AutoCloner

Multiple sequence alignment - TraesCS3A01G063300

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	TraesCS3A01G063300	chr3A	100.000	3152	0	0	1	3152	37831051	37834202	0.000000e+00	5821.0
1	TraesCS3A01G063300	chr3A	75.163	765	161	22	1405	2162	38198253	38198995	1.810000e-87	333.0
2	TraesCS3A01G063300	chr3A	74.453	411	87	10	1836	2245	10926889	10927282	9.050000e-36	161.0
3	TraesCS3A01G063300	chr3D	94.951	2258	84	10	102	2354	27941479	27939247	0.000000e+00	3511.0
4	TraesCS3A01G063300	chr3D	82.457	1807	248	29	544	2342	27559616	27561361	0.000000e+00	1517.0
5	TraesCS3A01G063300	chr3D	94.132	801	24	5	2352	3152	27955281	27956058	0.000000e+00	1197.0
6	TraesCS3A01G063300	chr3D	89.164	323	25	6	2561	2881	27954912	27955226	8.190000e-106	394.0
7	TraesCS3A01G063300	chr3D	77.778	675	120	22	1522	2187	27913422	27914075	3.810000e-104	388.0
8	TraesCS3A01G063300	chr3D	85.836	353	27	10	2596	2941	114343980	114343644	1.390000e-93	353.0
9	TraesCS3A01G063300	chr3D	73.242	1024	223	36	1175	2177	28233660	28234653	3.030000e-85	326.0
10	TraesCS3A01G063300	chr3D	82.063	223	37	2	553	775	27940910	27940691	1.490000e-43	187.0
11	TraesCS3A01G063300	chr3D	90.909	121	9	2	2352	2470	114344200	114344080	9.050000e-36	161.0
12	TraesCS3A01G063300	chr3D	100.000	32	0	0	2470	2501	27954837	27954868	3.400000e-05	60.2
13	TraesCS3A01G063300	chr3B	88.700	2115	182	22	236	2346	46789191	46787130	0.000000e+00	2529.0
14	TraesCS3A01G063300	chr3B	84.282	1686	210	25	661	2342	46059365	46060999	0.000000e+00	1594.0
15	TraesCS3A01G063300	chr3B	83.400	1500	216	27	685	2175	46593032	46591557	0.000000e+00	1360.0
16	TraesCS3A01G063300	chr3B	89.695	689	39	11	2470	3152	47128147	47128809	0.000000e+00	850.0
17	TraesCS3A01G063300	chr3B	93.354	316	12	7	2352	2666	46357559	46357252	2.860000e-125	459.0
18	TraesCS3A01G063300	chr3B	89.474	323	24	6	2561	2881	46357927	46357613	1.760000e-107	399.0
19	TraesCS3A01G063300	chr3B	74.669	983	160	48	1323	2272	46038193	46039119	1.390000e-93	353.0
20	TraesCS3A01G063300	chr3B	81.319	273	43	6	358	630	46593093	46592829	6.850000e-52	215.0
21	TraesCS3A01G063300	chr3B	80.498	241	45	2	556	795	46788764	46788525	1.930000e-42	183.0
22	TraesCS3A01G063300	chr3B	88.591	149	11	6	96	242	46793783	46793639	3.230000e-40	176.0
23	TraesCS3A01G063300	chr3B	76.327	245	52	6	553	795	46059322	46059562	3.300000e-25	126.0
