AutoCloner

Multiple sequence alignment - TraesCS6B01G211400

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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	TraesCS6B01G211400	chr6B	100.000	3455	0	0	1	3455	279189212	279192666	0.000000e+00	6381
1	TraesCS6B01G211400	chr6B	90.554	1101	68	20	2386	3455	440878442	440879537	0.000000e+00	1424
2	TraesCS6B01G211400	chr6B	81.743	1090	180	15	999	2078	403959957	403958877	0.000000e+00	893
3	TraesCS6B01G211400	chr6B	84.294	885	89	21	1	861	658742165	658741307	0.000000e+00	819
4	TraesCS6B01G211400	chr7B	91.024	1103	64	15	2384	3455	174254463	174253365	0.000000e+00	1456
5	TraesCS6B01G211400	chr7B	90.198	1112	73	16	2375	3455	491648959	491650065	0.000000e+00	1417
6	TraesCS6B01G211400	chr7B	83.608	1092	164	9	1300	2382	578782786	578783871	0.000000e+00	1011
7	TraesCS6B01G211400	chr7B	83.516	1092	165	9	1300	2382	578749922	578751007	0.000000e+00	1005
8	TraesCS6B01G211400	chr7B	76.329	207	41	8	2133	2335	679488701	679488499	1.700000e-18	104
9	TraesCS6B01G211400	chr4D	91.288	1079	72	15	2385	3455	418021705	418020641	0.000000e+00	1452
10	TraesCS6B01G211400	chr4B	90.926	1102	63	18	2385	3455	473814410	473813315	0.000000e+00	1447
11	TraesCS6B01G211400	chr4B	93.216	737	40	6	2381	3114	644261197	644260468	0.000000e+00	1075
12	TraesCS6B01G211400	chr4B	83.247	770	82	24	1	745	653310142	653310889	0.000000e+00	664
13	TraesCS6B01G211400	chr7D	90.614	1108	68	15	2379	3455	65825528	65826630	0.000000e+00	1437
14	TraesCS6B01G211400	chr7D	90.563	1102	69	18	2385	3455	536417630	536416533	0.000000e+00	1426
15	TraesCS6B01G211400	chr7D	92.378	761	35	10	3	759	416266788	416267529	0.000000e+00	1062
16	TraesCS6B01G211400	chr7D	84.942	518	53	14	1	509	167841656	167842157	5.150000e-138	501
17	TraesCS6B01G211400	chr7D	92.982	342	23	1	3115	3455	585223603	585223944	6.660000e-137	497
18	TraesCS6B01G211400	chr2B	90.352	1109	69	17	2380	3455	291984530	291983427	0.000000e+00	1421
19	TraesCS6B01G211400	chr2B	89.991	1109	75	16	2378	3455	455569782	455570885	0.000000e+00	1400
20	TraesCS6B01G211400	chr2B	93.567	342	21	1	3115	3455	427794577	427794236	3.080000e-140	508
21	TraesCS6B01G211400	chr2B	83.824	136	19	2	289	424	741523058	741522926	3.620000e-25	126
22	TraesCS6B01G211400	chr2D	90.036	1104	74	15	2374	3445	621254553	621253454	0.000000e+00	1397
23	TraesCS6B01G211400	chr2D	78.497	479	62	21	2	440	469922791	469922314	3.400000e-70	276
24	TraesCS6B01G211400	chr3D	86.881	1212	156	2	1173	2384	381272654	381273862	0.000000e+00	1354
25	TraesCS6B01G211400	chr3D	90.768	964	59	11	1	945	584417234	584416282	0.000000e+00	1260
