AutoCloner

Multiple sequence alignment - TraesCS2A01G465100

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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	TraesCS2A01G465100	chr2A	100.000	5041	0	0	1	5041	710186375	710191415	0.000000e+00	9310.0
1	TraesCS2A01G465100	chr2A	92.056	5048	312	39	1	4984	710204533	710209555	0.000000e+00	7018.0
2	TraesCS2A01G465100	chr2A	81.307	551	82	15	806	1347	710092600	710093138	1.300000e-115	427.0
3	TraesCS2A01G465100	chr2A	81.159	552	84	14	806	1348	709849839	709850379	4.660000e-115	425.0
4	TraesCS2A01G465100	chr2A	86.000	400	48	5	955	1347	710035892	710036290	6.030000e-114	422.0
5	TraesCS2A01G465100	chr2B	89.878	3290	323	6	1760	5041	683054274	683057561	0.000000e+00	4222.0
6	TraesCS2A01G465100	chr2B	89.107	2901	289	16	1786	4679	794694186	794691306	0.000000e+00	3581.0
7	TraesCS2A01G465100	chr2B	89.107	2901	289	16	1786	4679	794803087	794800207	0.000000e+00	3581.0
8	TraesCS2A01G465100	chr2B	87.827	3056	356	14	1632	4679	683128262	683131309	0.000000e+00	3568.0
9	TraesCS2A01G465100	chr2B	85.827	2907	358	26	1785	4679	683159767	683162631	0.000000e+00	3037.0
10	TraesCS2A01G465100	chr2B	87.337	1461	172	10	3589	5041	683044954	683046409	0.000000e+00	1661.0
11	TraesCS2A01G465100	chr2B	88.351	1322	114	17	59	1346	683126899	683128214	0.000000e+00	1552.0
12	TraesCS2A01G465100	chr2B	82.219	1794	305	10	1760	3549	683043161	683044944	0.000000e+00	1533.0
13	TraesCS2A01G465100	chr2B	91.116	484	35	4	874	1354	794696869	794696391	0.000000e+00	649.0
14	TraesCS2A01G465100	chr2B	83.986	587	59	18	39	618	683066484	683067042	9.610000e-147	531.0
15	TraesCS2A01G465100	chr2B	80.822	730	95	22	654	1347	683067038	683067758	9.610000e-147	531.0
16	TraesCS2A01G465100	chr2B	81.125	551	83	14	806	1347	683042513	683043051	6.030000e-114	422.0
17	TraesCS2A01G465100	chr2B	85.071	422	53	7	955	1366	683053771	683054192	6.030000e-114	422.0
18	TraesCS2A01G465100	chr2B	84.469	367	52	5	4678	5041	683162656	683163020	1.730000e-94	357.0
19	TraesCS2A01G465100	chr2B	81.351	370	66	3	4674	5041	683131330	683131698	1.060000e-76	298.0
20	TraesCS2A01G465100	chr2B	85.714	217	26	2	435	647	794697342	794697127	1.830000e-54	224.0
21	TraesCS2A01G465100	chr2B	81.579	228	38	4	4816	5041	794691214	794690989	8.620000e-43	185.0
22	TraesCS2A01G465100	chr2B	81.579	228	38	4	4816	5041	794800115	794799890	8.620000e-43	185.0
23	TraesCS2A01G465100	chr2B	90.323	62	1	1	1	62	683120689	683120745	5.410000e-10	76.8
24	TraesCS2A01G465100	chr2D	86.825	2907	334	26	1785	4679	571443451	571446320	0.000000e+00	3201.0
25	TraesCS2A01G465100	chr2D	87.397	1460	172	9	3589	5041	571197165	571198619	0.000000e+00	1666.0
