AutoCloner

Multiple sequence alignment - TraesCS2D01G379400

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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	TraesCS2D01G379400	chr2D	100.000	2654	0	0	1	2654	483839671	483837018	0.000000e+00	4902.0
1	TraesCS2D01G379400	chr2D	82.667	150	19	6	435	581	279041301	279041156	2.770000e-25	126.0
2	TraesCS2D01G379400	chr2D	82.051	156	20	7	431	582	619326428	619326579	2.770000e-25	126.0
3	TraesCS2D01G379400	chr2B	95.124	1497	51	10	683	2169	568659439	568657955	0.000000e+00	2340.0
4	TraesCS2D01G379400	chr2B	90.632	459	31	7	2202	2654	568657953	568657501	1.360000e-167	599.0
5	TraesCS2D01G379400	chr2B	90.909	88	6	1	1893	1978	258639665	258639578	1.670000e-22	117.0
6	TraesCS2D01G379400	chr2B	100.000	54	0	0	636	689	568659509	568659456	1.680000e-17	100.0
7	TraesCS2D01G379400	chr2A	92.291	1362	58	24	813	2169	627616826	627615507	0.000000e+00	1890.0
8	TraesCS2D01G379400	chr2A	83.688	423	36	17	1	397	630944799	630944384	4.170000e-98	368.0
9	TraesCS2D01G379400	chr2A	90.426	188	11	1	2206	2393	627615504	627615324	9.490000e-60	241.0
10	TraesCS2D01G379400	chr2A	85.841	226	20	6	2412	2633	627615241	627615024	2.050000e-56	230.0
11	TraesCS2D01G379400	chr2A	77.518	427	64	28	1	411	765009848	765009438	7.390000e-56	228.0
12	TraesCS2D01G379400	chr2A	77.049	427	67	27	1	411	764999142	764998731	1.600000e-52	217.0
13	TraesCS2D01G379400	chr2A	85.938	192	22	5	394	582	630944431	630944242	1.610000e-47	200.0
14	TraesCS2D01G379400	chr2A	89.888	89	6	2	1893	1978	278919347	278919435	7.770000e-21	111.0
15	TraesCS2D01G379400	chr2A	81.618	136	22	3	449	582	762659430	762659564	2.790000e-20	110.0
16	TraesCS2D01G379400	chr2A	97.222	36	1	0	683	718	627617091	627617056	7.930000e-06	62.1
17	TraesCS2D01G379400	chr7B	84.757	597	58	19	1	582	371450325	371449747	3.830000e-158	568.0
18	TraesCS2D01G379400	chr7B	79.867	601	83	31	2	581	20044573	20045156	3.180000e-109	405.0
19	TraesCS2D01G379400	chr7B	83.294	419	34	15	166	582	357968038	357967654	1.170000e-93	353.0
20	TraesCS2D01G379400	chr7B	90.217	92	8	1	1884	1974	471435460	471435369	4.640000e-23	119.0
21	TraesCS2D01G379400	chr4D	83.115	610	60	21	1	587	231200503	231199914	1.410000e-142	516.0
22	TraesCS2D01G379400	chr1D	83.361	607	48	16	1	584	414133855	414133279	1.820000e-141	512.0
