AutoCloner

Multiple sequence alignment - TraesCS5D01G524400

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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	TraesCS5D01G524400	chr5D	100.000	2990	0	0	1	2990	543537675	543534686	0.000000e+00	5522.0
1	TraesCS5D01G524400	chr5D	86.680	1021	115	14	1186	2189	551337128	551338144	0.000000e+00	1112.0
2	TraesCS5D01G524400	chr5D	85.698	888	117	7	1186	2071	551739004	551739883	0.000000e+00	928.0
3	TraesCS5D01G524400	chr5D	89.006	473	41	4	718	1189	551336709	551337171	2.580000e-160	575.0
4	TraesCS5D01G524400	chr5D	88.940	434	36	4	756	1189	551738626	551739047	2.640000e-145	525.0
5	TraesCS5D01G524400	chr5D	85.055	455	57	9	2073	2523	551739967	551740414	1.260000e-123	453.0
6	TraesCS5D01G524400	chr5D	88.750	240	23	3	2754	2990	551353475	551353713	1.050000e-74	291.0
7	TraesCS5D01G524400	chr5D	88.750	240	23	3	2754	2990	551389820	551390058	1.050000e-74	291.0
8	TraesCS5D01G524400	chr5D	87.273	165	14	5	2585	2745	551740489	551740650	6.580000e-42	182.0
9	TraesCS5D01G524400	chr5D	90.426	94	8	1	195	287	55904878	55904971	4.050000e-24	122.0
10	TraesCS5D01G524400	chr5D	100.000	44	0	0	1146	1189	543536490	543536447	6.870000e-12	82.4
11	TraesCS5D01G524400	chr5B	90.005	1841	124	16	1186	2990	685422595	685420779	0.000000e+00	2326.0
12	TraesCS5D01G524400	chr5B	90.221	1810	117	15	1186	2959	685444015	685445800	0.000000e+00	2307.0
13	TraesCS5D01G524400	chr5B	93.661	1199	60	7	1	1189	685442866	685444058	0.000000e+00	1779.0
14	TraesCS5D01G524400	chr5B	83.301	1533	177	45	1186	2673	699597399	699598897	0.000000e+00	1339.0
15	TraesCS5D01G524400	chr5B	82.850	1516	185	41	1186	2664	703716499	703717976	0.000000e+00	1290.0
16	TraesCS5D01G524400	chr5B	83.632	1393	187	26	1187	2553	700007284	700008661	0.000000e+00	1271.0
17	TraesCS5D01G524400	chr5B	90.976	676	27	11	519	1189	685423198	685422552	0.000000e+00	880.0
18	TraesCS5D01G524400	chr5B	76.784	1275	220	50	1202	2451	703644851	703646074	0.000000e+00	645.0
19	TraesCS5D01G524400	chr5B	86.964	560	55	5	648	1189	700006767	700007326	5.480000e-172	614.0
20	TraesCS5D01G524400	chr5B	83.284	682	84	22	527	1189	699596772	699597442	4.260000e-168	601.0
21	TraesCS5D01G524400	chr5B	79.247	877	150	20	1199	2064	703539807	703540662	1.540000e-162	582.0
22	TraesCS5D01G524400	chr5B	88.810	420	38	5	771	1189	703716131	703716542	9.560000e-140	507.0
23	TraesCS5D01G524400	chr5B	89.583	240	22	2	2754	2990	699598907	699599146	4.840000e-78	302.0
24	TraesCS5D01G524400	chr5B	84.722	288	24	9	2611	2894	700008764	700009035	1.370000e-68	270.0
25	TraesCS5D01G524400	chr5B	81.870	353	30	11	286	611	700006420	700006765	1.770000e-67	267.0
