AutoCloner

Multiple sequence alignment - TraesCS4A01G346500

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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	TraesCS4A01G346500	chr4A	100.000	4058	0	0	1	4058	625246045	625250102	0.000000e+00	7494.0
1	TraesCS4A01G346500	chr4A	85.724	1429	162	13	2070	3497	625176723	625178110	0.000000e+00	1471.0
2	TraesCS4A01G346500	chr4A	85.241	1450	175	18	2064	3500	624982267	624983690	0.000000e+00	1456.0
3	TraesCS4A01G346500	chr4A	88.636	132	15	0	1011	1142	625175691	625175822	1.170000e-35	161.0
4	TraesCS4A01G346500	chr5B	94.418	1863	95	5	1654	3510	685993372	685991513	0.000000e+00	2856.0
5	TraesCS4A01G346500	chr5B	95.971	1514	57	2	2042	3553	685648680	685650191	0.000000e+00	2455.0
6	TraesCS4A01G346500	chr5B	85.464	1541	199	17	1973	3500	685951447	685949919	0.000000e+00	1581.0
7	TraesCS4A01G346500	chr5B	91.273	1100	67	13	882	1966	685994480	685993395	0.000000e+00	1472.0
8	TraesCS4A01G346500	chr5B	81.658	1870	236	53	1903	3729	686051189	686049384	0.000000e+00	1454.0
9	TraesCS4A01G346500	chr5B	81.433	1745	244	32	1785	3506	686212506	686210819	0.000000e+00	1354.0
10	TraesCS4A01G346500	chr5B	91.959	485	32	3	3580	4058	685650269	685650752	0.000000e+00	673.0
11	TraesCS4A01G346500	chr5B	83.745	486	28	17	3580	4058	685991359	685990918	2.920000e-111	412.0
12	TraesCS4A01G346500	chr5B	92.216	167	10	1	997	1163	685952347	685952184	2.440000e-57	233.0
13	TraesCS4A01G346500	chr5B	90.411	146	14	0	997	1142	686051739	686051594	4.140000e-45	193.0
14	TraesCS4A01G346500	chr5B	96.154	52	1	1	3505	3555	685991486	685991435	2.600000e-12	84.2
15	TraesCS4A01G346500	chr5B	100.000	31	0	0	838	868	685994511	685994481	1.580000e-04	58.4
16	TraesCS4A01G346500	chr5D	95.296	1318	59	1	2193	3510	543840022	543838708	0.000000e+00	2087.0
17	TraesCS4A01G346500	chr5D	95.537	1210	47	4	997	2200	543841813	543840605	0.000000e+00	1929.0
18	TraesCS4A01G346500	chr5D	83.577	2052	269	38	1474	3500	544286832	544284824	0.000000e+00	1860.0
19	TraesCS4A01G346500	chr5D	83.112	1729	219	27	1782	3496	543858940	543857271	0.000000e+00	1507.0
20	TraesCS4A01G346500	chr5D	93.464	153	8	1	3580	3732	543838554	543838404	4.080000e-55	226.0
21	TraesCS4A01G346500	chr5D	79.273	275	18	16	3785	4058	543838400	543838164	5.430000e-34	156.0
22	TraesCS4A01G346500	chr5D	100.000	37	0	0	3513	3549	543838672	543838636	7.280000e-08	69.4
23	TraesCS4A01G346500	chr1D	95.652	460	20	0	1	460	479710445	479709986	0.000000e+00	739.0
24	TraesCS4A01G346500	chr1D	93.189	323	21	1	489	810	479709934	479709612	1.320000e-129	473.0
