621	596351528	596351417	3.140000e-41	180.0
36	TraesCS4A01G176600	chr6A	93.333	120	7	1	3511	3629	150232595	150232476	4.060000e-40	176.0
37	TraesCS4A01G176600	chr1B	95.536	112	5	0	3511	3622	15616935	15616824	3.140000e-41	180.0
38	TraesCS4A01G176600	chr3D	92.683	123	7	1	3495	3617	168186423	168186543	4.060000e-40	176.0
39	TraesCS4A01G176600	chr3D	87.037	54	7	0	1429	1482	538375082	538375029	1.190000e-05	62.1
40	TraesCS4A01G176600	chr3B	91.870	123	8	1	3495	3617	779534209	779534329	1.890000e-38	171.0
41	TraesCS4A01G176600	chr5D	87.037	54	7	0	1429	1482	457998904	457998851	1.190000e-05	62.1

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	TraesCS4A01G176600	chr4A	448102319	448106268	3949	False	7295.000000	7295	100.000000	1	3950	1	chr4A.!!$F2	3949
1	TraesCS4A01G176600	chr4B	185866790	185871770	4980	True	1970.000000	5225	92.348333	1	3950	3	chr4B.!!$R2	3949
2	TraesCS4A01G176600	chr4D	122256561	122259948	3387	True	2697.500000	4868	95.592500	624	3950	2	chr4D.!!$R2	3326
3	TraesCS4A01G176600	chr4D	122264514	122265152	638	True	983.000000	983	94.852000	1	624	1	chr4D.!!$R1	623
4	TraesCS4A01G176600	chr4D	489733351	489734001	650	False	250.000000	346	86.535500	2957	3939	2	chr4D.!!$F2	982
5	TraesCS4A01G176600	chr7B	88245927	88247310	1383	False	224.550000	387	80.649500	1429	2788	2	chr7B.!!$F1	1359
6	TraesCS4A01G176600	chr7B	87172328	87173726	1398	True	220.550000	379	80.538500	1429	2794	2	chr7B.!!$R2	1365
7	TraesCS4A01G176600	chr7A	127608376	127609309	933	False	387.000000	387	74.522000	1825	2749	1	chr7A.!!$F1	924
8	TraesCS4A01G176600	chr7D	126682749	126683872	1123	False	383.000000	383	73.263000	1825	2939	1	chr7D.!!$F1	1114
9	TraesCS4A01G176600	chr7D	126505350	126506745	1395	True	203.050000	344	80.494000	1429	2794	2	chr7D.!!$R2	1365
10	TraesCS4A01G176600	chr5A	671182741	671183391	650	False	245.333333	375	87.894333	2957	3939	3	chr5A.!!$F2	982

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
226	1373	0.464870	TTGCATTGCATGGGCCATAC	59.535	50.0	20.73	15.06	38.76	2.39	F
754	1932	0.756442	ACATGCTGCCAGGTGTGTTT	60.756	50.0	0.00	0.00	34.21	2.83	F
1323	2516	0.907704	TGCAGGGTATTCGTGGAGGT	60.908	55.0	0.00	0.00	0.00	3.85	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1143	2336	0.033228	CGATGTCCTCCTCCATCAGC	59.967	60.000	0.00	0.00	37.84	4.26	R
2538	3773	0.039035	AAAATGGGCCGCTAGAACCA	59.961	50.000	0.00	0.00	37.41	3.67	R