26	TraesCS5D01G524400	chr5B	91.444	187	13	2	2806	2990	703718097	703718282	1.380000e-63	254.0
27	TraesCS5D01G524400	chr5B	92.105	152	11	1	383	533	685423588	685423437	2.330000e-51	213.0
28	TraesCS5D01G524400	chr5B	95.455	88	4	0	286	373	699277749	699277836	1.120000e-29	141.0
29	TraesCS5D01G524400	chr5B	92.683	82	6	0	195	276	58672421	58672502	5.240000e-23	119.0
30	TraesCS5D01G524400	chr5B	100.000	54	0	0	286	339	685423644	685423591	1.900000e-17	100.0
31	TraesCS5D01G524400	chr4A	85.531	1016	119	20	1186	2189	616754542	616753543	0.000000e+00	1037.0
32	TraesCS5D01G524400	chr4A	86.288	423	36	10	778	1189	616754911	616754500	9.840000e-120	440.0
33	TraesCS5D01G524400	chr4A	89.030	237	23	2	2757	2990	616752876	616752640	1.050000e-74	291.0
34	TraesCS5D01G524400	chr4A	77.419	403	73	12	790	1188	616886011	616885623	1.080000e-54	224.0
35	TraesCS5D01G524400	chr3A	91.176	170	13	1	2815	2982	619187545	619187714	2.320000e-56	230.0
36	TraesCS5D01G524400	chr3A	92.941	85	6	0	195	279	602872501	602872585	1.130000e-24	124.0
37	TraesCS5D01G524400	chr7A	90.286	175	15	1	2818	2990	13758423	13758249	8.340000e-56	228.0
38	TraesCS5D01G524400	chr7A	87.500	104	11	1	195	298	640372091	640372192	5.240000e-23	119.0
39	TraesCS5D01G524400	chr7B	93.333	90	6	0	196	285	443651776	443651687	1.870000e-27	134.0
40	TraesCS5D01G524400	chr7B	93.590	78	4	1	13	90	598481485	598481409	6.770000e-22	115.0
41	TraesCS5D01G524400	chr1D	92.222	90	5	2	195	284	6173060	6172973	3.130000e-25	126.0
42	TraesCS5D01G524400	chr7D	91.111	90	6	2	195	284	5431584	5431671	1.460000e-23	121.0
43	TraesCS5D01G524400	chr5A	89.362	94	9	1	195	287	44879281	44879374	1.880000e-22	117.0

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	TraesCS5D01G524400	chr5D	543534686	543537675	2989	True	2802.200000	5522	100.000000	1	2990	2	chr5D.!!$R1	2989
1	TraesCS5D01G524400	chr5D	551336709	551338144	1435	False	843.500000	1112	87.843000	718	2189	2	chr5D.!!$F4	1471
2	TraesCS5D01G524400	chr5D	551738626	551740650	2024	False	522.000000	928	86.741500	756	2745	4	chr5D.!!$F5	1989
3	TraesCS5D01G524400	chr5B	685442866	685445800	2934	False	2043.000000	2307	91.941000	1	2959	2	chr5B.!!$F5	2958
4	TraesCS5D01G524400	chr5B	685420779	685423644	2865	True	879.750000	2326	93.271500	286	2990	4	chr5B.!!$R1	2704
5	TraesCS5D01G524400	chr5B	699596772	699599146	2374	False	747.333333	1339	85.389333	527	2990	3	chr5B.!!$F6	2463
6	TraesCS5D01G524400	chr5B	703716131	703718282	2151	False	683.666667	1290	87.701333	771	2990	3	chr5B.!!$F8	2219
7	TraesCS5D01G524400	chr5B	703644851	703646074	1223	False	645.000000	645	76.784000	1202	2451	1	chr5B.!!$F4	1249
