AutoCloner

Multiple sequence alignment - TraesCS2B01G224400

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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	TraesCS2B01G224400	chr2B	100.000	5455	0	0	1	5455	214320339	214314885	0.000000e+00	10074
1	TraesCS2B01G224400	chr2B	95.158	475	23	0	1053	1527	281487341	281486867	0.000000e+00	750
2	TraesCS2B01G224400	chr2B	94.191	482	26	2	1048	1527	673104350	673104831	0.000000e+00	734
3	TraesCS2B01G224400	chr2B	94.316	475	27	0	1053	1527	310456434	310456908	0.000000e+00	728
4	TraesCS2B01G224400	chr2B	95.455	66	3	0	210	275	214320089	214320024	7.470000e-19	106
5	TraesCS2B01G224400	chr2B	95.455	66	3	0	251	316	214320130	214320065	7.470000e-19	106
6	TraesCS2B01G224400	chr2A	94.268	5304	175	53	251	5455	166635317	166630044	0.000000e+00	7991
7	TraesCS2B01G224400	chr2A	90.894	1812	81	30	2206	3994	447942905	447944655	0.000000e+00	2355
8	TraesCS2B01G224400	chr2A	86.012	1823	185	29	2573	4347	197562010	197563810	0.000000e+00	1890
9	TraesCS2B01G224400	chr2A	87.345	1375	117	22	1033	2369	197560640	197561995	0.000000e+00	1522
10	TraesCS2B01G224400	chr2A	86.401	1228	116	18	3162	4347	197333277	197334495	0.000000e+00	1295
11	TraesCS2B01G224400	chr2A	90.985	721	28	14	2206	2917	398506765	398506073	0.000000e+00	937
12	TraesCS2B01G224400	chr2A	90.985	721	28	14	2206	2917	398765695	398765003	0.000000e+00	937
13	TraesCS2B01G224400	chr2A	88.768	276	25	3	5183	5455	197563957	197564229	3.150000e-87	333
14	TraesCS2B01G224400	chr2A	86.957	230	26	3	5230	5455	624449468	624449239	7.010000e-64	255
15	TraesCS2B01G224400	chr2A	91.304	184	15	1	2	185	29274223	29274041	3.260000e-62	250
16	TraesCS2B01G224400	chr2D	96.271	4774	122	25	721	5455	156714172	156709416	0.000000e+00	7779
17	TraesCS2B01G224400	chr2D	90.693	1096	87	12	1267	2355	182570519	182571606	0.000000e+00	1445
18	TraesCS2B01G224400	chr2D	87.936	688	52	12	3689	4347	182572865	182573550	0.000000e+00	782
19	TraesCS2B01G224400	chr2D	82.026	701	83	17	2431	3098	182571690	182572380	1.720000e-154	556
20	TraesCS2B01G224400	chr2D	89.493	276	23	3	5183	5455	182573697	182573969	1.450000e-90	344
21	TraesCS2B01G224400	chr2D	90.278	216	21	0	5240	5455	156594620	156594405	3.220000e-72	283
22	TraesCS2B01G224400	chr2D	93.548	93	3	2	2339	2429	182571621	182571712	9.530000e-28	135
23	TraesCS2B01G224400	chr4B	94.958	476	23	1	1053	1528	639306252	639306726	0.000000e+00	745
24	TraesCS2B01G224400	chr4B	74.866	374	67	22	3035	3398	75193655	75193299	1.580000e-30	145
25	TraesCS2B01G224400	chr5B	94.316	475	27	0	1053	1527	18174942	18175416	0.000000e+00	728
