AutoCloner

Multiple sequence alignment - TraesCS2D01G529500

Loading Multiple Alignment...

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	TraesCS2D01G529500	chr2D	100.000	3928	0	0	1	3928	616628907	616624980	0.000000e+00	7254.0
1	TraesCS2D01G529500	chr2D	83.601	1994	197	53	2029	3924	623790998	623792959	0.000000e+00	1751.0
2	TraesCS2D01G529500	chr2D	84.364	582	79	4	2235	2806	129941611	129942190	1.050000e-155	560.0
3	TraesCS2D01G529500	chr2D	85.780	436	41	6	2569	2990	623793660	623794088	3.980000e-120	442.0
4	TraesCS2D01G529500	chr2D	83.537	492	51	17	1682	2161	623790525	623790998	2.400000e-117	433.0
5	TraesCS2D01G529500	chr2D	81.366	322	41	12	3608	3913	623854456	623854774	1.200000e-60	244.0
6	TraesCS2D01G529500	chr2D	100.000	81	0	0	4257	4337	616624651	616624571	2.700000e-32	150.0
7	TraesCS2D01G529500	chr2A	90.648	3208	142	47	758	3874	746842129	746838989	0.000000e+00	4117.0
8	TraesCS2D01G529500	chr2A	85.921	1385	121	24	2029	3351	755060659	755062031	0.000000e+00	1410.0
9	TraesCS2D01G529500	chr2A	81.503	865	111	33	2228	3066	71683901	71683060	0.000000e+00	665.0
10	TraesCS2D01G529500	chr2A	93.443	244	13	3	285	528	746843199	746842959	4.120000e-95	359.0
11	TraesCS2D01G529500	chr2A	90.955	199	14	1	525	723	746842503	746842309	9.250000e-67	265.0
12	TraesCS2D01G529500	chr2A	89.937	159	13	2	2002	2157	755060497	755060655	7.350000e-48	202.0
13	TraesCS2D01G529500	chr2A	94.048	84	5	0	2906	2989	754708983	754708900	1.270000e-25	128.0
14	TraesCS2D01G529500	chr2A	95.161	62	3	0	49	110	21189300	21189239	9.930000e-17	99.0
15	TraesCS2D01G529500	chr2B	92.222	2957	96	41	595	3464	751605428	751602519	0.000000e+00	4063.0
16	TraesCS2D01G529500	chr2B	85.821	1333	114	32	2019	3286	765561882	765563204	0.000000e+00	1345.0
17	TraesCS2D01G529500	chr2B	82.877	876	116	25	2217	3073	110520863	110520003	0.000000e+00	756.0
18	TraesCS2D01G529500	chr2B	94.154	479	23	3	3455	3928	751588775	751588297	0.000000e+00	725.0
19	TraesCS2D01G529500	chr2B	80.166	721	94	31	3217	3913	765564140	765564835	1.080000e-135	494.0
20	TraesCS2D01G529500	chr2B	90.566	371	14	10	285	644	751605774	751605414	5.080000e-129	472.0
21	TraesCS2D01G529500	chr2B	88.028	284	23	9	5	281	751606384	751606105	4.180000e-85	326.0
22	TraesCS2D01G529500	chr2B	90.604	149	14	0	2029	2177	765561757	765561905	9.510000e-47	198.0
23	TraesCS2D01G529500	chr2B	95.062	81	4	0	4257	4337	751588166	751588086	1.270000e-25	128.0
24	TraesCS2D01G529500	chr2B	94.048	84	5	0	2906	2989	765486840	765486757	1.270000e-25	128.0
25	TraesCS2D01G529500	chr2B	85.263	95	14	0	109	203	717097589	717097495	9.930000e-17	99.0