24	TraesCS3A01G063300	chr3B	88.136	59	4	2	2288	2343	46041252	46041310	2.030000e-07	67.6
25	TraesCS3A01G063300	chr4A	96.766	402	10	3	2352	2752	89758814	89758415	0.000000e+00	667.0
26	TraesCS3A01G063300	chr4A	93.600	375	20	1	2778	3152	89758420	89758050	9.880000e-155	556.0
27	TraesCS3A01G063300	chr1D	86.119	353	26	10	2596	2941	262486879	262486543	2.990000e-95	359.0
28	TraesCS3A01G063300	chr7A	85.674	356	28	10	2593	2941	104380859	104381198	1.390000e-93	353.0
29	TraesCS3A01G063300	chr2A	85.552	353	28	11	2596	2941	547865638	547865302	6.470000e-92	348.0
30	TraesCS3A01G063300	chr6B	85.135	148	17	5	87	229	707141543	707141690	2.530000e-31	147.0
31	TraesCS3A01G063300	chrUn	76.889	225	50	2	1008	1231	197241947	197241724	3.300000e-25	126.0

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	TraesCS3A01G063300	chr3A	37831051	37834202	3151	False	5821.0	5821	100.0000	1	3152	1	chr3A.!!$F2	3151
1	TraesCS3A01G063300	chr3A	38198253	38198995	742	False	333.0	333	75.1630	1405	2162	1	chr3A.!!$F3	757
2	TraesCS3A01G063300	chr3D	27939247	27941479	2232	True	1849.0	3511	88.5070	102	2354	2	chr3D.!!$R1	2252
3	TraesCS3A01G063300	chr3D	27559616	27561361	1745	False	1517.0	1517	82.4570	544	2342	1	chr3D.!!$F1	1798
4	TraesCS3A01G063300	chr3D	27954837	27956058	1221	False	550.4	1197	94.4320	2352	3152	3	chr3D.!!$F4	800
5	TraesCS3A01G063300	chr3D	27913422	27914075	653	False	388.0	388	77.7780	1522	2187	1	chr3D.!!$F2	665
6	TraesCS3A01G063300	chr3D	28233660	28234653	993	False	326.0	326	73.2420	1175	2177	1	chr3D.!!$F3	1002
7	TraesCS3A01G063300	chr3D	114343644	114344200	556	True	257.0	353	88.3725	2352	2941	2	chr3D.!!$R2	589
8	TraesCS3A01G063300	chr3B	46787130	46789191	2061	True	1356.0	2529	84.5990	236	2346	2	chr3B.!!$R4	2110
9	TraesCS3A01G063300	chr3B	46059322	46060999	1677	False	860.0	1594	80.3045	553	2342	2	chr3B.!!$F3	1789
10	TraesCS3A01G063300	chr3B	47128147	47128809	662	False	850.0	850	89.6950	2470	3152	1	chr3B.!!$F1	682
11	TraesCS3A01G063300	chr3B	46591557	46593093	1536	True	787.5	1360	82.3595	358	2175	2	chr3B.!!$R3	1817
12	TraesCS3A01G063300	chr3B	46357252	46357927	675	True	429.0	459	91.4140	2352	2881	2	chr3B.!!$R2	529
13	TraesCS3A01G063300	chr3B	46038193	46041310	3117	False	210.3	353	81.4025	1323	2343	2	chr3B.!!$F2	1020
14	TraesCS3A01G063300	chr4A	89758050	89758814	764	True	611.5	667	95.1830	2352	3152	2	chr4A.!!$R1	800

