AutoCloner

Multiple sequence alignment - TraesCS2B01G149700

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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	TraesCS2B01G149700	chr2B	100.000	3416	0	0	1	3416	116309638	116313053	0.000000e+00	6309.0
1	TraesCS2B01G149700	chr2B	81.780	236	36	6	1756	1988	116391171	116391402	1.250000e-44	191.0
2	TraesCS2B01G149700	chr2A	93.640	2044	99	10	579	2609	75345704	75347729	0.000000e+00	3025.0
3	TraesCS2B01G149700	chr2A	90.058	513	47	1	2904	3416	71439795	71439287	0.000000e+00	662.0
4	TraesCS2B01G149700	chr2A	83.406	687	82	9	1498	2184	75351071	75351725	2.910000e-170	608.0
5	TraesCS2B01G149700	chr2A	89.700	466	47	1	1001	1465	75350604	75351069	8.160000e-166	593.0
6	TraesCS2B01G149700	chr2A	86.824	425	56	0	1001	1425	75556568	75556992	3.080000e-130	475.0
7	TraesCS2B01G149700	chr2A	91.288	264	22	1	2643	2906	554507067	554507329	3.240000e-95	359.0
8	TraesCS2B01G149700	chr2A	90.152	264	25	1	2643	2906	702954072	702954334	3.260000e-90	342.0
9	TraesCS2B01G149700	chr2D	92.513	1950	98	23	579	2492	75647657	75645720	0.000000e+00	2748.0
10	TraesCS2B01G149700	chr2D	84.141	227	33	3	1771	1996	75561853	75561629	2.060000e-52	217.0
11	TraesCS2B01G149700	chr2D	100.000	29	0	0	579	607	75649667	75649639	2.000000e-03	54.7
12	TraesCS2B01G149700	chr3D	94.932	513	26	0	2904	3416	433509292	433509804	0.000000e+00	804.0
13	TraesCS2B01G149700	chr3D	94.697	264	12	2	2643	2906	433508981	433509242	3.170000e-110	409.0
14	TraesCS2B01G149700	chr7B	93.177	513	35	0	2904	3416	580876798	580876286	0.000000e+00	754.0
15	TraesCS2B01G149700	chr7B	89.573	585	50	9	1	578	679575025	679574445	0.000000e+00	732.0
16	TraesCS2B01G149700	chr7B	88.514	592	56	8	1	582	678278254	678278843	0.000000e+00	706.0
17	TraesCS2B01G149700	chr7B	95.455	264	10	2	2643	2906	580877109	580876848	1.470000e-113	420.0
18	TraesCS2B01G149700	chr4A	90.119	587	48	6	1	578	662336499	662337084	0.000000e+00	754.0
19	TraesCS2B01G149700	chr4A	89.773	264	26	1	2643	2906	67263307	67263045	1.520000e-88	337.0
20	TraesCS2B01G149700	chr6B	92.788	513	36	1	2904	3416	159147491	159148002	0.000000e+00	741.0
21	TraesCS2B01G149700	chr6B	88.776	588	55	7	1	578	54405056	54404470	0.000000e+00	710.0
22	TraesCS2B01G149700	chr6B	95.455	264	11	1	2643	2906	159147179	159147441	1.470000e-113	420.0
23	TraesCS2B01G149700	chr1B	92.203	513	40	0	2904	3416	321687867	321688379	0.000000e+00	726.0