26	TraesCS2A01G465100	chr2D	80.888	1936	340	16	1632	3549	571195232	571197155	0.000000e+00	1498.0
27	TraesCS2A01G465100	chr2D	80.537	596	88	21	805	1387	571194650	571195230	2.790000e-117	433.0
28	TraesCS2A01G465100	chr2D	84.196	367	53	5	4678	5041	571446345	571446709	8.030000e-93	351.0
29	TraesCS2A01G465100	chr2D	80.523	344	61	6	4701	5041	571530171	571530511	5.010000e-65	259.0
30	TraesCS2A01G465100	chr6A	87.186	1631	189	12	3060	4679	617078180	617079801	0.000000e+00	1836.0
31	TraesCS2A01G465100	chrUn	87.535	1083	122	8	3604	4679	307300431	307301507	0.000000e+00	1240.0
32	TraesCS2A01G465100	chrUn	91.423	478	33	4	874	1348	332504345	332504817	0.000000e+00	649.0
33	TraesCS2A01G465100	chrUn	85.532	235	27	4	417	647	332503856	332504087	6.520000e-59	239.0
34	TraesCS2A01G465100	chr6B	80.442	588	80	10	4452	5005	717746109	717745523	2.810000e-112	416.0

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	TraesCS2A01G465100	chr2A	710186375	710191415	5040	False	9310.000000	9310	100.000000	1	5041	1	chr2A.!!$F4	5040
1	TraesCS2A01G465100	chr2A	710204533	710209555	5022	False	7018.000000	7018	92.056000	1	4984	1	chr2A.!!$F5	4983
2	TraesCS2A01G465100	chr2A	710092600	710093138	538	False	427.000000	427	81.307000	806	1347	1	chr2A.!!$F3	541
3	TraesCS2A01G465100	chr2A	709849839	709850379	540	False	425.000000	425	81.159000	806	1348	1	chr2A.!!$F1	542
4	TraesCS2A01G465100	chr2B	683053771	683057561	3790	False	2322.000000	4222	87.474500	955	5041	2	chr2B.!!$F3	4086
5	TraesCS2A01G465100	chr2B	794799890	794803087	3197	True	1883.000000	3581	85.343000	1786	5041	2	chr2B.!!$R2	3255
6	TraesCS2A01G465100	chr2B	683126899	683131698	4799	False	1806.000000	3568	85.843000	59	5041	3	chr2B.!!$F5	4982
7	TraesCS2A01G465100	chr2B	683159767	683163020	3253	False	1697.000000	3037	85.148000	1785	5041	2	chr2B.!!$F6	3256
8	TraesCS2A01G465100	chr2B	683042513	683046409	3896	False	1205.333333	1661	83.560333	806	5041	3	chr2B.!!$F2	4235
9	TraesCS2A01G465100	chr2B	794690989	794697342	6353	True	1159.750000	3581	86.879000	435	5041	4	chr2B.!!$R1	4606
10	TraesCS2A01G465100	chr2B	683066484	683067758	1274	False	531.000000	531	82.404000	39	1347	2	chr2B.!!$F4	1308
11	TraesCS2A01G465100	chr2D	571443451	571446709	3258	False	1776.000000	3201	85.510500	1785	5041	2	chr2D.!!$F3	3256
12	TraesCS2A01G465100	chr2D	571194650	571198619	3969	False	1199.000000	1666	82.940667	805	5041	3	chr2D.!!$F2	4236
13	TraesCS2A01G465100	chr6A	617078180	617079801	1621	False	1836.000000	1836	87.186000	3060	4679	1	chr6A.!!$F1	1619
14	TraesCS2A01G465100	chrUn	307300431	307301507	1076	False	1240.000000	1240	87.535000	3604	4679	1	chrUn.!!$F1	1075