26	TraesCS6B01G211400	chr3D	90.379	634	40	9	1	619	445096215	445096842	0.000000e+00	813
27	TraesCS6B01G211400	chr3B	93.179	733	43	4	2385	3114	393551811	393552539	0.000000e+00	1070
28	TraesCS6B01G211400	chr1D	85.042	956	129	10	1430	2384	399278619	399277677	0.000000e+00	961
29	TraesCS6B01G211400	chr1D	93.275	342	22	1	3115	3455	239792026	239791685	1.430000e-138	503
30	TraesCS6B01G211400	chr6D	86.039	881	85	17	1	861	464706061	464705199	0.000000e+00	911
31	TraesCS6B01G211400	chr6D	89.120	625	40	10	1	619	4220338	4220940	0.000000e+00	752
32	TraesCS6B01G211400	chrUn	82.785	1034	155	18	2383	3403	58831060	58832083	0.000000e+00	902
33	TraesCS6B01G211400	chrUn	83.379	367	46	9	1	354	2932907	2933271	3.330000e-85	326
34	TraesCS6B01G211400	chr2A	85.796	873	82	23	1	846	755826291	755825434	0.000000e+00	887
35	TraesCS6B01G211400	chr5D	86.293	518	59	5	1	509	513886194	513886708	1.400000e-153	553
36	TraesCS6B01G211400	chr1B	92.982	342	23	1	3115	3455	372758886	372758545	6.660000e-137	497

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	TraesCS6B01G211400	chr6B	279189212	279192666	3454	False	6381	6381	100.000	1	3455	1	chr6B.!!$F1	3454
1	TraesCS6B01G211400	chr6B	440878442	440879537	1095	False	1424	1424	90.554	2386	3455	1	chr6B.!!$F2	1069
2	TraesCS6B01G211400	chr6B	403958877	403959957	1080	True	893	893	81.743	999	2078	1	chr6B.!!$R1	1079
3	TraesCS6B01G211400	chr6B	658741307	658742165	858	True	819	819	84.294	1	861	1	chr6B.!!$R2	860
4	TraesCS6B01G211400	chr7B	174253365	174254463	1098	True	1456	1456	91.024	2384	3455	1	chr7B.!!$R1	1071
5	TraesCS6B01G211400	chr7B	491648959	491650065	1106	False	1417	1417	90.198	2375	3455	1	chr7B.!!$F1	1080
6	TraesCS6B01G211400	chr7B	578782786	578783871	1085	False	1011	1011	83.608	1300	2382	1	chr7B.!!$F3	1082
7	TraesCS6B01G211400	chr7B	578749922	578751007	1085	False	1005	1005	83.516	1300	2382	1	chr7B.!!$F2	1082
8	TraesCS6B01G211400	chr4D	418020641	418021705	1064	True	1452	1452	91.288	2385	3455	1	chr4D.!!$R1	1070
9	TraesCS6B01G211400	chr4B	473813315	473814410	1095	True	1447	1447	90.926	2385	3455	1	chr4B.!!$R1	1070
10	TraesCS6B01G211400	chr4B	644260468	644261197	729	True	1075	1075	93.216	2381	3114	1	chr4B.!!$R2	733
11	TraesCS6B01G211400	chr4B	653310142	653310889	747	False	664	664	83.247	1	745	1	chr4B.!!$F1	744
12	TraesCS6B01G211400	chr7D	65825528	65826630	1102	False	1437	1437	90.614	2379	3455	1	chr7D.!!$F1	1076
13	TraesCS6B01G211400	chr7D	536416533	536417630	1097	True	1426	1426	90.563	2385	3455	1	chr7D.!!$R1	1070
