AutoCloner

Multiple sequence alignment - TraesCS3D01G340100

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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	TraesCS3D01G340100	chr3D	100.000	3884	0	0	1	3884	453986593	453982710	0.000000e+00	7173.0
1	TraesCS3D01G340100	chr3D	90.063	2053	128	19	843	2879	1993368	1991376	0.000000e+00	2591.0
2	TraesCS3D01G340100	chr3D	85.714	126	5	4	3359	3481	1978653	1978538	1.900000e-23	121.0
3	TraesCS3D01G340100	chr3B	94.284	3674	146	34	256	3884	596413464	596409810	0.000000e+00	5563.0
4	TraesCS3D01G340100	chr3B	88.068	947	76	24	2534	3468	737563524	737562603	0.000000e+00	1088.0
5	TraesCS3D01G340100	chr3B	85.096	624	56	23	2854	3465	688176794	688177392	1.540000e-168	603.0
6	TraesCS3D01G340100	chr3B	84.776	624	58	23	2854	3465	688161174	688161772	3.340000e-165	592.0
7	TraesCS3D01G340100	chr3B	92.553	376	27	1	2528	2902	688159038	688159413	4.420000e-149	538.0
8	TraesCS3D01G340100	chr3B	85.043	234	11	12	3618	3839	688161887	688162108	2.350000e-52	217.0
9	TraesCS3D01G340100	chr3B	84.615	234	12	12	3618	3839	688177507	688177728	1.090000e-50	211.0
10	TraesCS3D01G340100	chr3B	81.695	295	14	17	3618	3884	737561791	737561509	3.930000e-50	209.0
11	TraesCS3D01G340100	chr3A	92.388	3731	150	47	228	3884	595935273	595931603	0.000000e+00	5193.0
12	TraesCS3D01G340100	chr3A	93.578	109	4	1	1	109	595935518	595935413	4.020000e-35	159.0
13	TraesCS3D01G340100	chr7A	92.257	904	48	8	881	1770	465714	464819	0.000000e+00	1262.0
14	TraesCS3D01G340100	chr7A	86.585	902	63	24	1914	2806	464735	463883	0.000000e+00	942.0
15	TraesCS3D01G340100	chr7A	88.235	51	6	0	3444	3494	463657	463607	1.170000e-05	62.1
16	TraesCS3D01G340100	chr5B	88.433	951	70	26	2528	3465	610348525	610349448	0.000000e+00	1110.0
17	TraesCS3D01G340100	chr5B	82.373	295	12	16	3618	3884	610349562	610349844	1.820000e-53	220.0
18	TraesCS3D01G340100	chr1B	80.034	1172	192	29	1001	2142	531535314	531536473	0.000000e+00	830.0
19	TraesCS3D01G340100	chr1B	82.368	397	62	8	2397	2792	531536581	531536970	4.810000e-89	339.0
20	TraesCS3D01G340100	chr1D	79.714	1188	186	40	1001	2149	391277857	391276686	0.000000e+00	808.0
21	TraesCS3D01G340100	chr1A	83.313	803	120	12	1003	1801	494024276	494025068	0.000000e+00	728.0
22	TraesCS3D01G340100	chr1A	83.123	397	59	8	2397	2792	494025546	494025935	4.770000e-94	355.0
23	TraesCS3D01G340100	chr2D	92.412	369	17	4	996	1362	636085982	636085623	2.070000e-142	516.0
24	TraesCS3D01G340100	chr2D	86.145	166	3	13	824	971	636086623	636086460	1.120000e-35	161.0
25	TraesCS3D01G340100	chrUn	91.008	367	24	2	996	1362	354266468	354266825	1.620000e-133	486.0
