AutoCloner

Multiple sequence alignment - TraesCS7D01G059500

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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	TraesCS7D01G059500	chr7D	100.000	4639	0	0	1	4639	32249181	32253819	0.000000e+00	8567.0
1	TraesCS7D01G059500	chr7D	85.250	1322	171	14	1789	3093	45706525	45705211	0.000000e+00	1339.0
2	TraesCS7D01G059500	chr7D	78.649	740	95	32	3158	3848	45705180	45704455	2.560000e-117	433.0
3	TraesCS7D01G059500	chr7D	74.827	723	135	29	2171	2856	16709076	16709788	2.730000e-72	283.0
4	TraesCS7D01G059500	chr7A	96.823	3022	81	8	1623	4639	32413142	32416153	0.000000e+00	5035.0
5	TraesCS7D01G059500	chr7A	84.367	1548	199	26	1567	3093	47903822	47902297	0.000000e+00	1478.0
6	TraesCS7D01G059500	chr7A	92.758	649	31	12	916	1561	32412489	32413124	0.000000e+00	924.0
7	TraesCS7D01G059500	chr7A	91.781	511	30	9	414	915	32410792	32411299	0.000000e+00	701.0
8	TraesCS7D01G059500	chr7A	75.272	736	137	26	2157	2856	15695573	15696299	4.510000e-80	309.0
9	TraesCS7D01G059500	chr7A	84.286	140	21	1	756	894	646081297	646081158	8.100000e-28	135.0
10	TraesCS7D01G059500	chr4A	94.225	2840	115	17	1490	4323	694849299	694846503	0.000000e+00	4290.0
11	TraesCS7D01G059500	chr4A	93.548	434	23	5	318	746	694850627	694850194	3.910000e-180	641.0
12	TraesCS7D01G059500	chr4A	95.597	318	14	0	4322	4639	694846421	694846104	1.150000e-140	510.0
13	TraesCS7D01G059500	chr4A	93.114	334	13	3	1	334	694850961	694850638	9.030000e-132	481.0
14	TraesCS7D01G059500	chr4A	74.728	736	141	26	2157	2856	717966490	717965764	2.110000e-73	287.0
15	TraesCS7D01G059500	chr4A	87.330	221	22	4	1268	1483	694849580	694849361	9.970000e-62	248.0
16	TraesCS7D01G059500	chr4A	91.447	152	11	2	951	1101	694849923	694849773	1.690000e-49	207.0
17	TraesCS7D01G059500	chr4A	89.655	145	15	0	748	892	694850074	694849930	7.930000e-43	185.0
18	TraesCS7D01G059500	chr4A	70.773	1112	243	62	1791	2850	624982433	624983514	1.330000e-40	178.0
19	TraesCS7D01G059500	chr4A	83.942	137	21	1	756	891	637534170	637534034	3.770000e-26	130.0
20	TraesCS7D01G059500	chr4A	73.298	382	67	25	2157	2516	625248645	625249013	1.770000e-19	108.0
21	TraesCS7D01G059500	chrUn	84.373	1555	193	24	1565	3093	320961660	320963190	0.000000e+00	1480.0
22	TraesCS7D01G059500	chr2B	75.262	1334	266	46	1786	3085	137188962	137190265	1.120000e-160	577.0
23	TraesCS7D01G059500	chr2B	75.214	1287	258	45	1786	3038	136806564	136807823	1.890000e-153	553.0
24	TraesCS7D01G059500	chr2B	75.214	1287	258	45	1786	3038	136951614	136952873	1.890000e-153	553.0
