AutoCloner

Multiple sequence alignment - TraesCS7B01G088500

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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	TraesCS7B01G088500	chr7B	100.000	3069	0	0	1	3069	103620418	103617350	0.000000e+00	5668.0
1	TraesCS7B01G088500	chr7B	84.891	781	75	22	1	771	573710969	573711716	0.000000e+00	749.0
2	TraesCS7B01G088500	chr7B	95.455	88	4	0	2347	2434	661996478	661996391	1.150000e-29	141.0
3	TraesCS7B01G088500	chr7A	95.845	1468	41	12	889	2349	138352012	138350558	0.000000e+00	2355.0
4	TraesCS7B01G088500	chr7A	80.236	678	69	34	2430	3069	138350560	138349910	1.680000e-122	449.0
5	TraesCS7B01G088500	chr7D	95.371	1469	40	12	889	2349	138338234	138336786	0.000000e+00	2311.0
6	TraesCS7B01G088500	chr7D	95.241	1408	51	7	949	2349	138312297	138310899	0.000000e+00	2215.0
7	TraesCS7B01G088500	chr7D	96.719	640	21	0	2430	3069	138310901	138310262	0.000000e+00	1066.0
8	TraesCS7B01G088500	chr7D	84.557	654	71	17	134	771	550570166	550570805	3.360000e-174	621.0
9	TraesCS7B01G088500	chr7D	86.047	86	7	2	1	86	550570084	550570164	1.520000e-13	87.9
10	TraesCS7B01G088500	chr2B	86.667	780	72	19	1	771	26933637	26934393	0.000000e+00	835.0
11	TraesCS7B01G088500	chr2B	86.514	786	69	22	1	776	94934603	94933845	0.000000e+00	830.0
12	TraesCS7B01G088500	chr2B	85.602	764	75	19	19	771	27670191	27669452	0.000000e+00	769.0
13	TraesCS7B01G088500	chr2B	91.489	94	8	0	2343	2436	103270298	103270391	2.480000e-26	130.0
14	TraesCS7B01G088500	chr1A	86.778	779	66	22	1	771	48795021	48795770	0.000000e+00	833.0
15	TraesCS7B01G088500	chr4B	85.385	780	71	24	1	771	4124243	4124988	0.000000e+00	769.0
16	TraesCS7B01G088500	chr4B	91.489	94	8	0	2348	2441	391596192	391596285	2.480000e-26	130.0
17	TraesCS7B01G088500	chr3B	84.856	799	74	24	1	776	758195832	758195058	0.000000e+00	761.0
18	TraesCS7B01G088500	chr6D	87.250	651	62	13	134	776	42449677	42449040	0.000000e+00	723.0
19	TraesCS7B01G088500	chr6D	76.204	1038	224	21	1154	2181	8397031	8396007	7.540000e-146	527.0
20	TraesCS7B01G088500	chr6D	75.962	1040	226	22	1154	2181	14689124	14688097	5.870000e-142	514.0
21	TraesCS7B01G088500	chr6D	76.408	746	166	9	1441	2181	14518057	14518797	7.980000e-106	394.0
22	TraesCS7B01G088500	chr6D	86.047	86	7	2	1	86	42449759	42449679	1.520000e-13	87.9
23	TraesCS7B01G088500	chr6A	76.177	1041	222	24	1154	2181	15873062	15872035	2.710000e-145	525.0
24	TraesCS7B01G088500	chr6B	75.924	1055	231	21	1154	2196	15234730	15233687	1.260000e-143	520.0
25	TraesCS7B01G088500	chr6B	74.715	1052	227	23	1154	2196	16267512	16268533	1.690000e-117	433.0
26	TraesCS7B01G088500	chr2D	82.075	636	64	21	281	879	110903988	110904610	5.910000e-137	497.0
