AutoCloner

Multiple sequence alignment - TraesCS7B01G500500

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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	TraesCS7B01G500500	chr7B	100.000	2795	0	0	1	2795	750106764	750103970	0.000000e+00	5162.0
1	TraesCS7B01G500500	chr7B	82.853	1423	185	33	820	2216	750096499	750095110	0.000000e+00	1221.0
2	TraesCS7B01G500500	chr7B	88.312	77	8	1	531	607	691996849	691996924	1.070000e-14	91.6
3	TraesCS7B01G500500	chr7A	92.490	1731	83	11	592	2307	732971394	732973092	0.000000e+00	2433.0
4	TraesCS7B01G500500	chr7A	81.294	1422	190	36	834	2216	733079319	733080703	0.000000e+00	1083.0
5	TraesCS7B01G500500	chr7A	87.409	548	54	9	61	594	732970786	732971332	1.420000e-172	616.0
6	TraesCS7B01G500500	chr7A	76.526	213	47	1	35	247	671915899	671915690	2.280000e-21	113.0
7	TraesCS7B01G500500	chr7D	83.422	1309	176	17	921	2216	633617097	633615817	0.000000e+00	1177.0
8	TraesCS7B01G500500	chr7D	79.358	218	35	4	175	391	35526231	35526439	8.070000e-31	145.0
9	TraesCS7B01G500500	chr7D	85.965	57	8	0	32	88	593909928	593909872	8.360000e-06	62.1
10	TraesCS7B01G500500	chr7D	97.143	35	0	1	36	69	57792005	57791971	1.080000e-04	58.4
11	TraesCS7B01G500500	chr5A	97.638	508	10	1	2290	2795	552159473	552158966	0.000000e+00	870.0
12	TraesCS7B01G500500	chr4B	99.272	412	1	1	2384	2795	540474839	540474430	0.000000e+00	743.0
13	TraesCS7B01G500500	chr2A	97.922	385	6	1	2413	2795	479838632	479839016	0.000000e+00	665.0
14	TraesCS7B01G500500	chr2A	85.143	175	24	2	1064	1237	3361387	3361560	7.960000e-41	178.0
15	TraesCS7B01G500500	chr2A	81.707	82	9	5	36	115	2816602	2816525	2.320000e-06	63.9
16	TraesCS7B01G500500	chr5B	98.413	378	4	1	2418	2795	669598820	669598445	0.000000e+00	664.0
17	TraesCS7B01G500500	chr5B	89.552	67	5	2	450	515	612636526	612636591	1.780000e-12	84.2
18	TraesCS7B01G500500	chr5B	77.372	137	21	9	1082	1210	613168155	613168021	3.860000e-09	73.1
19	TraesCS7B01G500500	chr5B	83.077	65	6	4	31	95	36336290	36336349	1.000000e-03	54.7
20	TraesCS7B01G500500	chr3B	98.760	242	3	0	2341	2582	144488439	144488198	5.530000e-117	431.0
21	TraesCS7B01G500500	chr3B	97.814	183	4	0	2613	2795	144488197	144488015	1.620000e-82	316.0
22	TraesCS7B01G500500	chr2B	82.332	549	46	17	2281	2795	559915100	559915631	1.990000e-116	429.0
23	TraesCS7B01G500500	chr2B	85.227	88	12	1	527	613	589340183	589340270	3.830000e-14	89.8
24	TraesCS7B01G500500	chr4D	80.594	505	51	17	2320	2795	207590796	207591282	2.060000e-91	346.0
