AutoCloner

Multiple sequence alignment - TraesCS7D01G274900

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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	TraesCS7D01G274900	chr7D	100.000	2708	0	0	1	2708	264325523	264328230	0.000000e+00	5001
1	TraesCS7D01G274900	chr7D	92.512	1843	109	25	380	2205	264360737	264362567	0.000000e+00	2612
2	TraesCS7D01G274900	chr7D	92.452	1603	101	17	450	2044	264338749	264340339	0.000000e+00	2272
3	TraesCS7D01G274900	chr7D	93.040	1523	80	22	378	1887	264370608	264372117	0.000000e+00	2202
4	TraesCS7D01G274900	chr7D	85.201	473	44	10	2234	2692	264344370	264344830	1.900000e-126	462
5	TraesCS7D01G274900	chr7D	82.007	289	16	16	1	253	264360443	264360731	2.110000e-51	213
6	TraesCS7D01G274900	chr7D	80.612	294	16	14	1	253	264370311	264370604	3.560000e-44	189
7	TraesCS7D01G274900	chr7D	78.231	294	23	17	1	253	264338408	264338701	1.680000e-32	150
8	TraesCS7D01G274900	chr7D	95.604	91	4	0	250	340	528060317	528060407	2.170000e-31	147
9	TraesCS7D01G274900	chr7A	95.290	1656	58	7	408	2044	287889480	287891134	0.000000e+00	2608
10	TraesCS7D01G274900	chr7A	95.755	1013	42	1	1192	2204	287862649	287863660	0.000000e+00	1631
11	TraesCS7D01G274900	chr7A	94.027	519	21	4	2198	2708	287863690	287864206	0.000000e+00	778
12	TraesCS7D01G274900	chr7A	84.631	488	50	11	2234	2708	287895142	287895617	1.900000e-126	462
13	TraesCS7D01G274900	chr7A	87.938	257	8	8	1	256	287862308	287862542	5.710000e-72	281
14	TraesCS7D01G274900	chr7A	86.547	223	13	8	16	230	287889261	287889474	2.100000e-56	230
15	TraesCS7D01G274900	chr7B	92.237	1842	113	27	378	2203	244644943	244646770	0.000000e+00	2582
16	TraesCS7D01G274900	chr7B	92.355	1622	96	23	380	1994	244692747	244694347	0.000000e+00	2283
17	TraesCS7D01G274900	chr7B	95.726	1357	58	0	688	2044	244651643	244652999	0.000000e+00	2185
18	TraesCS7D01G274900	chr7B	92.895	1520	83	21	380	1887	244716221	244717727	0.000000e+00	2185
19	TraesCS7D01G274900	chr7B	83.884	484	51	10	2234	2708	244656980	244657445	1.150000e-118	436
20	TraesCS7D01G274900	chr7B	93.651	252	15	1	375	626	244651394	244651644	2.550000e-100	375
21	TraesCS7D01G274900	chr7B	88.302	265	20	8	1	255	244651132	244651395	9.420000e-80	307
22	TraesCS7D01G274900	chr7B	88.824	170	14	2	2524	2690	244654683	244654850	1.270000e-48	204
23	TraesCS7D01G274900	chr7B	79.592	294	19	14	1	253	244692448	244692741	3.580000e-39	172
24	TraesCS7D01G274900	chr7B	84.431	167	15	3	98	253	244716049	244716215	1.300000e-33	154
25	TraesCS7D01G274900	chr7B	93.878	98	6	0	243	340	744290794	744290697	6.040000e-32	148