27	TraesCS7B01G088500	chr2D	91.011	89	8	0	158	246	110903898	110903986	1.490000e-23	121.0
28	TraesCS7B01G088500	chr5B	74.535	699	160	13	1508	2194	621235516	621234824	3.870000e-74	289.0
29	TraesCS7B01G088500	chr5B	95.294	85	4	0	2348	2432	696588015	696588099	5.340000e-28	135.0
30	TraesCS7B01G088500	chr1D	95.455	88	4	0	2348	2435	104427170	104427257	1.150000e-29	141.0
31	TraesCS7B01G088500	chrUn	90.816	98	8	1	2348	2444	17148683	17148586	2.480000e-26	130.0
32	TraesCS7B01G088500	chr2A	89.423	104	9	2	2343	2446	15846401	15846300	2.480000e-26	130.0
33	TraesCS7B01G088500	chr1B	90.722	97	7	2	2347	2442	129095803	129095898	8.930000e-26	128.0
34	TraesCS7B01G088500	chr4A	87.736	106	11	2	2343	2447	743141119	743141223	4.160000e-24	122.0

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	TraesCS7B01G088500	chr7B	103617350	103620418	3068	True	5668.00	5668	100.0000	1	3069	1	chr7B.!!$R1	3068
1	TraesCS7B01G088500	chr7B	573710969	573711716	747	False	749.00	749	84.8910	1	771	1	chr7B.!!$F1	770
2	TraesCS7B01G088500	chr7A	138349910	138352012	2102	True	1402.00	2355	88.0405	889	3069	2	chr7A.!!$R1	2180
3	TraesCS7B01G088500	chr7D	138336786	138338234	1448	True	2311.00	2311	95.3710	889	2349	1	chr7D.!!$R1	1460
4	TraesCS7B01G088500	chr7D	138310262	138312297	2035	True	1640.50	2215	95.9800	949	3069	2	chr7D.!!$R2	2120
5	TraesCS7B01G088500	chr7D	550570084	550570805	721	False	354.45	621	85.3020	1	771	2	chr7D.!!$F1	770
6	TraesCS7B01G088500	chr2B	26933637	26934393	756	False	835.00	835	86.6670	1	771	1	chr2B.!!$F1	770
7	TraesCS7B01G088500	chr2B	94933845	94934603	758	True	830.00	830	86.5140	1	776	1	chr2B.!!$R2	775
8	TraesCS7B01G088500	chr2B	27669452	27670191	739	True	769.00	769	85.6020	19	771	1	chr2B.!!$R1	752
9	TraesCS7B01G088500	chr1A	48795021	48795770	749	False	833.00	833	86.7780	1	771	1	chr1A.!!$F1	770
10	TraesCS7B01G088500	chr4B	4124243	4124988	745	False	769.00	769	85.3850	1	771	1	chr4B.!!$F1	770
11	TraesCS7B01G088500	chr3B	758195058	758195832	774	True	761.00	761	84.8560	1	776	1	chr3B.!!$R1	775
12	TraesCS7B01G088500	chr6D	8396007	8397031	1024	True	527.00	527	76.2040	1154	2181	1	chr6D.!!$R1	1027
13	TraesCS7B01G088500	chr6D	14688097	14689124	1027	True	514.00	514	75.9620	1154	2181	1	chr6D.!!$R2	1027
14	TraesCS7B01G088500	chr6D	42449040	42449759	719	True	405.45	723	86.6485	1	776	2	chr6D.!!$R3	775
15	TraesCS7B01G088500	chr6D	14518057	14518797	740	False	394.00	394	76.4080	1441	2181	1	chr6D.!!$F1	740
16	TraesCS7B01G088500	chr6A	15872035	15873062	1027	True	525.00	525	76.1770	1154	2181	1	chr6A.!!$R1	1027
17	TraesCS7B01G088500	chr6B	15233687	15234730	1043	True	520.00	520	75.9240	1154	2196	1	chr6B.!!$R1	1042
