AutoCloner

Multiple sequence alignment - TraesCS2D01G398100

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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	TraesCS2D01G398100	chr2D	100.000	5253	0	0	1	5253	510208092	510213344	0.000000e+00	9701.0
1	TraesCS2D01G398100	chr2D	92.913	635	31	12	2226	2849	510206420	510205789	0.000000e+00	911.0
2	TraesCS2D01G398100	chr2D	82.063	223	25	8	1981	2188	532167867	532168089	5.410000e-40	176.0
3	TraesCS2D01G398100	chr2D	100.000	30	0	0	4578	4607	222761142	222761171	7.350000e-04	56.5
4	TraesCS2D01G398100	chr2A	92.727	2475	97	29	785	3231	653857807	653860226	0.000000e+00	3496.0
5	TraesCS2D01G398100	chr2A	96.720	1250	30	4	3265	4505	653860223	653861470	0.000000e+00	2071.0
6	TraesCS2D01G398100	chr2A	95.803	548	21	2	4706	5253	653863589	653864134	0.000000e+00	883.0
7	TraesCS2D01G398100	chr2A	86.944	674	65	17	2186	2849	603860435	603861095	0.000000e+00	736.0
8	TraesCS2D01G398100	chr2A	88.769	463	34	10	1	451	653849011	653849467	7.690000e-153	551.0
9	TraesCS2D01G398100	chr2A	97.115	104	3	0	619	722	653857703	653857806	5.410000e-40	176.0
10	TraesCS2D01G398100	chr2A	91.892	74	6	0	423	496	653851173	653851246	2.590000e-18	104.0
11	TraesCS2D01G398100	chr2A	85.870	92	7	4	1964	2050	17221893	17221803	5.600000e-15	93.5
12	TraesCS2D01G398100	chr2B	94.041	1376	40	10	423	1771	599808268	599809628	0.000000e+00	2049.0
13	TraesCS2D01G398100	chr2B	95.215	1024	35	2	2855	3877	599813014	599814024	0.000000e+00	1607.0
14	TraesCS2D01G398100	chr2B	93.552	1008	43	11	3877	4864	599814054	599815059	0.000000e+00	1482.0
15	TraesCS2D01G398100	chr2B	89.444	900	49	19	1985	2849	599811273	599812161	0.000000e+00	1094.0
16	TraesCS2D01G398100	chr2B	95.482	332	9	6	4924	5253	599817654	599817981	4.660000e-145	525.0
17	TraesCS2D01G398100	chr2B	97.388	268	7	0	1716	1983	599809607	599809874	1.720000e-124	457.0
18	TraesCS2D01G398100	chr2B	94.022	184	8	3	272	455	599806316	599806496	5.180000e-70	276.0
19	TraesCS2D01G398100	chr2B	88.525	61	5	2	2833	2893	53989376	53989318	7.300000e-09	73.1
20	TraesCS2D01G398100	chr3D	90.579	743	34	16	2135	2849	84121331	84122065	0.000000e+00	952.0
21	TraesCS2D01G398100	chr3D	88.710	62	5	2	2831	2891	101798055	101797995	2.030000e-09	75.0
22	TraesCS2D01G398100	chr3A	92.054	667	38	9	2189	2844	100435430	100436092	0.000000e+00	924.0
23	TraesCS2D01G398100	chr3A	77.536	414	68	21	20	431	23195629	23195239	5.290000e-55	226.0
