AutoCloner

Multiple sequence alignment - TraesCS1D01G197700

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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	TraesCS1D01G197700	chr1D	100.000	2849	0	0	1	2849	279091871	279094719	0.000000e+00	5262.0
1	TraesCS1D01G197700	chr1D	97.059	68	2	0	784	851	382212981	382212914	6.450000e-22	115.0
2	TraesCS1D01G197700	chr1A	93.119	1831	49	18	874	2677	351340451	351342231	0.000000e+00	2612.0
3	TraesCS1D01G197700	chr1A	88.366	361	34	4	415	772	477347063	477347418	7.290000e-116	427.0
4	TraesCS1D01G197700	chr1A	85.047	107	6	3	2736	2842	351342220	351342316	1.810000e-17	100.0
5	TraesCS1D01G197700	chr1B	92.302	1351	50	22	874	2178	378828601	378829943	0.000000e+00	1869.0
6	TraesCS1D01G197700	chr1B	86.826	167	7	10	2680	2840	378830670	378830827	3.770000e-39	172.0
7	TraesCS1D01G197700	chr1B	95.652	69	3	0	784	852	467901618	467901686	8.340000e-21	111.0
8	TraesCS1D01G197700	chrUn	84.651	860	91	23	1	852	104864607	104865433	0.000000e+00	819.0
9	TraesCS1D01G197700	chr6A	86.894	763	55	16	13	772	201653038	201653758	0.000000e+00	813.0
10	TraesCS1D01G197700	chr6A	91.060	302	21	4	406	706	71691143	71690847	1.230000e-108	403.0
11	TraesCS1D01G197700	chr6D	85.020	761	81	16	1	738	362909030	362908280	0.000000e+00	743.0
12	TraesCS1D01G197700	chr6D	97.059	68	2	0	784	851	433638133	433638066	6.450000e-22	115.0
13	TraesCS1D01G197700	chr7B	84.547	783	84	23	1	780	584804796	584805544	0.000000e+00	741.0
14	TraesCS1D01G197700	chr3A	83.206	786	85	24	1	783	603788005	603788746	0.000000e+00	676.0
15	TraesCS1D01G197700	chr3A	87.566	378	31	6	406	783	502108507	502108868	9.440000e-115	424.0
16	TraesCS1D01G197700	chr6B	91.014	434	38	1	1	434	370135334	370134902	4.090000e-163	584.0
17	TraesCS1D01G197700	chr6B	90.691	333	25	5	405	737	53054851	53055177	3.370000e-119	438.0
18	TraesCS1D01G197700	chr2B	82.113	710	101	21	5	706	153614454	153613763	4.090000e-163	584.0
19	TraesCS1D01G197700	chr2B	88.506	435	34	3	1	434	545764082	545763663	1.960000e-141	512.0
20	TraesCS1D01G197700	chr2B	91.900	321	20	5	418	738	545763625	545763311	7.240000e-121	444.0
21	TraesCS1D01G197700	chr2B	86.141	368	32	15	424	783	356504572	356504216	2.070000e-101	379.0
22	TraesCS1D01G197700	chr5B	81.831	699	93	19	1	696	21423524	21424191	8.920000e-155	556.0
23	TraesCS1D01G197700	chr3D	80.619	743	116	12	42	783	598337932	598338647	1.490000e-152	549.0
24	TraesCS1D01G197700	chr3D	80.350	743	118	13	42	783	362876101	362876816	3.230000e-149	538.0
25	TraesCS1D01G197700	chr3D	97.059	68	2	0	784	851	598338686	598338753	6.450000e-22	115.0
26	TraesCS1D01G197700	chr7A	80.466	773	97	32	4	772	284789027	284788305	2.500000e-150	542.0