25	TraesCS7D01G059500	chr2B	75.136	1287	259	45	1786	3038	137608694	137609953	8.780000e-152	547.0
26	TraesCS7D01G059500	chr2D	74.850	1336	269	48	1786	3085	84916882	84918186	1.140000e-150	544.0
27	TraesCS7D01G059500	chr2D	85.401	137	15	5	756	889	139257631	139257765	2.250000e-28	137.0
28	TraesCS7D01G059500	chr2D	92.727	55	4	0	3702	3756	84918837	84918891	3.850000e-11	80.5
29	TraesCS7D01G059500	chr2D	97.436	39	1	0	901	939	193393215	193393253	3.000000e-07	67.6
30	TraesCS7D01G059500	chr2D	90.196	51	4	1	891	941	359664115	359664066	1.080000e-06	65.8
31	TraesCS7D01G059500	chr2A	74.146	1288	265	49	1789	3036	84153877	84152618	5.430000e-129	472.0
32	TraesCS7D01G059500	chr2A	84.559	136	20	1	756	890	39164544	39164679	2.910000e-27	134.0
33	TraesCS7D01G059500	chr5B	72.257	948	197	53	1942	2850	686050726	686049806	2.790000e-57	233.0
34	TraesCS7D01G059500	chr5B	72.000	725	147	47	1970	2666	685950996	685950300	3.710000e-36	163.0
35	TraesCS7D01G059500	chr5B	71.626	578	121	32	1978	2532	685649066	685649623	8.150000e-23	119.0
36	TraesCS7D01G059500	chr5B	80.153	131	26	0	2729	2859	685991823	685991693	1.060000e-16	99.0
37	TraesCS7D01G059500	chr5D	70.964	985	215	53	1912	2850	544285959	544285000	7.980000e-38	169.0
38	TraesCS7D01G059500	chr6B	83.221	149	20	5	755	899	598007682	598007535	1.050000e-26	132.0
39	TraesCS7D01G059500	chr3B	83.942	137	21	1	756	891	427579833	427579969	3.770000e-26	130.0
40	TraesCS7D01G059500	chr3B	97.500	40	1	0	901	940	202473548	202473587	8.330000e-08	69.4
41	TraesCS7D01G059500	chr4D	82.667	150	18	8	755	899	38450777	38450631	4.870000e-25	126.0
42	TraesCS7D01G059500	chr4D	97.436	39	1	0	901	939	451291104	451291142	3.000000e-07	67.6
43	TraesCS7D01G059500	chr6D	82.727	110	16	3	756	863	75893712	75893820	1.370000e-15	95.3
44	TraesCS7D01G059500	chr5A	100.000	37	0	0	904	940	6620422	6620386	8.330000e-08	69.4
45	TraesCS7D01G059500	chr5A	100.000	36	0	0	904	939	705906159	705906124	3.000000e-07	67.6
46	TraesCS7D01G059500	chr3D	91.837	49	3	1	891	939	333007730	333007683	3.000000e-07	67.6

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	TraesCS7D01G059500	chr7D	32249181	32253819	4638	False	8567.000000	8567	100.000000	1	4639	1	chr7D.!!$F2	4638
1	TraesCS7D01G059500	chr7D	45704455	45706525	2070	True	886.000000	1339	81.949500	1789	3848	2	chr7D.!!$R1	2059
2	TraesCS7D01G059500	chr7D	16709076	16709788	712	False	283.000000	283	74.827000	2171	2856	1	chr7D.!!$F1	685
3	TraesCS7D01G059500	chr7A	32410792	32416153	5361	False	2220.000000	5035	93.787333	414	4639	3	chr7A.!!$F2	4225
