AutoCloner

Multiple sequence alignment - TraesCS1A01G414200

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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	TraesCS1A01G414200	chr1A	100.000	2597	0	0	1	2597	573696449	573693853	0.000000e+00	4796.0
1	TraesCS1A01G414200	chr1A	84.296	1229	118	30	646	1846	573713262	573714443	0.000000e+00	1131.0
2	TraesCS1A01G414200	chr1A	88.254	315	20	8	1	302	573712643	573712953	6.830000e-96	361.0
3	TraesCS1A01G414200	chr1D	86.881	2020	117	50	1	1909	477417641	477415659	0.000000e+00	2126.0
4	TraesCS1A01G414200	chr1D	90.968	1229	70	18	701	1897	477427634	477428853	0.000000e+00	1616.0
5	TraesCS1A01G414200	chr1D	86.115	677	54	16	1947	2597	477415578	477414916	0.000000e+00	693.0
6	TraesCS1A01G414200	chr1D	93.478	276	9	6	1	274	477427046	477427314	4.030000e-108	401.0
7	TraesCS1A01G414200	chr1D	81.290	310	27	12	1537	1841	477425045	477425328	3.360000e-54	222.0
8	TraesCS1A01G414200	chr1D	87.407	135	11	3	2464	2592	219736286	219736420	1.610000e-32	150.0
9	TraesCS1A01G414200	chr1D	83.333	150	17	7	1949	2095	456851	456707	5.830000e-27	132.0
10	TraesCS1A01G414200	chr1D	78.279	244	19	15	419	628	477427356	477427599	2.710000e-25	126.0
11	TraesCS1A01G414200	chr1B	88.095	1386	87	26	560	1897	665028385	665027030	0.000000e+00	1574.0
12	TraesCS1A01G414200	chr1B	91.768	984	55	12	732	1698	665031623	665032597	0.000000e+00	1345.0
13	TraesCS1A01G414200	chr1B	92.512	414	11	9	1	414	665030006	665029613	2.240000e-160	575.0
14	TraesCS1A01G414200	chr1B	80.989	647	65	27	1947	2546	665026922	665026287	6.550000e-126	460.0
15	TraesCS1A01G414200	chr1B	85.014	347	21	10	1	342	665030915	665031235	8.960000e-85	324.0
16	TraesCS1A01G414200	chr1B	86.755	302	19	6	1	302	665028885	665028605	1.500000e-82	316.0
17	TraesCS1A01G414200	chr1B	81.433	307	18	12	416	683	665029441	665029135	5.630000e-52	215.0
18	TraesCS1A01G414200	chr1B	94.872	39	2	0	657	695	665031581	665031619	7.760000e-06	62.1
19	TraesCS1A01G414200	chr2D	88.782	624	48	12	1947	2552	520591885	520592504	0.000000e+00	745.0
20	TraesCS1A01G414200	chr2D	84.444	135	17	3	1964	2095	628165388	628165521	2.100000e-26	130.0
21	TraesCS1A01G414200	chr3A	90.411	146	9	2	2455	2595	76638381	76638236	1.230000e-43	187.0
22	TraesCS1A01G414200	chr3B	77.193	342	46	19	1241	1554	140394228	140393891	1.240000e-38	171.0
23	TraesCS1A01G414200	chr3B	81.046	153	21	8	1945	2095	468533457	468533603	5.870000e-22	115.0
24	TraesCS1A01G414200	chr2B	87.013	154	6	4	2456	2595	369467970	369467817	7.440000e-36	161.0
25	TraesCS1A01G414200	chr2B	80.263	152	25	5	1948	2098	28879230	28879083	2.730000e-20	110.0