27	TraesCS1D01G197700	chr2D	79.735	755	112	19	53	783	595555638	595556375	2.530000e-140	508.0
28	TraesCS1D01G197700	chr2D	97.059	68	2	0	784	851	595549458	595549525	6.450000e-22	115.0
29	TraesCS1D01G197700	chr3B	85.714	364	39	9	414	772	784849444	784849089	3.470000e-99	372.0
30	TraesCS1D01G197700	chr5D	76.738	748	121	30	53	772	555472086	555471364	4.480000e-98	368.0
31	TraesCS1D01G197700	chr5D	97.059	68	2	0	784	851	240855364	240855431	6.450000e-22	115.0
32	TraesCS1D01G197700	chr5D	97.059	68	2	0	784	851	368736282	368736349	6.450000e-22	115.0
33	TraesCS1D01G197700	chr4D	97.059	68	2	0	784	851	473839704	473839637	6.450000e-22	115.0
34	TraesCS1D01G197700	chr4D	97.059	68	2	0	784	851	473843734	473843667	6.450000e-22	115.0
35	TraesCS1D01G197700	chr7D	100.000	31	0	0	1027	1057	117527695	117527665	1.100000e-04	58.4

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	TraesCS1D01G197700	chr1D	279091871	279094719	2848	False	5262.0	5262	100.000	1	2849	1	chr1D.!!$F1	2848
1	TraesCS1D01G197700	chr1A	351340451	351342316	1865	False	1356.0	2612	89.083	874	2842	2	chr1A.!!$F2	1968
2	TraesCS1D01G197700	chr1B	378828601	378830827	2226	False	1020.5	1869	89.564	874	2840	2	chr1B.!!$F2	1966
3	TraesCS1D01G197700	chrUn	104864607	104865433	826	False	819.0	819	84.651	1	852	1	chrUn.!!$F1	851
4	TraesCS1D01G197700	chr6A	201653038	201653758	720	False	813.0	813	86.894	13	772	1	chr6A.!!$F1	759
5	TraesCS1D01G197700	chr6D	362908280	362909030	750	True	743.0	743	85.020	1	738	1	chr6D.!!$R1	737
6	TraesCS1D01G197700	chr7B	584804796	584805544	748	False	741.0	741	84.547	1	780	1	chr7B.!!$F1	779
7	TraesCS1D01G197700	chr3A	603788005	603788746	741	False	676.0	676	83.206	1	783	1	chr3A.!!$F2	782
8	TraesCS1D01G197700	chr2B	153613763	153614454	691	True	584.0	584	82.113	5	706	1	chr2B.!!$R1	701
9	TraesCS1D01G197700	chr2B	545763311	545764082	771	True	478.0	512	90.203	1	738	2	chr2B.!!$R3	737
10	TraesCS1D01G197700	chr5B	21423524	21424191	667	False	556.0	556	81.831	1	696	1	chr5B.!!$F1	695
11	TraesCS1D01G197700	chr3D	362876101	362876816	715	False	538.0	538	80.350	42	783	1	chr3D.!!$F1	741
12	TraesCS1D01G197700	chr3D	598337932	598338753	821	False	332.0	549	88.839	42	851	2	chr3D.!!$F2	809
13	TraesCS1D01G197700	chr7A	284788305	284789027	722	True	542.0	542	80.466	4	772	1	chr7A.!!$R1	768
14	TraesCS1D01G197700	chr2D	595555638	595556375	737	False	508.0	508	79.735	53	783	1	chr2D.!!$F2	730
15	TraesCS1D01G197700	chr5D	555471364	555472086	722	True	368.0	368	76.738	53	772	1	chr5D.!!$R1	719

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
775	944	1.2036	GAAGAGACGCGATCGAAGGC	61.204	60.0	21.57	14.25	39.41	4.35	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2024	2272	0.320596	TTCATTCGTTAACCGCCCGT	60.321	50.0	0.0	0.0	36.19	5.28	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