4	TraesCS7D01G059500	chr7A	47902297	47903822	1525	True	1478.000000	1478	84.367000	1567	3093	1	chr7A.!!$R1	1526
5	TraesCS7D01G059500	chr7A	15695573	15696299	726	False	309.000000	309	75.272000	2157	2856	1	chr7A.!!$F1	699
6	TraesCS7D01G059500	chr4A	694846104	694850961	4857	True	937.428571	4290	92.130857	1	4639	7	chr4A.!!$R3	4638
7	TraesCS7D01G059500	chr4A	717965764	717966490	726	True	287.000000	287	74.728000	2157	2856	1	chr4A.!!$R2	699
8	TraesCS7D01G059500	chrUn	320961660	320963190	1530	False	1480.000000	1480	84.373000	1565	3093	1	chrUn.!!$F1	1528
9	TraesCS7D01G059500	chr2B	137188962	137190265	1303	False	577.000000	577	75.262000	1786	3085	1	chr2B.!!$F3	1299
10	TraesCS7D01G059500	chr2B	136806564	136807823	1259	False	553.000000	553	75.214000	1786	3038	1	chr2B.!!$F1	1252
11	TraesCS7D01G059500	chr2B	136951614	136952873	1259	False	553.000000	553	75.214000	1786	3038	1	chr2B.!!$F2	1252
12	TraesCS7D01G059500	chr2B	137608694	137609953	1259	False	547.000000	547	75.136000	1786	3038	1	chr2B.!!$F4	1252
13	TraesCS7D01G059500	chr2D	84916882	84918891	2009	False	312.250000	544	83.788500	1786	3756	2	chr2D.!!$F3	1970
14	TraesCS7D01G059500	chr2A	84152618	84153877	1259	True	472.000000	472	74.146000	1789	3036	1	chr2A.!!$R1	1247
15	TraesCS7D01G059500	chr5B	686049806	686050726	920	True	233.000000	233	72.257000	1942	2850	1	chr5B.!!$R3	908

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	Hairpin	End Stability	Orientation
229	230	0.034186	GGGTGCATCCTTGGTCATCA	60.034	55.000	9.39	36.25	3.07	F
230	231	1.410648	GGGTGCATCCTTGGTCATCAT	60.411	52.381	9.39	36.25	2.45	F
231	232	1.679680	GGTGCATCCTTGGTCATCATG	59.320	52.381	0.00	0.00	3.07	F
1018	2363	2.091541	CCGAATAAAAAGCCAGGCAGA	58.908	47.619	15.80	0.00	4.26	F
1594	3058	1.203162	ACCCCCTGTTGCATGATTTGA	60.203	47.619	0.00	0.00	2.69	F
2590	4088	0.250684	TCAGCTTGGCATGTCGGAAA	60.251	50.000	2.12	0.00	3.13	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1209	2556	0.394488	CAGACCTAGGGACGAGAGCA	60.394	60.000	14.81	30.78	4.26	R
1295	2699	0.449786	TACACAATTTCATGGCCGCG	59.550	50.000	0.00	0.00	6.46	R
1371	2779	2.094854	CCCTAGGTGTTACACGACTGAC	60.095	54.545	8.29	34.83	3.51	R
2590	4088	1.897133	TCCGCACACTACAACTGGTAT	59.103	47.619	0.00	0.00	2.73	R
2810	4341	1.991230	CCCCATCGTTCAGGGTTCT	59.009	57.895	0.00	43.89	3.01	R
4161	5959	0.884704	TGCTCCGCTTTCTTCACCAC	60.885	55.000	0.00	0.00	4.16	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
27	28	3.119955	GGGACGAATGGAGTAGTTTTTGC	60.120	47.826	0.00	0.00	0.00	3.68
37	38	6.503524	TGGAGTAGTTTTTGCTTTCATCAAC	58.496	36.000	0.00	0.00	0.00	3.18