3014	4256	1.076705	GAAACAGGAGGGGATGCCC	60.077	63.158	15.97	15.97	44.51	5.36	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
66	67	6.595716	AGCAGAGTACATGATGTTCCTTTTAC	59.404	38.462	2.29	0.00	0.00	2.01
68	69	7.413438	GCAGAGTACATGATGTTCCTTTTACAG	60.413	40.741	2.29	0.00	0.00	2.74
133	134	7.159322	TCCTAACACACTCATCTCTAACTTC	57.841	40.000	0.00	0.00	0.00	3.01
169	1311	8.845227	TGTATCTCTTCACTTAGCATCTTCTAG	58.155	37.037	0.00	0.00	0.00	2.43
181	1323	4.940654	AGCATCTTCTAGTTCCTTTTGCTC	59.059	41.667	0.00	0.00	32.86	4.26
226	1373	0.464870	TTGCATTGCATGGGCCATAC	59.535	50.000	20.73	15.06	38.76	2.39
285	1432	4.273148	TGCCTCTGAAACTCTTCTAACC	57.727	45.455	0.00	0.00	32.33	2.85
544	1703	5.220989	GCTCATGAAAGATGAAAGCATGCTA	60.221	40.000	23.00	5.74	37.01	3.49
733	1911	5.777802	TCTTGGCGCTTTCATAATGAAAAA	58.222	33.333	7.64	0.00	44.69	1.94
754	1932	0.756442	ACATGCTGCCAGGTGTGTTT	60.756	50.000	0.00	0.00	34.21	2.83
799	1992	6.299805	ACAGTCATACTATTGTGTGATGGT	57.700	37.500	9.66	8.34	44.09	3.55
1143	2336	2.410939	CTCCCATACATCACTCGCATG	58.589	52.381	0.00	0.00	0.00	4.06
1293	2486	3.464907	CGACATGGAGAAGATGCATTCT	58.535	45.455	0.00	0.41	37.99	2.40
1323	2516	0.907704	TGCAGGGTATTCGTGGAGGT	60.908	55.000	0.00	0.00	0.00	3.85
1384	2577	1.892819	CTCGGATGGTGCTGAGGTGT	61.893	60.000	0.00	0.00	37.58	4.16
1654	2877	3.008517	TGGAAGAGGATGGCGCCA	61.009	61.111	34.80	34.80	0.00	5.69
2445	3668	2.920724	TCAACACCTTGATGGACGAA	57.079	45.000	0.00	0.00	39.71	3.85
2538	3773	2.616842	GTTCGTCCAAGGTGTTGTGAAT	59.383	45.455	0.00	0.00	30.95	2.57
2544	3779	2.958355	CCAAGGTGTTGTGAATGGTTCT	59.042	45.455	0.00	0.00	30.95	3.01
2617	3855	1.225855	GGTGTTCGACATGCTTGACA	58.774	50.000	6.60	0.00	0.00	3.58
2634	3872	3.941188	ACCACCACACCGCCAGAG	61.941	66.667	0.00	0.00	0.00	3.35
2727	3965	3.525545	GACCGGGTAGAGCGTCCC	61.526	72.222	6.32	0.00	40.26	4.46
2767	4005	0.380378	GCTGAGAAACCAACGTGCAA	59.620	50.000	0.00	0.00	0.00	4.08
2802	4040	2.213499	CCACTGAAGCCGATTATCACC	58.787	52.381	0.00	0.00	0.00	4.02
2940	4178	1.139947	GGCAGACGACACTAGCTCC	59.860	63.158	0.00	0.00	0.00	4.70
2964	4202	3.696548	AGTATTAGCTGCCTTTTTCTGCC	59.303	43.478	0.00	0.00	0.00	4.85
2967	4205	2.521547	AGCTGCCTTTTTCTGCCTAT	57.478	45.000	0.00	0.00	0.00	2.57
2968	4206	3.652057	AGCTGCCTTTTTCTGCCTATA	57.348	42.857	0.00	0.00	0.00	1.31