15	TraesCS2A01G465100	chrUn	332503856	332504817	961	False	444.000000	649	88.477500	417	1348	2	chrUn.!!$F2	931
16	TraesCS2A01G465100	chr6B	717745523	717746109	586	True	416.000000	416	80.442000	4452	5005	1	chr6B.!!$R1	553

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
82	83	0.109735	GTCGCTGGCTAAAAGGTTGC	60.110	55.000	0.00	0.00	4.17	F
165	185	0.521291	CGTGATGTTTTGTCCGGCAT	59.479	50.000	0.00	0.00	4.40	F
428	449	0.621082	TCACGGCCACCATAATTCCA	59.379	50.000	2.24	0.00	3.53	F
1016	1190	0.755686	GAGATGACGGGGCTTCTCAT	59.244	55.000	11.41	38.35	2.90	F
2033	4010	0.842467	AGGGGCCAGCTCAAAGTACT	60.842	55.000	4.39	0.00	2.73	F
2852	4832	1.003839	CCCACTAGCCGCACAAAGA	60.004	57.895	0.00	0.00	2.52	F
3066	5047	1.928868	AGAATTGGTTCCTGCTTGGG	58.071	50.000	0.00	34.81	4.12	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1016	1190	0.246910	TATTGCCGCGTCAACTACCA	59.753	50.000	4.03	0.00	3.25	R
1388	1595	1.698506	ACATTTTGGAACGCAGGGAA	58.301	45.000	0.00	0.00	3.97	R
2306	4283	1.836604	ACCACCAATGCCAACCACC	60.837	57.895	0.00	0.00	4.61	R
2816	4796	0.528017	GGCAGCCCTTTAGTGCTTTC	59.472	55.000	0.00	37.37	2.62	R
2898	4879	0.804989	CTCCATTTGTCCCGAACTGC	59.195	55.000	0.00	0.00	4.40	R
3746	5739	3.636300	TGTTTCCAACACAAGCTATTGCT	59.364	39.130	0.00	43.74	3.91	R
4385	6380	3.760684	GGAAACCATGATTTCTGCTCAGT	59.239	43.478	12.35	38.43	3.41	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
69	70	5.820131	TCTATATGCCAAAATTTGTCGCTG	58.180	37.500	4.92	0.00	0.00	5.18
82	83	0.109735	GTCGCTGGCTAAAAGGTTGC	60.110	55.000	0.00	0.00	0.00	4.17
100	112	4.214758	GGTTGCACATACTTAACGGAAACT	59.785	41.667	0.00	0.00	0.00	2.66
131	151	4.529897	TCAATTATGATCAGTGCCAAGCT	58.470	39.130	0.09	0.00	0.00	3.74
165	185	0.521291	CGTGATGTTTTGTCCGGCAT	59.479	50.000	0.00	0.00	0.00	4.40
187	207	3.674997	TGCTTGTACCATTTCTCCTGTC	58.325	45.455	0.00	0.00	0.00	3.51
223	243	3.169099	GAGATTCCAGGCTGCTATAGGA	58.831	50.000	9.56	0.00	0.00	2.94
254	274	4.708726	ATTGTTATTGCTGTTCTCTGGC	57.291	40.909	0.00	0.00	0.00	4.85
286	306	3.126001	TGAAAGTGCTCAGTAGTTGGG	57.874	47.619	0.00	0.00	0.00	4.12
294	314	3.187700	GCTCAGTAGTTGGGATGTTACG	58.812	50.000	0.00	0.00	0.00	3.18
304	324	4.481368	TGGGATGTTACGTCATAAGCTT	57.519	40.909	3.48	3.48	0.00	3.74
423	444	0.687920	TTGACTCACGGCCACCATAA	59.312	50.000	2.24	0.00	0.00	1.90
427	448	1.308998	CTCACGGCCACCATAATTCC	58.691	55.000	2.24	0.00	0.00	3.01
428	449	0.621082	TCACGGCCACCATAATTCCA	59.379	50.000	2.24	0.00	0.00	3.53
522	543	5.451354	AGTTGGGGAACTTAGCTGTTTTTA	58.549	37.500	0.00	0.00	0.00	1.52
597	625	4.396790	AGTTAGCTCTAGACTCAGTTTCCG	59.603	45.833	0.00	0.00	0.00	4.30
