AutoCloner

Multiple sequence alignment - TraesCS5D01G212400

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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	TraesCS5D01G212400	chr5D	100.000	2681	0	0	1466	4146	321669825	321672505	0.000000e+00	4951.0
1	TraesCS5D01G212400	chr5D	100.000	1146	0	0	1	1146	321668360	321669505	0.000000e+00	2117.0
2	TraesCS5D01G212400	chr5D	78.571	1050	180	31	1626	2652	321369498	321370525	0.000000e+00	651.0
3	TraesCS5D01G212400	chr5D	91.573	178	11	4	140	314	283106541	283106717	4.140000e-60	243.0
4	TraesCS5D01G212400	chr5D	83.908	174	13	4	440	610	493584099	493584260	7.180000e-33	152.0
5	TraesCS5D01G212400	chr5B	94.581	2676	101	17	1486	4143	372567063	372569712	0.000000e+00	4098.0
6	TraesCS5D01G212400	chr5B	79.356	1056	173	35	1622	2656	372158835	372159866	0.000000e+00	701.0
7	TraesCS5D01G212400	chr5B	94.505	91	1	4	948	1038	372566442	372566528	2.010000e-28	137.0
8	TraesCS5D01G212400	chr5B	100.000	28	0	0	3254	3281	228304629	228304656	7.000000e-03	52.8
9	TraesCS5D01G212400	chr5A	93.904	1903	64	26	1466	3340	416180831	416182709	0.000000e+00	2824.0
10	TraesCS5D01G212400	chr5A	87.407	810	51	12	3339	4146	416182766	416183526	0.000000e+00	883.0
11	TraesCS5D01G212400	chr5A	86.473	207	12	9	956	1146	416180611	416180817	3.250000e-51	213.0
12	TraesCS5D01G212400	chr5A	89.565	115	12	0	1622	1736	413240674	413240560	3.340000e-31	147.0
13	TraesCS5D01G212400	chr7D	87.638	542	46	9	39	560	612933124	612933664	9.850000e-171	610.0
14	TraesCS5D01G212400	chr7D	88.530	279	28	3	558	833	612933917	612934194	6.640000e-88	335.0
15	TraesCS5D01G212400	chr7D	81.356	118	14	8	3664	3776	267971470	267971356	5.710000e-14	89.8
16	TraesCS5D01G212400	chr1B	86.011	529	66	8	423	948	332007162	332006639	1.010000e-155	560.0
17	TraesCS5D01G212400	chr1B	84.708	497	58	11	440	928	129142501	129142015	8.060000e-132	481.0
18	TraesCS5D01G212400	chr1B	84.322	236	20	4	39	258	332007396	332007162	9.030000e-52	215.0
19	TraesCS5D01G212400	chr4B	84.674	522	54	15	440	948	621964958	621965466	8.000000e-137	497.0
20	TraesCS5D01G212400	chr4B	100.000	28	0	0	3254	3281	204926696	204926723	7.000000e-03	52.8
21	TraesCS5D01G212400	chr7A	84.096	459	49	15	9	449	151379196	151378744	4.960000e-114	422.0
22	TraesCS5D01G212400	chr7A	84.651	430	47	11	534	953	151378741	151378321	1.070000e-110	411.0
23	TraesCS5D01G212400	chr7A	80.674	564	80	18	323	869	526792810	526792259	1.070000e-110	411.0
24	TraesCS5D01G212400	chr7A	83.636	110	10	8	3664	3768	539238904	539238798	3.410000e-16	97.1
