AutoCloner

Multiple sequence alignment - TraesCS4A01G030400

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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	TraesCS4A01G030400	chr4A	100.000	2465	0	0	1	2465	23615502	23613038	0.000000e+00	4553
1	TraesCS4A01G030400	chr4A	94.049	1714	76	16	760	2465	23844249	23842554	0.000000e+00	2577
2	TraesCS4A01G030400	chr4A	95.600	250	9	2	487	734	23844805	23844556	1.370000e-107	399
3	TraesCS4A01G030400	chr4A	86.022	93	13	0	1508	1600	610898540	610898632	1.560000e-17	100
4	TraesCS4A01G030400	chr4D	92.178	1483	70	18	1003	2465	444173942	444175398	0.000000e+00	2054
5	TraesCS4A01G030400	chr4D	88.108	370	38	4	340	704	444171869	444172237	3.760000e-118	435
6	TraesCS4A01G030400	chr4D	83.607	305	39	5	1	295	40758692	40758389	2.410000e-70	276
7	TraesCS4A01G030400	chr4D	92.357	157	7	2	768	924	444173418	444173569	4.130000e-53	219
8	TraesCS4A01G030400	chr4B	90.062	1127	54	17	888	2000	553863652	553864734	0.000000e+00	1408
9	TraesCS4A01G030400	chr4B	91.101	427	25	6	465	890	553862651	553863065	1.280000e-157	566
10	TraesCS4A01G030400	chr4B	87.593	403	34	10	1	390	553853379	553853778	1.040000e-123	453
11	TraesCS4A01G030400	chr4B	89.773	176	14	2	2093	2268	553864735	553864906	3.190000e-54	222
12	TraesCS4A01G030400	chr4B	83.206	131	14	4	1506	1634	625595273	625595397	2.000000e-21	113
13	TraesCS4A01G030400	chr1B	88.219	713	56	18	767	1472	344375861	344375170	0.000000e+00	826
14	TraesCS4A01G030400	chr1B	95.354	495	17	2	989	1483	434335383	434335871	0.000000e+00	782
15	TraesCS4A01G030400	chr1B	80.519	308	46	9	1	295	423946256	423946562	8.870000e-55	224
16	TraesCS4A01G030400	chr1A	87.781	712	67	15	767	1472	344190016	344189319	0.000000e+00	815
17	TraesCS4A01G030400	chr2B	94.675	507	21	2	988	1494	473299911	473300411	0.000000e+00	782
18	TraesCS4A01G030400	chr2D	94.336	512	23	2	988	1499	399347615	399348120	0.000000e+00	780
19	TraesCS4A01G030400	chr2A	94.141	512	24	2	988	1499	537003389	537003894	0.000000e+00	774
20	TraesCS4A01G030400	chr7A	86.842	304	28	5	3	294	556101271	556100968	1.830000e-86	329
21	TraesCS4A01G030400	chr7A	86.557	305	29	5	3	295	556101870	556101566	2.360000e-85	326
22	TraesCS4A01G030400	chr7A	81.230	309	41	11	1	294	149318766	149319072	1.470000e-57	233
23	TraesCS4A01G030400	chr7B	89.286	252	21	2	1380	1631	648782925	648782680	6.620000e-81	311
24	TraesCS4A01G030400	chr7B	83.226	310	39	7	1	299	71148773	71149080	3.120000e-69	272
25	TraesCS4A01G030400	chr6D	83.766	308	33	9	1	294	42536474	42536778	2.410000e-70	276
26	TraesCS4A01G030400	chr6B	82.680	306	39	11	1	294	517441442	517441745	2.430000e-65	259

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	TraesCS4A01G030400	chr4A	23613038	23615502	2464	True	4553.000000	4553	100.0000	1	2465	1	chr4A.!!$R1	2464