18	TraesCS7B01G088500	chr6B	16267512	16268533	1021	False	433.00	433	74.7150	1154	2196	1	chr6B.!!$F1	1042
19	TraesCS7B01G088500	chr2D	110903898	110904610	712	False	309.00	497	86.5430	158	879	2	chr2D.!!$F1	721
20	TraesCS7B01G088500	chr5B	621234824	621235516	692	True	289.00	289	74.5350	1508	2194	1	chr5B.!!$R1	686

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
246	254	0.031616	AAGAGATCCTCCTCCGCCTT	60.032	55.0	0.0	0.0	33.76	4.35	F
587	616	0.036732	ATGACCCGTGTTGCATCAGT	59.963	50.0	0.0	0.0	0.00	3.41	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1209	1288	0.476611	AGAGGACCTTGGAGGCCTTT	60.477	55.0	6.77	0.0	40.43	3.11	R
2349	2460	1.424638	ACATTATGGGACGGAGGGAG	58.575	55.0	0.00	0.0	0.00	4.30	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
49	50	4.267536	CTGGTCATGGAGATTGACAACAT	58.732	43.478	6.20	0.00	44.22	2.71
79	85	3.637911	AAAATAGGCGTGTACCATGGA	57.362	42.857	21.47	0.00	0.00	3.41
178	184	1.523711	CAGCAACGGACACACCACT	60.524	57.895	0.00	0.00	38.90	4.00
246	254	0.031616	AAGAGATCCTCCTCCGCCTT	60.032	55.000	0.00	0.00	33.76	4.35
335	354	9.525826	CTTAGGAGGGCTATGAAATCAATTAAT	57.474	33.333	0.00	0.00	0.00	1.40
354	373	3.715648	ATAGAGGGTTCAGGTGGAGAT	57.284	47.619	0.00	0.00	0.00	2.75
406	425	3.131478	GGCGGCCGCTGTGTATTT	61.131	61.111	45.23	0.00	41.60	1.40
417	436	1.824852	CTGTGTATTTTCCTTGGCCCC	59.175	52.381	0.00	0.00	0.00	5.80
439	461	0.657840	GACGTGCTGCTGTTGTCTTT	59.342	50.000	0.00	0.00	0.00	2.52
463	485	1.373497	CGATCGCCATCCTGCTACC	60.373	63.158	0.26	0.00	0.00	3.18
468	490	3.043999	GCCATCCTGCTACCCCGTT	62.044	63.158	0.00	0.00	0.00	4.44
542	564	3.889815	TGGTAGGATTGCTTTGAGATGG	58.110	45.455	0.00	0.00	0.00	3.51
545	567	3.294038	AGGATTGCTTTGAGATGGGAG	57.706	47.619	0.00	0.00	0.00	4.30
547	569	3.117963	AGGATTGCTTTGAGATGGGAGAG	60.118	47.826	0.00	0.00	0.00	3.20
560	589	3.135161	TGGGAGAGGATTTCATCTGGA	57.865	47.619	0.00	0.00	37.10	3.86
565	594	4.350520	GGAGAGGATTTCATCTGGAGGAAT	59.649	45.833	0.00	0.00	37.10	3.01
576	605	1.762957	CTGGAGGAATGTATGACCCGT	59.237	52.381	0.00	0.00	0.00	5.28
579	608	2.093128	GGAGGAATGTATGACCCGTGTT	60.093	50.000	0.00	0.00	0.00	3.32
581	610	1.400494	GGAATGTATGACCCGTGTTGC	59.600	52.381	0.00	0.00	0.00	4.17
587	616	0.036732	ATGACCCGTGTTGCATCAGT	59.963	50.000	0.00	0.00	0.00	3.41
592	650	2.151202	CCCGTGTTGCATCAGTTTACT	58.849	47.619	0.00	0.00	0.00	2.24
632	690	4.334481	CGTTAATTAATGCCCTTCCTTCGT	59.666	41.667	4.52	0.00	0.00	3.85
639	697	1.600636	CCCTTCCTTCGTTGCAGCA	60.601	57.895	0.24	0.00	0.00	4.41
689	747	4.183916	TCCCTTTTAATCTGAGAACCCCT	58.816	43.478	0.00	0.00	0.00	4.79
773	847	4.586334	GAGAGGTAAGACGAACGTATGAC	58.414	47.826	0.00	0.15	0.00	3.06