26	TraesCS3D01G340100	chrUn	94.466	253	14	0	1110	1362	247902077	247902329	1.310000e-104	390.0

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	TraesCS3D01G340100	chr3D	453982710	453986593	3883	True	7173.000000	7173	100.000000	1	3884	1	chr3D.!!$R3	3883
1	TraesCS3D01G340100	chr3D	1991376	1993368	1992	True	2591.000000	2591	90.063000	843	2879	1	chr3D.!!$R2	2036
2	TraesCS3D01G340100	chr3B	596409810	596413464	3654	True	5563.000000	5563	94.284000	256	3884	1	chr3B.!!$R1	3628
3	TraesCS3D01G340100	chr3B	737561509	737563524	2015	True	648.500000	1088	84.881500	2534	3884	2	chr3B.!!$R2	1350
4	TraesCS3D01G340100	chr3B	688159038	688162108	3070	False	449.000000	592	87.457333	2528	3839	3	chr3B.!!$F1	1311
5	TraesCS3D01G340100	chr3B	688176794	688177728	934	False	407.000000	603	84.855500	2854	3839	2	chr3B.!!$F2	985
6	TraesCS3D01G340100	chr3A	595931603	595935518	3915	True	2676.000000	5193	92.983000	1	3884	2	chr3A.!!$R1	3883
7	TraesCS3D01G340100	chr7A	463607	465714	2107	True	755.366667	1262	89.025667	881	3494	3	chr7A.!!$R1	2613
8	TraesCS3D01G340100	chr5B	610348525	610349844	1319	False	665.000000	1110	85.403000	2528	3884	2	chr5B.!!$F1	1356
9	TraesCS3D01G340100	chr1B	531535314	531536970	1656	False	584.500000	830	81.201000	1001	2792	2	chr1B.!!$F1	1791
10	TraesCS3D01G340100	chr1D	391276686	391277857	1171	True	808.000000	808	79.714000	1001	2149	1	chr1D.!!$R1	1148
11	TraesCS3D01G340100	chr1A	494024276	494025935	1659	False	541.500000	728	83.218000	1003	2792	2	chr1A.!!$F1	1789
12	TraesCS3D01G340100	chr2D	636085623	636086623	1000	True	338.500000	516	89.278500	824	1362	2	chr2D.!!$R1	538

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
160	189	0.109689	CGTCGGACACAGAGAGGAAC	60.110	60.0	9.1	0.0	0.0	3.62	F
1586	2135	0.318762	AGGCTGTTCGACCTCAAGAC	59.681	55.0	0.0	0.0	0.0	3.01	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2049	2628	1.003233	GACCAGGGTGGAAGTCTGC	60.003	63.158	0.0	0.00	40.96	4.26	R
3027	5450	0.390866	AGTCCAGCTTGATCTGCGTG	60.391	55.000	0.0	0.17	35.28	5.34	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
48	49	0.678950	ACTGCATTTGAAAACGGGGG	59.321	50.000	0.00	0.00	0.00	5.40
109	110	1.945819	GCACGGCTGAATCTCCAAGAA	60.946	52.381	0.00	0.00	0.00	2.52
110	111	2.426522	CACGGCTGAATCTCCAAGAAA	58.573	47.619	0.00	0.00	0.00	2.52
111	112	2.160417	CACGGCTGAATCTCCAAGAAAC	59.840	50.000	0.00	0.00	0.00	2.78
112	113	1.394917	CGGCTGAATCTCCAAGAAACG	59.605	52.381	0.00	0.00	0.00	3.60
113	114	1.740025	GGCTGAATCTCCAAGAAACGG	59.260	52.381	0.00	0.00	0.00	4.44