14	TraesCS6B01G211400	chr7D	416266788	416267529	741	False	1062	1062	92.378	3	759	1	chr7D.!!$F3	756
15	TraesCS6B01G211400	chr7D	167841656	167842157	501	False	501	501	84.942	1	509	1	chr7D.!!$F2	508
16	TraesCS6B01G211400	chr2B	291983427	291984530	1103	True	1421	1421	90.352	2380	3455	1	chr2B.!!$R1	1075
17	TraesCS6B01G211400	chr2B	455569782	455570885	1103	False	1400	1400	89.991	2378	3455	1	chr2B.!!$F1	1077
18	TraesCS6B01G211400	chr2D	621253454	621254553	1099	True	1397	1397	90.036	2374	3445	1	chr2D.!!$R2	1071
19	TraesCS6B01G211400	chr3D	381272654	381273862	1208	False	1354	1354	86.881	1173	2384	1	chr3D.!!$F1	1211
20	TraesCS6B01G211400	chr3D	584416282	584417234	952	True	1260	1260	90.768	1	945	1	chr3D.!!$R1	944
21	TraesCS6B01G211400	chr3D	445096215	445096842	627	False	813	813	90.379	1	619	1	chr3D.!!$F2	618
22	TraesCS6B01G211400	chr3B	393551811	393552539	728	False	1070	1070	93.179	2385	3114	1	chr3B.!!$F1	729
23	TraesCS6B01G211400	chr1D	399277677	399278619	942	True	961	961	85.042	1430	2384	1	chr1D.!!$R2	954
24	TraesCS6B01G211400	chr6D	464705199	464706061	862	True	911	911	86.039	1	861	1	chr6D.!!$R1	860
25	TraesCS6B01G211400	chr6D	4220338	4220940	602	False	752	752	89.120	1	619	1	chr6D.!!$F1	618
26	TraesCS6B01G211400	chrUn	58831060	58832083	1023	False	902	902	82.785	2383	3403	1	chrUn.!!$F2	1020
27	TraesCS6B01G211400	chr2A	755825434	755826291	857	True	887	887	85.796	1	846	1	chr2A.!!$R1	845
28	TraesCS6B01G211400	chr5D	513886194	513886708	514	False	553	553	86.293	1	509	1	chr5D.!!$F1	508

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
978	1029	0.109735	CGTTCGACTGCTGCTACAGA	60.110	55.0	12.65	0.0	40.25	3.41	F
2128	2194	0.108233	CTCTGCTGAGTTCCTCCTGC	60.108	60.0	12.19	0.0	35.67	4.85	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2345	2411	0.027324	GTAGTCGACGGAGCTAACGG	59.973	60.0	10.46	0.0	35.23	4.44	R
2970	3049	0.450583	CACGACGAAGCTGCCTAGTA	59.549	55.0	0.00	0.0	0.00	1.82	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
34	35	9.278978	TCAACATCTAAAACTACACTATTGCAA	57.721	29.630	0.00	0.00	0.00	4.08
67	68	6.803320	ACTTTCAGTTGTTTTGATGCATATCG	59.197	34.615	0.00	0.00	36.04	2.92
113	114	1.827344	AGTCATGGAATCAGACGAGCA	59.173	47.619	0.00	0.00	0.00	4.26
213	214	4.759183	TGAAGTGCAATGCAACATACTACA	59.241	37.500	10.44	0.00	41.47	2.74
591	618	3.602390	TTCGTTCTCGCTTCCTTTTTG	57.398	42.857	0.00	0.00	36.96	2.44
628	655	3.172106	TTTGGCCGGTCCACAGGA	61.172	61.111	15.99	0.62	46.55	3.86
654	683	1.134788	CCGCCCCAGATATCGGATAAC	60.135	57.143	13.18	0.00	44.23	1.89
715	752	1.217942	GCCCCTAATCCTGGTCCAAAT	59.782	52.381	0.00	0.00	0.00	2.32