23	TraesCS2D01G379400	chr1D	91.011	89	8	0	1893	1981	449276393	449276305	1.290000e-23	121.0
24	TraesCS2D01G379400	chr6B	80.992	605	62	17	3	585	378290902	378290329	5.250000e-117	431.0
25	TraesCS2D01G379400	chr6B	89.796	98	7	3	1884	1979	680933320	680933224	3.590000e-24	122.0
26	TraesCS2D01G379400	chr7D	79.134	508	77	26	1	491	220180394	220179899	9.160000e-85	324.0
27	TraesCS2D01G379400	chr7D	77.307	401	58	23	199	582	119584595	119584211	3.460000e-49	206.0
28	TraesCS2D01G379400	chr6D	78.719	437	61	25	167	583	2936918	2936494	2.030000e-66	263.0
29	TraesCS2D01G379400	chr3D	75.676	629	92	37	1	582	174920254	174919640	9.430000e-65	257.0
30	TraesCS2D01G379400	chr3D	81.953	338	28	12	248	582	477238006	477238313	3.390000e-64	255.0
31	TraesCS2D01G379400	chr5A	83.401	247	26	8	348	581	684515473	684515717	5.750000e-52	215.0
32	TraesCS2D01G379400	chr5A	91.765	85	7	0	1894	1978	370102518	370102434	4.640000e-23	119.0
33	TraesCS2D01G379400	chr3B	76.371	474	63	31	126	582	697084114	697084555	2.680000e-50	209.0
34	TraesCS2D01G379400	chr3A	88.430	121	12	2	463	582	214272859	214272740	7.660000e-31	145.0
35	TraesCS2D01G379400	chr4A	89.773	88	9	0	1894	1981	472961343	472961256	2.160000e-21	113.0

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	TraesCS2D01G379400	chr2D	483837018	483839671	2653	True	4902.000	4902	100.000	1	2654	1	chr2D.!!$R2	2653
1	TraesCS2D01G379400	chr2B	568657501	568659509	2008	True	1013.000	2340	95.252	636	2654	3	chr2B.!!$R2	2018
2	TraesCS2D01G379400	chr2A	627615024	627617091	2067	True	605.775	1890	91.445	683	2633	4	chr2A.!!$R3	1950
3	TraesCS2D01G379400	chr2A	630944242	630944799	557	True	284.000	368	84.813	1	582	2	chr2A.!!$R4	581
4	TraesCS2D01G379400	chr7B	371449747	371450325	578	True	568.000	568	84.757	1	582	1	chr7B.!!$R2	581
5	TraesCS2D01G379400	chr7B	20044573	20045156	583	False	405.000	405	79.867	2	581	1	chr7B.!!$F1	579
6	TraesCS2D01G379400	chr4D	231199914	231200503	589	True	516.000	516	83.115	1	587	1	chr4D.!!$R1	586
7	TraesCS2D01G379400	chr1D	414133279	414133855	576	True	512.000	512	83.361	1	584	1	chr1D.!!$R1	583
8	TraesCS2D01G379400	chr6B	378290329	378290902	573	True	431.000	431	80.992	3	585	1	chr6B.!!$R1	582
9	TraesCS2D01G379400	chr3D	174919640	174920254	614	True	257.000	257	75.676	1	582	1	chr3D.!!$R1	581

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
