AutoCloner

Multiple sequence alignment - TraesCS5B01G042700

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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	TraesCS5B01G042700	chr5B	100.000	3356	0	0	1	3356	47570532	47567177	0.000000e+00	6198.0
1	TraesCS5B01G042700	chr5B	86.392	1433	122	36	1947	3342	48869528	48870924	0.000000e+00	1498.0
2	TraesCS5B01G042700	chr5B	95.642	849	13	6	5	831	551412084	551411238	0.000000e+00	1341.0
3	TraesCS5B01G042700	chr5B	93.984	881	7	13	4	839	37831815	37830936	0.000000e+00	1291.0
4	TraesCS5B01G042700	chr5B	82.682	895	124	17	1921	2798	47316686	47315806	0.000000e+00	765.0
5	TraesCS5B01G042700	chr5B	80.979	715	112	18	991	1684	47318024	47317313	2.280000e-151	545.0
6	TraesCS5B01G042700	chr5B	85.960	349	31	6	870	1218	48869177	48869507	1.150000e-94	357.0
7	TraesCS5B01G042700	chr5B	97.973	148	2	1	685	831	5871854	5872001	4.300000e-64	255.0
8	TraesCS5B01G042700	chr7B	99.278	831	5	1	1	830	625887658	625888488	0.000000e+00	1500.0
9	TraesCS5B01G042700	chr7B	96.158	859	9	10	4	839	650977551	650976694	0.000000e+00	1382.0
10	TraesCS5B01G042700	chr3A	98.441	834	8	3	4	834	552233870	552233039	0.000000e+00	1463.0
11	TraesCS5B01G042700	chr3A	97.847	836	12	4	1	832	16624748	16625581	0.000000e+00	1439.0
12	TraesCS5B01G042700	chr3A	87.448	239	6	5	628	843	689083488	689083251	1.550000e-63	254.0
13	TraesCS5B01G042700	chr5A	97.974	839	4	4	4	830	12875531	12874694	0.000000e+00	1443.0
14	TraesCS5B01G042700	chr5A	86.566	1057	91	26	1715	2744	37633664	37634696	0.000000e+00	1118.0
15	TraesCS5B01G042700	chr5A	90.969	753	59	5	937	1686	37632237	37632983	0.000000e+00	1005.0
16	TraesCS5B01G042700	chr5A	95.349	43	2	0	870	912	37632195	37632237	6.010000e-08	69.4
17	TraesCS5B01G042700	chr6B	97.749	844	6	3	1	832	707760462	707761304	0.000000e+00	1441.0
18	TraesCS5B01G042700	chr6B	98.246	627	6	4	218	843	127920631	127920009	0.000000e+00	1092.0
19	TraesCS5B01G042700	chr1B	97.663	813	7	3	32	833	419282530	419283341	0.000000e+00	1386.0
20	TraesCS5B01G042700	chr4B	97.775	809	4	4	36	832	603339438	603338632	0.000000e+00	1382.0
21	TraesCS5B01G042700	chr4B	96.377	828	6	5	29	833	472426267	472425441	0.000000e+00	1341.0
22	TraesCS5B01G042700	chr2B	96.131	853	8	4	1	830	278843300	278844150	0.000000e+00	1369.0
23	TraesCS5B01G042700	chr2B	88.235	238	3	7	628	841	63110966	63110730	9.240000e-66	261.0
24	TraesCS5B01G042700	chr2B	88.839	224	3	4	628	830	775410791	775411013	4.300000e-64	255.0
25	TraesCS5B01G042700	chr5D	84.337	1411	166	38	870	2269	46336473	46337839	0.000000e+00	1330.0
26	TraesCS5B01G042700	chr5D	89.133	911	69	13	1739	2639	46327981	46328871	0.000000e+00	1107.0