26	TraesCS2D01G529500	chr7D	85.073	1092	108	29	2034	3081	534655367	534654287	0.000000e+00	1062.0
27	TraesCS2D01G529500	chr7D	91.892	185	11	3	3165	3349	534653734	534653554	5.570000e-64	255.0
28	TraesCS2D01G529500	chr7D	90.798	163	12	2	2002	2161	534655534	534655372	9.450000e-52	215.0
29	TraesCS2D01G529500	chr7D	78.125	128	25	3	3786	3912	181851262	181851137	1.290000e-10	78.7
30	TraesCS2D01G529500	chr7B	81.507	146	19	4	41	178	165457828	165457683	3.540000e-21	113.0
31	TraesCS2D01G529500	chr7B	89.655	87	9	0	109	195	702385432	702385346	1.270000e-20	111.0
32	TraesCS2D01G529500	chr7B	96.774	62	1	1	48	108	504808402	504808341	7.670000e-18	102.0
33	TraesCS2D01G529500	chr6B	82.482	137	14	8	41	168	483589754	483589619	1.270000e-20	111.0
34	TraesCS2D01G529500	chr6B	78.462	130	22	5	3785	3912	347873268	347873143	3.600000e-11	80.5
35	TraesCS2D01G529500	chr6B	77.612	134	27	3	3780	3912	597758163	597758294	1.290000e-10	78.7
36	TraesCS2D01G529500	chr5D	86.735	98	13	0	106	203	15956916	15957013	4.590000e-20	110.0
37	TraesCS2D01G529500	chr5D	84.000	100	15	1	104	202	424938846	424938747	1.280000e-15	95.3
38	TraesCS2D01G529500	chr5D	83.673	98	14	2	3816	3912	442286250	442286346	1.660000e-14	91.6
39	TraesCS2D01G529500	chr1B	87.368	95	12	0	3816	3910	514823506	514823600	4.590000e-20	110.0
40	TraesCS2D01G529500	chr3D	87.500	96	9	3	111	205	114135954	114135861	1.650000e-19	108.0
41	TraesCS2D01G529500	chr3D	94.030	67	3	1	43	108	302932593	302932659	2.760000e-17	100.0
42	TraesCS2D01G529500	chr3D	85.714	98	10	1	106	203	511575678	511575771	2.760000e-17	100.0
43	TraesCS2D01G529500	chr3A	89.412	85	9	0	111	195	746151110	746151194	1.650000e-19	108.0
44	TraesCS2D01G529500	chr5B	95.238	63	3	0	48	110	565717065	565717127	2.760000e-17	100.0
45	TraesCS2D01G529500	chr5A	95.238	63	2	1	49	110	19674220	19674158	9.930000e-17	99.0
46	TraesCS2D01G529500	chr6A	93.750	64	2	2	47	108	48707559	48707622	1.280000e-15	95.3
47	TraesCS2D01G529500	chr1D	85.870	92	10	3	106	195	481338308	481338398	1.280000e-15	95.3
48	TraesCS2D01G529500	chr1D	78.358	134	18	8	3397	3523	324723465	324723594	4.650000e-10	76.8
49	TraesCS2D01G529500	chr3B	93.182	44	3	0	3383	3426	775096379	775096336	1.010000e-06	65.8

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	TraesCS2D01G529500	chr2D	616624571	616628907	4336	True	3702.000000	7254	100.000000	1	4337	2	chr2D.!!$R1	4336
1	TraesCS2D01G529500	chr2D	623790525	623794088	3563	False	875.333333	1751	84.306000	1682	3924	3	chr2D.!!$F3	2242