25	TraesCS4A01G346500	chr2A	88.415	492	54	3	1	491	45089428	45089917	1.260000e-164	590.0
26	TraesCS4A01G346500	chr2A	91.057	246	22	0	566	811	45089965	45090210	2.340000e-87	333.0
27	TraesCS4A01G346500	chr7A	86.997	323	40	2	170	491	507883692	507884013	2.980000e-96	363.0
28	TraesCS4A01G346500	chr7A	85.498	331	31	10	489	817	507884066	507884381	3.020000e-86	329.0
29	TraesCS4A01G346500	chr7A	80.952	294	39	8	516	807	296741421	296741143	2.460000e-52	217.0
30	TraesCS4A01G346500	chr1B	83.025	324	52	3	489	810	608356104	608355782	1.430000e-74	291.0
31	TraesCS4A01G346500	chr3D	82.972	323	34	6	509	810	569979525	569979847	5.170000e-69	272.0
32	TraesCS4A01G346500	chr2B	79.878	328	56	8	489	810	61029970	61030293	8.770000e-57	231.0
33	TraesCS4A01G346500	chr5A	79.918	244	44	5	567	808	626365650	626365890	1.500000e-39	174.0
34	TraesCS4A01G346500	chr6B	81.643	207	34	4	602	807	654692453	654692250	6.980000e-38	169.0

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	TraesCS4A01G346500	chr4A	625246045	625250102	4057	False	7494.00	7494	100.0000	1	4058	1	chr4A.!!$F2	4057
1	TraesCS4A01G346500	chr4A	624982267	624983690	1423	False	1456.00	1456	85.2410	2064	3500	1	chr4A.!!$F1	1436
2	TraesCS4A01G346500	chr4A	625175691	625178110	2419	False	816.00	1471	87.1800	1011	3497	2	chr4A.!!$F3	2486
3	TraesCS4A01G346500	chr5B	685648680	685650752	2072	False	1564.00	2455	93.9650	2042	4058	2	chr5B.!!$F1	2016
4	TraesCS4A01G346500	chr5B	686210819	686212506	1687	True	1354.00	1354	81.4330	1785	3506	1	chr5B.!!$R1	1721
5	TraesCS4A01G346500	chr5B	685990918	685994511	3593	True	976.52	2856	93.1180	838	4058	5	chr5B.!!$R3	3220
6	TraesCS4A01G346500	chr5B	685949919	685952347	2428	True	907.00	1581	88.8400	997	3500	2	chr5B.!!$R2	2503
7	TraesCS4A01G346500	chr5B	686049384	686051739	2355	True	823.50	1454	86.0345	997	3729	2	chr5B.!!$R4	2732
8	TraesCS4A01G346500	chr5D	544284824	544286832	2008	True	1860.00	1860	83.5770	1474	3500	1	chr5D.!!$R2	2026
9	TraesCS4A01G346500	chr5D	543857271	543858940	1669	True	1507.00	1507	83.1120	1782	3496	1	chr5D.!!$R1	1714
10	TraesCS4A01G346500	chr5D	543838164	543841813	3649	True	893.48	2087	92.7140	997	4058	5	chr5D.!!$R3	3061
11	TraesCS4A01G346500	chr1D	479709612	479710445	833	True	606.00	739	94.4205	1	810	2	chr1D.!!$R1	809
12	TraesCS4A01G346500	chr2A	45089428	45090210	782	False	461.50	590	89.7360	1	811	2	chr2A.!!$F1	810
13	TraesCS4A01G346500	chr7A	507883692	507884381	689	False	346.00	363	86.2475	170	817	2	chr7A.!!$F1	647

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
472	473	0.174845	CGACGGCCCACTAGAATGAA	59.825	55.0	0.00	0.00	2.57	F