747	784	3.083349	CCTCCCAGCCATCCGTCA	61.083	66.667	0.00	0.00	0.00	4.35
750	787	1.688884	TCCCAGCCATCCGTCATCA	60.689	57.895	0.00	0.00	0.00	3.07
752	789	0.179009	CCCAGCCATCCGTCATCATT	60.179	55.000	0.00	0.00	0.00	2.57
774	824	2.284995	GACAGAGGGTCCTGGGCT	60.285	66.667	0.00	0.00	40.83	5.19
775	825	2.284995	ACAGAGGGTCCTGGGCTC	60.285	66.667	0.00	0.00	38.44	4.70
776	826	2.040278	CAGAGGGTCCTGGGCTCT	59.960	66.667	0.00	0.00	0.00	4.09
779	829	3.663815	GAGGGTCCTGGGCTCTCGA	62.664	68.421	13.28	0.00	0.00	4.04
792	842	0.306840	CTCTCGACGCGCCATACTTA	59.693	55.000	5.73	0.00	0.00	2.24
901	952	2.237416	TCGTGTCGTTCGACTGCTA	58.763	52.632	22.49	8.21	36.23	3.49
912	963	0.248539	CGACTGCTACTACCGAAGCC	60.249	60.000	0.00	0.00	37.97	4.35
914	965	0.964358	ACTGCTACTACCGAAGCCGT	60.964	55.000	0.00	0.00	37.97	5.68
974	1025	2.126071	GCCGTTCGACTGCTGCTA	60.126	61.111	0.00	0.00	0.00	3.49
975	1026	2.445438	GCCGTTCGACTGCTGCTAC	61.445	63.158	0.00	0.00	0.00	3.58
976	1027	1.080772	CCGTTCGACTGCTGCTACA	60.081	57.895	0.00	0.00	0.00	2.74
977	1028	1.073216	CCGTTCGACTGCTGCTACAG	61.073	60.000	0.00	5.17	43.59	2.74
978	1029	0.109735	CGTTCGACTGCTGCTACAGA	60.110	55.000	12.65	0.00	40.25	3.41
979	1030	1.666023	CGTTCGACTGCTGCTACAGAA	60.666	52.381	12.65	0.00	40.25	3.02
980	1031	1.989165	GTTCGACTGCTGCTACAGAAG	59.011	52.381	12.65	0.82	42.60	2.85
989	1040	2.512515	CTACAGAAGCTGCCGCCC	60.513	66.667	0.00	0.00	34.37	6.13
990	1041	3.315142	CTACAGAAGCTGCCGCCCA	62.315	63.158	0.00	0.00	34.37	5.36
991	1042	3.605749	TACAGAAGCTGCCGCCCAC	62.606	63.158	0.00	0.00	34.37	4.61
1006	1057	2.985282	CACCCGCAGCCATGTGTT	60.985	61.111	0.00	0.00	35.02	3.32
1007	1058	2.672996	ACCCGCAGCCATGTGTTC	60.673	61.111	0.00	0.00	35.02	3.18
1012	1063	2.765969	CAGCCATGTGTTCCCCCT	59.234	61.111	0.00	0.00	0.00	4.79
1019	1070	3.003763	GTGTTCCCCCTCTCCGCT	61.004	66.667	0.00	0.00	0.00	5.52
1027	1078	4.521062	CCTCTCCGCTGGCCGAAG	62.521	72.222	0.00	0.00	40.02	3.79
1053	1104	4.373116	TGCTCGGACCGTTGCCTC	62.373	66.667	23.77	7.27	0.00	4.70
1058	1109	2.126031	GGACCGTTGCCTCGAGTC	60.126	66.667	12.31	0.00	33.62	3.36
1070	1121	3.213402	CGAGTCGAGCCCCTCCTC	61.213	72.222	6.73	0.00	0.00	3.71
1077	1128	3.357082	AGCCCCTCCTCTACCGGT	61.357	66.667	13.98	13.98	0.00	5.28
1078	1129	2.004408	GAGCCCCTCCTCTACCGGTA	62.004	65.000	14.95	14.95	0.00	4.02
1079	1130	1.831726	GCCCCTCCTCTACCGGTAC	60.832	68.421	11.16	0.00	0.00	3.34
1086	1137	1.445716	CCTCTACCGGTACCGCAGAG	61.446	65.000	34.94	34.94	41.96	3.35
1108	1159	2.838693	GGCCGTCCTCCTACCTCC	60.839	72.222	0.00	0.00	0.00	4.30
1112	1163	1.613610	CGTCCTCCTACCTCCAGGA	59.386	63.158	0.00	0.00	42.62	3.86