806	880	3.742248	CTCGAGGGGAGAGGGGGTC	62.742	73.684	3.91	0.00	46.23	4.46
813	887	1.152798	GGAGAGGGGGTCGTACGAT	60.153	63.158	22.57	4.35	0.00	3.73
818	892	1.151450	GGGGGTCGTACGATAGGGA	59.849	63.158	22.57	0.00	43.77	4.20
829	903	2.231529	ACGATAGGGATGGACGAAGAG	58.768	52.381	0.00	0.00	43.77	2.85
830	904	1.068194	CGATAGGGATGGACGAAGAGC	60.068	57.143	0.00	0.00	0.00	4.09
836	910	2.630592	GATGGACGAAGAGCGGGGAC	62.631	65.000	0.00	0.00	46.49	4.46
861	935	0.685660	GAGGGGAAACGGAACACTCT	59.314	55.000	0.00	0.00	0.00	3.24
862	936	1.897802	GAGGGGAAACGGAACACTCTA	59.102	52.381	0.00	0.00	0.00	2.43
866	940	4.077108	GGGGAAACGGAACACTCTATTTT	58.923	43.478	0.00	0.00	0.00	1.82
904	978	6.155827	AGATAGAGAAGATAACATTCTGCGC	58.844	40.000	0.00	0.00	37.14	6.09
912	986	1.852942	AACATTCTGCGCGACGATAT	58.147	45.000	12.10	0.00	0.00	1.63
919	993	3.756677	CGCGACGATATGCCGCTG	61.757	66.667	0.00	0.00	45.91	5.18
939	1013	0.038310	TCTCTTCGCTCTCCCTGTCA	59.962	55.000	0.00	0.00	0.00	3.58
940	1014	0.455410	CTCTTCGCTCTCCCTGTCAG	59.545	60.000	0.00	0.00	0.00	3.51
941	1015	0.038310	TCTTCGCTCTCCCTGTCAGA	59.962	55.000	0.00	0.00	0.00	3.27
942	1016	1.110442	CTTCGCTCTCCCTGTCAGAT	58.890	55.000	0.00	0.00	0.00	2.90
943	1017	2.092375	TCTTCGCTCTCCCTGTCAGATA	60.092	50.000	0.00	0.00	0.00	1.98
944	1018	2.666272	TCGCTCTCCCTGTCAGATAT	57.334	50.000	0.00	0.00	0.00	1.63
945	1019	2.509569	TCGCTCTCCCTGTCAGATATC	58.490	52.381	0.00	0.00	0.00	1.63
946	1020	2.107378	TCGCTCTCCCTGTCAGATATCT	59.893	50.000	0.00	0.00	0.00	1.98
1023	1102	2.807108	GCTTCTCCTCCAGAAACACGTT	60.807	50.000	0.00	0.00	40.83	3.99
1073	1152	0.413832	AGTGCCCTACTCTCCTTCCA	59.586	55.000	0.00	0.00	33.17	3.53
2214	2322	8.616076	CCAAGAACAGGCTTGAATAGTATTTAG	58.384	37.037	1.40	0.00	46.31	1.85
2253	2362	6.483307	CACAATGAAGTTTTCACTCTGGAGTA	59.517	38.462	2.75	0.00	43.48	2.59
2285	2394	2.301346	CTGGCAAGTCCTGTTTCTGTT	58.699	47.619	0.00	0.00	35.26	3.16
2286	2395	2.023673	TGGCAAGTCCTGTTTCTGTTG	58.976	47.619	0.00	0.00	35.26	3.33
2349	2460	3.865700	GCCACTTGCAGTTTGGTAC	57.134	52.632	10.91	0.00	40.77	3.34
2350	2461	1.318576	GCCACTTGCAGTTTGGTACT	58.681	50.000	10.91	0.00	40.77	2.73
2351	2462	1.266989	GCCACTTGCAGTTTGGTACTC	59.733	52.381	10.91	0.00	40.77	2.59
2352	2463	1.880027	CCACTTGCAGTTTGGTACTCC	59.120	52.381	0.00	0.00	33.85	3.85
2353	2464	1.880027	CACTTGCAGTTTGGTACTCCC	59.120	52.381	0.00	0.00	33.85	4.30
2354	2465	1.774856	ACTTGCAGTTTGGTACTCCCT	59.225	47.619	0.00	0.00	33.85	4.20
2355	2466	2.224548	ACTTGCAGTTTGGTACTCCCTC	60.225	50.000	0.00	0.00	33.85	4.30
2356	2467	0.690762	TGCAGTTTGGTACTCCCTCC	59.309	55.000	0.00	0.00	33.85	4.30
2357	2468	0.391263	GCAGTTTGGTACTCCCTCCG	60.391	60.000	0.00	0.00	33.85	4.63