25	TraesCS5D01G212400	chr7A	78.378	148	21	11	3664	3806	460451529	460451670	7.380000e-13	86.1
26	TraesCS5D01G212400	chr7A	76.875	160	24	12	3664	3816	49700061	49699908	1.240000e-10	78.7
27	TraesCS5D01G212400	chr4D	81.898	453	52	19	24	452	58642469	58642023	5.100000e-94	355.0
28	TraesCS5D01G212400	chr2A	83.333	384	43	9	81	443	89598327	89597944	6.640000e-88	335.0
29	TraesCS5D01G212400	chr2A	85.586	111	13	2	39	147	40008949	40009058	3.390000e-21	113.0
30	TraesCS5D01G212400	chr4A	82.064	407	48	19	534	928	744443713	744444106	1.440000e-84	324.0
31	TraesCS5D01G212400	chr4A	91.011	178	12	4	140	314	6804622	6804798	1.930000e-58	237.0
32	TraesCS5D01G212400	chr2B	81.728	405	52	16	534	928	79360199	79360591	6.690000e-83	318.0
33	TraesCS5D01G212400	chr1D	83.143	350	40	8	71	403	9728830	9728483	6.740000e-78	302.0
34	TraesCS5D01G212400	chr1D	78.652	445	54	14	1	430	46670573	46670155	1.480000e-64	257.0
35	TraesCS5D01G212400	chr1D	83.173	208	19	4	1	192	424136796	424136589	4.260000e-40	176.0
36	TraesCS5D01G212400	chr1D	84.685	111	13	3	39	147	465601035	465600927	1.580000e-19	108.0
37	TraesCS5D01G212400	chrUn	79.625	373	55	15	534	895	41893663	41894025	8.900000e-62	248.0
38	TraesCS5D01G212400	chrUn	87.805	123	14	1	1	122	132135887	132136009	4.320000e-30	143.0
39	TraesCS5D01G212400	chr3D	90.110	182	14	4	140	318	569990913	569990733	2.490000e-57	233.0
40	TraesCS5D01G212400	chr6D	78.142	366	67	13	1857	2214	432810800	432811160	1.940000e-53	220.0
41	TraesCS5D01G212400	chr6D	75.179	419	82	16	1690	2100	432672607	432672203	1.180000e-40	178.0
42	TraesCS5D01G212400	chr6D	84.906	106	13	2	39	142	38515480	38515584	2.040000e-18	104.0
43	TraesCS5D01G212400	chr6D	100.000	28	0	0	3254	3281	125612724	125612751	7.000000e-03	52.8
44	TraesCS5D01G212400	chr6A	75.137	547	95	32	1690	2214	578926132	578926659	6.980000e-53	219.0
45	TraesCS5D01G212400	chr6A	88.108	185	14	8	140	318	96793914	96794096	3.250000e-51	213.0
46	TraesCS5D01G212400	chr6A	75.656	419	80	16	1690	2100	578701595	578701191	5.470000e-44	189.0
47	TraesCS5D01G212400	chr6A	83.636	110	10	8	3664	3768	416378867	416378973	3.410000e-16	97.1
48	TraesCS5D01G212400	chr6A	77.852	149	21	12	3664	3806	52554149	52554291	9.550000e-12	82.4
49	TraesCS5D01G212400	chr6A	100.000	28	0	0	3254	3281	36403653	36403680	7.000000e-03	52.8
50	TraesCS5D01G212400	chr2D	92.806	139	9	1	9	147	309580720	309580857	2.530000e-47	200.0
51	TraesCS5D01G212400	chr2D	73.984	492	106	16	3672	4146	70373419	70372933	3.290000e-41	180.0