85	86	2.069273	CTGGACTAACGTCAGGCTTTG	58.931	52.381	0.00	0.00	42.05	2.77
111	112	2.050985	GCTGTTGACACGCTTGGC	60.051	61.111	0.00	0.00	0.00	4.52
206	207	6.752351	GTGCTGAATATATAATCCATCGTCGT	59.248	38.462	0.00	0.00	0.00	4.34
219	220	2.813908	GTCGTCACGGGTGCATCC	60.814	66.667	5.70	5.70	0.00	3.51
220	221	2.994995	TCGTCACGGGTGCATCCT	60.995	61.111	15.59	0.00	36.25	3.24
221	222	2.047274	CGTCACGGGTGCATCCTT	60.047	61.111	15.59	0.26	36.25	3.36
222	223	2.390599	CGTCACGGGTGCATCCTTG	61.391	63.158	16.25	16.25	36.25	3.61
223	224	2.040544	GTCACGGGTGCATCCTTGG	61.041	63.158	21.40	5.22	36.25	3.61
224	225	2.034066	CACGGGTGCATCCTTGGT	59.966	61.111	15.59	1.11	36.25	3.67
225	226	2.040544	CACGGGTGCATCCTTGGTC	61.041	63.158	15.59	0.00	36.25	4.02
226	227	2.350895	CGGGTGCATCCTTGGTCA	59.649	61.111	15.59	0.00	36.25	4.02
227	228	1.077501	CGGGTGCATCCTTGGTCAT	60.078	57.895	15.59	0.00	36.25	3.06
228	229	1.097547	CGGGTGCATCCTTGGTCATC	61.098	60.000	15.59	0.00	36.25	2.92
229	230	0.034186	GGGTGCATCCTTGGTCATCA	60.034	55.000	9.39	0.00	36.25	3.07
230	231	1.410648	GGGTGCATCCTTGGTCATCAT	60.411	52.381	9.39	0.00	36.25	2.45
231	232	1.679680	GGTGCATCCTTGGTCATCATG	59.320	52.381	0.00	0.00	0.00	3.07
232	233	2.372264	GTGCATCCTTGGTCATCATGT	58.628	47.619	0.00	0.00	0.00	3.21
277	278	2.257286	ATCGCTGCCGTGAACATTGC	62.257	55.000	0.00	0.00	32.63	3.56
348	376	5.861787	GCTGGTTGTTGGTTGTTTGATATAC	59.138	40.000	0.00	0.00	0.00	1.47
353	381	8.745590	GGTTGTTGGTTGTTTGATATACCTTAT	58.254	33.333	0.00	0.00	0.00	1.73
557	590	6.258230	TGCATCAATTTTCCAAGACTACAG	57.742	37.500	0.00	0.00	0.00	2.74
578	611	5.243060	ACAGGTTCTTAATTAAAGGGTGTGC	59.757	40.000	0.00	0.00	35.75	4.57
628	661	4.773323	AAGAAGAAAAGGAAATCGCCAG	57.227	40.909	0.00	0.00	0.00	4.85
634	667	3.644966	AAAGGAAATCGCCAGTCCATA	57.355	42.857	0.00	0.00	33.57	2.74
761	913	2.146920	ACTGCTACTCTGGTACTCCC	57.853	55.000	0.00	0.00	0.00	4.30
824	977	8.589701	TGGACTACATACAGAGTAAAATGAGA	57.410	34.615	0.00	0.00	0.00	3.27
845	998	6.531594	TGAGAGAGTACACAATCTAAAATGCG	59.468	38.462	0.00	0.00	0.00	4.73
847	1000	6.531948	AGAGAGTACACAATCTAAAATGCGTC	59.468	38.462	0.00	0.00	0.00	5.19
939	2283	7.232330	ACCTATATTTAGAAACGGAGGGAGTAC	59.768	40.741	0.00	0.00	0.00	2.73
1018	2363	2.091541	CCGAATAAAAAGCCAGGCAGA	58.908	47.619	15.80	0.00	0.00	4.26
1217	2564	4.385405	GGCACCTGCTGCTCTCGT	62.385	66.667	0.00	0.00	46.25	4.18
1257	2604	5.103643	ACCCTAACCTTGTTTTCTCCTCTTT	60.104	40.000	0.00	0.00	0.00	2.52
1272	2619	4.717877	TCCTCTTTCTGATGCAAGTTTGA	58.282	39.130	0.00	0.00	0.00	2.69
1273	2620	5.319453	TCCTCTTTCTGATGCAAGTTTGAT	58.681	37.500	0.00	0.00	0.00	2.57
