AutoCloner

Multiple sequence alignment - TraesCS2D01G387100

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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	TraesCS2D01G387100	chr2D	100.000	4639	0	0	1	4639	492513011	492508373	0.000000e+00	8567.0
1	TraesCS2D01G387100	chr2D	100.000	211	0	0	4961	5171	492508051	492507841	1.750000e-104	390.0
2	TraesCS2D01G387100	chr2B	92.958	4729	150	73	13	4639	578140814	578136167	0.000000e+00	6719.0
3	TraesCS2D01G387100	chr2B	84.921	126	3	4	5021	5146	578136104	578135995	4.230000e-21	113.0
4	TraesCS2D01G387100	chr2A	92.697	4368	132	62	380	4623	637681893	637677589	0.000000e+00	6126.0
5	TraesCS2D01G387100	chr2A	94.079	304	10	4	1	298	637682235	637681934	6.100000e-124	455.0
6	TraesCS2D01G387100	chr2A	91.324	219	10	5	4961	5171	637677555	637677338	1.820000e-74	291.0
7	TraesCS2D01G387100	chr2A	97.222	36	0	1	3253	3287	5186744	5186709	5.590000e-05	60.2
8	TraesCS2D01G387100	chr6B	94.004	517	15	7	3483	3993	505256916	505256410	0.000000e+00	769.0
9	TraesCS2D01G387100	chr6B	82.431	831	117	21	2204	3015	162546061	162546881	0.000000e+00	699.0
10	TraesCS2D01G387100	chr6B	84.839	310	41	6	3271	3577	512873515	512873821	1.810000e-79	307.0
11	TraesCS2D01G387100	chr6B	88.889	162	18	0	2204	2365	512872811	512872972	3.160000e-47	200.0
12	TraesCS2D01G387100	chr6B	86.076	158	20	2	1195	1351	162545860	162546016	8.900000e-38	169.0
13	TraesCS2D01G387100	chr5D	93.617	517	25	4	2517	3029	378325608	378326120	0.000000e+00	765.0
14	TraesCS2D01G387100	chr5D	93.686	491	23	5	3535	4023	378333758	378334242	0.000000e+00	728.0
15	TraesCS2D01G387100	chr6A	82.987	817	109	19	2201	2991	103264074	103264886	0.000000e+00	712.0
16	TraesCS2D01G387100	chr6A	85.577	312	37	6	3267	3577	450465277	450464973	2.320000e-83	320.0
17	TraesCS2D01G387100	chr6A	86.957	184	22	2	2204	2386	450465983	450465801	6.790000e-49	206.0
18	TraesCS2D01G387100	chr6D	82.416	836	103	27	2201	3015	85906197	85907009	0.000000e+00	689.0
19	TraesCS2D01G387100	chr6D	85.852	311	36	6	3268	3577	313281989	313281686	1.800000e-84	324.0
20	TraesCS2D01G387100	chr6D	89.506	162	17	0	2204	2365	313282693	313282532	6.790000e-49	206.0
21	TraesCS2D01G387100	chr6D	85.119	168	24	1	1195	1362	85906000	85906166	2.480000e-38	171.0
22	TraesCS2D01G387100	chr1D	87.455	279	35	0	3297	3575	231465068	231464790	6.460000e-84	322.0
23	TraesCS2D01G387100	chr1D	85.350	157	23	0	2204	2360	231466170	231466014	4.140000e-36	163.0