27	TraesCS5B01G042700	chr5D	90.990	788	57	7	870	1654	46326260	46327036	0.000000e+00	1050.0
28	TraesCS5B01G042700	chr5D	93.501	677	40	2	2672	3345	46329135	46329810	0.000000e+00	1003.0
29	TraesCS5B01G042700	chr5D	84.778	992	118	16	870	1836	46617444	46616461	0.000000e+00	965.0
30	TraesCS5B01G042700	chr5D	83.333	996	118	25	1921	2885	46334137	46335115	0.000000e+00	876.0
31	TraesCS5B01G042700	chr5D	87.612	783	55	16	2356	3117	46615435	46614674	0.000000e+00	870.0
32	TraesCS5B01G042700	chr5D	87.151	537	54	9	2359	2885	46342568	46343099	2.230000e-166	595.0
33	TraesCS5B01G042700	chr5D	81.913	481	57	18	2874	3343	46343194	46343655	2.440000e-101	379.0
34	TraesCS5B01G042700	chr5D	81.600	375	44	19	2981	3345	46614558	46614199	1.520000e-73	287.0
35	TraesCS5B01G042700	chr3B	87.601	621	41	19	1	609	28625295	28625891	0.000000e+00	688.0
36	TraesCS5B01G042700	chr3B	91.964	336	23	4	1	333	27502983	27503317	5.070000e-128	468.0
37	TraesCS5B01G042700	chr3B	88.889	225	3	4	628	831	6154875	6155098	1.190000e-64	257.0
38	TraesCS5B01G042700	chr2A	94.613	297	14	2	1	297	31556174	31556468	3.050000e-125	459.0

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	TraesCS5B01G042700	chr5B	47567177	47570532	3355	True	6198.000000	6198	100.000000	1	3356	1	chr5B.!!$R2	3355
1	TraesCS5B01G042700	chr5B	551411238	551412084	846	True	1341.000000	1341	95.642000	5	831	1	chr5B.!!$R3	826
2	TraesCS5B01G042700	chr5B	37830936	37831815	879	True	1291.000000	1291	93.984000	4	839	1	chr5B.!!$R1	835
3	TraesCS5B01G042700	chr5B	48869177	48870924	1747	False	927.500000	1498	86.176000	870	3342	2	chr5B.!!$F2	2472
4	TraesCS5B01G042700	chr5B	47315806	47318024	2218	True	655.000000	765	81.830500	991	2798	2	chr5B.!!$R4	1807
5	TraesCS5B01G042700	chr7B	625887658	625888488	830	False	1500.000000	1500	99.278000	1	830	1	chr7B.!!$F1	829
6	TraesCS5B01G042700	chr7B	650976694	650977551	857	True	1382.000000	1382	96.158000	4	839	1	chr7B.!!$R1	835
7	TraesCS5B01G042700	chr3A	552233039	552233870	831	True	1463.000000	1463	98.441000	4	834	1	chr3A.!!$R1	830
8	TraesCS5B01G042700	chr3A	16624748	16625581	833	False	1439.000000	1439	97.847000	1	832	1	chr3A.!!$F1	831
9	TraesCS5B01G042700	chr5A	12874694	12875531	837	True	1443.000000	1443	97.974000	4	830	1	chr5A.!!$R1	826
10	TraesCS5B01G042700	chr5A	37632195	37634696	2501	False	730.800000	1118	90.961333	870	2744	3	chr5A.!!$F1	1874
11	TraesCS5B01G042700	chr6B	707760462	707761304	842	False	1441.000000	1441	97.749000	1	832	1	chr6B.!!$F1	831
12	TraesCS5B01G042700	chr6B	127920009	127920631	622	True	1092.000000	1092	98.246000	218	843	1	chr6B.!!$R1	625
13	TraesCS5B01G042700	chr1B	419282530	419283341	811	False	1386.000000	1386	97.663000	32	833	1	chr1B.!!$F1	801