725	847	7.389607	GTCATACAAGTATACAACCAAACACCT	59.610	37.037	5.50	0.00	0.00	4.00
751	873	1.050204	AATGCAACTGTGGTGCCAAT	58.950	45.000	5.09	0.00	0.00	3.16
803	925	5.071788	TCCATATCTGTGGAAACCCTATCAC	59.928	44.000	0.00	0.00	45.03	3.06
867	1019	9.809096	CATAGTTTAACTCTCTCTCATTTGCTA	57.191	33.333	0.00	0.00	0.00	3.49
929	1084	7.201920	CGTTCTCCTTTCCTCTAAATCCATCTA	60.202	40.741	0.00	0.00	0.00	1.98
949	1104	2.080654	TTTTGGTTTCTCCCCTGTGG	57.919	50.000	0.00	0.00	34.77	4.17
976	1133	0.957362	ACTTTTGCTCCTGCTTGCTC	59.043	50.000	0.00	0.00	40.48	4.26
996	1159	4.335647	CTGCCTCCGGTGTGCCTT	62.336	66.667	0.00	0.00	0.00	4.35
1016	1190	0.755686	GAGATGACGGGGCTTCTCAT	59.244	55.000	11.41	0.00	38.35	2.90
1273	1447	1.337071	TGATGGACGAGCTCGATTACC	59.663	52.381	40.58	31.53	43.02	2.85
1375	1582	5.621197	TGCGTGATTGTAATTGCTACTTT	57.379	34.783	0.00	0.00	0.00	2.66
1416	1623	2.556622	CGTTCCAAAATGTTAGGCACCT	59.443	45.455	0.00	0.00	0.00	4.00
1453	1664	4.507756	GGTTTGAACAGCAATTTGAGGAAC	59.492	41.667	0.00	0.00	36.15	3.62
1507	1722	8.950208	ATTAGATTTGTACTTAGGAGCACTTC	57.050	34.615	0.00	0.00	0.00	3.01
1564	3448	7.767198	TGTATTTTGTCACATAACCTAGGTAGC	59.233	37.037	16.67	1.41	0.00	3.58
1577	3461	3.877508	CCTAGGTAGCATTAACTGTTGGC	59.122	47.826	0.00	4.57	0.00	4.52
2033	4010	0.842467	AGGGGCCAGCTCAAAGTACT	60.842	55.000	4.39	0.00	0.00	2.73
2247	4224	1.044611	GTATGGGAGGGAGTCAGAGC	58.955	60.000	0.00	0.00	0.00	4.09
2272	4249	6.416455	CGAGACAAGATAATAGAGCTGTTGAC	59.584	42.308	0.00	0.00	0.00	3.18
2306	4283	3.837213	AGTGATCTGAATGTTTTGCCG	57.163	42.857	0.00	0.00	0.00	5.69
2533	4513	8.299570	GCAGAAGAACCTTTTGAAGAATATCAA	58.700	33.333	2.00	0.00	37.53	2.57
2587	4567	1.420138	GTGGGAAGACAAGGACAGGAA	59.580	52.381	0.00	0.00	0.00	3.36
2766	4746	2.246469	AGGCATGTGCATTTGGTAACA	58.754	42.857	7.36	0.00	45.46	2.41
2815	4795	4.702131	GCAGTCTATTGGGAAACAGATTGT	59.298	41.667	0.00	0.00	30.06	2.71
2816	4796	5.392380	GCAGTCTATTGGGAAACAGATTGTG	60.392	44.000	0.00	0.00	30.06	3.33
2852	4832	1.003839	CCCACTAGCCGCACAAAGA	60.004	57.895	0.00	0.00	0.00	2.52
2898	4879	4.576463	GTGTTAGTGATAAGCATTGGAGGG	59.424	45.833	0.00	0.00	0.00	4.30
2928	4909	4.637977	GGGACAAATGGAGATCTCTTCAAC	59.362	45.833	21.81	5.87	34.65	3.18
2963	4944	6.177610	TGATATTTTACCCGTCTTGAAGCTT	58.822	36.000	0.00	0.00	0.00	3.74
3022	5003	7.152645	TGTTTCTCGTACTGCTCTTTATTTCT	58.847	34.615	0.00	0.00	0.00	2.52
3029	5010	7.502895	TCGTACTGCTCTTTATTTCTAGAGGAT	59.497	37.037	0.00	0.00	38.05	3.24
3035	5016	8.475639	TGCTCTTTATTTCTAGAGGATAAACGT	58.524	33.333	14.53	0.00	38.63	3.99
3036	5017	8.970293	GCTCTTTATTTCTAGAGGATAAACGTC	58.030	37.037	14.53	7.07	38.63	4.34
3058	5039	4.772100	TCTTCATGGGAAAGAATTGGTTCC	59.228	41.667	7.85	7.85	42.28	3.62