972	1324	0.047176	ACTCCCCATCCCATACCCAA	59.953	55.0	0.0	0.0	0.0	4.12	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2575	3009	0.038251	AGTCGCAATCAACTGCTCGA	60.038	50.0	0.0	0.0	40.33	4.04	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
37	38	7.353414	TGTGAACAATTTATGAAACTGGGAA	57.647	32.000	0.00	0.00	0.00	3.97
39	40	8.260818	TGTGAACAATTTATGAAACTGGGAAAA	58.739	29.630	0.00	0.00	0.00	2.29
41	42	9.270640	TGAACAATTTATGAAACTGGGAAAATG	57.729	29.630	0.00	0.00	0.00	2.32
58	62	5.048013	GGAAAATGTTTGAAACTCCGGAGAT	60.048	40.000	37.69	24.44	0.00	2.75
76	81	6.914215	CCGGAGATATGAAAACATGAACATTG	59.086	38.462	0.00	0.00	0.00	2.82
153	217	7.216130	GTGAAAATTTTGAACAAAAGCTTTCGG	59.784	33.333	24.70	10.53	42.07	4.30
154	218	6.735678	AAATTTTGAACAAAAGCTTTCGGT	57.264	29.167	13.10	11.20	42.72	4.69
155	219	6.735678	AATTTTGAACAAAAGCTTTCGGTT	57.264	29.167	22.08	22.08	42.72	4.44
229	295	8.447787	AATTTATGAACAATTTTCGAAGACCG	57.552	30.769	0.00	0.00	34.32	4.79
265	334	9.194716	GAAATTTTGAACGTTTCTTAAAAGCAC	57.805	29.630	0.46	1.85	0.00	4.40
488	658	2.419739	AAAACCGGCTGGCGTTGTT	61.420	52.632	22.22	16.29	39.70	2.83
492	662	3.964875	CGGCTGGCGTTGTTGCTT	61.965	61.111	16.07	0.00	34.52	3.91
493	663	2.612567	CGGCTGGCGTTGTTGCTTA	61.613	57.895	16.07	0.00	34.52	3.09
494	664	1.883021	GGCTGGCGTTGTTGCTTAT	59.117	52.632	0.00	0.00	34.52	1.73
541	712	3.043713	CGCTCGCCTGTGCAAAGA	61.044	61.111	5.12	0.00	37.32	2.52
586	757	5.186797	TGCGTCCAATAGAATTTTCCCAAAT	59.813	36.000	0.00	0.00	33.72	2.32
587	758	5.748630	GCGTCCAATAGAATTTTCCCAAATC	59.251	40.000	0.00	0.00	30.80	2.17
588	759	6.405842	GCGTCCAATAGAATTTTCCCAAATCT	60.406	38.462	0.00	0.00	30.80	2.40
589	760	7.201785	GCGTCCAATAGAATTTTCCCAAATCTA	60.202	37.037	0.00	0.00	30.80	1.98
590	761	8.129211	CGTCCAATAGAATTTTCCCAAATCTAC	58.871	37.037	0.00	0.00	30.80	2.59
591	762	8.129211	GTCCAATAGAATTTTCCCAAATCTACG	58.871	37.037	0.00	0.00	30.80	3.51
592	763	7.832187	TCCAATAGAATTTTCCCAAATCTACGT	59.168	33.333	0.00	0.00	30.80	3.57
593	764	8.466798	CCAATAGAATTTTCCCAAATCTACGTT	58.533	33.333	0.00	0.00	30.80	3.99
594	765	9.503427	CAATAGAATTTTCCCAAATCTACGTTC	57.497	33.333	0.00	0.00	30.80	3.95
595	766	6.178239	AGAATTTTCCCAAATCTACGTTCG	57.822	37.500	0.00	0.00	30.80	3.95
596	767	5.704053	AGAATTTTCCCAAATCTACGTTCGT	59.296	36.000	0.00	2.91	30.80	3.85
597	768	5.952526	ATTTTCCCAAATCTACGTTCGTT	57.047	34.783	2.62	0.00	0.00	3.85