26	TraesCS7D01G274900	chr7B	94.624	93	5	0	248	340	217312257	217312349	7.810000e-31	145
27	TraesCS7D01G274900	chr7B	78.088	251	18	12	1	214	244644357	244644607	1.020000e-24	124
28	TraesCS7D01G274900	chr5D	98.851	87	1	0	254	340	262838791	262838705	3.610000e-34	156
29	TraesCS7D01G274900	chr4B	96.591	88	3	0	253	340	99581209	99581296	2.170000e-31	147
30	TraesCS7D01G274900	chr4B	94.681	94	4	1	247	340	216815100	216815008	7.810000e-31	145
31	TraesCS7D01G274900	chr2D	96.591	88	3	0	253	340	488233729	488233642	2.170000e-31	147
32	TraesCS7D01G274900	chr1B	93.684	95	6	0	246	340	636267268	636267362	2.810000e-30	143
33	TraesCS7D01G274900	chr6A	88.793	116	9	4	225	340	507082123	507082012	3.640000e-29	139

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	TraesCS7D01G274900	chr7D	264325523	264328230	2707	False	5001.000000	5001	100.000000	1	2708	1	chr7D.!!$F1	2707
1	TraesCS7D01G274900	chr7D	264360443	264362567	2124	False	1412.500000	2612	87.259500	1	2205	2	chr7D.!!$F5	2204
2	TraesCS7D01G274900	chr7D	264338408	264340339	1931	False	1211.000000	2272	85.341500	1	2044	2	chr7D.!!$F4	2043
3	TraesCS7D01G274900	chr7D	264370311	264372117	1806	False	1195.500000	2202	86.826000	1	1887	2	chr7D.!!$F6	1886
4	TraesCS7D01G274900	chr7A	287889261	287891134	1873	False	1419.000000	2608	90.918500	16	2044	2	chr7A.!!$F3	2028
5	TraesCS7D01G274900	chr7A	287862308	287864206	1898	False	896.666667	1631	92.573333	1	2708	3	chr7A.!!$F2	2707
6	TraesCS7D01G274900	chr7B	244644357	244646770	2413	False	1353.000000	2582	85.162500	1	2203	2	chr7B.!!$F2	2202
7	TraesCS7D01G274900	chr7B	244692448	244694347	1899	False	1227.500000	2283	85.973500	1	1994	2	chr7B.!!$F4	1993
8	TraesCS7D01G274900	chr7B	244716049	244717727	1678	False	1169.500000	2185	88.663000	98	1887	2	chr7B.!!$F5	1789
9	TraesCS7D01G274900	chr7B	244651132	244657445	6313	False	701.400000	2185	90.077400	1	2708	5	chr7B.!!$F3	2707

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
553	890	0.168788	CAAGTAGCATGGGTTGTGCG	59.831	55.0	0.0	0.0	46.86	5.34	F
640	1000	0.687920	TCGGTTAGGACACCATGCAA	59.312	50.0	0.0	0.0	36.49	4.08	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1431	1793	0.179936	CCATCCTGCAGTCCTCCTTC	59.820	60.000	13.81	0.0	0.0	3.46	R
2044	2411	1.202879	TGGCCGTGAAGAAAATCTGGT	60.203	47.619	0.00	0.0	0.0	4.00	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
61	68	4.099881	AGGAGATTGATCAGAGCAGAGTTC	59.900	45.833	0.00	0.00	0.00	3.01
92	120	8.375506	TCTGAATGATACATTACCTATGGTTCC	58.624	37.037	0.00	0.00	38.64	3.62
93	121	8.040002	TGAATGATACATTACCTATGGTTCCA	57.960	34.615	0.00	0.00	38.64	3.53