24	TraesCS2D01G398100	chr3A	90.741	54	5	0	1976	2029	704690821	704690768	7.300000e-09	73.1
25	TraesCS2D01G398100	chr3A	95.349	43	2	0	1987	2029	481163122	481163164	9.440000e-08	69.4
26	TraesCS2D01G398100	chr3A	88.679	53	5	1	2839	2891	702007791	702007842	4.390000e-06	63.9
27	TraesCS2D01G398100	chr3A	87.273	55	6	1	1971	2025	704836661	704836608	1.580000e-05	62.1
28	TraesCS2D01G398100	chr7B	82.699	919	110	29	1970	2849	702192784	702193692	0.000000e+00	771.0
29	TraesCS2D01G398100	chr7B	87.651	332	38	1	1321	1649	612403854	612404185	2.970000e-102	383.0
30	TraesCS2D01G398100	chr7B	82.822	326	41	12	3928	4248	612405574	612405889	1.440000e-70	278.0
31	TraesCS2D01G398100	chr7B	85.714	259	37	0	2948	3206	612404520	612404778	1.860000e-69	274.0
32	TraesCS2D01G398100	chr7B	88.889	90	10	0	3582	3671	612405228	612405317	1.550000e-20	111.0
33	TraesCS2D01G398100	chr6A	86.834	676	66	18	2186	2849	510796454	510797118	0.000000e+00	734.0
34	TraesCS2D01G398100	chr4A	86.792	583	62	11	2276	2849	28657376	28656800	2.060000e-178	636.0
35	TraesCS2D01G398100	chr4A	90.000	100	6	4	1952	2047	6055043	6054944	5.520000e-25	126.0
36	TraesCS2D01G398100	chrUn	88.024	334	35	2	1310	1640	29287637	29287968	1.770000e-104	390.0
37	TraesCS2D01G398100	chrUn	91.209	91	8	0	3581	3671	29289177	29289267	1.990000e-24	124.0
38	TraesCS2D01G398100	chr5A	87.126	334	43	0	1325	1658	708124369	708124036	3.840000e-101	379.0
39	TraesCS2D01G398100	chr5A	76.727	550	95	25	3546	4069	708120869	708120327	5.180000e-70	276.0
40	TraesCS2D01G398100	chr5A	88.750	160	18	0	1791	1950	708073071	708072912	4.150000e-46	196.0
41	TraesCS2D01G398100	chr5A	91.489	47	4	0	4871	4917	697050718	697050764	1.220000e-06	65.8
42	TraesCS2D01G398100	chr5D	88.060	335	16	9	423	737	549430814	549430484	4.970000e-100	375.0
43	TraesCS2D01G398100	chr7D	95.420	131	6	0	604	734	249487321	249487191	5.330000e-50	209.0
44	TraesCS2D01G398100	chr7D	88.095	126	8	3	423	548	249487459	249487341	5.480000e-30	143.0
45	TraesCS2D01G398100	chr6D	92.308	52	4	0	2840	2891	45593283	45593232	2.030000e-09	75.0
46	TraesCS2D01G398100	chr6D	88.462	52	5	1	2840	2891	465751001	465751051	1.580000e-05	62.1
47	TraesCS2D01G398100	chr4B	78.899	109	20	3	4809	4915	658183832	658183725	2.620000e-08	71.3
48	TraesCS2D01G398100	chr1D	95.455	44	2	0	1987	2030	427329174	427329131	2.620000e-08	71.3
49	TraesCS2D01G398100	chr7A	93.333	45	3	0	1986	2030	470798763	470798719	3.390000e-07	67.6
50	TraesCS2D01G398100	chr7A	88.679	53	3	2	2839	2891	40135250	40135299	1.580000e-05	62.1