8	TraesCS5D01G524400	chr5B	700006420	700009035	2615	False	605.500000	1271	84.297000	286	2894	4	chr5B.!!$F7	2608
9	TraesCS5D01G524400	chr5B	703539807	703540662	855	False	582.000000	582	79.247000	1199	2064	1	chr5B.!!$F3	865
10	TraesCS5D01G524400	chr4A	616752640	616754911	2271	True	589.333333	1037	86.949667	778	2990	3	chr4A.!!$R2	2212

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
893	1198	0.037877	TCGAGGAGGTCTTCTTCCGT	59.962	55.0	0.0	0.0	43.46	4.69	F
1335	1653	0.180406	ATATGCCCTTGGACACCGAC	59.820	55.0	0.0	0.0	0.00	4.79	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1775	2115	0.390603	TGCAACTCCATCGTAACCCG	60.391	55.0	0.0	0.0	38.13	5.28	R
2284	2871	0.749454	GAGCCACATCGCAAGGGATT	60.749	55.0	0.0	0.0	38.47	3.01	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
77	78	1.070108	GTGGTCCGTCGAAGCTTTTTC	60.070	52.381	0.00	0.00	0.00	2.29
78	79	0.163146	GGTCCGTCGAAGCTTTTTCG	59.837	55.000	0.00	0.00	42.74	3.46
107	108	3.370953	GGTTGGTCTTGTCTGCCAGATAT	60.371	47.826	0.00	0.00	33.41	1.63
129	130	4.724074	ATCAAAATGATCACGTTGCCAT	57.276	36.364	13.12	3.16	29.59	4.40
220	224	2.607750	AGGCCGGGTGTCACTCAT	60.608	61.111	2.18	0.00	0.00	2.90
232	236	5.163754	GGGTGTCACTCATTATGCTTTGTAC	60.164	44.000	2.35	0.00	0.00	2.90
236	240	5.590259	GTCACTCATTATGCTTTGTACCCAT	59.410	40.000	0.00	0.00	0.00	4.00
243	247	3.591196	TGCTTTGTACCCATTTGATGC	57.409	42.857	0.00	0.00	0.00	3.91
259	263	8.627403	CCATTTGATGCTACATTCTGAGTTAAT	58.373	33.333	0.00	0.00	0.00	1.40
269	273	7.158099	ACATTCTGAGTTAATAAAAGCACCC	57.842	36.000	0.00	0.00	0.00	4.61
454	462	4.276926	GCAAAGTTTCAGGTCTTCAGTGAT	59.723	41.667	0.00	0.00	0.00	3.06
510	519	7.601856	TCTGCATTTATTTACCTTTTGAGGTG	58.398	34.615	8.32	0.00	43.03	4.00
525	787	3.091545	TGAGGTGGATTTCTGCATTTCC	58.908	45.455	0.00	0.00	0.00	3.13
624	891	6.706295	ACCAAGTCCTCTCTCTTCAATTTAG	58.294	40.000	0.00	0.00	0.00	1.85
629	897	7.093992	AGTCCTCTCTCTTCAATTTAGTTTCG	58.906	38.462	0.00	0.00	0.00	3.46
727	1015	2.185350	CCTCGCGTGATTGCCTCT	59.815	61.111	10.21	0.00	0.00	3.69
766	1054	3.058570	CGTAGTGCTACTGCTATCTCCTG	60.059	52.174	7.63	0.00	40.48	3.86
784	1072	1.681327	GCGTCCCAGACTCCCAGTA	60.681	63.158	0.00	0.00	0.00	2.74
799	1098	0.327576	CAGTACCCATTCCCCTCCCT	60.328	60.000	0.00	0.00	0.00	4.20
809	1108	0.728843	TCCCCTCCCTAAACCCTCAT	59.271	55.000	0.00	0.00	0.00	2.90
827	1126	0.676184	ATCTCCACCGATCGACCATG	59.324	55.000	18.66	9.02	0.00	3.66
828	1127	1.592669	CTCCACCGATCGACCATGC	60.593	63.158	18.66	0.00	0.00	4.06
829	1128	2.186644	CCACCGATCGACCATGCA	59.813	61.111	18.66	0.00	0.00	3.96
830	1129	1.884464	CCACCGATCGACCATGCAG	60.884	63.158	18.66	0.00	0.00	4.41