1383	1438	4.988598	CACCCGCGCTTGGAGTGT	62.989	66.667	18.43	0.00	0.00	3.55
1597	1658	2.682494	GCCACCCCACGTCCTCTA	60.682	66.667	0.00	0.00	0.00	2.43
1610	1671	3.141488	CTCTAGGTCGGCCAGCGT	61.141	66.667	9.71	0.00	37.19	5.07
1694	1756	1.749638	CGACCGGCTCTACCTCTGT	60.750	63.158	0.00	0.00	35.61	3.41
1755	1817	1.399744	CCGGTGCCATCTGCTACCTA	61.400	60.000	0.00	0.00	42.00	3.08
1885	1947	2.125147	GCACACGCTATGGCCTGA	60.125	61.111	3.32	0.00	34.30	3.86
1925	1987	1.516161	CACATCCACGCCTATGATGG	58.484	55.000	0.00	0.00	40.10	3.51
2078	2144	3.570540	TCCTCGTCTCCATCAAGATCAT	58.429	45.455	0.00	0.00	0.00	2.45
2084	2150	2.158711	TCTCCATCAAGATCATGGGCAC	60.159	50.000	9.94	0.00	41.25	5.01
2105	2171	1.548081	CCTGATCATGTTTGGCACCA	58.452	50.000	0.00	0.00	0.00	4.17
2128	2194	0.108233	CTCTGCTGAGTTCCTCCTGC	60.108	60.000	12.19	0.00	35.67	4.85
2146	2212	4.351938	CGTCGTTCTGCCGGGTCA	62.352	66.667	2.18	0.00	0.00	4.02
2178	2244	2.637383	GGAGACCAAGGACGCGTCT	61.637	63.158	35.50	20.42	39.54	4.18
2195	2261	2.607038	CGTCTGACATGTCGGTCTTTCA	60.607	50.000	29.34	10.51	38.61	2.69
2213	2279	1.539869	ACCTCACAGCCTGGACCAT	60.540	57.895	0.00	0.00	0.00	3.55
2217	2283	0.994247	TCACAGCCTGGACCATCAAT	59.006	50.000	0.00	0.00	0.00	2.57
2223	2289	0.179045	CCTGGACCATCAATCCCGAC	60.179	60.000	0.00	0.00	35.12	4.79
2253	2319	1.506718	CTTGTCGGAGCTGCTCGTA	59.493	57.895	22.25	10.68	0.00	3.43
2278	2344	2.046988	CTGATGCTGTGGCCGACA	60.047	61.111	0.00	2.81	37.74	4.35
2321	2387	2.185350	CCTCGCGCTTGGACTGAT	59.815	61.111	5.56	0.00	0.00	2.90
2345	2411	2.028125	TTCCCCGTCGAGATCCATGC	62.028	60.000	0.00	0.00	0.00	4.06
2365	2431	0.723414	CGTTAGCTCCGTCGACTACA	59.277	55.000	14.70	0.00	0.00	2.74
2399	2465	0.545309	CCACTGAGGGAGTCCTGGAA	60.545	60.000	9.58	0.00	45.05	3.53
2401	2467	1.209019	CACTGAGGGAGTCCTGGAATG	59.791	57.143	9.58	0.00	45.05	2.67
2405	2471	1.619669	GGGAGTCCTGGAATGGGGT	60.620	63.158	9.58	0.00	0.00	4.95
2523	2589	1.600636	CGTGGAAGGCAAGCTTGGA	60.601	57.895	27.10	0.00	0.00	3.53
2526	2592	1.620323	GTGGAAGGCAAGCTTGGAAAT	59.380	47.619	27.10	0.00	0.00	2.17
2576	2643	1.749634	CCGACTCTGTGTAACCCTAGG	59.250	57.143	0.06	0.06	34.36	3.02
2649	2724	8.509690	CAACAACAATCATAATCATAGGCTAGG	58.490	37.037	0.00	0.00	0.00	3.02
2803	2878	1.139058	CGCCTCCTGTTACCATTAGCT	59.861	52.381	0.00	0.00	0.00	3.32
2813	2888	4.868171	TGTTACCATTAGCTTTAGACGCAG	59.132	41.667	0.00	0.00	0.00	5.18
2970	3049	2.498644	GCTTTAGGCCAAACTCTCCT	57.501	50.000	5.01	0.00	34.27	3.69
2987	3066	0.029567	CCTACTAGGCAGCTTCGTCG	59.970	60.000	0.00	0.00	0.00	5.12
2994	3073	2.050351	CAGCTTCGTCGTGACCGT	60.050	61.111	0.00	0.00	35.01	4.83