51	TraesCS2D01G398100	chr7A	80.952	84	8	7	1990	2070	83516218	83516296	5.680000e-05	60.2
52	TraesCS2D01G398100	chr6B	94.444	36	1	1	4571	4605	529400003	529400038	3.000000e-03	54.7

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	TraesCS2D01G398100	chr2D	510208092	510213344	5252	False	9701.0	9701	100.000000	1	5253	1	chr2D.!!$F2	5252
1	TraesCS2D01G398100	chr2D	510205789	510206420	631	True	911.0	911	92.913000	2226	2849	1	chr2D.!!$R1	623
2	TraesCS2D01G398100	chr2A	653857703	653864134	6431	False	1656.5	3496	95.591250	619	5253	4	chr2A.!!$F3	4634
3	TraesCS2D01G398100	chr2A	603860435	603861095	660	False	736.0	736	86.944000	2186	2849	1	chr2A.!!$F1	663
4	TraesCS2D01G398100	chr2A	653849011	653851246	2235	False	327.5	551	90.330500	1	496	2	chr2A.!!$F2	495
5	TraesCS2D01G398100	chr2B	599806316	599817981	11665	False	1070.0	2049	94.163429	272	5253	7	chr2B.!!$F1	4981
6	TraesCS2D01G398100	chr3D	84121331	84122065	734	False	952.0	952	90.579000	2135	2849	1	chr3D.!!$F1	714
7	TraesCS2D01G398100	chr3A	100435430	100436092	662	False	924.0	924	92.054000	2189	2844	1	chr3A.!!$F1	655
8	TraesCS2D01G398100	chr7B	702192784	702193692	908	False	771.0	771	82.699000	1970	2849	1	chr7B.!!$F1	879
9	TraesCS2D01G398100	chr7B	612403854	612405889	2035	False	261.5	383	86.269000	1321	4248	4	chr7B.!!$F2	2927
10	TraesCS2D01G398100	chr6A	510796454	510797118	664	False	734.0	734	86.834000	2186	2849	1	chr6A.!!$F1	663
11	TraesCS2D01G398100	chr4A	28656800	28657376	576	True	636.0	636	86.792000	2276	2849	1	chr4A.!!$R2	573
12	TraesCS2D01G398100	chrUn	29287637	29289267	1630	False	257.0	390	89.616500	1310	3671	2	chrUn.!!$F1	2361
13	TraesCS2D01G398100	chr5A	708120327	708124369	4042	True	327.5	379	81.926500	1325	4069	2	chr5A.!!$R2	2744

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
193	194	1.135972	CGCAAGTGCCACTCATTGTAC	60.136	52.381	0.00	37.91	2.90	F
1026	2869	1.296715	CTACTCGCAGGTGCCCTTT	59.703	57.895	0.00	37.91	3.11	F
1700	3554	0.599558	TGAGTGCGCGGTTACTTACT	59.400	50.000	8.83	0.00	2.24	F
3074	7420	0.838122	ACAGAGTGGAAGGGGAGTGG	60.838	60.000	0.00	0.00	4.00	F
3989	10677	0.184933	CCATTCGGAGGGGGCATAAA	59.815	55.000	0.00	0.00	1.40	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1681	3535	0.599558	AGTAAGTAACCGCGCACTCA	59.400	50.000	8.75	0.00	3.41	R
2698	6195	0.734309	TTTATGCATGCACAGCCGAG	59.266	50.000	25.37	0.00	4.63	R
3238	9441	0.385029	AGTTGCAGCAAAATCACGCA	59.615	45.000	10.11	0.00	5.24	R