24	TraesCS2B01G149700	chr1B	92.161	472	37	0	2945	3416	539643139	539643610	0.000000e+00	667.0
25	TraesCS2B01G149700	chr1B	95.076	264	12	1	2643	2906	114678773	114678511	6.820000e-112	414.0
26	TraesCS2B01G149700	chr1B	94.318	264	14	1	2643	2906	321687555	321687817	1.480000e-108	403.0
27	TraesCS2B01G149700	chr3B	89.041	584	57	4	1	578	462052963	462053545	0.000000e+00	717.0
28	TraesCS2B01G149700	chr3B	88.946	588	54	7	1	579	39665454	39666039	0.000000e+00	715.0
29	TraesCS2B01G149700	chr3B	88.644	590	55	6	1	579	510283157	510282569	0.000000e+00	708.0
30	TraesCS2B01G149700	chr3B	88.605	588	57	6	1	579	68378900	68378314	0.000000e+00	706.0
31	TraesCS2B01G149700	chr5B	88.908	586	56	8	1	579	698010893	698011476	0.000000e+00	713.0
32	TraesCS2B01G149700	chr5A	91.813	513	41	1	2904	3416	572032198	572031687	0.000000e+00	713.0
33	TraesCS2B01G149700	chrUn	91.423	513	44	0	2904	3416	42178438	42177926	0.000000e+00	704.0
34	TraesCS2B01G149700	chrUn	94.340	265	14	1	2643	2907	42178750	42178487	4.100000e-109	405.0
35	TraesCS2B01G149700	chr4B	93.737	463	29	0	2954	3416	407744418	407744880	0.000000e+00	695.0

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	TraesCS2B01G149700	chr2B	116309638	116313053	3415	False	6309.000000	6309	100.000000	1	3416	1	chr2B.!!$F1	3415
1	TraesCS2B01G149700	chr2A	75345704	75351725	6021	False	1408.666667	3025	88.915333	579	2609	3	chr2A.!!$F4	2030
2	TraesCS2B01G149700	chr2A	71439287	71439795	508	True	662.000000	662	90.058000	2904	3416	1	chr2A.!!$R1	512
3	TraesCS2B01G149700	chr2D	75645720	75649667	3947	True	1401.350000	2748	96.256500	579	2492	2	chr2D.!!$R2	1913
4	TraesCS2B01G149700	chr3D	433508981	433509804	823	False	606.500000	804	94.814500	2643	3416	2	chr3D.!!$F1	773
5	TraesCS2B01G149700	chr7B	679574445	679575025	580	True	732.000000	732	89.573000	1	578	1	chr7B.!!$R1	577
6	TraesCS2B01G149700	chr7B	678278254	678278843	589	False	706.000000	706	88.514000	1	582	1	chr7B.!!$F1	581
7	TraesCS2B01G149700	chr7B	580876286	580877109	823	True	587.000000	754	94.316000	2643	3416	2	chr7B.!!$R2	773
8	TraesCS2B01G149700	chr4A	662336499	662337084	585	False	754.000000	754	90.119000	1	578	1	chr4A.!!$F1	577
9	TraesCS2B01G149700	chr6B	54404470	54405056	586	True	710.000000	710	88.776000	1	578	1	chr6B.!!$R1	577
10	TraesCS2B01G149700	chr6B	159147179	159148002	823	False	580.500000	741	94.121500	2643	3416	2	chr6B.!!$F1	773
11	TraesCS2B01G149700	chr1B	321687555	321688379	824	False	564.500000	726	93.260500	2643	3416	2	chr1B.!!$F2	773