23	24	2.282180	GCCCGCAGAAACCTCCAA	60.282	61.111	0.00	0.00	0.00	3.53
59	60	4.115199	GCCGGCACCTTCCATCCT	62.115	66.667	24.80	0.00	0.00	3.24
263	270	2.367202	GGTGGAGGCGGAGATCCAA	61.367	63.158	0.00	0.00	44.49	3.53
507	661	4.479993	GACGGCCTGCATCCTGCT	62.480	66.667	0.00	0.00	45.31	4.24
732	901	5.831702	AAATCTCTGTCTTGATTGATGGC	57.168	39.130	0.00	0.00	33.72	4.40
775	944	1.203600	GAAGAGACGCGATCGAAGGC	61.204	60.000	21.57	14.25	39.41	4.35
864	1071	8.793592	ACTAATTCTAACAGCTTTTACAAAGGG	58.206	33.333	0.00	0.00	0.00	3.95
865	1072	6.590234	ATTCTAACAGCTTTTACAAAGGGG	57.410	37.500	0.00	0.00	0.00	4.79
866	1073	5.313280	TCTAACAGCTTTTACAAAGGGGA	57.687	39.130	0.00	0.00	0.00	4.81
867	1074	5.887754	TCTAACAGCTTTTACAAAGGGGAT	58.112	37.500	0.00	0.00	0.00	3.85
868	1075	4.871933	AACAGCTTTTACAAAGGGGATG	57.128	40.909	0.00	0.00	0.00	3.51
869	1076	3.165071	ACAGCTTTTACAAAGGGGATGG	58.835	45.455	0.00	0.00	0.00	3.51
870	1077	3.181423	ACAGCTTTTACAAAGGGGATGGA	60.181	43.478	0.00	0.00	0.00	3.41
871	1078	3.193479	CAGCTTTTACAAAGGGGATGGAC	59.807	47.826	0.00	0.00	0.00	4.02
872	1079	3.076032	AGCTTTTACAAAGGGGATGGACT	59.924	43.478	0.00	0.00	0.00	3.85
912	1119	1.392853	GCAGCAAACATCTCGTCTCAG	59.607	52.381	0.00	0.00	0.00	3.35
979	1186	1.241315	CCTGTTAAACCCCACCGCAG	61.241	60.000	0.00	0.00	0.00	5.18
1293	1517	1.084289	GGTAAGTAGCCAGCCAAACG	58.916	55.000	0.00	0.00	0.00	3.60
1430	1654	1.891178	TAAGACTCGCGATGAACACG	58.109	50.000	10.36	0.00	0.00	4.49
1490	1718	4.867608	CCTCGTTTGATTTTCTCTCTCTCC	59.132	45.833	0.00	0.00	0.00	3.71
1637	1877	2.439519	CGGAATTGGGGAACGGGG	60.440	66.667	0.00	0.00	0.00	5.73
1723	1966	0.794981	CGCACGTCTCTTTCTCTCCG	60.795	60.000	0.00	0.00	0.00	4.63
1788	2031	1.115467	CGTCTTCCTGTGGCCTCTAT	58.885	55.000	3.32	0.00	0.00	1.98
1885	2130	1.515521	CCTTCGGTTGTTCACCTGCC	61.516	60.000	0.00	0.00	44.69	4.85
1897	2142	2.439409	TCACCTGCCATTGATTCTGTG	58.561	47.619	0.00	0.00	0.00	3.66
2007	2255	5.369685	ACTGGTTTTTGTTTTTGCCTTTG	57.630	34.783	0.00	0.00	0.00	2.77
2012	2260	2.700722	TTGTTTTTGCCTTTGGGGTC	57.299	45.000	0.00	0.00	37.43	4.46
2013	2261	0.461961	TGTTTTTGCCTTTGGGGTCG	59.538	50.000	0.00	0.00	37.43	4.79
2014	2262	0.747852	GTTTTTGCCTTTGGGGTCGA	59.252	50.000	0.00	0.00	37.43	4.20
2015	2263	1.137282	GTTTTTGCCTTTGGGGTCGAA	59.863	47.619	0.00	0.00	37.43	3.71
2016	2264	1.710816	TTTTGCCTTTGGGGTCGAAT	58.289	45.000	0.00	0.00	37.43	3.34
2017	2265	0.965439	TTTGCCTTTGGGGTCGAATG	59.035	50.000	0.00	0.00	37.43	2.67
2018	2266	0.111446	TTGCCTTTGGGGTCGAATGA	59.889	50.000	0.00	0.00	37.43	2.57
2019	2267	0.111446	TGCCTTTGGGGTCGAATGAA	59.889	50.000	0.00	0.00	37.43	2.57
