AutoCloner

Multiple sequence alignment - TraesCS7B01G111300

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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	TraesCS7B01G111300	chr7B	100.000	3948	0	0	1	3948	127654390	127650443	0.000000e+00	7291.0
1	TraesCS7B01G111300	chr7B	98.495	2791	40	2	1	2791	127775911	127773123	0.000000e+00	4920.0
2	TraesCS7B01G111300	chr7B	97.636	2792	60	2	1	2791	128072149	128069363	0.000000e+00	4785.0
3	TraesCS7B01G111300	chr7B	95.972	2110	53	9	875	2955	128436445	128438551	0.000000e+00	3397.0
4	TraesCS7B01G111300	chr7B	86.769	650	46	18	2342	2952	134493384	134494032	0.000000e+00	688.0
5	TraesCS7B01G111300	chr7B	84.414	648	92	7	1127	1771	134492380	134493021	2.590000e-176	628.0
6	TraesCS7B01G111300	chr7B	76.825	315	56	13	525	838	651193647	651193349	1.140000e-35	161.0
7	TraesCS7B01G111300	chr7B	88.636	88	8	2	3083	3168	128438628	128438715	5.400000e-19	106.0
8	TraesCS7B01G111300	chr7B	84.694	98	5	3	2992	3088	399888246	399888158	5.430000e-14	89.8
9	TraesCS7B01G111300	chr7B	94.231	52	3	0	3117	3168	134633855	134633804	3.270000e-11	80.5
10	TraesCS7B01G111300	chr7B	97.222	36	0	1	2959	2993	128438595	128438630	4.260000e-05	60.2
11	TraesCS7B01G111300	chr7D	91.276	2132	119	32	874	2959	164752991	164750881	0.000000e+00	2844.0
12	TraesCS7B01G111300	chr7D	89.864	1697	112	21	1305	2955	165118317	165119999	0.000000e+00	2126.0
13	TraesCS7B01G111300	chr7D	87.252	1059	88	25	1876	2905	169421831	169420791	0.000000e+00	1164.0
14	TraesCS7B01G111300	chr7D	85.201	1142	95	26	1885	2955	169440243	169439105	0.000000e+00	1105.0
15	TraesCS7B01G111300	chr7D	85.162	1112	104	32	1876	2956	169025261	169026342	0.000000e+00	1083.0
16	TraesCS7B01G111300	chr7D	94.385	659	31	4	3293	3948	164750649	164749994	0.000000e+00	1007.0
17	TraesCS7B01G111300	chr7D	83.602	744	102	15	1064	1794	169440989	169440253	0.000000e+00	680.0
18	TraesCS7B01G111300	chr7D	89.773	88	7	2	3083	3168	164750813	164750726	1.160000e-20	111.0
19	TraesCS7B01G111300	chr7D	88.608	79	9	0	701	779	260698117	260698039	3.250000e-16	97.1
20	TraesCS7B01G111300	chr7D	83.838	99	7	4	2991	3089	448858754	448858665	7.030000e-13	86.1
21	TraesCS7B01G111300	chr7D	100.000	35	0	0	2959	2993	164750845	164750811	9.160000e-07	65.8
22	TraesCS7B01G111300	chr7D	100.000	32	0	0	3199	3230	169420975	169420944	4.260000e-05	60.2
23	TraesCS7B01G111300	chr7A	90.643	2116	141	28	885	2955	166869089	166871192	0.000000e+00	2758.0
24	TraesCS7B01G111300	chr7A	90.909	1859	124	24	888	2712	166491748	166489901	0.000000e+00	2455.0
25	TraesCS7B01G111300	chr7A	89.711	865	58	16	2113	2956	166594876	166594022	0.000000e+00	1075.0