24	TraesCS2D01G387100	chr1D	88.235	102	10	2	2812	2912	263200582	263200682	2.530000e-23	121.0
25	TraesCS2D01G387100	chr1D	97.222	36	1	0	3253	3288	263200727	263200762	1.550000e-05	62.1
26	TraesCS2D01G387100	chr1B	86.806	288	38	0	3288	3575	365021471	365021758	6.460000e-84	322.0
27	TraesCS2D01G387100	chr1B	84.713	157	22	2	2204	2359	365020390	365020545	6.930000e-34	156.0
28	TraesCS2D01G387100	chr1A	86.458	288	39	0	3288	3575	317813374	317813661	3.010000e-82	316.0
29	TraesCS2D01G387100	chr1A	85.897	156	22	0	2204	2359	317812284	317812439	3.200000e-37	167.0
30	TraesCS2D01G387100	chr4B	86.268	284	36	3	3289	3570	671632088	671631806	6.510000e-79	305.0
31	TraesCS2D01G387100	chr4B	77.500	240	46	7	2718	2953	671632643	671632408	2.510000e-28	137.0
32	TraesCS2D01G387100	chrUn	77.500	240	46	7	2718	2953	28396399	28396634	2.510000e-28	137.0
33	TraesCS2D01G387100	chrUn	97.222	36	1	0	3253	3288	431347004	431346969	1.550000e-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	TraesCS2D01G387100	chr2D	492507841	492513011	5170	True	4478.500000	8567	100.0000	1	5171	2	chr2D.!!$R1	5170
1	TraesCS2D01G387100	chr2B	578135995	578140814	4819	True	3416.000000	6719	88.9395	13	5146	2	chr2B.!!$R1	5133
2	TraesCS2D01G387100	chr2A	637677338	637682235	4897	True	2290.666667	6126	92.7000	1	5171	3	chr2A.!!$R2	5170
3	TraesCS2D01G387100	chr6B	505256410	505256916	506	True	769.000000	769	94.0040	3483	3993	1	chr6B.!!$R1	510
4	TraesCS2D01G387100	chr6B	162545860	162546881	1021	False	434.000000	699	84.2535	1195	3015	2	chr6B.!!$F1	1820
5	TraesCS2D01G387100	chr6B	512872811	512873821	1010	False	253.500000	307	86.8640	2204	3577	2	chr6B.!!$F2	1373
6	TraesCS2D01G387100	chr5D	378325608	378326120	512	False	765.000000	765	93.6170	2517	3029	1	chr5D.!!$F1	512
7	TraesCS2D01G387100	chr6A	103264074	103264886	812	False	712.000000	712	82.9870	2201	2991	1	chr6A.!!$F1	790
8	TraesCS2D01G387100	chr6A	450464973	450465983	1010	True	263.000000	320	86.2670	2204	3577	2	chr6A.!!$R1	1373
9	TraesCS2D01G387100	chr6D	85906000	85907009	1009	False	430.000000	689	83.7675	1195	3015	2	chr6D.!!$F1	1820
10	TraesCS2D01G387100	chr6D	313281686	313282693	1007	True	265.000000	324	87.6790	2204	3577	2	chr6D.!!$R1	1373
11	TraesCS2D01G387100	chr1D	231464790	231466170	1380	True	242.500000	322	86.4025	2204	3575	2	chr1D.!!$R1	1371