2358	2469	0.974383	CAGTTTGGTACTCCCTCCGT	59.026	55.000	0.00	0.00	33.85	4.69
2359	2470	1.067071	CAGTTTGGTACTCCCTCCGTC	60.067	57.143	0.00	0.00	33.85	4.79
2360	2471	0.248565	GTTTGGTACTCCCTCCGTCC	59.751	60.000	0.00	0.00	0.00	4.79
2361	2472	0.906282	TTTGGTACTCCCTCCGTCCC	60.906	60.000	0.00	0.00	0.00	4.46
2362	2473	2.096707	TTGGTACTCCCTCCGTCCCA	62.097	60.000	0.00	0.00	0.00	4.37
2363	2474	1.075450	GGTACTCCCTCCGTCCCAT	60.075	63.158	0.00	0.00	0.00	4.00
2364	2475	0.186873	GGTACTCCCTCCGTCCCATA	59.813	60.000	0.00	0.00	0.00	2.74
2365	2476	1.412074	GGTACTCCCTCCGTCCCATAA	60.412	57.143	0.00	0.00	0.00	1.90
2366	2477	2.606378	GTACTCCCTCCGTCCCATAAT	58.394	52.381	0.00	0.00	0.00	1.28
2367	2478	1.424638	ACTCCCTCCGTCCCATAATG	58.575	55.000	0.00	0.00	0.00	1.90
2368	2479	1.344087	ACTCCCTCCGTCCCATAATGT	60.344	52.381	0.00	0.00	0.00	2.71
2369	2480	2.090943	ACTCCCTCCGTCCCATAATGTA	60.091	50.000	0.00	0.00	0.00	2.29
2370	2481	2.969950	CTCCCTCCGTCCCATAATGTAA	59.030	50.000	0.00	0.00	0.00	2.41
2371	2482	2.969950	TCCCTCCGTCCCATAATGTAAG	59.030	50.000	0.00	0.00	0.00	2.34
2372	2483	2.969950	CCCTCCGTCCCATAATGTAAGA	59.030	50.000	0.00	0.00	0.00	2.10
2373	2484	3.244112	CCCTCCGTCCCATAATGTAAGAC	60.244	52.174	0.00	0.00	0.00	3.01
2375	2486	3.025978	TCCGTCCCATAATGTAAGACGT	58.974	45.455	9.63	0.00	46.62	4.34
2376	2487	3.448301	TCCGTCCCATAATGTAAGACGTT	59.552	43.478	9.63	0.00	46.62	3.99
2377	2488	4.081531	TCCGTCCCATAATGTAAGACGTTT	60.082	41.667	9.63	0.00	46.62	3.60
2378	2489	4.632688	CCGTCCCATAATGTAAGACGTTTT	59.367	41.667	9.63	0.00	46.62	2.43
2379	2490	5.122711	CCGTCCCATAATGTAAGACGTTTTT	59.877	40.000	9.63	0.00	46.62	1.94
2398	2509	4.948341	TTTTGGCTCTACACTAGTGTCA	57.052	40.909	31.11	19.43	43.74	3.58
2399	2510	4.948341	TTTGGCTCTACACTAGTGTCAA	57.052	40.909	31.11	23.63	43.74	3.18
2400	2511	4.948341	TTGGCTCTACACTAGTGTCAAA	57.052	40.909	31.11	14.20	43.74	2.69
2401	2512	4.948341	TGGCTCTACACTAGTGTCAAAA	57.052	40.909	31.11	13.57	43.74	2.44
2402	2513	5.284861	TGGCTCTACACTAGTGTCAAAAA	57.715	39.130	31.11	13.19	43.74	1.94
2428	2539	9.566331	AATGTCTTATATTATGGGATGGAGAGA	57.434	33.333	0.00	0.00	0.00	3.10
2429	2540	8.601047	TGTCTTATATTATGGGATGGAGAGAG	57.399	38.462	0.00	0.00	0.00	3.20
2430	2541	8.180165	TGTCTTATATTATGGGATGGAGAGAGT	58.820	37.037	0.00	0.00	0.00	3.24
2431	2542	9.702253	GTCTTATATTATGGGATGGAGAGAGTA	57.298	37.037	0.00	0.00	0.00	2.59
2487	2598	5.742063	TGGTCGTCATCTAGTAGAGAAGAA	58.258	41.667	5.98	0.00	37.85	2.52
2488	2599	6.178324	TGGTCGTCATCTAGTAGAGAAGAAA	58.822	40.000	5.98	2.15	37.85	2.52
2489	2600	6.316640	TGGTCGTCATCTAGTAGAGAAGAAAG	59.683	42.308	5.98	2.83	37.85	2.62
2490	2601	6.539464	GGTCGTCATCTAGTAGAGAAGAAAGA	59.461	42.308	5.98	4.77	37.85	2.52