831	1130	2.202932	ACCGATCGACCATGCAGC	60.203	61.111	18.66	0.00	0.00	5.25
832	1131	2.969238	CCGATCGACCATGCAGCC	60.969	66.667	18.66	0.00	0.00	4.85
893	1198	0.037877	TCGAGGAGGTCTTCTTCCGT	59.962	55.000	0.00	0.00	43.46	4.69
1067	1379	4.143333	CGCCAACGGTCGGAGGAT	62.143	66.667	7.37	0.00	34.97	3.24
1070	1382	1.141881	CCAACGGTCGGAGGATCTG	59.858	63.158	0.00	0.00	44.94	2.90
1166	1478	3.712881	GAGTGCGGCGTGTTGGAC	61.713	66.667	9.37	0.00	0.00	4.02
1167	1479	4.235762	AGTGCGGCGTGTTGGACT	62.236	61.111	9.37	0.00	31.41	3.85
1168	1480	4.012895	GTGCGGCGTGTTGGACTG	62.013	66.667	9.37	0.00	0.00	3.51
1175	1487	2.672996	GTGTTGGACTGCCGGCAT	60.673	61.111	32.87	20.35	36.79	4.40
1176	1488	2.672651	TGTTGGACTGCCGGCATG	60.673	61.111	32.87	25.18	36.79	4.06
1177	1489	3.443045	GTTGGACTGCCGGCATGG	61.443	66.667	32.87	22.45	42.50	3.66
1190	1502	4.812476	CATGGCCGCGTTCTCCGA	62.812	66.667	4.92	0.00	39.56	4.55
1191	1503	4.514577	ATGGCCGCGTTCTCCGAG	62.515	66.667	4.92	0.00	39.56	4.63
1335	1653	0.180406	ATATGCCCTTGGACACCGAC	59.820	55.000	0.00	0.00	0.00	4.79
1336	1654	0.907704	TATGCCCTTGGACACCGACT	60.908	55.000	0.00	0.00	0.00	4.18
1383	1702	2.436646	GCAGGATGTGACCACCGG	60.437	66.667	0.00	0.00	39.31	5.28
1545	1870	3.123050	CGAATCATTCATCACGCCAGTA	58.877	45.455	0.00	0.00	0.00	2.74
1737	2074	1.289276	GCAGTTTGGGTTTTGCACAG	58.711	50.000	0.00	0.00	36.59	3.66
1775	2115	3.746045	TTACCTGTGGACAAGACAGAC	57.254	47.619	0.00	0.00	43.04	3.51
1851	2191	3.033909	CCTTCTTCCCATCCAAAATCCC	58.966	50.000	0.00	0.00	0.00	3.85
2171	2593	7.586714	TTGTGATAATATATCTGCTTGAGCG	57.413	36.000	0.00	0.00	45.83	5.03
2240	2826	9.326413	CAATTTTATATAGGGTCGTGTCTTCTT	57.674	33.333	0.00	0.00	0.00	2.52
2241	2827	9.901172	AATTTTATATAGGGTCGTGTCTTCTTT	57.099	29.630	0.00	0.00	0.00	2.52
2284	2871	3.153369	TCTATGTTTGCAGAAAGGGCA	57.847	42.857	0.00	0.00	40.00	5.36
2320	2907	1.918609	GCTCATTGACGACGTAGGAAC	59.081	52.381	0.00	0.00	0.00	3.62
2322	2909	3.427243	CTCATTGACGACGTAGGAACTC	58.573	50.000	0.00	0.00	41.75	3.01
2325	2912	3.928727	TTGACGACGTAGGAACTCAAT	57.071	42.857	0.00	0.00	41.75	2.57
2330	2917	6.722301	TGACGACGTAGGAACTCAATATAAG	58.278	40.000	0.00	0.00	41.75	1.73
2331	2918	6.069684	ACGACGTAGGAACTCAATATAAGG	57.930	41.667	0.00	0.00	41.75	2.69
2332	2919	5.009410	ACGACGTAGGAACTCAATATAAGGG	59.991	44.000	0.00	0.00	41.75	3.95
2333	2920	5.211174	ACGTAGGAACTCAATATAAGGGC	57.789	43.478	0.00	0.00	41.75	5.19
2336	2923	5.221461	CGTAGGAACTCAATATAAGGGCAGT	60.221	44.000	0.00	0.00	41.75	4.40
2339	2937	4.816925	GGAACTCAATATAAGGGCAGTCAC	59.183	45.833	0.00	0.00	0.00	3.67
2350	2949	2.158842	AGGGCAGTCACTCATCAATAGC	60.159	50.000	0.00	0.00	0.00	2.97