2994	4236	9.892130	AAGAGGTTAATCTTTGGACATTAGTAG	57.108	33.333	0.00	0.00	36.05	2.57
2995	4237	9.047947	AGAGGTTAATCTTTGGACATTAGTAGT	57.952	33.333	0.00	0.00	0.00	2.73
3035	4277	0.106967	GCATCCCCTCCTGTTTCCTC	60.107	60.000	0.00	0.00	0.00	3.71
3039	4281	0.038310	CCCCTCCTGTTTCCTCCAAC	59.962	60.000	0.00	0.00	0.00	3.77
3176	4428	9.956720	AGTTTCAATTTGATGAGTAAAGACTTG	57.043	29.630	0.00	0.00	35.45	3.16
3193	4445	7.823745	AAGACTTGATGTAAAGGTCAATTGT	57.176	32.000	5.13	0.00	0.00	2.71
3234	4486	6.072508	TGTTTATGTGCTTCCACTCATTCTTC	60.073	38.462	0.00	0.00	42.54	2.87
3235	4487	3.777106	TGTGCTTCCACTCATTCTTCT	57.223	42.857	0.00	0.00	42.54	2.85
3236	4488	4.090761	TGTGCTTCCACTCATTCTTCTT	57.909	40.909	0.00	0.00	42.54	2.52
3324	4581	7.861629	AGAGGACCAATAAATTCAGTGTCATA	58.138	34.615	0.00	0.00	0.00	2.15
3449	4706	0.034574	TTGCAGGTGTCCAAGTGTGT	60.035	50.000	0.00	0.00	0.00	3.72
3468	4725	6.770785	AGTGTGTAGCAGGAAAGAAACATAAA	59.229	34.615	0.00	0.00	0.00	1.40
3523	4782	1.031235	GGCTACTACTCCCTCCGTTC	58.969	60.000	0.00	0.00	0.00	3.95
3524	4783	1.684248	GGCTACTACTCCCTCCGTTCA	60.684	57.143	0.00	0.00	0.00	3.18
3525	4784	1.677052	GCTACTACTCCCTCCGTTCAG	59.323	57.143	0.00	0.00	0.00	3.02
3528	4787	3.103080	ACTACTCCCTCCGTTCAGAAT	57.897	47.619	0.00	0.00	0.00	2.40
3531	4790	3.889520	ACTCCCTCCGTTCAGAATTAC	57.110	47.619	0.00	0.00	0.00	1.89
3532	4791	3.442076	ACTCCCTCCGTTCAGAATTACT	58.558	45.455	0.00	0.00	0.00	2.24
3533	4792	3.838903	ACTCCCTCCGTTCAGAATTACTT	59.161	43.478	0.00	0.00	0.00	2.24
3537	4796	3.933332	CCTCCGTTCAGAATTACTTGTCC	59.067	47.826	0.00	0.00	0.00	4.02
3538	4797	3.933332	CTCCGTTCAGAATTACTTGTCCC	59.067	47.826	0.00	0.00	0.00	4.46
3539	4798	2.671396	CCGTTCAGAATTACTTGTCCCG	59.329	50.000	0.00	0.00	0.00	5.14
3546	4838	5.414454	TCAGAATTACTTGTCCCGAAAATGG	59.586	40.000	0.00	0.00	0.00	3.16
3550	4842	3.154827	ACTTGTCCCGAAAATGGATGT	57.845	42.857	0.00	0.00	33.65	3.06
3556	4848	5.853936	TGTCCCGAAAATGGATGTATCTAG	58.146	41.667	0.00	0.00	33.65	2.43
3558	4850	6.099125	TGTCCCGAAAATGGATGTATCTAGAA	59.901	38.462	0.00	0.00	33.65	2.10
3561	4854	6.647067	CCCGAAAATGGATGTATCTAGAACTC	59.353	42.308	0.00	0.00	0.00	3.01
3564	4857	9.098355	CGAAAATGGATGTATCTAGAACTCAAA	57.902	33.333	0.00	0.00	0.00	2.69
3589	4882	9.664332	AATATGTCTAGATACATCCATTTCTGC	57.336	33.333	0.00	0.00	40.52	4.26
3590	4883	5.532557	TGTCTAGATACATCCATTTCTGCG	58.467	41.667	0.00	0.00	0.00	5.18