119	148	1.612676	TCTCCAAGAAACGGTCTCGA	58.387	50.000	0.00	0.00	40.11	4.04
120	149	2.168496	TCTCCAAGAAACGGTCTCGAT	58.832	47.619	0.00	0.00	40.11	3.59
134	163	1.135489	TCTCGATCGAAACTGAACCCG	60.135	52.381	19.92	3.30	0.00	5.28
151	180	2.941333	GACTCGTCGTCGGACACA	59.059	61.111	9.10	0.00	43.61	3.72
152	181	1.154450	GACTCGTCGTCGGACACAG	60.154	63.158	9.10	8.18	43.61	3.66
153	182	1.563435	GACTCGTCGTCGGACACAGA	61.563	60.000	9.10	2.95	43.61	3.41
154	183	1.132844	CTCGTCGTCGGACACAGAG	59.867	63.158	9.10	8.79	43.61	3.35
155	184	1.289800	CTCGTCGTCGGACACAGAGA	61.290	60.000	9.10	0.00	43.61	3.10
156	185	1.132844	CGTCGTCGGACACAGAGAG	59.867	63.158	9.10	0.00	43.61	3.20
157	186	1.502640	GTCGTCGGACACAGAGAGG	59.497	63.158	9.10	0.00	42.91	3.69
158	187	0.954449	GTCGTCGGACACAGAGAGGA	60.954	60.000	9.10	0.00	42.91	3.71
159	188	0.250597	TCGTCGGACACAGAGAGGAA	60.251	55.000	9.10	0.00	0.00	3.36
160	189	0.109689	CGTCGGACACAGAGAGGAAC	60.110	60.000	9.10	0.00	0.00	3.62
162	191	2.434428	GTCGGACACAGAGAGGAACTA	58.566	52.381	2.62	0.00	41.55	2.24
163	192	2.818432	GTCGGACACAGAGAGGAACTAA	59.182	50.000	2.62	0.00	41.55	2.24
164	193	3.255149	GTCGGACACAGAGAGGAACTAAA	59.745	47.826	2.62	0.00	41.55	1.85
165	194	4.082136	GTCGGACACAGAGAGGAACTAAAT	60.082	45.833	2.62	0.00	41.55	1.40
166	195	4.158025	TCGGACACAGAGAGGAACTAAATC	59.842	45.833	0.00	0.00	41.55	2.17
167	196	4.425520	GGACACAGAGAGGAACTAAATCG	58.574	47.826	0.00	0.00	41.55	3.34
168	197	4.425520	GACACAGAGAGGAACTAAATCGG	58.574	47.826	0.00	0.00	41.55	4.18
169	198	3.195825	ACACAGAGAGGAACTAAATCGGG	59.804	47.826	0.00	0.00	41.55	5.14
170	199	3.447586	CACAGAGAGGAACTAAATCGGGA	59.552	47.826	0.00	0.00	41.55	5.14
171	200	3.702045	ACAGAGAGGAACTAAATCGGGAG	59.298	47.826	0.00	0.00	41.55	4.30
172	201	3.068873	CAGAGAGGAACTAAATCGGGAGG	59.931	52.174	0.00	0.00	41.55	4.30
173	202	3.052793	AGAGAGGAACTAAATCGGGAGGA	60.053	47.826	0.00	0.00	41.55	3.71
174	203	3.705072	GAGAGGAACTAAATCGGGAGGAA	59.295	47.826	0.00	0.00	41.55	3.36
175	204	3.707102	AGAGGAACTAAATCGGGAGGAAG	59.293	47.826	0.00	0.00	41.55	3.46
176	205	2.772515	AGGAACTAAATCGGGAGGAAGG	59.227	50.000	0.00	0.00	36.02	3.46
177	206	2.770232	GGAACTAAATCGGGAGGAAGGA	59.230	50.000	0.00	0.00	0.00	3.36
178	207	3.391626	GGAACTAAATCGGGAGGAAGGAT	59.608	47.826	0.00	0.00	0.00	3.24
179	208	4.141459	GGAACTAAATCGGGAGGAAGGATT	60.141	45.833	0.00	0.00	32.05	3.01
180	209	5.437946	GAACTAAATCGGGAGGAAGGATTT	58.562	41.667	4.01	4.01	41.69	2.17
181	210	6.408891	GGAACTAAATCGGGAGGAAGGATTTA	60.409	42.308	5.61	5.61	40.03	1.40
182	211	5.926663	ACTAAATCGGGAGGAAGGATTTAC	58.073	41.667	2.32	0.00	40.03	2.01