815	876	0.180406	AAAACGCCCCTCTCGCATAT	59.820	50.0	0.00	0.00	1.78	F
1614	1810	0.037697	AGCTGTCCGCGTAAACATCA	60.038	50.0	4.92	45.59	3.07	F
2789	4074	1.519408	CCCAAACTCCCACGTAACAG	58.481	55.0	0.00	0.00	3.16	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1359	1456	0.396811	ACCTTGTAGACAGTGGTGGC	59.603	55.000	8.14	34.73	5.01	R
2637	3922	0.391228	TAGGCACTGAACACGCAAGA	59.609	50.000	0.00	41.52	3.02	R
2834	4119	0.721718	GCGAGAGTTGGGTGAAATCG	59.278	55.000	0.00	33.73	3.34	R
3761	5169	1.526464	CCCGCAAACAATGAAAAGCAC	59.474	47.619	0.00	0.00	4.40	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
20	21	1.068741	GTCACCTTCTTGTCGGTCTGT	59.931	52.381	0.00	0.00	0.00	3.41
84	85	1.207488	TCACCTCCCCAACATCCTGG	61.207	60.000	0.00	0.00	36.10	4.45
191	192	2.431942	GCGAGAGGAACGGCGAAA	60.432	61.111	16.62	0.00	0.00	3.46
204	205	2.092291	GCGAAACGACGGCATCAGA	61.092	57.895	0.00	0.00	0.00	3.27
205	206	1.623081	GCGAAACGACGGCATCAGAA	61.623	55.000	0.00	0.00	0.00	3.02
255	256	0.814010	AACTCAAAGCTTGTCGCCGT	60.814	50.000	0.00	0.00	40.39	5.68
272	273	6.474427	TGTCGCCGTCTGTAATCTAAAATAAG	59.526	38.462	0.00	0.00	0.00	1.73
306	307	0.178926	TCTACCCGGAACCAACCTGA	60.179	55.000	0.73	0.00	0.00	3.86
314	315	2.951475	GAACCAACCTGACCACCGCA	62.951	60.000	0.00	0.00	0.00	5.69
472	473	0.174845	CGACGGCCCACTAGAATGAA	59.825	55.000	0.00	0.00	0.00	2.57
478	479	3.039011	GGCCCACTAGAATGAACTAGGA	58.961	50.000	0.00	0.00	42.68	2.94
481	482	5.119694	GCCCACTAGAATGAACTAGGAAAG	58.880	45.833	0.00	0.00	42.68	2.62
483	484	5.119694	CCACTAGAATGAACTAGGAAAGGC	58.880	45.833	0.00	0.00	42.68	4.35
485	486	4.710375	ACTAGAATGAACTAGGAAAGGCGA	59.290	41.667	0.00	0.00	42.68	5.54
486	487	4.130286	AGAATGAACTAGGAAAGGCGAG	57.870	45.455	0.00	0.00	0.00	5.03
487	488	3.769844	AGAATGAACTAGGAAAGGCGAGA	59.230	43.478	0.00	0.00	0.00	4.04
501	559	1.079819	CGAGAACAGGACGGCACAT	60.080	57.895	0.00	0.00	0.00	3.21
571	631	3.820590	CAAACGTGCTGGTCCACA	58.179	55.556	0.00	0.00	35.47	4.17
593	653	2.069273	CCTAGTCAGAAAGCCAACGTG	58.931	52.381	0.00	0.00	0.00	4.49
672	732	0.248054	CACGTCTTGCGCACTGTTTT	60.248	50.000	11.12	0.00	46.11	2.43
702	763	1.210967	TCGGGGGATTCGCTGTTTTAT	59.789	47.619	0.00	0.00	34.28	1.40
709	770	2.220315	TTCGCTGTTTTATTGACGCG	57.780	45.000	3.53	3.53	39.50	6.01
813	874	2.040544	CAAAACGCCCCTCTCGCAT	61.041	57.895	0.00	0.00	0.00	4.73
814	875	0.742990	CAAAACGCCCCTCTCGCATA	60.743	55.000	0.00	0.00	0.00	3.14
815	876	0.180406	AAAACGCCCCTCTCGCATAT	59.820	50.000	0.00	0.00	0.00	1.78
816	877	0.532862	AAACGCCCCTCTCGCATATG	60.533	55.000	0.00	0.00	0.00	1.78