12	TraesCS2B01G149700	chr3B	462052963	462053545	582	False	717.000000	717	89.041000	1	578	1	chr3B.!!$F2	577
13	TraesCS2B01G149700	chr3B	39665454	39666039	585	False	715.000000	715	88.946000	1	579	1	chr3B.!!$F1	578
14	TraesCS2B01G149700	chr3B	510282569	510283157	588	True	708.000000	708	88.644000	1	579	1	chr3B.!!$R2	578
15	TraesCS2B01G149700	chr3B	68378314	68378900	586	True	706.000000	706	88.605000	1	579	1	chr3B.!!$R1	578
16	TraesCS2B01G149700	chr5B	698010893	698011476	583	False	713.000000	713	88.908000	1	579	1	chr5B.!!$F1	578
17	TraesCS2B01G149700	chr5A	572031687	572032198	511	True	713.000000	713	91.813000	2904	3416	1	chr5A.!!$R1	512
18	TraesCS2B01G149700	chrUn	42177926	42178750	824	True	554.500000	704	92.881500	2643	3416	2	chrUn.!!$R1	773

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
839	2873	0.250858	TGTGCCCTGATTGACAGTGG	60.251	55.0	0.0	0.0	44.4	4.0	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2432	4497	0.034756	ATGTTGTGTACGCAGGAGCA	59.965	50.0	9.41	8.1	42.27	4.26	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
239	251	1.493854	ATAAACCGGTGTGAGCCCCA	61.494	55.000	8.52	0.00	0.00	4.96
275	287	0.741221	GGACTAAACTCTGGCCGCAG	60.741	60.000	0.00	0.00	0.00	5.18
397	409	0.698238	AGGAGCAAGGCACATTGGTA	59.302	50.000	0.00	0.00	40.78	3.25
398	410	1.285962	AGGAGCAAGGCACATTGGTAT	59.714	47.619	0.00	0.00	40.78	2.73
401	413	1.065491	AGCAAGGCACATTGGTATCGA	60.065	47.619	0.00	0.00	39.03	3.59
411	423	3.071023	ACATTGGTATCGATTCGTCCCAT	59.929	43.478	1.71	2.97	0.00	4.00
426	438	2.183409	CCATCAACCGGGAGCAAAG	58.817	57.895	6.32	0.00	0.00	2.77
512	525	2.565925	AATGCCCCCATTGGTCCCA	61.566	57.895	1.20	0.00	40.09	4.37
513	526	2.117248	AATGCCCCCATTGGTCCCAA	62.117	55.000	0.39	0.39	40.09	4.12
516	529	0.913934	GCCCCCATTGGTCCCAATTT	60.914	55.000	8.84	0.00	43.32	1.82
537	550	9.116067	CAATTTTAGATTGAACCGGGACTAATA	57.884	33.333	6.32	2.45	0.00	0.98
618	2648	5.108385	ACTTGCATTAGAAAACCAGAACG	57.892	39.130	0.00	0.00	0.00	3.95
686	2719	6.607004	ACGTATATAGTACCCCTACTACGT	57.393	41.667	0.00	0.00	42.77	3.57
689	2722	8.759782	ACGTATATAGTACCCCTACTACGTAAT	58.240	37.037	13.09	0.00	44.13	1.89
697	2730	6.661304	ACCCCTACTACGTAATGGAAATAG	57.339	41.667	0.00	0.00	0.00	1.73
701	2734	8.465201	CCCCTACTACGTAATGGAAATAGTATC	58.535	40.741	0.00	0.00	30.16	2.24
715	2748	6.481644	GGAAATAGTATCCTGAAACTCAGCTG	59.518	42.308	7.63	7.63	42.98	4.24