12	TraesCS2D01G387100	chr1B	365020390	365021758	1368	False	239.000000	322	85.7595	2204	3575	2	chr1B.!!$F1	1371
13	TraesCS2D01G387100	chr1A	317812284	317813661	1377	False	241.500000	316	86.1775	2204	3575	2	chr1A.!!$F1	1371
14	TraesCS2D01G387100	chr4B	671631806	671632643	837	True	221.000000	305	81.8840	2718	3570	2	chr4B.!!$R1	852

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
305	320	0.234884	GGCGCACACAAACTCTACAC	59.765	55.0	10.83	0.00	0.00	2.90	F
1483	1596	0.031817	CTTGGGCATGATTTCCCCCT	60.032	55.0	0.00	0.00	41.92	4.79	F
1534	1659	0.179129	GCGCTGGTTGGAATGGAATG	60.179	55.0	0.00	0.00	0.00	2.67	F
2344	2537	0.249398	GCTACCGCTTCTTCCAGGAA	59.751	55.0	0.71	0.71	0.00	3.36	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1993	2149	0.108424	CAAGGAGAGGCAAGGACGAG	60.108	60.000	0.00	0.00	0.00	4.18	R
2395	2624	4.988598	ACGACCAGCGGCAAGTGG	62.989	66.667	1.45	3.71	46.49	4.00	R
3771	4345	4.308458	CCAGGTCGAACGTGGCCA	62.308	66.667	0.00	0.00	45.60	5.36	R
4242	4820	0.320374	GGTGACTCGGTGATGGTGAA	59.680	55.000	0.00	0.00	0.00	3.18	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
110	113	2.725641	CACACGTGTCCGGTGAGA	59.274	61.111	20.49	0.00	37.41	3.27
209	216	7.449247	GCTCATTAATCTCCCCATATCTATCC	58.551	42.308	0.00	0.00	0.00	2.59
298	313	3.632107	TCGTCGGCGCACACAAAC	61.632	61.111	10.83	0.00	38.14	2.93
302	317	0.942410	GTCGGCGCACACAAACTCTA	60.942	55.000	10.83	0.00	0.00	2.43
305	320	0.234884	GGCGCACACAAACTCTACAC	59.765	55.000	10.83	0.00	0.00	2.90
307	322	1.070577	GCGCACACAAACTCTACACAG	60.071	52.381	0.30	0.00	0.00	3.66
308	323	2.201732	CGCACACAAACTCTACACAGT	58.798	47.619	0.00	0.00	0.00	3.55
310	325	3.425525	CGCACACAAACTCTACACAGTAG	59.574	47.826	0.00	0.00	0.00	2.57
311	326	4.369182	GCACACAAACTCTACACAGTAGT	58.631	43.478	4.30	0.00	0.00	2.73
313	328	5.401674	GCACACAAACTCTACACAGTAGTAC	59.598	44.000	4.30	0.00	0.00	2.73
316	331	5.624081	CACAAACTCTACACAGTAGTACACG	59.376	44.000	2.52	0.00	0.00	4.49
317	332	5.152097	CAAACTCTACACAGTAGTACACGG	58.848	45.833	2.52	0.00	0.00	4.94
318	333	4.013267	ACTCTACACAGTAGTACACGGT	57.987	45.455	2.52	0.00	35.80	4.83
319	334	5.152623	ACTCTACACAGTAGTACACGGTA	57.847	43.478	2.52	1.09	33.43	4.02
320	335	5.738909	ACTCTACACAGTAGTACACGGTAT	58.261	41.667	2.52	0.00	33.43	2.73
321	336	5.814705	ACTCTACACAGTAGTACACGGTATC	59.185	44.000	2.52	0.00	33.43	2.24
322	337	4.805719	TCTACACAGTAGTACACGGTATCG	59.194	45.833	2.52	0.00	43.02	2.92