26	TraesCS7B01G111300	chr7A	85.622	772	68	24	3174	3923	166488747	166487997	0.000000e+00	771.0
27	TraesCS7B01G111300	chr7A	87.424	660	50	13	2325	2955	171438297	171437642	0.000000e+00	728.0
28	TraesCS7B01G111300	chr7A	87.569	547	48	13	2429	2958	171547286	171546743	2.020000e-172	616.0
29	TraesCS7B01G111300	chr7A	85.799	507	38	20	2	490	166492676	166492186	1.270000e-139	507.0
30	TraesCS7B01G111300	chr7A	85.799	507	38	20	2	490	166868164	166868654	1.270000e-139	507.0
31	TraesCS7B01G111300	chr7A	77.104	297	51	13	525	820	726503833	726504113	5.280000e-34	156.0
32	TraesCS7B01G111300	chr7A	89.773	88	7	2	3083	3168	166871279	166871366	1.160000e-20	111.0
33	TraesCS7B01G111300	chr7A	100.000	35	0	0	2959	2993	166871247	166871281	9.160000e-07	65.8
34	TraesCS7B01G111300	chr7A	100.000	32	0	0	3199	3230	171546983	171546952	4.260000e-05	60.2
35	TraesCS7B01G111300	chrUn	88.912	956	70	14	2030	2956	218480268	218481216	0.000000e+00	1146.0
36	TraesCS7B01G111300	chrUn	89.339	469	36	8	2502	2958	309086272	309085806	9.510000e-161	577.0
37	TraesCS7B01G111300	chrUn	82.075	106	5	10	2992	3094	71667174	71667080	1.180000e-10	78.7
38	TraesCS7B01G111300	chrUn	95.455	44	2	0	3049	3092	307259646	307259689	1.970000e-08	71.3
39	TraesCS7B01G111300	chrUn	100.000	32	0	0	3199	3230	309086046	309086015	4.260000e-05	60.2
40	TraesCS7B01G111300	chr6A	83.745	769	101	14	1086	1836	124423003	124423765	0.000000e+00	706.0
41	TraesCS7B01G111300	chr5A	77.460	315	54	13	525	838	570379416	570379118	5.240000e-39	172.0
42	TraesCS7B01G111300	chr5A	84.211	95	6	2	2992	3086	425834588	425834673	2.530000e-12	84.2
43	TraesCS7B01G111300	chr2B	85.714	154	19	2	673	826	131882990	131883140	4.080000e-35	159.0
44	TraesCS7B01G111300	chr2B	95.349	43	2	0	3046	3088	701482447	701482489	7.080000e-08	69.4
45	TraesCS7B01G111300	chr1D	76.508	315	57	14	525	838	67973430	67973132	5.280000e-34	156.0
46	TraesCS7B01G111300	chr1D	88.235	102	3	2	2985	3086	411517707	411517799	3.220000e-21	113.0
47	TraesCS7B01G111300	chr1D	88.889	99	2	1	2989	3087	437574309	437574220	3.220000e-21	113.0
48	TraesCS7B01G111300	chr1D	95.522	67	3	0	2985	3051	413413545	413413479	1.500000e-19	108.0
49	TraesCS7B01G111300	chr4B	92.632	95	5	2	2991	3085	18449667	18449575	6.880000e-28	135.0
50	TraesCS7B01G111300	chr5D	90.000	100	1	2	2989	3088	310742410	310742500	1.930000e-23	121.0
51	TraesCS7B01G111300	chr3A	100.000	60	0	0	2992	3051	647416	647475	1.160000e-20	111.0
52	TraesCS7B01G111300	chr2A	96.923	65	1	1	2987	3051	762665008	762665071	1.500000e-19	108.0
53	TraesCS7B01G111300	chr2A	84.314	102	11	5	2992	3089	56940705	56940605	1.170000e-15	95.3