2020	2268	1.272425	TGCCTTTGGGGTCGAATGAAT	60.272	47.619	0.00	0.00	37.43	2.57
2021	2269	1.134946	GCCTTTGGGGTCGAATGAATG	59.865	52.381	0.00	0.00	37.43	2.67
2022	2270	1.750778	CCTTTGGGGTCGAATGAATGG	59.249	52.381	0.00	0.00	0.00	3.16
2023	2271	1.750778	CTTTGGGGTCGAATGAATGGG	59.249	52.381	0.00	0.00	0.00	4.00
2024	2272	0.995803	TTGGGGTCGAATGAATGGGA	59.004	50.000	0.00	0.00	0.00	4.37
2025	2273	0.254747	TGGGGTCGAATGAATGGGAC	59.745	55.000	0.00	0.00	0.00	4.46
2026	2274	0.814010	GGGGTCGAATGAATGGGACG	60.814	60.000	0.00	0.00	0.00	4.79
2027	2275	0.814010	GGGTCGAATGAATGGGACGG	60.814	60.000	0.00	0.00	0.00	4.79
2028	2276	0.814010	GGTCGAATGAATGGGACGGG	60.814	60.000	0.00	0.00	0.00	5.28
2029	2277	1.153249	TCGAATGAATGGGACGGGC	60.153	57.895	0.00	0.00	0.00	6.13
2030	2278	2.534019	CGAATGAATGGGACGGGCG	61.534	63.158	0.00	0.00	0.00	6.13
2031	2279	2.124320	AATGAATGGGACGGGCGG	60.124	61.111	0.00	0.00	0.00	6.13
2032	2280	2.886730	GAATGAATGGGACGGGCGGT	62.887	60.000	0.00	0.00	0.00	5.68
2033	2281	2.493273	AATGAATGGGACGGGCGGTT	62.493	55.000	0.00	0.00	0.00	4.44
2034	2282	1.628238	ATGAATGGGACGGGCGGTTA	61.628	55.000	0.00	0.00	0.00	2.85
2035	2283	1.078285	GAATGGGACGGGCGGTTAA	60.078	57.895	0.00	0.00	0.00	2.01
2036	2284	1.371337	GAATGGGACGGGCGGTTAAC	61.371	60.000	0.00	0.00	0.00	2.01
2103	2391	6.095440	CAGGGGATCACGAGAAAATTTATTGT	59.905	38.462	0.00	0.00	0.00	2.71
2276	3055	1.075748	GGAGCCAATGCCCTCCATT	60.076	57.895	11.62	0.00	45.55	3.16
2375	3154	9.046296	AGTATGTGCATCTTTGTATAAGTAAGC	57.954	33.333	0.00	0.00	0.00	3.09
2376	3155	9.046296	GTATGTGCATCTTTGTATAAGTAAGCT	57.954	33.333	0.00	0.00	0.00	3.74
2445	3226	0.106369	ACCATCACGGATCGAGGGTA	60.106	55.000	3.93	0.00	45.29	3.69
2458	3239	0.752376	GAGGGTAGTAGGCTCGCAGT	60.752	60.000	0.00	0.00	0.00	4.40
2460	3241	1.035932	GGGTAGTAGGCTCGCAGTGA	61.036	60.000	0.00	0.00	0.00	3.41
2510	3291	7.010552	AGTGCAAATGTAGCGTTAATTCTAGAG	59.989	37.037	0.00	0.00	33.85	2.43
2547	3328	9.143631	CAAATTTTGGACTAATGGATGACTTTC	57.856	33.333	0.97	0.00	0.00	2.62
2559	3340	1.206831	GACTTTCGCGGGACAAAGC	59.793	57.895	15.51	7.12	33.57	3.51
2623	3424	4.713553	TCCATGAACACTACAAAGCTTCA	58.286	39.130	0.00	0.00	30.95	3.02
2625	3426	5.412594	TCCATGAACACTACAAAGCTTCATC	59.587	40.000	0.00	0.00	33.87	2.92
2642	3443	5.750067	GCTTCATCTCTGAAACAAAAGCAAA	59.250	36.000	0.00	0.00	40.78	3.68
2658	3459	8.022550	ACAAAAGCAAACAAGAAAATGAAAAGG	58.977	29.630	0.00	0.00	0.00	3.11
2665	3466	9.323985	CAAACAAGAAAATGAAAAGGGAATACA	57.676	29.630	0.00	0.00	0.00	2.29
2669	3470	7.301868	AGAAAATGAAAAGGGAATACAGCAA	57.698	32.000	0.00	0.00	0.00	3.91
2670	3471	7.381323	AGAAAATGAAAAGGGAATACAGCAAG	58.619	34.615	0.00	0.00	0.00	4.01
2671	3472	5.665916	AATGAAAAGGGAATACAGCAAGG	57.334	39.130	0.00	0.00	0.00	3.61