26	TraesCS1A01G414200	chr4B	87.591	137	11	4	2463	2593	273227868	273227732	1.240000e-33	154.0
27	TraesCS1A01G414200	chr4B	81.579	152	22	5	1948	2098	568669186	568669040	1.260000e-23	121.0
28	TraesCS1A01G414200	chr5A	84.967	153	11	8	2455	2595	384707768	384707616	7.490000e-31	145.0
29	TraesCS1A01G414200	chr5A	82.000	150	22	4	1948	2095	608341359	608341213	3.510000e-24	122.0
30	TraesCS1A01G414200	chr4D	85.333	150	9	9	2456	2592	336505061	336505210	2.690000e-30	143.0
31	TraesCS1A01G414200	chr4D	80.392	153	23	6	1948	2098	455628361	455628214	2.730000e-20	110.0
32	TraesCS1A01G414200	chr3D	92.079	101	5	1	1454	1554	90775332	90775235	3.480000e-29	139.0
33	TraesCS1A01G414200	chr7D	83.893	149	18	5	1949	2095	606683346	606683202	1.250000e-28	137.0
34	TraesCS1A01G414200	chr7D	82.000	150	23	3	1948	2095	578817706	578817853	9.760000e-25	124.0
35	TraesCS1A01G414200	chr7B	84.286	140	16	5	1958	2095	463038509	463038644	5.830000e-27	132.0
36	TraesCS1A01G414200	chr5D	86.441	118	10	5	1949	2066	277135268	277135379	9.760000e-25	124.0
37	TraesCS1A01G414200	chr5D	82.707	133	18	4	1948	2079	515033756	515033628	2.110000e-21	113.0
38	TraesCS1A01G414200	chr5B	82.119	151	18	7	1949	2095	470401383	470401528	1.260000e-23	121.0
39	TraesCS1A01G414200	chr4A	83.088	136	16	7	1948	2081	590349766	590349896	1.630000e-22	117.0
40	TraesCS1A01G414200	chr2A	79.085	153	20	11	1948	2098	18463762	18463904	7.650000e-16	95.3

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	TraesCS1A01G414200	chr1A	573693853	573696449	2596	True	4796.000000	4796	100.000000	1	2597	1	chr1A.!!$R1	2596
1	TraesCS1A01G414200	chr1A	573712643	573714443	1800	False	746.000000	1131	86.275000	1	1846	2	chr1A.!!$F1	1845
2	TraesCS1A01G414200	chr1D	477414916	477417641	2725	True	1409.500000	2126	86.498000	1	2597	2	chr1D.!!$R2	2596
3	TraesCS1A01G414200	chr1D	477425045	477428853	3808	False	591.250000	1616	86.003750	1	1897	4	chr1D.!!$F2	1896
4	TraesCS1A01G414200	chr1B	665026287	665030006	3719	True	628.000000	1574	85.956800	1	2546	5	chr1B.!!$R1	2545
5	TraesCS1A01G414200	chr1B	665030915	665032597	1682	False	577.033333	1345	90.551333	1	1698	3	chr1B.!!$F1	1697
6	TraesCS1A01G414200	chr2D	520591885	520592504	619	False	745.000000	745	88.782000	1947	2552	1	chr2D.!!$F1	605

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
653	3926	1.201647	TCCGAGACGTTGAGAACATCC	59.798	52.381	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
1887	5311	0.181587	TTCTGAAGTGCCGGGTTCAA	59.818	50.0	2.18	0.0	32.36	2.69	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