598	769	5.754543	TTTTCCCAAATCTACGTTCGTTT	57.245	34.783	2.62	0.00	0.00	3.60
599	770	6.857777	TTTTCCCAAATCTACGTTCGTTTA	57.142	33.333	2.62	0.00	0.00	2.01
600	771	5.844301	TTCCCAAATCTACGTTCGTTTAC	57.156	39.130	2.62	0.00	0.00	2.01
601	772	3.919804	TCCCAAATCTACGTTCGTTTACG	59.080	43.478	2.62	0.00	46.52	3.18
607	778	2.765150	CGTTCGTTTACGTCGGCC	59.235	61.111	0.00	0.00	40.80	6.13
608	779	2.765150	GTTCGTTTACGTCGGCCG	59.235	61.111	22.12	22.12	44.03	6.13
609	780	2.430582	TTCGTTTACGTCGGCCGG	60.431	61.111	27.83	13.23	42.24	6.13
610	781	3.206211	TTCGTTTACGTCGGCCGGT	62.206	57.895	27.83	19.00	42.24	5.28
611	782	2.691674	TTCGTTTACGTCGGCCGGTT	62.692	55.000	27.83	12.42	42.24	4.44
612	783	2.855325	GTTTACGTCGGCCGGTTG	59.145	61.111	27.83	17.68	42.24	3.77
613	784	2.357275	TTTACGTCGGCCGGTTGG	60.357	61.111	27.83	14.40	42.24	3.77
614	785	2.865598	TTTACGTCGGCCGGTTGGA	61.866	57.895	27.83	9.41	42.24	3.53
615	786	2.768503	TTTACGTCGGCCGGTTGGAG	62.769	60.000	27.83	12.63	42.24	3.86
617	788	4.675029	CGTCGGCCGGTTGGAGTT	62.675	66.667	27.83	0.00	37.49	3.01
618	789	2.281276	GTCGGCCGGTTGGAGTTT	60.281	61.111	27.83	0.00	37.49	2.66
619	790	2.281208	TCGGCCGGTTGGAGTTTG	60.281	61.111	27.83	0.00	37.49	2.93
620	791	4.038080	CGGCCGGTTGGAGTTTGC	62.038	66.667	20.10	0.00	37.49	3.68
621	792	2.597510	GGCCGGTTGGAGTTTGCT	60.598	61.111	1.90	0.00	37.49	3.91
622	793	2.200337	GGCCGGTTGGAGTTTGCTT	61.200	57.895	1.90	0.00	37.49	3.91
623	794	1.007387	GCCGGTTGGAGTTTGCTTG	60.007	57.895	1.90	0.00	37.49	4.01
624	795	1.007387	CCGGTTGGAGTTTGCTTGC	60.007	57.895	0.00	0.00	37.49	4.01
625	796	1.007387	CGGTTGGAGTTTGCTTGCC	60.007	57.895	0.00	0.00	0.00	4.52
626	797	1.455383	CGGTTGGAGTTTGCTTGCCT	61.455	55.000	0.00	0.00	0.00	4.75
627	798	0.752658	GGTTGGAGTTTGCTTGCCTT	59.247	50.000	0.00	0.00	0.00	4.35
628	799	1.538849	GGTTGGAGTTTGCTTGCCTTG	60.539	52.381	0.00	0.00	0.00	3.61
629	800	0.752054	TTGGAGTTTGCTTGCCTTGG	59.248	50.000	0.00	0.00	0.00	3.61
630	801	1.114722	TGGAGTTTGCTTGCCTTGGG	61.115	55.000	0.00	0.00	0.00	4.12
631	802	0.827507	GGAGTTTGCTTGCCTTGGGA	60.828	55.000	0.00	0.00	0.00	4.37
632	803	1.039856	GAGTTTGCTTGCCTTGGGAA	58.960	50.000	0.00	0.00	0.00	3.97
633	804	0.752658	AGTTTGCTTGCCTTGGGAAC	59.247	50.000	0.00	0.00	0.00	3.62
634	805	0.463620	GTTTGCTTGCCTTGGGAACA	59.536	50.000	0.00	0.00	39.83	3.18