323	338	2.679837	ACACAGTAGTACACGGTATCGG	59.320	50.000	0.00	0.00	41.39	4.18
324	339	2.679837	CACAGTAGTACACGGTATCGGT	59.320	50.000	0.00	0.00	41.39	4.69
325	340	2.679837	ACAGTAGTACACGGTATCGGTG	59.320	50.000	0.00	0.00	41.39	4.94
327	342	1.672881	GTAGTACACGGTATCGGTGCT	59.327	52.381	0.00	6.59	41.39	4.40
328	343	0.737219	AGTACACGGTATCGGTGCTC	59.263	55.000	0.00	0.00	41.39	4.26
329	344	0.590732	GTACACGGTATCGGTGCTCG	60.591	60.000	0.00	0.00	41.39	5.03
330	345	1.026182	TACACGGTATCGGTGCTCGT	61.026	55.000	0.00	0.00	41.39	4.18
331	346	1.026182	ACACGGTATCGGTGCTCGTA	61.026	55.000	0.00	0.00	41.39	3.43
332	347	0.309922	CACGGTATCGGTGCTCGTAT	59.690	55.000	0.00	0.00	41.39	3.06
344	359	4.614946	GGTGCTCGTATTCGTATACCTTT	58.385	43.478	6.61	0.00	34.37	3.11
346	361	4.046462	TGCTCGTATTCGTATACCTTTGC	58.954	43.478	6.61	6.54	34.37	3.68
347	362	4.202080	TGCTCGTATTCGTATACCTTTGCT	60.202	41.667	6.61	0.00	34.37	3.91
348	363	4.148348	GCTCGTATTCGTATACCTTTGCTG	59.852	45.833	6.61	0.00	34.37	4.41
349	364	4.046462	TCGTATTCGTATACCTTTGCTGC	58.954	43.478	6.61	0.00	34.37	5.25
350	365	4.049186	CGTATTCGTATACCTTTGCTGCT	58.951	43.478	6.61	0.00	34.37	4.24
351	366	4.085055	CGTATTCGTATACCTTTGCTGCTG	60.085	45.833	6.61	0.00	34.37	4.41
352	367	3.603158	TTCGTATACCTTTGCTGCTGA	57.397	42.857	0.00	0.00	0.00	4.26
353	368	3.165058	TCGTATACCTTTGCTGCTGAG	57.835	47.619	0.00	0.00	0.00	3.35
354	369	2.496070	TCGTATACCTTTGCTGCTGAGT	59.504	45.455	0.00	0.00	0.00	3.41
355	370	3.697542	TCGTATACCTTTGCTGCTGAGTA	59.302	43.478	0.00	0.00	0.00	2.59
356	371	3.797256	CGTATACCTTTGCTGCTGAGTAC	59.203	47.826	0.00	0.00	0.00	2.73
358	373	0.393077	ACCTTTGCTGCTGAGTACGT	59.607	50.000	0.00	0.00	0.00	3.57
360	375	2.233922	ACCTTTGCTGCTGAGTACGTAT	59.766	45.455	0.00	0.00	0.00	3.06
361	376	3.262420	CCTTTGCTGCTGAGTACGTATT	58.738	45.455	0.00	0.00	0.00	1.89
362	377	3.684788	CCTTTGCTGCTGAGTACGTATTT	59.315	43.478	0.00	0.00	0.00	1.40
363	378	4.201724	CCTTTGCTGCTGAGTACGTATTTC	60.202	45.833	0.00	0.65	0.00	2.17
377	392	1.976045	GTATTTCGTTTGGTTGCGCTG	59.024	47.619	9.73	0.00	0.00	5.18
378	393	0.318614	ATTTCGTTTGGTTGCGCTGG	60.319	50.000	9.73	0.00	0.00	4.85
624	680	2.334653	CTCTCGCTCGCTCCCATC	59.665	66.667	0.00	0.00	0.00	3.51
625	681	3.206211	CTCTCGCTCGCTCCCATCC	62.206	68.421	0.00	0.00	0.00	3.51
626	682	4.292178	CTCGCTCGCTCCCATCCC	62.292	72.222	0.00	0.00	0.00	3.85
635	691	4.172232	TCCCATCCCCTCCCCTCG	62.172	72.222	0.00	0.00	0.00	4.63