54	TraesCS7B01G111300	chr2A	81.720	93	15	2	2994	3086	543766728	543766638	4.230000e-10	76.8
55	TraesCS7B01G111300	chr6B	75.210	238	42	11	543	779	399048849	399049070	3.250000e-16	97.1

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	TraesCS7B01G111300	chr7B	127650443	127654390	3947	True	7291.000000	7291	100.000000	1	3948	1	chr7B.!!$R1	3947
1	TraesCS7B01G111300	chr7B	127773123	127775911	2788	True	4920.000000	4920	98.495000	1	2791	1	chr7B.!!$R2	2790
2	TraesCS7B01G111300	chr7B	128069363	128072149	2786	True	4785.000000	4785	97.636000	1	2791	1	chr7B.!!$R3	2790
3	TraesCS7B01G111300	chr7B	128436445	128438715	2270	False	1187.733333	3397	93.943333	875	3168	3	chr7B.!!$F1	2293
4	TraesCS7B01G111300	chr7B	134492380	134494032	1652	False	658.000000	688	85.591500	1127	2952	2	chr7B.!!$F2	1825
5	TraesCS7B01G111300	chr7D	165118317	165119999	1682	False	2126.000000	2126	89.864000	1305	2955	1	chr7D.!!$F1	1650
6	TraesCS7B01G111300	chr7D	169025261	169026342	1081	False	1083.000000	1083	85.162000	1876	2956	1	chr7D.!!$F2	1080
7	TraesCS7B01G111300	chr7D	164749994	164752991	2997	True	1006.950000	2844	93.858500	874	3948	4	chr7D.!!$R3	3074
8	TraesCS7B01G111300	chr7D	169439105	169440989	1884	True	892.500000	1105	84.401500	1064	2955	2	chr7D.!!$R5	1891
9	TraesCS7B01G111300	chr7D	169420791	169421831	1040	True	612.100000	1164	93.626000	1876	3230	2	chr7D.!!$R4	1354
10	TraesCS7B01G111300	chr7A	166487997	166492676	4679	True	1244.333333	2455	87.443333	2	3923	3	chr7A.!!$R3	3921
11	TraesCS7B01G111300	chr7A	166594022	166594876	854	True	1075.000000	1075	89.711000	2113	2956	1	chr7A.!!$R1	843
12	TraesCS7B01G111300	chr7A	166868164	166871366	3202	False	860.450000	2758	91.553750	2	3168	4	chr7A.!!$F2	3166
13	TraesCS7B01G111300	chr7A	171437642	171438297	655	True	728.000000	728	87.424000	2325	2955	1	chr7A.!!$R2	630
14	TraesCS7B01G111300	chr7A	171546743	171547286	543	True	338.100000	616	93.784500	2429	3230	2	chr7A.!!$R4	801
15	TraesCS7B01G111300	chrUn	218480268	218481216	948	False	1146.000000	1146	88.912000	2030	2956	1	chrUn.!!$F1	926
16	TraesCS7B01G111300	chr6A	124423003	124423765	762	False	706.000000	706	83.745000	1086	1836	1	chr6A.!!$F1	750

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
234	240	2.159179	AAAGGCTCCACAAAAGTGGT	57.841	45.000	13.78	0.00	44.53	4.16	F
1882	2173	1.066858	TCGAAGGTCCTTCAGCATCAC	60.067	52.381	27.48	2.89	40.17	3.06	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2108	2457	0.251787	AAAACCATCTGCCTCCCCAC	60.252	55.0	0.00	0.00	0.0	4.61	R