2374	2976	1.480212	ATGACCAGTTGGAGGCGACA	61.480	55.000	4.92	0.00	38.94	4.35
2386	2988	1.210155	GGCGACAATGGTCTTGTGC	59.790	57.895	0.00	0.00	42.05	4.57
2451	3058	7.284489	TGCTTGTTTTCTCATAGTTTTGGTAGT	59.716	33.333	0.00	0.00	0.00	2.73
2459	3066	8.251750	TCTCATAGTTTTGGTAGTTTTCATCG	57.748	34.615	0.00	0.00	0.00	3.84
2479	3086	7.227873	TCATCGGTATGCTTTATAAATTCCCA	58.772	34.615	0.00	0.00	32.76	4.37
2483	3090	7.721842	TCGGTATGCTTTATAAATTCCCAATGA	59.278	33.333	0.00	0.00	0.00	2.57
2494	3101	4.689612	ATTCCCAATGATAGTAGCGTGT	57.310	40.909	0.00	0.00	0.00	4.49
2498	3117	4.403113	TCCCAATGATAGTAGCGTGTGTTA	59.597	41.667	0.00	0.00	0.00	2.41
2510	3130	2.159572	GCGTGTGTTATGGTGAATGGAC	60.160	50.000	0.00	0.00	0.00	4.02
2519	3139	1.073763	TGGTGAATGGACTGTCCTTGG	59.926	52.381	26.03	0.00	37.46	3.61
2534	3154	4.768448	TGTCCTTGGACTGAACGTCTAATA	59.232	41.667	19.11	0.00	41.47	0.98
2535	3155	5.244402	TGTCCTTGGACTGAACGTCTAATAA	59.756	40.000	19.11	0.00	41.47	1.40
2536	3156	6.070995	TGTCCTTGGACTGAACGTCTAATAAT	60.071	38.462	19.11	0.00	41.47	1.28
2557	3226	0.534873	TCTTGCCGCACAGCTATGTA	59.465	50.000	0.00	0.00	37.65	2.29
2558	3227	1.138859	TCTTGCCGCACAGCTATGTAT	59.861	47.619	0.00	0.00	37.65	2.29
2629	3338	9.638239	TCCTTATCTAAATTCATTTTGCACAAC	57.362	29.630	0.00	0.00	0.00	3.32
2673	3384	0.833287	GAGGGCATGTCCAGAGCTAA	59.167	55.000	20.74	0.00	36.21	3.09
2699	3412	5.115480	GTTTCTGTCTCTGAAGGGATCATC	58.885	45.833	0.00	0.00	37.44	2.92
2704	3417	3.703556	GTCTCTGAAGGGATCATCTGACA	59.296	47.826	0.00	0.00	37.44	3.58
2708	3421	6.267242	TCTCTGAAGGGATCATCTGACAATAG	59.733	42.308	0.00	0.00	37.44	1.73
2733	3446	1.082117	GCATGTTGGCTTGCTGATGC	61.082	55.000	0.00	0.00	41.05	3.91
2752	3465	3.852286	TGCGTCGTAATTAACAGTCCAT	58.148	40.909	0.00	0.00	0.00	3.41
2760	3473	8.241367	GTCGTAATTAACAGTCCATTGGATTTT	58.759	33.333	9.01	5.30	32.73	1.82
2900	3709	9.784531	CTCAGAATATGGAACCTATTTGTGTAT	57.215	33.333	0.00	0.00	0.00	2.29
2959	3768	1.460504	ACTGCCATGAATGCTCAGTG	58.539	50.000	12.59	0.00	38.08	3.66
2963	3772	2.946990	TGCCATGAATGCTCAGTGTATG	59.053	45.455	0.00	0.00	34.23	2.39

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
10	11	3.968649	TGTTCATGTGAAAGCTTCAAGC	58.031	40.909	0.00	0.00	42.15	4.01
77	78	2.056577	GACAAGACCAACCGTAGTTCG	58.943	52.381	0.00	0.00	32.45	3.95
78	79	3.057734	CAGACAAGACCAACCGTAGTTC	58.942	50.000	0.00	0.00	32.45	3.01
84	85	1.227823	TGGCAGACAAGACCAACCG	60.228	57.895	0.00	0.00	0.00	4.44
107	108	5.833406	ATGGCAACGTGATCATTTTGATA	57.167	34.783	18.63	9.52	36.81	2.15
135	136	0.754217	ATTGGCAGCGCATCCTCAAT	60.754	50.000	11.47	9.24	0.00	2.57
220	224	5.421693	AGCATCAAATGGGTACAAAGCATAA	59.578	36.000	0.00	0.00	0.00	1.90