1	TraesCS4A01G030400	chr4A	23842554	23844805	2251	True	1488.000000	2577	94.8245	487	2465	2	chr4A.!!$R2	1978
2	TraesCS4A01G030400	chr4D	444171869	444175398	3529	False	902.666667	2054	90.8810	340	2465	3	chr4D.!!$F1	2125
3	TraesCS4A01G030400	chr4B	553862651	553864906	2255	False	732.000000	1408	90.3120	465	2268	3	chr4B.!!$F3	1803
4	TraesCS4A01G030400	chr1B	344375170	344375861	691	True	826.000000	826	88.2190	767	1472	1	chr1B.!!$R1	705
5	TraesCS4A01G030400	chr1A	344189319	344190016	697	True	815.000000	815	87.7810	767	1472	1	chr1A.!!$R1	705
6	TraesCS4A01G030400	chr2B	473299911	473300411	500	False	782.000000	782	94.6750	988	1494	1	chr2B.!!$F1	506
7	TraesCS4A01G030400	chr2D	399347615	399348120	505	False	780.000000	780	94.3360	988	1499	1	chr2D.!!$F1	511
8	TraesCS4A01G030400	chr2A	537003389	537003894	505	False	774.000000	774	94.1410	988	1499	1	chr2A.!!$F1	511
9	TraesCS4A01G030400	chr7A	556100968	556101870	902	True	327.500000	329	86.6995	3	295	2	chr7A.!!$R1	292

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
381	394	0.108424	CCACCTCTCTCGCCTTCTTG	60.108	60.0	0.0	0.0	0.0	3.02	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1674	3977	0.179234	TGGCACAGTTCGGTTCAGAA	59.821	50.0	0.0	0.0	0.0	3.02	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
27	28	8.289618	GTGATGTGTATGTGTGTAAAACTTCAT	58.710	33.333	0.00	0.00	0.00	2.57
73	74	6.645700	TCTGTGCAAAAAGAACAAATTCAC	57.354	33.333	0.00	0.00	34.61	3.18
75	76	5.164233	TGTGCAAAAAGAACAAATTCACGA	58.836	33.333	0.00	0.00	37.29	4.35
76	77	5.809562	TGTGCAAAAAGAACAAATTCACGAT	59.190	32.000	0.00	0.00	37.29	3.73
83	84	8.925161	AAAAGAACAAATTCACGATCTTTTGA	57.075	26.923	14.32	0.00	42.37	2.69
113	114	7.886629	ATAGTATCATGTGTTGAAAAGCCAT	57.113	32.000	0.00	0.00	38.03	4.40
114	115	6.594788	AGTATCATGTGTTGAAAAGCCATT	57.405	33.333	0.00	0.00	38.03	3.16
140	149	1.268285	TGCACAACCGTCATTTCAACG	60.268	47.619	0.00	0.00	39.78	4.10
143	152	3.364565	GCACAACCGTCATTTCAACGTAT	60.365	43.478	0.00	0.00	38.44	3.06
167	177	4.443621	TCGTCCTGAAATTTACACACACA	58.556	39.130	0.00	0.00	0.00	3.72
191	201	4.881273	TGTGTTATGCCTTCATGTATGTCC	59.119	41.667	0.00	0.00	34.22	4.02
203	215	7.065803	CCTTCATGTATGTCCGTATTTTTCAGT	59.934	37.037	0.00	0.00	0.00	3.41
261	274	9.601217	TTCAATTTTGAATTTTTAGAAACCGGA	57.399	25.926	9.46	0.00	41.88	5.14
262	275	9.036671	TCAATTTTGAATTTTTAGAAACCGGAC	57.963	29.630	9.46	0.00	33.55	4.79
264	277	8.812147	ATTTTGAATTTTTAGAAACCGGACTC	57.188	30.769	9.46	3.52	0.00	3.36
269	282	4.627284	TTTTAGAAACCGGACTCCATGA	57.373	40.909	9.46	0.00	0.00	3.07
271	284	4.627284	TTAGAAACCGGACTCCATGAAA	57.373	40.909	9.46	0.00	0.00	2.69