25	TraesCS7B01G500500	chr4D	79.883	343	40	11	2321	2644	207588602	207588934	1.010000e-54	224.0
26	TraesCS7B01G500500	chr4D	92.754	69	4	1	527	594	41372576	41372508	6.370000e-17	99.0
27	TraesCS7B01G500500	chr4A	96.815	157	5	0	2412	2568	671929472	671929628	2.130000e-66	263.0
28	TraesCS7B01G500500	chr4A	95.614	114	3	1	2552	2663	671929634	671929747	6.150000e-42	182.0
29	TraesCS7B01G500500	chr4A	95.960	99	4	0	2697	2795	671929742	671929840	8.010000e-36	161.0
30	TraesCS7B01G500500	chr4A	91.379	58	4	1	458	515	180393970	180394026	8.300000e-11	78.7
31	TraesCS7B01G500500	chr4A	85.965	57	7	1	32	88	11730290	11730235	3.010000e-05	60.2
32	TraesCS7B01G500500	chr3A	89.744	78	6	2	531	606	661926746	661926669	6.370000e-17	99.0
33	TraesCS7B01G500500	chr2D	92.754	69	4	1	527	594	57203678	57203746	6.370000e-17	99.0
34	TraesCS7B01G500500	chr2D	92.754	69	4	1	527	594	412716098	412716030	6.370000e-17	99.0
35	TraesCS7B01G500500	chr2D	91.429	70	6	0	535	604	96099623	96099554	2.290000e-16	97.1
36	TraesCS7B01G500500	chr2D	77.863	131	25	3	1063	1190	5116355	5116484	8.300000e-11	78.7
37	TraesCS7B01G500500	chr2D	89.474	57	4	2	459	514	643737316	643737261	1.390000e-08	71.3
38	TraesCS7B01G500500	chr1B	92.754	69	4	1	527	594	335974929	335974861	6.370000e-17	99.0
39	TraesCS7B01G500500	chr1D	91.429	70	6	0	535	604	448801447	448801378	2.290000e-16	97.1
40	TraesCS7B01G500500	chr5D	82.243	107	19	0	1076	1182	449475058	449475164	2.960000e-15	93.5
41	TraesCS7B01G500500	chr5D	76.433	157	34	3	1072	1228	449291099	449290946	6.420000e-12	82.4
42	TraesCS7B01G500500	chr6D	90.323	62	6	0	138	199	387110202	387110263	6.420000e-12	82.4
43	TraesCS7B01G500500	chr6A	94.340	53	2	1	458	510	495417604	495417655	2.310000e-11	80.5
44	TraesCS7B01G500500	chr6A	85.000	60	5	3	36	95	498533221	498533166	1.080000e-04	58.4
45	TraesCS7B01G500500	chr1A	84.722	72	8	3	450	520	336317544	336317475	5.000000e-08	69.4
46	TraesCS7B01G500500	chr6B	100.000	35	0	0	32	66	184325892	184325926	6.460000e-07	65.8
47	TraesCS7B01G500500	chr3D	97.143	35	0	1	36	69	29784920	29784886	1.080000e-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	TraesCS7B01G500500	chr7B	750103970	750106764	2794	True	5162.0	5162	100.0000	1	2795	1	chr7B.!!$R2	2794
1	TraesCS7B01G500500	chr7B	750095110	750096499	1389	True	1221.0	1221	82.8530	820	2216	1	chr7B.!!$R1	1396
2	TraesCS7B01G500500	chr7A	732970786	732973092	2306	False	1524.5	2433	89.9495	61	2307	2	chr7A.!!$F2	2246
3	TraesCS7B01G500500	chr7A	733079319	733080703	1384	False	1083.0	1083	81.2940	834	2216	1	chr7A.!!$F1	1382
