AutoCloner

Multiple sequence alignment - TraesCS2A01G102900

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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	TraesCS2A01G102900	chr2A	100.000	3205	0	0	1	3205	56108813	56105609	0.000000e+00	5919.0
1	TraesCS2A01G102900	chr2A	93.454	1543	64	10	1674	3205	55972761	55971245	0.000000e+00	2255.0
2	TraesCS2A01G102900	chr2B	94.186	1978	89	11	1235	3205	87518103	87516145	0.000000e+00	2992.0
3	TraesCS2A01G102900	chr2B	91.034	1015	68	15	2123	3123	87529525	87528520	0.000000e+00	1349.0
4	TraesCS2A01G102900	chr2B	91.882	813	58	4	1235	2041	87530334	87529524	0.000000e+00	1129.0
5	TraesCS2A01G102900	chr2B	90.017	591	37	7	997	1582	87424048	87423475	0.000000e+00	745.0
6	TraesCS2A01G102900	chr2B	91.078	538	38	8	2133	2665	87422972	87422440	0.000000e+00	719.0
7	TraesCS2A01G102900	chr2B	92.227	476	34	1	1566	2041	87423459	87422987	0.000000e+00	671.0
8	TraesCS2A01G102900	chr2B	91.186	295	17	2	2664	2957	87422358	87422072	3.000000e-105	392.0
9	TraesCS2A01G102900	chr2B	92.000	250	19	1	2957	3205	87416221	87415972	1.830000e-92	350.0
10	TraesCS2A01G102900	chr2B	94.030	201	12	0	997	1197	87518294	87518094	4.020000e-79	305.0
11	TraesCS2A01G102900	chr2B	92.040	201	16	0	997	1197	87530525	87530325	1.880000e-72	283.0
12	TraesCS2A01G102900	chr2B	80.498	241	22	14	1385	1618	87774966	87774744	9.200000e-36	161.0
13	TraesCS2A01G102900	chr2B	79.070	258	34	7	997	1243	87775981	87775733	3.310000e-35	159.0
14	TraesCS2A01G102900	chr2B	92.105	76	5	1	1439	1513	87775724	87775649	4.370000e-19	106.0
15	TraesCS2A01G102900	chr2D	94.444	1458	67	7	588	2041	58638486	58639933	0.000000e+00	2231.0
16	TraesCS2A01G102900	chr2D	93.566	1088	47	11	2123	3202	58639932	58641004	0.000000e+00	1600.0
17	TraesCS2A01G102900	chr2D	93.684	1045	59	4	997	2041	55249846	55248809	0.000000e+00	1557.0
18	TraesCS2A01G102900	chr2D	92.491	1092	45	14	2123	3205	55248810	55247747	0.000000e+00	1528.0
19	TraesCS2A01G102900	chr2D	91.312	1082	67	11	2133	3205	55246604	55245541	0.000000e+00	1452.0
20	TraesCS2A01G102900	chr2D	92.550	604	41	4	1	600	58636311	58636914	0.000000e+00	863.0
21	TraesCS2A01G102900	chr2D	90.147	477	37	3	1565	2041	55247086	55246620	2.110000e-171	612.0
22	TraesCS2A01G102900	chr2D	97.255	255	7	0	719	973	55250160	55249906	1.770000e-117	433.0
23	TraesCS2A01G102900	chr2D	93.197	147	10	0	3059	3205	55242601	55242455	1.940000e-52	217.0
24	TraesCS2A01G102900	chr6B	93.069	101	7	0	2032	2132	96970752	96970852	7.160000e-32	148.0
25	TraesCS2A01G102900	chrUn	93.548	93	6	0	2039	2131	135090803	135090711	4.310000e-29	139.0
