AutoCloner

Multiple sequence alignment - TraesCS5D01G390100

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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	TraesCS5D01G390100	chr5D	100.000	5371	0	0	1	5371	458896538	458901908	0.000000e+00	9919
1	TraesCS5D01G390100	chr5D	86.903	565	30	15	950	1497	458866851	458867388	1.290000e-165	593
2	TraesCS5D01G390100	chr5D	84.211	551	74	11	3396	3942	458839632	458840173	1.710000e-144	523
3	TraesCS5D01G390100	chr5D	83.585	463	41	12	298	735	389452389	389452841	8.380000e-108	401
4	TraesCS5D01G390100	chr5D	86.250	240	26	2	996	1234	458818129	458818362	2.480000e-63	254
5	TraesCS5D01G390100	chr5D	84.739	249	29	3	989	1234	458836036	458836278	1.930000e-59	241
6	TraesCS5D01G390100	chr5D	78.333	300	52	10	2775	3068	458838013	458838305	1.190000e-41	182
7	TraesCS5D01G390100	chr5D	84.940	166	25	0	1632	1797	458818472	458818637	9.250000e-38	169
8	TraesCS5D01G390100	chr3D	90.834	3993	207	59	1047	4996	16163449	16167325	0.000000e+00	5199
9	TraesCS5D01G390100	chr3D	88.993	536	43	10	4672	5202	16161830	16162354	0.000000e+00	649
10	TraesCS5D01G390100	chr3D	82.081	346	33	13	5053	5371	16167811	16168154	8.870000e-68	268
11	TraesCS5D01G390100	chr3B	91.885	3019	169	31	1623	4597	23704117	23707103	0.000000e+00	4148
12	TraesCS5D01G390100	chr3B	84.857	350	18	7	1047	1391	23703791	23704110	2.410000e-83	320
13	TraesCS5D01G390100	chr3B	80.110	362	32	19	5045	5371	23707111	23707467	3.230000e-57	233
14	TraesCS5D01G390100	chr5B	93.341	1832	74	27	754	2577	562952003	562953794	0.000000e+00	2663
15	TraesCS5D01G390100	chr5B	94.672	1539	64	14	2606	4129	562953873	562955408	0.000000e+00	2372
16	TraesCS5D01G390100	chr5B	92.388	762	33	4	1	738	562951261	562952021	0.000000e+00	1062
17	TraesCS5D01G390100	chr5B	83.024	807	85	24	4082	4847	562955406	562956201	0.000000e+00	684
18	TraesCS5D01G390100	chr5B	87.554	466	52	6	3479	3942	562492188	562492649	7.920000e-148	534
19	TraesCS5D01G390100	chr5B	81.063	301	44	9	2775	3068	562490547	562490841	1.500000e-55	228
20	TraesCS5D01G390100	chr5B	85.714	98	10	4	5200	5295	562956294	562956389	3.420000e-17	100
21	TraesCS5D01G390100	chr5A	93.349	1699	65	14	897	2577	577932143	577933811	0.000000e+00	2468
22	TraesCS5D01G390100	chr5A	94.576	1475	70	8	2577	4044	577933849	577935320	0.000000e+00	2272
23	TraesCS5D01G390100	chr5A	94.029	1189	43	7	4201	5371	577935337	577936515	0.000000e+00	1777
24	TraesCS5D01G390100	chr5A	83.455	550	80	10	3396	3942	577901734	577902275	8.030000e-138	501