736	933	0.973496	TATGGAGTGCCGGCTGTGTA	60.973	55.000	29.70	11.90	36.79	2.90
972	1324	0.047176	ACTCCCCATCCCATACCCAA	59.953	55.000	0.00	0.00	0.00	4.12
1308	1666	2.097791	CGAGTACAAGGCAGGAGAGTAC	59.902	54.545	0.00	0.00	36.26	2.73
1563	1921	4.223923	ACCCTCACCAAGTATCAGAAGAAG	59.776	45.833	0.00	0.00	0.00	2.85
1608	1966	0.255890	AAGCTTATGTGGGTGGCGAT	59.744	50.000	0.00	0.00	0.00	4.58
1664	2022	1.002888	CACTGGGTGAACAGATCTGCT	59.997	52.381	22.83	10.95	40.97	4.24
1711	2069	7.767659	CACAAGATCTGATTAGAATGAGTCCAA	59.232	37.037	0.00	0.00	36.32	3.53
1848	2206	2.485903	TGCTGGTGTTACAAGGTTACG	58.514	47.619	0.00	0.00	0.00	3.18
1862	2220	9.793252	TTACAAGGTTACGATATCTGTAGTTTC	57.207	33.333	0.34	0.00	0.00	2.78
1867	2225	4.978083	ACGATATCTGTAGTTTCGTGGT	57.022	40.909	0.34	0.00	41.09	4.16
1881	2239	7.535489	AGTTTCGTGGTATAAACTATGCTTC	57.465	36.000	0.00	0.00	42.57	3.86
1981	2339	2.189521	GGGCGGAGGTGGTACATG	59.810	66.667	0.00	0.00	44.52	3.21
1999	2357	0.961019	TGTCAATGCTTTGCCCAGAC	59.039	50.000	7.44	1.51	32.61	3.51
2002	2360	0.109597	CAATGCTTTGCCCAGACGTC	60.110	55.000	7.70	7.70	0.00	4.34
2007	2365	3.454587	TTTGCCCAGACGTCACGCT	62.455	57.895	19.50	0.00	0.00	5.07
2120	2479	5.410924	TGACTATCTGTGCAACTCATGTAC	58.589	41.667	0.00	0.00	44.10	2.90
2121	2480	5.185828	TGACTATCTGTGCAACTCATGTACT	59.814	40.000	0.00	0.00	44.16	2.73
2123	2482	4.815533	ATCTGTGCAACTCATGTACTCT	57.184	40.909	0.00	0.00	44.16	3.24
2137	2496	3.033909	TGTACTCTAGCTGTGGATGCAT	58.966	45.455	0.00	0.00	0.00	3.96
2173	2532	6.959639	TGCAGATTTTTGGAATATACTCCC	57.040	37.500	0.00	0.00	34.22	4.30
2174	2533	6.672593	TGCAGATTTTTGGAATATACTCCCT	58.327	36.000	0.00	0.00	34.22	4.20
2175	2534	6.772716	TGCAGATTTTTGGAATATACTCCCTC	59.227	38.462	0.00	0.00	34.22	4.30
2176	2535	7.001073	GCAGATTTTTGGAATATACTCCCTCT	58.999	38.462	0.00	0.00	34.22	3.69
2177	2536	7.174080	GCAGATTTTTGGAATATACTCCCTCTC	59.826	40.741	0.00	0.00	34.22	3.20
2178	2537	8.435982	CAGATTTTTGGAATATACTCCCTCTCT	58.564	37.037	0.00	0.00	34.22	3.10
2179	2538	9.008584	AGATTTTTGGAATATACTCCCTCTCTT	57.991	33.333	0.00	0.00	34.22	2.85
2180	2539	9.278978	GATTTTTGGAATATACTCCCTCTCTTC	57.721	37.037	0.00	0.00	34.22	2.87
2181	2540	7.996758	TTTTGGAATATACTCCCTCTCTTCT	57.003	36.000	0.00	0.00	34.22	2.85
2182	2541	7.996758	TTTGGAATATACTCCCTCTCTTCTT	57.003	36.000	0.00	0.00	34.22	2.52
2183	2542	9.502035	TTTTGGAATATACTCCCTCTCTTCTTA	57.498	33.333	0.00	0.00	34.22	2.10