52	TraesCS5D01G212400	chr6B	80.000	245	47	2	1857	2100	652522432	652522189	3.290000e-41	180.0
53	TraesCS5D01G212400	chr3A	79.054	148	20	11	3664	3806	225549404	225549545	1.590000e-14	91.6
54	TraesCS5D01G212400	chr1A	80.000	130	17	9	3658	3781	192218012	192218138	2.050000e-13	87.9

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	TraesCS5D01G212400	chr5D	321668360	321672505	4145	False	3534.000000	4951	100.000000	1	4146	2	chr5D.!!$F4	4145
1	TraesCS5D01G212400	chr5D	321369498	321370525	1027	False	651.000000	651	78.571000	1626	2652	1	chr5D.!!$F2	1026
2	TraesCS5D01G212400	chr5B	372566442	372569712	3270	False	2117.500000	4098	94.543000	948	4143	2	chr5B.!!$F3	3195
3	TraesCS5D01G212400	chr5B	372158835	372159866	1031	False	701.000000	701	79.356000	1622	2656	1	chr5B.!!$F2	1034
4	TraesCS5D01G212400	chr5A	416180611	416183526	2915	False	1306.666667	2824	89.261333	956	4146	3	chr5A.!!$F1	3190
5	TraesCS5D01G212400	chr7D	612933124	612934194	1070	False	472.500000	610	88.084000	39	833	2	chr7D.!!$F1	794
6	TraesCS5D01G212400	chr1B	332006639	332007396	757	True	387.500000	560	85.166500	39	948	2	chr1B.!!$R2	909
7	TraesCS5D01G212400	chr4B	621964958	621965466	508	False	497.000000	497	84.674000	440	948	1	chr4B.!!$F2	508
8	TraesCS5D01G212400	chr7A	151378321	151379196	875	True	416.500000	422	84.373500	9	953	2	chr7A.!!$R4	944
9	TraesCS5D01G212400	chr7A	526792259	526792810	551	True	411.000000	411	80.674000	323	869	1	chr7A.!!$R2	546
10	TraesCS5D01G212400	chr6A	578926132	578926659	527	False	219.000000	219	75.137000	1690	2214	1	chr6A.!!$F5	524

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
949	1269	0.325296	AGCTCAGTATCGGGGTCCAA	60.325	55.0	0.0	0.0	0.0	3.53	F
2274	2743	0.617820	ACTGGGACGCCATCTACCTT	60.618	55.0	0.0	0.0	0.0	3.50	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2371	2840	1.150536	GGGTGTCCACAGGAAAGCA	59.849	57.895	7.64	0.0	39.05	3.91	R
3847	4388	0.604243	TTGCAACCGCCGAGTATTGT	60.604	50.000	0.00	0.0	37.32	2.71	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
28	29	7.713764	AACGTTTTTAGTTAAGTCCGTACAT	57.286	32.000	0.00	0.00	0.00	2.29
63	64	9.260002	CAAACATGGCAAACTTCTTTAACTAAT	57.740	29.630	0.00	0.00	0.00	1.73
67	68	9.023967	CATGGCAAACTTCTTTAACTAATATGC	57.976	33.333	0.00	0.00	0.00	3.14
69	71	9.456147	TGGCAAACTTCTTTAACTAATATGCTA	57.544	29.630	0.00	0.00	0.00	3.49
161	180	8.986477	AAACATGGCAACTAAAATCAGTATTC	57.014	30.769	0.00	0.00	37.61	1.75
240	265	2.094026	GTCTTTTTGCCATGTCCATCCC	60.094	50.000	0.00	0.00	0.00	3.85