25	TraesCS5D01G390100	chr5A	86.345	249	25	3	989	1234	577887164	577887406	4.130000e-66	263
26	TraesCS5D01G390100	chr5A	79.667	300	47	11	2775	3068	577889757	577890048	2.540000e-48	204
27	TraesCS5D01G390100	chr3A	92.000	1225	75	12	2012	3234	20225992	20224789	0.000000e+00	1698
28	TraesCS5D01G390100	chr3A	90.739	1177	77	10	3338	4486	20229781	20228609	0.000000e+00	1541
29	TraesCS5D01G390100	chr3A	95.204	834	34	6	3238	4069	20218838	20218009	0.000000e+00	1314
30	TraesCS5D01G390100	chr3A	91.570	949	52	9	4068	4996	20217847	20216907	0.000000e+00	1284
31	TraesCS5D01G390100	chr3A	92.367	773	47	8	2577	3343	20231443	20230677	0.000000e+00	1090
32	TraesCS5D01G390100	chr3A	89.294	878	49	13	1047	1917	20226879	20226040	0.000000e+00	1059
33	TraesCS5D01G390100	chr3A	87.599	629	50	14	4580	5202	20228544	20227938	0.000000e+00	704
34	TraesCS5D01G390100	chr3A	87.432	183	17	4	5193	5371	20216302	20216122	7.050000e-49	206
35	TraesCS5D01G390100	chr2D	81.406	441	60	13	417	856	473094860	473095279	1.850000e-89	340
36	TraesCS5D01G390100	chr2D	89.011	273	22	4	408	679	431525931	431526196	1.120000e-86	331
37	TraesCS5D01G390100	chr2D	88.278	273	24	4	408	679	52015711	52015976	2.410000e-83	320
38	TraesCS5D01G390100	chr2D	88.627	255	25	4	408	660	370823281	370823533	1.880000e-79	307
39	TraesCS5D01G390100	chr6D	85.303	347	28	7	358	681	434774873	434775219	2.400000e-88	337
40	TraesCS5D01G390100	chr4D	88.583	254	22	3	427	679	490979841	490979594	8.740000e-78	302

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	TraesCS5D01G390100	chr5D	458896538	458901908	5370	False	9919.000000	9919	100.000000	1	5371	1	chr5D.!!$F3	5370
1	TraesCS5D01G390100	chr5D	458866851	458867388	537	False	593.000000	593	86.903000	950	1497	1	chr5D.!!$F2	547
2	TraesCS5D01G390100	chr5D	458836036	458840173	4137	False	315.333333	523	82.427667	989	3942	3	chr5D.!!$F5	2953
3	TraesCS5D01G390100	chr5D	458818129	458818637	508	False	211.500000	254	85.595000	996	1797	2	chr5D.!!$F4	801
4	TraesCS5D01G390100	chr3D	16161830	16168154	6324	False	2038.666667	5199	87.302667	1047	5371	3	chr3D.!!$F1	4324
5	TraesCS5D01G390100	chr3B	23703791	23707467	3676	False	1567.000000	4148	85.617333	1047	5371	3	chr3B.!!$F1	4324
6	TraesCS5D01G390100	chr5B	562951261	562956389	5128	False	1376.200000	2663	89.827800	1	5295	5	chr5B.!!$F2	5294
7	TraesCS5D01G390100	chr5B	562490547	562492649	2102	False	381.000000	534	84.308500	2775	3942	2	chr5B.!!$F1	1167
8	TraesCS5D01G390100	chr5A	577932143	577936515	4372	False	2172.333333	2468	93.984667	897	5371	3	chr5A.!!$F3	4474