14	TraesCS5B01G042700	chr4B	603338632	603339438	806	True	1382.000000	1382	97.775000	36	832	1	chr4B.!!$R2	796
15	TraesCS5B01G042700	chr4B	472425441	472426267	826	True	1341.000000	1341	96.377000	29	833	1	chr4B.!!$R1	804
16	TraesCS5B01G042700	chr2B	278843300	278844150	850	False	1369.000000	1369	96.131000	1	830	1	chr2B.!!$F1	829
17	TraesCS5B01G042700	chr5D	46334137	46337839	3702	False	1103.000000	1330	83.835000	870	2885	2	chr5D.!!$F2	2015
18	TraesCS5B01G042700	chr5D	46326260	46329810	3550	False	1053.333333	1107	91.208000	870	3345	3	chr5D.!!$F1	2475
19	TraesCS5B01G042700	chr5D	46614199	46617444	3245	True	707.333333	965	84.663333	870	3345	3	chr5D.!!$R1	2475
20	TraesCS5B01G042700	chr5D	46342568	46343655	1087	False	487.000000	595	84.532000	2359	3343	2	chr5D.!!$F3	984
21	TraesCS5B01G042700	chr3B	28625295	28625891	596	False	688.000000	688	87.601000	1	609	1	chr3B.!!$F3	608

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
852	945	0.104304	AGTATAGTTGGCGCTTCCCG	59.896	55.0	7.64	40.75	5.14	F
853	946	0.179092	GTATAGTTGGCGCTTCCCGT	60.179	55.0	7.64	39.71	5.28	F
858	951	0.311477	GTTGGCGCTTCCCGTAAAAA	59.689	50.0	7.64	39.71	1.94	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1862	5064	0.034089	GGCCACCAAACTATCAGCCT	60.034	55.000	0.00	36.00	4.58	R
2100	5696	0.037697	TGCGTGTCTTAACATCGGCT	60.038	50.000	0.00	37.81	5.52	R
2484	6677	1.277273	CTGCAGATTGACAGTGGAGGA	59.723	52.381	8.42	0.00	3.71	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
842	935	9.661563	TTTTTCCACCAGTGTATAGTATAGTTG	57.338	33.333	0.00	0.00	0.00	3.16
845	938	5.220381	CACCAGTGTATAGTATAGTTGGCG	58.780	45.833	11.68	3.00	0.00	5.69
848	941	5.509163	CCAGTGTATAGTATAGTTGGCGCTT	60.509	44.000	7.64	0.00	0.00	4.68
849	942	5.629849	CAGTGTATAGTATAGTTGGCGCTTC	59.370	44.000	7.64	0.00	0.00	3.86
850	943	4.922103	GTGTATAGTATAGTTGGCGCTTCC	59.078	45.833	7.64	0.00	0.00	3.46
852	945	0.104304	AGTATAGTTGGCGCTTCCCG	59.896	55.000	7.64	0.00	40.75	5.14
853	946	0.179092	GTATAGTTGGCGCTTCCCGT	60.179	55.000	7.64	0.00	39.71	5.28
854	947	1.067516	GTATAGTTGGCGCTTCCCGTA	59.932	52.381	7.64	0.00	39.71	4.02
856	949	0.321021	TAGTTGGCGCTTCCCGTAAA	59.679	50.000	7.64	0.00	39.71	2.01
858	951	0.311477	GTTGGCGCTTCCCGTAAAAA	59.689	50.000	7.64	0.00	39.71	1.94
912	2380	0.805322	GCATGACTCTGTCTCTGCCG	60.805	60.000	0.00	0.00	36.60	5.69
915	2383	1.244697	TGACTCTGTCTCTGCCGGTC	61.245	60.000	1.90	0.00	33.15	4.79
916	2384	0.963355	GACTCTGTCTCTGCCGGTCT	60.963	60.000	1.90	0.00	0.00	3.85
917	2385	1.247419	ACTCTGTCTCTGCCGGTCTG	61.247	60.000	1.90	0.00	0.00	3.51
918	2386	2.125753	CTGTCTCTGCCGGTCTGC	60.126	66.667	1.90	0.00	0.00	4.26
919	2387	3.655810	CTGTCTCTGCCGGTCTGCC	62.656	68.421	1.90	0.00	0.00	4.85