2	TraesCS2D01G529500	chr2D	129941611	129942190	579	False	560.000000	560	84.364000	2235	2806	1	chr2D.!!$F1	571
3	TraesCS2D01G529500	chr2A	746838989	746843199	4210	True	1580.333333	4117	91.682000	285	3874	3	chr2A.!!$R4	3589
4	TraesCS2D01G529500	chr2A	755060497	755062031	1534	False	806.000000	1410	87.929000	2002	3351	2	chr2A.!!$F1	1349
5	TraesCS2D01G529500	chr2A	71683060	71683901	841	True	665.000000	665	81.503000	2228	3066	1	chr2A.!!$R2	838
6	TraesCS2D01G529500	chr2B	751602519	751606384	3865	True	1620.333333	4063	90.272000	5	3464	3	chr2B.!!$R5	3459
7	TraesCS2D01G529500	chr2B	110520003	110520863	860	True	756.000000	756	82.877000	2217	3073	1	chr2B.!!$R1	856
8	TraesCS2D01G529500	chr2B	765561757	765564835	3078	False	679.000000	1345	85.530333	2019	3913	3	chr2B.!!$F1	1894
9	TraesCS2D01G529500	chr2B	751588086	751588775	689	True	426.500000	725	94.608000	3455	4337	2	chr2B.!!$R4	882
10	TraesCS2D01G529500	chr7D	534653554	534655534	1980	True	510.666667	1062	89.254333	2002	3349	3	chr7D.!!$R2	1347

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
206	208	0.495612	CGCGCATCATCGAAAAATGC	59.504	50.0	8.75	15.96	41.82	3.56	F
660	1489	0.597637	GATGGTAGCAGCGCACGTAT	60.598	55.0	11.47	0.00	0.00	3.06	F
1677	2691	0.666374	TCAAAGTCAGCGTCGACTCA	59.334	50.0	14.70	0.00	45.56	3.41	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1930	2950	0.249073	CATTCGACGGGAAGAGCGAT	60.249	55.000	0.00	38.24	4.58	R
2200	3388	2.284699	CTTGGGGAGGAGGTCGGT	60.285	66.667	0.00	0.00	4.69	R
3590	6425	1.298014	CTTCTCACCCAGTGGCTCC	59.702	63.158	2.61	33.87	4.70	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	3.766068	TTTGATTTTGCAATGGGCTGA	57.234	38.095	0.00	0.00	45.15	4.26
77	78	2.027625	GGTACAGACGCAAGCGCTT	61.028	57.895	18.98	18.98	44.19	4.68
120	122	2.092753	CCCTATGAATGAGCCGGCATAT	60.093	50.000	31.54	19.46	0.00	1.78
121	123	3.201290	CCTATGAATGAGCCGGCATATC	58.799	50.000	31.54	18.63	0.00	1.63
138	140	9.166173	CCGGCATATCATCTTAAGATTTATGAA	57.834	33.333	29.10	14.59	33.82	2.57
149	151	9.383519	TCTTAAGATTTATGAAGCAACTGTAGG	57.616	33.333	0.00	0.00	0.00	3.18
156	158	2.047274	GCAACTGTAGGCGCCTCA	60.047	61.111	36.73	27.51	0.00	3.86
187	189	3.688185	GGGAACGTCTCCTTCCATTAAAC	59.312	47.826	13.94	0.00	44.68	2.01
196	198	2.033299	CCTTCCATTAAACGCGCATCAT	59.967	45.455	5.73	0.00	0.00	2.45
204	206	2.542766	AACGCGCATCATCGAAAAAT	57.457	40.000	5.73	0.00	0.00	1.82
205	207	1.813896	ACGCGCATCATCGAAAAATG	58.186	45.000	5.73	0.00	0.00	2.32
206	208	0.495612	CGCGCATCATCGAAAAATGC	59.504	50.000	8.75	15.96	41.82	3.56
224	227	1.569479	GCGAGCACTGGGACTTGAAC	61.569	60.000	0.00	0.00	0.00	3.18