288	313	5.508200	AATTAGTTTGAGAACACGGCAAA	57.492	34.783	0.00	0.00	38.26	3.68
314	339	5.862811	TGTTCTTTCAAATTTGTTTTGCCG	58.137	33.333	17.47	2.06	43.68	5.69
318	343	3.252974	TCAAATTTGTTTTGCCGTGGT	57.747	38.095	17.47	0.00	43.68	4.16
319	344	3.600388	TCAAATTTGTTTTGCCGTGGTT	58.400	36.364	17.47	0.00	43.68	3.67
321	346	4.806247	TCAAATTTGTTTTGCCGTGGTTAG	59.194	37.500	17.47	0.00	43.68	2.34
336	361	4.326548	CGTGGTTAGAAGTTTCGATCCTTC	59.673	45.833	13.82	13.82	37.85	3.46
337	362	5.235516	GTGGTTAGAAGTTTCGATCCTTCA	58.764	41.667	20.35	8.83	39.61	3.02
354	379	7.520292	CGATCCTTCAAAATTTGTTTTGCCATT	60.520	33.333	5.56	0.00	40.65	3.16
362	387	6.551385	AATTTGTTTTGCCATTGCGATTAA	57.449	29.167	0.00	0.00	41.78	1.40
370	395	3.242903	TGCCATTGCGATTAAATGTACGG	60.243	43.478	0.00	0.00	41.78	4.02
387	412	8.652810	AATGTACGGTATCATTACAACTTACC	57.347	34.615	11.61	0.00	33.32	2.85
437	463	5.578005	TTTCTATGTGTCTAGGGAGAACG	57.422	43.478	0.00	0.00	31.96	3.95
487	524	9.783256	GATGGCAAATTTCGTATAGTAAACTTT	57.217	29.630	0.00	0.00	0.00	2.66
575	872	4.067972	AGTGTAAACTTCGTGGTGATGT	57.932	40.909	0.00	0.00	36.60	3.06
583	880	4.699637	ACTTCGTGGTGATGTCAACTTTA	58.300	39.130	0.00	0.00	33.92	1.85
599	898	9.772973	TGTCAACTTTATGTAGTGTAAAGATGT	57.227	29.630	11.36	0.00	40.19	3.06
661	966	6.577103	TCAAAACATAAACTTGAACATGGCA	58.423	32.000	0.00	0.00	0.00	4.92
734	1043	7.849804	AAGCCAGTGTTTATTAGTCACATAG	57.150	36.000	0.00	0.00	34.94	2.23
756	1065	5.135383	AGAAAAACCGGGCTTTTACTAGTT	58.865	37.500	14.44	0.00	0.00	2.24
771	1080	9.706691	CTTTTACTAGTTGTGACTTAATCTGGA	57.293	33.333	0.00	0.00	37.33	3.86
834	1153	3.881104	GGTGGGTGGGGTGTTCGT	61.881	66.667	0.00	0.00	0.00	3.85
836	1155	2.768769	TGGGTGGGGTGTTCGTGA	60.769	61.111	0.00	0.00	0.00	4.35
880	1200	2.056223	TGGTTCGGACGATCTCCCC	61.056	63.158	0.00	3.18	35.21	4.81
915	1235	3.316760	GTTCGGTCCGGGGGTCTT	61.317	66.667	12.29	0.00	0.00	3.01
928	1248	3.857909	GTCTTCCAGACCGAACGC	58.142	61.111	0.00	0.00	39.28	4.84
933	1253	4.379243	CCAGACCGAACGCCAGCT	62.379	66.667	0.00	0.00	0.00	4.24
935	1255	3.303135	AGACCGAACGCCAGCTCA	61.303	61.111	0.00	0.00	0.00	4.26
936	1256	2.811317	GACCGAACGCCAGCTCAG	60.811	66.667	0.00	0.00	0.00	3.35
949	1269	0.325296	AGCTCAGTATCGGGGTCCAA	60.325	55.000	0.00	0.00	0.00	3.53
1089	1416	0.693430	ATCGACTAAACCCCTCCCCC	60.693	60.000	0.00	0.00	0.00	5.40
1112	1439	1.541672	CCTCCCTCTCCTCTCCTCC	59.458	68.421	0.00	0.00	0.00	4.30
1114	1441	0.998945	CTCCCTCTCCTCTCCTCCCT	60.999	65.000	0.00	0.00	0.00	4.20