920	2388	4.459089	GTCTCTGCCGGTCTGCCC	62.459	72.222	1.90	0.00	0.00	5.36
971	2470	6.644248	AAGTACCCCACTTTTTGTACAATC	57.356	37.500	9.56	0.00	45.54	2.67
974	2473	7.166167	AGTACCCCACTTTTTGTACAATCTAG	58.834	38.462	9.56	9.44	36.81	2.43
975	2474	5.948842	ACCCCACTTTTTGTACAATCTAGT	58.051	37.500	9.56	10.05	0.00	2.57
976	2475	7.081857	ACCCCACTTTTTGTACAATCTAGTA	57.918	36.000	9.56	0.00	0.00	1.82
979	2478	7.827236	CCCCACTTTTTGTACAATCTAGTATCA	59.173	37.037	9.56	0.00	0.00	2.15
1056	2559	4.124351	CTCGTTGTCGCCGGCCTA	62.124	66.667	23.46	6.42	36.96	3.93
1154	2657	1.153086	CAGCCCAGCTACCATGGAC	60.153	63.158	21.47	7.45	40.51	4.02
1187	2694	1.374252	GCGAAGTCGTCACACCCAT	60.374	57.895	2.25	0.00	42.22	4.00
1207	2714	1.835712	AACGGTCCCTCGGAACACT	60.836	57.895	0.00	0.00	39.88	3.55
1222	2729	0.475632	ACACTCCACCTTCATCCCCA	60.476	55.000	0.00	0.00	0.00	4.96
1297	2819	1.682849	CGGACCCCCAAACTCATCA	59.317	57.895	0.00	0.00	0.00	3.07
1413	2935	4.722700	ATGCAGTCCACCGCCCAC	62.723	66.667	0.00	0.00	0.00	4.61
1536	3058	7.151999	TGTTTATATCGTTGACATTGCCTTT	57.848	32.000	0.00	0.00	0.00	3.11
1543	3065	3.123050	GTTGACATTGCCTTTTGTGGAC	58.877	45.455	0.00	0.00	0.00	4.02
1608	3130	3.838565	TGACCTAGGGCTAGATGAAGAG	58.161	50.000	17.75	0.00	35.21	2.85
1646	3168	3.818210	ACCATTGCAAGACGTGTAATTCA	59.182	39.130	4.94	0.00	40.20	2.57
1666	4060	5.313520	TCAACGACCACTTGATTACGATA	57.686	39.130	0.00	0.00	0.00	2.92
1691	4085	5.077134	TGGGATGATGATTATAGCGACAG	57.923	43.478	0.00	0.00	0.00	3.51
1726	4742	2.412870	GTGATGGTGATGACGACAACA	58.587	47.619	0.00	0.00	39.31	3.33
1727	4743	2.413112	GTGATGGTGATGACGACAACAG	59.587	50.000	0.00	0.00	38.37	3.16
1751	4791	3.123157	AGAAGGCGATGATGATGAAGG	57.877	47.619	0.00	0.00	0.00	3.46
1793	4833	6.146760	AGGAAGAGGTAGATATTGATGTGGT	58.853	40.000	0.00	0.00	0.00	4.16
1798	4838	5.754782	AGGTAGATATTGATGTGGTTGCAA	58.245	37.500	0.00	0.00	0.00	4.08
1819	4859	3.492311	GATGAGGACGAGGGCGAGC	62.492	68.421	0.00	0.00	41.64	5.03
1837	4877	1.836802	AGCAGAAGATGGAGGAGGAAC	59.163	52.381	0.00	0.00	0.00	3.62
1848	5050	3.766691	GAGGAACAGGCCGCGGTA	61.767	66.667	28.70	0.00	0.00	4.02
1862	5064	2.683859	CGGTAGACGTGACAGCCGA	61.684	63.158	0.00	0.00	41.45	5.54
1880	5082	1.383523	GAGGCTGATAGTTTGGTGGC	58.616	55.000	0.00	0.00	0.00	5.01
1898	5230	2.117865	GGCCAATGATTTTCATGGGGA	58.882	47.619	11.90	0.00	46.08	4.81
1899	5231	2.103601	GGCCAATGATTTTCATGGGGAG	59.896	50.000	11.90	0.00	46.08	4.30
1982	5578	1.536766	ACATCATGGATTTATGCGCGG	59.463	47.619	8.83	0.00	0.00	6.46
2100	5696	3.680490	TCGCCAGGTTGATGTTTTCATA	58.320	40.909	0.00	0.00	41.05	2.15
2181	5890	3.009723	ACTATTCATCGGCCAACACTTG	58.990	45.455	2.24	0.00	0.00	3.16
2303	6012	0.389426	GCGAGGTTTTACGAGCCTGA	60.389	55.000	0.00	0.00	31.89	3.86