3592	4885	5.631512	GTCTAGATACATCCATTTCTGCGAC	59.368	44.000	0.00	0.00	0.00	5.19
3593	4886	4.406648	AGATACATCCATTTCTGCGACA	57.593	40.909	0.00	0.00	0.00	4.35
3594	4887	4.769688	AGATACATCCATTTCTGCGACAA	58.230	39.130	0.00	0.00	0.00	3.18
3595	4888	4.813161	AGATACATCCATTTCTGCGACAAG	59.187	41.667	0.00	0.00	0.00	3.16
3596	4889	2.783135	ACATCCATTTCTGCGACAAGT	58.217	42.857	0.00	0.00	0.00	3.16
3597	4890	3.937814	ACATCCATTTCTGCGACAAGTA	58.062	40.909	0.00	0.00	0.00	2.24
3598	4891	4.323417	ACATCCATTTCTGCGACAAGTAA	58.677	39.130	0.00	0.00	0.00	2.24
3600	4893	5.415701	ACATCCATTTCTGCGACAAGTAATT	59.584	36.000	0.00	0.00	0.00	1.40
3601	4894	5.545658	TCCATTTCTGCGACAAGTAATTC	57.454	39.130	0.00	0.00	0.00	2.17
3602	4895	4.394920	TCCATTTCTGCGACAAGTAATTCC	59.605	41.667	0.00	0.00	0.00	3.01
3607	4924	2.734606	CTGCGACAAGTAATTCCGAACA	59.265	45.455	0.00	0.00	0.00	3.18
3624	4941	3.673594	CGAACAGAGGGAGTACATGTGAC	60.674	52.174	9.11	3.04	0.00	3.67
3687	5004	9.627395	ATTATTTTATCTGCTAGTGCTACTACG	57.373	33.333	0.00	0.00	40.48	3.51
3695	5012	4.397103	TGCTAGTGCTACTACGTACATGTT	59.603	41.667	2.30	0.00	40.48	2.71
3718	5035	2.498167	ACTCACAACAGCCTGACATTC	58.502	47.619	0.00	0.00	0.00	2.67

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
181	1323	1.224592	GTGACATACCCCAGCCAGG	59.775	63.158	0.00	0.00	37.03	4.45
232	1379	8.824756	TTGGTTACCATATTTGCTATTGGTAA	57.175	30.769	4.38	8.84	38.92	2.85
233	1380	9.427821	AATTGGTTACCATATTTGCTATTGGTA	57.572	29.630	4.38	0.00	31.53	3.25
234	1381	7.912778	ATTGGTTACCATATTTGCTATTGGT	57.087	32.000	4.38	0.00	31.53	3.67
235	1382	9.260002	GAAATTGGTTACCATATTTGCTATTGG	57.740	33.333	20.64	0.00	31.53	3.16
236	1383	8.967218	CGAAATTGGTTACCATATTTGCTATTG	58.033	33.333	20.64	5.61	31.53	1.90
237	1384	8.691797	ACGAAATTGGTTACCATATTTGCTATT	58.308	29.630	20.64	8.06	31.53	1.73
238	1385	8.232913	ACGAAATTGGTTACCATATTTGCTAT	57.767	30.769	20.64	3.06	31.53	2.97
285	1432	1.603455	ACAATGGGCACAGGTTCGG	60.603	57.895	0.00	0.00	0.00	4.30
733	1911	1.303074	CACACCTGGCAGCATGTCT	60.303	57.895	16.93	0.00	44.57	3.41
754	1932	8.383175	ACTGTCCTAGGTTGATTATTTTTCTCA	58.617	33.333	9.08	0.00	0.00	3.27
799	1992	1.003580	GGCTGATCCTCCTGTTTGTCA	59.996	52.381	0.00	0.00	0.00	3.58
1062	2255	1.191535	TGTCAAGGTAGACGGATGGG	58.808	55.000	0.00	0.00	41.41	4.00
1143	2336	0.033228	CGATGTCCTCCTCCATCAGC	59.967	60.000	0.00	0.00	37.84	4.26