3066	5047	1.928868	AGAATTGGTTCCTGCTTGGG	58.071	50.000	0.00	0.00	34.81	4.12
3369	5350	9.784531	AGAAGTTTGATGAAATACTTCAGAAGA	57.215	29.630	17.56	1.14	44.68	2.87
3606	5590	6.040247	TCATTGTATAGAGGCTACAACAACG	58.960	40.000	2.85	0.00	40.73	4.10
3646	5636	6.037610	GCATCGACAAGATTTTATCACCTTCT	59.962	38.462	0.00	0.00	37.52	2.85
3705	5698	7.906327	TGTGCCTACTGATATGCATAATCTTA	58.094	34.615	11.13	0.00	34.87	2.10
3723	5716	9.846248	ATAATCTTATTAATTTGCGCCATCTTC	57.154	29.630	4.18	0.00	0.00	2.87
3732	5725	2.715046	TGCGCCATCTTCTTTCTCATT	58.285	42.857	4.18	0.00	0.00	2.57
3733	5726	2.421073	TGCGCCATCTTCTTTCTCATTG	59.579	45.455	4.18	0.00	0.00	2.82
3746	5739	5.775686	CTTTCTCATTGGAAAGTGCATCAA	58.224	37.500	14.50	0.00	44.00	2.57
3802	5795	5.054477	TCAGGAACTAAGTTTCAAGGTTCG	58.946	41.667	0.00	0.00	36.02	3.95
4385	6380	6.479972	TCCAGAGTTACTCTTCTTTCAACA	57.520	37.500	12.76	0.00	38.99	3.33
4500	6496	8.674263	TTCCTGTTCAATACATTTGCAAATTT	57.326	26.923	21.95	18.10	35.85	1.82
4610	6610	3.258372	TGGACCTACATGTTGTCAGAGTC	59.742	47.826	22.29	14.29	0.00	3.36
4617	6617	5.028549	ACATGTTGTCAGAGTCTCAGTTT	57.971	39.130	1.94	0.00	0.00	2.66
4660	6660	4.098914	TGACTAAAATGACAAGCCTGGT	57.901	40.909	0.00	0.00	0.00	4.00
4679	6679	3.756434	TGGTATTTTGCAGCAGTCTAACC	59.244	43.478	0.00	2.28	0.00	2.85
4807	6834	0.107459	GAGTTGTCCATCAGGGGAGC	60.107	60.000	0.00	0.00	37.71	4.70
4810	6837	0.252881	TTGTCCATCAGGGGAGCTCT	60.253	55.000	14.64	0.00	37.71	4.09
4822	6849	1.675415	GGGAGCTCTGAGACTTGCAAG	60.675	57.143	24.84	24.84	0.00	4.01
4848	6875	8.663209	AATGAGTATAGAGCATAGATGGTTCT	57.337	34.615	0.00	0.00	38.85	3.01
4940	6967	5.699839	ACATCGTTTGGAATAAGAAACTGC	58.300	37.500	0.00	0.00	31.15	4.40
4942	6969	4.138290	TCGTTTGGAATAAGAAACTGCCA	58.862	39.130	0.00	0.00	31.15	4.92
4965	6992	7.335422	GCCAAAATCTGATCTCTCTTTCAAGTA	59.665	37.037	0.00	0.00	0.00	2.24
5000	7027	4.612932	GCTCATTGCTTTAGAGTCCTTG	57.387	45.455	0.00	0.00	38.95	3.61

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
39	40	9.289782	GACAAATTTTGGCATATAGAGTAGGAT	57.710	33.333	10.16	0.00	38.99	3.24
69	70	4.783764	AAGTATGTGCAACCTTTTAGCC	57.216	40.909	0.00	0.00	34.36	3.93
82	83	7.124347	TGCTTTAGTTTCCGTTAAGTATGTG	57.876	36.000	0.00	0.00	0.00	3.21
100	112	7.040892	GGCACTGATCATAATTGAGATGCTTTA	60.041	37.037	0.00	0.00	34.73	1.85
131	151	3.135712	ACATCACGAAGGGCCATGTTATA	59.864	43.478	6.18	0.00	0.00	0.98
187	207	0.461516	ATCTCTGGACGCACATGCAG	60.462	55.000	4.49	0.00	42.21	4.41
223	243	7.834181	AGAACAGCAATAACAATAGGTATTGGT	59.166	33.333	11.03	11.03	45.54	3.67
242	262	0.036022	AACTGAGGCCAGAGAACAGC	59.964	55.000	5.01	0.00	43.02	4.40