2424	6612	5.278604	TCGTTCATATACGACAGTGGATTG	58.721	41.667	0.00	0.00	44.82	2.67
2425	6613	4.444388	CGTTCATATACGACAGTGGATTGG	59.556	45.833	0.00	0.00	43.99	3.16
2426	6614	5.597806	GTTCATATACGACAGTGGATTGGA	58.402	41.667	0.00	0.00	0.00	3.53
2427	6615	6.223852	GTTCATATACGACAGTGGATTGGAT	58.776	40.000	0.00	0.00	0.00	3.41
2428	6616	6.419484	TCATATACGACAGTGGATTGGATT	57.581	37.500	0.00	0.00	0.00	3.01
2481	6674	7.224167	CGTTACTTTGGAAACTAGAGTTCAACT	59.776	37.037	0.00	0.00	37.25	3.16
2482	6675	6.927294	ACTTTGGAAACTAGAGTTCAACTG	57.073	37.500	0.00	0.00	37.25	3.16
2483	6676	6.415573	ACTTTGGAAACTAGAGTTCAACTGT	58.584	36.000	0.00	0.00	37.25	3.55
2484	6677	6.884836	ACTTTGGAAACTAGAGTTCAACTGTT	59.115	34.615	0.00	0.00	37.25	3.16
2485	6678	6.920569	TTGGAAACTAGAGTTCAACTGTTC	57.079	37.500	0.00	0.00	37.25	3.18
2644	6839	2.954318	GTCACATGGCTATTTGGAGCAT	59.046	45.455	0.00	0.00	44.76	3.79
2722	7151	5.863397	GCAATGTTCGAAGAAATCAAATGGA	59.137	36.000	0.00	0.00	45.90	3.41
2784	7220	2.863809	TGAGGCTTGGGTTCTTTCTTC	58.136	47.619	0.00	0.00	0.00	2.87
2831	7267	9.347934	TGTTGTTGTAATTTCTTTGTAACTGTG	57.652	29.630	0.00	0.00	0.00	3.66
2854	7290	4.261280	GCTAGTGGTGTAGCTTAGCTCTAC	60.261	50.000	11.09	10.98	41.99	2.59
2871	7307	9.998106	TTAGCTCTACAGTTTCTTCTTTGTAAT	57.002	29.630	0.00	0.00	0.00	1.89
2906	7450	2.095567	GCGAGCTTGCTTCAAAAGATCA	60.096	45.455	19.25	0.00	39.47	2.92
2959	7508	6.863126	GCATTGCTGTTAACTGATGTTTTAGT	59.137	34.615	15.89	0.00	37.59	2.24
2978	7527	4.213564	AGTTTCTTCCTACAGGCATGAG	57.786	45.455	4.84	0.00	34.44	2.90
2990	7539	4.207165	ACAGGCATGAGTTGTAAAGTGTT	58.793	39.130	4.84	0.00	0.00	3.32
3072	7623	8.870116	AGGGAAATTACTTAGTTGATGCTTTTT	58.130	29.630	0.00	0.00	0.00	1.94
3135	7972	0.111061	AGCCAGTTGCATCACCAAGA	59.889	50.000	0.00	0.00	44.83	3.02
3221	8059	0.984961	TGGGCTCCTCCTTGGATGAG	60.985	60.000	14.85	14.85	45.16	2.90
3247	8085	0.471617	AGCTGTCTCAGTGTTGCCTT	59.528	50.000	0.00	0.00	33.43	4.35
3345	8188	7.023575	CAGTAACAAATTATGAAGCCTCACAC	58.976	38.462	0.00	0.00	33.30	3.82
3346	8189	6.714810	AGTAACAAATTATGAAGCCTCACACA	59.285	34.615	0.00	0.00	33.30	3.72
3347	8190	5.376854	ACAAATTATGAAGCCTCACACAC	57.623	39.130	0.00	0.00	33.30	3.82
3348	8191	5.072741	ACAAATTATGAAGCCTCACACACT	58.927	37.500	0.00	0.00	33.30	3.55
3349	8192	6.237901	ACAAATTATGAAGCCTCACACACTA	58.762	36.000	0.00	0.00	33.30	2.74
3350	8193	6.149474	ACAAATTATGAAGCCTCACACACTAC	59.851	38.462	0.00	0.00	33.30	2.73
3351	8194	2.770164	ATGAAGCCTCACACACTACC	57.230	50.000	0.00	0.00	33.30	3.18
3352	8195	0.317160	TGAAGCCTCACACACTACCG	59.683	55.000	0.00	0.00	0.00	4.02
3353	8196	0.389948	GAAGCCTCACACACTACCGG	60.390	60.000	0.00	0.00	0.00	5.28