2672	3473	4.380843	TGAAAAGGGAATACAGCAAGGA	57.619	40.909	0.00	0.00	0.00	3.36
2673	3474	4.735369	TGAAAAGGGAATACAGCAAGGAA	58.265	39.130	0.00	0.00	0.00	3.36
2674	3475	4.522789	TGAAAAGGGAATACAGCAAGGAAC	59.477	41.667	0.00	0.00	0.00	3.62
2675	3476	3.806949	AAGGGAATACAGCAAGGAACA	57.193	42.857	0.00	0.00	0.00	3.18
2676	3477	3.356529	AGGGAATACAGCAAGGAACAG	57.643	47.619	0.00	0.00	0.00	3.16
2677	3478	2.912956	AGGGAATACAGCAAGGAACAGA	59.087	45.455	0.00	0.00	0.00	3.41
2678	3479	3.330701	AGGGAATACAGCAAGGAACAGAA	59.669	43.478	0.00	0.00	0.00	3.02
2679	3480	3.691609	GGGAATACAGCAAGGAACAGAAG	59.308	47.826	0.00	0.00	0.00	2.85
2680	3481	3.127721	GGAATACAGCAAGGAACAGAAGC	59.872	47.826	0.00	0.00	0.00	3.86
2681	3482	2.928801	TACAGCAAGGAACAGAAGCA	57.071	45.000	0.00	0.00	0.00	3.91
2682	3483	2.057137	ACAGCAAGGAACAGAAGCAA	57.943	45.000	0.00	0.00	0.00	3.91
2683	3484	1.952296	ACAGCAAGGAACAGAAGCAAG	59.048	47.619	0.00	0.00	0.00	4.01
2684	3485	2.224606	CAGCAAGGAACAGAAGCAAGA	58.775	47.619	0.00	0.00	0.00	3.02
2685	3486	2.620115	CAGCAAGGAACAGAAGCAAGAA	59.380	45.455	0.00	0.00	0.00	2.52
2686	3487	2.883386	AGCAAGGAACAGAAGCAAGAAG	59.117	45.455	0.00	0.00	0.00	2.85
2687	3488	2.880890	GCAAGGAACAGAAGCAAGAAGA	59.119	45.455	0.00	0.00	0.00	2.87
2688	3489	3.058363	GCAAGGAACAGAAGCAAGAAGAG	60.058	47.826	0.00	0.00	0.00	2.85
2689	3490	4.384056	CAAGGAACAGAAGCAAGAAGAGA	58.616	43.478	0.00	0.00	0.00	3.10
2690	3491	4.906747	AGGAACAGAAGCAAGAAGAGAT	57.093	40.909	0.00	0.00	0.00	2.75
2691	3492	4.577875	AGGAACAGAAGCAAGAAGAGATG	58.422	43.478	0.00	0.00	0.00	2.90
2692	3493	3.126686	GGAACAGAAGCAAGAAGAGATGC	59.873	47.826	0.00	0.00	42.87	3.91
2746	3549	2.281070	AACTGAGCAGTGGCCACG	60.281	61.111	29.68	23.87	41.58	4.94
2748	3551	4.007644	CTGAGCAGTGGCCACGGA	62.008	66.667	36.08	16.88	42.56	4.69
2801	3604	2.590092	GCAGCGTACCCCATTCCT	59.410	61.111	0.00	0.00	0.00	3.36
2842	3646	3.603857	CGACAAGGAGCTTTAAACACACG	60.604	47.826	0.00	0.00	0.00	4.49
2843	3647	3.537580	ACAAGGAGCTTTAAACACACGA	58.462	40.909	0.00	0.00	0.00	4.35
2844	3648	3.942748	ACAAGGAGCTTTAAACACACGAA	59.057	39.130	0.00	0.00	0.00	3.85
2845	3649	4.578928	ACAAGGAGCTTTAAACACACGAAT	59.421	37.500	0.00	0.00	0.00	3.34
2846	3650	4.749245	AGGAGCTTTAAACACACGAATG	57.251	40.909	0.00	0.00	0.00	2.67
2847	3651	3.058224	AGGAGCTTTAAACACACGAATGC	60.058	43.478	0.00	0.00	0.00	3.56
2848	3652	3.058224	GGAGCTTTAAACACACGAATGCT	60.058	43.478	0.00	0.00	36.58	3.79

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
23	24	1.767692	GTCAACTCCCCACCACCAT	59.232	57.895	0.00	0.00	0.00	3.55
292	300	1.302033	GAGCGCCCCGATGATGAAT	60.302	57.895	2.29	0.00	0.00	2.57
732	901	6.094186	TCAGATGATATAAGTAGCGCCTGTAG	59.906	42.308	2.29	0.00	0.00	2.74