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
780	852	0.106719	GGCTCAATCCCCAAATCCGA	60.107	55.000	0.0	0.0	0.0	4.55	F
1239	1380	1.083401	GCGCTTCAACACACGACAG	60.083	57.895	0.0	0.0	0.0	3.51	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1731	1910	1.863155	TTGGAGGCCCCTTGATCACC	61.863	60.000	0.0	0.0	35.38	4.02	R
2189	2375	2.812011	GGAAGCACAACGAAGGTATTGT	59.188	45.455	0.0	0.0	39.63	2.71	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
19	20	2.293677	TCGATGACGTTTGGATCAGG	57.706	50.000	0.00	0.00	40.69	3.86
20	21	0.652592	CGATGACGTTTGGATCAGGC	59.347	55.000	0.00	0.00	34.56	4.85
22	23	0.744414	ATGACGTTTGGATCAGGCGG	60.744	55.000	0.00	0.00	0.00	6.13
24	25	1.359459	GACGTTTGGATCAGGCGGAC	61.359	60.000	0.00	0.00	0.00	4.79
25	26	1.375396	CGTTTGGATCAGGCGGACA	60.375	57.895	0.00	0.00	0.00	4.02
27	28	0.734889	GTTTGGATCAGGCGGACATG	59.265	55.000	0.00	0.00	0.00	3.21
28	29	1.031571	TTTGGATCAGGCGGACATGC	61.032	55.000	0.00	0.00	0.00	4.06
29	30	2.969238	GGATCAGGCGGACATGCG	60.969	66.667	0.00	0.00	35.06	4.73
30	31	2.969238	GATCAGGCGGACATGCGG	60.969	66.667	0.00	0.00	35.06	5.69
32	33	2.721971	GATCAGGCGGACATGCGGAT	62.722	60.000	0.00	0.00	33.84	4.18
33	34	3.274586	CAGGCGGACATGCGGATG	61.275	66.667	16.07	16.07	35.06	3.51
34	35	3.469970	AGGCGGACATGCGGATGA	61.470	61.111	24.66	0.00	35.06	2.92
36	37	2.320587	GGCGGACATGCGGATGATC	61.321	63.158	24.66	15.90	35.06	2.92
37	38	1.301244	GCGGACATGCGGATGATCT	60.301	57.895	24.66	0.19	33.36	2.75
38	39	0.882042	GCGGACATGCGGATGATCTT	60.882	55.000	24.66	0.00	33.36	2.40
39	40	1.143305	CGGACATGCGGATGATCTTC	58.857	55.000	24.66	10.20	33.36	2.87
40	41	1.143305	GGACATGCGGATGATCTTCG	58.857	55.000	24.66	0.00	33.36	3.79
41	42	1.143305	GACATGCGGATGATCTTCGG	58.857	55.000	24.66	10.70	33.36	4.30
42	43	0.882042	ACATGCGGATGATCTTCGGC	60.882	55.000	24.66	25.26	41.02	5.54
43	44	1.302033	ATGCGGATGATCTTCGGCC	60.302	57.895	27.41	15.91	40.21	6.13
44	45	3.038417	GCGGATGATCTTCGGCCG	61.038	66.667	22.12	22.12	44.47	6.13
47	48	1.661821	GGATGATCTTCGGCCGACG	60.662	63.158	31.19	27.59	46.11	5.12
59	60	2.668280	GCCGACGAGCCACAAAGAC	61.668	63.158	0.00	0.00	0.00	3.01
60	61	1.006102	CCGACGAGCCACAAAGACT	60.006	57.895	0.00	0.00	0.00	3.24
64	65	3.567473	GAGCCACAAAGACTCGGC	58.433	61.111	0.00	0.00	45.23	5.54