26	TraesCS2B01G224400	chr1B	94.105	475	28	0	1053	1527	649829135	649828661	0.000000e+00	723
27	TraesCS2B01G224400	chr1B	83.988	331	26	12	5125	5455	148414034	148414337	5.340000e-75	292
28	TraesCS2B01G224400	chr4A	87.361	538	46	13	186	723	65714624	65715139	1.010000e-166	597
29	TraesCS2B01G224400	chr3D	86.940	536	47	13	186	721	300680133	300680645	1.020000e-161	580
30	TraesCS2B01G224400	chr3D	92.010	413	32	1	311	723	23089461	23089050	3.660000e-161	579
31	TraesCS2B01G224400	chr3D	90.811	185	16	1	1	185	300679835	300680018	4.220000e-61	246
32	TraesCS2B01G224400	chr4D	91.283	413	34	2	311	723	465183000	465183410	3.690000e-156	562
33	TraesCS2B01G224400	chr5A	85.688	538	55	13	186	723	510491092	510491607	1.030000e-151	547
34	TraesCS2B01G224400	chr5D	90.750	400	34	2	323	722	519644724	519644328	1.040000e-146	531
35	TraesCS2B01G224400	chr5D	85.093	161	22	2	25	185	430523907	430523749	4.370000e-36	163
36	TraesCS2B01G224400	chr1A	87.565	386	13	6	2208	2584	512491084	512491443	1.090000e-111	414
37	TraesCS2B01G224400	chr1A	90.090	222	20	2	5235	5455	90161333	90161553	2.490000e-73	287
38	TraesCS2B01G224400	chr6A	82.064	407	71	2	316	722	556538312	556537908	4.040000e-91	346
39	TraesCS2B01G224400	chr6A	81.623	419	74	3	316	734	603647325	603646910	1.450000e-90	344
40	TraesCS2B01G224400	chr6A	70.701	1611	309	103	3030	4599	46698241	46696753	5.540000e-50	209
41	TraesCS2B01G224400	chr6A	74.004	527	96	28	3028	3532	32884983	32884476	5.620000e-40	176
42	TraesCS2B01G224400	chr6A	90.000	90	8	1	1	89	546924976	546925065	1.240000e-21	115
43	TraesCS2B01G224400	chrUn	71.455	1615	301	109	3030	4599	27474181	27475680	1.160000e-71	281
44	TraesCS2B01G224400	chr1D	89.189	222	22	2	5235	5455	93102998	93103218	5.380000e-70	276
45	TraesCS2B01G224400	chr6D	73.814	527	98	28	3028	3532	29851966	29852474	7.260000e-39	172

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	TraesCS2B01G224400	chr2B	214314885	214320339	5454	True	3428.666667	10074	96.9700	1	5455	3	chr2B.!!$R2	5454
1	TraesCS2B01G224400	chr2A	166630044	166635317	5273	True	7991.000000	7991	94.2680	251	5455	1	chr2A.!!$R2	5204
2	TraesCS2B01G224400	chr2A	447942905	447944655	1750	False	2355.000000	2355	90.8940	2206	3994	1	chr2A.!!$F2	1788
3	TraesCS2B01G224400	chr2A	197333277	197334495	1218	False	1295.000000	1295	86.4010	3162	4347	1	chr2A.!!$F1	1185
4	TraesCS2B01G224400	chr2A	197560640	197564229	3589	False	1248.333333	1890	87.3750	1033	5455	3	chr2A.!!$F3	4422
5	TraesCS2B01G224400	chr2A	398506073	398506765	692	True	937.000000	937	90.9850	2206	2917	1	chr2A.!!$R3	711
6	TraesCS2B01G224400	chr2A	398765003	398765695	692	True	937.000000	937	90.9850	2206	2917	1	chr2A.!!$R4	711