766	2800	0.446222	CCACGAAAATACCCTGTGCG	59.554	55.000	0.00	0.00	0.00	5.34
798	2832	0.946221	GAGCATGGGTTAGATCGCCG	60.946	60.000	0.00	0.00	0.00	6.46
839	2873	0.250858	TGTGCCCTGATTGACAGTGG	60.251	55.000	0.00	0.00	44.40	4.00
840	2874	0.250901	GTGCCCTGATTGACAGTGGT	60.251	55.000	0.00	0.00	44.40	4.16
841	2875	1.003118	GTGCCCTGATTGACAGTGGTA	59.997	52.381	0.00	0.00	44.40	3.25
842	2876	1.702401	TGCCCTGATTGACAGTGGTAA	59.298	47.619	0.00	0.00	44.40	2.85
950	2986	3.403038	GCGCCTGCCTATATAATATGGG	58.597	50.000	0.00	0.00	33.98	4.00
952	2988	4.263068	GCGCCTGCCTATATAATATGGGAT	60.263	45.833	0.00	0.00	33.98	3.85
963	2999	1.660167	ATATGGGATCATGCATCGCG	58.340	50.000	0.00	0.00	45.57	5.87
996	3058	3.551659	GCTCAAGCAAGTTTCTTTCCCAG	60.552	47.826	0.00	0.00	41.59	4.45
1020	3082	4.184439	TCTGTGGCACGGACACTA	57.816	55.556	24.78	2.63	42.96	2.74
1196	3258	2.046314	CATTGACCCGGCGAAGGT	60.046	61.111	9.30	8.30	41.50	3.50
1197	3259	2.046314	ATTGACCCGGCGAAGGTG	60.046	61.111	12.62	0.00	37.88	4.00
1386	3448	3.107661	CCGGTGCCGTGTTACGAC	61.108	66.667	9.90	0.00	46.05	4.34
1437	3499	2.332514	GTTGTCGTCGACCGTCCA	59.667	61.111	22.05	0.39	37.94	4.02
1706	3768	1.304217	TGGTCTCCTCCTCGGACAC	60.304	63.158	0.00	0.00	36.69	3.67
1722	3784	2.031163	ACCTTCTCGCAGCACACC	59.969	61.111	0.00	0.00	0.00	4.16
1941	4003	2.910994	CCGAGGGGCTACTACGGG	60.911	72.222	0.00	0.00	39.92	5.28
2140	4202	1.001268	CGTACCTCATCTCGGACATGG	60.001	57.143	0.00	0.00	0.00	3.66
2143	4205	1.689243	CCTCATCTCGGACATGGCCA	61.689	60.000	20.22	8.56	0.00	5.36
2145	4207	0.617935	TCATCTCGGACATGGCCAAA	59.382	50.000	20.22	3.58	0.00	3.28
2180	4242	2.036572	GGATTTCGGGTGGGGCAA	59.963	61.111	0.00	0.00	0.00	4.52
2227	4289	1.176527	CATTCTGGCCACGTTCCATT	58.823	50.000	0.00	0.00	32.37	3.16
2235	4297	0.037590	CCACGTTCCATTTGGAGGGA	59.962	55.000	0.00	0.00	46.36	4.20
2244	4306	2.554344	CCATTTGGAGGGAAGGAACGAA	60.554	50.000	0.00	0.00	37.39	3.85
2299	4361	4.680237	CGGTGCAGGCGTTGGAGA	62.680	66.667	0.00	0.00	0.00	3.71
2301	4363	2.343758	GTGCAGGCGTTGGAGAGA	59.656	61.111	0.00	0.00	0.00	3.10
2318	4380	1.273886	GAGACTGAAGGTGGAGGTGAC	59.726	57.143	0.00	0.00	0.00	3.67
2328	4390	2.539081	GGAGGTGACCAAGGGGCTT	61.539	63.158	3.63	0.00	37.90	4.35
2331	4396	1.001269	GGTGACCAAGGGGCTTACC	60.001	63.158	0.00	0.00	37.90	2.85
2336	4401	1.376812	CCAAGGGGCTTACCGTCAC	60.377	63.158	0.00	0.00	41.60	3.67
2338	4403	1.844289	AAGGGGCTTACCGTCACCA	60.844	57.895	0.00	0.00	41.60	4.17