1115	1442	0.996762	TCCCTCTCCTCTCCTCCCTC	60.997	65.000	0.00	0.00	0.00	4.30
1119	1446	3.430497	TCCTCTCCTCCCTCCCCG	61.430	72.222	0.00	0.00	0.00	5.73
1783	2234	1.380112	GACTACCTGGTCCTCCGCT	60.380	63.158	0.63	0.00	36.30	5.52
1844	2295	2.045926	CGGAAGCCTGGGGACAAG	60.046	66.667	0.00	0.00	42.06	3.16
2274	2743	0.617820	ACTGGGACGCCATCTACCTT	60.618	55.000	0.00	0.00	0.00	3.50
2371	2840	1.542187	GGTGTACCCTCCGAGCAAGT	61.542	60.000	0.00	0.00	0.00	3.16
2488	2957	2.502213	TCGGCATTATGTCTACACGG	57.498	50.000	0.00	0.00	0.00	4.94
2669	3138	4.511527	TCTGTCTACTGTTCCTACTACCG	58.488	47.826	0.00	0.00	0.00	4.02
2874	3343	6.198237	TGTATCCCTAGTTCCCTACTACTC	57.802	45.833	0.00	0.00	38.33	2.59
2889	3358	4.494091	ACTACTCCATTTGGTGAGGATG	57.506	45.455	5.71	0.00	36.34	3.51
3070	3542	2.477863	GCTGCGTATTCCATTTGGTGAC	60.478	50.000	0.00	0.00	36.34	3.67
3108	3580	5.301555	GGGCAAACCATCTACTCTCTATTC	58.698	45.833	0.00	0.00	39.85	1.75
3422	3962	7.523415	TGGGGTAATTCTTTCTAAGTTTGACT	58.477	34.615	0.00	0.00	0.00	3.41
3530	4070	6.867662	ACTGATTGTGAACACCTAAAAGAG	57.132	37.500	2.46	0.00	0.00	2.85
3534	4074	7.874940	TGATTGTGAACACCTAAAAGAGATTG	58.125	34.615	2.46	0.00	0.00	2.67
3546	4086	9.620259	ACCTAAAAGAGATTGGATGAAGAATAC	57.380	33.333	0.00	0.00	0.00	1.89
3556	4096	5.500234	TGGATGAAGAATACTTTGGTCCAG	58.500	41.667	0.00	0.00	36.86	3.86
3600	4140	9.834628	CGTCTAAACTCTTATAATCAGATCTCC	57.165	37.037	0.00	0.00	0.00	3.71
3626	4166	0.758123	GGCAAGAGATCTCCTCCAGG	59.242	60.000	19.30	4.12	42.97	4.45
3693	4233	7.673926	AGGGAAGTATCACAACCAAAATGTATT	59.326	33.333	0.00	0.00	0.00	1.89
3718	4258	4.381505	GGTCTGACACAAGAAAAGCCAAAA	60.382	41.667	10.38	0.00	0.00	2.44
3719	4259	4.800471	GTCTGACACAAGAAAAGCCAAAAG	59.200	41.667	2.24	0.00	0.00	2.27
3721	4261	5.184864	TCTGACACAAGAAAAGCCAAAAGAA	59.815	36.000	0.00	0.00	0.00	2.52
3722	4262	5.976458	TGACACAAGAAAAGCCAAAAGAAT	58.024	33.333	0.00	0.00	0.00	2.40
3723	4263	7.068103	TCTGACACAAGAAAAGCCAAAAGAATA	59.932	33.333	0.00	0.00	0.00	1.75
3726	4266	8.962884	ACACAAGAAAAGCCAAAAGAATATTT	57.037	26.923	0.00	0.00	0.00	1.40
3760	4301	4.992688	GTTGAGTTGTCAATTCAACCACA	58.007	39.130	29.81	8.46	46.35	4.17
3761	4302	4.630894	TGAGTTGTCAATTCAACCACAC	57.369	40.909	8.22	0.00	45.90	3.82
3762	4303	3.064682	TGAGTTGTCAATTCAACCACACG	59.935	43.478	8.22	0.00	45.90	4.49
3763	4304	3.013921	AGTTGTCAATTCAACCACACGT	58.986	40.909	6.44	0.00	45.90	4.49
3764	4305	3.105203	GTTGTCAATTCAACCACACGTG	58.895	45.455	15.48	15.48	40.97	4.49
3765	4306	2.633488	TGTCAATTCAACCACACGTGA	58.367	42.857	25.01	0.00	0.00	4.35