7	TraesCS2B01G224400	chr2D	156709416	156714172	4756	True	7779.000000	7779	96.2710	721	5455	1	chr2D.!!$R2	4734
8	TraesCS2B01G224400	chr2D	182570519	182573969	3450	False	652.400000	1445	88.7392	1267	5455	5	chr2D.!!$F1	4188
9	TraesCS2B01G224400	chr4A	65714624	65715139	515	False	597.000000	597	87.3610	186	723	1	chr4A.!!$F1	537
10	TraesCS2B01G224400	chr3D	300679835	300680645	810	False	413.000000	580	88.8755	1	721	2	chr3D.!!$F1	720
11	TraesCS2B01G224400	chr5A	510491092	510491607	515	False	547.000000	547	85.6880	186	723	1	chr5A.!!$F1	537
12	TraesCS2B01G224400	chr6A	46696753	46698241	1488	True	209.000000	209	70.7010	3030	4599	1	chr6A.!!$R2	1569
13	TraesCS2B01G224400	chrUn	27474181	27475680	1499	False	281.000000	281	71.4550	3030	4599	1	chrUn.!!$F1	1569

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
93	94	0.037975	CTTGTGATGCTTTGGTGGGC	60.038	55.000	0.00	0.00	5.36	F
1599	1778	0.032130	TGGTCTGAGAGTTCGTGTGC	59.968	55.000	0.00	0.00	4.57	F
2435	2704	2.182030	GAGACCTCACGCCGGAAG	59.818	66.667	5.05	0.00	3.46	F
2436	2705	3.991536	GAGACCTCACGCCGGAAGC	62.992	68.421	5.05	38.52	3.86	F
3244	3603	1.537776	CGTCTCCTTGCAGCTATCCAG	60.538	57.143	0.00	0.00	3.86	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1731	1911	2.135933	GAGGTTGTTCACTTGTCTCCG	58.864	52.381	0.00	0.00	4.63	R
2437	2706	0.250597	TTCACGTGAGGTCTCTCCGA	60.251	55.000	19.11	41.99	4.55	R
3244	3603	2.016096	GCAGATTCCTCAGCCAACTCC	61.016	57.143	0.00	0.00	3.85	R
4133	4544	2.945668	GGATGAACCGAGGGAAAAGATG	59.054	50.000	0.00	0.00	2.90	R
4934	5350	0.041400	TTTCACGTCGCACTGCAATG	60.041	50.000	1.11	0.00	2.82	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
36	37	4.016444	GGGAAAGAATGGTTGCTACATGA	58.984	43.478	0.00	0.00	0.00	3.07
38	39	5.127682	GGGAAAGAATGGTTGCTACATGATT	59.872	40.000	0.00	0.00	0.00	2.57
41	42	7.917505	GGAAAGAATGGTTGCTACATGATTTAG	59.082	37.037	0.00	0.00	0.00	1.85
43	44	7.798596	AGAATGGTTGCTACATGATTTAGAG	57.201	36.000	0.00	0.00	0.00	2.43
53	54	6.015010	GCTACATGATTTAGAGCCTCTTCCTA	60.015	42.308	0.00	0.00	0.00	2.94
89	90	4.942761	ATGTTTCTTGTGATGCTTTGGT	57.057	36.364	0.00	0.00	0.00	3.67
93	94	0.037975	CTTGTGATGCTTTGGTGGGC	60.038	55.000	0.00	0.00	0.00	5.36
118	119	0.719465	CACATTCGTAACGAGGTGGC	59.281	55.000	0.00	0.00	38.42	5.01
123	124	0.454600	TCGTAACGAGGTGGCTCATC	59.545	55.000	0.00	0.00	0.00	2.92
134	135	0.813610	TGGCTCATCATAAACCGCCG	60.814	55.000	0.00	0.00	40.31	6.46
137	138	0.813610	CTCATCATAAACCGCCGCCA	60.814	55.000	0.00	0.00	0.00	5.69
158	159	1.728490	CCATGGAGGCCTTTAAGCGC	61.728	60.000	6.77	0.00	0.00	5.92
190	305	6.760298	GTGAGCTATCTTGATTCAATGAGTGA	59.240	38.462	0.00	0.00	0.00	3.41