2380	4445	0.880278	TGCGGACAAGAGCAAGTCAC	60.880	55.000	0.00	0.00	40.78	3.67
2382	4447	1.284982	CGGACAAGAGCAAGTCACCG	61.285	60.000	0.00	0.00	36.50	4.94
2432	4497	1.672854	TAGAAGCGGTGCGGTGCTAT	61.673	55.000	0.00	0.00	41.76	2.97
2457	4523	3.249799	TCCTGCGTACACAACATCAAAAG	59.750	43.478	0.00	0.00	0.00	2.27
2497	4563	2.613595	CTGTTGTGCTTGTGCTAGACAA	59.386	45.455	0.00	0.76	42.55	3.18
2499	4565	1.217001	TGTGCTTGTGCTAGACAACG	58.783	50.000	0.00	0.00	39.78	4.10
2527	4593	3.491267	GTGGCGTTAGTAATGCATCTCTC	59.509	47.826	24.71	9.81	45.20	3.20
2531	4597	3.180584	CGTTAGTAATGCATCTCTCGTGC	59.819	47.826	0.00	0.00	42.81	5.34
2539	4605	1.267235	GCATCTCTCGTGCATCGTTTG	60.267	52.381	8.22	2.34	42.08	2.93
2584	4651	9.132521	CTGGTTTTCTTTGATAATGCTTGTAAG	57.867	33.333	0.00	0.00	0.00	2.34
2585	4652	8.855110	TGGTTTTCTTTGATAATGCTTGTAAGA	58.145	29.630	0.00	0.00	0.00	2.10
2588	4655	8.635765	TTTCTTTGATAATGCTTGTAAGAGGT	57.364	30.769	0.00	0.00	0.00	3.85
2592	4659	9.346725	CTTTGATAATGCTTGTAAGAGGTTTTC	57.653	33.333	0.00	0.00	0.00	2.29
2605	4672	4.195225	GAGGTTTTCTTCCTCGTCATCT	57.805	45.455	0.00	0.00	41.36	2.90
2606	4673	4.570930	GAGGTTTTCTTCCTCGTCATCTT	58.429	43.478	0.00	0.00	41.36	2.40
2607	4674	4.319177	AGGTTTTCTTCCTCGTCATCTTG	58.681	43.478	0.00	0.00	0.00	3.02
2608	4675	4.065789	GGTTTTCTTCCTCGTCATCTTGT	58.934	43.478	0.00	0.00	0.00	3.16
2609	4676	4.515567	GGTTTTCTTCCTCGTCATCTTGTT	59.484	41.667	0.00	0.00	0.00	2.83
2610	4677	5.334182	GGTTTTCTTCCTCGTCATCTTGTTC	60.334	44.000	0.00	0.00	0.00	3.18
2611	4678	3.217599	TCTTCCTCGTCATCTTGTTCG	57.782	47.619	0.00	0.00	0.00	3.95
2632	4699	7.760794	TGTTCGGTCGTGTGTTTTTATCTATAT	59.239	33.333	0.00	0.00	0.00	0.86
2633	4700	9.236691	GTTCGGTCGTGTGTTTTTATCTATATA	57.763	33.333	0.00	0.00	0.00	0.86
2635	4702	9.454585	TCGGTCGTGTGTTTTTATCTATATAAG	57.545	33.333	0.00	0.00	0.00	1.73
2636	4703	9.454585	CGGTCGTGTGTTTTTATCTATATAAGA	57.545	33.333	0.00	0.00	39.02	2.10
2665	5913	7.243604	AGTGGAAAATGCAAGATAAATTGGA	57.756	32.000	0.00	0.00	34.85	3.53
2815	6100	2.807676	GGAACCCCTTGTGATGACAAT	58.192	47.619	0.00	0.00	41.33	2.71
2865	6150	1.337167	GGTTGAAGTTGGCAATGGCTC	60.337	52.381	8.59	1.48	40.87	4.70
2989	6326	0.170116	CACTGTCGAGCACCTCTCTC	59.830	60.000	0.00	0.00	39.70	3.20
3042	6379	1.005037	GCACCTCGACATGGACACA	60.005	57.895	0.00	0.00	0.00	3.72
3068	6405	4.499183	GACACTATCACCTGGAAGTTCAG	58.501	47.826	0.00	0.65	34.70	3.02
3186	6722	4.021981	GTGCCTCCTAAATGCAAGTTCTTT	60.022	41.667	0.00	0.00	36.65	2.52