839	1046	8.244113	CCCCTTTGTAAAAGCTGTTAGAATTAG	58.756	37.037	7.04	3.28	0.00	1.73
852	1059	5.125578	GCTTAGTCCATCCCCTTTGTAAAAG	59.874	44.000	0.00	0.00	0.00	2.27
853	1060	5.014202	GCTTAGTCCATCCCCTTTGTAAAA	58.986	41.667	0.00	0.00	0.00	1.52
854	1061	4.569015	GGCTTAGTCCATCCCCTTTGTAAA	60.569	45.833	0.00	0.00	0.00	2.01
855	1062	3.053917	GGCTTAGTCCATCCCCTTTGTAA	60.054	47.826	0.00	0.00	0.00	2.41
856	1063	2.508300	GGCTTAGTCCATCCCCTTTGTA	59.492	50.000	0.00	0.00	0.00	2.41
857	1064	1.285078	GGCTTAGTCCATCCCCTTTGT	59.715	52.381	0.00	0.00	0.00	2.83
858	1065	1.284785	TGGCTTAGTCCATCCCCTTTG	59.715	52.381	0.00	0.00	0.00	2.77
859	1066	1.285078	GTGGCTTAGTCCATCCCCTTT	59.715	52.381	0.00	0.00	38.57	3.11
860	1067	0.919710	GTGGCTTAGTCCATCCCCTT	59.080	55.000	0.00	0.00	38.57	3.95
861	1068	1.338136	CGTGGCTTAGTCCATCCCCT	61.338	60.000	0.00	0.00	38.57	4.79
862	1069	1.146263	CGTGGCTTAGTCCATCCCC	59.854	63.158	0.00	0.00	38.57	4.81
863	1070	1.523938	GCGTGGCTTAGTCCATCCC	60.524	63.158	0.00	0.00	38.57	3.85
864	1071	0.811616	CAGCGTGGCTTAGTCCATCC	60.812	60.000	0.00	0.00	36.40	3.51
865	1072	0.108138	ACAGCGTGGCTTAGTCCATC	60.108	55.000	0.00	0.00	36.40	3.51
866	1073	0.108138	GACAGCGTGGCTTAGTCCAT	60.108	55.000	0.00	0.00	36.40	3.41
867	1074	1.292223	GACAGCGTGGCTTAGTCCA	59.708	57.895	0.00	0.00	36.40	4.02
868	1075	0.108138	ATGACAGCGTGGCTTAGTCC	60.108	55.000	5.86	0.00	36.40	3.85
869	1076	1.726853	AATGACAGCGTGGCTTAGTC	58.273	50.000	2.23	2.23	36.40	2.59
870	1077	2.076863	GAAATGACAGCGTGGCTTAGT	58.923	47.619	0.00	0.00	36.40	2.24
871	1078	2.094894	CAGAAATGACAGCGTGGCTTAG	59.905	50.000	0.00	0.00	36.40	2.18
872	1079	2.076100	CAGAAATGACAGCGTGGCTTA	58.924	47.619	0.00	0.00	36.40	3.09
945	1152	2.933834	AGGGGAACGGGAAGGTGG	60.934	66.667	0.00	0.00	0.00	4.61
1021	1239	2.090775	GGAGGAGAAGGAGGAGGAGATT	60.091	54.545	0.00	0.00	0.00	2.40
1027	1245	2.131067	GGCGGAGGAGAAGGAGGAG	61.131	68.421	0.00	0.00	0.00	3.69
1028	1246	2.042843	GGCGGAGGAGAAGGAGGA	60.043	66.667	0.00	0.00	0.00	3.71
1029	1247	3.532155	CGGCGGAGGAGAAGGAGG	61.532	72.222	0.00	0.00	0.00	4.30
1030	1248	4.214327	GCGGCGGAGGAGAAGGAG	62.214	72.222	9.78	0.00	0.00	3.69
1293	1517	1.079057	GGAAGGGAGTGGAGCGAAC	60.079	63.158	0.00	0.00	0.00	3.95
1423	1647	2.338620	CGGAGACTGCCGTGTTCA	59.661	61.111	0.00	0.00	46.07	3.18
1490	1718	1.576421	GCTGCAGGAACGAACAAGG	59.424	57.895	17.12	0.00	0.00	3.61
1685	1925	1.699656	GCTGAGGACGCGTCGTAGTA	61.700	60.000	31.77	20.07	41.37	1.82
1686	1926	3.036783	GCTGAGGACGCGTCGTAGT	62.037	63.158	31.77	17.01	41.37	2.73
1687	1927	2.277373	GCTGAGGACGCGTCGTAG	60.277	66.667	31.77	26.87	41.37	3.51
1788	2031	5.833131	GGCTGGTAATCTAATCCCAATTTCA	59.167	40.000	0.00	0.00	0.00	2.69
1885	2130	7.086376	ACGGAAAAAGAATCACAGAATCAATG	58.914	34.615	0.00	0.00	0.00	2.82