3170	4290	0.323629	TCCTGGGTTAACAAGGAGCG	59.676	55.0	20.02	1.75	0.0	5.03	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
234	240	2.159179	AAAGGCTCCACAAAAGTGGT	57.841	45.000	13.78	0.00	44.53	4.16
254	261	4.280677	TGGTTTTACTTTCTTCAGCCATGG	59.719	41.667	7.63	7.63	0.00	3.66
352	371	7.173390	GGATGAGCTATAATTTGTTCCAGTACC	59.827	40.741	0.00	0.00	0.00	3.34
705	795	5.549742	TGTCCTCCAGATTGCAAAATTTT	57.450	34.783	1.71	0.00	0.00	1.82
1735	1996	1.134280	CCAACAAGAGGATGCGAGGAT	60.134	52.381	0.00	0.00	0.00	3.24
1882	2173	1.066858	TCGAAGGTCCTTCAGCATCAC	60.067	52.381	27.48	2.89	40.17	3.06
2179	2549	1.697432	ACGACCCAATTGAGGTTGAGA	59.303	47.619	27.19	0.00	40.76	3.27
2349	2890	1.820519	GCCTTCCATGATGCTGACAAA	59.179	47.619	0.00	0.00	0.00	2.83
2831	3759	4.070009	GCATGATGCAGTTATGATCTGGA	58.930	43.478	13.36	0.00	44.26	3.86
2940	4005	3.930634	AGTTCCAGAGCAAATTCAAGC	57.069	42.857	0.00	0.00	0.00	4.01
2993	4111	3.118261	TCCTTCTGGGAGATGCAATGTAC	60.118	47.826	0.00	0.00	39.58	2.90
2994	4112	3.118112	CCTTCTGGGAGATGCAATGTACT	60.118	47.826	0.00	0.00	37.23	2.73
2995	4113	3.827008	TCTGGGAGATGCAATGTACTC	57.173	47.619	0.00	0.00	0.00	2.59
2996	4114	2.435805	TCTGGGAGATGCAATGTACTCC	59.564	50.000	14.46	14.46	45.50	3.85
2999	4117	3.118905	GGAGATGCAATGTACTCCCTC	57.881	52.381	12.82	0.00	41.89	4.30
3000	4118	2.703007	GGAGATGCAATGTACTCCCTCT	59.297	50.000	12.82	0.00	41.89	3.69
3001	4119	3.494048	GGAGATGCAATGTACTCCCTCTG	60.494	52.174	12.82	0.00	41.89	3.35
3002	4120	3.110705	AGATGCAATGTACTCCCTCTGT	58.889	45.455	0.00	0.00	0.00	3.41
3003	4121	3.133721	AGATGCAATGTACTCCCTCTGTC	59.866	47.826	0.00	0.00	0.00	3.51
3004	4122	1.555075	TGCAATGTACTCCCTCTGTCC	59.445	52.381	0.00	0.00	0.00	4.02
3005	4123	1.134371	GCAATGTACTCCCTCTGTCCC	60.134	57.143	0.00	0.00	0.00	4.46
3006	4124	2.187958	CAATGTACTCCCTCTGTCCCA	58.812	52.381	0.00	0.00	0.00	4.37
3007	4125	2.571653	CAATGTACTCCCTCTGTCCCAA	59.428	50.000	0.00	0.00	0.00	4.12
3008	4126	2.409064	TGTACTCCCTCTGTCCCAAA	57.591	50.000	0.00	0.00	0.00	3.28
3009	4127	2.696775	TGTACTCCCTCTGTCCCAAAA	58.303	47.619	0.00	0.00	0.00	2.44
3010	4128	3.256704	TGTACTCCCTCTGTCCCAAAAT	58.743	45.455	0.00	0.00	0.00	1.82
3011	4129	4.431378	TGTACTCCCTCTGTCCCAAAATA	58.569	43.478	0.00	0.00	0.00	1.40
3012	4130	5.036916	TGTACTCCCTCTGTCCCAAAATAT	58.963	41.667	0.00	0.00	0.00	1.28
3013	4131	6.206787	TGTACTCCCTCTGTCCCAAAATATA	58.793	40.000	0.00	0.00	0.00	0.86
3014	4132	6.674861	TGTACTCCCTCTGTCCCAAAATATAA	59.325	38.462	0.00	0.00	0.00	0.98
3015	4133	6.253946	ACTCCCTCTGTCCCAAAATATAAG	57.746	41.667	0.00	0.00	0.00	1.73
3016	4134	5.970640	ACTCCCTCTGTCCCAAAATATAAGA	59.029	40.000	0.00	0.00	0.00	2.10