26	TraesCS2A01G102900	chr3D	88.496	113	12	1	2026	2138	424006084	424005973	5.580000e-28	135.0
27	TraesCS2A01G102900	chr1B	91.837	98	7	1	2040	2137	538168114	538168018	5.580000e-28	135.0
28	TraesCS2A01G102900	chr4B	89.623	106	8	3	2021	2124	399783265	399783161	7.210000e-27	132.0
29	TraesCS2A01G102900	chr4B	94.737	76	4	0	1	76	170073984	170073909	5.620000e-23	119.0
30	TraesCS2A01G102900	chr6A	85.385	130	13	6	2040	2169	1139610	1139487	2.590000e-26	130.0
31	TraesCS2A01G102900	chr4D	86.842	114	15	0	2040	2153	182071716	182071829	9.330000e-26	128.0
32	TraesCS2A01G102900	chr4D	93.590	78	5	0	1	78	336505134	336505057	2.020000e-22	117.0
33	TraesCS2A01G102900	chr4D	92.500	80	6	0	1	80	293616426	293616347	7.270000e-22	115.0
34	TraesCS2A01G102900	chr4A	95.946	74	3	0	1	74	87045511	87045438	1.560000e-23	121.0
35	TraesCS2A01G102900	chr7D	88.043	92	9	2	1	92	391808749	391808838	1.220000e-19	108.0
36	TraesCS2A01G102900	chr7A	86.458	96	12	1	3	98	231631840	231631934	1.570000e-18	104.0
37	TraesCS2A01G102900	chr7A	82.258	124	17	4	1	119	219371055	219370932	5.660000e-18	102.0
38	TraesCS2A01G102900	chr7A	80.137	146	13	13	1	140	537244046	537244181	9.470000e-16	95.3

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	TraesCS2A01G102900	chr2A	56105609	56108813	3204	True	5919.000000	5919	100.000000	1	3205	1	chr2A.!!$R2	3204
1	TraesCS2A01G102900	chr2A	55971245	55972761	1516	True	2255.000000	2255	93.454000	1674	3205	1	chr2A.!!$R1	1531
2	TraesCS2A01G102900	chr2B	87516145	87518294	2149	True	1648.500000	2992	94.108000	997	3205	2	chr2B.!!$R3	2208
3	TraesCS2A01G102900	chr2B	87528520	87530525	2005	True	920.333333	1349	91.652000	997	3123	3	chr2B.!!$R4	2126
4	TraesCS2A01G102900	chr2B	87422072	87424048	1976	True	631.750000	745	91.127000	997	2957	4	chr2B.!!$R2	1960
5	TraesCS2A01G102900	chr2D	58636311	58641004	4693	False	1564.666667	2231	93.520000	1	3202	3	chr2D.!!$F1	3201
6	TraesCS2A01G102900	chr2D	55242455	55250160	7705	True	966.500000	1557	93.014333	719	3205	6	chr2D.!!$R1	2486

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	End Stability	Orientation
471	475	0.319297	ACGGCGGTTACTTCACAGAC	60.319	55.000	13.24	3.51	F
533	537	1.804151	GTTGCTCATGTTTCCTGCGTA	59.196	47.619	0.00	4.42	F
2054	3780	1.844497	TCATCTACTCCCTCCGTCTCA	59.156	52.381	0.00	3.27	F

Position	MSA Position	Penalty	Sequence	TM	GC	End Stability	Orientation
2108	3834	0.115745	AAACTACTCCCTCCGTCCCA	59.884	55.000	4.37	R
2109	3835	1.273759	AAAACTACTCCCTCCGTCCC	58.726	55.000	4.46	R