817	878	2.047844	CGCCCCTCTCGCATATGG	60.048	66.667	4.56	0.00	0.00	2.74
818	879	2.348998	GCCCCTCTCGCATATGGG	59.651	66.667	13.38	13.38	39.37	4.00
819	880	2.217038	GCCCCTCTCGCATATGGGA	61.217	63.158	20.12	20.12	42.11	4.37
827	888	2.263077	CTCGCATATGGGAGTATTCGC	58.737	52.381	31.54	3.33	46.26	4.70
828	889	1.893137	TCGCATATGGGAGTATTCGCT	59.107	47.619	17.80	0.00	37.19	4.93
829	890	3.086282	TCGCATATGGGAGTATTCGCTA	58.914	45.455	17.80	0.00	37.19	4.26
830	891	3.128764	TCGCATATGGGAGTATTCGCTAG	59.871	47.826	17.80	0.00	37.19	3.42
831	892	3.128764	CGCATATGGGAGTATTCGCTAGA	59.871	47.826	14.32	0.00	37.19	2.43
832	893	4.380550	CGCATATGGGAGTATTCGCTAGAA	60.381	45.833	14.32	0.00	41.13	2.10
833	894	5.479306	GCATATGGGAGTATTCGCTAGAAA	58.521	41.667	4.56	0.00	40.15	2.52
834	895	5.932303	GCATATGGGAGTATTCGCTAGAAAA	59.068	40.000	4.56	0.00	40.15	2.29
835	896	6.426937	GCATATGGGAGTATTCGCTAGAAAAA	59.573	38.462	4.56	0.00	40.15	1.94
836	897	7.571428	GCATATGGGAGTATTCGCTAGAAAAAC	60.571	40.741	4.56	0.00	40.15	2.43
868	929	3.499737	GTCCAACCAGCGATGCGG	61.500	66.667	0.00	0.00	0.00	5.69
906	967	1.073199	CTGGGCTGGTCCTCGTTTT	59.927	57.895	0.00	0.00	34.39	2.43
909	970	1.971695	GGCTGGTCCTCGTTTTGGG	60.972	63.158	0.00	0.00	0.00	4.12
956	1017	1.707989	TCCCCTATGCCAAAAGACACA	59.292	47.619	0.00	0.00	0.00	3.72
967	1031	1.238439	AAAGACACAGTCGCATTGGG	58.762	50.000	0.00	0.00	37.67	4.12
1097	1164	2.183046	GACCGCTCTCAGCTCCAC	59.817	66.667	0.00	0.00	39.60	4.02
1206	1273	9.043079	GTTTAATTAAAGTAGAATCGGGAGAGG	57.957	37.037	10.92	0.00	45.48	3.69
1298	1395	9.941664	CTTGATGATTTGACAGGTGATATTTAC	57.058	33.333	0.00	0.00	0.00	2.01
1359	1456	1.475213	GCCTCCCCTAAACTTGGATCG	60.475	57.143	0.00	0.00	0.00	3.69
1382	1488	1.202651	ACCACTGTCTACAAGGTGTGC	60.203	52.381	6.20	0.00	34.36	4.57
1521	1716	3.405831	TCAGTGATTGCCTGAAACTCAG	58.594	45.455	0.00	0.00	43.91	3.35
1566	1762	7.957484	CGATTCTTTTACTGTGACTGTTATTGG	59.043	37.037	0.00	0.00	0.00	3.16
1573	1769	4.256920	CTGTGACTGTTATTGGGAAGGAG	58.743	47.826	0.00	0.00	0.00	3.69
1603	1799	8.964420	TTAAAATTTCTTATCAAAGCTGTCCG	57.036	30.769	0.00	0.00	32.36	4.79
1614	1810	0.037697	AGCTGTCCGCGTAAACATCA	60.038	50.000	4.92	0.00	45.59	3.07
1933	2252	3.278574	AGCATGCTATTCCGCTTTTACA	58.721	40.909	21.21	0.00	0.00	2.41
2434	3719	7.934855	ATTATTGCTCTGTTTGACTCATTCT	57.065	32.000	0.00	0.00	0.00	2.40
2637	3922	6.597280	GTGATCCTAGCAAGAAAAACTCATCT	59.403	38.462	0.00	0.00	0.00	2.90
2789	4074	1.519408	CCCAAACTCCCACGTAACAG	58.481	55.000	0.00	0.00	0.00	3.16
2834	4119	1.600916	GCATCCTTACGGCCCCATC	60.601	63.158	0.00	0.00	0.00	3.51
2935	4220	4.160439	CAGAGCACACCCTTACTCTTGATA	59.840	45.833	0.00	0.00	37.40	2.15