94	122	8.156820	TGAATGATACATTACCTATGGTTCCAG	58.843	37.037	0.00	0.00	38.64	3.86
95	123	7.872061	ATGATACATTACCTATGGTTCCAGA	57.128	36.000	0.00	0.00	38.64	3.86
100	135	5.011738	ACATTACCTATGGTTCCAGATACCG	59.988	44.000	0.00	0.00	38.64	4.02
102	137	3.858135	ACCTATGGTTCCAGATACCGAT	58.142	45.455	0.00	0.00	38.55	4.18
256	591	3.386726	TGGCCGTCATACAAGCTAATACT	59.613	43.478	0.00	0.00	0.00	2.12
257	592	3.988517	GGCCGTCATACAAGCTAATACTC	59.011	47.826	0.00	0.00	0.00	2.59
258	593	3.988517	GCCGTCATACAAGCTAATACTCC	59.011	47.826	0.00	0.00	0.00	3.85
259	594	4.557205	CCGTCATACAAGCTAATACTCCC	58.443	47.826	0.00	0.00	0.00	4.30
260	595	4.281182	CCGTCATACAAGCTAATACTCCCT	59.719	45.833	0.00	0.00	0.00	4.20
261	596	5.462405	CGTCATACAAGCTAATACTCCCTC	58.538	45.833	0.00	0.00	0.00	4.30
262	597	5.565045	CGTCATACAAGCTAATACTCCCTCC	60.565	48.000	0.00	0.00	0.00	4.30
263	598	4.523173	TCATACAAGCTAATACTCCCTCCG	59.477	45.833	0.00	0.00	0.00	4.63
264	599	2.748388	ACAAGCTAATACTCCCTCCGT	58.252	47.619	0.00	0.00	0.00	4.69
265	600	3.105283	ACAAGCTAATACTCCCTCCGTT	58.895	45.455	0.00	0.00	0.00	4.44
266	601	3.132467	ACAAGCTAATACTCCCTCCGTTC	59.868	47.826	0.00	0.00	0.00	3.95
267	602	2.317973	AGCTAATACTCCCTCCGTTCC	58.682	52.381	0.00	0.00	0.00	3.62
268	603	2.037144	GCTAATACTCCCTCCGTTCCA	58.963	52.381	0.00	0.00	0.00	3.53
269	604	2.433239	GCTAATACTCCCTCCGTTCCAA	59.567	50.000	0.00	0.00	0.00	3.53
270	605	3.118519	GCTAATACTCCCTCCGTTCCAAA	60.119	47.826	0.00	0.00	0.00	3.28
271	606	4.624604	GCTAATACTCCCTCCGTTCCAAAA	60.625	45.833	0.00	0.00	0.00	2.44
272	607	4.586306	AATACTCCCTCCGTTCCAAAAT	57.414	40.909	0.00	0.00	0.00	1.82
273	608	5.703730	AATACTCCCTCCGTTCCAAAATA	57.296	39.130	0.00	0.00	0.00	1.40
274	609	3.629142	ACTCCCTCCGTTCCAAAATAG	57.371	47.619	0.00	0.00	0.00	1.73
275	610	3.178865	ACTCCCTCCGTTCCAAAATAGA	58.821	45.455	0.00	0.00	0.00	1.98
276	611	3.780850	ACTCCCTCCGTTCCAAAATAGAT	59.219	43.478	0.00	0.00	0.00	1.98
277	612	4.130118	CTCCCTCCGTTCCAAAATAGATG	58.870	47.826	0.00	0.00	0.00	2.90
278	613	3.778075	TCCCTCCGTTCCAAAATAGATGA	59.222	43.478	0.00	0.00	0.00	2.92
279	614	3.877508	CCCTCCGTTCCAAAATAGATGAC	59.122	47.826	0.00	0.00	0.00	3.06
280	615	3.877508	CCTCCGTTCCAAAATAGATGACC	59.122	47.826	0.00	0.00	0.00	4.02
281	616	3.877508	CTCCGTTCCAAAATAGATGACCC	59.122	47.826	0.00	0.00	0.00	4.46
282	617	3.264706	TCCGTTCCAAAATAGATGACCCA	59.735	43.478	0.00	0.00	0.00	4.51
283	618	4.013728	CCGTTCCAAAATAGATGACCCAA	58.986	43.478	0.00	0.00	0.00	4.12
284	619	4.142469	CCGTTCCAAAATAGATGACCCAAC	60.142	45.833	0.00	0.00	0.00	3.77
285	620	4.700213	CGTTCCAAAATAGATGACCCAACT	59.300	41.667	0.00	0.00	0.00	3.16