283	296	0.465097	CCATGAAAGCCGAGCTCCAT	60.465	55.000	8.47	1.36	38.25	3.41
299	312	3.699067	CTCCATAAGCAATTTTCCGCAG	58.301	45.455	0.00	0.00	0.00	5.18
301	314	2.159198	CCATAAGCAATTTTCCGCAGCT	60.159	45.455	0.00	0.00	37.08	4.24
302	315	2.634982	TAAGCAATTTTCCGCAGCTG	57.365	45.000	10.11	10.11	35.42	4.24
304	317	0.242017	AGCAATTTTCCGCAGCTGAC	59.758	50.000	20.43	8.06	33.67	3.51
305	318	0.242017	GCAATTTTCCGCAGCTGACT	59.758	50.000	20.43	0.00	0.00	3.41
306	319	1.468520	GCAATTTTCCGCAGCTGACTA	59.531	47.619	20.43	0.00	0.00	2.59
307	320	2.098117	GCAATTTTCCGCAGCTGACTAT	59.902	45.455	20.43	0.00	0.00	2.12
308	321	3.312421	GCAATTTTCCGCAGCTGACTATA	59.688	43.478	20.43	0.00	0.00	1.31
309	322	4.786609	GCAATTTTCCGCAGCTGACTATAC	60.787	45.833	20.43	0.00	0.00	1.47
310	323	3.887621	TTTTCCGCAGCTGACTATACT	57.112	42.857	20.43	0.00	0.00	2.12
311	324	4.994907	TTTTCCGCAGCTGACTATACTA	57.005	40.909	20.43	0.00	0.00	1.82
312	325	5.531122	TTTTCCGCAGCTGACTATACTAT	57.469	39.130	20.43	0.00	0.00	2.12
313	326	5.531122	TTTCCGCAGCTGACTATACTATT	57.469	39.130	20.43	0.00	0.00	1.73
314	327	6.644248	TTTCCGCAGCTGACTATACTATTA	57.356	37.500	20.43	0.00	0.00	0.98
315	328	6.644248	TTCCGCAGCTGACTATACTATTAA	57.356	37.500	20.43	0.00	0.00	1.40
316	329	6.010294	TCCGCAGCTGACTATACTATTAAC	57.990	41.667	20.43	0.00	0.00	2.01
317	330	5.048224	TCCGCAGCTGACTATACTATTAACC	60.048	44.000	20.43	0.00	0.00	2.85
318	331	5.278808	CCGCAGCTGACTATACTATTAACCA	60.279	44.000	20.43	0.00	0.00	3.67
319	332	6.390721	CGCAGCTGACTATACTATTAACCAT	58.609	40.000	20.43	0.00	0.00	3.55
320	333	6.528423	CGCAGCTGACTATACTATTAACCATC	59.472	42.308	20.43	0.00	0.00	3.51
321	334	7.575909	CGCAGCTGACTATACTATTAACCATCT	60.576	40.741	20.43	0.00	0.00	2.90
322	335	8.091449	GCAGCTGACTATACTATTAACCATCTT	58.909	37.037	20.43	0.00	0.00	2.40
323	336	9.632807	CAGCTGACTATACTATTAACCATCTTC	57.367	37.037	8.42	0.00	0.00	2.87
324	337	9.594936	AGCTGACTATACTATTAACCATCTTCT	57.405	33.333	0.00	0.00	0.00	2.85
371	384	5.072464	GGGAGCTTTTAATATCCACCTCTCT	59.928	44.000	0.00	0.00	33.24	3.10
381	394	0.108424	CCACCTCTCTCGCCTTCTTG	60.108	60.000	0.00	0.00	0.00	3.02
385	398	1.273606	CCTCTCTCGCCTTCTTGTTCA	59.726	52.381	0.00	0.00	0.00	3.18
392	408	1.251251	GCCTTCTTGTTCATGGCACT	58.749	50.000	0.00	0.00	42.79	4.40
406	422	2.517959	TGGCACTCCATTTCCTTTCAG	58.482	47.619	0.00	0.00	37.47	3.02
762	1890	1.227527	GGTTTTTGCCACCACAGCC	60.228	57.895	0.00	0.00	34.04	4.85
1380	3674	1.231641	CCGGGAGATCCAGACCTCT	59.768	63.158	0.00	0.00	37.91	3.69
1487	3781	4.644103	TTCCGTTGCCTGTATCTAGTAC	57.356	45.455	0.00	0.00	0.00	2.73
1490	3784	3.243434	CCGTTGCCTGTATCTAGTACCAG	60.243	52.174	0.00	0.00	32.03	4.00
1495	3789	4.584743	TGCCTGTATCTAGTACCAGATGTG	59.415	45.833	13.35	4.19	35.99	3.21