9	TraesCS5D01G390100	chr5A	577901734	577902275	541	False	501.000000	501	83.455000	3396	3942	1	chr5A.!!$F1	546
10	TraesCS5D01G390100	chr5A	577887164	577890048	2884	False	233.500000	263	83.006000	989	3068	2	chr5A.!!$F2	2079
11	TraesCS5D01G390100	chr3A	20224789	20231443	6654	True	1218.400000	1698	90.399800	1047	5202	5	chr3A.!!$R2	4155
12	TraesCS5D01G390100	chr3A	20216122	20218838	2716	True	934.666667	1314	91.402000	3238	5371	3	chr3A.!!$R1	2133

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
858	884	0.173708	GACTACTGCTTCCCTGGACG	59.826	60.000	0.00	0.00	0.00	4.79	F
1334	4945	1.565305	GTGAAGCAGATACTCCAGCG	58.435	55.000	0.00	0.00	0.00	5.18	F
2104	7016	1.153706	CCTAGCACCAACGTACCGG	60.154	63.158	0.00	0.00	0.00	5.28	F
2278	7190	1.808411	TTCCTCTTGGCTTAAGCACG	58.192	50.000	27.83	15.21	44.36	5.34	F
3116	8122	1.884579	CAGAAACTCTGCAGGCATGTT	59.115	47.619	15.13	11.09	37.72	2.71	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1689	5325	0.392193	CCTCGCTTGGCTTCTCATGT	60.392	55.000	0.00	0.00	0.00	3.21	R
3102	8108	2.223876	ACACAAAAACATGCCTGCAGAG	60.224	45.455	17.39	6.56	0.00	3.35	R
4025	10165	1.676746	AGCAGGTGCATCATGATCAC	58.323	50.000	20.83	20.83	45.16	3.06	R
4055	10195	7.331687	GCATGCAATTTTCTATAAACCAGTTGT	59.668	33.333	14.21	0.00	0.00	3.32	R
4873	11276	0.459585	TGAGGCGTGCTCCGTTATTC	60.460	55.000	0.00	0.00	39.32	1.75	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
44	45	1.601903	CCTTGTTGCTTCTTGTGCGTA	59.398	47.619	0.00	0.00	0.00	4.42
62	63	4.948608	CGTAGCATCTATGATCTACGGT	57.051	45.455	16.15	0.00	46.03	4.83
64	65	5.700846	CGTAGCATCTATGATCTACGGTTT	58.299	41.667	16.15	0.00	46.03	3.27
132	133	5.070981	TCTCTCATAGGTGCTCATAAAAGGG	59.929	44.000	0.00	0.00	0.00	3.95
140	141	0.734889	CTCATAAAAGGGCAGTGGCG	59.265	55.000	10.99	0.00	42.47	5.69
165	166	8.883731	CGGAGCTATAATTAATTTATCAGTGGG	58.116	37.037	5.91	0.00	32.66	4.61
167	168	8.581253	AGCTATAATTAATTTATCAGTGGGGC	57.419	34.615	5.91	0.00	32.66	5.80
190	191	3.423867	CGAGTGCCGTTAAAATTTGTTGG	59.576	43.478	0.00	0.00	0.00	3.77
191	192	3.723260	AGTGCCGTTAAAATTTGTTGGG	58.277	40.909	0.00	0.00	0.00	4.12
229	230	9.638239	CATTGAAAAATAGCCTTTTAGCAGTAA	57.362	29.630	0.00	0.00	34.23	2.24
260	261	5.532032	ACGAATTATGCATTGATCATCACCA	59.468	36.000	3.54	0.00	0.00	4.17
275	276	7.760794	TGATCATCACCAATTGAGCATAAAAAC	59.239	33.333	7.12	0.00	37.77	2.43
463	487	2.664851	TTCGAGCGGGCAACAGTG	60.665	61.111	0.00	0.00	39.74	3.66