4	TraesCS7B01G500500	chr7D	633615817	633617097	1280	True	1177.0	1177	83.4220	921	2216	1	chr7D.!!$R3	1295
5	TraesCS7B01G500500	chr5A	552158966	552159473	507	True	870.0	870	97.6380	2290	2795	1	chr5A.!!$R1	505
6	TraesCS7B01G500500	chr2B	559915100	559915631	531	False	429.0	429	82.3320	2281	2795	1	chr2B.!!$F1	514
7	TraesCS7B01G500500	chr4D	207588602	207591282	2680	False	285.0	346	80.2385	2320	2795	2	chr4D.!!$F1	475

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
154	155	0.100682	GACGGATTCTAGAGCGTGCA	59.899	55.0	0.0	0.0	0.0	4.57	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1846	1961	0.5966	GACACAAAGACGGTCTCGCA	60.597	55.0	11.71	0.0	40.63	5.1	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
27	28	6.927381	ACGGATACAACACTAATAGTTATGGC	59.073	38.462	7.01	0.00	0.00	4.40
28	29	6.089016	CGGATACAACACTAATAGTTATGGCG	59.911	42.308	7.01	0.00	0.00	5.69
29	30	7.149973	GGATACAACACTAATAGTTATGGCGA	58.850	38.462	7.01	0.00	0.00	5.54
31	32	6.844696	ACAACACTAATAGTTATGGCGATG	57.155	37.500	7.01	0.00	0.00	3.84
32	33	5.758296	ACAACACTAATAGTTATGGCGATGG	59.242	40.000	7.01	0.00	0.00	3.51
33	34	5.801531	ACACTAATAGTTATGGCGATGGA	57.198	39.130	0.00	0.00	0.00	3.41
34	35	6.360370	ACACTAATAGTTATGGCGATGGAT	57.640	37.500	0.00	0.00	0.00	3.41
35	36	6.166279	ACACTAATAGTTATGGCGATGGATG	58.834	40.000	0.00	0.00	0.00	3.51
36	37	5.582269	CACTAATAGTTATGGCGATGGATGG	59.418	44.000	0.00	0.00	0.00	3.51
37	38	4.640771	AATAGTTATGGCGATGGATGGT	57.359	40.909	0.00	0.00	0.00	3.55
38	39	2.260844	AGTTATGGCGATGGATGGTG	57.739	50.000	0.00	0.00	0.00	4.17
39	40	1.202806	AGTTATGGCGATGGATGGTGG	60.203	52.381	0.00	0.00	0.00	4.61
41	42	2.730066	TATGGCGATGGATGGTGGCG	62.730	60.000	0.00	0.00	0.00	5.69
44	45	3.274586	CGATGGATGGTGGCGCTG	61.275	66.667	7.64	0.00	0.00	5.18
45	46	2.124570	GATGGATGGTGGCGCTGT	60.125	61.111	7.64	0.00	0.00	4.40
46	47	2.124570	ATGGATGGTGGCGCTGTC	60.125	61.111	7.64	0.00	0.00	3.51
47	48	2.599645	GATGGATGGTGGCGCTGTCT	62.600	60.000	7.64	0.00	0.00	3.41
48	49	2.821366	GGATGGTGGCGCTGTCTG	60.821	66.667	7.64	0.00	0.00	3.51
49	50	2.821366	GATGGTGGCGCTGTCTGG	60.821	66.667	7.64	0.00	0.00	3.86
58	59	2.046892	GCTGTCTGGCGTCATGGT	60.047	61.111	0.00	0.00	0.00	3.55
59	60	2.393768	GCTGTCTGGCGTCATGGTG	61.394	63.158	0.00	0.00	0.00	4.17
118	119	6.526526	CATTGATCTGTCCTGAAGATGAGAT	58.473	40.000	0.00	0.00	34.50	2.75
119	120	5.532664	TGATCTGTCCTGAAGATGAGATG	57.467	43.478	0.00	0.00	34.50	2.90