1897	2142	9.159364	AGTACTACCAATTACGGAAAAAGAATC	57.841	33.333	0.00	0.00	0.00	2.52
2007	2255	0.814010	CGTCCCATTCATTCGACCCC	60.814	60.000	0.00	0.00	0.00	4.95
2012	2260	2.534019	CGCCCGTCCCATTCATTCG	61.534	63.158	0.00	0.00	0.00	3.34
2013	2261	2.186826	CCGCCCGTCCCATTCATTC	61.187	63.158	0.00	0.00	0.00	2.67
2014	2262	2.124320	CCGCCCGTCCCATTCATT	60.124	61.111	0.00	0.00	0.00	2.57
2015	2263	1.628238	TAACCGCCCGTCCCATTCAT	61.628	55.000	0.00	0.00	0.00	2.57
2016	2264	1.839148	TTAACCGCCCGTCCCATTCA	61.839	55.000	0.00	0.00	0.00	2.57
2017	2265	1.078285	TTAACCGCCCGTCCCATTC	60.078	57.895	0.00	0.00	0.00	2.67
2018	2266	1.377594	GTTAACCGCCCGTCCCATT	60.378	57.895	0.00	0.00	0.00	3.16
2019	2267	2.269883	GTTAACCGCCCGTCCCAT	59.730	61.111	0.00	0.00	0.00	4.00
2020	2268	4.376176	CGTTAACCGCCCGTCCCA	62.376	66.667	0.00	0.00	0.00	4.37
2021	2269	2.857575	ATTCGTTAACCGCCCGTCCC	62.858	60.000	0.00	0.00	36.19	4.46
2022	2270	1.448365	ATTCGTTAACCGCCCGTCC	60.448	57.895	0.00	0.00	36.19	4.79
2023	2271	0.737019	TCATTCGTTAACCGCCCGTC	60.737	55.000	0.00	0.00	36.19	4.79
2024	2272	0.320596	TTCATTCGTTAACCGCCCGT	60.321	50.000	0.00	0.00	36.19	5.28
2025	2273	1.011333	ATTCATTCGTTAACCGCCCG	58.989	50.000	0.00	0.00	36.19	6.13
2026	2274	1.064952	CCATTCATTCGTTAACCGCCC	59.935	52.381	0.00	0.00	36.19	6.13
2027	2275	1.064952	CCCATTCATTCGTTAACCGCC	59.935	52.381	0.00	0.00	36.19	6.13
2028	2276	1.533129	GCCCATTCATTCGTTAACCGC	60.533	52.381	0.00	0.00	36.19	5.68
2029	2277	2.014128	AGCCCATTCATTCGTTAACCG	58.986	47.619	0.00	0.00	38.13	4.44
2030	2278	2.099098	CCAGCCCATTCATTCGTTAACC	59.901	50.000	0.00	0.00	0.00	2.85
2031	2279	2.752903	ACCAGCCCATTCATTCGTTAAC	59.247	45.455	0.00	0.00	0.00	2.01
2032	2280	3.080300	ACCAGCCCATTCATTCGTTAA	57.920	42.857	0.00	0.00	0.00	2.01
2033	2281	2.799126	ACCAGCCCATTCATTCGTTA	57.201	45.000	0.00	0.00	0.00	3.18
2034	2282	1.818674	GAACCAGCCCATTCATTCGTT	59.181	47.619	0.00	0.00	0.00	3.85
2035	2283	1.463674	GAACCAGCCCATTCATTCGT	58.536	50.000	0.00	0.00	0.00	3.85
2036	2284	0.740737	GGAACCAGCCCATTCATTCG	59.259	55.000	0.00	0.00	0.00	3.34
2103	2391	0.394938	TCCACTTTACTGCTGCCGAA	59.605	50.000	0.00	0.00	0.00	4.30
2364	3143	4.684703	CACGGTGGCATAGCTTACTTATAC	59.315	45.833	0.00	0.00	0.00	1.47
2373	3152	1.054406	ATACCCACGGTGGCATAGCT	61.054	55.000	21.88	0.00	36.19	3.32
2374	3153	0.884704	CATACCCACGGTGGCATAGC	60.885	60.000	21.88	0.00	36.19	2.97
2375	3154	0.884704	GCATACCCACGGTGGCATAG	60.885	60.000	21.88	10.44	37.31	2.23
2376	3155	1.147376	GCATACCCACGGTGGCATA	59.853	57.895	21.88	15.51	37.31	3.14
2377	3156	2.124320	GCATACCCACGGTGGCAT	60.124	61.111	21.88	13.40	37.31	4.40
2445	3226	2.716017	GCCTCACTGCGAGCCTACT	61.716	63.158	0.00	0.00	40.78	2.57