3160	10463	6.173427	ACCAAACAAATGACTTTTATGCCT	57.827	33.333	4.75	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
100	101	4.120331	GGCGCAGGTGATTGGTGC	62.120	66.667	10.83	0.00	37.32	5.01
159	160	4.592936	CGCGACGTCCTCCTAGCG	62.593	72.222	16.54	16.54	41.56	4.26
190	191	2.592861	GCGAGGTGGCATCCATCC	60.593	66.667	0.00	0.00	34.66	3.51
191	192	2.910360	CGAGGTGGCATCCATCCA	59.090	61.111	0.00	0.00	34.66	3.41
306	308	2.550606	GGTTGCACGTGGAAGTTTCATA	59.449	45.455	23.57	0.00	0.00	2.15
317	319	5.527582	GTGGAAGTTTCATAGCGGTTATGAT	59.472	40.000	14.14	1.11	45.70	2.45
335	337	9.354673	GGTTATGATCCCTTCAAAAAGATATGA	57.645	33.333	0.00	0.00	38.03	2.15
353	355	3.706389	TGAGAAGGTCATCTCCCCATA	57.294	47.619	2.16	0.00	44.27	2.74
361	363	3.070018	GTCATCTCCCCATAAATCAGCG	58.930	50.000	0.00	0.00	0.00	5.18
383	386	4.564821	CGGGGAGAAATGACCTCTTTTACA	60.565	45.833	0.00	0.00	0.00	2.41
428	432	6.281405	AGTTTACGAGAACTGTTGAAGATGT	58.719	36.000	0.00	0.00	38.39	3.06
467	471	2.134346	TGTAAACGGCGGTTACTTCAC	58.866	47.619	37.89	21.92	34.62	3.18
471	475	0.319297	ACGGCGGTTACTTCACAGAC	60.319	55.000	13.24	0.00	0.00	3.51
533	537	1.804151	GTTGCTCATGTTTCCTGCGTA	59.196	47.619	0.00	0.00	0.00	4.42
600	2189	5.886992	ACGTTACTTCTTCCCTTGTTTTTG	58.113	37.500	0.00	0.00	0.00	2.44
613	2202	5.304357	CCCTTGTTTTTGTCTATCAACCCTT	59.696	40.000	0.00	0.00	35.61	3.95
624	2213	8.073467	TGTCTATCAACCCTTTCTTTTGTTTT	57.927	30.769	0.00	0.00	0.00	2.43
642	2231	3.570912	TTTTGACGAGGGGACTTCTTT	57.429	42.857	0.00	0.00	44.43	2.52
650	2239	4.017808	CGAGGGGACTTCTTTTCTCTCTA	58.982	47.826	0.00	0.00	44.43	2.43
683	2272	5.545063	TTCTTTTGAGGTTTTCATTCCCC	57.455	39.130	0.00	0.00	35.27	4.81
813	2406	6.127168	CGATGGGCTTTATATACATCCTACCA	60.127	42.308	0.00	0.00	35.67	3.25
975	2568	4.509970	GGCAACACACAAAAACCCTAATTC	59.490	41.667	0.00	0.00	0.00	2.17
976	2569	4.509970	GCAACACACAAAAACCCTAATTCC	59.490	41.667	0.00	0.00	0.00	3.01
1202	2831	6.371595	TGAATGCCAAAATTCCCAAAGTAT	57.628	33.333	0.00	0.00	35.98	2.12
1406	3097	8.208224	TCGCCTTACTTGGATCTGAATTTAATA	58.792	33.333	0.00	0.00	0.00	0.98
1407	3098	8.836413	CGCCTTACTTGGATCTGAATTTAATAA	58.164	33.333	0.00	0.00	0.00	1.40
1476	3170	2.044650	GCAGGCAGAGATTGGGCA	60.045	61.111	0.00	0.00	0.00	5.36
1668	3394	4.713946	TGAATGGCAGACGGTTCC	57.286	55.556	0.00	0.00	0.00	3.62
1861	3587	2.644676	GGTTCAGGTCATTTAGGGCTC	58.355	52.381	0.00	0.00	0.00	4.70
2048	3774	8.602472	ATTATATGAACTCATCTACTCCCTCC	57.398	38.462	0.00	0.00	37.76	4.30
2049	3775	2.656002	TGAACTCATCTACTCCCTCCG	58.344	52.381	0.00	0.00	0.00	4.63
2050	3776	2.025226	TGAACTCATCTACTCCCTCCGT	60.025	50.000	0.00	0.00	0.00	4.69