167	3290	2.009774	GCTACGTGGATCATGCAAAGT	58.990	47.619	1.81	0.00	0.00	2.66
207	3335	5.238650	ACAAGTGTCCTTTATCCGAACAAAG	59.761	40.000	0.00	0.00	0.00	2.77
234	3362	3.637273	GAAGGACGTGGCCCTGGT	61.637	66.667	0.00	0.00	33.55	4.00
262	3395	5.183713	TCCAAAGCAGATTAAGACACCAATG	59.816	40.000	0.00	0.00	0.00	2.82
364	3552	6.875076	ACTTTATAAGCACGTAGATTCAGGT	58.125	36.000	0.00	0.00	0.00	4.00
371	3559	2.170607	CACGTAGATTCAGGTGGGGATT	59.829	50.000	0.00	0.00	32.09	3.01
375	3563	3.142579	AGATTCAGGTGGGGATTCTCT	57.857	47.619	0.00	0.00	0.00	3.10
396	3584	4.830600	TCTTCCCCCTGTGATTGTTTAAAC	59.169	41.667	11.54	11.54	0.00	2.01
442	3635	8.196771	TGTTAGTTTGATGAAATTGTTCTTGCT	58.803	29.630	0.00	0.00	34.60	3.91
483	3681	1.405872	TACAGACCCTCACAACACGT	58.594	50.000	0.00	0.00	0.00	4.49
493	3691	3.003275	CCTCACAACACGTATGCAAACTT	59.997	43.478	0.00	0.00	0.00	2.66
496	3694	4.812091	TCACAACACGTATGCAAACTTACT	59.188	37.500	0.00	0.00	0.00	2.24
501	3699	3.370978	CACGTATGCAAACTTACTCCCTG	59.629	47.826	0.00	0.00	0.00	4.45
508	3713	5.626142	TGCAAACTTACTCCCTGTGAATAA	58.374	37.500	0.00	0.00	0.00	1.40
509	3714	6.245408	TGCAAACTTACTCCCTGTGAATAAT	58.755	36.000	0.00	0.00	0.00	1.28
510	3715	7.398829	TGCAAACTTACTCCCTGTGAATAATA	58.601	34.615	0.00	0.00	0.00	0.98
511	3716	7.335924	TGCAAACTTACTCCCTGTGAATAATAC	59.664	37.037	0.00	0.00	0.00	1.89
512	3717	7.335924	GCAAACTTACTCCCTGTGAATAATACA	59.664	37.037	0.00	0.00	0.00	2.29
516	3743	5.615925	ACTCCCTGTGAATAATACAGTCC	57.384	43.478	0.00	0.00	43.05	3.85
584	3838	3.566853	CTATGCCGCACTGCACCG	61.567	66.667	0.00	0.00	45.48	4.94
640	3911	1.474879	CTCCAAGTCCTTCTCCGAGAC	59.525	57.143	0.00	0.00	0.00	3.36
653	3926	1.201647	TCCGAGACGTTGAGAACATCC	59.798	52.381	0.00	0.00	0.00	3.51
654	3927	1.260206	CGAGACGTTGAGAACATCCG	58.740	55.000	0.00	0.00	0.00	4.18
688	3989	1.476833	GCAGACACTGAAAACCTGGGA	60.477	52.381	0.00	0.00	32.44	4.37
696	4010	3.181434	ACTGAAAACCTGGGATTGCACTA	60.181	43.478	0.00	0.00	0.00	2.74
822	4156	3.312421	CGACCAATAATGTAAGCCACCAG	59.688	47.826	0.00	0.00	0.00	4.00
950	4316	4.024302	TGACAGCATCGTTAGTACCTATCG	60.024	45.833	0.00	0.00	32.49	2.92
1005	4383	1.392589	CCTATCGGTTGCAAATGGCT	58.607	50.000	0.00	0.00	45.15	4.75
1524	4908	2.983546	AGGTTCTACCAGCAACTGCGT	61.984	52.381	0.00	0.00	41.95	5.24
1599	4986	2.160813	GGTCGCCGCTCAATTTTAGAAA	59.839	45.455	0.00	0.00	0.00	2.52
1603	4990	6.199393	GTCGCCGCTCAATTTTAGAAATATT	58.801	36.000	0.00	0.00	0.00	1.28
1606	4993	6.303259	CGCCGCTCAATTTTAGAAATATTAGC	59.697	38.462	0.00	0.00	0.00	3.09
1679	5072	3.603532	TGCCATGTCTTCATCTTCAGAC	58.396	45.455	0.00	0.00	40.03	3.51