2458	3239	1.194121	TTGTCTGCTAGCCTGCCTCA	61.194	55.000	13.29	0.35	0.00	3.86
2460	3241	1.415659	CTATTGTCTGCTAGCCTGCCT	59.584	52.381	13.29	0.00	0.00	4.75
2510	3291	4.219288	AGTCCAAAATTTGCTCATCACTCC	59.781	41.667	0.00	0.00	0.00	3.85
2623	3424	6.866480	TCTTGTTTGCTTTTGTTTCAGAGAT	58.134	32.000	0.00	0.00	0.00	2.75
2625	3426	6.949578	TTCTTGTTTGCTTTTGTTTCAGAG	57.050	33.333	0.00	0.00	0.00	3.35
2642	3443	7.154656	GCTGTATTCCCTTTTCATTTTCTTGT	58.845	34.615	0.00	0.00	0.00	3.16
2658	3459	3.127721	GCTTCTGTTCCTTGCTGTATTCC	59.872	47.826	0.00	0.00	0.00	3.01
2665	3466	2.645838	TCTTGCTTCTGTTCCTTGCT	57.354	45.000	0.00	0.00	0.00	3.91
2669	3470	4.577875	CATCTCTTCTTGCTTCTGTTCCT	58.422	43.478	0.00	0.00	0.00	3.36
2670	3471	3.126686	GCATCTCTTCTTGCTTCTGTTCC	59.873	47.826	0.00	0.00	35.95	3.62
2671	3472	3.181522	CGCATCTCTTCTTGCTTCTGTTC	60.182	47.826	0.00	0.00	36.71	3.18
2672	3473	2.740981	CGCATCTCTTCTTGCTTCTGTT	59.259	45.455	0.00	0.00	36.71	3.16
2673	3474	2.028658	TCGCATCTCTTCTTGCTTCTGT	60.029	45.455	0.00	0.00	36.71	3.41
2674	3475	2.604011	CTCGCATCTCTTCTTGCTTCTG	59.396	50.000	0.00	0.00	36.71	3.02
2675	3476	2.233431	ACTCGCATCTCTTCTTGCTTCT	59.767	45.455	0.00	0.00	36.71	2.85
2676	3477	2.348059	CACTCGCATCTCTTCTTGCTTC	59.652	50.000	0.00	0.00	36.71	3.86
2677	3478	2.344950	CACTCGCATCTCTTCTTGCTT	58.655	47.619	0.00	0.00	36.71	3.91
2678	3479	1.405256	CCACTCGCATCTCTTCTTGCT	60.405	52.381	0.00	0.00	36.71	3.91
2679	3480	1.005340	CCACTCGCATCTCTTCTTGC	58.995	55.000	0.00	0.00	35.50	4.01
2680	3481	1.005340	GCCACTCGCATCTCTTCTTG	58.995	55.000	0.00	0.00	37.47	3.02
2681	3482	0.610174	TGCCACTCGCATCTCTTCTT	59.390	50.000	0.00	0.00	44.64	2.52
2682	3483	2.280835	TGCCACTCGCATCTCTTCT	58.719	52.632	0.00	0.00	44.64	2.85
2683	3484	4.919653	TGCCACTCGCATCTCTTC	57.080	55.556	0.00	0.00	44.64	2.87
2691	3492	3.554692	CCGACGATTGCCACTCGC	61.555	66.667	4.21	0.00	39.71	5.03
2692	3493	2.126071	ACCGACGATTGCCACTCG	60.126	61.111	2.65	2.65	41.77	4.18
2746	3549	3.865745	CACTTGTGTATGGATCTCGTTCC	59.134	47.826	0.00	0.00	36.24	3.62
2748	3551	3.055819	AGCACTTGTGTATGGATCTCGTT	60.056	43.478	2.61	0.00	0.00	3.85
2782	3585	2.895372	GAATGGGGTACGCTGCCG	60.895	66.667	10.04	0.00	43.80	5.69
2783	3586	2.516225	GGAATGGGGTACGCTGCC	60.516	66.667	10.04	2.98	43.80	4.85
2784	3587	1.523938	GAGGAATGGGGTACGCTGC	60.524	63.158	10.04	0.00	43.80	5.25
2785	3588	1.146263	GGAGGAATGGGGTACGCTG	59.854	63.158	10.04	0.00	43.80	5.18
2786	3589	2.432300	CGGAGGAATGGGGTACGCT	61.432	63.158	10.04	0.00	43.80	5.07
2787	3590	2.108362	CGGAGGAATGGGGTACGC	59.892	66.667	0.29	0.29	43.69	4.42
2801	3604	1.003839	GTGGATGTGACTTGCCGGA	60.004	57.895	5.05	0.00	0.00	5.14

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.