225	228	0.951040	CGAGCACTGGGACTTGAACC	60.951	60.000	0.00	0.00	0.00	3.62
226	229	0.606673	GAGCACTGGGACTTGAACCC	60.607	60.000	0.00	0.00	46.87	4.11
231	234	1.352352	ACTGGGACTTGAACCCTGATG	59.648	52.381	14.87	2.01	46.82	3.07
358	689	4.525487	TCTCCGGTTGTAAGAAGTGTGTAT	59.475	41.667	0.00	0.00	0.00	2.29
448	779	4.863131	TCGAGGAAAAGCGAAAGAAGTATC	59.137	41.667	0.00	0.00	33.04	2.24
543	1333	0.809241	CTAAGCTCAGCTTCCAGCCG	60.809	60.000	17.33	0.00	46.77	5.52
659	1488	1.226859	GATGGTAGCAGCGCACGTA	60.227	57.895	11.47	0.00	0.00	3.57
660	1489	0.597637	GATGGTAGCAGCGCACGTAT	60.598	55.000	11.47	0.00	0.00	3.06
661	1490	0.875908	ATGGTAGCAGCGCACGTATG	60.876	55.000	11.47	0.00	0.00	2.39
662	1491	1.518572	GGTAGCAGCGCACGTATGT	60.519	57.895	11.47	0.00	0.00	2.29
706	1535	2.104111	TCACGTTTGACCCATCTTCTGT	59.896	45.455	0.00	0.00	0.00	3.41
713	1548	0.921896	ACCCATCTTCTGTCCCCATG	59.078	55.000	0.00	0.00	0.00	3.66
751	1588	2.832201	ACCTACGGCTACGGGCTC	60.832	66.667	2.91	0.00	46.48	4.70
791	1771	7.213678	GGTTTGGATCAAAACATTCCAGTTAA	58.786	34.615	23.92	0.00	40.38	2.01
792	1772	7.170828	GGTTTGGATCAAAACATTCCAGTTAAC	59.829	37.037	23.92	0.00	40.38	2.01
793	1773	7.595819	TTGGATCAAAACATTCCAGTTAACT	57.404	32.000	1.12	1.12	40.48	2.24
870	1858	2.115291	GGCCGGCTGATTTGAGGAC	61.115	63.158	28.56	0.00	0.00	3.85
871	1859	2.464459	GCCGGCTGATTTGAGGACG	61.464	63.158	22.15	0.00	0.00	4.79
872	1860	1.218047	CCGGCTGATTTGAGGACGA	59.782	57.895	0.00	0.00	0.00	4.20
874	1862	1.438651	CGGCTGATTTGAGGACGAAA	58.561	50.000	0.00	0.00	0.00	3.46
875	1863	2.009774	CGGCTGATTTGAGGACGAAAT	58.990	47.619	0.00	0.00	0.00	2.17
876	1864	2.030946	CGGCTGATTTGAGGACGAAATC	59.969	50.000	0.00	0.00	39.36	2.17
925	1913	3.017314	GCGAGTCGTACGCGGATG	61.017	66.667	15.08	7.96	46.05	3.51
926	1914	2.705220	CGAGTCGTACGCGGATGA	59.295	61.111	9.77	9.77	37.75	2.92
927	1915	1.278937	CGAGTCGTACGCGGATGAT	59.721	57.895	17.84	5.85	37.75	2.45
1497	2504	4.262506	GGGGGTGTATCTGTATTGTCTAGC	60.263	50.000	0.00	0.00	0.00	3.42
1634	2642	1.742831	CAACGAACATACCACCATGGG	59.257	52.381	18.09	4.89	43.37	4.00
1677	2691	0.666374	TCAAAGTCAGCGTCGACTCA	59.334	50.000	14.70	0.00	45.56	3.41
1701	2715	0.963962	AAACTAGGCGAGAACGTGGA	59.036	50.000	0.28	0.00	41.98	4.02
1754	2768	1.148310	CCCATGTTGATCGCCGATAC	58.852	55.000	0.00	0.00	0.00	2.24
1769	2783	1.270839	CGATACCAATGGGGATTCGCT	60.271	52.381	3.55	0.00	38.09	4.93
1859	2879	0.830648	ATCCTCAAATCCCGCTTCGA	59.169	50.000	0.00	0.00	0.00	3.71
1930	2950	3.939939	TGAAGCAGCGCCAGGACA	61.940	61.111	2.29	0.00	0.00	4.02