2051	3777	2.351706	ACTCATCTACTCCCTCCGTC	57.648	55.000	0.00	0.00	0.00	4.79
2052	3778	1.847737	ACTCATCTACTCCCTCCGTCT	59.152	52.381	0.00	0.00	0.00	4.18
2053	3779	2.158726	ACTCATCTACTCCCTCCGTCTC	60.159	54.545	0.00	0.00	0.00	3.36
2054	3780	1.844497	TCATCTACTCCCTCCGTCTCA	59.156	52.381	0.00	0.00	0.00	3.27
2055	3781	2.443632	TCATCTACTCCCTCCGTCTCAT	59.556	50.000	0.00	0.00	0.00	2.90
2056	3782	3.651423	TCATCTACTCCCTCCGTCTCATA	59.349	47.826	0.00	0.00	0.00	2.15
2057	3783	4.104261	TCATCTACTCCCTCCGTCTCATAA	59.896	45.833	0.00	0.00	0.00	1.90
2058	3784	4.726035	TCTACTCCCTCCGTCTCATAAT	57.274	45.455	0.00	0.00	0.00	1.28
2059	3785	4.399219	TCTACTCCCTCCGTCTCATAATG	58.601	47.826	0.00	0.00	0.00	1.90
2060	3786	3.033659	ACTCCCTCCGTCTCATAATGT	57.966	47.619	0.00	0.00	0.00	2.71
2061	3787	4.180377	ACTCCCTCCGTCTCATAATGTA	57.820	45.455	0.00	0.00	0.00	2.29
2062	3788	4.543689	ACTCCCTCCGTCTCATAATGTAA	58.456	43.478	0.00	0.00	0.00	2.41
2063	3789	4.585162	ACTCCCTCCGTCTCATAATGTAAG	59.415	45.833	0.00	0.00	0.00	2.34
2064	3790	4.800023	TCCCTCCGTCTCATAATGTAAGA	58.200	43.478	0.00	0.00	0.00	2.10
2065	3791	4.583489	TCCCTCCGTCTCATAATGTAAGAC	59.417	45.833	0.00	0.00	36.82	3.01
2073	3799	7.938971	GTCTCATAATGTAAGACGCTTTTTG	57.061	36.000	0.00	0.00	31.01	2.44
2074	3800	7.739295	GTCTCATAATGTAAGACGCTTTTTGA	58.261	34.615	0.00	0.00	31.01	2.69
2075	3801	7.688578	GTCTCATAATGTAAGACGCTTTTTGAC	59.311	37.037	0.00	0.00	31.01	3.18
2076	3802	7.386573	TCTCATAATGTAAGACGCTTTTTGACA	59.613	33.333	0.00	0.00	0.00	3.58
2077	3803	8.039603	TCATAATGTAAGACGCTTTTTGACAT	57.960	30.769	0.00	0.25	0.00	3.06
2078	3804	8.511321	TCATAATGTAAGACGCTTTTTGACATT	58.489	29.630	15.86	15.86	38.95	2.71
2079	3805	9.767684	CATAATGTAAGACGCTTTTTGACATTA	57.232	29.630	17.77	17.77	40.56	1.90
2082	3808	8.673626	ATGTAAGACGCTTTTTGACATTATTG	57.326	30.769	0.00	0.00	0.00	1.90
2083	3809	7.644490	TGTAAGACGCTTTTTGACATTATTGT	58.356	30.769	0.00	0.00	39.32	2.71
2084	3810	8.775527	TGTAAGACGCTTTTTGACATTATTGTA	58.224	29.630	0.00	0.00	35.79	2.41
2085	3811	9.262472	GTAAGACGCTTTTTGACATTATTGTAG	57.738	33.333	0.00	0.00	35.79	2.74
2086	3812	7.435068	AGACGCTTTTTGACATTATTGTAGT	57.565	32.000	0.00	0.00	35.79	2.73
2087	3813	7.298122	AGACGCTTTTTGACATTATTGTAGTG	58.702	34.615	0.00	0.00	35.79	2.74
2088	3814	6.966021	ACGCTTTTTGACATTATTGTAGTGT	58.034	32.000	0.00	0.00	35.79	3.55
2089	3815	7.422399	ACGCTTTTTGACATTATTGTAGTGTT	58.578	30.769	0.00	0.00	35.79	3.32
2090	3816	8.561212	ACGCTTTTTGACATTATTGTAGTGTTA	58.439	29.630	0.00	0.00	35.79	2.41