3118	3224	0.319555	TGAACGAGTTCTTGGCGGAG	60.320	55.000	15.80	0.00	40.14	4.63
3130	3236	2.209690	TGGCGGAGTATGATCGGATA	57.790	50.000	0.00	0.00	0.00	2.59
3151	3257	1.546099	GGGCTTAAACCCGACCAAAGA	60.546	52.381	0.00	0.00	40.98	2.52
3172	3278	0.460311	AGATTAACTCTCCGCCGGTG	59.540	55.000	8.42	8.42	0.00	4.94
3208	3314	2.648059	GTAGTGGAGGAGCAATGCATT	58.352	47.619	5.99	5.99	0.00	3.56
3248	3354	3.175109	GGACGAACTATGTCCGGATTT	57.825	47.619	7.81	0.00	45.82	2.17
3322	3431	0.744874	CTTAGAATCGGACAGCGGGA	59.255	55.000	0.00	0.00	0.00	5.14
3429	3538	4.116113	TGGACTTAAATCTACCCACCCAT	58.884	43.478	0.00	0.00	0.00	4.00

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
213	214	7.578557	AGGGGCTCCTACTATAGATGATATAGT	59.421	40.741	0.94	11.23	42.75	2.12
229	230	2.041508	CCTGCTCAGGGGCTCCTA	60.042	66.667	3.71	0.00	44.87	2.94
354	365	6.919662	GGTTGCTACATGTTGATGATTATTGG	59.080	38.462	11.66	0.00	33.36	3.16
445	456	8.347729	TCGCATGTATGTGTATTTACAGTAAG	57.652	34.615	5.43	0.00	39.25	2.34
591	618	1.177401	GGCCCATCTCTGTCCAAAAC	58.823	55.000	0.00	0.00	0.00	2.43
670	699	2.227757	TCAATGGGGACGGAAGCCA	61.228	57.895	0.00	0.00	0.00	4.75
736	773	0.182061	AGCAATGATGACGGATGGCT	59.818	50.000	0.00	0.00	0.00	4.75
745	782	1.211212	CCCTCTGTCCAGCAATGATGA	59.789	52.381	0.00	0.00	0.00	2.92
747	784	1.211457	GACCCTCTGTCCAGCAATGAT	59.789	52.381	0.00	0.00	38.09	2.45
772	822	2.938539	AAGTATGGCGCGTCGAGAGC	62.939	60.000	6.09	2.93	45.31	4.09
773	823	0.306840	TAAGTATGGCGCGTCGAGAG	59.693	55.000	6.09	0.00	0.00	3.20
774	824	0.949397	ATAAGTATGGCGCGTCGAGA	59.051	50.000	6.09	0.00	0.00	4.04
775	825	1.328439	GATAAGTATGGCGCGTCGAG	58.672	55.000	6.09	0.00	0.00	4.04
776	826	0.039798	GGATAAGTATGGCGCGTCGA	60.040	55.000	6.09	0.00	0.00	4.20
779	829	1.000163	CAGAGGATAAGTATGGCGCGT	60.000	52.381	8.43	0.00	0.00	6.01
792	842	6.928492	GCGAGATAAATTCTTCTTCAGAGGAT	59.072	38.462	0.00	0.00	33.74	3.24
876	927	2.681666	GAACGACACGACGATGCG	59.318	61.111	0.00	4.11	37.03	4.73
886	937	1.466167	GGTAGTAGCAGTCGAACGACA	59.534	52.381	25.13	5.70	46.76	4.35
888	939	0.723414	CGGTAGTAGCAGTCGAACGA	59.277	55.000	0.00	0.00	0.00	3.85
922	973	2.046023	CAGTGAGGCATTCCGGCA	60.046	61.111	0.00	0.00	44.47	5.69
956	1007	3.964221	TAGCAGCAGTCGAACGGCG	62.964	63.158	4.80	4.80	44.04	6.46
957	1008	2.126071	TAGCAGCAGTCGAACGGC	60.126	61.111	0.00	0.00	39.63	5.68
958	1009	1.073216	CTGTAGCAGCAGTCGAACGG	61.073	60.000	0.00	0.00	0.00	4.44
959	1010	0.109735	TCTGTAGCAGCAGTCGAACG	60.110	55.000	0.00	0.00	37.70	3.95
960	1011	1.989165	CTTCTGTAGCAGCAGTCGAAC	59.011	52.381	0.00	0.00	37.70	3.95