3203	6739	4.255833	TCTTTGCTTGGTTGGCAATTAG	57.744	40.909	1.92	2.55	46.81	1.73
3228	6764	1.145945	AGGATCTGGACAGCGGATAGA	59.854	52.381	0.00	0.00	0.00	1.98
3237	6773	2.541762	GACAGCGGATAGACTTCAATGC	59.458	50.000	0.00	0.00	0.00	3.56
3255	6791	3.365265	CGAGGGTGGCCAAACTGC	61.365	66.667	7.24	0.00	0.00	4.40
3259	7652	2.430610	GGGTGGCCAAACTGCAACA	61.431	57.895	7.24	0.00	36.88	3.33
3388	8744	4.847198	TGATGTGCATTCTAGTGATTGGT	58.153	39.130	0.00	0.00	0.00	3.67
3394	8750	4.002982	GCATTCTAGTGATTGGTGTGACA	58.997	43.478	0.00	0.00	0.00	3.58

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
77	88	9.494271	TGAATTTTCTCTATAAGCGCATCTATT	57.506	29.630	11.47	0.00	0.00	1.73
184	196	1.410517	TGCCTTATTGAGCTCCTCTCG	59.589	52.381	12.15	0.00	44.86	4.04
239	251	2.046314	CCACCTCGCCAACCGAAT	60.046	61.111	0.00	0.00	46.81	3.34
275	287	2.067013	GACTAAAGTGTTGGTCCTCGC	58.933	52.381	0.00	0.00	38.85	5.03
384	396	2.872245	CGAATCGATACCAATGTGCCTT	59.128	45.455	0.00	0.00	0.00	4.35
397	409	1.538204	CGGTTGATGGGACGAATCGAT	60.538	52.381	10.55	0.00	0.00	3.59
398	410	0.179121	CGGTTGATGGGACGAATCGA	60.179	55.000	10.55	0.00	0.00	3.59
401	413	4.954933	CCGGTTGATGGGACGAAT	57.045	55.556	0.00	0.00	0.00	3.34
411	423	2.406002	GACCCTTTGCTCCCGGTTGA	62.406	60.000	0.00	0.00	0.00	3.18
426	438	4.078516	CCCGGTTCGTCTGGACCC	62.079	72.222	0.00	0.00	45.09	4.46
512	525	9.338622	CTATTAGTCCCGGTTCAATCTAAAATT	57.661	33.333	0.00	0.00	0.00	1.82
513	526	7.937394	CCTATTAGTCCCGGTTCAATCTAAAAT	59.063	37.037	0.00	0.00	0.00	1.82
516	529	5.221581	GCCTATTAGTCCCGGTTCAATCTAA	60.222	44.000	0.00	0.63	0.00	2.10
618	2648	5.582665	GGATTCTCCGAGCCATGTAAATATC	59.417	44.000	0.00	0.00	0.00	1.63
665	2698	9.331282	CCATTACGTAGTAGGGGTACTATATAC	57.669	40.741	0.00	0.00	46.93	1.47
697	2730	3.182967	CGACAGCTGAGTTTCAGGATAC	58.817	50.000	23.35	0.00	44.43	2.24
701	2734	0.318441	TCCGACAGCTGAGTTTCAGG	59.682	55.000	23.35	12.61	44.43	3.86
715	2748	3.707793	ACGAATCTAGCATCTTTCCGAC	58.292	45.455	0.00	0.00	0.00	4.79
798	2832	3.890147	AGGCTGTATGTGTAGCTAGGTAC	59.110	47.826	22.42	22.42	39.80	3.34
841	2875	8.793592	GGTAGTTCTTCACAGAAAATGGTTATT	58.206	33.333	0.00	0.00	40.90	1.40
842	2876	7.393515	GGGTAGTTCTTCACAGAAAATGGTTAT	59.606	37.037	0.00	0.00	40.90	1.89
950	2986	0.657312	TGGTTTCGCGATGCATGATC	59.343	50.000	10.88	0.00	0.00	2.92
952	2988	1.093972	ATTGGTTTCGCGATGCATGA	58.906	45.000	10.88	0.00	0.00	3.07
963	2999	2.704725	TGCTTGAGCGAATTGGTTTC	57.295	45.000	0.00	0.00	45.83	2.78