2091	3817	9.388346	CGCTTTTTGACATTATTGTAGTGTTAA	57.612	29.630	0.00	0.00	35.79	2.01
2116	3842	5.623956	AATGTCTTACATTATGGGACGGA	57.376	39.130	3.51	0.00	46.11	4.69
2117	3843	4.665833	TGTCTTACATTATGGGACGGAG	57.334	45.455	0.00	0.00	0.00	4.63
2118	3844	3.386726	TGTCTTACATTATGGGACGGAGG	59.613	47.826	0.00	0.00	0.00	4.30
2119	3845	2.969950	TCTTACATTATGGGACGGAGGG	59.030	50.000	0.00	0.00	0.00	4.30
2120	3846	2.779429	TACATTATGGGACGGAGGGA	57.221	50.000	0.00	0.00	0.00	4.20
2121	3847	1.424638	ACATTATGGGACGGAGGGAG	58.575	55.000	0.00	0.00	0.00	4.30
2248	4147	3.190535	GCCATCGTCAACCTGTTATGTTT	59.809	43.478	0.00	0.00	0.00	2.83
2305	6405	8.517878	ACAACCATCACTAAATTCTTTCATGAG	58.482	33.333	0.00	0.00	0.00	2.90
2395	6495	1.732259	CGCCAACAAGACTATGGTGAC	59.268	52.381	8.89	0.00	45.43	3.67
2479	6585	6.920758	AGAGAAGATGCAATTAGTTAGCTACG	59.079	38.462	0.00	0.00	0.00	3.51
2521	6627	8.239038	TCCTACTACCTTCATTACTTCATGAG	57.761	38.462	0.00	0.00	34.59	2.90
2568	6674	1.538512	GACCTGTTTTAAACCCTCCGC	59.461	52.381	5.32	0.00	0.00	5.54
2632	6739	3.954200	TGCCATGAGATTGACAAGCTTA	58.046	40.909	7.50	3.66	0.00	3.09
3142	10445	8.851145	TCTTTTGCACACAACCATTACTAAATA	58.149	29.630	0.00	0.00	34.87	1.40
3194	10497	0.662619	TTGTTTGGTCGAGCTGCTTG	59.337	50.000	16.64	10.76	0.00	4.01

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
142	143	4.592936	CGCTAGGAGGACGTCGCG	62.593	72.222	16.54	16.54	38.99	5.87
174	175	1.227764	CTGGATGGATGCCACCTCG	60.228	63.158	0.00	0.00	35.80	4.63
177	178	1.152610	ATGCTGGATGGATGCCACC	60.153	57.895	0.00	0.00	35.80	4.61
194	195	3.353836	GTGTTGTCGCGCCACCAT	61.354	61.111	0.00	0.00	0.00	3.55
273	275	2.335011	GCAACCTGTCAAACGCCC	59.665	61.111	0.00	0.00	0.00	6.13
275	277	1.654137	CGTGCAACCTGTCAAACGC	60.654	57.895	0.00	0.00	0.00	4.84
276	278	0.588730	CACGTGCAACCTGTCAAACG	60.589	55.000	0.82	0.00	37.09	3.60
280	282	0.813610	CTTCCACGTGCAACCTGTCA	60.814	55.000	10.91	0.00	0.00	3.58
306	308	3.644966	TTTGAAGGGATCATAACCGCT	57.355	42.857	0.00	0.00	38.03	5.52
335	337	4.977739	TGATTTATGGGGAGATGACCTTCT	59.022	41.667	0.00	0.00	0.00	2.85
353	355	2.369394	GTCATTTCTCCCCGCTGATTT	58.631	47.619	0.00	0.00	0.00	2.17
361	363	4.918588	TGTAAAAGAGGTCATTTCTCCCC	58.081	43.478	0.00	0.00	31.96	4.81
453	457	0.319211	TGTCTGTGAAGTAACCGCCG	60.319	55.000	0.00	0.00	0.00	6.46
467	471	1.302511	CCAACGGTTCCCCTGTCTG	60.303	63.158	0.00	0.00	0.00	3.51
471	475	0.889186	CAACTCCAACGGTTCCCCTG	60.889	60.000	0.00	0.00	0.00	4.45
505	509	4.776322	CATGAGCAACGCCCCCGA	62.776	66.667	0.00	0.00	38.29	5.14
533	537	0.326618	AGGTGCTAGGCTACCCACAT	60.327	55.000	17.44	10.81	37.70	3.21