1274	2621	5.413833	TCCTCTTTCTGATGCAAGTTTGATC	59.586	40.000	0.00	0.00	0.00	2.92
1275	2622	5.415077	CCTCTTTCTGATGCAAGTTTGATCT	59.585	40.000	0.00	0.00	0.00	2.75
1276	2623	6.072064	CCTCTTTCTGATGCAAGTTTGATCTT	60.072	38.462	0.00	0.00	0.00	2.40
1277	2624	6.675026	TCTTTCTGATGCAAGTTTGATCTTG	58.325	36.000	0.00	2.58	45.09	3.02
1278	2625	6.263842	TCTTTCTGATGCAAGTTTGATCTTGT	59.736	34.615	0.00	0.00	44.41	3.16
1279	2626	6.395426	TTCTGATGCAAGTTTGATCTTGTT	57.605	33.333	0.00	0.00	44.41	2.83
1280	2627	5.765176	TCTGATGCAAGTTTGATCTTGTTG	58.235	37.500	0.00	0.00	44.41	3.33
1282	2629	6.486320	TCTGATGCAAGTTTGATCTTGTTGTA	59.514	34.615	0.00	0.00	44.41	2.41
1283	2630	7.013178	TCTGATGCAAGTTTGATCTTGTTGTAA	59.987	33.333	0.00	0.00	44.41	2.41
1295	2699	3.496884	TCTTGTTGTAAGAACATGCGGAC	59.503	43.478	0.00	0.00	34.97	4.79
1326	2730	4.704540	TGAAATTGTGTAACTATGGGCCTG	59.295	41.667	4.53	0.00	38.04	4.85
1333	2737	3.783642	TGTAACTATGGGCCTGGTGTTAT	59.216	43.478	4.53	0.00	0.00	1.89
1337	2741	2.442236	ATGGGCCTGGTGTTATTCTG	57.558	50.000	4.53	0.00	0.00	3.02
1371	2779	2.442212	TGGCATGATGCTTTGTGTTG	57.558	45.000	17.84	0.00	44.28	3.33
1594	3058	1.203162	ACCCCCTGTTGCATGATTTGA	60.203	47.619	0.00	0.00	0.00	2.69
1671	3145	8.800370	TGCTGTACCTTATTGTGATTGAAATA	57.200	30.769	0.00	0.00	0.00	1.40
2040	3520	1.444119	GGCGTGCCACAGTTTCTTCA	61.444	55.000	5.89	0.00	35.81	3.02
2155	3638	3.371273	GGACTACCCTTTATCCAACACCC	60.371	52.174	0.00	0.00	0.00	4.61
2163	3646	2.612285	TATCCAACACCCAATGGCAA	57.388	45.000	0.00	0.00	36.62	4.52
2590	4088	0.250684	TCAGCTTGGCATGTCGGAAA	60.251	50.000	2.12	0.00	0.00	3.13
2751	4282	5.584649	CGCTAAGTGGATGAAGTTGGATAAA	59.415	40.000	0.00	0.00	0.00	1.40
2810	4341	5.241506	CCAGGAGTTCTACATTTTCTTGCAA	59.758	40.000	0.00	0.00	0.00	4.08
2919	4450	0.753867	TTGGTCAGTTCGTGCCTACA	59.246	50.000	0.00	0.00	0.00	2.74
2944	4475	7.174363	AGTTCCCACCCCATTACATATATTT	57.826	36.000	0.00	0.00	0.00	1.40
3080	4612	2.203337	GCCCTGTCAACTGGTGCA	60.203	61.111	11.74	0.00	34.13	4.57
3191	4728	5.765677	TCCGTTCAGTGAATAATTTGGTTGA	59.234	36.000	9.18	0.00	0.00	3.18
3345	4892	2.095212	GCTGGGATCCTTCGTTTTTCAC	60.095	50.000	12.58	0.00	0.00	3.18
3392	4939	9.424319	GTGGAATACACAGTTGTATATAGGATG	57.576	37.037	0.00	0.00	46.45	3.51
3404	4951	6.210796	TGTATATAGGATGTGGTTTCGTTCG	58.789	40.000	0.00	0.00	0.00	3.95
3508	5268	6.705381	CCACAAAAGGTAATCTGAATTGCAAA	59.295	34.615	1.71	0.00	0.00	3.68
3783	5581	1.808411	TTTTCTCTGCAACGCCTAGG	58.192	50.000	3.67	3.67	0.00	3.02
3926	5724	4.098914	TGGACCTAGTTTGAACAGCATT	57.901	40.909	0.00	0.00	0.00	3.56