120	121	4.344390	TGATCTGTCCTGAAGATGAGATGG	59.656	45.833	0.00	0.00	34.50	3.51
125	126	1.539929	CCTGAAGATGAGATGGCGGAC	60.540	57.143	0.00	0.00	0.00	4.79
132	133	1.048160	TGAGATGGCGGACTATGGCA	61.048	55.000	0.00	0.00	46.52	4.92
134	135	1.050988	AGATGGCGGACTATGGCAGT	61.051	55.000	0.00	0.00	45.62	4.40
136	137	1.337384	ATGGCGGACTATGGCAGTGA	61.337	55.000	0.00	0.00	45.62	3.41
154	155	0.100682	GACGGATTCTAGAGCGTGCA	59.899	55.000	0.00	0.00	0.00	4.57
199	200	2.028130	CTAGATCGGTTGGTGCTCTCT	58.972	52.381	0.00	0.00	0.00	3.10
272	273	1.672030	CGCCAGTGCACTCCATCAA	60.672	57.895	18.64	0.00	37.32	2.57
284	285	3.679980	CACTCCATCAAAGTTGTAGGTCG	59.320	47.826	5.05	0.00	0.00	4.79
348	349	5.104259	TGTATCTGCTCTGTCAGACTCTA	57.896	43.478	0.00	0.00	44.88	2.43
354	355	5.655974	TCTGCTCTGTCAGACTCTATTGAAT	59.344	40.000	0.00	0.00	38.11	2.57
403	404	1.079405	GATTGACGTTGAGGCCCGA	60.079	57.895	0.00	0.00	0.00	5.14
418	419	2.436911	GGCCCGAGGTAATCCTTCTTTA	59.563	50.000	0.00	0.00	45.24	1.85
419	420	3.118149	GGCCCGAGGTAATCCTTCTTTAA	60.118	47.826	0.00	0.00	45.24	1.52
420	421	4.445879	GGCCCGAGGTAATCCTTCTTTAAT	60.446	45.833	0.00	0.00	45.24	1.40
466	469	3.804873	GCAAGCTAAGATTTACTCCCTCG	59.195	47.826	0.00	0.00	0.00	4.63
467	470	4.372656	CAAGCTAAGATTTACTCCCTCGG	58.627	47.826	0.00	0.00	0.00	4.63
473	476	3.930035	AGATTTACTCCCTCGGATTCCT	58.070	45.455	0.30	0.00	0.00	3.36
506	509	7.037586	AGGTCTTTGTAAAGATTCCACTATGGA	60.038	37.037	9.98	0.00	44.55	3.41
525	538	8.074363	ACTATGGACCATATATATAGTGGCCTT	58.926	37.037	14.69	11.40	36.47	4.35
528	541	5.823045	GGACCATATATATAGTGGCCTTTGC	59.177	44.000	3.32	0.00	36.47	3.68
531	544	6.012508	ACCATATATATAGTGGCCTTTGCACT	60.013	38.462	3.32	0.08	40.13	4.40
539	552	5.310409	AGTGGCCTTTGCACTATATACAT	57.690	39.130	3.32	0.00	40.13	2.29
540	553	5.694995	AGTGGCCTTTGCACTATATACATT	58.305	37.500	3.32	0.00	40.13	2.71
541	554	5.765182	AGTGGCCTTTGCACTATATACATTC	59.235	40.000	3.32	0.00	40.13	2.67
593	671	9.379791	ACAAAGACTTATATTTAAGAACGGAGG	57.620	33.333	9.58	0.00	38.56	4.30
699	778	0.549469	TCCTCTGTGCATGCATGGAT	59.451	50.000	25.64	0.00	0.00	3.41
772	851	7.798982	GTCGTTCTGAAGTTTGATTAGGAAAAG	59.201	37.037	0.00	0.00	0.00	2.27
791	870	5.358298	AAAGAAACTGAAATCCGCAGTAC	57.642	39.130	0.00	0.00	45.27	2.73
804	883	3.751175	TCCGCAGTACCTTTTCAGAATTG	59.249	43.478	0.00	0.00	0.00	2.32
809	888	4.217118	CAGTACCTTTTCAGAATTGCAGCT	59.783	41.667	0.00	0.00	0.00	4.24
814	893	5.525012	ACCTTTTCAGAATTGCAGCTTTTTC	59.475	36.000	0.00	0.00	0.00	2.29