961	1012	2.354109	CTTCTGTAGCAGCAGTCGAA	57.646	50.000	0.00	0.00	37.70	3.71
972	1023	2.512515	GGGCGGCAGCTTCTGTAG	60.513	66.667	12.47	0.00	44.37	2.74
973	1024	3.318384	TGGGCGGCAGCTTCTGTA	61.318	61.111	12.47	0.00	44.37	2.74
989	1040	2.981560	GAACACATGGCTGCGGGTG	61.982	63.158	13.13	13.13	37.29	4.61
990	1041	2.672996	GAACACATGGCTGCGGGT	60.673	61.111	0.00	0.00	0.00	5.28
991	1042	3.443045	GGAACACATGGCTGCGGG	61.443	66.667	0.00	0.00	0.00	6.13
992	1043	3.443045	GGGAACACATGGCTGCGG	61.443	66.667	0.00	0.00	0.00	5.69
993	1044	3.443045	GGGGAACACATGGCTGCG	61.443	66.667	0.00	0.00	0.00	5.18
994	1045	3.070576	GGGGGAACACATGGCTGC	61.071	66.667	0.00	0.00	0.00	5.25
995	1046	1.379044	GAGGGGGAACACATGGCTG	60.379	63.158	0.00	0.00	34.58	4.85
996	1047	1.542375	AGAGGGGGAACACATGGCT	60.542	57.895	0.00	0.00	34.58	4.75
997	1048	1.077429	GAGAGGGGGAACACATGGC	60.077	63.158	0.00	0.00	34.58	4.40
998	1049	1.609783	GGAGAGGGGGAACACATGG	59.390	63.158	0.00	0.00	34.58	3.66
999	1050	1.221840	CGGAGAGGGGGAACACATG	59.778	63.158	0.00	0.00	34.58	3.21
1000	1051	2.670148	GCGGAGAGGGGGAACACAT	61.670	63.158	0.00	0.00	34.58	3.21
1001	1052	3.319198	GCGGAGAGGGGGAACACA	61.319	66.667	0.00	0.00	34.58	3.72
1002	1053	3.003763	AGCGGAGAGGGGGAACAC	61.004	66.667	0.00	0.00	0.00	3.32
1003	1054	3.003173	CAGCGGAGAGGGGGAACA	61.003	66.667	0.00	0.00	0.00	3.18
1004	1055	3.787001	CCAGCGGAGAGGGGGAAC	61.787	72.222	0.00	0.00	0.00	3.62
1036	1087	4.373116	GAGGCAACGGTCCGAGCA	62.373	66.667	26.22	0.00	46.39	4.26
1053	1104	2.326773	TAGAGGAGGGGCTCGACTCG	62.327	65.000	5.85	0.00	34.58	4.18
1058	1109	2.907917	CGGTAGAGGAGGGGCTCG	60.908	72.222	0.00	0.00	0.00	5.03
1070	1121	2.412112	GCTCTGCGGTACCGGTAG	59.588	66.667	33.98	22.25	40.19	3.18
1092	1143	2.043248	TGGAGGTAGGAGGACGGC	60.043	66.667	0.00	0.00	0.00	5.68
1376	1431	2.523168	TGTCCCTGCGACACTCCA	60.523	61.111	0.00	0.00	46.80	3.86
1383	1438	2.264480	CAACGGATGTCCCTGCGA	59.736	61.111	0.00	0.00	33.81	5.10
1398	1453	2.586635	AAACGACAGCGACCGCAA	60.587	55.556	16.97	0.00	44.88	4.85
1459	1514	3.086600	CTGGGTGGAGGAGGAGGC	61.087	72.222	0.00	0.00	0.00	4.70
1498	1553	4.980805	GGCAGAACCACGGCGACA	62.981	66.667	16.62	0.00	40.43	4.35
1500	1555	4.373116	GAGGCAGAACCACGGCGA	62.373	66.667	16.62	0.00	43.14	5.54
1525	1580	1.977293	GAAGCAGATTCCTCCGGGCT	61.977	60.000	0.00	0.00	31.14	5.19
1583	1644	1.000107	GACCTAGAGGACGTGGGGT	60.000	63.158	1.60	0.00	38.94	4.95
1596	1657	4.077184	CCAACGCTGGCCGACCTA	62.077	66.667	0.00	0.00	41.02	3.08
1678	1740	1.682684	CCACAGAGGTAGAGCCGGT	60.683	63.158	1.90	0.00	43.70	5.28
1779	1841	2.440247	TCGAGATCCAGCTCCGCA	60.440	61.111	0.00	0.00	0.00	5.69