66	67	3.567473	GCCACAAAGACTCGGCTC	58.433	61.111	0.00	0.00	41.50	4.70
67	68	1.004440	GCCACAAAGACTCGGCTCT	60.004	57.895	0.00	0.00	41.50	4.09
68	69	0.603975	GCCACAAAGACTCGGCTCTT	60.604	55.000	0.00	0.00	41.50	2.85
70	71	1.801178	CCACAAAGACTCGGCTCTTTC	59.199	52.381	5.54	0.00	38.24	2.62
72	73	1.068741	ACAAAGACTCGGCTCTTTCGT	59.931	47.619	5.54	5.63	38.24	3.85
74	75	1.249407	AAGACTCGGCTCTTTCGTCT	58.751	50.000	0.00	0.00	36.58	4.18
75	76	1.249407	AGACTCGGCTCTTTCGTCTT	58.751	50.000	0.00	0.00	31.36	3.01
76	77	1.068194	AGACTCGGCTCTTTCGTCTTG	60.068	52.381	0.00	0.00	31.36	3.02
77	78	0.674534	ACTCGGCTCTTTCGTCTTGT	59.325	50.000	0.00	0.00	0.00	3.16
78	79	1.063806	CTCGGCTCTTTCGTCTTGTG	58.936	55.000	0.00	0.00	0.00	3.33
82	83	1.221414	GCTCTTTCGTCTTGTGCTGT	58.779	50.000	0.00	0.00	0.00	4.40
84	85	2.800544	GCTCTTTCGTCTTGTGCTGTTA	59.199	45.455	0.00	0.00	0.00	2.41
85	86	3.433615	GCTCTTTCGTCTTGTGCTGTTAT	59.566	43.478	0.00	0.00	0.00	1.89
87	88	5.292101	GCTCTTTCGTCTTGTGCTGTTATAT	59.708	40.000	0.00	0.00	0.00	0.86
90	91	7.739295	TCTTTCGTCTTGTGCTGTTATATTTC	58.261	34.615	0.00	0.00	0.00	2.17
91	92	7.602644	TCTTTCGTCTTGTGCTGTTATATTTCT	59.397	33.333	0.00	0.00	0.00	2.52
93	94	7.060600	TCGTCTTGTGCTGTTATATTTCTTG	57.939	36.000	0.00	0.00	0.00	3.02
95	96	7.549134	TCGTCTTGTGCTGTTATATTTCTTGAT	59.451	33.333	0.00	0.00	0.00	2.57
96	97	7.637519	CGTCTTGTGCTGTTATATTTCTTGATG	59.362	37.037	0.00	0.00	0.00	3.07
97	98	8.668353	GTCTTGTGCTGTTATATTTCTTGATGA	58.332	33.333	0.00	0.00	0.00	2.92
100	101	9.791820	TTGTGCTGTTATATTTCTTGATGATTG	57.208	29.630	0.00	0.00	0.00	2.67
177	178	4.457466	TCTGTTTTTCTGTAAGGGTGTCC	58.543	43.478	0.00	0.00	0.00	4.02
180	181	3.935818	TTTTCTGTAAGGGTGTCCACA	57.064	42.857	0.00	0.00	34.83	4.17
189	190	4.755266	AAGGGTGTCCACATATGTACTC	57.245	45.455	8.32	3.00	34.83	2.59
229	234	4.566759	TCAATGAATACGTAGTGCTGCTTC	59.433	41.667	0.00	0.00	45.73	3.86
230	235	3.586100	TGAATACGTAGTGCTGCTTCA	57.414	42.857	0.00	0.54	45.73	3.02
232	237	3.926527	TGAATACGTAGTGCTGCTTCAAG	59.073	43.478	0.00	0.00	45.73	3.02
244	249	4.984161	TGCTGCTTCAAGAAAAAGTTATGC	59.016	37.500	0.00	0.00	0.00	3.14
249	254	6.039717	TGCTTCAAGAAAAAGTTATGCACTCT	59.960	34.615	0.00	0.00	32.94	3.24
401	410	4.409574	CCATTCCATTCCATTCCAATCCAA	59.590	41.667	0.00	0.00	0.00	3.53
605	677	3.461773	CATCGGTGAGGAGGGCGT	61.462	66.667	0.00	0.00	0.00	5.68