1562	3856	2.877097	TGGGAGTTGCTGAATGCTTA	57.123	45.000	0.00	0.00	43.37	3.09
1635	3929	4.430137	TTTGCAAGCTGAGATTTAGCAG	57.570	40.909	0.00	0.00	43.53	4.24
1665	3968	6.569226	GCTTATGATCTGACTGTTGTTTGCTT	60.569	38.462	0.00	0.00	0.00	3.91
1671	3974	3.510719	TGACTGTTGTTTGCTTTTCTGC	58.489	40.909	0.00	0.00	0.00	4.26
1672	3975	3.193267	TGACTGTTGTTTGCTTTTCTGCT	59.807	39.130	0.00	0.00	0.00	4.24
1673	3976	3.774066	ACTGTTGTTTGCTTTTCTGCTC	58.226	40.909	0.00	0.00	0.00	4.26
1674	3977	3.445096	ACTGTTGTTTGCTTTTCTGCTCT	59.555	39.130	0.00	0.00	0.00	4.09
1675	3978	4.082026	ACTGTTGTTTGCTTTTCTGCTCTT	60.082	37.500	0.00	0.00	0.00	2.85
1676	3979	4.423732	TGTTGTTTGCTTTTCTGCTCTTC	58.576	39.130	0.00	0.00	0.00	2.87
1677	3980	4.158394	TGTTGTTTGCTTTTCTGCTCTTCT	59.842	37.500	0.00	0.00	0.00	2.85
1678	3981	4.297299	TGTTTGCTTTTCTGCTCTTCTG	57.703	40.909	0.00	0.00	0.00	3.02
1695	3998	0.532862	CTGAACCGAACTGTGCCACT	60.533	55.000	0.00	0.00	0.00	4.00
1707	4010	1.160137	GTGCCACTGGACTGAACATC	58.840	55.000	0.00	0.00	0.00	3.06
1721	4024	7.336679	TGGACTGAACATCTGTATTGTTAATGG	59.663	37.037	0.00	0.00	37.43	3.16
1763	4066	5.543507	ACTTATTGGATTGGTTGCAACAA	57.456	34.783	29.55	17.93	38.59	2.83
1882	4185	5.716094	TGTAACGCTAGAAGTTAGCATTGA	58.284	37.500	10.32	0.00	40.39	2.57
1988	4389	5.449107	AATTTGCAGCATCAGTATCATCC	57.551	39.130	0.00	0.00	0.00	3.51
2030	4431	8.507524	AAGCAAATTTGGTTATCTCTAGTACC	57.492	34.615	29.03	3.90	45.96	3.34
2083	4489	8.956426	TGAATTTTATGGACTGTTAGTGAATCC	58.044	33.333	0.00	0.00	0.00	3.01
2119	4525	3.006537	TCTGCTACCTGTAGTTGTTGACC	59.993	47.826	6.22	0.00	35.65	4.02
2123	4529	1.202770	ACCTGTAGTTGTTGACCTGGC	60.203	52.381	0.00	0.00	0.00	4.85
2144	4550	1.687123	GTGCCGGTATCATGGACTAGT	59.313	52.381	1.90	0.00	0.00	2.57
2145	4551	2.102588	GTGCCGGTATCATGGACTAGTT	59.897	50.000	1.90	0.00	0.00	2.24
2146	4552	2.364324	TGCCGGTATCATGGACTAGTTC	59.636	50.000	1.90	0.00	0.00	3.01
2216	4622	3.615155	TGGAATGTGAAATATCCGCACA	58.385	40.909	0.00	0.00	45.40	4.57
2225	4631	5.065218	GTGAAATATCCGCACAGAACTGAAT	59.935	40.000	8.87	0.00	32.96	2.57
2252	4658	2.135933	GAAGTTTGTGACCTGAGACGG	58.864	52.381	0.00	0.00	0.00	4.79
2270	4676	5.589192	AGACGGCAGTATTATGTACAGTTC	58.411	41.667	0.33	0.00	0.00	3.01
2276	4682	6.073548	GGCAGTATTATGTACAGTTCTGCATC	60.074	42.308	26.38	15.56	45.59	3.91
2338	4757	1.687123	ACTTCAGAAGTACTGGCACGT	59.313	47.619	14.58	0.00	45.76	4.49
2350	4769	1.205820	GGCACGTCTGTTTAACCGC	59.794	57.895	0.00	0.00	0.00	5.68
2383	4802	9.364989	TGTTATAGCCACATTAAAAGAAATTGC	57.635	29.630	0.00	0.00	0.00	3.56
2386	4805	3.431572	GCCACATTAAAAGAAATTGCGCA	59.568	39.130	5.66	5.66	0.00	6.09
2428	4849	9.500785	TCGTGCTAAAATTTCATATCCATGATA	57.499	29.630	0.00	0.00	40.85	2.15