206	321	3.781965	TGAGTGATCCCAAATCTGGATGA	59.218	43.478	0.00	0.00	46.92	2.92
213	328	2.686915	CCCAAATCTGGATGAGTCAAGC	59.313	50.000	0.00	0.00	46.92	4.01
215	330	3.377485	CCAAATCTGGATGAGTCAAGCTG	59.623	47.826	0.00	0.00	46.92	4.24
222	337	0.969149	ATGAGTCAAGCTGTCCACGA	59.031	50.000	0.00	0.00	0.00	4.35
239	354	2.936498	CACGAATGGGTCTTATGGTGAC	59.064	50.000	0.00	0.00	0.00	3.67
262	377	3.559024	CTCAGCAAGCTGTCCACG	58.441	61.111	20.34	3.52	43.96	4.94
263	378	1.005748	CTCAGCAAGCTGTCCACGA	60.006	57.895	20.34	0.70	43.96	4.35
289	404	2.107366	TCTTATGGTGATGACGGCTCA	58.893	47.619	0.00	0.00	0.00	4.26
290	405	2.499693	TCTTATGGTGATGACGGCTCAA	59.500	45.455	0.00	0.00	0.00	3.02
293	408	0.107643	TGGTGATGACGGCTCAACAA	59.892	50.000	6.05	0.00	37.39	2.83
304	419	3.289128	CTCAACAAGCTGTCCACGA	57.711	52.632	0.00	0.00	0.00	4.35
305	420	1.581934	CTCAACAAGCTGTCCACGAA	58.418	50.000	0.00	0.00	0.00	3.85
307	422	1.872952	TCAACAAGCTGTCCACGAATG	59.127	47.619	0.00	0.00	0.00	2.67
417	552	3.997021	CGCAATACAGAGAAGTGACCTTT	59.003	43.478	0.00	0.00	0.00	3.11
444	579	8.689061	CAGTGGAGATAAAAATGGATTCAATCA	58.311	33.333	0.00	0.00	0.00	2.57
505	640	4.130118	TCGGTCTACTCGTCCCTTATTAC	58.870	47.826	0.00	0.00	0.00	1.89
533	668	9.877178	GAGATTAGAAAACCTTATGTCTCTTCA	57.123	33.333	0.00	0.00	0.00	3.02
680	815	7.860373	GGAGCTAGCTACGATTGATTATATGAG	59.140	40.741	19.38	0.00	0.00	2.90
846	985	2.606725	GCGAACTTCCTCTCACATGATG	59.393	50.000	0.00	0.00	0.00	3.07
851	990	4.017126	ACTTCCTCTCACATGATGACGTA	58.983	43.478	0.00	0.00	32.37	3.57
897	1036	4.023291	GCTCATCCTTTCCCCAAATAACA	58.977	43.478	0.00	0.00	0.00	2.41
1229	1401	2.362369	CCATCTCCTCGCCACCACT	61.362	63.158	0.00	0.00	0.00	4.00
1327	1499	2.742116	GCCGGGGAGCAGGTAATGA	61.742	63.158	2.18	0.00	0.00	2.57
1545	1724	3.648339	TTGCTCTTCTTTGTGCATTCC	57.352	42.857	0.00	0.00	36.53	3.01
1586	1765	2.353011	GGGATGTGCAATTTGTGGTCTG	60.353	50.000	0.00	0.00	0.00	3.51
1599	1778	0.032130	TGGTCTGAGAGTTCGTGTGC	59.968	55.000	0.00	0.00	0.00	4.57
1731	1911	5.124457	TGCTCTTCTTGCAATCTTGGAATAC	59.876	40.000	0.00	0.00	37.86	1.89
1761	1942	5.304686	AGTGAACAACCTCCTGTGATTAA	57.695	39.130	0.00	0.00	0.00	1.40
1826	2007	8.739039	CCTGTACCAATTCATTCTTGTATCAAA	58.261	33.333	0.00	0.00	0.00	2.69
1854	2035	5.696724	GGTAGCATATTCATCGCAGTTTACT	59.303	40.000	0.00	0.00	0.00	2.24
1895	2078	5.000012	ACATGTTTTTGTTTTAGGCGTGA	58.000	34.783	0.00	0.00	0.00	4.35
1992	2175	7.765695	ATGGATGGTTTTATAGGCATAGTTG	57.234	36.000	0.00	0.00	0.00	3.16
2055	2238	4.948847	TCCGTAGATCATTGGTCATTCAG	58.051	43.478	0.00	0.00	0.00	3.02
2204	2387	8.465999	TCACAACATGATTCTTGTAAACAGTTT	58.534	29.630	0.00	3.49	29.99	2.66