4042	10730	1.880027	CCTGTACTTTGTCACCAAGGC	59.120	52.381	0.00	31.18	4.35	R
4861	13586	4.019174	ACTTTCATGGTATTCTGGCTTGG	58.981	43.478	0.00	0.00	3.61	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
193	194	1.135972	CGCAAGTGCCACTCATTGTAC	60.136	52.381	0.00	0.00	37.91	2.90
195	196	2.350772	GCAAGTGCCACTCATTGTACAC	60.351	50.000	0.00	0.00	36.03	2.90
211	212	4.200874	TGTACACAATGTTTCCGGTCTTT	58.799	39.130	0.00	0.00	0.00	2.52
228	229	8.364142	TCCGGTCTTTTGATGAAACATAAATTT	58.636	29.630	0.00	0.00	0.00	1.82
229	230	9.632807	CCGGTCTTTTGATGAAACATAAATTTA	57.367	29.630	0.00	0.00	0.00	1.40
428	2251	4.615912	GCAAAAATGAACGGTGATGCTAGT	60.616	41.667	0.00	0.00	0.00	2.57
442	2265	5.020795	TGATGCTAGTGGAGTTGGTTAGTA	58.979	41.667	0.00	0.00	0.00	1.82
574	2397	5.414454	AGCTCATTAAACACGCCAATTAAGA	59.586	36.000	0.00	0.00	0.00	2.10
575	2398	6.095440	AGCTCATTAAACACGCCAATTAAGAT	59.905	34.615	0.00	0.00	0.00	2.40
576	2399	7.282224	AGCTCATTAAACACGCCAATTAAGATA	59.718	33.333	0.00	0.00	0.00	1.98
578	2401	7.925993	TCATTAAACACGCCAATTAAGATAGG	58.074	34.615	0.00	0.00	0.00	2.57
579	2402	6.687081	TTAAACACGCCAATTAAGATAGGG	57.313	37.500	0.00	0.00	0.00	3.53
580	2403	3.208747	ACACGCCAATTAAGATAGGGG	57.791	47.619	0.00	0.00	39.70	4.79
581	2404	2.158667	ACACGCCAATTAAGATAGGGGG	60.159	50.000	0.00	0.00	38.30	5.40
582	2405	2.105821	CACGCCAATTAAGATAGGGGGA	59.894	50.000	0.00	0.00	38.30	4.81
626	2467	9.566432	AATGGTCCATTAAGAGATCATTAAGAC	57.434	33.333	15.83	5.21	41.03	3.01
694	2535	4.026804	CGGGTCAATTAAGAGATTCGAACG	60.027	45.833	0.00	0.00	0.00	3.95
1007	2850	4.202357	ACACTGTAGCTTCAACATGGAAGA	60.202	41.667	13.91	0.00	45.66	2.87
1023	2866	1.889530	AAGACTACTCGCAGGTGCCC	61.890	60.000	0.00	0.00	37.91	5.36
1025	2868	1.889530	GACTACTCGCAGGTGCCCTT	61.890	60.000	0.00	0.00	37.91	3.95
1026	2869	1.296715	CTACTCGCAGGTGCCCTTT	59.703	57.895	0.00	0.00	37.91	3.11
1044	2887	4.496336	GCATCCCTCTGCGGCCTT	62.496	66.667	0.00	0.00	31.49	4.35
1215	3058	2.028385	GCCGGTCTTCTACAAGGAAAGA	60.028	50.000	1.90	0.00	31.24	2.52
1512	3363	2.167693	CGGCTCCTTCCACAAGTACATA	59.832	50.000	0.00	0.00	0.00	2.29
1689	3543	5.852738	AATCAGATTATACATGAGTGCGC	57.147	39.130	0.00	0.00	0.00	6.09
1698	3552	1.067425	ACATGAGTGCGCGGTTACTTA	60.067	47.619	8.83	0.00	0.00	2.24
1699	3553	1.323534	CATGAGTGCGCGGTTACTTAC	59.676	52.381	8.83	0.00	0.00	2.34
1700	3554	0.599558	TGAGTGCGCGGTTACTTACT	59.400	50.000	8.83	0.00	0.00	2.24
1701	3555	1.000060	TGAGTGCGCGGTTACTTACTT	60.000	47.619	8.83	0.00	0.00	2.24