1293	2486	0.323302	TACCCTGCAAAGACGCATCA	59.677	50.000	0.00	0.00	42.06	3.07
1384	2577	7.112122	AGTTTGCTCTGATCACCATTATTGTA	58.888	34.615	0.00	0.00	0.00	2.41
1654	2877	6.039047	AGCATTATTTTGTTGATCATCTCGCT	59.961	34.615	0.00	0.00	0.00	4.93
2445	3668	2.354805	GGGTCTGTCGATAACAAGGCTT	60.355	50.000	0.00	0.00	37.45	4.35
2538	3773	0.039035	AAAATGGGCCGCTAGAACCA	59.961	50.000	0.00	0.00	37.41	3.67
2544	3779	1.181786	CCAAGAAAAATGGGCCGCTA	58.818	50.000	0.00	0.00	34.15	4.26
2580	3818	5.470047	ACACCGATGAGTAAAAGAAGAGT	57.530	39.130	0.00	0.00	0.00	3.24
2617	3855	3.941188	CTCTGGCGGTGTGGTGGT	61.941	66.667	0.00	0.00	0.00	4.16
2682	3920	1.269723	TCGCAGGCGATAGTATTCAGG	59.730	52.381	12.94	0.00	44.01	3.86
2727	3965	2.412870	TGCCACTGTTTGTATGTCTCG	58.587	47.619	0.00	0.00	0.00	4.04
2767	4005	2.926779	TGGCAGCTGTCTGAGGCT	60.927	61.111	20.86	0.00	42.95	4.58
2802	4040	1.364901	CTTGCCTGTTGCCACCTTG	59.635	57.895	0.00	0.00	40.16	3.61
2940	4178	4.494855	GCAGAAAAAGGCAGCTAATACTCG	60.495	45.833	0.00	0.00	0.00	4.18
2968	4206	9.892130	CTACTAATGTCCAAAGATTAACCTCTT	57.108	33.333	0.00	0.00	37.06	2.85
2992	4234	6.267014	GCCCCAGTTGTATCTCATAAGTACTA	59.733	42.308	0.00	0.00	0.00	1.82
2993	4235	5.070580	GCCCCAGTTGTATCTCATAAGTACT	59.929	44.000	0.00	0.00	0.00	2.73
2994	4236	5.163343	TGCCCCAGTTGTATCTCATAAGTAC	60.163	44.000	0.00	0.00	0.00	2.73
2995	4237	4.966168	TGCCCCAGTTGTATCTCATAAGTA	59.034	41.667	0.00	0.00	0.00	2.24
2996	4238	3.780294	TGCCCCAGTTGTATCTCATAAGT	59.220	43.478	0.00	0.00	0.00	2.24
2997	4239	4.422073	TGCCCCAGTTGTATCTCATAAG	57.578	45.455	0.00	0.00	0.00	1.73
2998	4240	4.202461	GGATGCCCCAGTTGTATCTCATAA	60.202	45.833	0.00	0.00	34.14	1.90
3002	4244	2.262423	GGATGCCCCAGTTGTATCTC	57.738	55.000	0.00	0.00	34.14	2.75
3014	4256	1.076705	GAAACAGGAGGGGATGCCC	60.077	63.158	15.97	15.97	44.51	5.36
3035	4277	5.567138	AGAGCGAAATTTAAGATGGTTGG	57.433	39.130	0.00	0.00	0.00	3.77
3039	4281	7.402640	GTGTCTAAGAGCGAAATTTAAGATGG	58.597	38.462	0.00	0.00	0.00	3.51
3176	4428	5.982516	TGCAACAACAATTGACCTTTACATC	59.017	36.000	13.59	0.00	0.00	3.06
3375	4632	9.132521	CGCAGAGAAAGAAATTACAAATTCAAT	57.867	29.630	0.00	0.00	0.00	2.57
3449	4706	8.402798	TGTTCATTTATGTTTCTTTCCTGCTA	57.597	30.769	0.00	0.00	0.00	3.49
3468	4725	6.210385	TGCATGTAACCTTTAACCATGTTCAT	59.790	34.615	0.00	0.00	36.23	2.57
3523	4782	5.414454	TCCATTTTCGGGACAAGTAATTCTG	59.586	40.000	0.00	0.00	0.00	3.02