594	618	8.491605	GACAGCAGTCGACTTATATACTTAAC	57.508	38.462	17.26	0.00	34.60	2.01
671	695	4.581824	AGCCATGGACTAATGCTGTTAATG	59.418	41.667	18.40	0.00	0.00	1.90
736	761	8.934023	TTTTTGGGAAGACTAATGATGTTAGT	57.066	30.769	0.42	0.42	37.89	2.24
737	762	8.561738	TTTTGGGAAGACTAATGATGTTAGTC	57.438	34.615	16.31	16.31	46.85	2.59
858	884	0.173708	GACTACTGCTTCCCTGGACG	59.826	60.000	0.00	0.00	0.00	4.79
1305	4916	4.706476	CCTTTTCAGCATGGGATTAGTTCA	59.294	41.667	0.00	0.00	36.16	3.18
1334	4945	1.565305	GTGAAGCAGATACTCCAGCG	58.435	55.000	0.00	0.00	0.00	5.18
1391	5007	5.108517	GGAGCACTTAGATAGCTGCATATC	58.891	45.833	1.02	6.70	44.73	1.63
1497	5118	3.068024	TGTGTGCCATTTTGGAGTCTTTC	59.932	43.478	0.00	0.00	40.96	2.62
1640	5270	6.205853	CGCTACTCTCCTTACATTCTACTGAT	59.794	42.308	0.00	0.00	0.00	2.90
1689	5325	5.560722	TGAAGTTAGATTGGAGGTTGTCA	57.439	39.130	0.00	0.00	0.00	3.58
1963	6336	7.824289	CCTAGAGATGTTTGTTCCAGTTAATCA	59.176	37.037	0.00	0.00	0.00	2.57
1964	6337	7.678947	AGAGATGTTTGTTCCAGTTAATCAG	57.321	36.000	0.00	0.00	0.00	2.90
1965	6338	7.227156	AGAGATGTTTGTTCCAGTTAATCAGT	58.773	34.615	0.00	0.00	0.00	3.41
1966	6339	8.375506	AGAGATGTTTGTTCCAGTTAATCAGTA	58.624	33.333	0.00	0.00	0.00	2.74
1969	6342	6.296026	TGTTTGTTCCAGTTAATCAGTAGCT	58.704	36.000	0.00	0.00	0.00	3.32
2104	7016	1.153706	CCTAGCACCAACGTACCGG	60.154	63.158	0.00	0.00	0.00	5.28
2278	7190	1.808411	TTCCTCTTGGCTTAAGCACG	58.192	50.000	27.83	15.21	44.36	5.34
2376	7296	5.163343	GCTACCCTTCCTTGTATGTGTCATA	60.163	44.000	0.00	0.00	0.00	2.15
2466	7386	6.159988	GGGATGCATGAATAGTAGAGTACAC	58.840	44.000	2.46	0.00	0.00	2.90
2541	7461	9.803315	AGGTTGTTTTCTAGTCTTTGAAAAATC	57.197	29.630	12.19	5.42	41.74	2.17
2542	7462	9.803315	GGTTGTTTTCTAGTCTTTGAAAAATCT	57.197	29.630	12.19	0.00	41.74	2.40
2597	7555	5.064071	GGAAAGAGAACTTAAATCTGGCTCG	59.936	44.000	0.00	0.00	35.05	5.03
2662	7632	7.657354	AGGATGCTTAAAACAACTGAAAATTCC	59.343	33.333	0.00	0.00	0.00	3.01
2769	7768	4.816385	CACGAATAAACATCCAGGCTACAT	59.184	41.667	0.00	0.00	0.00	2.29
2772	7771	5.178252	CGAATAAACATCCAGGCTACATGAG	59.822	44.000	0.00	0.00	0.00	2.90
2816	7815	8.989980	GTGAAGTACACTTTATAAGTTTCTGCT	58.010	33.333	0.00	0.00	45.13	4.24
3068	8073	4.354587	GCATACAAGGTAGCATGCTTTTC	58.645	43.478	28.02	16.10	40.46	2.29
3116	8122	1.884579	CAGAAACTCTGCAGGCATGTT	59.115	47.619	15.13	11.09	37.72	2.71
3129	8138	4.749099	GCAGGCATGTTTTTGTGTAAATGA	59.251	37.500	0.00	0.00	0.00	2.57
3192	8204	4.034285	ACAGGGAGATAAACTGGGTTTG	57.966	45.455	5.99	0.00	36.37	2.93