1762	3650	2.031870	AGGGGAATATTTTTGCGCCTC	58.968	47.619	4.18	0.00	39.16	4.70
1780	3668	4.675114	CGCCTCGTATATTTTTGCCATTTC	59.325	41.667	0.00	0.00	0.00	2.17
2005	5409	9.186837	CTATCGCTACCTAATATTAAAGGGAGA	57.813	37.037	17.64	13.49	45.54	3.71
2081	5492	3.296709	CTTCGTACGTGCCCAGCCT	62.297	63.158	16.05	0.00	0.00	4.58
2330	5808	4.272489	TGTTATGAGCATGGAAGGAAAGG	58.728	43.478	0.00	0.00	0.00	3.11
2454	5933	4.569865	GGCAGGAAGGGAAGGAATTAAAGA	60.570	45.833	0.00	0.00	0.00	2.52
2461	5948	8.816894	GGAAGGGAAGGAATTAAAGAAAAGAAT	58.183	33.333	0.00	0.00	0.00	2.40
2697	6194	6.921857	CCGTTGTGGACCGATTATATATATCC	59.078	42.308	0.00	3.31	42.00	2.59
2698	6195	6.921857	CGTTGTGGACCGATTATATATATCCC	59.078	42.308	0.00	0.00	0.00	3.85
2743	6240	4.684724	AGTCCCATTGTGACTCTACCTAA	58.315	43.478	0.00	0.00	38.71	2.69
2906	7251	4.753610	AGATGCATACAGTACATGATGCAC	59.246	41.667	22.87	17.80	46.03	4.57
3074	7420	0.838122	ACAGAGTGGAAGGGGAGTGG	60.838	60.000	0.00	0.00	0.00	4.00
3085	7431	1.104630	GGGGAGTGGTAGACGAGAAG	58.895	60.000	0.00	0.00	0.00	2.85
3237	9440	7.030768	TGTTTACTCCTAAAAGTGTTTGTTGC	58.969	34.615	0.00	0.00	0.00	4.17
3238	9441	7.094118	TGTTTACTCCTAAAAGTGTTTGTTGCT	60.094	33.333	0.00	0.00	0.00	3.91
3239	9442	5.248870	ACTCCTAAAAGTGTTTGTTGCTG	57.751	39.130	0.00	0.00	0.00	4.41
3242	9445	2.362169	AAAAGTGTTTGTTGCTGCGT	57.638	40.000	0.00	0.00	0.00	5.24
3244	9447	0.808125	AAGTGTTTGTTGCTGCGTGA	59.192	45.000	0.00	0.00	0.00	4.35
3245	9448	1.024271	AGTGTTTGTTGCTGCGTGAT	58.976	45.000	0.00	0.00	0.00	3.06
3246	9449	1.405105	AGTGTTTGTTGCTGCGTGATT	59.595	42.857	0.00	0.00	0.00	2.57
3261	9464	3.786048	GCGTGATTTTGCTGCAACTATAC	59.214	43.478	15.72	11.03	0.00	1.47
3569	10143	2.420642	CATGCACACTGCTACTCAAGT	58.579	47.619	0.00	0.00	45.31	3.16
3570	10144	2.620251	TGCACACTGCTACTCAAGTT	57.380	45.000	0.00	0.00	45.31	2.66
3657	10236	1.654317	AACACTAACGGACGTGCAAA	58.346	45.000	8.11	0.00	34.58	3.68
3989	10677	0.184933	CCATTCGGAGGGGGCATAAA	59.815	55.000	0.00	0.00	0.00	1.40
4042	10730	1.135257	AGATCGCACTCTTCCTTCACG	60.135	52.381	0.00	0.00	0.00	4.35
4262	10950	6.852404	CCTAGGGAGGGATAAAATGATTCAA	58.148	40.000	0.00	0.00	39.48	2.69
4276	10964	7.642071	AAATGATTCAACAATGGAAAACTCG	57.358	32.000	0.00	0.00	0.00	4.18
4342	11030	7.500559	AGCAACTTGATGGATAATCTTACTTCC	59.499	37.037	0.00	0.00	36.15	3.46
4411	11099	9.083422	TCTACCATCTCTCCTCTATAAAATGTG	57.917	37.037	0.00	0.00	0.00	3.21
4501	11189	9.383519	TGTCATGGAATTTCTAAACTCATACTC	57.616	33.333	0.00	0.00	0.00	2.59