815	894	5.756833	CCTTTTCAGAATTGCAGCTTTTTCT	59.243	36.000	0.00	0.00	0.00	2.52
816	895	6.925165	CCTTTTCAGAATTGCAGCTTTTTCTA	59.075	34.615	0.00	0.00	0.00	2.10
928	1014	2.682269	GCCTTCTTCTCCTTTGCCCTAG	60.682	54.545	0.00	0.00	0.00	3.02
971	1057	3.245087	CGATCTCTCCTATCCTCCCAAGA	60.245	52.174	0.00	0.00	0.00	3.02
972	1058	4.569653	CGATCTCTCCTATCCTCCCAAGAT	60.570	50.000	0.00	0.00	0.00	2.40
973	1059	4.396357	TCTCTCCTATCCTCCCAAGATC	57.604	50.000	0.00	0.00	0.00	2.75
974	1060	3.076785	TCTCTCCTATCCTCCCAAGATCC	59.923	52.174	0.00	0.00	0.00	3.36
976	1062	1.787058	TCCTATCCTCCCAAGATCCGA	59.213	52.381	0.00	0.00	0.00	4.55
977	1063	2.383683	TCCTATCCTCCCAAGATCCGAT	59.616	50.000	0.00	0.00	0.00	4.18
979	1065	3.196685	CCTATCCTCCCAAGATCCGATTC	59.803	52.174	0.00	0.00	0.00	2.52
1104	1196	2.630214	CGATCTACCGCTGGAGCTA	58.370	57.895	1.50	0.00	39.32	3.32
1108	1200	0.814410	TCTACCGCTGGAGCTACTCG	60.814	60.000	0.00	0.30	39.32	4.18
1119	1211	0.538118	AGCTACTCGTCGAGGTCTCT	59.462	55.000	25.25	13.46	33.35	3.10
1237	1329	1.525077	TGGGTTCTCACGTTGTGCC	60.525	57.895	0.00	0.00	32.98	5.01
1623	1727	1.156736	CCTGGACGGTCATGACAAAC	58.843	55.000	26.47	15.59	0.00	2.93
1627	1731	1.542547	GGACGGTCATGACAAACAGGT	60.543	52.381	26.47	13.44	0.00	4.00
1634	1738	4.321230	GGTCATGACAAACAGGTTGGAATC	60.321	45.833	26.47	0.26	41.97	2.52
1639	1743	4.201970	TGACAAACAGGTTGGAATCGTTTC	60.202	41.667	2.51	0.00	41.97	2.78
1725	1829	2.278026	TCATGATGACGACGGACTTG	57.722	50.000	0.00	0.00	0.00	3.16
1736	1840	1.301401	CGGACTTGGAAGCCAACGA	60.301	57.895	0.00	0.00	38.75	3.85
1773	1888	5.013547	AGAGTCGAGTTGGGATCTATATGG	58.986	45.833	0.00	0.00	0.00	2.74
1832	1947	1.206132	AGTCACACGGTGAGTTGTTGA	59.794	47.619	16.29	3.90	42.73	3.18
1846	1961	0.327924	TGTTGATGGCATCCGTCCTT	59.672	50.000	23.92	0.00	38.69	3.36
1887	2002	2.401583	TACGAATGCAGCAATCCAGT	57.598	45.000	0.00	0.00	0.00	4.00
2019	2134	3.965539	CTCCTGCCAGCTTCACGGG	62.966	68.421	0.00	0.00	36.56	5.28
2090	2205	4.216731	GCGTGTTTAGGTACAGCTTTTTC	58.783	43.478	0.00	0.00	0.00	2.29
2141	2256	3.138798	CCTGGATGCTGTGCTGGC	61.139	66.667	0.00	0.00	30.91	4.85
2149	2264	2.656646	CTGTGCTGGCGAGGTGTA	59.343	61.111	0.00	0.00	0.00	2.90
2266	2381	6.658831	TGCTTTTCGAAGTGAAATAGACAAG	58.341	36.000	0.00	0.00	45.62	3.16
2274	2389	8.248253	TCGAAGTGAAATAGACAAGCTGTAATA	58.752	33.333	0.00	0.00	0.00	0.98
2573	2720	7.684529	AGATCTCTCTCTCTCTCTCTAAATCC	58.315	42.308	0.00	0.00	0.00	3.01

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	9.622004	CCATAACTATTAGTGTTGTATCCGTAG	57.378	37.037	0.00	0.00	0.00	3.51