1808	5224	2.989824	CGTCCGGGGACTGTCAGT	60.990	66.667	15.40	4.81	42.54	3.41
1873	5297	0.998145	AAGAAAGCATGGGAGGAGCT	59.002	50.000	0.00	0.00	41.03	4.09
1887	5311	3.372025	GGAGGAGCTGGAAAATACATGGT	60.372	47.826	0.00	0.00	0.00	3.55
1897	5321	1.470051	AATACATGGTTGAACCCGGC	58.530	50.000	12.53	0.00	37.50	6.13
1898	5322	0.329931	ATACATGGTTGAACCCGGCA	59.670	50.000	12.53	0.00	37.50	5.69
1899	5323	0.606944	TACATGGTTGAACCCGGCAC	60.607	55.000	12.53	0.00	37.50	5.01
1900	5324	1.603455	CATGGTTGAACCCGGCACT	60.603	57.895	12.53	0.00	37.50	4.40
1901	5325	1.152830	ATGGTTGAACCCGGCACTT	59.847	52.632	12.53	0.00	37.50	3.16
1902	5326	0.893727	ATGGTTGAACCCGGCACTTC	60.894	55.000	12.53	0.00	37.50	3.01
1904	5328	1.515521	GGTTGAACCCGGCACTTCAG	61.516	60.000	2.08	0.00	30.04	3.02
1930	5387	7.454260	AAATATTCTGAGAAACAGTTCCACC	57.546	36.000	0.00	0.00	45.86	4.61
1931	5388	2.930826	TCTGAGAAACAGTTCCACCC	57.069	50.000	0.00	0.00	45.86	4.61
1934	5391	1.226746	GAGAAACAGTTCCACCCGTG	58.773	55.000	0.00	0.00	33.92	4.94
1973	5455	1.530720	CAACATTTTCTTTTGGCCCGC	59.469	47.619	0.00	0.00	0.00	6.13
1979	5461	2.962697	TTCTTTTGGCCCGCGCAAAC	62.963	55.000	8.75	0.00	36.38	2.93
1985	5468	4.700365	GCCCGCGCAAACAAGACC	62.700	66.667	8.75	0.00	34.03	3.85
1986	5469	3.283684	CCCGCGCAAACAAGACCA	61.284	61.111	8.75	0.00	0.00	4.02
1987	5470	2.051345	CCGCGCAAACAAGACCAC	60.051	61.111	8.75	0.00	0.00	4.16
1993	5476	2.607180	GCGCAAACAAGACCACAAAAAT	59.393	40.909	0.30	0.00	0.00	1.82
2060	5543	2.974794	AGGAGGCAAAAGAAAAAGGCAT	59.025	40.909	0.00	0.00	0.00	4.40
2107	5615	8.607459	TCGCACACATATTTTGTTTTGAAAATT	58.393	25.926	0.00	0.00	36.94	1.82
2148	5656	9.786105	CATGTTTAAAATGCCTTTTTGAAAAGT	57.214	25.926	13.45	0.00	42.92	2.66
2158	5666	5.465390	GCCTTTTTGAAAAGTGGGTTCATAC	59.535	40.000	13.45	0.00	42.92	2.39
2164	5672	4.202336	TGAAAAGTGGGTTCATACGTACCA	60.202	41.667	7.50	2.84	34.34	3.25
2186	5694	5.067674	CCAGGTTTCAAAGATGTTCAGTTCA	59.932	40.000	0.00	0.00	0.00	3.18
2200	5708	7.402811	TGTTCAGTTCAGATACAAACTTACG	57.597	36.000	0.00	0.00	33.53	3.18
2204	5712	5.854866	CAGTTCAGATACAAACTTACGTCGA	59.145	40.000	0.00	0.00	33.53	4.20
2205	5713	5.855395	AGTTCAGATACAAACTTACGTCGAC	59.145	40.000	5.18	5.18	31.81	4.20
2206	5714	5.618056	TCAGATACAAACTTACGTCGACT	57.382	39.130	14.70	3.37	0.00	4.18
2207	5715	6.726258	TCAGATACAAACTTACGTCGACTA	57.274	37.500	14.70	2.35	0.00	2.59
2208	5716	6.537566	TCAGATACAAACTTACGTCGACTAC	58.462	40.000	14.70	0.00	0.00	2.73
2209	5717	6.147656	TCAGATACAAACTTACGTCGACTACA	59.852	38.462	14.70	0.00	0.00	2.74