1885	1947	4.719369	GGAGAACTCGTGCGCGGT	62.719	66.667	21.04	13.66	38.89	5.68
1925	1987	4.257731	GGAGGAGAACTTGATGAGGAAAC	58.742	47.826	0.00	0.00	0.00	2.78
1969	2035	4.065281	GCGTAGACCACCAGCGGT	62.065	66.667	0.00	0.00	43.91	5.68
2001	2067	1.622811	CTCCAAGGAGTGAAGAGCAGT	59.377	52.381	7.98	0.00	37.47	4.40
2031	2097	1.672854	CCTTCACCGGGATAGCGTCA	61.673	60.000	6.32	0.00	0.00	4.35
2084	2150	0.819582	GTGCCAAACATGATCAGGGG	59.180	55.000	12.66	4.58	0.00	4.79
2091	2157	0.478072	AGGACTGGTGCCAAACATGA	59.522	50.000	0.00	0.00	0.00	3.07
2096	2162	1.228245	GCAGAGGACTGGTGCCAAA	60.228	57.895	0.00	0.00	43.62	3.28
2105	2171	3.784429	AGGAACTCAGCAGAGGACT	57.216	52.632	11.18	2.67	46.44	3.85
2146	2212	3.391382	CTCCGGGGCGAGGTTCTT	61.391	66.667	0.00	0.00	0.00	2.52
2168	2234	1.213013	GACATGTCAGACGCGTCCT	59.787	57.895	34.08	19.25	0.00	3.85
2178	2244	2.163818	GGTGAAAGACCGACATGTCA	57.836	50.000	24.93	0.93	37.73	3.58
2195	2261	1.539869	ATGGTCCAGGCTGTGAGGT	60.540	57.895	14.43	0.00	0.00	3.85
2213	2279	2.504032	GGATGCCGTCGGGATTGA	59.496	61.111	20.08	0.00	32.75	2.57
2345	2411	0.027324	GTAGTCGACGGAGCTAACGG	59.973	60.000	10.46	0.00	35.23	4.44
2417	2483	1.202770	GGCCAAAGCATATAGTCCGGT	60.203	52.381	0.00	0.00	42.56	5.28
2429	2495	2.644992	CAACAGTCCGGCCAAAGC	59.355	61.111	2.24	0.00	38.76	3.51
2523	2589	8.875168	AGAAGGAGATCTACATATCCGAAATTT	58.125	33.333	7.93	0.00	44.22	1.82
2526	2592	7.175816	CAGAGAAGGAGATCTACATATCCGAAA	59.824	40.741	7.93	0.00	44.22	3.46
2621	2695	8.297470	AGCCTATGATTATGATTGTTGTTGTT	57.703	30.769	0.00	0.00	0.00	2.83
2622	2696	7.886629	AGCCTATGATTATGATTGTTGTTGT	57.113	32.000	0.00	0.00	0.00	3.32
2649	2724	3.950395	TCGTAGAGGCTAAACCCTAGAAC	59.050	47.826	0.00	0.00	40.58	3.01
2803	2878	1.134907	GGATCCCGAACTGCGTCTAAA	60.135	52.381	0.00	0.00	38.67	1.85
2817	2892	1.268066	GGATCTCGGGTAAGGATCCC	58.732	60.000	8.55	0.00	45.69	3.85
2824	2902	0.974010	AACTGGCGGATCTCGGGTAA	60.974	55.000	0.00	0.00	39.69	2.85
2970	3049	0.450583	CACGACGAAGCTGCCTAGTA	59.549	55.000	0.00	0.00	0.00	1.82
3118	3224	5.176592	GGTTTAAGCCCTATCCGATCATAC	58.823	45.833	0.00	0.00	0.00	2.39
3130	3236	0.479378	TTTGGTCGGGTTTAAGCCCT	59.521	50.000	23.42	0.00	46.47	5.19
3172	3278	2.029828	CACTACCGCTATCTGATGGGTC	60.030	54.545	11.51	0.00	32.29	4.46
3208	3314	8.074613	TCGTCCTTAAAATAGAGGAAGAATCA	57.925	34.615	5.72	0.00	44.09	2.57
3322	3431	4.006780	GGATGTTGCCCAATTTTTCTGT	57.993	40.909	0.00	0.00	0.00	3.41
3429	3538	4.782691	TGGGAAAGATCACTTGTATCTGGA	59.217	41.667	0.00	0.00	36.39	3.86

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.