3766	4307	3.010420	TGTCAATTCAACCACACGTGAA	58.990	40.909	25.01	4.89	0.00	3.18
3767	4308	3.440522	TGTCAATTCAACCACACGTGAAA	59.559	39.130	25.01	6.63	0.00	2.69
3768	4309	4.082733	TGTCAATTCAACCACACGTGAAAA	60.083	37.500	25.01	6.99	0.00	2.29
3769	4310	4.859798	GTCAATTCAACCACACGTGAAAAA	59.140	37.500	25.01	7.69	0.00	1.94
3779	4320	8.476142	CAACCACACGTGAAAAATAAATACTTG	58.524	33.333	25.01	4.22	0.00	3.16
3787	4328	8.629986	CGTGAAAAATAAATACTTGCTTGACAG	58.370	33.333	0.00	0.00	0.00	3.51
3847	4388	0.322322	ATTGCGGTAAGGTGACGGAA	59.678	50.000	0.00	0.00	41.82	4.30
3859	4400	0.457166	TGACGGAACAATACTCGGCG	60.457	55.000	0.00	0.00	32.63	6.46
3920	4461	3.838244	AAAAGCGTAGGCATGAGGATA	57.162	42.857	10.48	0.00	43.41	2.59
3922	4463	2.294449	AGCGTAGGCATGAGGATAGA	57.706	50.000	10.48	0.00	43.41	1.98
3929	4470	6.502652	CGTAGGCATGAGGATAGATAATGAG	58.497	44.000	0.00	0.00	0.00	2.90
3942	4483	7.065563	GGATAGATAATGAGATGTTGCATGGAC	59.934	40.741	0.00	0.00	0.00	4.02
3950	4491	5.529800	TGAGATGTTGCATGGACATAATCAG	59.470	40.000	2.52	0.00	37.83	2.90
3988	4529	5.883673	GGTAGCATAGGGAGATAGTAGTCTG	59.116	48.000	0.00	0.00	0.00	3.51
4009	4550	7.395489	AGTCTGGCTCAAATTCATCAACTTATT	59.605	33.333	0.00	0.00	0.00	1.40
4012	4553	9.859427	CTGGCTCAAATTCATCAACTTATTTAA	57.141	29.630	0.00	0.00	0.00	1.52

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
1	2	5.265477	ACGGACTTAACTAAAAACGTTTGC	58.735	37.500	15.46	0.00	0.00	3.68
2	3	7.397970	TGTACGGACTTAACTAAAAACGTTTG	58.602	34.615	15.46	4.73	34.89	2.93
14	15	7.718272	TGCCATATTTATGTACGGACTTAAC	57.282	36.000	5.65	0.00	31.82	2.01
21	22	6.148948	CCATGTTTGCCATATTTATGTACGG	58.851	40.000	0.00	0.00	30.71	4.02
22	23	5.629020	GCCATGTTTGCCATATTTATGTACG	59.371	40.000	0.00	0.00	30.71	3.67
28	29	6.047511	AGTTTGCCATGTTTGCCATATTTA	57.952	33.333	0.00	0.00	30.71	1.40
32	33	3.577848	AGAAGTTTGCCATGTTTGCCATA	59.422	39.130	0.00	0.00	30.71	2.74
204	225	3.963383	AAAGACACAACGAACCATGAC	57.037	42.857	0.00	0.00	0.00	3.06
240	265	3.947910	AGGCCATGACAAACATTCTTG	57.052	42.857	5.01	0.00	37.07	3.02
314	339	5.235516	TGAAGGATCGAAACTTCTAACCAC	58.764	41.667	24.06	6.23	42.67	4.16
318	343	9.677567	CAAATTTTGAAGGATCGAAACTTCTAA	57.322	29.630	24.06	21.06	40.81	2.10
319	344	8.846211	ACAAATTTTGAAGGATCGAAACTTCTA	58.154	29.630	24.06	17.74	40.81	2.10
321	346	7.930513	ACAAATTTTGAAGGATCGAAACTTC	57.069	32.000	19.70	19.70	40.81	3.01
337	362	4.889832	TCGCAATGGCAAAACAAATTTT	57.110	31.818	0.00	0.00	41.24	1.82
354	379	7.652507	TGTAATGATACCGTACATTTAATCGCA	59.347	33.333	0.00	0.00	37.75	5.10