2429	4850	9.764870	CGTGCTAAAATTTCATATCCATGATAG	57.235	33.333	0.00	0.00	40.85	2.08

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	7.281100	TGAAGTTTTACACACATACACATCACA	59.719	33.333	0.00	0.00	0.00	3.58
1	2	7.635423	TGAAGTTTTACACACATACACATCAC	58.365	34.615	0.00	0.00	0.00	3.06
22	23	8.013947	CGCATCTCAAGGTATTTCATTATGAAG	58.986	37.037	7.72	0.00	37.70	3.02
27	28	7.386025	CAGATCGCATCTCAAGGTATTTCATTA	59.614	37.037	0.00	0.00	37.58	1.90
126	135	4.316375	CGAAATACGTTGAAATGACGGT	57.684	40.909	0.00	0.00	44.34	4.83
167	177	5.532406	GGACATACATGAAGGCATAACACAT	59.468	40.000	0.00	0.00	32.27	3.21
180	190	9.607988	AATACTGAAAAATACGGACATACATGA	57.392	29.630	0.00	0.00	0.00	3.07
237	249	9.040939	AGTCCGGTTTCTAAAAATTCAAAATTG	57.959	29.630	0.00	0.00	0.00	2.32
261	274	0.107945	GAGCTCGGCTTTCATGGAGT	60.108	55.000	0.00	0.00	39.88	3.85
262	275	0.813210	GGAGCTCGGCTTTCATGGAG	60.813	60.000	7.83	0.00	39.88	3.86
264	277	0.465097	ATGGAGCTCGGCTTTCATGG	60.465	55.000	7.83	0.00	39.88	3.66
283	296	2.095263	GTCAGCTGCGGAAAATTGCTTA	60.095	45.455	9.47	0.00	0.00	3.09
287	300	4.572389	AGTATAGTCAGCTGCGGAAAATTG	59.428	41.667	9.47	0.00	0.00	2.32
295	308	5.769367	TGGTTAATAGTATAGTCAGCTGCG	58.231	41.667	9.47	0.00	0.00	5.18
296	309	7.607250	AGATGGTTAATAGTATAGTCAGCTGC	58.393	38.462	9.47	4.26	0.00	5.25
297	310	9.632807	GAAGATGGTTAATAGTATAGTCAGCTG	57.367	37.037	7.63	7.63	0.00	4.24
323	336	9.420551	CCCGCTCCTTATAAACTTTATACTTAG	57.579	37.037	1.33	1.68	0.00	2.18
324	337	9.146586	TCCCGCTCCTTATAAACTTTATACTTA	57.853	33.333	1.33	0.00	0.00	2.24
325	338	8.026396	TCCCGCTCCTTATAAACTTTATACTT	57.974	34.615	1.33	0.00	0.00	2.24
326	339	7.607615	TCCCGCTCCTTATAAACTTTATACT	57.392	36.000	1.33	0.00	0.00	2.12
327	340	6.368243	GCTCCCGCTCCTTATAAACTTTATAC	59.632	42.308	1.33	0.00	0.00	1.47
328	341	6.269307	AGCTCCCGCTCCTTATAAACTTTATA	59.731	38.462	0.00	0.00	45.15	0.98
329	342	5.071923	AGCTCCCGCTCCTTATAAACTTTAT	59.928	40.000	0.00	0.00	45.15	1.40
330	343	4.407945	AGCTCCCGCTCCTTATAAACTTTA	59.592	41.667	0.00	0.00	45.15	1.85
331	344	3.200165	AGCTCCCGCTCCTTATAAACTTT	59.800	43.478	0.00	0.00	45.15	2.66
332	345	2.772515	AGCTCCCGCTCCTTATAAACTT	59.227	45.455	0.00	0.00	45.15	2.66
333	346	2.399580	AGCTCCCGCTCCTTATAAACT	58.600	47.619	0.00	0.00	45.15	2.66
334	347	2.912690	AGCTCCCGCTCCTTATAAAC	57.087	50.000	0.00	0.00	45.15	2.01
371	384	2.555123	GCCATGAACAAGAAGGCGA	58.445	52.632	0.00	0.00	35.42	5.54
439	455	8.804688	AAATACGAAGAATCTACATAGCTGTC	57.195	34.615	0.00	0.00	36.79	3.51
762	1890	1.634757	TTTGCTGCGGTGCGTCTATG	61.635	55.000	0.00	0.00	35.36	2.23
1487	3781	2.810274	CAGAGTGAACAACCACATCTGG	59.190	50.000	0.00	0.00	44.26	3.86
1490	3784	2.851195	ACCAGAGTGAACAACCACATC	58.149	47.619	0.00	0.00	39.42	3.06
1495	3789	2.415512	GCGATAACCAGAGTGAACAACC	59.584	50.000	0.00	0.00	0.00	3.77