3017	4135	6.447084	ACTCCCTCTGTCCCAAAATATAAGAA	59.553	38.462	0.00	0.00	0.00	2.52
3018	4136	6.659824	TCCCTCTGTCCCAAAATATAAGAAC	58.340	40.000	0.00	0.00	0.00	3.01
3019	4137	6.216662	TCCCTCTGTCCCAAAATATAAGAACA	59.783	38.462	0.00	0.00	0.00	3.18
3020	4138	7.062957	CCCTCTGTCCCAAAATATAAGAACAT	58.937	38.462	0.00	0.00	0.00	2.71
3021	4139	7.561356	CCCTCTGTCCCAAAATATAAGAACATT	59.439	37.037	0.00	0.00	0.00	2.71
3022	4140	8.971073	CCTCTGTCCCAAAATATAAGAACATTT	58.029	33.333	0.00	0.00	0.00	2.32
3076	4194	7.486802	AAAACGTTCTTATATTATGGGACGG	57.513	36.000	0.00	1.76	0.00	4.79
3077	4195	6.409524	AACGTTCTTATATTATGGGACGGA	57.590	37.500	0.00	0.00	0.00	4.69
3078	4196	6.409524	ACGTTCTTATATTATGGGACGGAA	57.590	37.500	13.18	0.00	0.00	4.30
3079	4197	6.453092	ACGTTCTTATATTATGGGACGGAAG	58.547	40.000	13.18	0.00	0.00	3.46
3080	4198	5.867716	CGTTCTTATATTATGGGACGGAAGG	59.132	44.000	0.00	0.00	0.00	3.46
3081	4199	6.294899	CGTTCTTATATTATGGGACGGAAGGA	60.295	42.308	0.00	0.00	0.00	3.36
3082	4200	6.852420	TCTTATATTATGGGACGGAAGGAG	57.148	41.667	0.00	0.00	0.00	3.69
3083	4201	6.320518	TCTTATATTATGGGACGGAAGGAGT	58.679	40.000	0.00	0.00	0.00	3.85
3084	4202	7.472741	TCTTATATTATGGGACGGAAGGAGTA	58.527	38.462	0.00	0.00	0.00	2.59
3094	4212	5.163683	GGGACGGAAGGAGTATTTAAAAAGC	60.164	44.000	0.00	0.00	0.00	3.51
3096	4214	6.820152	GGACGGAAGGAGTATTTAAAAAGCTA	59.180	38.462	0.00	0.00	0.00	3.32
3159	4279	3.829948	CAGCTTGCCAGTTGAAACATAG	58.170	45.455	0.00	0.00	33.07	2.23
3168	4288	4.692625	CCAGTTGAAACATAGACAGACCTG	59.307	45.833	0.00	0.00	0.00	4.00
3169	4289	4.692625	CAGTTGAAACATAGACAGACCTGG	59.307	45.833	1.82	0.00	34.19	4.45
3170	4290	3.334583	TGAAACATAGACAGACCTGGC	57.665	47.619	0.00	0.00	39.43	4.85
3172	4292	0.108138	AACATAGACAGACCTGGCGC	60.108	55.000	0.00	0.00	45.19	6.53
3193	4590	3.146847	CTCCTTGTTAACCCAGGACAAC	58.853	50.000	16.32	0.00	0.00	3.32
3195	4592	3.139397	TCCTTGTTAACCCAGGACAACAT	59.861	43.478	16.32	0.00	31.45	2.71
3197	4594	2.870175	TGTTAACCCAGGACAACATGG	58.130	47.619	2.48	0.00	46.10	3.66
3202	4599	2.401766	CCAGGACAACATGGCGCTC	61.402	63.158	7.64	0.00	41.02	5.03
3204	4601	2.045926	GGACAACATGGCGCTCCT	60.046	61.111	7.64	0.00	0.00	3.69
3206	4603	3.044059	GACAACATGGCGCTCCTGC	62.044	63.158	7.64	0.00	0.00	4.85
3234	4634	5.717178	AGTACTTCTGCTCTGTTTCCAGATA	59.283	40.000	0.00	0.00	46.38	1.98
3236	4636	4.081198	ACTTCTGCTCTGTTTCCAGATAGG	60.081	45.833	0.00	0.00	46.38	2.57
3241	4641	7.013220	TCTGCTCTGTTTCCAGATAGGTATAT	58.987	38.462	0.00	0.00	46.38	0.86
3247	4647	7.879677	TCTGTTTCCAGATAGGTATATGCATTG	59.120	37.037	3.54	0.00	42.80	2.82
3248	4648	7.517320	TGTTTCCAGATAGGTATATGCATTGT	58.483	34.615	3.54	0.00	39.02	2.71