2557	2672	9.227777	GTTAATAACTATGTTTCTGAACCTGGT	57.772	33.333	0.00	0.00	34.80	4.00
2799	2920	2.435422	TCCACATGAATTCGTGCACAT	58.565	42.857	24.48	5.25	36.36	3.21
2815	2939	2.826428	CACATGGAGGATAGTGTTCCG	58.174	52.381	0.00	0.00	40.94	4.30
2853	2995	2.289010	CGAAAGGCCAATGGAGCTTTTT	60.289	45.455	5.01	0.00	39.34	1.94
2890	3033	2.290387	GGGAAAGAGAAAGGGGACACTC	60.290	54.545	0.00	0.00	0.00	3.51
2952	3095	3.724478	TGTCATATCCAGGGTTCACTCT	58.276	45.455	0.00	0.00	0.00	3.24
3014	3157	6.127054	TGCAGCATTACTACCTAATGAAGAGT	60.127	38.462	0.00	0.00	43.24	3.24
3043	3186	6.378710	TCTATACACTGACTTTCCATCTCG	57.621	41.667	0.00	0.00	0.00	4.04
3064	3214	8.070034	TCTCGAGGTAGGTGTTGAATAAAATA	57.930	34.615	13.56	0.00	0.00	1.40

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
79	85	2.031163	GTCTTCCGCACCTGCACT	59.969	61.111	0.00	0.00	42.21	4.40
178	184	4.329545	GGAGACGCCAAGGTGCCA	62.330	66.667	0.00	0.00	36.34	4.92
214	221	2.433970	GGATCTCTTGCTAGAGCTTGGT	59.566	50.000	18.93	3.98	46.24	3.67
228	236	0.758685	CAAGGCGGAGGAGGATCTCT	60.759	60.000	0.00	0.00	34.39	3.10
255	263	4.609018	CGCCTATCCCACCCTGCG	62.609	72.222	0.00	0.00	35.81	5.18
267	275	0.899019	TGCTCACATAACACCGCCTA	59.101	50.000	0.00	0.00	0.00	3.93
335	354	4.834406	ATATCTCCACCTGAACCCTCTA	57.166	45.455	0.00	0.00	0.00	2.43
398	417	1.888826	CGGGGCCAAGGAAAATACACA	60.889	52.381	4.39	0.00	0.00	3.72
406	425	4.323477	CGTCACGGGGCCAAGGAA	62.323	66.667	4.39	0.00	0.00	3.36
417	436	2.246397	CAACAGCAGCACGTCACG	59.754	61.111	0.00	0.00	0.00	4.35
439	461	0.600057	CAGGATGGCGATCGATCAGA	59.400	55.000	24.40	8.21	0.00	3.27
560	589	2.939640	GCAACACGGGTCATACATTCCT	60.940	50.000	0.00	0.00	0.00	3.36
565	594	1.002544	TGATGCAACACGGGTCATACA	59.997	47.619	0.00	0.00	0.00	2.29
576	605	2.480037	CTGCGAGTAAACTGATGCAACA	59.520	45.455	0.00	0.00	31.16	3.33
579	608	2.455674	ACTGCGAGTAAACTGATGCA	57.544	45.000	0.00	0.00	0.00	3.96
581	610	6.641062	GCTAATTACTGCGAGTAAACTGATG	58.359	40.000	11.18	3.53	43.16	3.07
654	712	7.013655	CAGATTAAAAGGGAATCGGATCAATGT	59.986	37.037	0.00	0.00	38.18	2.71
712	770	0.108585	AGCAGCCTTTCCTTTCGTGA	59.891	50.000	0.00	0.00	0.00	4.35
784	858	2.203422	CCTCTCCCCTCGAGCGAT	60.203	66.667	6.99	0.00	38.62	4.58
785	859	4.507916	CCCTCTCCCCTCGAGCGA	62.508	72.222	6.99	3.48	38.62	4.93
788	862	3.742248	GACCCCCTCTCCCCTCGAG	62.742	73.684	5.13	5.13	40.30	4.04
789	863	3.752167	GACCCCCTCTCCCCTCGA	61.752	72.222	0.00	0.00	0.00	4.04
806	880	1.516161	TCGTCCATCCCTATCGTACG	58.484	55.000	9.53	9.53	0.00	3.67
813	887	1.107538	CCGCTCTTCGTCCATCCCTA	61.108	60.000	0.00	0.00	36.19	3.53
818	892	2.363795	TCCCCGCTCTTCGTCCAT	60.364	61.111	0.00	0.00	36.19	3.41