2012	3032	3.282157	CGATGGCGAGGGCAATGG	61.282	66.667	0.00	0.00	42.43	3.16
2021	3041	1.303309	GAGGGCAATGGAGATTCACG	58.697	55.000	0.00	0.00	0.00	4.35
2072	3239	1.447140	CCAAGTGCATGCATGTGGC	60.447	57.895	29.11	16.17	45.13	5.01
2200	3388	4.028490	GGCATCACCCCACCGACA	62.028	66.667	0.00	0.00	0.00	4.35
2201	3389	2.746277	GCATCACCCCACCGACAC	60.746	66.667	0.00	0.00	0.00	3.67
2393	3590	3.257561	CAAGGTCGCTCGCATCGG	61.258	66.667	0.00	0.00	0.00	4.18
2682	3908	4.521062	CAGAAGCTCGGGCCGGAG	62.521	72.222	30.69	30.69	39.73	4.63
2834	4078	4.800023	TCCATCATCCTACGTTCTCCTTA	58.200	43.478	0.00	0.00	0.00	2.69
2836	4080	5.839063	TCCATCATCCTACGTTCTCCTTATT	59.161	40.000	0.00	0.00	0.00	1.40
2837	4081	5.928839	CCATCATCCTACGTTCTCCTTATTG	59.071	44.000	0.00	0.00	0.00	1.90
2838	4082	6.463049	CCATCATCCTACGTTCTCCTTATTGT	60.463	42.308	0.00	0.00	0.00	2.71
3078	4388	5.654497	CCATGTTAATTTCCTCAAGCCTTC	58.346	41.667	0.00	0.00	0.00	3.46
3105	4617	3.537793	AAAATGTTTCCTCGAGCGAAC	57.462	42.857	17.32	17.32	0.00	3.95
3196	4978	0.250124	TGTCGGTGTGGATTGGTGAC	60.250	55.000	0.00	0.00	0.00	3.67
3295	6092	4.218635	TGTTTTATAATGTCCGGCTTGCAA	59.781	37.500	0.00	0.00	0.00	4.08
3447	6273	9.338291	GCTATATTCACAATTTATGCATGAGTG	57.662	33.333	10.16	9.92	0.00	3.51
3458	6288	3.696281	TGCATGAGTGGCATAATTTCG	57.304	42.857	0.00	0.00	36.11	3.46
3465	6295	5.639757	TGAGTGGCATAATTTCGTTGATTG	58.360	37.500	0.00	0.00	0.00	2.67
3524	6355	5.631512	TCAGTTGTTGTTTTTGGACTTTTCG	59.368	36.000	0.00	0.00	0.00	3.46
3585	6420	7.506328	AAAAATAGGACGCTAGTTTTCAAGT	57.494	32.000	0.00	0.00	33.59	3.16
3590	6425	3.675698	GGACGCTAGTTTTCAAGTCAGAG	59.324	47.826	0.00	0.00	0.00	3.35
3620	6455	3.673201	GGGTGAGAAGCTCAACTGGAGA	61.673	54.545	11.78	0.00	46.38	3.71
3823	6694	9.258629	TGTCATAGGGAAATTTTGATCTTCATT	57.741	29.630	0.00	0.00	0.00	2.57
3920	6791	0.608130	AGCTATGTGTTCACTGGCGA	59.392	50.000	4.59	0.00	0.00	5.54
3921	6792	1.002366	GCTATGTGTTCACTGGCGAG	58.998	55.000	4.59	0.00	0.00	5.03
3922	6793	1.002366	CTATGTGTTCACTGGCGAGC	58.998	55.000	0.00	0.00	0.00	5.03
3923	6794	0.608130	TATGTGTTCACTGGCGAGCT	59.392	50.000	0.00	0.00	0.00	4.09
3924	6795	0.952497	ATGTGTTCACTGGCGAGCTG	60.952	55.000	0.00	0.00	0.00	4.24
3925	6796	1.300931	GTGTTCACTGGCGAGCTGA	60.301	57.895	0.00	0.00	0.00	4.26
3926	6797	1.005748	TGTTCACTGGCGAGCTGAG	60.006	57.895	0.00	0.00	0.00	3.35
3927	6798	1.005630	GTTCACTGGCGAGCTGAGT	60.006	57.895	0.00	0.00	0.00	3.41
4311	7902	9.426534	TTCTATCTCTCTCCTTTGATCATGTAA	57.573	33.333	0.00	0.00	0.00	2.41

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