2386	2607	3.884037	ACCCATCTCTTGTGGAAAAGT	57.116	42.857	0.00	0.00	39.12	2.66
2430	2699	2.750637	TCGGAGAGACCTCACGCC	60.751	66.667	8.56	2.70	41.20	5.68
2431	2700	4.180946	CGGAGAGACCTCACGCCG	62.181	72.222	10.08	10.08	41.20	6.46
2432	2701	3.827898	GGAGAGACCTCACGCCGG	61.828	72.222	0.00	0.00	41.20	6.13
2433	2702	2.750637	GAGAGACCTCACGCCGGA	60.751	66.667	5.05	0.00	39.24	5.14
2434	2703	2.282958	AGAGACCTCACGCCGGAA	60.283	61.111	5.05	0.00	0.00	4.30
2435	2704	2.182030	GAGACCTCACGCCGGAAG	59.818	66.667	5.05	0.00	0.00	3.46
2436	2705	3.991536	GAGACCTCACGCCGGAAGC	62.992	68.421	5.05	0.00	38.52	3.86
2437	2706	4.070552	GACCTCACGCCGGAAGCT	62.071	66.667	5.05	0.00	40.39	3.74
2438	2707	3.991536	GACCTCACGCCGGAAGCTC	62.992	68.421	5.05	0.00	40.39	4.09
2478	2747	6.154363	TGAATCAACAGGTTTGACTCCTTTTT	59.846	34.615	0.00	0.00	32.37	1.94
2504	2774	8.482128	TGTCTTTGGTTATTTCAAAGTGGAAAT	58.518	29.630	13.84	6.41	46.50	2.17
3160	3459	4.125703	GCATGTTCCCTGATCTAACTCTG	58.874	47.826	0.00	0.00	0.00	3.35
3202	3561	4.380973	CGACAGGAGCAAGTTCTTGATAGA	60.381	45.833	15.52	0.00	0.00	1.98
3244	3603	1.537776	CGTCTCCTTGCAGCTATCCAG	60.538	57.143	0.00	0.00	0.00	3.86
3313	3676	1.899814	AGGAGCCACGATGTAAGTTCA	59.100	47.619	0.00	0.00	0.00	3.18
3865	4269	6.560711	ACCAAATGCGATTTATTAACTCACC	58.439	36.000	0.00	0.00	0.00	4.02
4133	4544	5.104259	ACTTATCCTTCAGTCATCAACCC	57.896	43.478	0.00	0.00	0.00	4.11
4137	4548	3.184628	TCCTTCAGTCATCAACCCATCT	58.815	45.455	0.00	0.00	0.00	2.90
4297	4709	2.221169	GACAGTGTGGCAAATGTGAGA	58.779	47.619	0.00	0.00	0.00	3.27
4424	4838	1.237533	TACAGCACGTTACTCCACGA	58.762	50.000	0.00	0.00	43.15	4.35
4454	4868	1.003839	GGGCCGTGTTCAGATGTGA	60.004	57.895	0.00	0.00	0.00	3.58
4622	5036	4.696479	ATAAGTCTCCCATTGCTAGGTG	57.304	45.455	0.00	0.00	0.00	4.00
4633	5047	4.142534	CCATTGCTAGGTGAATGTTGAGTG	60.143	45.833	0.00	0.00	0.00	3.51
4708	5122	1.982073	GCATACACTGAAGCGGGTGC	61.982	60.000	0.00	0.00	43.24	5.01
4734	5148	8.328864	CGCTTATACTTGTACATTCTTTCTTCC	58.671	37.037	0.00	0.00	0.00	3.46
4804	5218	5.181748	ACTAGTTCTGATGTGCTGAAATCC	58.818	41.667	0.00	0.00	36.40	3.01
4883	5299	8.771920	TCAAACATGTATGATAGTCGAAGTTT	57.228	30.769	0.00	0.00	0.00	2.66
4934	5350	5.112686	CAACCTGGTGCTATTTCTCTCTAC	58.887	45.833	0.00	0.00	0.00	2.59
4983	5399	5.869753	ACATTTGACATGAGTAAGTCTGC	57.130	39.130	0.00	0.00	35.81	4.26
5007	5423	2.286294	CGAGGAGAATGTGCTTGTATGC	59.714	50.000	0.00	0.00	0.00	3.14
5054	5496	7.009999	GCTGATTCAGTAGTAGAACATCAACAG	59.990	40.741	14.90	0.00	33.43	3.16
5136	5606	1.383248	AATGGCCTCTAGCTCCGGT	60.383	57.895	3.32	0.00	43.05	5.28
5174	5644	5.237236	TCAACGTTTTAGAAGAGGGGAAT	57.763	39.130	0.00	0.00	0.00	3.01