4505	11193	9.927081	ATGGAATTTCTAAACTCATACTCCATT	57.073	29.630	0.00	0.00	36.75	3.16
4511	11199	6.338146	TCTAAACTCATACTCCATTTGTCCG	58.662	40.000	0.00	0.00	0.00	4.79
4605	12373	6.652205	TTATTTTGGGATGGAGGAAGTAGT	57.348	37.500	0.00	0.00	0.00	2.73
4611	12379	6.742559	TGGGATGGAGGAAGTAGTATAAAC	57.257	41.667	0.00	0.00	0.00	2.01
4648	12416	2.047213	TTGGGAAGTGGGTCACGGTC	62.047	60.000	0.00	0.00	39.64	4.79
4649	12417	2.346365	GGAAGTGGGTCACGGTCC	59.654	66.667	7.64	7.64	39.64	4.46
4650	12418	2.346365	GAAGTGGGTCACGGTCCC	59.654	66.667	5.12	5.12	44.81	4.46
4651	12419	3.246880	AAGTGGGTCACGGTCCCC	61.247	66.667	5.60	5.60	44.00	4.81
4684	12473	1.024271	TGCCAGCGCATCCTAATTTC	58.976	50.000	11.47	0.00	41.12	2.17
4692	12481	6.128282	CCAGCGCATCCTAATTTCGTAAATAT	60.128	38.462	11.47	0.00	0.00	1.28
4694	12483	7.898309	CAGCGCATCCTAATTTCGTAAATATAC	59.102	37.037	11.47	0.00	0.00	1.47
4841	13566	3.198068	AGCGTGAACCATAGCTTGTATG	58.802	45.455	0.00	0.00	36.41	2.39
4863	13588	9.400638	GTATGTATCGTTCAATTTGTTTTTCCA	57.599	29.630	0.00	0.00	0.00	3.53
4942	16232	7.636150	ACTTGATCATATTTGTCTCCCAAAG	57.364	36.000	0.00	0.00	45.79	2.77
4943	16233	7.177878	ACTTGATCATATTTGTCTCCCAAAGT	58.822	34.615	0.00	0.00	45.79	2.66
4944	16234	7.337942	ACTTGATCATATTTGTCTCCCAAAGTC	59.662	37.037	0.00	0.00	45.79	3.01
5203	16495	6.543831	ACCCTAGAACATGAATGCATCTAAAC	59.456	38.462	0.00	0.00	32.58	2.01

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
35	36	8.496088	AGATAGAGAGTACAGTGGTATTGTAGT	58.504	37.037	0.00	0.00	37.38	2.73
38	39	9.696572	TTTAGATAGAGAGTACAGTGGTATTGT	57.303	33.333	0.00	0.00	0.00	2.71
129	130	6.514947	TGCAATGTTAAATGCTCTCTTGTTT	58.485	32.000	9.66	0.00	42.97	2.83
165	166	3.193903	TGAGTGGCACTTGCGTATAGTTA	59.806	43.478	22.98	0.00	43.26	2.24
193	194	4.300189	TCAAAAGACCGGAAACATTGTG	57.700	40.909	9.46	0.46	0.00	3.33
195	196	5.119931	TCATCAAAAGACCGGAAACATTG	57.880	39.130	9.46	6.94	0.00	2.82
428	2251	6.877668	TCCATACAATACTAACCAACTCCA	57.122	37.500	0.00	0.00	0.00	3.86
442	2265	5.045286	GCCCTCTCCATTCTATCCATACAAT	60.045	44.000	0.00	0.00	0.00	2.71
504	2327	6.095432	AGCATGTTATTTTTGTGCCAAGTA	57.905	33.333	0.00	0.00	36.50	2.24
524	2347	8.050325	TCCTAATTAGTACTGCCATTTAAAGCA	58.950	33.333	11.50	2.55	37.46	3.91
574	2397	4.724279	AGCACGATTTAATTCCCCCTAT	57.276	40.909	0.00	0.00	0.00	2.57
575	2398	5.633655	TTAGCACGATTTAATTCCCCCTA	57.366	39.130	0.00	0.00	0.00	3.53
576	2399	4.513406	TTAGCACGATTTAATTCCCCCT	57.487	40.909	0.00	0.00	0.00	4.79