183	212	3.859061	AATCGGGAGGAAGGATTTACC	57.141	47.619	0.00	0.00	39.35	2.85
201	230	7.769507	GGATTTACCTTCTTCTTTTCGTAGGAT	59.230	37.037	0.00	0.00	35.41	3.24
203	232	8.543862	TTTACCTTCTTCTTTTCGTAGGATTC	57.456	34.615	0.00	0.00	0.00	2.52
205	234	5.012768	ACCTTCTTCTTTTCGTAGGATTCCA	59.987	40.000	5.29	0.00	0.00	3.53
207	236	7.093024	ACCTTCTTCTTTTCGTAGGATTCCATA	60.093	37.037	5.29	0.00	0.00	2.74
213	242	8.014070	TCTTTTCGTAGGATTCCATACATACA	57.986	34.615	5.29	0.00	0.00	2.29
215	244	9.104965	CTTTTCGTAGGATTCCATACATACAAA	57.895	33.333	5.29	0.68	0.00	2.83
216	245	9.621629	TTTTCGTAGGATTCCATACATACAAAT	57.378	29.630	5.29	0.00	0.00	2.32
218	247	9.701098	TTCGTAGGATTCCATACATACAAATAC	57.299	33.333	5.29	0.00	0.00	1.89
219	248	8.862085	TCGTAGGATTCCATACATACAAATACA	58.138	33.333	5.29	0.00	0.00	2.29
220	249	9.653287	CGTAGGATTCCATACATACAAATACAT	57.347	33.333	5.29	0.00	0.00	2.29
235	297	6.578944	ACAAATACATCGTGATACTAGGCAA	58.421	36.000	0.00	0.00	0.00	4.52
458	529	2.224159	TGAACCCTGCAGTCTCCCC	61.224	63.158	13.81	0.00	0.00	4.81
522	593	3.157252	GGCCAGGAGCTCGATCCA	61.157	66.667	7.83	0.00	42.26	3.41
836	907	0.802494	CCGGTGATTTACAGCCACAC	59.198	55.000	0.00	0.00	43.16	3.82
1472	2021	4.463879	CACCAGCCTGGCCGAGAG	62.464	72.222	16.57	2.16	42.67	3.20
1586	2135	0.318762	AGGCTGTTCGACCTCAAGAC	59.681	55.000	0.00	0.00	0.00	3.01
1731	2280	1.882167	GATCAGCCTCAGCGTGCTC	60.882	63.158	0.00	0.00	46.67	4.26
1774	2323	2.956964	CGGCGCTCAAGATCCGTC	60.957	66.667	7.64	0.00	37.33	4.79
1832	2387	1.006805	GGATCCACGATCTCGGCAG	60.007	63.158	6.95	0.00	44.95	4.85
1895	2474	0.741915	AAGGAGGAAGAGATCGTCGC	59.258	55.000	0.00	0.00	42.57	5.19
2184	2765	7.482743	CACACACACTTGCATGATTAGATTAAC	59.517	37.037	6.60	0.00	0.00	2.01
2185	2766	7.174772	ACACACACTTGCATGATTAGATTAACA	59.825	33.333	6.60	0.00	0.00	2.41
2334	2931	4.309099	TCTGCTTTTGTCCATGCAATTTC	58.691	39.130	0.00	0.00	34.90	2.17
2366	2964	0.868406	AAGCAGAAGAAACGGAAGCG	59.132	50.000	0.00	0.00	0.00	4.68
2382	2984	1.352056	GCGGCGGCTAACTGAATTC	59.648	57.895	9.78	0.00	35.83	2.17
3018	5441	0.744874	GACTGATCGATCCCACGGAA	59.255	55.000	22.31	1.07	34.34	4.30
3030	5453	1.876714	CACGGAAGGGATACGCACG	60.877	63.158	0.00	0.00	39.78	5.34
3143	5567	9.167239	GAATAGCAGATTTTCTTTTCATCATCG	57.833	33.333	0.00	0.00	0.00	3.84
3149	5581	9.861138	CAGATTTTCTTTTCATCATCGAGTATC	57.139	33.333	0.00	0.00	0.00	2.24
3165	5611	6.577103	TCGAGTATCATGCTTCTTCATTTCT	58.423	36.000	0.00	0.00	33.17	2.52
3191	5637	0.251354	AGTGCCAGCATGTAGGAGTG	59.749	55.000	9.41	0.00	0.00	3.51
3270	5719	5.127519	TGCATGAAAGCAACTATTAATGGCT	59.872	36.000	0.00	0.00	42.46	4.75
3283	5734	8.863872	ACTATTAATGGCTTGTTTAGACTTGT	57.136	30.769	0.00	0.00	30.89	3.16