362	387	8.259411	TGGTAAGTTGTAATGATACCGTACATT	58.741	33.333	0.00	0.00	39.07	2.71
407	433	8.561738	TCCCTAGACACATAGAAAATTTTGAC	57.438	34.615	8.47	0.00	0.00	3.18
568	865	8.542497	TTACACTACATAAAGTTGACATCACC	57.458	34.615	0.00	0.00	0.00	4.02
583	880	5.817816	GGCAAGCTACATCTTTACACTACAT	59.182	40.000	0.00	0.00	0.00	2.29
599	898	3.009473	AGGAAGAAAGTCATGGCAAGCTA	59.991	43.478	0.00	0.00	0.00	3.32
602	901	4.861102	AAAGGAAGAAAGTCATGGCAAG	57.139	40.909	0.00	0.00	0.00	4.01
638	943	6.841443	TGCCATGTTCAAGTTTATGTTTTG	57.159	33.333	0.00	0.00	0.00	2.44
734	1043	5.217393	CAACTAGTAAAAGCCCGGTTTTTC	58.783	41.667	14.59	6.50	31.96	2.29
756	1065	9.349713	ACAAAATAAAGTCCAGATTAAGTCACA	57.650	29.630	0.00	0.00	0.00	3.58
804	1123	1.073706	CCCACCAGGCCCTATAGGT	60.074	63.158	17.72	0.00	38.26	3.08
834	1153	1.378514	GAGGAAAAGCGCCCCATCA	60.379	57.895	2.29	0.00	0.00	3.07
836	1155	2.043953	GGAGGAAAAGCGCCCCAT	60.044	61.111	2.29	0.00	0.00	4.00
880	1200	1.804326	CAACTCGTTCGCTACCGGG	60.804	63.158	6.32	0.00	34.56	5.73
915	1235	4.373116	GCTGGCGTTCGGTCTGGA	62.373	66.667	0.00	0.00	0.00	3.86
928	1248	1.742768	GACCCCGATACTGAGCTGG	59.257	63.158	0.00	0.00	0.00	4.85
1089	1416	2.018086	AGAGGAGAGGGAGGGAGGG	61.018	68.421	0.00	0.00	0.00	4.30
1090	1417	1.541672	GAGAGGAGAGGGAGGGAGG	59.458	68.421	0.00	0.00	0.00	4.30
1502	1929	3.370131	CGCGCGCGGTATATTAGG	58.630	61.111	43.28	13.53	35.56	2.69
1571	1998	1.358759	GCGAAGGGTGGTGTGTTTG	59.641	57.895	0.00	0.00	0.00	2.93
1625	2070	0.875059	CACTCCACGCCTTCCTTTTC	59.125	55.000	0.00	0.00	0.00	2.29
1752	2203	1.909781	GTAGTCCACCACGTCCCCA	60.910	63.158	0.00	0.00	0.00	4.96
2013	2467	1.679305	GTGGAGCAGGACGAGGAGA	60.679	63.158	0.00	0.00	0.00	3.71
2274	2743	3.579685	CTCTGGAGCTCGACGTCA	58.420	61.111	17.16	1.87	0.00	4.35
2371	2840	1.150536	GGGTGTCCACAGGAAAGCA	59.849	57.895	7.64	0.00	39.05	3.91
2669	3138	2.361438	ACACCGAATTCCGAGGAGTATC	59.639	50.000	5.02	0.00	41.76	2.24
2846	3315	4.913154	AGGGAACTAGGGATACAAGGTA	57.087	45.455	0.00	0.00	40.61	3.08
2847	3316	3.797671	AGGGAACTAGGGATACAAGGT	57.202	47.619	0.00	0.00	40.61	3.50
2874	3343	3.301794	TCCATCATCCTCACCAAATGG	57.698	47.619	0.00	0.00	42.17	3.16
3070	3542	2.125512	CCCGTCTTCTTCCTGGCG	60.126	66.667	0.00	0.00	0.00	5.69
3433	3973	9.917129	CTCCATTCAAAATATAATGCATGCTAA	57.083	29.630	20.33	4.37	32.79	3.09
3436	3976	8.821147	TTCTCCATTCAAAATATAATGCATGC	57.179	30.769	11.82	11.82	32.79	4.06
3470	4010	2.237143	CCTTGGTTGAGCTGGAGTATCA	59.763	50.000	0.00	0.00	36.25	2.15
3471	4011	2.420687	CCCTTGGTTGAGCTGGAGTATC	60.421	54.545	0.00	0.00	0.00	2.24