2210	5718	6.798476	CAGATACAAACTTACGTCGACTACAA	59.202	38.462	14.70	3.73	0.00	2.41
2211	5719	7.324375	CAGATACAAACTTACGTCGACTACAAA	59.676	37.037	14.70	1.60	0.00	2.83
2212	5720	5.626258	ACAAACTTACGTCGACTACAAAC	57.374	39.130	14.70	0.00	0.00	2.93
2213	5721	5.343249	ACAAACTTACGTCGACTACAAACT	58.657	37.500	14.70	0.00	0.00	2.66
2227	5745	7.041167	TCGACTACAAACTACTGCAAACTACTA	60.041	37.037	0.00	0.00	0.00	1.82
2257	5803	0.247460	CCAGTCAATGTCGGAGCTCA	59.753	55.000	17.19	0.00	0.00	4.26
2281	5830	2.581354	CTTGAGGGACCAGCCTCG	59.419	66.667	0.00	0.00	35.99	4.63
2284	5833	3.827898	GAGGGACCAGCCTCGTCG	61.828	72.222	0.00	0.00	36.66	5.12
2291	5840	3.062466	CAGCCTCGTCGTCCTCCA	61.062	66.667	0.00	0.00	0.00	3.86
2302	5851	2.037381	GTCGTCCTCCACCTTCTTCTTT	59.963	50.000	0.00	0.00	0.00	2.52
2335	5884	0.035458	CCTTCTTCACCGGCTTGTCT	59.965	55.000	0.00	0.00	0.00	3.41
2405	5954	1.210967	CCCTAAACCTCGCCATGGTAA	59.789	52.381	14.67	0.38	36.69	2.85
2431	5980	0.815213	CCCACCGATGAATGTCGCAT	60.815	55.000	0.00	0.00	40.17	4.73
2459	6008	2.305928	AGATGACCCGAGTCTCTGATG	58.694	52.381	0.00	0.00	43.91	3.07
2461	6010	0.611896	TGACCCGAGTCTCTGATGCA	60.612	55.000	0.00	0.00	43.91	3.96
2469	6018	3.243805	CGAGTCTCTGATGCATCTCCAAT	60.244	47.826	26.32	9.11	0.00	3.16
2566	6128	9.216117	CATTTTAACTAACCTAGTGCTTAGTGT	57.784	33.333	5.81	1.75	39.39	3.55
2582	6144	5.739161	GCTTAGTGTCAGTTGTTGTTTTCTG	59.261	40.000	0.00	0.00	0.00	3.02
2586	6148	4.324402	GTGTCAGTTGTTGTTTTCTGCTTG	59.676	41.667	0.00	0.00	0.00	4.01

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
23	2025	6.479990	TCAAGTGCTCAATAGATTGTTATCCG	59.520	38.462	2.32	0.00	38.84	4.18
167	3290	4.099266	ACACTTGTTGCCAAAATAAGAGCA	59.901	37.500	2.18	0.00	0.00	4.26
207	3335	2.480802	GCCACGTCCTTCTCTTTTCTTC	59.519	50.000	0.00	0.00	0.00	2.87
234	3362	6.070251	TGGTGTCTTAATCTGCTTTGGATAGA	60.070	38.462	0.00	0.00	0.00	1.98
371	3559	2.044793	ACAATCACAGGGGGAAGAGA	57.955	50.000	0.00	0.00	0.00	3.10
375	3563	4.547671	TGTTTAAACAATCACAGGGGGAA	58.452	39.130	18.54	0.00	35.67	3.97
414	3602	9.520204	CAAGAACAATTTCATCAAACTAACAGT	57.480	29.630	0.00	0.00	33.72	3.55
483	3681	4.901197	TCACAGGGAGTAAGTTTGCATA	57.099	40.909	0.00	0.00	0.00	3.14
493	3691	5.601313	GGGACTGTATTATTCACAGGGAGTA	59.399	44.000	7.35	0.00	46.25	2.59
496	3694	4.367166	TGGGACTGTATTATTCACAGGGA	58.633	43.478	7.35	0.00	46.25	4.20
501	3699	6.281405	ACGAAGATGGGACTGTATTATTCAC	58.719	40.000	0.00	0.00	0.00	3.18
508	3713	6.295719	ACTTTAACGAAGATGGGACTGTAT	57.704	37.500	0.00	0.00	38.77	2.29
509	3714	5.733620	ACTTTAACGAAGATGGGACTGTA	57.266	39.130	0.00	0.00	38.77	2.74