232	236	4.885907	ACTCAGAATGTAGCATCAAATGGG	59.114	41.667	0.00	0.00	37.40	4.00
243	247	8.398665	GGGTGCTTTTATTAACTCAGAATGTAG	58.601	37.037	0.00	0.00	37.40	2.74
259	263	6.636562	TTTGTTCGATAAAGGGTGCTTTTA	57.363	33.333	0.00	0.00	0.00	1.52
443	451	5.876612	AAGAGCAAATGATCACTGAAGAC	57.123	39.130	10.19	0.00	31.88	3.01
480	489	8.303876	TCAAAAGGTAAATAAATGCAGAAGTCC	58.696	33.333	0.00	0.00	0.00	3.85
510	519	7.330262	TCCAATTAAAGGAAATGCAGAAATCC	58.670	34.615	0.00	0.00	30.71	3.01
574	836	2.304470	GGGCCTGGGAAGAGAGATATTC	59.696	54.545	0.84	0.00	0.00	1.75
624	891	1.658114	GCCCAGGTGGAAACGAAAC	59.342	57.895	0.00	0.00	37.39	2.78
629	897	1.908299	CCAAGGCCCAGGTGGAAAC	60.908	63.158	0.00	0.00	37.39	2.78
766	1054	1.681327	TACTGGGAGTCTGGGACGC	60.681	63.158	0.00	0.00	37.67	5.19
784	1072	1.305886	GTTTAGGGAGGGGAATGGGT	58.694	55.000	0.00	0.00	0.00	4.51
799	1098	2.241281	TCGGTGGAGATGAGGGTTTA	57.759	50.000	0.00	0.00	0.00	2.01
809	1108	2.016393	GCATGGTCGATCGGTGGAGA	62.016	60.000	16.41	0.00	0.00	3.71
994	1306	2.440980	GGGGTGCTCCATGGAAGC	60.441	66.667	17.00	20.20	37.22	3.86
1067	1379	1.649321	AGAACTGTGGGATGAGCAGA	58.351	50.000	0.00	0.00	34.60	4.26
1070	1382	1.680249	GGGAAGAACTGTGGGATGAGC	60.680	57.143	0.00	0.00	0.00	4.26
1158	1470	2.672996	ATGCCGGCAGTCCAACAC	60.673	61.111	35.36	0.00	0.00	3.32
1159	1471	2.672651	CATGCCGGCAGTCCAACA	60.673	61.111	35.36	8.54	0.00	3.33
1160	1472	3.443045	CCATGCCGGCAGTCCAAC	61.443	66.667	35.36	0.00	0.00	3.77
1173	1485	4.812476	TCGGAGAACGCGGCCATG	62.812	66.667	12.47	0.00	43.86	3.66
1174	1486	4.514577	CTCGGAGAACGCGGCCAT	62.515	66.667	12.47	0.00	43.86	4.40
1189	1501	3.712881	GTCCAACACGCCGCACTC	61.713	66.667	0.00	0.00	0.00	3.51
1190	1502	4.235762	AGTCCAACACGCCGCACT	62.236	61.111	0.00	0.00	0.00	4.40
1191	1503	4.012895	CAGTCCAACACGCCGCAC	62.013	66.667	0.00	0.00	0.00	5.34
1545	1870	0.995024	CTTGGATGAAGACAGGGGGT	59.005	55.000	0.00	0.00	32.82	4.95
1602	1933	4.952262	TTTGAGAATTCCTGCTTGATCG	57.048	40.909	0.65	0.00	0.00	3.69
1775	2115	0.390603	TGCAACTCCATCGTAACCCG	60.391	55.000	0.00	0.00	38.13	5.28
1851	2191	8.438676	ACCCAATCAATCTAAGTCTTTTATCG	57.561	34.615	0.00	0.00	0.00	2.92
2260	2847	5.714333	TGCCCTTTCTGCAAACATAGATTTA	59.286	36.000	0.00	0.00	35.40	1.40
2284	2871	0.749454	GAGCCACATCGCAAGGGATT	60.749	55.000	0.00	0.00	38.47	3.01
2320	2907	5.282055	TGAGTGACTGCCCTTATATTGAG	57.718	43.478	0.00	0.00	0.00	3.02
2322	2909	5.614308	TGATGAGTGACTGCCCTTATATTG	58.386	41.667	0.00	0.00	0.00	1.90
2325	2912	5.894298	ATTGATGAGTGACTGCCCTTATA	57.106	39.130	0.00	0.00	0.00	0.98
2330	2917	2.216898	GCTATTGATGAGTGACTGCCC	58.783	52.381	0.00	0.00	0.00	5.36