660	732	3.470567	CAAGTCCACGCGAGCGAC	61.471	66.667	24.72	14.68	42.83	5.19
678	750	2.588034	GAGGGTGGCGCCGTAATC	60.588	66.667	23.90	13.77	38.44	1.75
779	851	1.447317	CGGCTCAATCCCCAAATCCG	61.447	60.000	0.00	0.00	0.00	4.18
780	852	0.106719	GGCTCAATCCCCAAATCCGA	60.107	55.000	0.00	0.00	0.00	4.55
1072	1213	4.069232	CCTCCGCCGTCTGCAAGA	62.069	66.667	0.00	0.00	43.69	3.02
1239	1380	1.083401	GCGCTTCAACACACGACAG	60.083	57.895	0.00	0.00	0.00	3.51
1731	1910	0.461548	TGGATAGGCAGAGTCTTGCG	59.538	55.000	0.00	0.00	45.00	4.85
1750	1929	1.691219	GTGATCAAGGGGCCTCCAA	59.309	57.895	0.00	0.00	38.24	3.53
2189	2375	8.906867	AGTAACGTTCTATATACTTGGTTGCTA	58.093	33.333	2.82	0.00	29.49	3.49
2264	2451	9.608617	GTTAGAAATTGTTCCTTTACTAGTTGC	57.391	33.333	0.00	0.00	33.92	4.17
2431	4739	5.796502	TCCTGGGATTCAGATAAAAAGGT	57.203	39.130	0.00	0.00	46.18	3.50
2434	4742	7.016296	TCCTGGGATTCAGATAAAAAGGTTTT	58.984	34.615	0.00	0.00	46.18	2.43
2543	4898	9.382244	GAAAATGTATACATCAAGAATTACGGC	57.618	33.333	18.52	0.00	35.10	5.68
2544	4899	8.445275	AAATGTATACATCAAGAATTACGGCA	57.555	30.769	18.52	0.00	35.10	5.69
2545	4900	8.445275	AATGTATACATCAAGAATTACGGCAA	57.555	30.769	18.52	0.00	35.10	4.52
2546	4901	7.477144	TGTATACATCAAGAATTACGGCAAG	57.523	36.000	0.08	0.00	0.00	4.01
2547	4902	7.269316	TGTATACATCAAGAATTACGGCAAGA	58.731	34.615	0.08	0.00	0.00	3.02
2548	4903	7.766738	TGTATACATCAAGAATTACGGCAAGAA	59.233	33.333	0.08	0.00	0.00	2.52
2549	4904	7.807977	ATACATCAAGAATTACGGCAAGAAT	57.192	32.000	0.00	0.00	0.00	2.40
2550	4905	6.515272	ACATCAAGAATTACGGCAAGAATT	57.485	33.333	0.00	0.00	0.00	2.17
2551	4906	7.624360	ACATCAAGAATTACGGCAAGAATTA	57.376	32.000	0.00	0.00	0.00	1.40
2638	5003	4.272018	GCTCTAACGCATTCATTCATCAGT	59.728	41.667	0.00	0.00	0.00	3.41
2652	5017	5.694231	TTCATCAGTGAAACATGGTGAAG	57.306	39.130	0.00	0.00	38.90	3.02
2659	5024	4.022589	AGTGAAACATGGTGAAGCAGAATG	60.023	41.667	0.00	0.00	41.43	2.67
2838	5213	9.768662	AAAAGAGAATTGACAGCATTAAATTGT	57.231	25.926	0.00	0.00	0.00	2.71
2968	5343	3.552273	GGCGTTGAGAGTTGAGAGTTGTA	60.552	47.826	0.00	0.00	0.00	2.41
2969	5344	3.425858	GCGTTGAGAGTTGAGAGTTGTAC	59.574	47.826	0.00	0.00	0.00	2.90
2970	5345	3.982058	CGTTGAGAGTTGAGAGTTGTACC	59.018	47.826	0.00	0.00	0.00	3.34
2971	5346	4.499188	CGTTGAGAGTTGAGAGTTGTACCA	60.499	45.833	0.00	0.00	0.00	3.25
3091	5466	4.143333	CGTCGTGCAGGGGGTAGG	62.143	72.222	6.56	0.00	0.00	3.18