510	3715	4.618920	ACTTTAACGAAGATGGGACTGT	57.381	40.909	0.00	0.00	38.77	3.55
511	3716	4.994852	TCAACTTTAACGAAGATGGGACTG	59.005	41.667	0.00	0.00	38.35	3.51
512	3717	5.223449	TCAACTTTAACGAAGATGGGACT	57.777	39.130	0.00	0.00	38.35	3.85
516	3743	6.539649	TGAGTTCAACTTTAACGAAGATGG	57.460	37.500	0.00	0.00	38.35	3.51
557	3785	1.227380	GCGGCATAGGTCACTCTGG	60.227	63.158	0.00	0.00	0.00	3.86
558	3786	0.807667	GTGCGGCATAGGTCACTCTG	60.808	60.000	5.72	0.00	0.00	3.35
584	3838	1.485838	CTGATGATGCTCGTGCCGTC	61.486	60.000	7.05	6.06	38.71	4.79
640	3911	0.652592	GGATGCGGATGTTCTCAACG	59.347	55.000	0.00	0.00	0.00	4.10
653	3926	1.736126	GTCTGCATGGATATGGATGCG	59.264	52.381	9.80	6.23	46.66	4.73
654	3927	2.486982	GTGTCTGCATGGATATGGATGC	59.513	50.000	8.12	8.12	44.42	3.91
717	4031	2.917713	AAGGTTGCATGATTGGGGTA	57.082	45.000	0.00	0.00	0.00	3.69
822	4156	1.376037	CTGGGTCTGAAACGAGGGC	60.376	63.158	0.00	0.00	0.00	5.19
950	4316	1.066114	CGTCTCGCTCTTGGTCGTTC	61.066	60.000	0.00	0.00	0.00	3.95
1216	4594	2.989253	TGCGACGAAGGAGGAGCA	60.989	61.111	0.00	0.00	0.00	4.26
1301	4682	0.635731	GTCGTTGAGCATCTCGAACG	59.364	55.000	17.20	17.20	41.54	3.95
1328	4709	2.504244	CGTCGTCGAAGAGGTGCC	60.504	66.667	12.09	0.00	43.64	5.01
1329	4710	1.512310	CTCGTCGTCGAAGAGGTGC	60.512	63.158	24.96	0.00	45.61	5.01
1330	4711	4.747543	CTCGTCGTCGAAGAGGTG	57.252	61.111	24.96	13.23	45.61	4.00
1524	4908	2.650116	GGAGACGCTCTTCTGGGCA	61.650	63.158	6.78	0.00	0.00	5.36
1577	4964	1.083489	CTAAAATTGAGCGGCGACCA	58.917	50.000	12.98	3.92	0.00	4.02
1599	4986	2.820197	TCGAGCAGTCCATCGCTAATAT	59.180	45.455	0.00	0.00	38.99	1.28
1603	4990	1.448119	CCTCGAGCAGTCCATCGCTA	61.448	60.000	6.99	0.00	38.99	4.26
1606	4993	2.279120	GCCTCGAGCAGTCCATCG	60.279	66.667	6.99	0.00	42.97	3.84
1657	5050	3.622163	GTCTGAAGATGAAGACATGGCAG	59.378	47.826	0.00	0.00	42.01	4.85
1679	5072	4.394610	TGGTCATGTGGATGATTTACGTTG	59.605	41.667	0.00	0.00	40.78	4.10
1808	5224	2.429930	CTGCTTTCACCCGGGTCA	59.570	61.111	27.51	17.94	0.00	4.02
1873	5297	3.508012	CGGGTTCAACCATGTATTTTCCA	59.492	43.478	9.35	0.00	41.02	3.53
1887	5311	0.181587	TTCTGAAGTGCCGGGTTCAA	59.818	50.000	2.18	0.00	32.36	2.69
1904	5328	8.023706	GGTGGAACTGTTTCTCAGAATATTTTC	58.976	37.037	0.00	0.00	46.27	2.29
1917	5374	1.098712	TGCACGGGTGGAACTGTTTC	61.099	55.000	0.43	0.00	36.74	2.78
1930	5387	1.236616	TTCAATGTGGAGCTGCACGG	61.237	55.000	29.82	22.04	0.00	4.94
1931	5388	0.592637	TTTCAATGTGGAGCTGCACG	59.407	50.000	29.82	17.81	0.00	5.34
1934	5391	3.096489	TGTTTTTCAATGTGGAGCTGC	57.904	42.857	0.00	0.00	0.00	5.25
1973	5455	3.616379	ACATTTTTGTGGTCTTGTTTGCG	59.384	39.130	0.00	0.00	0.00	4.85