5	6	4.458397	TCAGCCCATTGCAAAATCAAAAA	58.542	34.783	1.71	0.00	44.83	1.94
6	7	4.082665	TCAGCCCATTGCAAAATCAAAA	57.917	36.364	1.71	0.00	44.83	2.44
7	8	3.766068	TCAGCCCATTGCAAAATCAAA	57.234	38.095	1.71	0.00	44.83	2.69
8	9	3.766068	TTCAGCCCATTGCAAAATCAA	57.234	38.095	1.71	0.00	44.83	2.57
59	60	0.734942	TAAGCGCTTGCGTCTGTACC	60.735	55.000	32.23	0.00	45.69	3.34
77	78	5.220912	GGGTGAGTGTATGCGCGTATATATA	60.221	44.000	19.79	7.33	0.00	0.86
87	88	3.452755	TTCATAGGGTGAGTGTATGCG	57.547	47.619	0.00	0.00	38.29	4.73
93	94	2.804572	CGGCTCATTCATAGGGTGAGTG	60.805	54.545	10.76	0.00	43.70	3.51
120	122	9.453572	ACAGTTGCTTCATAAATCTTAAGATGA	57.546	29.630	18.61	10.27	34.49	2.92
138	140	1.903877	ATGAGGCGCCTACAGTTGCT	61.904	55.000	32.97	10.75	0.00	3.91
140	142	1.137086	ACTATGAGGCGCCTACAGTTG	59.863	52.381	32.97	21.47	0.00	3.16
141	143	1.409427	GACTATGAGGCGCCTACAGTT	59.591	52.381	32.97	14.54	0.00	3.16
178	180	1.260297	CGATGATGCGCGTTTAATGGA	59.740	47.619	8.43	0.00	0.00	3.41
180	182	2.643875	TCGATGATGCGCGTTTAATG	57.356	45.000	8.43	0.00	0.00	1.90
182	184	3.457198	TTTTCGATGATGCGCGTTTAA	57.543	38.095	8.43	0.00	0.00	1.52
184	186	2.323939	TTTTTCGATGATGCGCGTTT	57.676	40.000	8.43	0.00	0.00	3.60
187	189	0.495612	GCATTTTTCGATGATGCGCG	59.504	50.000	0.00	0.00	37.09	6.86
196	198	0.516877	CCAGTGCTCGCATTTTTCGA	59.483	50.000	0.00	0.00	34.52	3.71
204	206	2.031012	CAAGTCCCAGTGCTCGCA	59.969	61.111	0.00	0.00	0.00	5.10
205	207	1.301716	TTCAAGTCCCAGTGCTCGC	60.302	57.895	0.00	0.00	0.00	5.03
206	208	0.951040	GGTTCAAGTCCCAGTGCTCG	60.951	60.000	0.00	0.00	0.00	5.03
224	227	6.840780	AAAGTTAATCAAAGTCCATCAGGG	57.159	37.500	0.00	0.00	34.83	4.45
312	643	9.723447	GAGACGACCATGTTATATGATATACAG	57.277	37.037	0.00	0.00	0.00	2.74
358	689	1.347062	GGCCCACCCATTCTGAAAAA	58.653	50.000	0.00	0.00	0.00	1.94
543	1333	1.480954	TGGCCGATAGAGGAAGAACAC	59.519	52.381	0.00	0.00	39.76	3.32
579	1380	4.398549	TGTCTACGTTGTTGCTAAATGC	57.601	40.909	0.00	0.00	43.25	3.56
791	1771	9.213799	CTCTTTTGCACTTCTTTAATCTAGAGT	57.786	33.333	0.00	0.00	0.00	3.24
792	1772	8.663911	CCTCTTTTGCACTTCTTTAATCTAGAG	58.336	37.037	0.00	0.00	0.00	2.43
793	1773	8.375506	TCCTCTTTTGCACTTCTTTAATCTAGA	58.624	33.333	0.00	0.00	0.00	2.43
815	1803	0.609406	GTGGCCTGTTTCCCTTCCTC	60.609	60.000	3.32	0.00	0.00	3.71
871	1859	4.015977	CGTCGAAATTTCAGCTCGATTTC	58.984	43.478	17.99	12.62	42.93	2.17
872	1860	3.181520	CCGTCGAAATTTCAGCTCGATTT	60.182	43.478	17.99	0.00	42.93	2.17
874	1862	1.927174	CCGTCGAAATTTCAGCTCGAT	59.073	47.619	17.99	0.00	42.93	3.59
875	1863	1.336517	ACCGTCGAAATTTCAGCTCGA	60.337	47.619	17.99	7.02	39.16	4.04