5328	5800	0.963856	CTTGAGGCATTCCAGCAGCA	60.964	55.000	0.00	0.00	35.83	4.41

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
5	6	7.460910	AGCAACCATTCTTTCCCATTATTTTT	58.539	30.769	0.00	0.00	0.00	1.94
36	37	8.100164	GCTCAATATTAGGAAGAGGCTCTAAAT	58.900	37.037	19.07	16.22	0.00	1.40
38	39	6.294787	CGCTCAATATTAGGAAGAGGCTCTAA	60.295	42.308	19.07	8.77	0.00	2.10
41	42	4.241681	CGCTCAATATTAGGAAGAGGCTC	58.758	47.826	6.34	6.34	0.00	4.70
43	44	3.996480	ACGCTCAATATTAGGAAGAGGC	58.004	45.455	2.88	0.00	0.00	4.70
73	74	1.619654	CCCACCAAAGCATCACAAGA	58.380	50.000	0.00	0.00	0.00	3.02
77	78	2.973082	GGCCCACCAAAGCATCAC	59.027	61.111	0.00	0.00	35.26	3.06
93	94	1.009903	TCGTTACGAATGTGCCACGG	61.010	55.000	4.50	0.00	31.06	4.94
104	105	0.454600	GATGAGCCACCTCGTTACGA	59.545	55.000	7.39	7.39	41.13	3.43
118	119	0.813610	TGGCGGCGGTTTATGATGAG	60.814	55.000	9.78	0.00	0.00	2.90
123	124	3.514362	GGGTGGCGGCGGTTTATG	61.514	66.667	9.78	0.00	0.00	1.90
137	138	0.033109	GCTTAAAGGCCTCCATGGGT	60.033	55.000	13.02	0.00	36.00	4.51
151	152	1.156736	GCTCACCAAGAAGCGCTTAA	58.843	50.000	25.11	1.94	34.31	1.85
158	159	6.111382	TGAATCAAGATAGCTCACCAAGAAG	58.889	40.000	0.00	0.00	0.00	2.85
190	305	4.789807	CTTGACTCATCCAGATTTGGGAT	58.210	43.478	1.81	0.00	45.98	3.85
206	321	1.609061	CCATTCGTGGACAGCTTGACT	60.609	52.381	0.00	0.00	0.00	3.41
213	328	3.198068	CATAAGACCCATTCGTGGACAG	58.802	50.000	0.00	0.00	0.00	3.51
215	330	2.093128	ACCATAAGACCCATTCGTGGAC	60.093	50.000	0.00	0.00	33.09	4.02
222	337	2.418197	CGTCGTCACCATAAGACCCATT	60.418	50.000	0.00	0.00	32.41	3.16
262	377	3.809832	CGTCATCACCATAAGACCCATTC	59.190	47.826	0.00	0.00	0.00	2.67
263	378	3.433598	CCGTCATCACCATAAGACCCATT	60.434	47.826	0.00	0.00	0.00	3.16
289	404	1.238439	CCATTCGTGGACAGCTTGTT	58.762	50.000	0.00	0.00	0.00	2.83
290	405	0.606401	CCCATTCGTGGACAGCTTGT	60.606	55.000	0.00	0.00	0.00	3.16
293	408	1.296715	GACCCATTCGTGGACAGCT	59.703	57.895	0.00	0.00	0.00	4.24
295	410	2.979814	TATGACCCATTCGTGGACAG	57.020	50.000	0.00	0.00	0.00	3.51
297	412	4.881850	AGAAAATATGACCCATTCGTGGAC	59.118	41.667	0.00	0.00	0.00	4.02
299	414	5.356751	TGAAGAAAATATGACCCATTCGTGG	59.643	40.000	0.00	0.00	0.00	4.94
300	415	6.435430	TGAAGAAAATATGACCCATTCGTG	57.565	37.500	0.00	0.00	0.00	4.35
302	417	5.916883	GCATGAAGAAAATATGACCCATTCG	59.083	40.000	0.00	0.00	0.00	3.34
303	418	6.808829	TGCATGAAGAAAATATGACCCATTC	58.191	36.000	0.00	0.00	0.00	2.67
304	419	6.183360	CCTGCATGAAGAAAATATGACCCATT	60.183	38.462	0.74	0.00	0.00	3.16
305	420	5.303589	CCTGCATGAAGAAAATATGACCCAT	59.696	40.000	0.74	0.00	0.00	4.00
307	422	4.500375	GCCTGCATGAAGAAAATATGACCC	60.500	45.833	0.74	0.00	0.00	4.46