3284	5735	9.953565	ACTATTAATGGCTTGTTTAGACTTGTA	57.046	29.630	0.00	0.00	30.89	2.41
3349	5800	2.175035	TTGTGTAGTACCGGCAGGCC	62.175	60.000	0.00	0.00	42.76	5.19
3395	5856	1.734465	GAGAAGAATCTGTTGGGCACG	59.266	52.381	0.00	0.00	35.54	5.34
3481	5971	4.976116	GCCATAACAATTCCGCAAAGTATC	59.024	41.667	0.00	0.00	0.00	2.24
3495	5985	6.255020	CCGCAAAGTATCTGTTCGTAAGTTAT	59.745	38.462	0.00	0.00	39.48	1.89
3511	6001	6.784227	CGTAAGTTATCACGAAAGTTGTCAAC	59.216	38.462	7.68	7.68	46.40	3.18
3513	6003	4.514066	AGTTATCACGAAAGTTGTCAACCC	59.486	41.667	12.17	1.71	46.40	4.11

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
23	24	3.490761	CCGTTTTCAAATGCAGTGAACCT	60.491	43.478	13.62	0.00	34.78	3.50
24	25	2.794350	CCGTTTTCAAATGCAGTGAACC	59.206	45.455	13.62	7.91	34.78	3.62
25	26	2.794350	CCCGTTTTCAAATGCAGTGAAC	59.206	45.455	13.62	5.36	34.78	3.18
26	27	2.223923	CCCCGTTTTCAAATGCAGTGAA	60.224	45.455	10.70	10.70	33.21	3.18
27	28	1.339610	CCCCGTTTTCAAATGCAGTGA	59.660	47.619	0.00	0.00	0.00	3.41
28	29	1.605202	CCCCCGTTTTCAAATGCAGTG	60.605	52.381	0.00	0.00	0.00	3.66
29	30	0.678950	CCCCCGTTTTCAAATGCAGT	59.321	50.000	0.00	0.00	0.00	4.40
30	31	0.678950	ACCCCCGTTTTCAAATGCAG	59.321	50.000	0.00	0.00	0.00	4.41
48	49	1.433879	CCACTCGGATCGACCTCAC	59.566	63.158	0.00	0.00	36.31	3.51
91	92	2.427506	GTTTCTTGGAGATTCAGCCGT	58.572	47.619	0.00	0.00	0.00	5.68
109	110	1.538512	TCAGTTTCGATCGAGACCGTT	59.461	47.619	28.99	12.98	37.05	4.44
110	111	1.162698	TCAGTTTCGATCGAGACCGT	58.837	50.000	28.99	13.64	37.05	4.83
111	112	1.912110	GTTCAGTTTCGATCGAGACCG	59.088	52.381	28.99	21.80	30.58	4.79
112	113	2.260481	GGTTCAGTTTCGATCGAGACC	58.740	52.381	28.99	20.24	30.58	3.85
113	114	2.260481	GGGTTCAGTTTCGATCGAGAC	58.740	52.381	26.45	26.45	0.00	3.36
119	148	1.402456	CGAGTCGGGTTCAGTTTCGAT	60.402	52.381	4.10	0.00	34.13	3.59
120	149	0.039798	CGAGTCGGGTTCAGTTTCGA	60.040	55.000	4.10	0.00	0.00	3.71
134	163	1.154450	CTGTGTCCGACGACGAGTC	60.154	63.158	9.28	0.00	46.16	3.36
148	177	3.447586	TCCCGATTTAGTTCCTCTCTGTG	59.552	47.826	0.00	0.00	0.00	3.66
151	180	3.052793	TCCTCCCGATTTAGTTCCTCTCT	60.053	47.826	0.00	0.00	0.00	3.10
152	181	3.297736	TCCTCCCGATTTAGTTCCTCTC	58.702	50.000	0.00	0.00	0.00	3.20
153	182	3.399952	TCCTCCCGATTTAGTTCCTCT	57.600	47.619	0.00	0.00	0.00	3.69
154	183	3.181464	CCTTCCTCCCGATTTAGTTCCTC	60.181	52.174	0.00	0.00	0.00	3.71
155	184	2.772515	CCTTCCTCCCGATTTAGTTCCT	59.227	50.000	0.00	0.00	0.00	3.36
156	185	2.770232	TCCTTCCTCCCGATTTAGTTCC	59.230	50.000	0.00	0.00	0.00	3.62
157	186	4.691326	ATCCTTCCTCCCGATTTAGTTC	57.309	45.455	0.00	0.00	0.00	3.01