814	885	2.558359	GAGAGGAAGGAGATGAGCTAGC	59.442	54.545	6.62	6.62	0.00	3.42
858	933	5.934402	TTCCCTACAATTCACTAGTCCTC	57.066	43.478	0.00	0.00	0.00	3.71
902	977	0.250727	TTCTACAGCCAACCACCTGC	60.251	55.000	0.00	0.00	32.37	4.85
932	1007	3.243975	ACAGATTTTGCCTTCCTTTGCTG	60.244	43.478	0.00	0.00	0.00	4.41
944	1019	0.539438	CTTTGCTGGCTTGGTACCCA	60.539	55.000	10.07	0.00	0.00	4.51
984	1070	2.904866	GTTCAAGGCGGTGGTGCA	60.905	61.111	0.00	0.00	36.28	4.57
1156	1254	1.966972	CAGCAGCAGCAGCAGAACT	60.967	57.895	12.92	0.00	45.49	3.01
1402	1515	3.090037	TCCAGGTAAGAAAGAGGTCGAG	58.910	50.000	0.00	0.00	0.00	4.04
1412	1525	7.479897	AAGAAAGAGGTCGAGAAAGTAAAAC	57.520	36.000	0.00	0.00	0.00	2.43
1432	1545	0.869068	CGCACGGTAATTTCCACACA	59.131	50.000	1.75	0.00	0.00	3.72
1454	1567	1.790090	TTTCGCAATTCACCGCAGCA	61.790	50.000	0.00	0.00	0.00	4.41
1483	1596	0.031817	CTTGGGCATGATTTCCCCCT	60.032	55.000	0.00	0.00	41.92	4.79
1534	1659	0.179129	GCGCTGGTTGGAATGGAATG	60.179	55.000	0.00	0.00	0.00	2.67
1535	1660	0.457035	CGCTGGTTGGAATGGAATGG	59.543	55.000	0.00	0.00	0.00	3.16
1536	1661	0.826062	GCTGGTTGGAATGGAATGGG	59.174	55.000	0.00	0.00	0.00	4.00
1537	1662	1.619432	GCTGGTTGGAATGGAATGGGA	60.619	52.381	0.00	0.00	0.00	4.37
1538	1663	2.956385	GCTGGTTGGAATGGAATGGGAT	60.956	50.000	0.00	0.00	0.00	3.85
1543	1668	2.749600	TGGAATGGAATGGGATGGTTG	58.250	47.619	0.00	0.00	0.00	3.77
1583	1708	1.434555	TATGCGCGCTTGTTGTTACT	58.565	45.000	33.29	6.14	0.00	2.24
1587	1712	1.081442	GCGCTTGTTGTTACTGCCC	60.081	57.895	0.00	0.00	0.00	5.36
1608	1733	1.523095	GCGATTCTCCTCGAATTTCCG	59.477	52.381	0.00	0.00	42.31	4.30
1678	1803	1.380112	GAGGCCGTGGAGTAGGAGT	60.380	63.158	0.00	0.00	0.00	3.85
1882	2036	4.672899	TCTTTGTTTATTTCCCTCCCCAG	58.327	43.478	0.00	0.00	0.00	4.45
1949	2105	1.077716	AGATGGCCTGCGGTTAACC	60.078	57.895	15.13	15.13	0.00	2.85
1957	2113	0.450184	CTGCGGTTAACCAATTCCCG	59.550	55.000	24.14	9.58	41.50	5.14
1992	2148	1.076339	CCTTCCTCGCCCTCTCTCT	60.076	63.158	0.00	0.00	0.00	3.10
1993	2149	1.106944	CCTTCCTCGCCCTCTCTCTC	61.107	65.000	0.00	0.00	0.00	3.20
2002	2158	1.388547	CCCTCTCTCTCTCGTCCTTG	58.611	60.000	0.00	0.00	0.00	3.61
2049	2205	3.997681	CCGGAGAGGAAGAAAAAGAGAAC	59.002	47.826	0.00	0.00	45.00	3.01
2150	2327	5.419788	TCCAGTCCTTTGATTGATTGATTGG	59.580	40.000	0.00	0.00	32.66	3.16
2194	2375	4.143052	CGCGAGTAATTAACCTTCCGTTTT	60.143	41.667	0.00	0.00	35.79	2.43