308	423	4.098349	TGCCTGCATGAAGAAAATATGACC	59.902	41.667	0.74	0.00	0.00	4.02
309	424	5.252969	TGCCTGCATGAAGAAAATATGAC	57.747	39.130	0.74	0.00	0.00	3.06
417	552	8.827832	ATTGAATCCATTTTTATCTCCACTGA	57.172	30.769	0.00	0.00	0.00	3.41
444	579	3.087031	CCTGGATCAACTTGACAGCAAT	58.913	45.455	0.00	0.00	32.68	3.56
505	640	7.493367	AGAGACATAAGGTTTTCTAATCTCCG	58.507	38.462	0.00	0.00	32.28	4.63
590	725	4.766373	TGCCTTCTACATGAGCAAATTTGA	59.234	37.500	22.31	1.15	0.00	2.69
626	761	0.249398	CGAAGGACCCGAACCAATCT	59.751	55.000	0.00	0.00	0.00	2.40
674	809	4.484537	ACTCAACTGAAGCAGCTCATAT	57.515	40.909	0.00	0.00	34.37	1.78
680	815	6.428385	AATGTATTACTCAACTGAAGCAGC	57.572	37.500	0.00	0.00	34.37	5.25
787	922	4.344104	TCAATTGTCTGGATTTTCCCCTC	58.656	43.478	5.13	0.00	35.03	4.30
820	956	0.671796	TGAGAGGAAGTTCGCGAACA	59.328	50.000	42.89	23.89	43.47	3.18
851	990	5.439721	GGTTATTTATAAAGGTGGACGGGT	58.560	41.667	3.94	0.00	0.00	5.28
958	1097	4.778143	CGGGTGGAGCGGAAAGGG	62.778	72.222	0.00	0.00	0.00	3.95
1248	1420	2.266055	CTCCCGGTCTGCACTTCC	59.734	66.667	0.00	0.00	0.00	3.46
1545	1724	2.539274	CCGAACACAAAAATTGGCACAG	59.461	45.455	0.00	0.00	42.39	3.66
1586	1765	2.349817	CCAACATTGCACACGAACTCTC	60.350	50.000	0.00	0.00	0.00	3.20
1599	1778	7.948034	TTACCCTAAATCCTTACCAACATTG	57.052	36.000	0.00	0.00	0.00	2.82
1731	1911	2.135933	GAGGTTGTTCACTTGTCTCCG	58.864	52.381	0.00	0.00	0.00	4.63
1826	2007	3.999001	CTGCGATGAATATGCTACCACAT	59.001	43.478	0.00	0.00	0.00	3.21
1854	2035	2.283532	CCCAATGTTTCCCCCGCA	60.284	61.111	0.00	0.00	0.00	5.69
1992	2175	4.807304	CAGCCCTGAATAAACAAATGCATC	59.193	41.667	0.00	0.00	0.00	3.91
2055	2238	3.829948	CTGTGGTCAGTGATTTTGCATC	58.170	45.455	0.00	0.00	36.97	3.91
2204	2387	7.573096	GCAAAATCCGAAACATCTTACTTCAGA	60.573	37.037	0.00	0.00	0.00	3.27
2322	2510	8.630054	TGCCAAACTTAGAAGTAATTGTACAT	57.370	30.769	0.00	0.00	38.57	2.29
2430	2699	2.802106	GGTCTCTCCGAGCTTCCG	59.198	66.667	0.00	0.00	37.18	4.30
2435	2704	2.041686	ACGTGAGGTCTCTCCGAGC	61.042	63.158	14.13	0.00	41.99	5.03
2436	2705	0.673956	TCACGTGAGGTCTCTCCGAG	60.674	60.000	15.76	8.67	41.99	4.63
2437	2706	0.250597	TTCACGTGAGGTCTCTCCGA	60.251	55.000	19.11	0.00	41.99	4.55
2438	2707	0.811915	ATTCACGTGAGGTCTCTCCG	59.188	55.000	19.11	4.71	41.99	4.63
2439	2708	1.819288	TGATTCACGTGAGGTCTCTCC	59.181	52.381	24.37	9.99	39.23	3.71
2440	2709	3.246619	GTTGATTCACGTGAGGTCTCTC	58.753	50.000	24.37	14.67	40.36	3.20
2441	2710	2.628178	TGTTGATTCACGTGAGGTCTCT	59.372	45.455	24.37	8.05	0.00	3.10
2442	2711	2.989840	CTGTTGATTCACGTGAGGTCTC	59.010	50.000	24.37	17.79	0.00	3.36