254	274	3.679389	AGCACTTTCATGGTAACTGAGG	58.321	45.455	0.00	0.00	37.61	3.86
286	306	9.210426	CAAAATACAAGCTTATGACGTAACATC	57.790	33.333	0.00	0.00	0.00	3.06
304	324	4.215399	GCTGTCAGCCTTGTACAAAATACA	59.785	41.667	14.27	8.76	34.48	2.29
357	378	0.040942	ATGGTGTATTTGGCTGGGCA	59.959	50.000	0.00	0.00	0.00	5.36
423	444	1.075482	CTGCACAGGGGTGTGGAAT	59.925	57.895	7.59	0.00	46.95	3.01
427	448	2.281761	GGTCTGCACAGGGGTGTG	60.282	66.667	1.01	1.01	46.95	3.82
428	449	3.570212	GGGTCTGCACAGGGGTGT	61.570	66.667	0.00	0.00	46.95	4.16
597	625	3.467803	ACCAACTACAGAGCAGTTTCAC	58.532	45.455	0.00	0.00	33.99	3.18
603	631	6.163476	TGTTAACATACCAACTACAGAGCAG	58.837	40.000	3.59	0.00	0.00	4.24
725	847	5.221521	TGGCACCACAGTTGCATTAATTAAA	60.222	36.000	1.21	0.00	0.00	1.52
751	873	4.202357	ACAAGGAAGCACATGAGTCAAGTA	60.202	41.667	0.00	0.00	0.00	2.24
793	915	5.347978	AGTAACAACTAGGGTGATAGGGTT	58.652	41.667	2.93	0.00	32.58	4.11
803	925	3.057526	GCTTTGCCAAGTAACAACTAGGG	60.058	47.826	0.00	0.00	31.86	3.53
867	1019	1.068352	AAGGAAGGAACTGGGCAGGT	61.068	55.000	0.00	0.00	40.86	4.00
929	1084	2.178984	TCCACAGGGGAGAAACCAAAAT	59.821	45.455	0.00	0.00	42.15	1.82
949	1104	2.087646	CAGGAGCAAAAGTAGGCCTTC	58.912	52.381	12.58	5.68	31.27	3.46
996	1159	0.614697	TGAGAAGCCCCGTCATCTCA	60.615	55.000	0.46	0.46	44.35	3.27
1016	1190	0.246910	TATTGCCGCGTCAACTACCA	59.753	50.000	4.03	0.00	0.00	3.25
1096	1270	1.702182	TCAGCAAGCCCAATTTCACA	58.298	45.000	0.00	0.00	0.00	3.58
1273	1447	2.236223	ATCTGCTGCTGGAGTCGGTG	62.236	60.000	11.73	0.00	33.13	4.94
1388	1595	1.698506	ACATTTTGGAACGCAGGGAA	58.301	45.000	0.00	0.00	0.00	3.97
1416	1623	6.148811	GCTGTTCAAACCTATACTTTGCACTA	59.851	38.462	0.00	0.00	29.40	2.74
1453	1664	7.816945	TCAGATGTATATAATGCATGTGTCG	57.183	36.000	0.00	0.00	43.65	4.35
1496	1711	2.868964	ACCATAGGGAAGTGCTCCTA	57.131	50.000	0.00	0.00	44.68	2.94
1507	1722	7.773224	TCATGTGACAAAAAGTATACCATAGGG	59.227	37.037	0.00	0.00	41.29	3.53
1564	3448	2.557924	TGAGCTTGGCCAACAGTTAATG	59.442	45.455	16.05	3.07	0.00	1.90
1577	3461	3.476552	TGTAGTTCAGGTTTGAGCTTGG	58.523	45.455	0.00	0.00	41.46	3.61
1798	3775	2.925306	GCCACTTGAGCAAAAGCAGATG	60.925	50.000	0.00	0.00	0.00	2.90
2033	4010	8.260114	TCATGTTTAATCTCAGAAGTCAGCATA	58.740	33.333	0.00	0.00	0.00	3.14
2247	4224	6.416455	GTCAACAGCTCTATTATCTTGTCTCG	59.584	42.308	0.00	0.00	0.00	4.04
2282	4259	5.122239	CGGCAAAACATTCAGATCACTAGAA	59.878	40.000	0.00	0.00	0.00	2.10
2306	4283	1.836604	ACCACCAATGCCAACCACC	60.837	57.895	0.00	0.00	0.00	4.61
2533	4513	7.382218	CCAATACGAGCAGAAATCTTTTGTTTT	59.618	33.333	0.00	0.00	0.00	2.43
2587	4567	5.134725	AGCCAAGAGTTTAATCCATCCAT	57.865	39.130	0.00	0.00	0.00	3.41