3932	5730	5.221244	ACCTAGTTTGAACAGCATTGGAAAC	60.221	40.000	0.00	0.00	0.00	2.78
4025	5823	0.743345	GTAGAAATTCGCACCGCCCT	60.743	55.000	0.00	0.00	0.00	5.19
4026	5824	0.035820	TAGAAATTCGCACCGCCCTT	60.036	50.000	0.00	0.00	0.00	3.95
4227	6025	4.581824	ACTACAAGGTGTTTGACTCGTCTA	59.418	41.667	0.00	0.00	39.21	2.59
4301	6099	8.472007	TGTATGTTCCTTGTTTTACTTTGGAT	57.528	30.769	0.00	0.00	0.00	3.41
4374	6259	0.598065	GCCGTCAATGAGCTGGTTTT	59.402	50.000	0.00	0.00	0.00	2.43
4482	6367	6.468333	TTGTCATATGCAGCCATTATTTGT	57.532	33.333	0.00	0.00	32.85	2.83
4505	6390	4.445557	TGCATTATTAGCACCACCCATA	57.554	40.909	0.00	0.00	37.02	2.74
4541	6426	5.408909	TCGTTCGTTAGGCAAAATGTTATGA	59.591	36.000	0.00	0.00	0.00	2.15
4622	6507	8.871686	AAAGAGTACAAATGGTTCATGTTTTC	57.128	30.769	0.00	0.00	0.00	2.29
4634	6519	3.861840	TCATGTTTTCGGAGGATGAGAC	58.138	45.455	0.00	0.00	0.00	3.36

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
7	8	5.358298	AAGCAAAAACTACTCCATTCGTC	57.642	39.130	0.00	0.00	0.00	4.20
85	86	1.480205	GTGTCAACAGCATGCACAAC	58.520	50.000	21.98	10.71	42.53	3.32
111	112	1.804326	CCCGTAAGTTGCCGAGTCG	60.804	63.158	5.29	5.29	0.00	4.18
115	116	2.677765	TTTGCCCCGTAAGTTGCCGA	62.678	55.000	0.00	0.00	0.00	5.54
175	176	6.398095	TGGATTATATATTCAGCACGTCTGG	58.602	40.000	12.89	0.00	43.06	3.86
178	179	6.752351	ACGATGGATTATATATTCAGCACGTC	59.248	38.462	6.89	1.13	0.00	4.34
206	207	2.350895	CCAAGGATGCACCCGTGA	59.649	61.111	15.57	0.00	37.81	4.35
219	220	4.182339	CTCTCTCACACATGATGACCAAG	58.818	47.826	0.00	0.00	33.22	3.61
220	221	3.618263	GCTCTCTCACACATGATGACCAA	60.618	47.826	0.00	0.00	33.22	3.67
221	222	2.093816	GCTCTCTCACACATGATGACCA	60.094	50.000	0.00	0.00	33.22	4.02
222	223	2.548875	GCTCTCTCACACATGATGACC	58.451	52.381	0.00	0.00	33.22	4.02
223	224	2.191802	CGCTCTCTCACACATGATGAC	58.808	52.381	0.00	0.00	33.22	3.06
224	225	1.135721	CCGCTCTCTCACACATGATGA	59.864	52.381	0.00	1.67	33.22	2.92
225	226	1.568606	CCGCTCTCTCACACATGATG	58.431	55.000	0.00	0.00	33.22	3.07
226	227	0.179089	GCCGCTCTCTCACACATGAT	60.179	55.000	0.00	0.00	33.22	2.45
227	228	1.216444	GCCGCTCTCTCACACATGA	59.784	57.895	0.00	0.00	0.00	3.07
228	229	0.390866	AAGCCGCTCTCTCACACATG	60.391	55.000	0.00	0.00	0.00	3.21
229	230	0.322975	AAAGCCGCTCTCTCACACAT	59.677	50.000	0.00	0.00	0.00	3.21
230	231	0.601046	CAAAGCCGCTCTCTCACACA	60.601	55.000	0.00	0.00	0.00	3.72
231	232	1.294659	CCAAAGCCGCTCTCTCACAC	61.295	60.000	0.00	0.00	0.00	3.82
232	233	1.004560	CCAAAGCCGCTCTCTCACA	60.005	57.895	0.00	0.00	0.00	3.58
277	278	3.243704	CCTTCCGAGCTCTATCCTTGAAG	60.244	52.174	12.85	10.94	0.00	3.02