3251	4651	7.175347	TCCAGATAGGTATATGCATTGTCTC	57.825	40.000	3.54	0.00	39.02	3.36
3259	4667	2.787473	ATGCATTGTCTCTTCCCGAA	57.213	45.000	0.00	0.00	0.00	4.30
3265	4673	3.402628	TTGTCTCTTCCCGAAGAAAGG	57.597	47.619	8.43	0.00	45.75	3.11
3267	4675	2.704065	TGTCTCTTCCCGAAGAAAGGTT	59.296	45.455	8.43	0.00	45.75	3.50
3271	4679	2.436542	TCTTCCCGAAGAAAGGTTGTCA	59.563	45.455	4.66	0.00	43.79	3.58
3283	4691	8.541133	AAGAAAGGTTGTCAAAAATCGAAAAA	57.459	26.923	0.00	0.00	0.00	1.94
3310	4718	0.615331	TGACCCAGGACAAGATCTGC	59.385	55.000	0.00	0.00	0.00	4.26
3323	4731	1.364626	GATCTGCGCAAGGTCCAGTG	61.365	60.000	13.05	0.00	38.28	3.66
3358	4766	4.245054	GCGAGAAGCGAGTGACAA	57.755	55.556	0.00	0.00	44.57	3.18
3363	4771	2.596419	CGAGAAGCGAGTGACAAGATTC	59.404	50.000	1.16	1.16	44.57	2.52
3413	4821	6.255887	CACGATCTTAAAGTCCAACATACTCC	59.744	42.308	0.00	0.00	0.00	3.85
3474	4883	8.722480	ACATCTTTCATCGACAAATGAATAGA	57.278	30.769	0.31	6.83	43.30	1.98
3475	4884	8.824781	ACATCTTTCATCGACAAATGAATAGAG	58.175	33.333	0.31	0.00	43.30	2.43
3516	4925	0.644843	CAAAGGCAACGCACACAAAC	59.355	50.000	0.00	0.00	46.39	2.93
3517	4926	0.800300	AAAGGCAACGCACACAAACG	60.800	50.000	0.00	0.00	46.39	3.60
3521	4930	0.835120	GCAACGCACACAAACGTAAC	59.165	50.000	0.00	0.00	42.68	2.50
3539	4948	7.797038	ACGTAACAAAATCCAACTCTTAACT	57.203	32.000	0.00	0.00	0.00	2.24
3648	5057	1.224592	CGCTAGGGCATTTGGGACT	59.775	57.895	0.00	0.00	38.60	3.85
3723	5135	8.540388	ACATGATTTACCACTATACACTCTTGT	58.460	33.333	0.00	0.00	40.02	3.16
3748	5163	1.541588	GGCTGGCGAAAAGAATGAGTT	59.458	47.619	0.00	0.00	0.00	3.01
3756	5171	3.057315	CGAAAAGAATGAGTTGCCATGGT	60.057	43.478	14.67	0.00	0.00	3.55
3915	5330	1.164041	TCGTCTCGCTGTGAGTGTCA	61.164	55.000	17.04	0.00	45.46	3.58
3918	5333	0.877743	TCTCGCTGTGAGTGTCAGAG	59.122	55.000	17.04	0.00	45.46	3.35
3923	5338	1.405256	GCTGTGAGTGTCAGAGGATGG	60.405	57.143	3.53	0.00	38.13	3.51

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
234	240	4.519540	GCCATGGCTGAAGAAAGTAAAA	57.480	40.909	29.98	0.00	38.26	1.52
275	282	3.446799	CTCAGAGAGTCATAGCTGCAAC	58.553	50.000	1.02	0.00	0.00	4.17
352	371	9.748708	TCAGAAATTGTACAAAAAGAATCCTTG	57.251	29.630	13.23	1.53	31.91	3.61
705	795	2.689658	TCAACCTCAGGTGGAAGAAGA	58.310	47.619	0.00	0.00	31.84	2.87
1882	2173	1.269166	GATGTTGTAGTGGACTCGCG	58.731	55.000	0.00	0.00	0.00	5.87
2108	2457	0.251787	AAAACCATCTGCCTCCCCAC	60.252	55.000	0.00	0.00	0.00	4.61
2179	2549	2.426023	GTTGGCTCCAGTGACCGT	59.574	61.111	0.00	0.00	0.00	4.83
2349	2890	1.134670	GCGGCATTGTACCTCTTCTCT	60.135	52.381	0.00	0.00	0.00	3.10
2831	3759	6.376581	AGTTACTACTACTTATCTGCGGTTGT	59.623	38.462	0.00	0.00	31.21	3.32