3	4	6.089016	CGCCATAACTATTAGTGTTGTATCCG	59.911	42.308	0.00	0.00	0.00	4.18
4	5	7.149973	TCGCCATAACTATTAGTGTTGTATCC	58.850	38.462	0.00	0.00	0.00	2.59
5	6	8.648097	CATCGCCATAACTATTAGTGTTGTATC	58.352	37.037	0.00	0.00	0.00	2.24
9	10	5.989168	TCCATCGCCATAACTATTAGTGTTG	59.011	40.000	0.00	0.00	0.00	3.33
11	12	5.801531	TCCATCGCCATAACTATTAGTGT	57.198	39.130	0.00	0.00	0.00	3.55
12	13	5.582269	CCATCCATCGCCATAACTATTAGTG	59.418	44.000	0.00	0.00	0.00	2.74
13	14	5.248477	ACCATCCATCGCCATAACTATTAGT	59.752	40.000	0.00	0.00	0.00	2.24
14	15	5.582269	CACCATCCATCGCCATAACTATTAG	59.418	44.000	0.00	0.00	0.00	1.73
16	17	4.326826	CACCATCCATCGCCATAACTATT	58.673	43.478	0.00	0.00	0.00	1.73
17	18	3.307691	CCACCATCCATCGCCATAACTAT	60.308	47.826	0.00	0.00	0.00	2.12
18	19	2.038426	CCACCATCCATCGCCATAACTA	59.962	50.000	0.00	0.00	0.00	2.24
19	20	1.202806	CCACCATCCATCGCCATAACT	60.203	52.381	0.00	0.00	0.00	2.24
20	21	1.238439	CCACCATCCATCGCCATAAC	58.762	55.000	0.00	0.00	0.00	1.89
22	23	1.073025	GCCACCATCCATCGCCATA	59.927	57.895	0.00	0.00	0.00	2.74
23	24	2.203394	GCCACCATCCATCGCCAT	60.203	61.111	0.00	0.00	0.00	4.40
27	28	3.274586	CAGCGCCACCATCCATCG	61.275	66.667	2.29	0.00	0.00	3.84
28	29	2.124570	ACAGCGCCACCATCCATC	60.125	61.111	2.29	0.00	0.00	3.51
29	30	2.124570	GACAGCGCCACCATCCAT	60.125	61.111	2.29	0.00	0.00	3.41
31	32	2.821366	CAGACAGCGCCACCATCC	60.821	66.667	2.29	0.00	0.00	3.51
32	33	2.821366	CCAGACAGCGCCACCATC	60.821	66.667	2.29	0.00	0.00	3.51
41	42	2.046892	ACCATGACGCCAGACAGC	60.047	61.111	0.00	0.00	0.00	4.40
43	44	2.347114	CCACCATGACGCCAGACA	59.653	61.111	0.00	0.00	0.00	3.41
44	45	3.127533	GCCACCATGACGCCAGAC	61.128	66.667	0.00	0.00	0.00	3.51
45	46	4.758251	CGCCACCATGACGCCAGA	62.758	66.667	0.00	0.00	0.00	3.86
51	52	3.490759	CTGCGACGCCACCATGAC	61.491	66.667	18.69	0.00	0.00	3.06
54	55	3.939837	CTGTCTGCGACGCCACCAT	62.940	63.158	18.69	0.00	34.95	3.55
55	56	4.662961	CTGTCTGCGACGCCACCA	62.663	66.667	18.69	9.64	34.95	4.17
56	57	4.664677	ACTGTCTGCGACGCCACC	62.665	66.667	18.69	5.06	34.95	4.61
57	58	2.661866	AACTGTCTGCGACGCCAC	60.662	61.111	18.69	14.36	34.95	5.01
58	59	2.661537	CAACTGTCTGCGACGCCA	60.662	61.111	18.69	7.25	34.95	5.69
59	60	3.414700	CCAACTGTCTGCGACGCC	61.415	66.667	18.69	2.07	34.95	5.68
118	119	1.987306	TCACTGCCATAGTCCGCCA	60.987	57.895	0.00	0.00	37.60	5.69
119	120	1.521681	GTCACTGCCATAGTCCGCC	60.522	63.158	0.00	0.00	37.60	6.13
120	121	1.878522	CGTCACTGCCATAGTCCGC	60.879	63.158	0.00	0.00	37.60	5.54