836	910	4.926207	CCGTTTCCCCTCTTACGG	57.074	61.111	0.00	0.00	46.22	4.02
879	953	6.307800	GCGCAGAATGTTATCTTCTCTATCTC	59.692	42.308	0.30	0.00	39.31	2.75
880	954	6.155827	GCGCAGAATGTTATCTTCTCTATCT	58.844	40.000	0.30	0.00	39.31	1.98
881	955	5.060323	CGCGCAGAATGTTATCTTCTCTATC	59.940	44.000	8.75	0.00	39.31	2.08
882	956	4.920340	CGCGCAGAATGTTATCTTCTCTAT	59.080	41.667	8.75	0.00	39.31	1.98
883	957	4.036380	TCGCGCAGAATGTTATCTTCTCTA	59.964	41.667	8.75	0.00	39.31	2.43
884	958	3.119291	CGCGCAGAATGTTATCTTCTCT	58.881	45.455	8.75	0.00	39.31	3.10
885	959	3.060873	GTCGCGCAGAATGTTATCTTCTC	60.061	47.826	8.75	0.00	39.31	2.87
886	960	2.860735	GTCGCGCAGAATGTTATCTTCT	59.139	45.455	8.75	0.00	39.31	2.85
887	961	2.346741	CGTCGCGCAGAATGTTATCTTC	60.347	50.000	8.75	0.00	39.31	2.87
912	986	3.633094	GAGCGAAGAGACAGCGGCA	62.633	63.158	1.45	0.00	35.78	5.69
919	993	0.454196	GACAGGGAGAGCGAAGAGAC	59.546	60.000	0.00	0.00	0.00	3.36
939	1013	1.883275	CCGGCGAGAGTCAAGATATCT	59.117	52.381	9.30	0.00	33.27	1.98
940	1014	1.667467	GCCGGCGAGAGTCAAGATATC	60.667	57.143	12.58	0.00	33.27	1.63
941	1015	0.315568	GCCGGCGAGAGTCAAGATAT	59.684	55.000	12.58	0.00	33.27	1.63
942	1016	1.734137	GCCGGCGAGAGTCAAGATA	59.266	57.895	12.58	0.00	33.27	1.98
943	1017	2.496817	GCCGGCGAGAGTCAAGAT	59.503	61.111	12.58	0.00	33.27	2.40
944	1018	4.116328	CGCCGGCGAGAGTCAAGA	62.116	66.667	44.86	0.00	42.83	3.02
992	1071	2.044650	GGAGAAGCATGGCTGGCA	60.045	61.111	6.31	6.31	39.62	4.92
1023	1102	0.834612	GACGGAGAGAGAGGAGGAGA	59.165	60.000	0.00	0.00	0.00	3.71
1209	1288	0.476611	AGAGGACCTTGGAGGCCTTT	60.477	55.000	6.77	0.00	40.43	3.11
2253	2362	2.154798	CTTGCCAGCTTGCTGTGCAT	62.155	55.000	26.52	0.00	38.76	3.96
2285	2394	7.990886	ACATCCAGTTAGAGTGTTAGAAAAACA	59.009	33.333	0.00	0.00	0.00	2.83
2286	2395	8.379457	ACATCCAGTTAGAGTGTTAGAAAAAC	57.621	34.615	0.00	0.00	0.00	2.43
2314	2425	4.547671	AGTGGCATACTATAGTGGACACT	58.452	43.478	28.64	28.64	43.49	3.55
2349	2460	1.424638	ACATTATGGGACGGAGGGAG	58.575	55.000	0.00	0.00	0.00	4.30
2350	2461	2.779429	TACATTATGGGACGGAGGGA	57.221	50.000	0.00	0.00	0.00	4.20
2351	2462	2.969950	TCTTACATTATGGGACGGAGGG	59.030	50.000	0.00	0.00	0.00	4.30
2352	2463	3.552273	CGTCTTACATTATGGGACGGAGG	60.552	52.174	20.50	5.87	43.69	4.30
2353	2464	3.639538	CGTCTTACATTATGGGACGGAG	58.360	50.000	20.50	2.74	43.69	4.63
2354	2465	3.720949	CGTCTTACATTATGGGACGGA	57.279	47.619	20.50	2.30	43.69	4.69
2376	2487	5.284861	TGACACTAGTGTAGAGCCAAAAA	57.715	39.130	27.98	2.12	45.05	1.94
2377	2488	4.948341	TGACACTAGTGTAGAGCCAAAA	57.052	40.909	27.98	3.58	45.05	2.44
2378	2489	4.948341	TTGACACTAGTGTAGAGCCAAA	57.052	40.909	27.98	11.09	45.05	3.28