3159	4445	0.249120	TGGGTGGCTCATCTAACACG	59.751	55.000	0.00	0.00	34.78	4.49
3403	4689	2.661566	CCAGACAGTGCAGTTCGCG	61.662	63.158	0.00	0.00	46.97	5.87
3589	4962	7.692460	TGATTAATCTGTATGGGATTGCATC	57.308	36.000	16.24	0.00	35.40	3.91
3606	4979	0.251354	ATCTGTCATCTGGTTGCGCT	59.749	50.000	9.73	0.00	0.00	5.92
3712	5085	5.048991	GGGTACTATTGTGGACAAACTTGTG	60.049	44.000	0.00	0.00	42.43	3.33
3734	5107	5.047235	GTGGTGTATTCAACTGTACCTCTCT	60.047	44.000	0.00	0.00	31.63	3.10
3743	5116	5.987347	TCAACTGTACCTCTCTTAAAAACGG	59.013	40.000	0.00	0.00	0.00	4.44
3761	5169	1.335810	CGGCACCTTGGATCATTCATG	59.664	52.381	0.00	0.00	0.00	3.07
3778	5186	5.406767	TTCATGTGCTTTTCATTGTTTGC	57.593	34.783	0.00	0.00	0.00	3.68
3781	5189	1.526464	GTGCTTTTCATTGTTTGCGGG	59.474	47.619	0.00	0.00	0.00	6.13
3794	5202	2.426738	GTTTGCGGGATTGGATCATTCA	59.573	45.455	0.00	0.00	0.00	2.57
3795	5203	2.662535	TGCGGGATTGGATCATTCAT	57.337	45.000	0.00	0.00	0.00	2.57
3828	5242	8.267183	ACTGAATGAATGTACTGATTATGGTGA	58.733	33.333	0.00	0.00	0.00	4.02
3849	5263	7.440856	TGGTGATTTTCTTGCCATTTTTAGTTC	59.559	33.333	0.00	0.00	0.00	3.01
3858	5272	8.034215	TCTTGCCATTTTTAGTTCATAATGTGG	58.966	33.333	0.00	0.00	0.00	4.17
3862	5276	7.981225	GCCATTTTTAGTTCATAATGTGGTGAT	59.019	33.333	0.00	0.00	0.00	3.06
3866	5280	8.642935	TTTTAGTTCATAATGTGGTGATGGAA	57.357	30.769	0.00	0.00	0.00	3.53
3921	5335	0.514691	GTCTTGCGCTTTCCTCTGTG	59.485	55.000	9.73	0.00	0.00	3.66
3939	5353	6.072618	CCTCTGTGATCAAATCATAGGAATGC	60.073	42.308	9.45	0.00	45.29	3.56
3960	5379	1.974236	ACTGTCCTCTCCTCCAGTTTG	59.026	52.381	0.00	0.00	34.64	2.93
3968	5387	4.714308	CCTCTCCTCCAGTTTGTTATCTCT	59.286	45.833	0.00	0.00	0.00	3.10

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
20	21	1.038130	GGAGGACGAAGGAGCAGCTA	61.038	60.000	0.00	0.00	0.00	3.32
84	85	1.002011	GGAGAAGGGGAGTGCAACC	60.002	63.158	0.00	0.00	37.80	3.77
191	192	0.817654	TCTGATTCTGATGCCGTCGT	59.182	50.000	0.00	0.00	0.00	4.34
204	205	4.105377	ACTGCCCTGCCTATAAATCTGATT	59.895	41.667	0.00	0.00	0.00	2.57
205	206	3.654806	ACTGCCCTGCCTATAAATCTGAT	59.345	43.478	0.00	0.00	0.00	2.90
247	248	3.853831	TTTAGATTACAGACGGCGACA	57.146	42.857	16.62	0.00	0.00	4.35
272	273	4.035675	CCGGGTAGATCTCTGCAAATTTTC	59.964	45.833	0.00	0.00	0.00	2.29
290	291	2.826003	GGTCAGGTTGGTTCCGGGT	61.826	63.158	0.00	0.00	0.00	5.28
306	307	2.360350	CCTGCTTGATGCGGTGGT	60.360	61.111	0.00	0.00	46.27	4.16
314	315	2.173569	GGGTATGGAGTTCCTGCTTGAT	59.826	50.000	0.00	0.00	36.82	2.57
412	413	1.609501	GGGGGACAAAAAGGGGAGC	60.610	63.158	0.00	0.00	0.00	4.70