578	2401	6.385649	TTCATTAGCACGATTTAATTCCCC	57.614	37.500	0.00	0.00	0.00	4.81
579	2402	6.863126	CCATTCATTAGCACGATTTAATTCCC	59.137	38.462	0.00	0.00	0.00	3.97
580	2403	7.425606	ACCATTCATTAGCACGATTTAATTCC	58.574	34.615	0.00	0.00	0.00	3.01
581	2404	7.591426	GGACCATTCATTAGCACGATTTAATTC	59.409	37.037	0.00	0.00	0.00	2.17
582	2405	7.068103	TGGACCATTCATTAGCACGATTTAATT	59.932	33.333	0.00	0.00	0.00	1.40
626	2467	6.618287	TTAGCATGATTTAATTCTCCCGTG	57.382	37.500	0.00	0.00	0.00	4.94
740	2581	4.460263	GCCAGAAAAAGGGGAAACAAAAT	58.540	39.130	0.00	0.00	0.00	1.82
745	2586	0.317160	CCGCCAGAAAAAGGGGAAAC	59.683	55.000	0.00	0.00	41.25	2.78
746	2587	1.468506	GCCGCCAGAAAAAGGGGAAA	61.469	55.000	0.00	0.00	41.25	3.13
747	2588	1.906333	GCCGCCAGAAAAAGGGGAA	60.906	57.895	0.00	0.00	41.25	3.97
748	2589	2.282887	GCCGCCAGAAAAAGGGGA	60.283	61.111	0.00	0.00	41.25	4.81
749	2590	1.877576	GAAGCCGCCAGAAAAAGGGG	61.878	60.000	0.00	0.00	39.04	4.79
750	2591	1.178534	TGAAGCCGCCAGAAAAAGGG	61.179	55.000	0.00	0.00	0.00	3.95
799	2641	4.909696	TGCACCTTTCGAATTTTGAAGA	57.090	36.364	0.00	0.00	0.00	2.87
1023	2866	2.768492	GCCGCAGAGGGATGCAAAG	61.768	63.158	0.00	0.00	46.87	2.77
1025	2868	4.802051	GGCCGCAGAGGGATGCAA	62.802	66.667	0.00	0.00	46.87	4.08
1044	2887	2.494445	CCTGCTACGATGACGGCA	59.506	61.111	0.00	0.00	44.46	5.69
1051	2894	2.786495	CGAGCCACCCTGCTACGAT	61.786	63.158	0.00	0.00	42.95	3.73
1215	3058	6.003950	TGCTTAGCTTGATTACCTTTTCAGT	58.996	36.000	5.60	0.00	0.00	3.41
1399	3250	1.138568	CCCTCCTGCTGGAAGATGAT	58.861	55.000	13.89	0.00	42.66	2.45
1681	3535	0.599558	AGTAAGTAACCGCGCACTCA	59.400	50.000	8.75	0.00	0.00	3.41
1689	3543	5.284660	CACGTAGCACTAAAGTAAGTAACCG	59.715	44.000	0.00	0.00	0.00	4.44
1698	3552	8.173130	GCAAAAATATACACGTAGCACTAAAGT	58.827	33.333	0.00	0.00	0.00	2.66
1699	3553	7.369800	CGCAAAAATATACACGTAGCACTAAAG	59.630	37.037	0.00	0.00	0.00	1.85
1700	3554	7.174746	CGCAAAAATATACACGTAGCACTAAA	58.825	34.615	0.00	0.00	0.00	1.85
1701	3555	6.698107	CGCAAAAATATACACGTAGCACTAA	58.302	36.000	0.00	0.00	0.00	2.24
1762	3650	6.264518	AGGTAGGGAAATGGCAAAAATATACG	59.735	38.462	0.00	0.00	0.00	3.06
1780	3668	2.267174	CATCTGCATGGAAGGTAGGG	57.733	55.000	0.00	0.00	29.06	3.53
1850	3857	4.831155	TCGAAGTTCTTCCTGAGTTTCCTA	59.169	41.667	0.56	0.00	0.00	2.94
2081	5492	3.770040	CAGGACGACGGATGGGCA	61.770	66.667	0.00	0.00	0.00	5.36
2697	6194	1.096967	TTATGCATGCACAGCCGAGG	61.097	55.000	25.37	0.00	0.00	4.63
2698	6195	0.734309	TTTATGCATGCACAGCCGAG	59.266	50.000	25.37	0.00	0.00	4.63