2331	2918	2.910199	TGCTATTGATGAGTGACTGCC	58.090	47.619	0.00	0.00	0.00	4.85
2332	2919	4.633126	TCTTTGCTATTGATGAGTGACTGC	59.367	41.667	0.00	0.00	0.00	4.40
2333	2920	6.537660	TCATCTTTGCTATTGATGAGTGACTG	59.462	38.462	0.00	0.00	40.81	3.51
2336	2923	5.819379	GGTCATCTTTGCTATTGATGAGTGA	59.181	40.000	12.09	0.00	44.59	3.41
2339	2937	5.821470	ACTGGTCATCTTTGCTATTGATGAG	59.179	40.000	12.09	6.37	44.59	2.90
2350	2949	1.815003	GCCTCCAACTGGTCATCTTTG	59.185	52.381	0.00	0.00	36.34	2.77
2374	2976	5.948162	ACTTCATATTCAGCACAAGACCATT	59.052	36.000	0.00	0.00	0.00	3.16
2386	2988	5.549347	AGCAGCCAGATACTTCATATTCAG	58.451	41.667	0.00	0.00	0.00	3.02
2451	3058	9.959749	GGAATTTATAAAGCATACCGATGAAAA	57.040	29.630	3.94	0.00	34.73	2.29
2456	3063	8.522830	CATTGGGAATTTATAAAGCATACCGAT	58.477	33.333	3.94	5.56	0.00	4.18
2479	3086	5.753438	CACCATAACACACGCTACTATCATT	59.247	40.000	0.00	0.00	0.00	2.57
2483	3090	4.994907	TCACCATAACACACGCTACTAT	57.005	40.909	0.00	0.00	0.00	2.12
2488	3095	2.083774	CCATTCACCATAACACACGCT	58.916	47.619	0.00	0.00	0.00	5.07
2494	3101	3.587061	AGGACAGTCCATTCACCATAACA	59.413	43.478	22.31	0.00	39.61	2.41
2498	3117	2.291153	CCAAGGACAGTCCATTCACCAT	60.291	50.000	22.31	0.00	39.61	3.55
2510	3130	1.784525	GACGTTCAGTCCAAGGACAG	58.215	55.000	20.52	13.14	46.76	3.51
2534	3154	1.533625	TAGCTGTGCGGCAAGAAATT	58.466	45.000	3.23	0.00	34.17	1.82
2535	3155	1.402968	CATAGCTGTGCGGCAAGAAAT	59.597	47.619	3.23	0.00	34.17	2.17
2536	3156	0.804364	CATAGCTGTGCGGCAAGAAA	59.196	50.000	3.23	0.00	34.17	2.52
2589	3290	5.456921	AGATAAGGATCAAAGCTTGGGAA	57.543	39.130	0.00	0.00	34.17	3.97
2620	3329	5.126222	TCATGAGTTTTACCTGTTGTGCAAA	59.874	36.000	0.00	0.00	0.00	3.68
2629	3338	5.181009	TCATCTGCTCATGAGTTTTACCTG	58.819	41.667	23.38	11.98	0.00	4.00
2673	3384	3.251484	TCCCTTCAGAGACAGAAACCAT	58.749	45.455	0.00	0.00	0.00	3.55
2699	3412	5.396484	CCAACATGCAGAAACTATTGTCAG	58.604	41.667	0.00	0.00	0.00	3.51
2704	3417	4.813027	CAAGCCAACATGCAGAAACTATT	58.187	39.130	0.00	0.00	0.00	1.73
2708	3421	1.142474	GCAAGCCAACATGCAGAAAC	58.858	50.000	0.00	0.00	40.23	2.78
2733	3446	4.865925	TCCAATGGACTGTTAATTACGACG	59.134	41.667	0.00	0.00	0.00	5.12
2752	3465	8.800370	TGACATGTAGCACTAATAAAATCCAA	57.200	30.769	0.00	0.00	0.00	3.53
2760	3473	7.564793	ACAGGATTTGACATGTAGCACTAATA	58.435	34.615	0.00	0.00	33.07	0.98
2900	3709	9.046846	TCAAAATTAAGGAGAGATAGGTCAGAA	57.953	33.333	0.00	0.00	0.00	3.02
2959	3768	9.778993	CCAGCATATAAACATCTAAATGCATAC	57.221	33.333	0.00	0.00	41.61	2.39
2963	3772	7.596248	CCAACCAGCATATAAACATCTAAATGC	59.404	37.037	0.00	0.00	39.93	3.56

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.