2344	2537	0.249398	GCTACCGCTTCTTCCAGGAA	59.751	55.000	0.71	0.71	0.00	3.36
2395	2624	3.432588	CAGCAGCAGCAGCAGGAC	61.433	66.667	12.92	0.00	45.49	3.85
3043	3497	4.394712	CGACAGCACCTCCCACCC	62.395	72.222	0.00	0.00	0.00	4.61
3165	3673	3.836176	AAACGACGCGCGAAGAGGT	62.836	57.895	39.36	21.73	44.57	3.85
3771	4345	2.809601	GCAGACAACGCCGACGAT	60.810	61.111	0.00	0.00	43.93	3.73
4074	4650	1.971695	GTTCCAGAGGCCAAACCCG	60.972	63.158	5.01	0.00	40.58	5.28
4212	4790	2.237143	TCAGCATACTTCCAGTTCCAGG	59.763	50.000	0.00	0.00	0.00	4.45
4239	4817	3.845781	ATAACCTCGAAGCATCACCAT	57.154	42.857	0.00	0.00	0.00	3.55
4242	4820	1.487976	ACCTCGAAGCATCACCATCAT	59.512	47.619	0.00	0.00	0.00	2.45
4305	4883	0.712222	CGATCATCGCCATCACATCG	59.288	55.000	0.00	0.00	31.14	3.84
4991	5594	5.403166	TCGTTACAGTGTATACTTTGTGTGC	59.597	40.000	17.57	9.75	34.07	4.57
5030	5634	3.243602	GCGGGAACTTTGTGTGGTTATTT	60.244	43.478	0.00	0.00	0.00	1.40
5138	5749	6.658816	TGCCAATATGACTTTTCTTAAGCTCA	59.341	34.615	0.00	0.00	0.00	4.26
5145	5756	6.588204	TGACTTTTCTTAAGCTCAGGTGTTA	58.412	36.000	0.00	0.00	0.00	2.41

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
110	113	4.052518	GCCTGCATGGGGTGAGGT	62.053	66.667	0.00	0.00	36.00	3.85
298	313	5.051173	CGATACCGTGTACTACTGTGTAGAG	60.051	48.000	11.17	0.00	0.00	2.43
302	317	2.679837	CCGATACCGTGTACTACTGTGT	59.320	50.000	0.00	0.00	0.00	3.72
305	320	2.540361	GCACCGATACCGTGTACTACTG	60.540	54.545	0.00	0.00	0.00	2.74
307	322	1.672881	AGCACCGATACCGTGTACTAC	59.327	52.381	0.00	0.00	0.00	2.73
308	323	1.942657	GAGCACCGATACCGTGTACTA	59.057	52.381	0.00	0.00	0.00	1.82
310	325	0.590732	CGAGCACCGATACCGTGTAC	60.591	60.000	0.00	0.00	41.76	2.90
311	326	1.026182	ACGAGCACCGATACCGTGTA	61.026	55.000	5.53	0.00	41.76	2.90
313	328	0.309922	ATACGAGCACCGATACCGTG	59.690	55.000	5.53	0.00	41.76	4.94
316	331	1.002033	ACGAATACGAGCACCGATACC	60.002	52.381	5.53	0.00	42.66	2.73
317	332	2.396160	ACGAATACGAGCACCGATAC	57.604	50.000	5.53	0.00	42.66	2.24
318	333	4.093408	GGTATACGAATACGAGCACCGATA	59.907	45.833	5.53	0.00	39.16	2.92
319	334	3.120060	GGTATACGAATACGAGCACCGAT	60.120	47.826	5.53	0.00	39.16	4.18
320	335	2.224079	GGTATACGAATACGAGCACCGA	59.776	50.000	5.53	0.00	39.16	4.69
321	336	2.225019	AGGTATACGAATACGAGCACCG	59.775	50.000	0.00	0.00	39.16	4.94
322	337	3.911661	AGGTATACGAATACGAGCACC	57.088	47.619	0.00	0.00	39.16	5.01