158	187	5.452341	AAATCCTTCCTCCCGATTTAGTT	57.548	39.130	0.00	0.00	35.10	2.24
159	188	5.163227	GGTAAATCCTTCCTCCCGATTTAGT	60.163	44.000	0.00	0.00	38.49	2.24
160	189	5.071923	AGGTAAATCCTTCCTCCCGATTTAG	59.928	44.000	0.00	0.00	45.67	1.85
161	190	4.973211	AGGTAAATCCTTCCTCCCGATTTA	59.027	41.667	0.00	0.00	45.67	1.40
162	191	3.786450	AGGTAAATCCTTCCTCCCGATTT	59.214	43.478	0.00	0.00	45.67	2.17
163	192	3.394645	AGGTAAATCCTTCCTCCCGATT	58.605	45.455	0.00	0.00	45.67	3.34
164	193	3.061909	AGGTAAATCCTTCCTCCCGAT	57.938	47.619	0.00	0.00	45.67	4.18
165	194	2.563039	AGGTAAATCCTTCCTCCCGA	57.437	50.000	0.00	0.00	45.67	5.14
175	204	7.101700	TCCTACGAAAAGAAGAAGGTAAATCC	58.898	38.462	0.00	0.00	0.00	3.01
176	205	8.719560	ATCCTACGAAAAGAAGAAGGTAAATC	57.280	34.615	0.00	0.00	0.00	2.17
177	206	9.163899	GAATCCTACGAAAAGAAGAAGGTAAAT	57.836	33.333	0.00	0.00	0.00	1.40
178	207	7.605309	GGAATCCTACGAAAAGAAGAAGGTAAA	59.395	37.037	0.00	0.00	0.00	2.01
179	208	7.101700	GGAATCCTACGAAAAGAAGAAGGTAA	58.898	38.462	0.00	0.00	0.00	2.85
180	209	6.211986	TGGAATCCTACGAAAAGAAGAAGGTA	59.788	38.462	0.00	0.00	0.00	3.08
181	210	5.012768	TGGAATCCTACGAAAAGAAGAAGGT	59.987	40.000	0.00	0.00	0.00	3.50
182	211	5.488341	TGGAATCCTACGAAAAGAAGAAGG	58.512	41.667	0.00	0.00	0.00	3.46
183	212	7.764443	TGTATGGAATCCTACGAAAAGAAGAAG	59.236	37.037	0.00	0.00	0.00	2.85
184	213	7.617225	TGTATGGAATCCTACGAAAAGAAGAA	58.383	34.615	0.00	0.00	0.00	2.52
185	214	7.177832	TGTATGGAATCCTACGAAAAGAAGA	57.822	36.000	0.00	0.00	0.00	2.87
186	215	8.979574	GTATGTATGGAATCCTACGAAAAGAAG	58.020	37.037	0.00	0.00	0.00	2.85
187	216	8.479689	TGTATGTATGGAATCCTACGAAAAGAA	58.520	33.333	0.00	0.00	0.00	2.52
188	217	8.014070	TGTATGTATGGAATCCTACGAAAAGA	57.986	34.615	0.00	0.00	0.00	2.52
189	218	8.657074	TTGTATGTATGGAATCCTACGAAAAG	57.343	34.615	0.00	0.00	0.00	2.27
190	219	9.621629	ATTTGTATGTATGGAATCCTACGAAAA	57.378	29.630	0.00	2.15	0.00	2.29
192	221	9.701098	GTATTTGTATGTATGGAATCCTACGAA	57.299	33.333	0.00	1.03	0.00	3.85
198	227	8.443160	CACGATGTATTTGTATGTATGGAATCC	58.557	37.037	0.00	0.00	0.00	3.01
203	232	9.639601	AGTATCACGATGTATTTGTATGTATGG	57.360	33.333	0.00	0.00	0.00	2.74
207	236	7.813148	GCCTAGTATCACGATGTATTTGTATGT	59.187	37.037	0.00	0.00	0.00	2.29
213	242	6.817184	ACTTGCCTAGTATCACGATGTATTT	58.183	36.000	0.00	0.00	34.56	1.40
215	244	7.704578	ATACTTGCCTAGTATCACGATGTAT	57.295	36.000	0.00	0.00	44.97	2.29
216	245	7.013942	ACAATACTTGCCTAGTATCACGATGTA	59.986	37.037	8.53	0.00	46.92	2.29
217	246	6.183360	ACAATACTTGCCTAGTATCACGATGT	60.183	38.462	8.53	6.74	46.92	3.06