286	621	5.183140	CGTTCCAAAATAGATGACCCAACTT	59.817	40.000	0.00	0.00	0.00	2.66
287	622	6.294508	CGTTCCAAAATAGATGACCCAACTTT	60.295	38.462	0.00	0.00	0.00	2.66
288	623	6.588719	TCCAAAATAGATGACCCAACTTTG	57.411	37.500	0.00	0.00	0.00	2.77
289	624	6.074648	TCCAAAATAGATGACCCAACTTTGT	58.925	36.000	0.00	0.00	0.00	2.83
290	625	7.235079	TCCAAAATAGATGACCCAACTTTGTA	58.765	34.615	0.00	0.00	0.00	2.41
291	626	7.175990	TCCAAAATAGATGACCCAACTTTGTAC	59.824	37.037	0.00	0.00	0.00	2.90
292	627	7.176690	CCAAAATAGATGACCCAACTTTGTACT	59.823	37.037	0.00	0.00	0.00	2.73
293	628	9.226606	CAAAATAGATGACCCAACTTTGTACTA	57.773	33.333	0.00	0.00	0.00	1.82
294	629	9.802039	AAAATAGATGACCCAACTTTGTACTAA	57.198	29.630	0.00	0.00	0.00	2.24
295	630	8.788325	AATAGATGACCCAACTTTGTACTAAC	57.212	34.615	0.00	0.00	0.00	2.34
296	631	6.435292	AGATGACCCAACTTTGTACTAACT	57.565	37.500	0.00	0.00	0.00	2.24
297	632	6.838382	AGATGACCCAACTTTGTACTAACTT	58.162	36.000	0.00	0.00	0.00	2.66
298	633	7.287810	AGATGACCCAACTTTGTACTAACTTT	58.712	34.615	0.00	0.00	0.00	2.66
299	634	6.687081	TGACCCAACTTTGTACTAACTTTG	57.313	37.500	0.00	0.00	0.00	2.77
300	635	6.181908	TGACCCAACTTTGTACTAACTTTGT	58.818	36.000	0.00	0.00	0.00	2.83
301	636	7.337167	TGACCCAACTTTGTACTAACTTTGTA	58.663	34.615	0.00	0.00	0.00	2.41
302	637	7.280652	TGACCCAACTTTGTACTAACTTTGTAC	59.719	37.037	6.58	6.58	40.27	2.90
303	638	7.341030	ACCCAACTTTGTACTAACTTTGTACT	58.659	34.615	12.73	0.00	40.44	2.73
304	639	8.485392	ACCCAACTTTGTACTAACTTTGTACTA	58.515	33.333	12.73	4.86	40.44	1.82
305	640	8.768019	CCCAACTTTGTACTAACTTTGTACTAC	58.232	37.037	12.73	0.00	40.44	2.73
306	641	9.316730	CCAACTTTGTACTAACTTTGTACTACA	57.683	33.333	12.73	0.00	40.44	2.74
341	676	9.793259	AAAGTTGAGTCATCTATTTTAGAACCA	57.207	29.630	4.14	0.00	38.50	3.67
342	677	9.965902	AAGTTGAGTCATCTATTTTAGAACCAT	57.034	29.630	4.14	0.00	38.50	3.55
355	690	7.883391	TTTTAGAACCATACTGTTCAAACCA	57.117	32.000	6.67	0.00	45.62	3.67
356	691	8.472007	TTTTAGAACCATACTGTTCAAACCAT	57.528	30.769	6.67	0.00	45.62	3.55
357	692	9.575868	TTTTAGAACCATACTGTTCAAACCATA	57.424	29.630	6.67	0.00	45.62	2.74
358	693	8.786826	TTAGAACCATACTGTTCAAACCATAG	57.213	34.615	6.67	0.00	45.62	2.23
359	694	6.180472	AGAACCATACTGTTCAAACCATAGG	58.820	40.000	6.67	0.00	45.62	2.57
360	695	5.514500	ACCATACTGTTCAAACCATAGGT	57.486	39.130	0.00	0.00	37.65	3.08
361	696	6.630203	ACCATACTGTTCAAACCATAGGTA	57.370	37.500	0.00	0.00	33.12	3.08
362	697	7.023171	ACCATACTGTTCAAACCATAGGTAA	57.977	36.000	0.00	0.00	33.12	2.85
363	698	7.639378	ACCATACTGTTCAAACCATAGGTAAT	58.361	34.615	0.00	0.00	33.12	1.89
364	699	8.774183	ACCATACTGTTCAAACCATAGGTAATA	58.226	33.333	0.00	0.00	33.12	0.98