876	1864	1.068474	ACCGTCGAAATTTCAGCTCG	58.932	50.000	17.99	14.19	0.00	5.03
925	1913	0.784778	GCGTACGGCTCAAGCATATC	59.215	55.000	18.39	0.00	44.36	1.63
926	1914	0.939577	CGCGTACGGCTCAAGCATAT	60.940	55.000	18.39	0.00	44.36	1.78
927	1915	1.587876	CGCGTACGGCTCAAGCATA	60.588	57.895	18.39	0.00	44.36	3.14
961	1955	0.034896	TCCGGTCAAGGTCTTTCAGC	59.965	55.000	0.00	0.00	0.00	4.26
1444	2445	4.607557	CGCGCGGTGGTAGAATTAATTAAG	60.608	45.833	24.84	0.00	0.00	1.85
1497	2504	3.426525	GGCAAATTTTGAGCTCGTTTCTG	59.573	43.478	13.26	3.37	0.00	3.02
1618	2626	1.682854	CATGCCCATGGTGGTATGTTC	59.317	52.381	11.73	0.00	41.84	3.18
1677	2691	1.711206	GTTCTCGCCTAGTTTCGCTT	58.289	50.000	0.00	0.00	0.00	4.68
1730	2744	1.449601	GCGATCAACATGGGGTCGT	60.450	57.895	19.23	0.00	34.97	4.34
1754	2768	1.076777	ACCAGCGAATCCCCATTGG	60.077	57.895	0.00	0.00	0.00	3.16
1797	2817	1.323271	TGGGGCAGTAGAAGAGCTCG	61.323	60.000	8.37	0.00	0.00	5.03
1930	2950	0.249073	CATTCGACGGGAAGAGCGAT	60.249	55.000	0.00	0.00	38.24	4.58
2012	3032	2.582498	CGTCCGCCCGTGAATCTC	60.582	66.667	0.00	0.00	0.00	2.75
2200	3388	2.284699	CTTGGGGAGGAGGTCGGT	60.285	66.667	0.00	0.00	0.00	4.69
2834	4078	8.382030	TGCATGATGAGATCGTAATTTACAAT	57.618	30.769	0.00	0.00	0.00	2.71
2836	4080	7.571798	GCATGCATGATGAGATCGTAATTTACA	60.572	37.037	30.64	0.00	33.31	2.41
2837	4081	6.740002	GCATGCATGATGAGATCGTAATTTAC	59.260	38.462	30.64	1.71	33.31	2.01
2838	4082	6.427547	TGCATGCATGATGAGATCGTAATTTA	59.572	34.615	30.64	0.00	33.31	1.40
3098	4610	4.870426	TGACTAGATTTCCATTGTTCGCTC	59.130	41.667	0.00	0.00	0.00	5.03
3105	4617	7.928307	TCTTTTCCTGACTAGATTTCCATTG	57.072	36.000	0.00	0.00	0.00	2.82
3196	4978	9.520204	AAATCGAAAGTGGCAAGAATATTATTG	57.480	29.630	16.71	16.71	32.81	1.90
3295	6092	5.381174	TTGTAGTAGTGTGCATAGTTCGT	57.619	39.130	0.00	0.00	0.00	3.85
3330	6134	2.562738	ACGGTCAGTGATGAGTGATCAA	59.437	45.455	0.00	0.00	42.96	2.57
3439	6265	3.698029	ACGAAATTATGCCACTCATGC	57.302	42.857	0.00	0.00	36.63	4.06
3447	6273	7.704472	TCCAATAACAATCAACGAAATTATGCC	59.296	33.333	0.00	0.00	0.00	4.40
3453	6282	7.120579	TGCTAGTCCAATAACAATCAACGAAAT	59.879	33.333	0.00	0.00	0.00	2.17
3477	6307	7.306213	TGACTCTACGCACTAGATTAATATGC	58.694	38.462	0.00	0.00	30.60	3.14
3585	6420	1.915266	CACCCAGTGGCTCCTCTGA	60.915	63.158	16.97	0.00	39.18	3.27
3590	6425	1.298014	CTTCTCACCCAGTGGCTCC	59.702	63.158	2.61	0.00	33.87	4.70
3823	6694	2.439507	GCAAGGGATGATGGAGAGGTTA	59.560	50.000	0.00	0.00	0.00	2.85
4311	7902	2.027745	ACCGCAATCAAGATCAGACACT	60.028	45.455	0.00	0.00	0.00	3.55

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.