1979	5461	3.790820	CACGACACATTTTTGTGGTCTTG	59.209	43.478	10.54	6.12	43.59	3.02
1985	5468	3.300880	GCGTTTCACGACACATTTTTGTG	60.301	43.478	0.00	4.64	46.05	3.33
1986	5469	2.849473	GCGTTTCACGACACATTTTTGT	59.151	40.909	0.00	0.00	46.05	2.83
1987	5470	3.105203	AGCGTTTCACGACACATTTTTG	58.895	40.909	0.00	0.00	46.05	2.44
1993	5476	4.548494	TCTAAATAGCGTTTCACGACACA	58.452	39.130	0.00	0.00	46.05	3.72
2039	5522	2.397597	TGCCTTTTTCTTTTGCCTCCT	58.602	42.857	0.00	0.00	0.00	3.69
2060	5543	5.722592	GCGACACAAAATTTTGCGAGAAAAA	60.723	36.000	26.94	0.00	41.79	1.94
2065	5548	2.097925	GTGCGACACAAAATTTTGCGAG	60.098	45.455	26.94	19.68	41.79	5.03
2148	5656	1.941377	ACCTGGTACGTATGAACCCA	58.059	50.000	0.00	0.00	34.69	4.51
2158	5666	4.513692	TGAACATCTTTGAAACCTGGTACG	59.486	41.667	0.00	0.00	0.00	3.67
2164	5672	6.122277	TCTGAACTGAACATCTTTGAAACCT	58.878	36.000	0.00	0.00	0.00	3.50
2200	5708	4.743644	AGTTTGCAGTAGTTTGTAGTCGAC	59.256	41.667	7.70	7.70	0.00	4.20
2204	5712	8.636213	TCTTAGTAGTTTGCAGTAGTTTGTAGT	58.364	33.333	0.00	0.00	0.00	2.73
2205	5713	9.130312	CTCTTAGTAGTTTGCAGTAGTTTGTAG	57.870	37.037	0.00	0.00	0.00	2.74
2206	5714	8.853126	TCTCTTAGTAGTTTGCAGTAGTTTGTA	58.147	33.333	0.00	0.00	0.00	2.41
2207	5715	7.723324	TCTCTTAGTAGTTTGCAGTAGTTTGT	58.277	34.615	0.00	0.00	0.00	2.83
2208	5716	8.764524	ATCTCTTAGTAGTTTGCAGTAGTTTG	57.235	34.615	0.00	0.00	0.00	2.93
2209	5717	9.209175	CAATCTCTTAGTAGTTTGCAGTAGTTT	57.791	33.333	0.00	0.00	0.00	2.66
2210	5718	8.368668	ACAATCTCTTAGTAGTTTGCAGTAGTT	58.631	33.333	0.00	0.00	31.97	2.24
2211	5719	7.897864	ACAATCTCTTAGTAGTTTGCAGTAGT	58.102	34.615	0.00	0.00	31.97	2.73
2212	5720	7.489757	GGACAATCTCTTAGTAGTTTGCAGTAG	59.510	40.741	0.00	0.00	31.97	2.57
2213	5721	7.321153	GGACAATCTCTTAGTAGTTTGCAGTA	58.679	38.462	0.00	0.00	31.97	2.74
2227	5745	4.583871	GACATTGACTGGGACAATCTCTT	58.416	43.478	0.00	0.00	34.67	2.85
2281	5830	1.258676	AGAAGAAGGTGGAGGACGAC	58.741	55.000	0.00	0.00	0.00	4.34
2284	5833	3.073209	AGGAAAAGAAGAAGGTGGAGGAC	59.927	47.826	0.00	0.00	0.00	3.85
2291	5840	4.446455	GGTGAGGAAGGAAAAGAAGAAGGT	60.446	45.833	0.00	0.00	0.00	3.50
2302	5851	0.196118	AGAAGGGGGTGAGGAAGGAA	59.804	55.000	0.00	0.00	0.00	3.36
2335	5884	1.389555	ATGAGTACTCGGTGCATCGA	58.610	50.000	22.68	22.68	37.60	3.59
2431	5980	2.168521	GACTCGGGTCATCTTGGATCAA	59.831	50.000	11.49	0.00	41.75	2.57
2560	6122	5.414454	AGCAGAAAACAACAACTGACACTAA	59.586	36.000	0.00	0.00	32.90	2.24
2566	6128	4.782019	ACAAGCAGAAAACAACAACTGA	57.218	36.364	0.00	0.00	32.90	3.41

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.