2184	2543	9.502035	TTTGGAATATACTCCCTCTCTTCTTAA	57.498	33.333	0.00	0.00	34.22	1.85
2185	2544	9.502035	TTGGAATATACTCCCTCTCTTCTTAAA	57.498	33.333	0.00	0.00	34.22	1.52
2186	2545	9.676129	TGGAATATACTCCCTCTCTTCTTAAAT	57.324	33.333	0.00	0.00	34.22	1.40
2194	2553	9.052365	ACTCCCTCTCTTCTTAAATATTTGTCT	57.948	33.333	11.05	0.00	0.00	3.41
2195	2554	9.898152	CTCCCTCTCTTCTTAAATATTTGTCTT	57.102	33.333	11.05	0.00	0.00	3.01
2340	2699	3.500343	AGAACCTGAACTTTGATTGGGG	58.500	45.455	0.00	0.00	0.00	4.96
2354	2713	3.637694	TGATTGGGGTTGCATATGACATG	59.362	43.478	6.97	0.00	0.00	3.21
2455	2882	7.753309	GGTTAATAAAAACCCTGGCAAAAAT	57.247	32.000	0.00	0.00	42.68	1.82
2547	2975	0.180642	AGAGGATGCCGTCGAGACTA	59.819	55.000	0.00	0.00	32.77	2.59
2551	2979	1.134560	GGATGCCGTCGAGACTACTTT	59.865	52.381	0.00	0.00	0.00	2.66
2575	3009	4.382470	CCTTTCATCGTCATCACCTCTCTT	60.382	45.833	0.00	0.00	0.00	2.85
2576	3010	4.377839	TTCATCGTCATCACCTCTCTTC	57.622	45.455	0.00	0.00	0.00	2.87
2587	3021	2.094286	CACCTCTCTTCGAGCAGTTGAT	60.094	50.000	0.00	0.00	38.49	2.57
2588	3022	2.564947	ACCTCTCTTCGAGCAGTTGATT	59.435	45.455	0.00	0.00	38.49	2.57
2589	3023	2.928757	CCTCTCTTCGAGCAGTTGATTG	59.071	50.000	0.00	0.00	38.49	2.67
2590	3024	2.341257	TCTCTTCGAGCAGTTGATTGC	58.659	47.619	0.00	0.00	44.41	3.56
2622	3056	0.971386	GACGACCTGTTAAGACCCCA	59.029	55.000	0.00	0.00	0.00	4.96
2625	3059	1.470979	CGACCTGTTAAGACCCCATCG	60.471	57.143	0.00	0.00	0.00	3.84
2642	3076	3.242091	CCATCGAACGAATGACACATGAC	60.242	47.826	0.00	0.00	0.00	3.06

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
37	38	6.884295	TCATATCTCCGGAGTTTCAAACATTT	59.116	34.615	30.17	6.97	0.00	2.32
39	40	5.989477	TCATATCTCCGGAGTTTCAAACAT	58.011	37.500	30.17	16.16	0.00	2.71
41	42	6.737254	TTTCATATCTCCGGAGTTTCAAAC	57.263	37.500	30.17	0.00	0.00	2.93
58	62	8.429493	TTGCAAACAATGTTCATGTTTTCATA	57.571	26.923	0.00	0.00	45.97	2.15
76	81	6.551812	AAAAATTGTTCGCAAATTGCAAAC	57.448	29.167	18.65	16.37	45.36	2.93
439	566	4.232091	TCTAGAAGGTTCCCTGAACTGTT	58.768	43.478	6.89	0.00	41.70	3.16
440	567	3.858135	TCTAGAAGGTTCCCTGAACTGT	58.142	45.455	6.89	0.00	41.70	3.55
541	712	2.282391	TGCATCAAACTGCCGGCT	60.282	55.556	29.70	4.80	41.58	5.52
559	730	4.412207	GGAAAATTCTATTGGACGCACAC	58.588	43.478	0.00	0.00	0.00	3.82
591	762	2.719774	CCGGCCGACGTAAACGAAC	61.720	63.158	30.73	2.36	43.02	3.95