2856	7201	1.692042	CAGAGGCTGGGGGTCATCT	60.692	63.158	0.00	0.00	0.00	2.90
2891	7236	8.560355	TTAACTTTATGTGCATCATGTACTGT	57.440	30.769	7.44	0.00	37.91	3.55
3046	7392	2.416162	CCTTCCACTCTGTAGCTCGTTC	60.416	54.545	0.00	0.00	0.00	3.95
3085	7431	1.661112	GCCATCAAGTCTACAGCGAAC	59.339	52.381	0.00	0.00	0.00	3.95
3237	9440	0.780002	GTTGCAGCAAAATCACGCAG	59.220	50.000	10.11	0.00	33.48	5.18
3238	9441	0.385029	AGTTGCAGCAAAATCACGCA	59.615	45.000	10.11	0.00	0.00	5.24
3239	9442	2.330231	TAGTTGCAGCAAAATCACGC	57.670	45.000	10.11	0.00	0.00	5.34
3242	9445	4.935205	ACGAGTATAGTTGCAGCAAAATCA	59.065	37.500	10.11	0.00	0.00	2.57
3244	9447	4.695455	ACACGAGTATAGTTGCAGCAAAAT	59.305	37.500	10.11	9.30	0.00	1.82
3245	9448	4.062293	ACACGAGTATAGTTGCAGCAAAA	58.938	39.130	10.11	1.15	0.00	2.44
3246	9449	3.659786	ACACGAGTATAGTTGCAGCAAA	58.340	40.909	10.11	0.00	0.00	3.68
3518	10077	6.204882	ACTGTTTCTATGCTCCAACTTGTAAC	59.795	38.462	0.00	0.00	0.00	2.50
3569	10143	3.069872	TGGTAACCTGCAGAGAACGTTAA	59.930	43.478	17.39	0.00	0.00	2.01
3570	10144	2.629137	TGGTAACCTGCAGAGAACGTTA	59.371	45.455	17.39	11.64	0.00	3.18
3657	10236	7.397761	ACTGTCTAAGCTAAGAGTACCTTTCAT	59.602	37.037	0.00	0.00	36.34	2.57
3723	10340	4.323417	TGTTGGTCCATTAACTAGCACAG	58.677	43.478	0.00	0.00	0.00	3.66
4042	10730	1.880027	CCTGTACTTTGTCACCAAGGC	59.120	52.381	0.00	0.00	31.18	4.35
4262	10950	2.749621	GAGCCATCGAGTTTTCCATTGT	59.250	45.455	0.00	0.00	0.00	2.71
4276	10964	6.344500	TCTCTTTCTTGTATCAAGAGCCATC	58.656	40.000	11.17	0.00	42.25	3.51
4342	11030	2.954318	CTGCCAATCCCCAACTTATGAG	59.046	50.000	0.00	0.00	0.00	2.90
4411	11099	3.258372	TGGTAGTCACATGTTGGAGAGTC	59.742	47.826	0.00	0.00	0.00	3.36
4501	11189	6.254281	AGACACTTATTTTCGGACAAATGG	57.746	37.500	7.80	4.86	0.00	3.16
4505	11193	4.873817	TCGAGACACTTATTTTCGGACAA	58.126	39.130	0.00	0.00	32.52	3.18
4511	11199	9.872757	TTGTACAAAATCGAGACACTTATTTTC	57.127	29.630	5.64	0.00	31.05	2.29
4575	12343	5.043432	TCCTCCATCCCAAAATAAATGTCCT	60.043	40.000	0.00	0.00	0.00	3.85
4611	12379	5.007034	TCCCAAACACAATACCATACACAG	58.993	41.667	0.00	0.00	0.00	3.66
4732	13457	7.305474	ACTTTTTATTCGAGTGCAATAGTTGG	58.695	34.615	0.00	0.00	0.00	3.77
4841	13566	7.280769	GCTTGGAAAAACAAATTGAACGATAC	58.719	34.615	0.00	0.00	0.00	2.24
4861	13586	4.019174	ACTTTCATGGTATTCTGGCTTGG	58.981	43.478	0.00	0.00	0.00	3.61
4863	13588	4.922206	TGACTTTCATGGTATTCTGGCTT	58.078	39.130	0.00	0.00	0.00	4.35

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.