2379	2490	4.948341	TTTGACACTAGTGTAGAGCCAA	57.052	40.909	27.98	22.31	45.05	4.52
2380	2491	4.948341	TTTTGACACTAGTGTAGAGCCA	57.052	40.909	27.98	17.99	45.05	4.75
2402	2513	9.566331	TCTCTCCATCCCATAATATAAGACATT	57.434	33.333	0.00	0.00	0.00	2.71
2403	2514	9.211410	CTCTCTCCATCCCATAATATAAGACAT	57.789	37.037	0.00	0.00	0.00	3.06
2404	2515	8.180165	ACTCTCTCCATCCCATAATATAAGACA	58.820	37.037	0.00	0.00	0.00	3.41
2405	2516	8.602472	ACTCTCTCCATCCCATAATATAAGAC	57.398	38.462	0.00	0.00	0.00	3.01
2406	2517	9.928618	CTACTCTCTCCATCCCATAATATAAGA	57.071	37.037	0.00	0.00	0.00	2.10
2407	2518	9.707957	ACTACTCTCTCCATCCCATAATATAAG	57.292	37.037	0.00	0.00	0.00	1.73
2409	2520	9.480861	CAACTACTCTCTCCATCCCATAATATA	57.519	37.037	0.00	0.00	0.00	0.86
2410	2521	7.093112	GCAACTACTCTCTCCATCCCATAATAT	60.093	40.741	0.00	0.00	0.00	1.28
2411	2522	6.211584	GCAACTACTCTCTCCATCCCATAATA	59.788	42.308	0.00	0.00	0.00	0.98
2412	2523	5.012561	GCAACTACTCTCTCCATCCCATAAT	59.987	44.000	0.00	0.00	0.00	1.28
2413	2524	4.345257	GCAACTACTCTCTCCATCCCATAA	59.655	45.833	0.00	0.00	0.00	1.90
2414	2525	3.898123	GCAACTACTCTCTCCATCCCATA	59.102	47.826	0.00	0.00	0.00	2.74
2415	2526	2.703007	GCAACTACTCTCTCCATCCCAT	59.297	50.000	0.00	0.00	0.00	4.00
2416	2527	2.111384	GCAACTACTCTCTCCATCCCA	58.889	52.381	0.00	0.00	0.00	4.37
2417	2528	2.393646	AGCAACTACTCTCTCCATCCC	58.606	52.381	0.00	0.00	0.00	3.85
2418	2529	5.799827	ATTAGCAACTACTCTCTCCATCC	57.200	43.478	0.00	0.00	0.00	3.51
2419	2530	9.771534	AAAATATTAGCAACTACTCTCTCCATC	57.228	33.333	0.00	0.00	0.00	3.51
2446	2557	7.083875	ACGACCAAAACATATTCGAATTCAT	57.916	32.000	17.19	1.34	33.87	2.57
2487	2598	2.226437	CGTAACTGTGCCATGCTTTCTT	59.774	45.455	0.00	0.00	0.00	2.52
2488	2599	1.806542	CGTAACTGTGCCATGCTTTCT	59.193	47.619	0.00	0.00	0.00	2.52
2489	2600	1.804151	TCGTAACTGTGCCATGCTTTC	59.196	47.619	0.00	0.00	0.00	2.62
2490	2601	1.890876	TCGTAACTGTGCCATGCTTT	58.109	45.000	0.00	0.00	0.00	3.51
2557	2672	3.840890	ACAAAACGCAGACTGAACAAA	57.159	38.095	6.65	0.00	0.00	2.83
2759	2880	7.453393	TGTGGATGGGAGAAGATAAATCATAC	58.547	38.462	0.00	0.00	0.00	2.39
2799	2920	1.335132	GCCCGGAACACTATCCTCCA	61.335	60.000	0.73	0.00	37.34	3.86
2815	2939	0.392461	TCGTTGTATCAGCAAGGCCC	60.392	55.000	0.00	0.00	35.12	5.80
2853	2995	4.221703	TCTTTCCCTTTTGCTGTTTCACAA	59.778	37.500	0.00	0.00	0.00	3.33
2890	3033	7.842525	TTTCTTACTACTACTTTCGACAACG	57.157	36.000	0.00	0.00	41.26	4.10
2952	3095	8.077386	CCTAGCAAAACCGTAAAAAGATTGTAA	58.923	33.333	0.00	0.00	0.00	2.41
3014	3157	6.530120	TGGAAAGTCAGTGTATAGAGCAAAA	58.470	36.000	0.00	0.00	0.00	2.44
3024	3167	3.444034	CCTCGAGATGGAAAGTCAGTGTA	59.556	47.826	15.71	0.00	0.00	2.90

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.