365	700	9.793259	CCATACTGTTCAAACCATAGGTAATAT	57.207	33.333	0.00	0.00	33.12	1.28
406	742	4.993029	TCAAACCGAGTTTTGGAATGTT	57.007	36.364	0.03	0.00	37.13	2.71
527	864	3.312697	GCCAACTCGAATATCCAAGGTTC	59.687	47.826	0.00	0.00	0.00	3.62
553	890	0.168788	CAAGTAGCATGGGTTGTGCG	59.831	55.000	0.00	0.00	46.86	5.34
577	917	6.128309	CGACACATCACACCTATTCAAATCAA	60.128	38.462	0.00	0.00	0.00	2.57
629	972	1.835531	ACCAACCCATACTCGGTTAGG	59.164	52.381	0.00	0.00	41.78	2.69
637	980	3.492656	CCATACTCGGTTAGGACACCATG	60.493	52.174	0.00	0.00	36.49	3.66
640	1000	0.687920	TCGGTTAGGACACCATGCAA	59.312	50.000	0.00	0.00	36.49	4.08
858	1220	5.762179	TGATTCCTTGTGTCTACCATTCT	57.238	39.130	0.00	0.00	0.00	2.40
900	1262	6.226787	CAGTTCCTCTGTATAAATAGGCCTG	58.773	44.000	17.99	0.00	39.17	4.85
1067	1429	1.063183	AAGGTTGAAGAGGAGCTGCT	58.937	50.000	7.79	7.79	0.00	4.24
1185	1547	1.927487	TCATGTGCCTTCCAAGCAAT	58.073	45.000	0.00	0.00	43.02	3.56
1431	1793	2.854777	CGCGAAGAAGGTTACATCTGAG	59.145	50.000	0.00	0.00	0.00	3.35
1483	1845	1.519751	CGAGGCTAGGGAGATCACCG	61.520	65.000	2.87	0.00	0.00	4.94
1910	2275	1.134491	GCGCTGGTCCATAACTACCTT	60.134	52.381	0.00	0.00	36.67	3.50
1923	2288	4.942761	AACTACCTTCTTGTTCGTACCA	57.057	40.909	0.00	0.00	0.00	3.25
1931	2298	7.208080	ACCTTCTTGTTCGTACCATGTATATC	58.792	38.462	0.00	0.00	0.00	1.63
1937	2304	9.471084	CTTGTTCGTACCATGTATATCAATGTA	57.529	33.333	0.00	0.00	0.00	2.29
1950	2317	1.276705	TCAATGTAGCCACGTTGCCTA	59.723	47.619	11.81	0.00	46.80	3.93
2044	2411	4.678574	GCTTGCAAATGGATAACATGCTGA	60.679	41.667	0.00	0.00	40.44	4.26
2093	2460	1.150827	GCCTGCCATTGCTTTGTTTC	58.849	50.000	0.00	0.00	38.71	2.78
2425	3409	2.919666	GCGTAAGGCATGTTCAACAT	57.080	45.000	0.00	0.00	42.87	2.71

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
81	109	3.323774	TCGGTATCTGGAACCATAGGT	57.676	47.619	0.00	0.00	36.78	3.08
92	120	8.153479	CTGATCCTCTAATAGATCGGTATCTG	57.847	42.308	0.00	0.00	42.60	2.90
167	209	5.393135	CGTCTGAGTTAAATGCTCCAGAGTA	60.393	44.000	0.00	0.00	32.31	2.59
256	591	3.778075	TCATCTATTTTGGAACGGAGGGA	59.222	43.478	0.00	0.00	0.00	4.20
257	592	3.877508	GTCATCTATTTTGGAACGGAGGG	59.122	47.826	0.00	0.00	0.00	4.30
258	593	3.877508	GGTCATCTATTTTGGAACGGAGG	59.122	47.826	0.00	0.00	0.00	4.30
259	594	3.877508	GGGTCATCTATTTTGGAACGGAG	59.122	47.826	0.00	0.00	0.00	4.63
260	595	3.264706	TGGGTCATCTATTTTGGAACGGA	59.735	43.478	0.00	0.00	0.00	4.69
261	596	3.616219	TGGGTCATCTATTTTGGAACGG	58.384	45.455	0.00	0.00	0.00	4.44
262	597	4.700213	AGTTGGGTCATCTATTTTGGAACG	59.300	41.667	0.00	0.00	0.00	3.95