125	126	2.898729	AGAATCCGTCACTGCCATAG	57.101	50.000	0.00	0.00	0.00	2.23
132	133	1.402259	CACGCTCTAGAATCCGTCACT	59.598	52.381	9.10	0.00	0.00	3.41
134	135	0.100682	GCACGCTCTAGAATCCGTCA	59.899	55.000	9.10	0.00	0.00	4.35
136	137	0.179134	GTGCACGCTCTAGAATCCGT	60.179	55.000	0.00	6.87	0.00	4.69
154	155	1.965930	ATCAACGCACACCGCATGT	60.966	52.632	0.00	0.00	44.81	3.21
168	169	2.388735	ACCGATCTAGCAGACCATCAA	58.611	47.619	0.00	0.00	0.00	2.57
172	173	0.824109	CCAACCGATCTAGCAGACCA	59.176	55.000	0.00	0.00	0.00	4.02
199	200	2.434884	GCTGCCTAACTGCGAGCA	60.435	61.111	0.00	0.00	36.25	4.26
227	228	4.281435	CCATGCATGCCATCTAATTTGGTA	59.719	41.667	21.69	0.00	36.57	3.25
272	273	4.421948	CTTAATCGCTCGACCTACAACTT	58.578	43.478	0.00	0.00	0.00	2.66
373	374	2.536365	ACGTCAATCGATGCGTACAAT	58.464	42.857	17.35	0.00	42.86	2.71
379	380	0.298707	CCTCAACGTCAATCGATGCG	59.701	55.000	0.00	7.20	41.08	4.73
418	419	9.408648	CCCTTACACTCCATATTCTTTGTTATT	57.591	33.333	0.00	0.00	0.00	1.40
419	420	7.502561	GCCCTTACACTCCATATTCTTTGTTAT	59.497	37.037	0.00	0.00	0.00	1.89
420	421	6.826741	GCCCTTACACTCCATATTCTTTGTTA	59.173	38.462	0.00	0.00	0.00	2.41
427	428	3.565902	GCTTGCCCTTACACTCCATATTC	59.434	47.826	0.00	0.00	0.00	1.75
430	433	2.196595	AGCTTGCCCTTACACTCCATA	58.803	47.619	0.00	0.00	0.00	2.74
434	437	3.611766	TCTTAGCTTGCCCTTACACTC	57.388	47.619	0.00	0.00	0.00	3.51
439	442	5.397559	GGGAGTAAATCTTAGCTTGCCCTTA	60.398	44.000	0.00	0.00	0.00	2.69
506	509	6.012508	AGTGCAAAGGCCACTATATATATGGT	60.013	38.462	5.01	5.94	40.13	3.55
518	531	5.334105	CGAATGTATATAGTGCAAAGGCCAC	60.334	44.000	5.01	0.00	40.13	5.01
519	532	4.754618	CGAATGTATATAGTGCAAAGGCCA	59.245	41.667	5.01	0.00	40.13	5.36
520	533	4.755123	ACGAATGTATATAGTGCAAAGGCC	59.245	41.667	0.00	0.00	40.13	5.19
521	534	5.924475	ACGAATGTATATAGTGCAAAGGC	57.076	39.130	0.00	0.00	41.68	4.35
522	535	8.435430	CACATACGAATGTATATAGTGCAAAGG	58.565	37.037	0.00	0.00	44.70	3.11
525	538	7.438564	ACCACATACGAATGTATATAGTGCAA	58.561	34.615	0.00	0.00	44.70	4.08
528	541	7.599171	TGGACCACATACGAATGTATATAGTG	58.401	38.462	0.00	0.00	44.70	2.74
531	544	8.410912	GCTATGGACCACATACGAATGTATATA	58.589	37.037	0.00	0.00	44.70	0.86
539	552	1.067974	CCGCTATGGACCACATACGAA	59.932	52.381	0.00	0.00	42.00	3.85
540	553	0.671796	CCGCTATGGACCACATACGA	59.328	55.000	0.00	0.00	42.00	3.43
541	554	0.671796	TCCGCTATGGACCACATACG	59.328	55.000	0.00	0.00	43.74	3.06
622	700	2.797786	CCGGGATGTTAAACCAAAGGA	58.202	47.619	0.00	0.00	0.00	3.36
772	851	3.335579	AGGTACTGCGGATTTCAGTTTC	58.664	45.455	0.00	0.00	41.61	2.78