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
2	3	0.652592	CGCCTGATCCAAACGTCATC	59.347	55.000	0.00	0.00	0.00	2.92
4	5	1.375396	CCGCCTGATCCAAACGTCA	60.375	57.895	0.00	0.00	0.00	4.35
5	6	1.079405	TCCGCCTGATCCAAACGTC	60.079	57.895	0.00	0.00	0.00	4.34
6	7	1.375523	GTCCGCCTGATCCAAACGT	60.376	57.895	0.00	0.00	0.00	3.99
8	9	0.734889	CATGTCCGCCTGATCCAAAC	59.265	55.000	0.00	0.00	0.00	2.93
10	11	1.451927	GCATGTCCGCCTGATCCAA	60.452	57.895	0.00	0.00	0.00	3.53
11	12	2.190313	GCATGTCCGCCTGATCCA	59.810	61.111	0.00	0.00	0.00	3.41
12	13	2.969238	CGCATGTCCGCCTGATCC	60.969	66.667	0.00	0.00	0.00	3.36
14	15	2.811514	ATCCGCATGTCCGCCTGAT	61.812	57.895	0.00	0.00	0.00	2.90
16	17	3.274586	CATCCGCATGTCCGCCTG	61.275	66.667	0.00	0.00	0.00	4.85
17	18	2.721971	GATCATCCGCATGTCCGCCT	62.722	60.000	0.00	0.00	0.00	5.52
18	19	2.281070	ATCATCCGCATGTCCGCC	60.281	61.111	0.00	0.00	0.00	6.13
19	20	0.882042	AAGATCATCCGCATGTCCGC	60.882	55.000	0.00	0.00	0.00	5.54
20	21	1.143305	GAAGATCATCCGCATGTCCG	58.857	55.000	0.00	0.00	0.00	4.79
22	23	1.143305	CCGAAGATCATCCGCATGTC	58.857	55.000	0.00	0.00	0.00	3.06
24	25	1.572085	GGCCGAAGATCATCCGCATG	61.572	60.000	12.19	0.00	0.00	4.06
25	26	1.302033	GGCCGAAGATCATCCGCAT	60.302	57.895	12.19	0.00	0.00	4.73
27	28	3.038417	CGGCCGAAGATCATCCGC	61.038	66.667	24.07	3.12	33.36	5.54
28	29	1.661821	GTCGGCCGAAGATCATCCG	60.662	63.158	32.93	0.00	41.30	4.18
29	30	1.661821	CGTCGGCCGAAGATCATCC	60.662	63.158	33.68	16.17	39.56	3.51
30	31	0.661780	CTCGTCGGCCGAAGATCATC	60.662	60.000	37.62	20.22	46.75	2.92
32	33	2.798689	CTCGTCGGCCGAAGATCA	59.201	61.111	37.62	20.31	46.75	2.92
33	34	2.655685	GCTCGTCGGCCGAAGATC	60.656	66.667	37.62	31.24	46.75	2.75
34	35	4.208686	GGCTCGTCGGCCGAAGAT	62.209	66.667	37.62	0.00	46.75	2.40
41	42	2.357034	TCTTTGTGGCTCGTCGGC	60.357	61.111	0.00	0.00	38.97	5.54
42	43	1.006102	AGTCTTTGTGGCTCGTCGG	60.006	57.895	0.00	0.00	0.00	4.79
43	44	2.435741	GAGTCTTTGTGGCTCGTCG	58.564	57.895	0.00	0.00	37.69	5.12
47	48	3.567473	GCCGAGTCTTTGTGGCTC	58.433	61.111	0.00	0.00	44.16	4.70
49	50	2.147960	AAAGAGCCGAGTCTTTGTGGC	61.148	52.381	10.20	0.00	43.66	5.01
50	51	1.801178	GAAAGAGCCGAGTCTTTGTGG	59.199	52.381	14.46	0.00	45.00	4.17
51	52	1.457303	CGAAAGAGCCGAGTCTTTGTG	59.543	52.381	14.46	5.67	45.00	3.33
52	53	1.068741	ACGAAAGAGCCGAGTCTTTGT	59.931	47.619	14.46	10.64	45.00	2.83