348	376	7.448161	TGCTACATCCCAATCACAATAATAAGG	59.552	37.037	0.00	0.00	0.00	2.69
353	381	6.461370	GCAATGCTACATCCCAATCACAATAA	60.461	38.462	0.00	0.00	0.00	1.40
365	393	4.129380	TGTATGTCAGCAATGCTACATCC	58.871	43.478	23.36	17.05	36.40	3.51
480	512	5.104193	ACACAGCTTCTCCATCATAAGGAAT	60.104	40.000	0.00	0.00	34.08	3.01
557	590	4.770531	AGGCACACCCTTTAATTAAGAACC	59.229	41.667	0.00	0.00	43.06	3.62
578	611	3.084039	ACATAAAGATGTGTGTGGCAGG	58.916	45.455	0.00	0.00	44.90	4.85
727	761	3.728385	AGCAGTTAAGCCCAGAAGATT	57.272	42.857	0.00	0.00	34.23	2.40
824	977	6.398918	AGACGCATTTTAGATTGTGTACTCT	58.601	36.000	0.00	0.00	36.75	3.24
915	1069	8.298140	CAGTACTCCCTCCGTTTCTAAATATAG	58.702	40.741	0.00	0.00	0.00	1.31
916	1070	7.232127	CCAGTACTCCCTCCGTTTCTAAATATA	59.768	40.741	0.00	0.00	0.00	0.86
928	2272	0.970937	TGCTTCCAGTACTCCCTCCG	60.971	60.000	0.00	0.00	0.00	4.63
939	2283	1.298859	GCTTACCCGTGTGCTTCCAG	61.299	60.000	0.00	0.00	0.00	3.86
978	2323	2.434359	GGAACGAACCTGCTCGGG	60.434	66.667	0.00	0.00	43.22	5.14
1018	2363	1.995376	ATTTGGCTGGAACGAACCTT	58.005	45.000	0.00	0.00	0.00	3.50
1156	2503	1.743252	GTGGCTCTTGGCTTCCGAG	60.743	63.158	0.00	0.00	41.46	4.63
1209	2556	0.394488	CAGACCTAGGGACGAGAGCA	60.394	60.000	14.81	0.00	30.78	4.26
1217	2564	2.295143	AGGGTTCTACAGACCTAGGGA	58.705	52.381	14.81	0.00	0.00	4.20
1272	2619	4.154195	GTCCGCATGTTCTTACAACAAGAT	59.846	41.667	0.00	0.00	37.91	2.40
1273	2620	3.496884	GTCCGCATGTTCTTACAACAAGA	59.503	43.478	0.00	0.00	37.91	3.02
1274	2621	3.664276	CGTCCGCATGTTCTTACAACAAG	60.664	47.826	0.00	0.00	37.91	3.16
1275	2622	2.222213	CGTCCGCATGTTCTTACAACAA	59.778	45.455	0.00	0.00	37.91	2.83
1276	2623	1.795872	CGTCCGCATGTTCTTACAACA	59.204	47.619	0.00	0.00	37.91	3.33
1277	2624	1.463528	GCGTCCGCATGTTCTTACAAC	60.464	52.381	6.82	0.00	41.49	3.32
1278	2625	0.793861	GCGTCCGCATGTTCTTACAA	59.206	50.000	6.82	0.00	41.49	2.41
1279	2626	1.348538	CGCGTCCGCATGTTCTTACA	61.349	55.000	12.58	0.00	42.06	2.41
1280	2627	1.343821	CGCGTCCGCATGTTCTTAC	59.656	57.895	12.58	0.00	42.06	2.34
1282	2629	3.118454	CCGCGTCCGCATGTTCTT	61.118	61.111	12.58	0.00	42.06	2.52
1295	2699	0.449786	TACACAATTTCATGGCCGCG	59.550	50.000	0.00	0.00	0.00	6.46
1326	2730	3.934068	TCTTTCGGGTCAGAATAACACC	58.066	45.455	0.00	0.00	0.00	4.16
1333	2737	3.005367	GCCAAAATTCTTTCGGGTCAGAA	59.995	43.478	0.00	0.00	33.55	3.02
1337	2741	3.056891	TCATGCCAAAATTCTTTCGGGTC	60.057	43.478	0.00	0.00	0.00	4.46
1371	2779	2.094854	CCCTAGGTGTTACACGACTGAC	60.095	54.545	8.29	0.00	34.83	3.51