4055	10195	1.905894	TGCACCTGCTTATGTGTCCTA	59.094	47.619	0.00	0.00	42.66	2.94
4059	10199	3.684788	CACCTGCTTATGTGTCCTACAAC	59.315	47.826	0.00	0.00	43.77	3.32
4114	10417	7.097192	TGAGCTGGCTTATAATATTTAGACCG	58.903	38.462	0.00	0.00	0.00	4.79
4147	10497	9.521841	TTTATCATTTTCCCATGTACACTGTAA	57.478	29.630	0.00	0.00	0.00	2.41
4467	10842	0.611618	TTTTGTCAGATGCCGGCCAT	60.612	50.000	26.77	17.61	36.70	4.40
4487	10862	5.594926	CCATGATTACTGATTCCTTTTGCC	58.405	41.667	0.00	0.00	0.00	4.52
4593	10990	7.041107	CCTCTCTTTATCTGACTCTGGAAAAG	58.959	42.308	0.00	0.00	0.00	2.27
4731	11129	3.117701	TCAGTTTGTTGATTGACCCCTCA	60.118	43.478	0.00	0.00	0.00	3.86
4839	11242	7.709182	TCCCTATTACATCACAGTTCATTAACG	59.291	37.037	0.00	0.00	40.73	3.18
4873	11276	2.097142	GCCACAGCTGAAGCAGAATAAG	59.903	50.000	23.35	0.00	45.16	1.73
4874	11277	3.603532	CCACAGCTGAAGCAGAATAAGA	58.396	45.455	23.35	0.00	45.16	2.10
4875	11278	4.005650	CCACAGCTGAAGCAGAATAAGAA	58.994	43.478	23.35	0.00	45.16	2.52
4876	11279	4.639310	CCACAGCTGAAGCAGAATAAGAAT	59.361	41.667	23.35	0.00	45.16	2.40
4877	11280	5.819379	CCACAGCTGAAGCAGAATAAGAATA	59.181	40.000	23.35	0.00	45.16	1.75
4878	11281	6.317140	CCACAGCTGAAGCAGAATAAGAATAA	59.683	38.462	23.35	0.00	45.16	1.40
4879	11282	7.185453	CACAGCTGAAGCAGAATAAGAATAAC	58.815	38.462	23.35	0.00	45.16	1.89
4880	11283	6.036517	ACAGCTGAAGCAGAATAAGAATAACG	59.963	38.462	23.35	0.00	45.16	3.18
4881	11284	5.525378	AGCTGAAGCAGAATAAGAATAACGG	59.475	40.000	4.90	0.00	45.16	4.44
4882	11285	5.523916	GCTGAAGCAGAATAAGAATAACGGA	59.476	40.000	0.00	0.00	41.59	4.69
4883	11286	6.292596	GCTGAAGCAGAATAAGAATAACGGAG	60.293	42.308	0.00	0.00	41.59	4.63
4996	11399	2.846206	TCCTATGTCCAGCATTTCCTGT	59.154	45.455	0.00	0.00	38.94	4.00
5008	11411	8.646900	TCCAGCATTTCCTGTTTTAATAAAGTT	58.353	29.630	0.00	0.00	0.00	2.66
5009	11412	9.921637	CCAGCATTTCCTGTTTTAATAAAGTTA	57.078	29.630	0.00	0.00	0.00	2.24
5107	11945	7.440523	AGTTACATCAAGTCATGTTCCTTTC	57.559	36.000	0.00	0.00	38.07	2.62
5252	12121	4.430441	AGGAACAGAGGTACAAGATTCCT	58.570	43.478	10.31	10.31	39.67	3.36
5297	12166	6.448207	CTCATTCCTTGGAGGATTCTTTTC	57.552	41.667	0.00	0.00	45.34	2.29
5363	12235	7.538678	CACGGAAATTTTCTAAGGATTTGAGTG	59.461	37.037	8.93	0.00	30.24	3.51

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
44	45	4.752101	GCAAAACCGTAGATCATAGATGCT	59.248	41.667	0.00	0.00	0.00	3.79
62	63	1.664873	CCAAGTGATGCGGGCAAAA	59.335	52.632	0.00	0.00	0.00	2.44
64	65	2.676121	CCCAAGTGATGCGGGCAA	60.676	61.111	0.00	0.00	31.89	4.52
126	127	2.282462	CTCCGCCACTGCCCTTTT	60.282	61.111	0.00	0.00	0.00	2.27