3530	4070	6.603201	TGGACCAAAGTATTCTTCATCCAATC	59.397	38.462	0.00	0.00	36.65	2.67
3534	4074	5.501156	ACTGGACCAAAGTATTCTTCATCC	58.499	41.667	0.00	3.58	33.33	3.51
3546	4086	2.584835	TCCATGGAACTGGACCAAAG	57.415	50.000	13.46	0.00	40.43	2.77
3556	4096	1.084370	CGACGAGCCTTCCATGGAAC	61.084	60.000	23.63	14.61	0.00	3.62
3600	4140	1.569708	GAGATCTCTTGCCGCTGAAG	58.430	55.000	15.80	0.00	0.00	3.02
3602	4142	0.685785	AGGAGATCTCTTGCCGCTGA	60.686	55.000	21.81	0.00	0.00	4.26
3626	4166	3.863041	AGGAAAAGAGTAAGATGACGGC	58.137	45.455	0.00	0.00	0.00	5.68
3662	4202	5.255397	TGGTTGTGATACTTCCCTCAAAT	57.745	39.130	0.00	0.00	0.00	2.32
3664	4204	4.715534	TTGGTTGTGATACTTCCCTCAA	57.284	40.909	0.00	0.00	0.00	3.02
3665	4205	4.715534	TTTGGTTGTGATACTTCCCTCA	57.284	40.909	0.00	0.00	0.00	3.86
3666	4206	5.476945	ACATTTTGGTTGTGATACTTCCCTC	59.523	40.000	0.00	0.00	0.00	4.30
3667	4207	5.393866	ACATTTTGGTTGTGATACTTCCCT	58.606	37.500	0.00	0.00	0.00	4.20
3693	4233	2.687935	GGCTTTTCTTGTGTCAGACCAA	59.312	45.455	0.00	1.49	0.00	3.67
3736	4277	5.883115	TGTGGTTGAATTGACAACTCAACTA	59.117	36.000	30.54	25.75	45.33	2.24
3754	4295	7.168469	GCAAGTATTTATTTTTCACGTGTGGTT	59.832	33.333	16.51	0.94	0.00	3.67
3755	4296	6.639279	GCAAGTATTTATTTTTCACGTGTGGT	59.361	34.615	16.51	1.45	0.00	4.16
3756	4297	6.861055	AGCAAGTATTTATTTTTCACGTGTGG	59.139	34.615	16.51	0.00	0.00	4.17
3757	4298	7.851822	AGCAAGTATTTATTTTTCACGTGTG	57.148	32.000	16.51	1.99	0.00	3.82
3758	4299	8.132362	TCAAGCAAGTATTTATTTTTCACGTGT	58.868	29.630	16.51	0.00	0.00	4.49
3759	4300	8.417176	GTCAAGCAAGTATTTATTTTTCACGTG	58.583	33.333	9.94	9.94	0.00	4.49
3760	4301	8.132362	TGTCAAGCAAGTATTTATTTTTCACGT	58.868	29.630	0.00	0.00	0.00	4.49
3761	4302	8.500837	TGTCAAGCAAGTATTTATTTTTCACG	57.499	30.769	0.00	0.00	0.00	4.35
3762	4303	9.677567	TCTGTCAAGCAAGTATTTATTTTTCAC	57.322	29.630	0.00	0.00	0.00	3.18
3779	4320	9.495754	CTTTGCTAGTAATAAATTCTGTCAAGC	57.504	33.333	0.00	0.00	0.00	4.01
3847	4388	0.604243	TTGCAACCGCCGAGTATTGT	60.604	50.000	0.00	0.00	37.32	2.71
3899	4440	3.838244	ATCCTCATGCCTACGCTTTTA	57.162	42.857	0.00	0.00	35.36	1.52
3920	4461	5.687780	TGTCCATGCAACATCTCATTATCT	58.312	37.500	0.00	0.00	0.00	1.98
3922	4463	8.645814	ATTATGTCCATGCAACATCTCATTAT	57.354	30.769	13.38	0.00	38.31	1.28
3929	4470	5.762825	ACTGATTATGTCCATGCAACATC	57.237	39.130	13.38	4.21	38.31	3.06
3950	4491	6.040878	CCTATGCTACCCGCTATTACATAAC	58.959	44.000	0.00	0.00	40.11	1.89

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.