218	247	6.144563	CACAATACTTGCCTAGTATCACGATG	59.855	42.308	8.53	6.26	46.92	3.84
219	248	6.216569	CACAATACTTGCCTAGTATCACGAT	58.783	40.000	8.53	0.00	46.92	3.73
220	249	5.588240	CACAATACTTGCCTAGTATCACGA	58.412	41.667	8.53	0.00	46.92	4.35
271	333	2.423577	GCTTGGCTTCGTCCTTCTTAA	58.576	47.619	0.00	0.00	0.00	1.85
272	334	1.338769	GGCTTGGCTTCGTCCTTCTTA	60.339	52.381	0.00	0.00	0.00	2.10
522	593	1.130054	ATGGCGGATGACCTATGGCT	61.130	55.000	0.00	0.00	0.00	4.75
624	695	1.873486	GCCGGTTGCTTGCAAGATTTT	60.873	47.619	30.39	0.00	36.87	1.82
806	877	2.525105	AATCACCGGCAATTAAGGGT	57.475	45.000	0.00	0.00	0.00	4.34
1586	2135	4.147449	TGCTCGCCATGGAGTCGG	62.147	66.667	18.40	8.58	36.41	4.79
1773	2322	3.370209	CCCAGATCTTGTTCATGCTCTGA	60.370	47.826	15.88	0.00	33.59	3.27
1774	2323	2.943690	CCCAGATCTTGTTCATGCTCTG	59.056	50.000	0.00	10.50	0.00	3.35
2049	2628	1.003233	GACCAGGGTGGAAGTCTGC	60.003	63.158	0.00	0.00	40.96	4.26
2184	2765	4.041723	GCCCAATCGGACGAAAATAAATG	58.958	43.478	0.00	0.00	0.00	2.32
2185	2766	3.067601	GGCCCAATCGGACGAAAATAAAT	59.932	43.478	0.00	0.00	0.00	1.40
2198	2779	0.471617	AGATCTCAAGGGCCCAATCG	59.528	55.000	27.56	9.85	0.00	3.34
2334	2931	3.879295	TCTTCTGCTTCTGGAAACAAGTG	59.121	43.478	0.00	0.00	42.06	3.16
2366	2964	1.084289	AACGAATTCAGTTAGCCGCC	58.916	50.000	6.22	0.00	0.00	6.13
2382	2984	0.453793	TTCTGCACCACAAACCAACG	59.546	50.000	0.00	0.00	0.00	4.10
3018	5441	1.364171	GATCTGCGTGCGTATCCCT	59.636	57.895	0.00	0.00	0.00	4.20
3027	5450	0.390866	AGTCCAGCTTGATCTGCGTG	60.391	55.000	0.00	0.17	35.28	5.34
3030	5453	1.066286	ACTCAGTCCAGCTTGATCTGC	60.066	52.381	10.55	0.00	32.87	4.26
3143	5567	7.983307	ACAAGAAATGAAGAAGCATGATACTC	58.017	34.615	0.00	0.00	0.00	2.59
3149	5581	8.697067	CACTAAAACAAGAAATGAAGAAGCATG	58.303	33.333	0.00	0.00	0.00	4.06
3165	5611	3.505680	CCTACATGCTGGCACTAAAACAA	59.494	43.478	0.00	0.00	0.00	2.83
3191	5637	1.068474	CTCAACATCCCAACGTCGAC	58.932	55.000	5.18	5.18	0.00	4.20
3303	5754	7.285629	TCAATCAGTAGTAGAATTCCACGATCT	59.714	37.037	0.65	0.00	0.00	2.75
3306	5757	6.769134	TCAATCAGTAGTAGAATTCCACGA	57.231	37.500	0.65	0.00	0.00	4.35
3495	5985	1.292061	CGGGTTGACAACTTTCGTGA	58.708	50.000	17.52	0.00	0.00	4.35
3511	6001	1.130561	GTTTTCCTTGATCTTCGCGGG	59.869	52.381	6.13	0.00	0.00	6.13
3513	6003	1.130561	GGGTTTTCCTTGATCTTCGCG	59.869	52.381	0.00	0.00	40.46	5.87
3562	6065	7.038659	CACCATTTTTCTACAGTTTGGTTTGA	58.961	34.615	0.00	0.00	33.88	2.69
3704	6934	2.928416	GGAACCCTACACTGTGTGC	58.072	57.895	22.97	5.64	36.98	4.57
3768	6998	2.319011	GACGCATGCCAGTGATGCTG	62.319	60.000	13.15	9.79	43.45	4.41

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.