592	763	2.430582	CCGGCCGACGTAAACGAA	60.431	61.111	30.73	0.00	43.02	3.85
593	764	3.206211	AACCGGCCGACGTAAACGA	62.206	57.895	30.73	0.00	43.02	3.85
594	765	2.734346	AACCGGCCGACGTAAACG	60.734	61.111	30.73	9.82	46.33	3.60
595	766	2.670210	CCAACCGGCCGACGTAAAC	61.670	63.158	30.73	0.00	42.24	2.01
596	767	2.357275	CCAACCGGCCGACGTAAA	60.357	61.111	30.73	0.00	42.24	2.01
597	768	3.285523	CTCCAACCGGCCGACGTAA	62.286	63.158	30.73	8.10	42.24	3.18
598	769	3.751246	CTCCAACCGGCCGACGTA	61.751	66.667	30.73	6.87	42.24	3.57
600	771	4.675029	AACTCCAACCGGCCGACG	62.675	66.667	30.73	14.21	43.80	5.12
601	772	2.281276	AAACTCCAACCGGCCGAC	60.281	61.111	30.73	0.00	0.00	4.79
602	773	2.281208	CAAACTCCAACCGGCCGA	60.281	61.111	30.73	4.63	0.00	5.54
603	774	4.038080	GCAAACTCCAACCGGCCG	62.038	66.667	21.04	21.04	0.00	6.13
604	775	2.200337	AAGCAAACTCCAACCGGCC	61.200	57.895	0.00	0.00	0.00	6.13
605	776	1.007387	CAAGCAAACTCCAACCGGC	60.007	57.895	0.00	0.00	0.00	6.13
606	777	1.007387	GCAAGCAAACTCCAACCGG	60.007	57.895	0.00	0.00	0.00	5.28
607	778	1.007387	GGCAAGCAAACTCCAACCG	60.007	57.895	0.00	0.00	0.00	4.44
608	779	0.752658	AAGGCAAGCAAACTCCAACC	59.247	50.000	0.00	0.00	0.00	3.77
609	780	1.538849	CCAAGGCAAGCAAACTCCAAC	60.539	52.381	0.00	0.00	0.00	3.77
610	781	0.752054	CCAAGGCAAGCAAACTCCAA	59.248	50.000	0.00	0.00	0.00	3.53
611	782	1.114722	CCCAAGGCAAGCAAACTCCA	61.115	55.000	0.00	0.00	0.00	3.86
612	783	0.827507	TCCCAAGGCAAGCAAACTCC	60.828	55.000	0.00	0.00	0.00	3.85
613	784	1.039856	TTCCCAAGGCAAGCAAACTC	58.960	50.000	0.00	0.00	0.00	3.01
614	785	0.752658	GTTCCCAAGGCAAGCAAACT	59.247	50.000	0.00	0.00	0.00	2.66
615	786	0.463620	TGTTCCCAAGGCAAGCAAAC	59.536	50.000	0.00	0.00	0.00	2.93
616	787	1.138661	CTTGTTCCCAAGGCAAGCAAA	59.861	47.619	0.00	0.00	43.62	3.68
617	788	0.752054	CTTGTTCCCAAGGCAAGCAA	59.248	50.000	0.00	0.00	43.62	3.91
618	789	2.428834	CTTGTTCCCAAGGCAAGCA	58.571	52.632	0.00	0.00	43.62	3.91
624	795	3.131850	ACAAGGCTTGTTCCCAAGG	57.868	52.632	26.54	0.22	46.72	3.61
633	804	1.654220	CACCACGGAACAAGGCTTG	59.346	57.895	25.06	25.06	0.00	4.01
634	805	1.528309	CCACCACGGAACAAGGCTT	60.528	57.895	0.00	0.00	36.56	4.35
736	933	6.271159	TGAATGGTTAAGGCCCAAAAATACTT	59.729	34.615	0.00	0.00	35.14	2.24
946	1298	1.461655	GGGATGGGGAGTAGGGTCC	60.462	68.421	0.00	0.00	35.64	4.46