132	133	1.884235	AATTATAGCTCCGCCACTGC	58.116	50.000	0.00	0.00	0.00	4.40
140	141	9.178758	CCCCACTGATAAATTAATTATAGCTCC	57.821	37.037	0.01	0.00	34.30	4.70
167	168	3.276882	ACAAATTTTAACGGCACTCGG	57.723	42.857	0.00	0.00	44.45	4.63
190	191	0.033208	TTCAATGGCATGACCCTCCC	60.033	55.000	0.00	0.00	37.83	4.30
191	192	1.851304	TTTCAATGGCATGACCCTCC	58.149	50.000	0.00	0.00	37.83	4.30
237	238	6.004408	TGGTGATGATCAATGCATAATTCG	57.996	37.500	0.00	0.00	0.00	3.34
251	252	7.844009	AGTTTTTATGCTCAATTGGTGATGAT	58.156	30.769	5.42	0.00	35.07	2.45
573	597	8.638685	TTTGGTTAAGTATATAAGTCGACTGC	57.361	34.615	20.85	0.00	0.00	4.40
614	638	1.402325	GCGTTTGGGATGTGGCTAAAC	60.402	52.381	0.00	0.00	0.00	2.01
754	779	9.448438	TGCATTACTGACTAACATCATTAGTTT	57.552	29.630	1.13	0.00	35.54	2.66
858	884	0.389757	GTGGAACCGGCTCCTCTATC	59.610	60.000	24.04	6.64	36.35	2.08
1182	4770	1.299976	GAGGTTGGACGCCTGGAAT	59.700	57.895	0.00	0.00	36.29	3.01
1305	4916	1.131638	TCTGCTTCACCTGGTTCTGT	58.868	50.000	0.00	0.00	0.00	3.41
1334	4945	8.672823	AGATAAACGGAATAAATTACTCCCAC	57.327	34.615	0.00	0.00	0.00	4.61
1391	5007	1.202533	ACCCTGGCATCGAAACGATAG	60.203	52.381	6.34	1.70	45.19	2.08
1481	5102	5.726980	TGGATTGAAAGACTCCAAAATGG	57.273	39.130	0.00	0.00	36.15	3.16
1497	5118	2.736144	AATGCACAGCACTTGGATTG	57.264	45.000	0.00	0.00	43.04	2.67
1640	5270	6.995686	TGTAGCAAATTACAGTGGAGAAAGAA	59.004	34.615	0.00	0.00	0.00	2.52
1689	5325	0.392193	CCTCGCTTGGCTTCTCATGT	60.392	55.000	0.00	0.00	0.00	3.21
1913	6286	5.753744	CGACTAGGCATACTTCTAAGACAG	58.246	45.833	0.00	0.00	0.00	3.51
1917	6290	3.903360	GGCGACTAGGCATACTTCTAAG	58.097	50.000	0.00	0.00	45.92	2.18
1963	6336	4.442192	GGCTATGCAGTTAGTGAAGCTACT	60.442	45.833	0.00	0.00	31.80	2.57
1964	6337	3.804873	GGCTATGCAGTTAGTGAAGCTAC	59.195	47.826	0.00	0.00	31.80	3.58
1965	6338	3.450817	TGGCTATGCAGTTAGTGAAGCTA	59.549	43.478	0.00	2.02	31.80	3.32
1966	6339	2.237143	TGGCTATGCAGTTAGTGAAGCT	59.763	45.455	0.00	0.00	31.80	3.74
1969	6342	4.842574	TCAATGGCTATGCAGTTAGTGAA	58.157	39.130	0.00	0.00	0.00	3.18
2104	7016	2.494471	CCCGGGTAAAGAAAATTCACCC	59.506	50.000	14.18	9.18	44.59	4.61
2122	7034	4.814294	GACCGTAGCAGTGCCCCG	62.814	72.222	12.58	14.07	0.00	5.73
2376	7296	2.489619	CCATGTGCAGTATAATGGGCCT	60.490	50.000	4.53	0.00	36.68	5.19
2515	7435	9.803315	GATTTTTCAAAGACTAGAAAACAACCT	57.197	29.630	12.67	0.00	41.77	3.50
2541	7461	9.449719	AGTAATTGTGTACCCTTCAATTAAGAG	57.550	33.333	16.48	0.00	42.00	2.85