2443	2712	2.289072	CCTGTTGATTCACGTGAGGTCT	60.289	50.000	24.37	11.49	0.00	3.85
2444	2713	2.069273	CCTGTTGATTCACGTGAGGTC	58.931	52.381	19.11	19.68	0.00	3.85
2445	2714	1.416401	ACCTGTTGATTCACGTGAGGT	59.584	47.619	19.11	17.02	0.00	3.85
2446	2715	2.169832	ACCTGTTGATTCACGTGAGG	57.830	50.000	19.11	16.35	0.00	3.86
2447	2716	3.559655	TCAAACCTGTTGATTCACGTGAG	59.440	43.478	19.11	6.98	0.00	3.51
2448	2717	3.311322	GTCAAACCTGTTGATTCACGTGA	59.689	43.478	15.76	15.76	0.00	4.35
2449	2718	3.312421	AGTCAAACCTGTTGATTCACGTG	59.688	43.478	9.94	9.94	0.00	4.49
2450	2719	3.541632	AGTCAAACCTGTTGATTCACGT	58.458	40.909	0.00	0.00	0.00	4.49
2451	2720	3.058914	GGAGTCAAACCTGTTGATTCACG	60.059	47.826	11.97	0.00	37.04	4.35
2452	2721	4.137543	AGGAGTCAAACCTGTTGATTCAC	58.862	43.478	11.97	4.04	37.04	3.18
2504	2774	3.643199	TTGATCCCGACATTTCATGGA	57.357	42.857	0.00	0.00	33.60	3.41
2720	2995	5.778241	TGTAAGAGACCCTTCATTGACACTA	59.222	40.000	0.00	0.00	36.34	2.74
3160	3459	5.453648	TGTCGTACATTGGCATAAACAAAC	58.546	37.500	0.00	0.00	0.00	2.93
3202	3561	2.029918	GCGTTCCTCATTTCTGCCTTTT	60.030	45.455	0.00	0.00	0.00	2.27
3244	3603	2.016096	GCAGATTCCTCAGCCAACTCC	61.016	57.143	0.00	0.00	0.00	3.85
3865	4269	5.106157	ACTCCTTAAATGCCTGAAACAATCG	60.106	40.000	0.00	0.00	0.00	3.34
4107	4516	6.825721	GGTTGATGACTGAAGGATAAGTTGAT	59.174	38.462	0.00	0.00	0.00	2.57
4133	4544	2.945668	GGATGAACCGAGGGAAAAGATG	59.054	50.000	0.00	0.00	0.00	2.90
4137	4548	3.970205	GGGATGAACCGAGGGAAAA	57.030	52.632	0.00	0.00	40.11	2.29
4297	4709	7.129457	TGATGTAAAGGTAGAGATGCTGATT	57.871	36.000	0.00	0.00	0.00	2.57
4622	5036	2.549754	CAGTCACCCACACTCAACATTC	59.450	50.000	0.00	0.00	0.00	2.67
4633	5047	2.292267	CATTCATAGGCAGTCACCCAC	58.708	52.381	0.00	0.00	0.00	4.61
4668	5082	6.569127	TGCCAAATTATCTACCACCTAGAA	57.431	37.500	0.00	0.00	34.99	2.10
4708	5122	8.328864	GGAAGAAAGAATGTACAAGTATAAGCG	58.671	37.037	0.00	0.00	0.00	4.68
4804	5218	8.072321	ACAATAGGCATGAGAGGTATATACAG	57.928	38.462	14.70	0.00	0.00	2.74
4883	5299	4.082245	TGTCATACAAGCACATTCTCGAGA	60.082	41.667	12.08	12.08	0.00	4.04
4934	5350	0.041400	TTTCACGTCGCACTGCAATG	60.041	50.000	1.11	0.00	0.00	2.82
4983	5399	2.146342	ACAAGCACATTCTCCTCGTTG	58.854	47.619	0.00	0.00	0.00	4.10
5007	5423	3.612860	GCACGTTCAGACTTACTGTATGG	59.387	47.826	5.80	0.00	45.86	2.74
5054	5496	4.379652	AGGGCACAAATTTTCATGTCAAC	58.620	39.130	0.00	0.00	0.00	3.18
5136	5606	3.469899	GTTGATGCATGCAACGTTCTA	57.530	42.857	26.68	11.69	36.63	2.10
5174	5644	9.627395	TTGTTTGATTTCGTTCTTTCTTTGTTA	57.373	25.926	0.00	0.00	0.00	2.41
5328	5800	0.108804	CAGGGTAAGCACATCGACGT	60.109	55.000	0.00	0.00	0.00	4.34

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.