456	457	2.224066	CCTAGTTCATTCTAGTGGGCCG	60.224	54.545	0.00	0.00	36.59	6.13
462	463	4.710375	TCGCCTTTCCTAGTTCATTCTAGT	59.290	41.667	0.00	0.00	36.59	2.57
465	466	3.769844	TCTCGCCTTTCCTAGTTCATTCT	59.230	43.478	0.00	0.00	0.00	2.40
472	473	1.550976	CCTGTTCTCGCCTTTCCTAGT	59.449	52.381	0.00	0.00	0.00	2.57
478	479	1.004918	CCGTCCTGTTCTCGCCTTT	60.005	57.895	0.00	0.00	0.00	3.11
481	482	4.373116	TGCCGTCCTGTTCTCGCC	62.373	66.667	0.00	0.00	0.00	5.54
483	484	0.172578	TATGTGCCGTCCTGTTCTCG	59.827	55.000	0.00	0.00	0.00	4.04
485	486	1.066858	CAGTATGTGCCGTCCTGTTCT	60.067	52.381	0.00	0.00	0.00	3.01
486	487	1.359848	CAGTATGTGCCGTCCTGTTC	58.640	55.000	0.00	0.00	0.00	3.18
487	488	3.532896	CAGTATGTGCCGTCCTGTT	57.467	52.632	0.00	0.00	0.00	3.16
501	559	4.710695	CGTGACGGTGGCGCAGTA	62.711	66.667	10.83	0.00	0.00	2.74
571	631	1.338200	CGTTGGCTTTCTGACTAGGCT	60.338	52.381	0.00	0.00	37.78	4.58
640	700	3.310860	GACGTGGGGTCGGCTTGAT	62.311	63.158	0.00	0.00	35.61	2.57
641	701	3.998672	GACGTGGGGTCGGCTTGA	61.999	66.667	0.00	0.00	35.61	3.02
702	763	0.796870	CTGTCAGATACGCGCGTCAA	60.797	55.000	41.35	24.77	0.00	3.18
709	770	0.457851	AGCTGGACTGTCAGATACGC	59.542	55.000	6.91	4.05	36.93	4.42
813	874	6.880484	TGTTTTTCTAGCGAATACTCCCATA	58.120	36.000	0.00	0.00	0.00	2.74
814	875	5.741011	TGTTTTTCTAGCGAATACTCCCAT	58.259	37.500	0.00	0.00	0.00	4.00
815	876	5.155278	TGTTTTTCTAGCGAATACTCCCA	57.845	39.130	0.00	0.00	0.00	4.37
816	877	6.490566	TTTGTTTTTCTAGCGAATACTCCC	57.509	37.500	0.00	0.00	0.00	4.30
817	878	7.021790	CCTTTTGTTTTTCTAGCGAATACTCC	58.978	38.462	0.00	0.00	0.00	3.85
818	879	6.523546	GCCTTTTGTTTTTCTAGCGAATACTC	59.476	38.462	0.00	0.00	0.00	2.59
819	880	6.206829	AGCCTTTTGTTTTTCTAGCGAATACT	59.793	34.615	0.00	0.00	0.00	2.12
820	881	6.305638	CAGCCTTTTGTTTTTCTAGCGAATAC	59.694	38.462	0.00	0.00	0.00	1.89
821	882	6.378582	CAGCCTTTTGTTTTTCTAGCGAATA	58.621	36.000	0.00	0.00	0.00	1.75
822	883	5.222631	CAGCCTTTTGTTTTTCTAGCGAAT	58.777	37.500	0.00	0.00	0.00	3.34
823	884	4.606961	CAGCCTTTTGTTTTTCTAGCGAA	58.393	39.130	0.00	0.00	0.00	4.70
824	885	3.550030	GCAGCCTTTTGTTTTTCTAGCGA	60.550	43.478	0.00	0.00	0.00	4.93
825	886	2.726241	GCAGCCTTTTGTTTTTCTAGCG	59.274	45.455	0.00	0.00	0.00	4.26
826	887	2.726241	CGCAGCCTTTTGTTTTTCTAGC	59.274	45.455	0.00	0.00	0.00	3.42
888	949	1.073199	AAAACGAGGACCAGCCCAG	59.927	57.895	0.00	0.00	37.37	4.45
906	967	2.428925	GCGTAGGTTCCCGATCCCA	61.429	63.158	0.00	0.00	0.00	4.37
909	970	1.143969	CGTTGCGTAGGTTCCCGATC	61.144	60.000	0.00	0.00	0.00	3.69
1097	1164	4.394712	GGGGTGAGGGTGCAGACG	62.395	72.222	0.00	0.00	0.00	4.18