3354	8197	0.830444	AAGCCTCACACACTACCGGA	60.830	55.000	9.46	0.00	0.00	5.14
3355	8198	0.830444	AGCCTCACACACTACCGGAA	60.830	55.000	9.46	0.00	0.00	4.30

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
213	218	5.750067	CAGTTTGACCAGATTTGACCAAAAG	59.250	40.000	0.00	0.00	33.56	2.27
834	927	0.179092	ACGGGAAGCGCCAACTATAC	60.179	55.000	2.29	0.00	38.95	1.47
839	932	0.311477	TTTTTACGGGAAGCGCCAAC	59.689	50.000	2.29	0.00	38.95	3.77
858	951	3.366985	GCCAAGCGCCAACTATACTTTTT	60.367	43.478	2.29	0.00	0.00	1.94
859	952	2.163613	GCCAAGCGCCAACTATACTTTT	59.836	45.455	2.29	0.00	0.00	2.27
860	953	1.743394	GCCAAGCGCCAACTATACTTT	59.257	47.619	2.29	0.00	0.00	2.66
861	954	1.379527	GCCAAGCGCCAACTATACTT	58.620	50.000	2.29	0.00	0.00	2.24
862	955	3.080647	GCCAAGCGCCAACTATACT	57.919	52.632	2.29	0.00	0.00	2.12
921	2389	1.453148	GTCTTGCACCGTACGTACAAC	59.547	52.381	24.50	11.12	0.00	3.32
922	2390	1.337703	AGTCTTGCACCGTACGTACAA	59.662	47.619	24.50	13.51	0.00	2.41
923	2391	0.953727	AGTCTTGCACCGTACGTACA	59.046	50.000	24.50	6.27	0.00	2.90
974	2473	8.994429	AGGAATCGATCATTGATACTTGATAC	57.006	34.615	0.00	0.17	32.84	2.24
976	2475	9.597170	CATAGGAATCGATCATTGATACTTGAT	57.403	33.333	0.00	0.00	35.33	2.57
979	2478	6.820656	GCCATAGGAATCGATCATTGATACTT	59.179	38.462	0.00	0.00	0.00	2.24
981	2480	5.233050	CGCCATAGGAATCGATCATTGATAC	59.767	44.000	0.00	0.00	0.00	2.24
988	2488	1.068541	CGACGCCATAGGAATCGATCA	60.069	52.381	0.00	0.00	34.83	2.92
1154	2657	0.389817	TTCGCCATCAGTGAAGACCG	60.390	55.000	0.00	0.00	40.06	4.79
1187	2694	1.833492	TGTTCCGAGGGACCGTTGA	60.833	57.895	2.78	0.00	0.00	3.18
1207	2714	1.753903	TTCTTGGGGATGAAGGTGGA	58.246	50.000	0.00	0.00	0.00	4.02
1222	2729	2.503356	AGCCGGAGAGATGTGAATTCTT	59.497	45.455	5.05	0.00	0.00	2.52
1413	2935	1.662629	GTGATGACTGCCATGAAGTCG	59.337	52.381	18.15	0.00	45.81	4.18
1477	2999	1.526917	GTTCTGGCAGCCACACACT	60.527	57.895	11.22	0.00	0.00	3.55
1543	3065	1.602851	GCTGATGCCATAGAGCTTGTG	59.397	52.381	0.00	0.00	0.00	3.33
1618	3140	0.238289	CGTCTTGCAATGGTGACCAC	59.762	55.000	6.40	0.00	35.80	4.16
1646	3168	5.320549	ACTATCGTAATCAAGTGGTCGTT	57.679	39.130	0.00	0.00	0.00	3.85
1666	4060	5.012046	TGTCGCTATAATCATCATCCCAACT	59.988	40.000	0.00	0.00	0.00	3.16
1691	4085	4.215613	CACCATCACCATCATCATCATCAC	59.784	45.833	0.00	0.00	0.00	3.06
1726	4742	0.461548	TCATCATCGCCTTCTTCGCT	59.538	50.000	0.00	0.00	0.00	4.93
1727	4743	1.194098	CATCATCATCGCCTTCTTCGC	59.806	52.381	0.00	0.00	0.00	4.70
1751	4791	1.668337	CCTCATCCTCGTCATCATCGC	60.668	57.143	0.00	0.00	0.00	4.58
1793	4833	2.358957	CCTCGTCCTCATCATTTGCAA	58.641	47.619	0.00	0.00	0.00	4.08
1798	4838	1.043116	TCGCCCTCGTCCTCATCATT	61.043	55.000	0.00	0.00	36.96	2.57
1819	4859	2.170187	CCTGTTCCTCCTCCATCTTCTG	59.830	54.545	0.00	0.00	0.00	3.02