323	338	4.085210	GCAAAGGTATACGAATACGAGCAC	60.085	45.833	0.00	0.00	39.16	4.40
324	339	4.046462	GCAAAGGTATACGAATACGAGCA	58.954	43.478	0.00	0.00	39.16	4.26
325	340	4.148348	CAGCAAAGGTATACGAATACGAGC	59.852	45.833	0.00	0.00	39.16	5.03
327	342	4.046462	GCAGCAAAGGTATACGAATACGA	58.954	43.478	0.00	0.00	39.16	3.43
328	343	4.049186	AGCAGCAAAGGTATACGAATACG	58.951	43.478	0.00	0.00	39.16	3.06
329	344	5.047847	TCAGCAGCAAAGGTATACGAATAC	58.952	41.667	0.00	0.00	37.78	1.89
330	345	5.163447	ACTCAGCAGCAAAGGTATACGAATA	60.163	40.000	0.00	0.00	0.00	1.75
331	346	4.122776	CTCAGCAGCAAAGGTATACGAAT	58.877	43.478	0.00	0.00	0.00	3.34
332	347	3.056107	ACTCAGCAGCAAAGGTATACGAA	60.056	43.478	0.00	0.00	0.00	3.85
344	359	2.526077	CGAAATACGTACTCAGCAGCA	58.474	47.619	0.00	0.00	37.22	4.41
358	373	1.068885	CCAGCGCAACCAAACGAAATA	60.069	47.619	11.47	0.00	0.00	1.40
360	375	1.064946	CCAGCGCAACCAAACGAAA	59.935	52.632	11.47	0.00	0.00	3.46
361	376	2.718731	CCAGCGCAACCAAACGAA	59.281	55.556	11.47	0.00	0.00	3.85
362	377	3.283684	CCCAGCGCAACCAAACGA	61.284	61.111	11.47	0.00	0.00	3.85
363	378	4.341502	CCCCAGCGCAACCAAACG	62.342	66.667	11.47	0.00	0.00	3.60
377	392	0.256177	GATCTCCCACCAAGAACCCC	59.744	60.000	0.00	0.00	0.00	4.95
378	393	0.107654	CGATCTCCCACCAAGAACCC	60.108	60.000	0.00	0.00	0.00	4.11
591	647	2.675348	CGAGAGGATGGTGAAAAAGAGC	59.325	50.000	0.00	0.00	0.00	4.09
814	885	0.901580	AATTGTGGCTTCTGGGCTGG	60.902	55.000	0.00	0.00	41.48	4.85
825	900	6.756542	GTGAATTGTAGGGAATTAATTGTGGC	59.243	38.462	5.17	0.00	0.00	5.01
902	977	4.418392	GAAGGCAAAATCTGTATGTGCAG	58.582	43.478	0.00	0.00	36.93	4.41
944	1019	1.021390	CGCTCTCAAATTGTCCGGCT	61.021	55.000	0.00	0.00	0.00	5.52
984	1070	1.282738	TGCATGGATGATGACACCACT	59.717	47.619	0.00	0.00	36.49	4.00
989	1075	1.675552	CTGCTGCATGGATGATGACA	58.324	50.000	1.31	0.00	33.31	3.58
991	1077	0.106918	TGCTGCTGCATGGATGATGA	60.107	50.000	14.93	0.00	45.31	2.92
1140	1238	2.868920	GAGTTCTGCTGCTGCTGC	59.131	61.111	22.51	22.51	40.48	5.25
1212	1313	3.060000	AGCATGTCGTCGTCGGGA	61.060	61.111	1.55	0.00	37.69	5.14
1412	1525	0.167251	GTGTGGAAATTACCGTGCGG	59.833	55.000	9.29	9.29	42.03	5.69
1432	1545	0.595588	TGCGGTGAATTGCGAAATGT	59.404	45.000	0.00	0.00	0.00	2.71
1454	1567	1.005097	TCATGCCCAAGACAAGATGCT	59.995	47.619	0.00	0.00	0.00	3.79
1483	1596	3.109547	CCGTTAGTCGCTTGCGCA	61.110	61.111	5.66	5.66	38.35	6.09
1493	1613	4.152938	GCTAAATTCCACGAAACCGTTAGT	59.847	41.667	0.00	0.00	38.35	2.24