996	3058	1.069227	GTCCGTGCCACAGACATTTTC	60.069	52.381	6.33	0.00	0.00	2.29
1020	3082	2.337532	CGGACGGACAAGGTCGTT	59.662	61.111	0.00	0.00	39.88	3.85
1196	3258	0.029433	CGAGATCGCCGACTTGATCA	59.971	55.000	4.85	0.00	42.72	2.92
1197	3259	0.661780	CCGAGATCGCCGACTTGATC	60.662	60.000	11.26	0.00	41.02	2.92
1329	3391	0.323542	AGTCTTCCATCCGGACGTCT	60.324	55.000	16.46	0.00	42.67	4.18
1706	3768	1.294659	GAAGGTGTGCTGCGAGAAGG	61.295	60.000	0.00	0.00	0.00	3.46
1941	4003	2.091603	GCGAACGCGAACGAGTTC	59.908	61.111	25.13	25.13	46.43	3.01
2227	4289	0.036306	GCTTCGTTCCTTCCCTCCAA	59.964	55.000	0.00	0.00	0.00	3.53
2235	4297	1.004918	CTCACCGGCTTCGTTCCTT	60.005	57.895	0.00	0.00	0.00	3.36
2288	4350	0.605589	CTTCAGTCTCTCCAACGCCT	59.394	55.000	0.00	0.00	0.00	5.52
2293	4355	2.251818	CTCCACCTTCAGTCTCTCCAA	58.748	52.381	0.00	0.00	0.00	3.53
2299	4361	1.343069	GTCACCTCCACCTTCAGTCT	58.657	55.000	0.00	0.00	0.00	3.24
2301	4363	0.399949	TGGTCACCTCCACCTTCAGT	60.400	55.000	0.00	0.00	34.66	3.41
2318	4380	1.376812	GTGACGGTAAGCCCCTTGG	60.377	63.158	0.00	0.00	0.00	3.61
2338	4403	0.674534	GGTTCAGTGACAGTCCGACT	59.325	55.000	0.00	0.00	0.00	4.18
2380	4445	1.959226	CGTGACCAGGAACCAACGG	60.959	63.158	0.00	0.00	0.00	4.44
2382	4447	1.227853	AGCGTGACCAGGAACCAAC	60.228	57.895	0.00	0.00	0.00	3.77
2424	4489	2.349969	TACGCAGGAGCATAGCACCG	62.350	60.000	0.00	0.00	43.81	4.94
2432	4497	0.034756	ATGTTGTGTACGCAGGAGCA	59.965	50.000	9.41	8.10	42.27	4.26
2457	4523	1.896660	TGGCCGAACTTGGTGCTTC	60.897	57.895	0.00	0.00	0.00	3.86
2499	4565	2.190981	CATTACTAACGCCACGACCTC	58.809	52.381	0.00	0.00	0.00	3.85
2531	4597	0.726827	ATACCGCAGTGCAAACGATG	59.273	50.000	16.83	0.00	0.00	3.84
2534	4600	1.663643	ACATATACCGCAGTGCAAACG	59.336	47.619	16.83	1.33	0.00	3.60
2539	4605	2.285220	CAGACAACATATACCGCAGTGC	59.715	50.000	4.58	4.58	0.00	4.40
2543	4609	3.620427	AACCAGACAACATATACCGCA	57.380	42.857	0.00	0.00	0.00	5.69
2576	4643	4.152580	CGAGGAAGAAAACCTCTTACAAGC	59.847	45.833	11.35	0.00	46.39	4.01
2585	4652	4.202367	ACAAGATGACGAGGAAGAAAACCT	60.202	41.667	0.00	0.00	40.80	3.50
2588	4655	4.447724	CGAACAAGATGACGAGGAAGAAAA	59.552	41.667	0.00	0.00	0.00	2.29
2592	4659	2.263077	CCGAACAAGATGACGAGGAAG	58.737	52.381	0.00	0.00	0.00	3.46
2603	4670	2.012937	AAACACACGACCGAACAAGA	57.987	45.000	0.00	0.00	0.00	3.02
2604	4671	2.817538	AAAACACACGACCGAACAAG	57.182	45.000	0.00	0.00	0.00	3.16
2605	4672	4.571580	AGATAAAAACACACGACCGAACAA	59.428	37.500	0.00	0.00	0.00	2.83