2542	7462	9.802039	AAGTAATTGTGTACCCTTCAATTAAGA	57.198	29.630	16.48	3.82	42.00	2.10
2655	7625	6.435428	GTGACTTCATGTTACGTGGAATTTT	58.565	36.000	4.63	0.00	0.00	1.82
2763	7762	8.962912	ACATTAGGTTTGACAAGCTCATGTAGC	61.963	40.741	10.69	8.56	46.40	3.58
2769	7768	4.275689	CACACATTAGGTTTGACAAGCTCA	59.724	41.667	1.88	0.00	41.18	4.26
2772	7771	4.829064	TCACACATTAGGTTTGACAAGC	57.171	40.909	0.00	0.00	31.45	4.01
2816	7815	3.398406	TGCGTAGACTTCAGCAATTTGA	58.602	40.909	0.00	0.00	36.60	2.69
3102	8108	2.223876	ACACAAAAACATGCCTGCAGAG	60.224	45.455	17.39	6.56	0.00	3.35
3656	9785	7.008810	GCATTTGAAAACGAACACAAAGTAAGA	59.991	33.333	0.00	0.00	36.07	2.10
4012	10151	7.142021	GCATCATGATCACTATACCCTATACG	58.858	42.308	4.86	0.00	0.00	3.06
4025	10165	1.676746	AGCAGGTGCATCATGATCAC	58.323	50.000	20.83	20.83	45.16	3.06
4055	10195	7.331687	GCATGCAATTTTCTATAAACCAGTTGT	59.668	33.333	14.21	0.00	0.00	3.32
4059	10199	7.707464	TCATGCATGCAATTTTCTATAAACCAG	59.293	33.333	26.68	0.00	0.00	4.00
4114	10417	9.736023	GTACATGGGAAAATGATAAATCAAGAC	57.264	33.333	0.00	0.00	40.69	3.01
4467	10842	3.694072	CGGGCAAAAGGAATCAGTAATCA	59.306	43.478	0.00	0.00	0.00	2.57
4487	10862	1.275291	ACAACCTCAGGTGTACATCGG	59.725	52.381	0.00	0.00	35.34	4.18
4873	11276	0.459585	TGAGGCGTGCTCCGTTATTC	60.460	55.000	0.00	0.00	39.32	1.75
4874	11277	0.739813	GTGAGGCGTGCTCCGTTATT	60.740	55.000	0.00	0.00	39.32	1.40
4875	11278	1.153628	GTGAGGCGTGCTCCGTTAT	60.154	57.895	0.00	0.00	39.32	1.89
4876	11279	2.260434	GTGAGGCGTGCTCCGTTA	59.740	61.111	0.00	0.00	39.32	3.18
4877	11280	4.681978	GGTGAGGCGTGCTCCGTT	62.682	66.667	0.00	0.00	39.32	4.44
4879	11282	4.680237	TTGGTGAGGCGTGCTCCG	62.680	66.667	0.00	0.00	40.40	4.63
4880	11283	2.743928	CTTGGTGAGGCGTGCTCC	60.744	66.667	0.00	0.00	0.00	4.70
4881	11284	2.029844	GACTTGGTGAGGCGTGCTC	61.030	63.158	0.00	0.00	0.00	4.26
4882	11285	2.031163	GACTTGGTGAGGCGTGCT	59.969	61.111	0.00	0.00	0.00	4.40
4883	11286	1.891919	TTGACTTGGTGAGGCGTGC	60.892	57.895	0.00	0.00	35.50	5.34
5025	11428	9.760660	CCTCTTCGTTTAGTTCTATTCATTTTG	57.239	33.333	0.00	0.00	0.00	2.44
5226	12091	5.568620	ATCTTGTACCTCTGTTCCTTTGT	57.431	39.130	0.00	0.00	0.00	2.83
5229	12094	4.846940	AGGAATCTTGTACCTCTGTTCCTT	59.153	41.667	9.53	0.00	40.64	3.36
5252	12121	6.611236	TGAGGTCAATATAGACACAATCCTCA	59.389	38.462	0.00	0.00	43.19	3.86
5314	12183	4.745649	AGGTCTCACGTAATGCTAAGAAC	58.254	43.478	0.00	0.00	0.00	3.01
5339	12211	7.029563	CCACTCAAATCCTTAGAAAATTTCCG	58.970	38.462	1.57	0.00	0.00	4.30

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.