1534	1659	2.496871	TCATTTCATGTGCAACCATCCC	59.503	45.455	0.00	0.00	34.36	3.85
1535	1660	3.872511	TCATTTCATGTGCAACCATCC	57.127	42.857	0.00	0.00	34.36	3.51
1536	1661	4.116961	CCATCATTTCATGTGCAACCATC	58.883	43.478	0.00	0.00	34.36	3.51
1537	1662	3.680475	GCCATCATTTCATGTGCAACCAT	60.680	43.478	0.00	0.00	34.36	3.55
1538	1663	2.353903	GCCATCATTTCATGTGCAACCA	60.354	45.455	0.00	0.00	34.36	3.67
1543	1668	2.565210	TTCGCCATCATTTCATGTGC	57.435	45.000	0.00	0.00	0.00	4.57
1560	1685	1.895051	ACAACAAGCGCGCATAATTC	58.105	45.000	35.10	0.72	0.00	2.17
1571	1696	1.081442	GCGGGCAGTAACAACAAGC	60.081	57.895	0.00	0.00	0.00	4.01
1583	1708	4.207281	CGAGGAGAATCGCGGGCA	62.207	66.667	6.13	0.00	35.66	5.36
1608	1733	1.344438	CCAGGAAAGGCAAGGAAAACC	59.656	52.381	0.00	0.00	0.00	3.27
1678	1803	0.184451	CCCTACGCCTACCACTCCTA	59.816	60.000	0.00	0.00	0.00	2.94
1786	1928	5.064579	CCCAAAAACTGAAAGCGAAAAACAT	59.935	36.000	0.00	0.00	37.60	2.71
1949	2105	3.189287	GCATATAGGCAGAACGGGAATTG	59.811	47.826	4.13	0.00	0.00	2.32
1957	2113	4.068599	GGAAGGAAGCATATAGGCAGAAC	58.931	47.826	12.54	0.00	35.83	3.01
1992	2148	0.251832	AAGGAGAGGCAAGGACGAGA	60.252	55.000	0.00	0.00	0.00	4.04
1993	2149	0.108424	CAAGGAGAGGCAAGGACGAG	60.108	60.000	0.00	0.00	0.00	4.18
2002	2158	1.273886	ACGAAAGAGACAAGGAGAGGC	59.726	52.381	0.00	0.00	0.00	4.70
2049	2205	1.083401	GAAGCTTCGCGTGTGTGTG	60.083	57.895	11.40	0.00	0.00	3.82
2194	2375	2.430465	GCAAGCTTCCTGAGATCACAA	58.570	47.619	0.00	0.00	0.00	3.33
2395	2624	4.988598	ACGACCAGCGGCAAGTGG	62.989	66.667	1.45	3.71	46.49	4.00
3771	4345	4.308458	CCAGGTCGAACGTGGCCA	62.308	66.667	0.00	0.00	45.60	5.36
4074	4650	2.258286	GCATTGTTGGTGCCGACC	59.742	61.111	6.17	0.00	43.48	4.79
4212	4790	2.346803	TGCTTCGAGGTTATTGTCTGC	58.653	47.619	0.00	0.00	0.00	4.26
4239	4817	1.899142	TGACTCGGTGATGGTGAATGA	59.101	47.619	0.00	0.00	0.00	2.57
4242	4820	0.320374	GGTGACTCGGTGATGGTGAA	59.680	55.000	0.00	0.00	0.00	3.18
4305	4883	3.179265	CGTCGTCGGTGATGGTGC	61.179	66.667	0.00	0.00	0.00	5.01
4968	5571	5.389098	GGCACACAAAGTATACACTGTAACG	60.389	44.000	5.50	0.00	34.36	3.18
5005	5609	0.673437	CCACACAAAGTTCCCGCAAT	59.327	50.000	0.00	0.00	0.00	3.56
5030	5634	7.894708	ACCAAAAACATGTGAACATATGATCA	58.105	30.769	11.32	11.32	34.26	2.92
5138	5749	7.568349	TGATGAGCTCATAATTTCTAACACCT	58.432	34.615	28.78	1.75	36.57	4.00

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.