53	54	1.721926	GACGAAAGAGCCGAGTCTTTG	59.278	52.381	14.46	10.18	45.00	2.77
54	55	2.036089	AAGACGAAAGAGCCGAGTCTTT	59.964	45.455	10.65	10.65	46.23	2.52
55	56	1.249407	AGACGAAAGAGCCGAGTCTT	58.751	50.000	0.00	0.00	38.86	3.01
59	60	1.063806	CACAAGACGAAAGAGCCGAG	58.936	55.000	0.00	0.00	0.00	4.63
60	61	0.944311	GCACAAGACGAAAGAGCCGA	60.944	55.000	0.00	0.00	0.00	5.54
63	64	1.221414	ACAGCACAAGACGAAAGAGC	58.779	50.000	0.00	0.00	0.00	4.09
64	65	6.893958	ATATAACAGCACAAGACGAAAGAG	57.106	37.500	0.00	0.00	0.00	2.85
66	67	7.743104	AGAAATATAACAGCACAAGACGAAAG	58.257	34.615	0.00	0.00	0.00	2.62
67	68	7.667043	AGAAATATAACAGCACAAGACGAAA	57.333	32.000	0.00	0.00	0.00	3.46
68	69	7.386573	TCAAGAAATATAACAGCACAAGACGAA	59.613	33.333	0.00	0.00	0.00	3.85
70	71	7.060600	TCAAGAAATATAACAGCACAAGACG	57.939	36.000	0.00	0.00	0.00	4.18
72	73	8.791327	TCATCAAGAAATATAACAGCACAAGA	57.209	30.769	0.00	0.00	0.00	3.02
74	75	9.791820	CAATCATCAAGAAATATAACAGCACAA	57.208	29.630	0.00	0.00	0.00	3.33
75	76	8.959548	ACAATCATCAAGAAATATAACAGCACA	58.040	29.630	0.00	0.00	0.00	4.57
76	77	9.229784	CACAATCATCAAGAAATATAACAGCAC	57.770	33.333	0.00	0.00	0.00	4.40
77	78	8.959548	ACACAATCATCAAGAAATATAACAGCA	58.040	29.630	0.00	0.00	0.00	4.41
78	79	9.793252	AACACAATCATCAAGAAATATAACAGC	57.207	29.630	0.00	0.00	0.00	4.40
120	121	5.118286	CCTGAAGGTTTGCACAAAGAATTT	58.882	37.500	0.00	0.00	40.26	1.82
136	137	4.709397	ACAGAGAGACATAAGACCTGAAGG	59.291	45.833	0.00	0.00	42.17	3.46
153	154	5.365619	GACACCCTTACAGAAAAACAGAGA	58.634	41.667	0.00	0.00	0.00	3.10
157	158	3.949113	GTGGACACCCTTACAGAAAAACA	59.051	43.478	0.00	0.00	0.00	2.83
189	190	8.592105	ATTCATTGAACAAATTTGGTACACAG	57.408	30.769	21.74	12.20	39.29	3.66
197	198	8.365210	GCACTACGTATTCATTGAACAAATTTG	58.635	33.333	16.67	16.67	0.00	2.32
315	323	8.776680	TCGTATGCTTTTACTTTTTCAGTTTC	57.223	30.769	0.00	0.00	36.88	2.78
337	345	1.215647	GACACAGGGCTCGATTCGT	59.784	57.895	5.89	0.00	0.00	3.85
385	394	3.958798	CTCTGCTTGGATTGGAATGGAAT	59.041	43.478	0.00	0.00	0.00	3.01
401	410	0.748450	GCTCATCTCTGCTCTCTGCT	59.252	55.000	0.00	0.00	43.37	4.24
507	516	3.992641	GGGGTTTGGGGGTGGAGG	61.993	72.222	0.00	0.00	0.00	4.30
660	732	4.524318	ATTACGGCGCCACCCTCG	62.524	66.667	28.98	13.91	33.26	4.63
779	851	4.838486	CACCCTCGTCGCTCGCTC	62.838	72.222	0.00	0.00	39.67	5.03