1503	3797	3.362706	TCTACTTGGCGATAACCAGAGT	58.637	45.455	0.00	0.00	41.82	3.24
1505	3799	3.767673	ACTTCTACTTGGCGATAACCAGA	59.232	43.478	0.00	0.00	41.82	3.86
1633	3927	3.001026	CAGTCAGATCATAAGCAACGCTG	59.999	47.826	0.00	0.00	39.62	5.18
1635	3929	2.932614	ACAGTCAGATCATAAGCAACGC	59.067	45.455	0.00	0.00	0.00	4.84
1639	3933	5.335113	GCAAACAACAGTCAGATCATAAGCA	60.335	40.000	0.00	0.00	0.00	3.91
1665	3968	3.131396	GTTCGGTTCAGAAGAGCAGAAA	58.869	45.455	0.00	0.00	39.81	2.52
1671	3974	1.795286	GCACAGTTCGGTTCAGAAGAG	59.205	52.381	0.00	0.00	0.00	2.85
1672	3975	1.540363	GGCACAGTTCGGTTCAGAAGA	60.540	52.381	0.00	0.00	0.00	2.87
1673	3976	0.868406	GGCACAGTTCGGTTCAGAAG	59.132	55.000	0.00	0.00	0.00	2.85
1674	3977	0.179234	TGGCACAGTTCGGTTCAGAA	59.821	50.000	0.00	0.00	0.00	3.02
1675	3978	0.531974	GTGGCACAGTTCGGTTCAGA	60.532	55.000	13.86	0.00	41.80	3.27
1676	3979	0.532862	AGTGGCACAGTTCGGTTCAG	60.533	55.000	21.41	0.00	40.27	3.02
1677	3980	0.813610	CAGTGGCACAGTTCGGTTCA	60.814	55.000	21.41	0.00	40.27	3.18
1678	3981	1.507141	CCAGTGGCACAGTTCGGTTC	61.507	60.000	21.41	0.00	40.27	3.62
1695	3998	7.336679	CCATTAACAATACAGATGTTCAGTCCA	59.663	37.037	0.00	0.00	41.11	4.02
1707	4010	8.561738	ACTGAAACCTACCATTAACAATACAG	57.438	34.615	0.00	0.00	0.00	2.74
1763	4066	7.926555	CGGTACTCATAAACTCATAACCTGAAT	59.073	37.037	0.00	0.00	32.14	2.57
1988	4389	6.817765	TTTGCTTATAGGAACCAACTTCTG	57.182	37.500	0.00	0.00	0.00	3.02
2023	4424	7.550712	ACTTATGTTCGGTAAAAGGGTACTAG	58.449	38.462	0.00	0.00	0.00	2.57
2024	4425	7.480760	ACTTATGTTCGGTAAAAGGGTACTA	57.519	36.000	0.00	0.00	0.00	1.82
2030	4431	9.550811	GAATTGTAACTTATGTTCGGTAAAAGG	57.449	33.333	0.00	0.00	37.59	3.11
2037	4443	9.840427	AAATTCAGAATTGTAACTTATGTTCGG	57.160	29.630	9.24	0.00	37.59	4.30
2103	4509	1.202770	GCCAGGTCAACAACTACAGGT	60.203	52.381	0.00	0.00	0.00	4.00
2161	4567	1.071605	CCTACAAGCAGAACAGTCGC	58.928	55.000	0.00	0.00	0.00	5.19
2170	4576	2.568623	AGTCCAAACCCTACAAGCAG	57.431	50.000	0.00	0.00	0.00	4.24
2225	4631	6.706270	GTCTCAGGTCACAAACTTCTGAATTA	59.294	38.462	0.00	0.00	34.58	1.40
2235	4641	0.531974	TGCCGTCTCAGGTCACAAAC	60.532	55.000	0.00	0.00	0.00	2.93
2244	4650	5.183014	TGTACATAATACTGCCGTCTCAG	57.817	43.478	0.00	0.00	39.86	3.35
2252	4658	6.703607	AGATGCAGAACTGTACATAATACTGC	59.296	38.462	21.91	21.91	46.07	4.40
2276	4682	3.802948	AGTTCGTTACTGCTATCCCAG	57.197	47.619	0.00	0.00	35.19	4.45
2338	4757	1.068885	CAATTGCCGCGGTTAAACAGA	60.069	47.619	28.70	6.98	0.00	3.41
2428	4849	7.195374	TCTTGCTACCCATACTTAATTGTCT	57.805	36.000	0.00	0.00	0.00	3.41
2429	4850	9.726438	ATATCTTGCTACCCATACTTAATTGTC	57.274	33.333	0.00	0.00	0.00	3.18

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.