1563	1921	0.109132	CCATCTTTGCAAGCCCGAAC	60.109	55.000	0.00	0.00	0.00	3.95
1608	1966	0.190069	ACTCCCCCTCACACACTACA	59.810	55.000	0.00	0.00	0.00	2.74
1664	2022	1.276138	AGAGGATCACATCGCACACAA	59.724	47.619	0.00	0.00	37.82	3.33
1711	2069	7.814264	ACTCAATTCTCTCAACAATTGAACT	57.186	32.000	13.59	0.00	44.52	3.01
1735	2093	7.026562	CACATGTTGTAAGTTCAGTTCACAAA	58.973	34.615	0.00	0.00	31.44	2.83
1848	2206	9.962783	AGTTTATACCACGAAACTACAGATATC	57.037	33.333	0.00	0.00	42.62	1.63
1981	2339	0.109597	CGTCTGGGCAAAGCATTGAC	60.110	55.000	5.73	1.48	44.37	3.18
2002	2360	3.423154	GGGTTCGGCAAGAGCGTG	61.423	66.667	0.00	0.00	43.41	5.34
2007	2365	3.343617	CTTGATTAAGGGTTCGGCAAGA	58.656	45.455	0.00	0.00	34.71	3.02
2087	2446	6.538945	TGCACAGATAGTCAACCACTATAA	57.461	37.500	0.00	0.00	46.76	0.98
2120	2479	4.333913	ACTTATGCATCCACAGCTAGAG	57.666	45.455	0.19	0.00	0.00	2.43
2121	2480	5.539955	TCATACTTATGCATCCACAGCTAGA	59.460	40.000	0.19	0.00	33.76	2.43
2123	2482	5.806654	TCATACTTATGCATCCACAGCTA	57.193	39.130	0.19	0.00	33.76	3.32
2169	2528	9.898152	AAGACAAATATTTAAGAAGAGAGGGAG	57.102	33.333	0.00	0.00	0.00	4.30
2197	2556	9.696572	AGTGTGAAACCATCTAGTAGTATCTAA	57.303	33.333	0.00	0.00	34.36	2.10
2198	2557	9.696572	AAGTGTGAAACCATCTAGTAGTATCTA	57.303	33.333	0.00	0.00	34.36	1.98
2199	2558	8.596781	AAGTGTGAAACCATCTAGTAGTATCT	57.403	34.615	0.00	0.00	34.36	1.98
2200	2559	9.088512	CAAAGTGTGAAACCATCTAGTAGTATC	57.911	37.037	0.00	0.00	34.36	2.24
2214	2573	4.098416	GCAGACAACTCAAAGTGTGAAAC	58.902	43.478	0.00	0.00	35.22	2.78
2340	2699	7.182761	GTGTTTACTCTCATGTCATATGCAAC	58.817	38.462	0.00	0.00	0.00	4.17
2379	2738	1.534336	AATCGGCCAATTGCTGCACA	61.534	50.000	0.00	0.00	46.56	4.57
2455	2882	4.681074	TCTTATGGGCATGTTGTATCGA	57.319	40.909	0.00	0.00	0.00	3.59
2547	2975	4.003648	GGTGATGACGATGAAAGGAAAGT	58.996	43.478	0.00	0.00	0.00	2.66
2551	2979	3.099905	AGAGGTGATGACGATGAAAGGA	58.900	45.455	0.00	0.00	0.00	3.36
2575	3009	0.038251	AGTCGCAATCAACTGCTCGA	60.038	50.000	0.00	0.00	40.33	4.04
2576	3010	0.792640	AAGTCGCAATCAACTGCTCG	59.207	50.000	0.00	0.00	40.33	5.03
2591	3025	3.173240	GTCGTCTGCGGCGAAGTC	61.173	66.667	15.80	8.60	40.19	3.01
2622	3056	2.598637	CGTCATGTGTCATTCGTTCGAT	59.401	45.455	0.00	0.00	0.00	3.59
2625	3059	2.092211	GGTCGTCATGTGTCATTCGTTC	59.908	50.000	0.00	0.00	0.00	3.95

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.