600	2189	8.817100	CAAAAACAAAAGAAAGGGTTGATAGAC	58.183	33.333	0.00	0.00	0.00	2.59
613	2202	4.017808	TCCCCTCGTCAAAAACAAAAGAA	58.982	39.130	0.00	0.00	0.00	2.52
624	2213	2.704065	AGAAAAGAAGTCCCCTCGTCAA	59.296	45.455	0.00	0.00	0.00	3.18
660	2249	5.452636	CGGGGAATGAAAACCTCAAAAGAAA	60.453	40.000	0.00	0.00	37.67	2.52
813	2406	1.893919	GCCGAAACTGAGAGGCTCCT	61.894	60.000	11.71	0.00	45.67	3.69
906	2499	1.433534	CTCTCTTGAAGCCGTTGGAC	58.566	55.000	0.00	0.00	0.00	4.02
976	2569	2.233605	TATGTCGGGGCGTGGTTCTG	62.234	60.000	0.00	0.00	0.00	3.02
1202	2831	9.573166	TGAAATTCAGATCCAAGTAAGAAGAAA	57.427	29.630	0.00	0.00	0.00	2.52
1476	3170	5.791336	TGCTAGATGTCCGAATGAATAGT	57.209	39.130	0.00	0.00	0.00	2.12
1668	3394	3.060098	GTGCGAGATTTTCTTCTGACTCG	59.940	47.826	0.00	0.00	46.11	4.18
1806	3532	2.005370	TATGGTCACGAGATACCCCC	57.995	55.000	0.00	0.00	34.69	5.40
1861	3587	3.600717	TTTGTACACAGACATTGCACG	57.399	42.857	0.00	0.00	0.00	5.34
2039	3765	4.180377	ACATTATGAGACGGAGGGAGTA	57.820	45.455	0.00	0.00	0.00	2.59
2040	3766	3.033659	ACATTATGAGACGGAGGGAGT	57.966	47.619	0.00	0.00	0.00	3.85
2041	3767	4.827835	TCTTACATTATGAGACGGAGGGAG	59.172	45.833	0.00	0.00	0.00	4.30
2042	3768	4.583489	GTCTTACATTATGAGACGGAGGGA	59.417	45.833	0.00	0.00	34.53	4.20
2043	3769	4.872664	GTCTTACATTATGAGACGGAGGG	58.127	47.826	0.00	0.00	34.53	4.30
2049	3775	7.688578	GTCAAAAAGCGTCTTACATTATGAGAC	59.311	37.037	0.00	1.64	39.92	3.36
2050	3776	7.386573	TGTCAAAAAGCGTCTTACATTATGAGA	59.613	33.333	0.00	0.00	0.00	3.27
2051	3777	7.518161	TGTCAAAAAGCGTCTTACATTATGAG	58.482	34.615	0.00	0.00	0.00	2.90
2052	3778	7.428282	TGTCAAAAAGCGTCTTACATTATGA	57.572	32.000	0.00	0.00	0.00	2.15
2053	3779	8.673626	AATGTCAAAAAGCGTCTTACATTATG	57.326	30.769	12.58	0.00	35.08	1.90
2056	3782	9.128107	CAATAATGTCAAAAAGCGTCTTACATT	57.872	29.630	15.86	15.86	38.96	2.71
2057	3783	8.296713	ACAATAATGTCAAAAAGCGTCTTACAT	58.703	29.630	0.00	0.00	33.41	2.29
2058	3784	7.644490	ACAATAATGTCAAAAAGCGTCTTACA	58.356	30.769	0.00	0.00	33.41	2.41
2059	3785	9.262472	CTACAATAATGTCAAAAAGCGTCTTAC	57.738	33.333	0.00	0.00	41.05	2.34
2060	3786	8.995220	ACTACAATAATGTCAAAAAGCGTCTTA	58.005	29.630	0.00	0.00	41.05	2.10
2061	3787	7.803189	CACTACAATAATGTCAAAAAGCGTCTT	59.197	33.333	0.00	0.00	41.05	3.01
2062	3788	7.041372	ACACTACAATAATGTCAAAAAGCGTCT	60.041	33.333	0.00	0.00	41.05	4.18
2063	3789	7.075741	ACACTACAATAATGTCAAAAAGCGTC	58.924	34.615	0.00	0.00	41.05	5.19
2064	3790	6.966021	ACACTACAATAATGTCAAAAAGCGT	58.034	32.000	0.00	0.00	41.05	5.07