263	598	6.590234	AAGTTGGGTCATCTATTTTGGAAC	57.410	37.500	0.00	0.00	0.00	3.62
264	599	6.553100	ACAAAGTTGGGTCATCTATTTTGGAA	59.447	34.615	0.00	0.00	0.00	3.53
265	600	6.074648	ACAAAGTTGGGTCATCTATTTTGGA	58.925	36.000	0.00	0.00	0.00	3.53
266	601	6.345096	ACAAAGTTGGGTCATCTATTTTGG	57.655	37.500	0.00	0.00	0.00	3.28
267	602	8.110860	AGTACAAAGTTGGGTCATCTATTTTG	57.889	34.615	0.00	0.00	0.00	2.44
268	603	9.802039	TTAGTACAAAGTTGGGTCATCTATTTT	57.198	29.630	0.00	0.00	0.00	1.82
269	604	9.227777	GTTAGTACAAAGTTGGGTCATCTATTT	57.772	33.333	0.00	0.00	0.00	1.40
270	605	8.603304	AGTTAGTACAAAGTTGGGTCATCTATT	58.397	33.333	0.00	0.00	0.00	1.73
271	606	8.147244	AGTTAGTACAAAGTTGGGTCATCTAT	57.853	34.615	0.00	0.00	0.00	1.98
272	607	7.549147	AGTTAGTACAAAGTTGGGTCATCTA	57.451	36.000	0.00	0.00	0.00	1.98
273	608	6.435292	AGTTAGTACAAAGTTGGGTCATCT	57.565	37.500	0.00	0.00	0.00	2.90
274	609	7.012989	ACAAAGTTAGTACAAAGTTGGGTCATC	59.987	37.037	0.00	0.00	0.00	2.92
275	610	6.831868	ACAAAGTTAGTACAAAGTTGGGTCAT	59.168	34.615	0.00	0.00	0.00	3.06
276	611	6.181908	ACAAAGTTAGTACAAAGTTGGGTCA	58.818	36.000	0.00	0.00	0.00	4.02
277	612	6.688637	ACAAAGTTAGTACAAAGTTGGGTC	57.311	37.500	0.00	0.00	0.00	4.46
278	613	7.341030	AGTACAAAGTTAGTACAAAGTTGGGT	58.659	34.615	6.30	0.00	43.24	4.51
279	614	7.797038	AGTACAAAGTTAGTACAAAGTTGGG	57.203	36.000	6.30	0.00	43.24	4.12
280	615	9.316730	TGTAGTACAAAGTTAGTACAAAGTTGG	57.683	33.333	0.00	0.00	43.24	3.77
315	650	9.793259	TGGTTCTAAAATAGATGACTCAACTTT	57.207	29.630	0.00	0.00	34.22	2.66
316	651	9.965902	ATGGTTCTAAAATAGATGACTCAACTT	57.034	29.630	0.00	0.00	34.22	2.66
329	664	9.575868	TGGTTTGAACAGTATGGTTCTAAAATA	57.424	29.630	7.47	0.00	33.00	1.40
330	665	8.472007	TGGTTTGAACAGTATGGTTCTAAAAT	57.528	30.769	7.47	0.00	33.00	1.82
331	666	7.883391	TGGTTTGAACAGTATGGTTCTAAAA	57.117	32.000	7.47	0.00	33.00	1.52
332	667	9.226606	CTATGGTTTGAACAGTATGGTTCTAAA	57.773	33.333	7.47	4.38	33.00	1.85
333	668	7.827236	CCTATGGTTTGAACAGTATGGTTCTAA	59.173	37.037	7.47	3.74	33.00	2.10
334	669	7.037873	ACCTATGGTTTGAACAGTATGGTTCTA	60.038	37.037	7.47	0.00	39.55	2.10
335	670	6.180472	CCTATGGTTTGAACAGTATGGTTCT	58.820	40.000	7.47	0.00	33.00	3.01
336	671	5.944007	ACCTATGGTTTGAACAGTATGGTTC	59.056	40.000	0.00	0.00	39.40	3.62
337	672	5.887754	ACCTATGGTTTGAACAGTATGGTT	58.112	37.500	0.00	0.00	32.96	3.67
338	673	5.514500	ACCTATGGTTTGAACAGTATGGT	57.486	39.130	0.00	0.00	32.96	3.55
339	674	9.793259	ATATTACCTATGGTTTGAACAGTATGG	57.207	33.333	0.00	0.00	37.55	2.74
352	687	9.228077	TGGTACCAAGTTTATATTACCTATGGT	57.772	33.333	13.60	0.00	41.27	3.55
364	699	8.789762	GTTTGAACAGTATGGTACCAAGTTTAT	58.210	33.333	20.76	3.33	33.00	1.40