1206	1273	1.202533	TCGCTAGGGCAAGATTACTGC	60.203	52.381	1.02	0.00	38.60	4.40
1298	1395	4.385447	CACCACTAATTCACAAAAATGCCG	59.615	41.667	0.00	0.00	0.00	5.69
1359	1456	0.396811	ACCTTGTAGACAGTGGTGGC	59.603	55.000	8.14	0.00	34.73	5.01
1382	1488	1.948104	TCAACAACTGAACCGAGTGG	58.052	50.000	0.00	0.00	42.84	4.00
1521	1716	5.998454	ATCGATCAAATCACATTGGACTC	57.002	39.130	0.00	0.00	0.00	3.36
1603	1799	5.177696	GTGATAATCCCTCTGATGTTTACGC	59.822	44.000	0.00	0.00	32.68	4.42
1933	2252	8.345724	AGTTCTAAGTGATGATTTTGCTTGAT	57.654	30.769	0.00	0.00	0.00	2.57
2434	3719	4.098349	GCCAATGAATGCAAGGAAGTCATA	59.902	41.667	0.00	0.00	0.00	2.15
2637	3922	0.391228	TAGGCACTGAACACGCAAGA	59.609	50.000	0.00	0.00	41.52	3.02
2789	4074	3.057526	GCCACAAAAGTACCCAAGATCAC	60.058	47.826	0.00	0.00	0.00	3.06
2834	4119	0.721718	GCGAGAGTTGGGTGAAATCG	59.278	55.000	0.00	0.00	33.73	3.34
2935	4220	5.819379	ACACAATCTGATAGATGCGTTCATT	59.181	36.000	0.00	0.00	34.65	2.57
3159	4445	2.295070	GAGGCGAGAGACCCTAAAGATC	59.705	54.545	0.00	0.00	43.69	2.75
3403	4689	4.565962	CGACATATCATAGAAGAGCATGGC	59.434	45.833	0.00	0.00	0.00	4.40
3565	4896	7.692460	GATGCAATCCCATACAGATTAATCA	57.308	36.000	17.56	0.00	37.38	2.57
3589	4962	1.642037	CCAGCGCAACCAGATGACAG	61.642	60.000	11.47	0.00	0.00	3.51
3606	4979	3.181462	CCATTCTACTGCTGCATCTACCA	60.181	47.826	1.31	0.00	0.00	3.25
3712	5085	5.662674	AGAGAGGTACAGTTGAATACACC	57.337	43.478	0.00	0.00	0.00	4.16
3734	5107	3.223435	TGATCCAAGGTGCCGTTTTTAA	58.777	40.909	0.00	0.00	0.00	1.52
3743	5116	2.480759	GCACATGAATGATCCAAGGTGC	60.481	50.000	0.00	11.75	39.68	5.01
3761	5169	1.526464	CCCGCAAACAATGAAAAGCAC	59.474	47.619	0.00	0.00	0.00	4.40
3778	5186	4.338964	TCAACAATGAATGATCCAATCCCG	59.661	41.667	0.00	0.00	30.99	5.14
3781	5189	7.541162	TCAGTTCAACAATGAATGATCCAATC	58.459	34.615	0.00	0.00	46.67	2.67
3794	5202	8.394971	TCAGTACATTCATTCAGTTCAACAAT	57.605	30.769	0.00	0.00	0.00	2.71
3795	5203	7.800155	TCAGTACATTCATTCAGTTCAACAA	57.200	32.000	0.00	0.00	0.00	2.83
3849	5263	4.525996	TCCTGTTCCATCACCACATTATG	58.474	43.478	0.00	0.00	0.00	1.90
3858	5272	3.425162	AGGTTTCTCCTGTTCCATCAC	57.575	47.619	0.00	0.00	46.19	3.06
3877	5291	6.138761	GTCATTTGCAGAGTAAACAGACAAG	58.861	40.000	8.81	0.00	31.30	3.16
3921	5335	6.293845	GGACAGTGCATTCCTATGATTTGATC	60.294	42.308	0.00	0.00	33.37	2.92
3939	5353	1.638529	AACTGGAGGAGAGGACAGTG	58.361	55.000	0.00	0.00	42.85	3.66
3960	5379	8.780249	CAAGAGTAGTCTTAGGCTAGAGATAAC	58.220	40.741	12.50	9.60	41.40	1.89
3968	5387	3.954904	CTGCCAAGAGTAGTCTTAGGCTA	59.045	47.826	31.64	23.54	46.51	3.93

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.