2993	4111	6.500589	TCTTATATTTTGGGACAGAGGGAG	57.499	41.667	0.00	0.00	42.39	4.30
2994	4112	6.216662	TGTTCTTATATTTTGGGACAGAGGGA	59.783	38.462	0.00	0.00	42.39	4.20
2995	4113	6.423182	TGTTCTTATATTTTGGGACAGAGGG	58.577	40.000	0.00	0.00	42.39	4.30
2996	4114	8.525290	AATGTTCTTATATTTTGGGACAGAGG	57.475	34.615	0.00	0.00	42.39	3.69
3050	4168	9.044150	CCGTCCCATAATATAAGAACGTTTTTA	57.956	33.333	13.02	13.02	0.00	1.52
3051	4169	7.769970	TCCGTCCCATAATATAAGAACGTTTTT	59.230	33.333	9.22	9.22	0.00	1.94
3052	4170	7.274447	TCCGTCCCATAATATAAGAACGTTTT	58.726	34.615	0.46	0.00	0.00	2.43
3053	4171	6.819284	TCCGTCCCATAATATAAGAACGTTT	58.181	36.000	0.46	0.00	0.00	3.60
3054	4172	6.409524	TCCGTCCCATAATATAAGAACGTT	57.590	37.500	0.00	0.00	0.00	3.99
3055	4173	6.409524	TTCCGTCCCATAATATAAGAACGT	57.590	37.500	0.00	0.00	0.00	3.99
3056	4174	5.867716	CCTTCCGTCCCATAATATAAGAACG	59.132	44.000	0.00	0.00	0.00	3.95
3057	4175	7.001099	TCCTTCCGTCCCATAATATAAGAAC	57.999	40.000	0.00	0.00	0.00	3.01
3058	4176	6.785963	ACTCCTTCCGTCCCATAATATAAGAA	59.214	38.462	0.00	0.00	0.00	2.52
3059	4177	6.320518	ACTCCTTCCGTCCCATAATATAAGA	58.679	40.000	0.00	0.00	0.00	2.10
3060	4178	6.607004	ACTCCTTCCGTCCCATAATATAAG	57.393	41.667	0.00	0.00	0.00	1.73
3061	4179	8.674925	AATACTCCTTCCGTCCCATAATATAA	57.325	34.615	0.00	0.00	0.00	0.98
3062	4180	8.674925	AAATACTCCTTCCGTCCCATAATATA	57.325	34.615	0.00	0.00	0.00	0.86
3063	4181	7.569599	AAATACTCCTTCCGTCCCATAATAT	57.430	36.000	0.00	0.00	0.00	1.28
3064	4182	8.495160	TTAAATACTCCTTCCGTCCCATAATA	57.505	34.615	0.00	0.00	0.00	0.98
3065	4183	5.906772	AAATACTCCTTCCGTCCCATAAT	57.093	39.130	0.00	0.00	0.00	1.28
3066	4184	6.811634	TTAAATACTCCTTCCGTCCCATAA	57.188	37.500	0.00	0.00	0.00	1.90
3067	4185	6.811634	TTTAAATACTCCTTCCGTCCCATA	57.188	37.500	0.00	0.00	0.00	2.74
3068	4186	5.703730	TTTAAATACTCCTTCCGTCCCAT	57.296	39.130	0.00	0.00	0.00	4.00
3069	4187	5.502089	TTTTAAATACTCCTTCCGTCCCA	57.498	39.130	0.00	0.00	0.00	4.37
3070	4188	5.163683	GCTTTTTAAATACTCCTTCCGTCCC	60.164	44.000	0.00	0.00	0.00	4.46
3071	4189	5.646793	AGCTTTTTAAATACTCCTTCCGTCC	59.353	40.000	0.00	0.00	0.00	4.79
3072	4190	6.738832	AGCTTTTTAAATACTCCTTCCGTC	57.261	37.500	0.00	0.00	0.00	4.79
3073	4191	7.881751	AGTTAGCTTTTTAAATACTCCTTCCGT	59.118	33.333	0.00	0.00	0.00	4.69
3074	4192	8.175716	CAGTTAGCTTTTTAAATACTCCTTCCG	58.824	37.037	0.00	0.00	0.00	4.30
3075	4193	9.227777	TCAGTTAGCTTTTTAAATACTCCTTCC	57.772	33.333	0.00	0.00	0.00	3.46
3112	4230	8.567104	GCAAAATAAGGATTGTTTGACCAATTT	58.433	29.630	0.00	0.00	38.50	1.82
3114	4232	7.222872	TGCAAAATAAGGATTGTTTGACCAAT	58.777	30.769	0.00	0.00	38.50	3.16