365	700	7.229106	GGTTTGAACAGTATGGTACCAAGTTTA	59.771	37.037	20.76	14.47	33.00	2.01
366	701	6.040054	GGTTTGAACAGTATGGTACCAAGTTT	59.960	38.462	20.76	4.60	33.00	2.66
367	702	5.533528	GGTTTGAACAGTATGGTACCAAGTT	59.466	40.000	20.76	19.72	33.00	2.66
368	703	5.067954	GGTTTGAACAGTATGGTACCAAGT	58.932	41.667	20.76	12.40	33.00	3.16
369	704	4.153475	CGGTTTGAACAGTATGGTACCAAG	59.847	45.833	20.76	11.74	33.00	3.61
370	705	4.066490	CGGTTTGAACAGTATGGTACCAA	58.934	43.478	20.76	5.65	33.00	3.67
371	706	3.324268	TCGGTTTGAACAGTATGGTACCA	59.676	43.478	18.99	18.99	33.00	3.25
372	707	3.929094	TCGGTTTGAACAGTATGGTACC	58.071	45.455	4.43	4.43	33.00	3.34
373	708	4.563061	ACTCGGTTTGAACAGTATGGTAC	58.437	43.478	0.00	0.00	33.00	3.34
374	709	4.877378	ACTCGGTTTGAACAGTATGGTA	57.123	40.909	0.00	0.00	33.00	3.25
375	710	3.764237	ACTCGGTTTGAACAGTATGGT	57.236	42.857	0.00	0.00	42.46	3.55
376	711	5.212194	CAAAACTCGGTTTGAACAGTATGG	58.788	41.667	1.24	0.00	39.69	2.74
406	742	4.574674	AACATGGCCATCTTGTAGAGAA	57.425	40.909	17.61	0.00	38.06	2.87
527	864	0.454600	CCCATGCTACTTGCTTGCTG	59.545	55.000	0.00	0.00	43.09	4.41
553	890	6.741992	TGATTTGAATAGGTGTGATGTGTC	57.258	37.500	0.00	0.00	0.00	3.67
629	972	6.389091	TCTTGACATAATTTTGCATGGTGTC	58.611	36.000	0.00	0.00	36.09	3.67
637	980	5.964758	TGGTGGATCTTGACATAATTTTGC	58.035	37.500	0.00	0.00	0.00	3.68
640	1000	9.347240	CTCTATTGGTGGATCTTGACATAATTT	57.653	33.333	0.00	0.00	0.00	1.82
900	1262	6.374578	GTTTGATGTGTTTAGCCTTCTTCTC	58.625	40.000	0.00	0.00	0.00	2.87
1185	1547	2.596346	TGCTGGGAAGAGCAAATTTGA	58.404	42.857	22.31	0.00	46.05	2.69
1431	1793	0.179936	CCATCCTGCAGTCCTCCTTC	59.820	60.000	13.81	0.00	0.00	3.46
1910	2275	8.201464	ACATTGATATACATGGTACGAACAAGA	58.799	33.333	0.00	0.00	0.00	3.02
1923	2288	5.179368	GCAACGTGGCTACATTGATATACAT	59.821	40.000	13.47	0.00	0.00	2.29
1950	2317	7.318141	CAAAATCATGAGATTAAGCAGGTGTT	58.682	34.615	0.09	0.00	43.52	3.32
2044	2411	1.202879	TGGCCGTGAAGAAAATCTGGT	60.203	47.619	0.00	0.00	0.00	4.00
2310	3289	7.632721	ACAACATTCAAAATCAAAACTGATGC	58.367	30.769	0.00	0.00	0.00	3.91
2383	3362	4.236935	CACATGTCACCACTAAATTTGGC	58.763	43.478	0.00	0.00	37.69	4.52
2387	3366	2.487762	CGCCACATGTCACCACTAAATT	59.512	45.455	0.00	0.00	0.00	1.82
2431	3415	2.432444	CCACCAATACAACGTGATGGT	58.568	47.619	0.00	0.00	44.95	3.55
2460	3444	4.232188	ACACATCCTCTACTAGGTTCGA	57.768	45.455	0.00	0.00	46.62	3.71
2468	3452	6.405953	CCAAACGATCTTACACATCCTCTACT	60.406	42.308	0.00	0.00	0.00	2.57
2470	3454	5.655090	TCCAAACGATCTTACACATCCTCTA	59.345	40.000	0.00	0.00	0.00	2.43

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.