2656	4636	9.761504	TCATTTTTGCAACTGAATTCATTCTAA	57.238	25.926	8.96	0.00	37.67	2.10
2766	4746	2.761208	CAGGATCACCCTCGTAGTTCTT	59.239	50.000	0.00	0.00	45.60	2.52
2815	4795	1.247567	GCAGCCCTTTAGTGCTTTCA	58.752	50.000	0.00	0.00	35.12	2.69
2816	4796	0.528017	GGCAGCCCTTTAGTGCTTTC	59.472	55.000	0.00	0.00	37.37	2.62
2852	4832	2.560542	TGTGTTCAAAAGTGCACCAACT	59.439	40.909	14.63	0.00	0.00	3.16
2898	4879	0.804989	CTCCATTTGTCCCGAACTGC	59.195	55.000	0.00	0.00	0.00	4.40
2928	4909	8.099364	ACGGGTAAAATATCATTAGCATCTTG	57.901	34.615	10.69	0.00	33.52	3.02
3022	5003	5.205821	TCCCATGAAGACGTTTATCCTCTA	58.794	41.667	0.00	0.00	0.00	2.43
3029	5010	6.072175	CCAATTCTTTCCCATGAAGACGTTTA	60.072	38.462	0.00	0.00	33.15	2.01
3035	5016	4.772100	GGAACCAATTCTTTCCCATGAAGA	59.228	41.667	0.00	0.00	36.07	2.87
3036	5017	4.774200	AGGAACCAATTCTTTCCCATGAAG	59.226	41.667	9.97	0.00	42.14	3.02
3039	5020	3.368739	GCAGGAACCAATTCTTTCCCATG	60.369	47.826	9.97	5.62	42.14	3.66
3058	5039	5.047802	ACAAAATTCTGTGATACCCAAGCAG	60.048	40.000	0.00	0.00	0.00	4.24
3369	5350	5.065235	CCTCAATTTTTGCAAAGGTCCAAT	58.935	37.500	12.41	6.12	0.00	3.16
3574	5558	9.143155	TGTAGCCTCTATACAATGATCTGTTTA	57.857	33.333	0.00	0.00	30.37	2.01
3595	5579	2.372350	GAAACACAGCGTTGTTGTAGC	58.628	47.619	0.63	0.00	39.70	3.58
3606	5590	1.135859	CGATGCTTGAGGAAACACAGC	60.136	52.381	0.00	0.00	30.79	4.40
3657	5647	7.388500	CACAGAAAAATTGCCTGAAATACCAAT	59.612	33.333	8.43	0.00	0.00	3.16
3705	5698	6.127647	TGAGAAAGAAGATGGCGCAAATTAAT	60.128	34.615	10.83	0.00	0.00	1.40
3746	5739	3.636300	TGTTTCCAACACAAGCTATTGCT	59.364	39.130	0.00	0.00	43.74	3.91
3802	5795	8.561738	TCTTATCTCAAAACTACCACCATTTC	57.438	34.615	0.00	0.00	0.00	2.17
3848	5841	9.614792	AGTTGAGAAATTTCAAGTAGTACAAGT	57.385	29.630	19.99	11.32	38.59	3.16
3944	5937	4.458397	CTGTTATCTGCCATGACAAGGAT	58.542	43.478	0.00	0.00	0.00	3.24
4135	6130	6.015180	CAGGAGTTGGAAGAATTTTCCATTCA	60.015	38.462	17.35	5.89	46.85	2.57
4385	6380	3.760684	GGAAACCATGATTTCTGCTCAGT	59.239	43.478	12.35	0.00	38.43	3.41
4660	6660	4.261801	GGAGGTTAGACTGCTGCAAAATA	58.738	43.478	3.02	0.00	0.00	1.40
4807	6834	4.567971	ACTCATTCTTGCAAGTCTCAGAG	58.432	43.478	25.19	23.61	0.00	3.35
4810	6837	7.410120	TCTATACTCATTCTTGCAAGTCTCA	57.590	36.000	25.19	9.26	0.00	3.27
4822	6849	8.748412	AGAACCATCTATGCTCTATACTCATTC	58.252	37.037	0.00	0.00	32.88	2.67
4848	6875	6.071896	ACACTCAACTCATTAGATTCGACAGA	60.072	38.462	0.00	0.00	0.00	3.41
4940	6967	7.684937	ACTTGAAAGAGAGATCAGATTTTGG	57.315	36.000	0.00	0.00	0.00	3.28
5000	7027	5.934625	CAGATTAGGGCAGTTGTGTATATCC	59.065	44.000	0.00	0.00	0.00	2.59

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.