3159	4279	2.948720	AAGGAGCGCCAGGTCTGTC	61.949	63.158	9.88	0.00	43.89	3.51
3168	4288	1.302993	TGGGTTAACAAGGAGCGCC	60.303	57.895	2.29	0.00	0.00	6.53
3169	4289	1.305930	CCTGGGTTAACAAGGAGCGC	61.306	60.000	17.63	0.00	0.00	5.92
3170	4290	0.323629	TCCTGGGTTAACAAGGAGCG	59.676	55.000	20.02	1.75	0.00	5.03
3172	4292	3.146847	GTTGTCCTGGGTTAACAAGGAG	58.853	50.000	22.95	7.28	33.84	3.69
3202	4599	2.757868	AGAGCAGAAGTACTAGTGCAGG	59.242	50.000	24.11	0.87	38.44	4.85
3204	4601	3.157881	ACAGAGCAGAAGTACTAGTGCA	58.842	45.455	24.11	0.00	38.44	4.57
3206	4603	5.164954	GGAAACAGAGCAGAAGTACTAGTG	58.835	45.833	5.39	0.00	0.00	2.74
3234	4634	4.262635	CGGGAAGAGACAATGCATATACCT	60.263	45.833	0.00	0.00	0.00	3.08
3236	4636	4.883083	TCGGGAAGAGACAATGCATATAC	58.117	43.478	0.00	0.00	0.00	1.47
3241	4641	1.623311	TCTTCGGGAAGAGACAATGCA	59.377	47.619	7.02	0.00	42.06	3.96
3247	4647	3.067833	CAACCTTTCTTCGGGAAGAGAC	58.932	50.000	10.69	0.00	46.80	3.36
3248	4648	2.704065	ACAACCTTTCTTCGGGAAGAGA	59.296	45.455	10.69	6.39	46.80	3.10
3251	4651	2.846193	TGACAACCTTTCTTCGGGAAG	58.154	47.619	1.97	1.97	39.71	3.46
3259	4667	8.716646	ATTTTTCGATTTTTGACAACCTTTCT	57.283	26.923	0.00	0.00	0.00	2.52
3265	4673	9.753669	AACAAGAATTTTTCGATTTTTGACAAC	57.246	25.926	6.72	0.00	35.70	3.32
3267	4675	9.144747	TCAACAAGAATTTTTCGATTTTTGACA	57.855	25.926	6.72	0.00	35.70	3.58
3271	4679	7.550906	TGGGTCAACAAGAATTTTTCGATTTTT	59.449	29.630	0.00	0.00	34.02	1.94
3283	4691	3.593442	TTGTCCTGGGTCAACAAGAAT	57.407	42.857	0.00	0.00	0.00	2.40
3310	4718	1.642037	CTCATGCACTGGACCTTGCG	61.642	60.000	12.37	2.05	41.96	4.85
3323	4731	1.941999	GCTTGGCCTCAACCTCATGC	61.942	60.000	3.32	0.00	0.00	4.06
3358	4766	4.649674	TGCTACCGTTAGGATTCAGAATCT	59.350	41.667	20.41	10.58	41.02	2.40
3363	4771	2.098607	TCGTGCTACCGTTAGGATTCAG	59.901	50.000	0.00	0.00	41.02	3.02
3413	4821	1.427809	TGGGATGATGCCTACAGAGG	58.572	55.000	4.19	0.00	46.93	3.69
3474	4883	1.903877	CTTGGTGATCCACTCCGGCT	61.904	60.000	0.00	0.00	44.22	5.52
3475	4884	1.450312	CTTGGTGATCCACTCCGGC	60.450	63.158	0.00	0.00	44.22	6.13
3516	4925	7.857569	TGAGTTAAGAGTTGGATTTTGTTACG	58.142	34.615	0.00	0.00	0.00	3.18
3517	4926	9.052759	TCTGAGTTAAGAGTTGGATTTTGTTAC	57.947	33.333	0.00	0.00	0.00	2.50
3521	4930	7.359598	CGTCTCTGAGTTAAGAGTTGGATTTTG	60.360	40.741	4.32	0.00	43.57	2.44
3648	5057	2.299013	TGGCGACTTAGAGAGAAAAGCA	59.701	45.455	0.00	0.00	0.00	3.91
3723	5135	4.776349	TCATTCTTTTCGCCAGCCTTATA	58.224	39.130	0.00	0.00	0.00	0.98
3756	5171	3.872696	TGTTATCGAGTAGTGACGGGTA	58.127	45.455	0.00	0.00	0.00	3.69

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.