791	870	5.756833	AGAAAAAGCTGCAATTCTGAAAAGG	59.243	36.000	11.94	0.00	31.25	3.11
804	883	7.100458	TGAAATTCCCTATAGAAAAAGCTGC	57.900	36.000	0.00	0.00	0.00	5.25
928	1014	1.736365	GCAGCTCCCGTAGTAGGACC	61.736	65.000	0.00	0.00	0.00	4.46
972	1058	0.604511	TCGGATCGGATCGAATCGGA	60.605	55.000	11.62	10.34	39.99	4.55
973	1059	0.452184	ATCGGATCGGATCGAATCGG	59.548	55.000	9.82	4.02	39.99	4.18
974	1060	1.532090	GGATCGGATCGGATCGAATCG	60.532	57.143	27.38	9.46	43.00	3.34
976	1062	0.452184	CGGATCGGATCGGATCGAAT	59.548	55.000	27.38	7.53	43.00	3.34
977	1063	0.604511	TCGGATCGGATCGGATCGAA	60.605	55.000	27.38	18.85	43.00	3.71
979	1065	2.099143	ATCGGATCGGATCGGATCG	58.901	57.895	26.28	23.09	43.26	3.69
1104	1196	2.843669	GTCAGAGACCTCGACGAGT	58.156	57.895	22.61	11.34	34.09	4.18
1232	1324	1.591504	TAGCATCTCGTCGTGGCACA	61.592	55.000	19.09	1.83	0.00	4.57
1237	1329	1.532090	GGAGTGTAGCATCTCGTCGTG	60.532	57.143	0.00	0.00	0.00	4.35
1243	1335	3.254411	TCGATGATGGAGTGTAGCATCTC	59.746	47.826	0.00	0.00	38.46	2.75
1293	1385	4.353437	AAGTCGCGGTGGTCGTCC	62.353	66.667	6.13	0.00	41.72	4.79
1623	1727	2.139917	TGTCGAAACGATTCCAACCTG	58.860	47.619	0.00	0.00	38.42	4.00
1627	1731	1.874872	GGGTTGTCGAAACGATTCCAA	59.125	47.619	0.00	0.00	38.42	3.53
1634	1738	0.725117	GGCATAGGGTTGTCGAAACG	59.275	55.000	0.00	0.00	0.00	3.60
1639	1743	2.210116	GTACATGGCATAGGGTTGTCG	58.790	52.381	0.00	0.00	0.00	4.35
1725	1829	1.375523	ATCACCGTCGTTGGCTTCC	60.376	57.895	0.00	0.00	0.00	3.46
1736	1840	2.214181	GACTCTGCCGACATCACCGT	62.214	60.000	0.00	0.00	0.00	4.83
1832	1947	2.514592	CGCAAGGACGGATGCCAT	60.515	61.111	0.00	0.00	39.39	4.40
1846	1961	0.596600	GACACAAAGACGGTCTCGCA	60.597	55.000	11.71	0.00	40.63	5.10
2019	2134	3.491652	GCCTTCGTCCAGCTTCGC	61.492	66.667	0.00	0.00	0.00	4.70
2141	2256	1.359848	GAAGCCACACATACACCTCG	58.640	55.000	0.00	0.00	0.00	4.63
2167	2282	5.491078	TCTTGGATGGGAGTAATTTGTAGGT	59.509	40.000	0.00	0.00	0.00	3.08
2221	2336	6.819284	AGCAATCCTTTTTCATCTTGTTTCA	58.181	32.000	0.00	0.00	0.00	2.69
2323	2438	8.812972	ACAAGCGATGGTAGAAAGGATTATATA	58.187	33.333	0.00	0.00	0.00	0.86
2324	2439	7.680730	ACAAGCGATGGTAGAAAGGATTATAT	58.319	34.615	0.00	0.00	0.00	0.86
2325	2440	7.062749	ACAAGCGATGGTAGAAAGGATTATA	57.937	36.000	0.00	0.00	0.00	0.98
2327	2442	5.353394	ACAAGCGATGGTAGAAAGGATTA	57.647	39.130	0.00	0.00	0.00	1.75
2573	2720	2.283617	CAGATCCAATTCTTCTCACGCG	59.716	50.000	3.53	3.53	0.00	6.01

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.