2065	3791	7.851822	AACACTACAATAATGTCAAAAAGCG	57.148	32.000	0.00	0.00	41.05	4.68
2091	3817	6.887545	TCCGTCCCATAATGTAAGACATTTTT	59.112	34.615	9.92	0.00	45.80	1.94
2092	3818	6.419791	TCCGTCCCATAATGTAAGACATTTT	58.580	36.000	9.92	0.33	45.80	1.82
2093	3819	5.996644	TCCGTCCCATAATGTAAGACATTT	58.003	37.500	9.92	0.00	45.80	2.32
2095	3821	4.040461	CCTCCGTCCCATAATGTAAGACAT	59.960	45.833	0.00	0.00	41.31	3.06
2096	3822	3.386726	CCTCCGTCCCATAATGTAAGACA	59.613	47.826	0.00	0.00	0.00	3.41
2097	3823	3.244112	CCCTCCGTCCCATAATGTAAGAC	60.244	52.174	0.00	0.00	0.00	3.01
2098	3824	2.969950	CCCTCCGTCCCATAATGTAAGA	59.030	50.000	0.00	0.00	0.00	2.10
2099	3825	2.969950	TCCCTCCGTCCCATAATGTAAG	59.030	50.000	0.00	0.00	0.00	2.34
2100	3826	2.969950	CTCCCTCCGTCCCATAATGTAA	59.030	50.000	0.00	0.00	0.00	2.41
2101	3827	2.090943	ACTCCCTCCGTCCCATAATGTA	60.091	50.000	0.00	0.00	0.00	2.29
2102	3828	1.344087	ACTCCCTCCGTCCCATAATGT	60.344	52.381	0.00	0.00	0.00	2.71
2103	3829	1.424638	ACTCCCTCCGTCCCATAATG	58.575	55.000	0.00	0.00	0.00	1.90
2104	3830	2.179424	ACTACTCCCTCCGTCCCATAAT	59.821	50.000	0.00	0.00	0.00	1.28
2105	3831	1.572415	ACTACTCCCTCCGTCCCATAA	59.428	52.381	0.00	0.00	0.00	1.90
2106	3832	1.229131	ACTACTCCCTCCGTCCCATA	58.771	55.000	0.00	0.00	0.00	2.74
2107	3833	0.338814	AACTACTCCCTCCGTCCCAT	59.661	55.000	0.00	0.00	0.00	4.00
2108	3834	0.115745	AAACTACTCCCTCCGTCCCA	59.884	55.000	0.00	0.00	0.00	4.37
2109	3835	1.273759	AAAACTACTCCCTCCGTCCC	58.726	55.000	0.00	0.00	0.00	4.46
2110	3836	4.750021	ATAAAAACTACTCCCTCCGTCC	57.250	45.455	0.00	0.00	0.00	4.79
2111	3837	8.728337	AAATAATAAAAACTACTCCCTCCGTC	57.272	34.615	0.00	0.00	0.00	4.79
2112	3838	9.170734	GAAAATAATAAAAACTACTCCCTCCGT	57.829	33.333	0.00	0.00	0.00	4.69
2113	3839	9.392259	AGAAAATAATAAAAACTACTCCCTCCG	57.608	33.333	0.00	0.00	0.00	4.63
2159	4058	5.877012	CCAAGTTCACTACACATAAGAGCAT	59.123	40.000	0.00	0.00	0.00	3.79
2248	4147	5.468540	TGCAAGCTAAAGAAGACTGACTA	57.531	39.130	0.00	0.00	0.00	2.59
2305	6405	7.553044	ACAAATAACTTCTATGCCCTACACTTC	59.447	37.037	0.00	0.00	0.00	3.01
2395	6495	6.673154	TGATCACAGCAGAACTTGATATTG	57.327	37.500	0.00	0.00	30.88	1.90
2479	6585	6.181206	AGTAGGAGCAAAGGATAAGGATTC	57.819	41.667	0.00	0.00	0.00	2.52
2521	6627	5.689383	TTTGAGTCTATGTGCAGGTTTTC	57.311	39.130	0.00	0.00	0.00	2.29
2568	6674	1.944024	TCTGTTTTACACGGGTTGCTG	59.056	47.619	0.00	0.00	31.75	4.41
3119	10422	9.416794	CAATATTTAGTAATGGTTGTGTGCAAA	57.583	29.630	0.00	0.00	36.22	3.68
3160	10463	6.173427	ACCAAACAAATGACTTTTATGCCT	57.827	33.333	0.00	0.00	0.00	4.75

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.