2606	4673	4.121317	AGATAAAAACACACGACCGAACA	58.879	39.130	0.00	0.00	0.00	3.18
2607	4674	4.720530	AGATAAAAACACACGACCGAAC	57.279	40.909	0.00	0.00	0.00	3.95
2608	4675	9.800433	TTATATAGATAAAAACACACGACCGAA	57.200	29.630	0.00	0.00	0.00	4.30
2609	4676	9.454585	CTTATATAGATAAAAACACACGACCGA	57.545	33.333	0.00	0.00	0.00	4.69
2610	4677	9.454585	TCTTATATAGATAAAAACACACGACCG	57.545	33.333	0.00	0.00	0.00	4.79
2632	4699	7.581213	TCTTGCATTTTCCACTTTTCTCTTA	57.419	32.000	0.00	0.00	0.00	2.10
2633	4700	6.469782	TCTTGCATTTTCCACTTTTCTCTT	57.530	33.333	0.00	0.00	0.00	2.85
2635	4702	8.816640	TTTATCTTGCATTTTCCACTTTTCTC	57.183	30.769	0.00	0.00	0.00	2.87
2636	4703	9.783081	AATTTATCTTGCATTTTCCACTTTTCT	57.217	25.926	0.00	0.00	0.00	2.52
2637	4704	9.815936	CAATTTATCTTGCATTTTCCACTTTTC	57.184	29.630	0.00	0.00	0.00	2.29
2639	4706	8.156165	TCCAATTTATCTTGCATTTTCCACTTT	58.844	29.630	0.00	0.00	0.00	2.66
2640	4707	7.678837	TCCAATTTATCTTGCATTTTCCACTT	58.321	30.769	0.00	0.00	0.00	3.16
2665	5913	6.553524	CAGTTTGGAATTTGCACATTTGTTT	58.446	32.000	0.00	0.00	0.00	2.83
2671	5919	3.472283	TGCAGTTTGGAATTTGCACAT	57.528	38.095	0.00	0.00	41.23	3.21
2679	5927	1.188863	GCCTCCATGCAGTTTGGAAT	58.811	50.000	8.80	0.00	42.56	3.01
2815	6100	4.484236	CTGCAGCAAAAATATTTCGGTCA	58.516	39.130	0.00	2.72	0.00	4.02
2989	6326	1.956477	CTCCCAAAGGGTGACAAACTG	59.044	52.381	1.36	0.00	44.74	3.16
3016	6353	0.397941	ATGTCGAGGTGCATATGGGG	59.602	55.000	4.56	0.00	0.00	4.96
3024	6361	1.005037	TGTGTCCATGTCGAGGTGC	60.005	57.895	0.00	0.00	0.00	5.01
3042	6379	0.040646	TCCAGGTGATAGTGTCGGGT	59.959	55.000	0.00	0.00	0.00	5.28
3068	6405	2.205074	CCGAGTAGTGTCCATCAATGC	58.795	52.381	0.00	0.00	0.00	3.56
3156	6493	2.501316	GCATTTAGGAGGCACCCAAATT	59.499	45.455	4.76	0.00	37.76	1.82
3186	6722	1.336131	TGCTAATTGCCAACCAAGCA	58.664	45.000	6.19	6.19	42.00	3.91
3203	6739	1.506493	CGCTGTCCAGATCCTATTGC	58.494	55.000	0.00	0.00	0.00	3.56
3228	6764	1.002134	CCACCCTCGGCATTGAAGT	60.002	57.895	0.00	0.00	0.00	3.01
3237	6773	2.672996	CAGTTTGGCCACCCTCGG	60.673	66.667	3.88	0.00	0.00	4.63
3255	6791	4.704540	TGCTTACATAGGGGACAAATGTTG	59.295	41.667	0.00	0.00	39.21	3.33
3259	7652	3.527665	ACCTGCTTACATAGGGGACAAAT	59.472	43.478	0.00	0.00	38.42	2.32
3388	8744	4.951254	TCTTTAATGGAAGTCGTGTCACA	58.049	39.130	3.42	0.00	0.00	3.58
3394	8750	4.618920	ACCACTCTTTAATGGAAGTCGT	57.381	40.909	0.00	0.00	39.46	4.34

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.