1848	5050	4.057428	GCCTCGGCTGTCACGTCT	62.057	66.667	0.00	0.00	38.26	4.18
1862	5064	0.034089	GGCCACCAAACTATCAGCCT	60.034	55.000	0.00	0.00	36.00	4.58
1880	5082	4.100498	CCTTCTCCCCATGAAAATCATTGG	59.900	45.833	0.00	3.99	38.88	3.16
1898	5230	1.352622	TGGCACTGTTGACCCCTTCT	61.353	55.000	0.00	0.00	0.00	2.85
1899	5231	0.467290	TTGGCACTGTTGACCCCTTC	60.467	55.000	0.00	0.00	0.00	3.46
1933	5529	8.786826	ACATTCCGATAATTGAAGTTACTTCA	57.213	30.769	22.16	22.16	46.93	3.02
1982	5578	4.229876	GTGCCAGCAAGTGTATTCTTTTC	58.770	43.478	0.00	0.00	0.00	2.29
2100	5696	0.037697	TGCGTGTCTTAACATCGGCT	60.038	50.000	0.00	0.00	37.81	5.52
2181	5890	2.427095	AGGTGCAGAAACAAACTTGGAC	59.573	45.455	0.00	0.00	0.00	4.02
2303	6012	2.747177	TGACATTCGATCCCAGGTAGT	58.253	47.619	0.00	0.00	0.00	2.73
2403	6586	5.597806	TCCAATCCACTGTCGTATATGAAC	58.402	41.667	0.00	0.00	0.00	3.18
2412	6600	7.279981	TGAATAACTAAATCCAATCCACTGTCG	59.720	37.037	0.00	0.00	0.00	4.35
2481	6674	2.550855	GCAGATTGACAGTGGAGGAACA	60.551	50.000	0.00	0.00	0.00	3.18
2482	6675	2.079925	GCAGATTGACAGTGGAGGAAC	58.920	52.381	0.00	0.00	0.00	3.62
2483	6676	1.699083	TGCAGATTGACAGTGGAGGAA	59.301	47.619	0.00	0.00	0.00	3.36
2484	6677	1.277273	CTGCAGATTGACAGTGGAGGA	59.723	52.381	8.42	0.00	0.00	3.71
2485	6678	1.735386	CTGCAGATTGACAGTGGAGG	58.265	55.000	8.42	0.00	0.00	4.30
2644	6839	5.559770	TGGCTTTGAAGATGTATTCACTCA	58.440	37.500	0.00	0.00	38.87	3.41
2722	7151	6.240586	CCCCCTTAAATAGCTCCCTGAATAAT	60.241	42.308	0.00	0.00	0.00	1.28
2784	7220	4.944372	GCCGCACGGACTATCGGG	62.944	72.222	14.43	0.00	41.96	5.14
2831	7267	2.691011	AGAGCTAAGCTACACCACTAGC	59.309	50.000	3.60	3.60	39.88	3.42
2854	7290	8.345565	AGCTGTACAATTACAAAGAAGAAACTG	58.654	33.333	0.00	0.00	37.77	3.16
2871	7307	2.279582	GCTCGCTTCTAGCTGTACAA	57.720	50.000	0.00	0.00	39.60	2.41
2896	7440	7.702386	TCGACATTCTTGTTTTGATCTTTTGA	58.298	30.769	0.00	0.00	35.79	2.69
2906	7450	5.032220	GGAACGTTTCGACATTCTTGTTTT	58.968	37.500	0.46	0.00	35.79	2.43
2959	7508	4.202461	ACAACTCATGCCTGTAGGAAGAAA	60.202	41.667	1.17	0.00	37.39	2.52
2978	7527	6.708949	TCAGTTATCCCTGAACACTTTACAAC	59.291	38.462	0.00	0.00	38.49	3.32
2990	7539	4.835615	GCTATCTCCTTCAGTTATCCCTGA	59.164	45.833	0.00	0.00	39.65	3.86
3072	7623	2.108168	CGTGATGAAGGGGTAGGAGAA	58.892	52.381	0.00	0.00	0.00	2.87
3152	7989	9.406828	CTAATGCAAAGTAGTTATACGCTATGA	57.593	33.333	0.00	0.00	36.97	2.15
3305	8145	8.691661	ATTTGTTACTGGTGATACTTTCTTGT	57.308	30.769	0.00	0.00	0.00	3.16
3319	8162	6.150976	TGTGAGGCTTCATAATTTGTTACTGG	59.849	38.462	0.30	0.00	35.39	4.00
3334	8177	0.389948	CCGGTAGTGTGTGAGGCTTC	60.390	60.000	0.00	0.00	0.00	3.86

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.