1561	3025	2.774234	ACAGGGGGTGATTCATACTCTG	59.226	50.000	15.05	15.05	0.00	3.35
1563	3027	3.545703	CAACAGGGGGTGATTCATACTC	58.454	50.000	0.00	0.00	0.00	2.59
1603	3067	7.806409	TGTTCAGCACAACAGCATAATATAT	57.194	32.000	0.00	0.00	36.85	0.86
1671	3145	8.922931	TGTATATCAAGTTATCAACATGGCAT	57.077	30.769	0.00	0.00	31.41	4.40
2040	3520	5.045286	GGAGAAGTGATATATGGGCAGGAAT	60.045	44.000	0.00	0.00	0.00	3.01
2155	3638	3.737047	GCAGGATCATGAAGTTGCCATTG	60.737	47.826	12.39	3.50	0.00	2.82
2163	3646	2.234661	TGTCTTCGCAGGATCATGAAGT	59.765	45.455	12.39	0.00	39.05	3.01
2590	4088	1.897133	TCCGCACACTACAACTGGTAT	59.103	47.619	0.00	0.00	0.00	2.73
2751	4282	7.500629	AATAAAGAGAGCCCAATTTTCCAAT	57.499	32.000	0.00	0.00	0.00	3.16
2810	4341	1.991230	CCCCATCGTTCAGGGTTCT	59.009	57.895	0.00	0.00	43.89	3.01
2919	4450	6.796867	ATATATGTAATGGGGTGGGAACTT	57.203	37.500	0.00	0.00	0.00	2.66
2944	4475	3.486383	ACTGCTTTCTTTTCCATCCGAA	58.514	40.909	0.00	0.00	0.00	4.30
2958	4489	2.502295	CAGAAGCTCTCCAACTGCTTT	58.498	47.619	0.00	0.00	45.56	3.51
3191	4728	5.804639	TGTTCAGCATACAGGATTAACACT	58.195	37.500	0.00	0.00	0.00	3.55
3391	4938	2.312722	TCTTTCCGAACGAAACCACA	57.687	45.000	0.00	0.00	35.49	4.17
3392	4939	2.664698	GCATCTTTCCGAACGAAACCAC	60.665	50.000	0.00	0.00	35.49	4.16
3404	4951	4.202441	TGCAATCTTAGGAGCATCTTTCC	58.798	43.478	0.00	0.00	33.73	3.13
3465	5219	4.180817	TGTGGCTACATCAATGTAAGACG	58.819	43.478	0.00	0.00	42.20	4.18
3476	5230	5.880332	TCAGATTACCTTTTGTGGCTACATC	59.120	40.000	2.83	0.00	36.53	3.06
3508	5268	4.374399	CCTGCTGCTGAAAGAAAACAATT	58.626	39.130	8.20	0.00	34.07	2.32
3623	5416	8.993121	CAAGCTTTTATTCTGAGTTCTGTCTTA	58.007	33.333	0.00	0.00	0.00	2.10
3642	5435	3.155501	AGCTTCATCTTCTGCAAGCTTT	58.844	40.909	0.00	0.00	41.47	3.51
3692	5486	5.316167	TGATTTTCTGTACAAGAGCACCAT	58.684	37.500	0.00	0.00	35.91	3.55
3783	5581	7.765307	TCCTTCTTAATGAAAATGTCATGCTC	58.235	34.615	0.00	0.00	46.80	4.26
3926	5724	5.310409	AGGTCTCAGATCTTTTGTTTCCA	57.690	39.130	0.00	0.00	0.00	3.53
3932	5730	5.123027	GGTGCTTTAGGTCTCAGATCTTTTG	59.877	44.000	0.00	0.00	0.00	2.44
4025	5823	2.113774	CAGCTGGTCTGGGTGCAA	59.886	61.111	5.57	0.00	39.15	4.08
4161	5959	0.884704	TGCTCCGCTTTCTTCACCAC	60.885	55.000	0.00	0.00	0.00	4.16
4227	6025	2.710096	ACTACAGTTTGCAGTGTGGT	57.290	45.000	8.52	8.52	41.86	4.16
4374	6259	5.947663	TCAAACAAAGGAATCTACAAGGGA	58.052	37.500	0.00	0.00	0.00	4.20
4505	6390	6.982141	TGCCTAACGAACGATTCACTATAAAT	59.018	34.615	0.14	0.00	0.00	1.40
4541	6426	8.692682	ATTTATAGGGCCTCTAAGATCTTCAT	57.307	34.615	10.74	0.00	0.00	2.57

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.