831	903	4.351054	CTGTGGAGGTGGGGGTGC	62.351	72.222	0.00	0.00	0.00	5.01
1239	1380	1.883084	CCGGAAGCCACGTATCTGC	60.883	63.158	0.00	0.00	0.00	4.26
1281	1431	4.496336	AGGAGGATGCGGCCTTGC	62.496	66.667	0.00	0.00	38.73	4.01
1307	1457	2.108075	ACAATGAACCAGTCCATGTCCA	59.892	45.455	0.00	0.00	0.00	4.02
1310	1460	4.272489	CCATACAATGAACCAGTCCATGT	58.728	43.478	0.00	0.00	0.00	3.21
1311	1461	3.633525	CCCATACAATGAACCAGTCCATG	59.366	47.826	0.00	0.00	0.00	3.66
1731	1910	1.863155	TTGGAGGCCCCTTGATCACC	61.863	60.000	0.00	0.00	35.38	4.02
1750	1929	5.241403	TGTGTGGTGGAATGATTAAGACT	57.759	39.130	0.00	0.00	0.00	3.24
2189	2375	2.812011	GGAAGCACAACGAAGGTATTGT	59.188	45.455	0.00	0.00	39.63	2.71
2264	2451	4.570772	ACACAGTACAGCTACAAGTTTGTG	59.429	41.667	7.73	13.20	42.31	3.33
2399	4706	4.712337	TCTGAATCCCAGGAAGAAGTAGAC	59.288	45.833	0.00	0.00	43.12	2.59
2431	4739	7.233962	GGTTCTTGGATAGGTCCCTTTTTAAAA	59.766	37.037	0.00	0.00	44.41	1.52
2434	4742	5.313772	TGGTTCTTGGATAGGTCCCTTTTTA	59.686	40.000	0.00	0.00	44.41	1.52
2540	4895	6.758886	AGATTCTAGTCACTTAATTCTTGCCG	59.241	38.462	0.00	0.00	0.00	5.69
2541	4896	7.766278	TCAGATTCTAGTCACTTAATTCTTGCC	59.234	37.037	0.00	0.00	0.00	4.52
2542	4897	8.709386	TCAGATTCTAGTCACTTAATTCTTGC	57.291	34.615	0.00	0.00	0.00	4.01
2544	4899	9.323985	GCATCAGATTCTAGTCACTTAATTCTT	57.676	33.333	0.00	0.00	0.00	2.52
2545	4900	8.481314	TGCATCAGATTCTAGTCACTTAATTCT	58.519	33.333	0.00	0.00	0.00	2.40
2546	4901	8.547069	GTGCATCAGATTCTAGTCACTTAATTC	58.453	37.037	0.00	0.00	0.00	2.17
2547	4902	8.263640	AGTGCATCAGATTCTAGTCACTTAATT	58.736	33.333	0.00	0.00	30.30	1.40
2548	4903	7.790027	AGTGCATCAGATTCTAGTCACTTAAT	58.210	34.615	0.00	0.00	30.30	1.40
2549	4904	7.175347	AGTGCATCAGATTCTAGTCACTTAA	57.825	36.000	0.00	0.00	30.30	1.85
2550	4905	6.782082	AGTGCATCAGATTCTAGTCACTTA	57.218	37.500	0.00	0.00	30.30	2.24
2551	4906	5.674052	AGTGCATCAGATTCTAGTCACTT	57.326	39.130	0.00	0.00	30.30	3.16
2638	5003	3.890756	ACATTCTGCTTCACCATGTTTCA	59.109	39.130	0.00	0.00	0.00	2.69
2652	5017	4.424626	TGTCGATGAGTTCTACATTCTGC	58.575	43.478	0.00	0.00	0.00	4.26
2659	5024	4.425520	CTCCCTTTGTCGATGAGTTCTAC	58.574	47.826	0.00	0.00	0.00	2.59
2838	5213	5.067954	GGGTTGCTGTTAGTTTTCCTTCTA	58.932	41.667	0.00	0.00	0.00	2.10
2915	5290	4.638963	GTTTCTTCGATTCGAATCACCAC	58.361	43.478	31.57	17.39	44.85	4.16

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.