3524	4783	5.566469	TCCATTTTCGGGACAAGTAATTCT	58.434	37.500	0.00	0.00	0.00	2.40
3525	4784	5.890424	TCCATTTTCGGGACAAGTAATTC	57.110	39.130	0.00	0.00	0.00	2.17
3528	4787	4.658063	ACATCCATTTTCGGGACAAGTAA	58.342	39.130	0.00	0.00	37.23	2.24
3531	4790	5.126067	AGATACATCCATTTTCGGGACAAG	58.874	41.667	0.00	0.00	37.23	3.16
3532	4791	5.110814	AGATACATCCATTTTCGGGACAA	57.889	39.130	0.00	0.00	37.23	3.18
3533	4792	4.771114	AGATACATCCATTTTCGGGACA	57.229	40.909	0.00	0.00	37.23	4.02
3537	4796	7.210174	TGAGTTCTAGATACATCCATTTTCGG	58.790	38.462	0.00	0.00	0.00	4.30
3538	4797	8.648557	TTGAGTTCTAGATACATCCATTTTCG	57.351	34.615	0.00	0.00	0.00	3.46
3564	4857	7.978414	CGCAGAAATGGATGTATCTAGACATAT	59.022	37.037	0.00	0.00	40.18	1.78
3573	4866	4.572389	ACTTGTCGCAGAAATGGATGTATC	59.428	41.667	0.00	0.00	39.69	2.24
3582	4875	4.250464	TCGGAATTACTTGTCGCAGAAAT	58.750	39.130	0.00	0.00	39.69	2.17
3584	4877	3.306917	TCGGAATTACTTGTCGCAGAA	57.693	42.857	0.00	0.00	39.69	3.02
3586	4879	2.734606	TGTTCGGAATTACTTGTCGCAG	59.265	45.455	0.00	0.00	0.00	5.18
3589	4882	3.612860	CCTCTGTTCGGAATTACTTGTCG	59.387	47.826	0.00	0.00	0.00	4.35
3590	4883	3.933332	CCCTCTGTTCGGAATTACTTGTC	59.067	47.826	0.00	0.00	0.00	3.18
3592	4885	4.184629	CTCCCTCTGTTCGGAATTACTTG	58.815	47.826	0.00	0.00	0.00	3.16
3593	4886	3.838903	ACTCCCTCTGTTCGGAATTACTT	59.161	43.478	0.00	0.00	0.00	2.24
3594	4887	3.442076	ACTCCCTCTGTTCGGAATTACT	58.558	45.455	0.00	0.00	0.00	2.24
3595	4888	3.889520	ACTCCCTCTGTTCGGAATTAC	57.110	47.619	0.00	0.00	0.00	1.89
3596	4889	4.346730	TGTACTCCCTCTGTTCGGAATTA	58.653	43.478	0.00	0.00	0.00	1.40
3597	4890	3.170717	TGTACTCCCTCTGTTCGGAATT	58.829	45.455	0.00	0.00	0.00	2.17
3598	4891	2.816411	TGTACTCCCTCTGTTCGGAAT	58.184	47.619	0.00	0.00	0.00	3.01
3600	4893	2.100197	CATGTACTCCCTCTGTTCGGA	58.900	52.381	0.00	0.00	0.00	4.55
3601	4894	1.825474	ACATGTACTCCCTCTGTTCGG	59.175	52.381	0.00	0.00	0.00	4.30
3602	4895	2.492088	TCACATGTACTCCCTCTGTTCG	59.508	50.000	0.00	0.00	0.00	3.95
3607	4924	2.930109	AGGTCACATGTACTCCCTCT	57.070	50.000	0.00	0.00	0.00	3.69
3684	5001	5.893512	GTTGTGAGTTCAACATGTACGTA	57.106	39.130	0.00	0.00	44.65	3.57
3685	5002	4.789095	GTTGTGAGTTCAACATGTACGT	57.211	40.909	0.00	0.00	44.65	3.57
3695	5012	1.209261	TGTCAGGCTGTTGTGAGTTCA	59.791	47.619	15.27	0.00	0.00	3.18

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.